@article{zhao_sandercock_mejia-guerra_mollinari_heller-uszynska_wadl_webster_beil_sheehan_2024, title={A Public Mid-Density Genotyping Platform for Hexaploid Sweetpotato (<i>Ipomoea batatas</i> [L.] Lam)}, volume={15}, ISSN={["2073-4425"]}, url={https://www.mdpi.com/2073-4425/15/8/1047}, DOI={10.3390/genes15081047}, abstractNote={Small public breeding programs focused on specialty crops have many barriers to adopting technology, particularly creating and using genetic marker panels for genomic-based decisions in selection. Here, we report the creation of a DArTag panel of 3120 loci distributed across the sweetpotato (}, number={8}, journal={GENES}, author={Zhao, Dongyan and Sandercock, Alexander M. and Mejia-Guerra, Maria Katherine and Mollinari, Marcelo and Heller-Uszynska, Kasia and Wadl, Phillip A. and Webster, Seymour A. and Beil, Craig T. and Sheehan, Moira J.}, year={2024}, month={Aug} }
 @article{fraher_schwarz_heim_gesteira_mollinari_pereira_zeng_brown-guedira_gorny_yencho_2024, title={Discovery of a major QTL for resistance to the guava root-knot nematode (<i>Meloidogyne enterolobii</i>) in 'Tanzania', an African landrace sweetpotato (<i>Ipomoea batatas</i>)}, volume={137}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-024-04739-1}, abstractNote={Sweetpotato, Ipomoea batatas (L.) Lam. (2n = 6x = 90), is among the world's most important food crops and is North Carolina's most important vegetable crop. The recent introduction of Meloidogyne enterolobii poses a significant economic threat to North Carolina's sweetpotato industry and breeding resistance into new varieties has become a high priority for the US sweetpotato industry. Previous studies have shown that 'Tanzania', a released African landrace, is resistant to M. enterolobii. We screened the biparental sweetpotato mapping population, 'Tanzania' x 'Beauregard', for resistance to M. enterolobii by inoculating 246 full-sibs with 10,000 eggs each under greenhouse conditions. 'Tanzania', the female parent, was highly resistant, while 'Beauregard' was highly susceptible. Our bioassays exhibited strong skewing toward resistance for three measures of resistance: reproductive factor, eggs per gram of root tissue, and root gall severity ratings. A 1:1 segregation for resistance suggested a major gene conferred M. enterolobii resistance. Using a random-effect multiple interval mapping model, we identified a single major QTL, herein designated as qIbMe-4.1, on linkage group 4 that explained 70% of variation in resistance to M. enterolobii. This study provides a new understanding of the genetic basis of M. enterolobii resistance in sweetpotato and represents a major step towards the identification of selectable markers for nematode resistance breeding.}, number={10}, journal={THEORETICAL AND APPLIED GENETICS}, author={Fraher, Simon and Schwarz, Tanner and Heim, Chris and Gesteira, Gabriel De Siqueira and Mollinari, Marcelo and Pereira, Guilherme Da Silva and Zeng, Zhao-Bang and Brown-Guedira, Gina and Gorny, Adrienne and Yencho, G. Craig}, year={2024}, month={Oct} }
 @article{oh_stapleton_giongo_johanningsmeier_mollinari_mainland_perkins-veazie_iorizzo_2024, title={Prediction of blueberry sensory texture attributes by integrating multiple instrumental measurements}, volume={218}, ISSN={["1873-2356"]}, DOI={10.1016/j.postharvbio.2024.113160}, journal={POSTHARVEST BIOLOGY AND TECHNOLOGY}, author={Oh, Heeduk and Stapleton, Lee and Giongo, Lara and Johanningsmeier, Suzanne and Mollinari, Marcelo and Mainland, Charles M. and Perkins-Veazie, Penelope and Iorizzo, Massimo}, year={2024}, month={Dec} }
 @article{zhao_mejia-guerra_mollinari_samac_irish_heller-uszynska_beil_sheehan_2023, title={A public mid-density genotyping platform for alfalfa (Medicago sativa L.)}, volume={4}, ISSN={2708-3764}, url={http://dx.doi.org/10.46265/genresj.EMOR6509}, DOI={10.46265/genresj.emor6509}, abstractNote={Small public breeding programmes have many barriers to adopting technology, particularly creating and using genetic marker panels for genomic-based decisions in selection. Here we report the creation of a DArTag panel of 3,000 loci distributed across the alfalfa (Medicago sativa L.) genome for use in molecular breeding and genomic insight. The creation of this marker panel brings cost-effective and rapid genotyping capabilities to alfalfa breeding programmes. The open access provided by this platform will allow genetic data sets generated on the marker panel to be compared and joined across projects, institutions and countries. This genotyping resource has the power to make routine genotyping a reality for any breeder of alfalfa.}, number={8}, journal={Genetic Resources}, publisher={Alliance of Bioversity International and CIAT}, author={Zhao, Dongyan and Mejia-Guerra, Katherine Maria and Mollinari, Marcelo and Samac, Deborah and Irish, Brian and Heller-Uszynska, Katarzyna and Beil, Craig Thomas and Sheehan, Moira Jane}, year={2023}, month={Oct}, pages={55–63} }
 @article{da costa lima moraes_mollinari_ferreira_aono_de castro lara_pessoa-filho_barrios_garcia_do valle_de souza_et al._2023, title={Advances in genomic characterization of Urochloa humidicola: exploring polyploid inheritance and apomixis}, volume={136}, ISSN={0040-5752 1432-2242}, url={http://dx.doi.org/10.1007/s00122-023-04485-w}, DOI={10.1007/s00122-023-04485-w}, number={11}, journal={Theoretical and Applied Genetics}, publisher={Springer Science and Business Media LLC}, author={da Costa Lima Moraes, Aline and Mollinari, Marcelo and Ferreira, Rebecca Caroline Ulbricht and Aono, Alexandre and de Castro Lara, Letícia Aparecida and Pessoa-Filho, Marco and Barrios, Sanzio Carvalho Lima and Garcia, Antonio Augusto Franco and do Valle, Cacilda Borges and de Souza, Anete Pereira and et al.}, year={2023}, month={Nov} }
 @article{c. l. moraes aline_mollinari_ulbricht_aono_castro lara_pessoa-filho_l_garcia_valle_souza_et al._2023, title={Advances in genomic characterization of<i>Urochloa humidicola</i>: exploring polyploid inheritance and apomixis}, volume={9}, url={http://dx.doi.org/10.1101/2023.08.31.555743}, DOI={10.1101/2023.08.31.555743}, abstractNote={AbstractTropical forage grasses are an important food source for animal feeding, withUrochloa humidicola, also known as Koronivia grass, being one of the main pasture grasses for poorly drained soils in the tropics. However, genetic and genomic resources for this species are lacking due to its genomic complexity, including high heterozygosity, evidence of segmental allopolyploidy, and reproduction by apomixis. These complexities hinder the application of marker-assisted selection (MAS) in breeding programs. Here, we developed the highest-density linkage map currently available for the hexaploid tropical forage grassU. humidicola. This map was constructed using a biparental F1 population generated from a cross between the female parent H031 (CIAT 26146), the only known sexual genotype for the species, and the apomictic male parent H016 (BRS cv. Tupi). The linkage analysis included 4,873 single nucleotide polymorphism (SNP) markers with allele dosage information. It allowed mapping of the apospory locus and phenotype to linkage group 3, in a region syntenic with chromosome 3 ofUrochloa ruziziensisand chromosome 1 ofSetaria italica. We also identified hexaploid haplotypes for all individuals, assessed the meiotic configuration, and estimated the level of preferential pairing in parents during the meiotic process, which revealed the autopolyploid origin of sexual H031 in contrast to H016, which presented allopolyploid behavior in preferential pairing analysis. These results provide new information regarding the genetic organization, mode of reproduction, and allopolyploid origin ofU. humidicola, potential SNPs markers associated to apomixes for MAS and resources for research on polyploids and tropical forage grasses.Key messageWe present the highest-density genetic map for the hexaploidUrochloa humidicola. SNP markers expose genetic organization, reproduction, and species origin, aiding polyploid and tropical forage research.}, publisher={Cold Spring Harbor Laboratory}, author={C. L. Moraes Aline and Mollinari, Marcelo and Ulbricht, Rebecca and Aono, Alexandre and Castro Lara, Letícia Aparecida and Pessoa-Filho, Marco and L, Barrios S C and Garcia, Antonio Augusto Franco and VALLE, CACILDA BORGGES DO and Souza, Anete P and et al.}, year={2023}, month={Sep} }
 @inproceedings{wu_sun_kitavi_hamilton_gesteira_mollinari_zeng_yencho_buell_fei_2023, title={Advances in the Development of Chromosome-Scale Haplotype-Resolved Genome Assemblies of Hexaploid Sweetpotatoes}, booktitle={International Plant & Animal Genome 30 Conference}, author={Wu, S. and Sun, H. and Kitavi, M. and Hamilton, J.P. and Gesteira, G.S. and Mollinari, M. and Zeng, Z.-B. and Yencho, C. and Buell, R. and Fei, Z.}, year={2023} }
 @inproceedings{gesteira_mollinari_pereira_olukolu_oloka_yencho_zeng_2023, title={Genetic Mapping in Interconnected Hexaploid Sweetpotato Populations}, booktitle={International Plant & Animal Genome 30 Conference}, author={Gesteira, G.S. and Mollinari, M. and Pereira, G. da S. and Olukolu, B.A. and Oloka, B.M. and Yencho, C. and Zeng, Z.-B.}, year={2023} }
 @inproceedings{taniguti_taniguti_lau_garcia_mollinari_byrne_riera-lizarazu_2023, title={Selecting the Best Bioinformatic Pipeline for Evaluating Diploid and Auto-Tetraploid Garden Rose Genotype-by-Sequencing Data}, booktitle={International Plant & Animal Genome 30 Conference}, author={Taniguti, C.H. and Taniguti, L.M. and Lau, J. and Garcia, A.A.F. and Mollinari, M. and Byrne, D. and Riera-Lizarazu, O.}, year={2023} }
 @article{taniguti_taniguti_amadeu_lau_gesteira_oliveira_ferreira_pereira_byrne_mollinari_et al._2023, title={Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps}, volume={12}, ISSN={2047-217X}, url={http://dx.doi.org/10.1093/gigascience/giad092}, DOI={10.1093/gigascience/giad092}, abstractNote={Abstract
               
                  Background
                  Genotyping-by-sequencing (GBS) provides affordable methods for genotyping hundreds of individuals using millions of markers. However, this challenges bioinformatic procedures that must overcome possible artifacts such as the bias generated by polymerase chain reaction duplicates and sequencing errors. Genotyping errors lead to data that deviate from what is expected from regular meiosis. This, in turn, leads to difficulties in grouping and ordering markers, resulting in inflated and incorrect linkage maps. Therefore, genotyping errors can be easily detected by linkage map quality evaluations.
               
               
                  Results
                  We developed and used the Reads2Map workflow to build linkage maps with simulated and empirical GBS data of diploid outcrossing populations. The workflows run GATK, Stacks, TASSEL, and Freebayes for single-nucleotide polymorphism calling and updog, polyRAD, and SuperMASSA for genotype calling, as well as OneMap and GUSMap to build linkage maps. Using simulated data, we observed which genotype call software fails in identifying common errors in GBS sequencing data and proposed specific filters to better handle them. We tested whether it is possible to overcome errors in a linkage map using genotype probabilities from each software or global error rates to estimate genetic distances with an updated version of OneMap. We also evaluated the impact of segregation distortion, contaminant samples, and haplotype-based multiallelic markers in the final linkage maps. Through our evaluations, we observed that some of the approaches produce different results depending on the dataset (dataset dependent) and others produce consistent advantageous results among them (dataset independent).
               
               
                  Conclusions
                  We set as default in the Reads2Map workflows the approaches that showed to be dataset independent for GBS datasets according to our results. This reduces the number of required tests to identify optimal pipelines and parameters for other empirical datasets. Using Reads2Map, users can select the pipeline and parameters that best fit their data context. The Reads2MapApp shiny app provides a graphical representation of the results to facilitate their interpretation.
               }, journal={GigaScience}, publisher={Oxford University Press (OUP)}, author={Taniguti, Cristiane Hayumi and Taniguti, Lucas Mitsuo and Amadeu, Rodrigo Rampazo and Lau, Jeekin and Gesteira, Gabriel de Siqueira and Oliveira, Thiago de Paula and Ferreira, Getulio Caixeta and Pereira, Guilherme da Silva and Byrne, David and Mollinari, Marcelo and et al.}, year={2023} }
 @article{taniguti_taniguti_amadeu_lau_gesteira_paula oliveira_ferreira_pereira_byrne_mollinari_et al._2022, title={Developing best practices for genotyping-by-sequencing analysis using linkage maps as benchmarks}, volume={11}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85146963616&partnerID=MN8TOARS}, DOI={10.1101/2022.11.24.517847}, abstractNote={Background: Genotyping-by-Sequencing (GBS) provides affordable methods for genotyping hundreds of individuals using millions of markers. However, this challenges bioinformatic procedures that must overcome possible artifacts such as the bias generated by PCR duplicates and sequencing errors. Genotyping errors lead to data that deviate from what is expected from regular meiosis. This, in turn, leads to difficulties in grouping and ordering markers resulting in inflated and incorrect linkage maps. Therefore, genotyping errors can be easily detected by linkage map quality evaluations. Results: We developed and used the Reads2Map workflow to build linkage maps with simulated and empirical GBS data of diploid outcrossing populations. The workflows run GATK, Stacks, TASSEL, and Freebayes for SNP calling and updog, polyRAD, and SuperMASSA for genotype calling, and OneMap and GUSMap to build linkage maps. Using simulated data, we observed which genotype call software fails in identifying common errors in GBS sequencing data and proposed specific filters to better handle them. We tested whether it is possible to overcome errors in a linkage map using genotype probabilities from each software or global error rates to estimate genetic distances with an updated version of OneMap. We also evaluated the impact of segregation distortion, contaminant samples, and haplotype-based multiallelic markers in the final linkage maps. Through our evaluations, we observed that some of the approaches produce different results depending on the dataset (dataset-dependent) and others produce consistent advantageous results among them (dataset-independent). Conclusions: We set as default in the Reads2Map workflows the approaches that showed to be dataset-independent for GBS datasets according to our results. This reduces the number required of tests to identify optimal pipelines and parameters for other empirical datasets. Using Reads2Map, users can select the pipeline and parameters that best fit their data context. The Reads2MapApp shiny app provides a graphical representation of the results to facilitate their interpretation.}, journal={bioRxiv}, publisher={Cold Spring Harbor Laboratory}, author={Taniguti, C. H. and Taniguti, Lucas Mitsuo and Amadeu, Rodrigo Rampazo and Lau, Jeekin and Gesteira, Gabriel De Siqueira and Paula Oliveira, Thiago and Ferreira, Getulio Caixeta and Pereira, Guilherme Da Silva and Byrne, David and Mollinari, Marcelo and et al.}, year={2022} }
 @article{zeng_mollinari_da silva pereira_olukolu_yencho_2022, title={Polyploid Goes to Genomics}, volume={2}, number={2}, journal={21st Century Pathology}, author={Zeng, Z.-B. and Mollinari, M. and da Silva Pereira, G. and Olukolu, B.A. and Yencho, G.C.}, year={2022}, pages={113} }
 @article{taniguti_de siqueira gesteira_lau_da silva pereira_zeng_byrne_riera-lizarazu_mollinari_2022, title={VIEWpoly: a visualization tool to integrate and explore
results of polyploid genetic analysis}, volume={7}, ISSN={2475-9066}, url={http://dx.doi.org/10.21105/joss.04242}, DOI={10.21105/joss.04242}, abstractNote={Autopolyploid species comprise a significant part of the agronomic market. Some examples are potato, sweet potato, roses, and blueberries. They all present more than two copies of their entire genome, which increase the complexity of genetic models. Advancements in computational tools for linkage and quantitative trait loci (QTL) analysis in autopolyploids have allowed the in-depth exploration and understanding of their genetics. Despite providing advanced methods, the results of these tools may be challenging to interpret and connect to other sources of genomic information and consequently apply them in practical breeding applications. VIEWpoly is an R package for visualizing, exploring, and integrating results from different polyploid computational tools using an interactive graphical user interface. The package allows users to explore linkage and QTL analysis results and integrates these with genomic information in a genome browser, facilitating the search for candidate genes. In addition, it provides features to download comprehensive tables and graphics for further analysis and presentation. VIEWpoly is freely available as an R package at https://CRAN.Rproject.org/package=viewpoly.}, number={74}, journal={Journal of Open Source Software}, publisher={The Open Journal}, author={Taniguti, Cristiane Hayumi and de Siqueira Gesteira, Gabriel and Lau, Jeekin and da Silva Pereira, Guilherme and Zeng, Zhao-Bang and Byrne, David and Riera-Lizarazu, Oscar and Mollinari, Marcelo}, year={2022}, month={Jun}, pages={4242} }
 @inproceedings{taniguti_gesteira_lau_pereira_zeng_byrne_riera-lizarazu_mollinari_2022, title={VIEWpoly: a visualization tool to integrate and explore results of polyploid genetic analysis in}, booktitle={International Plant & Animal Genome XXIX Conference}, author={Taniguti, C.H. and Gesteira, G. de S. and Lau, J. and Pereira, G. da S. and Zeng, Z.-B. and Byrne, D.H. and Riera-Lizarazu, O. and Mollinari, M.}, year={2022} }
 @article{oloka_da silva pereira_amankwaah_mollinari_pecota_yada_olukolu_zeng_yencho_2021, title={Discovery of a major QTL for root-knot nematode (Meloidogyne incognita) resistance in cultivated sweetpotato (Ipomoea batatas)}, volume={134}, ISSN={0040-5752 1432-2242}, url={http://dx.doi.org/10.1007/s00122-021-03797-z}, DOI={10.1007/s00122-021-03797-z}, abstractNote={AbstractKey messageUtilizing a high-density integrated genetic linkage map of hexaploid sweetpotato, we discovered a major dominant QTL for root-knot nematode (RKN) resistance and modeled its effects. This discovery is useful for development of a modern sweetpotato breeding program that utilizes marker-assisted selection and genomic selection approaches for faster genetic gain of RKN resistance.AbstractThe root-knot nematode [Meloidogyne incognita (Kofoid & White) Chitwood] (RKN) causes significant storage root quality reduction and yields losses in cultivated sweetpotato [Ipomoea batatas (L.) Lam.]. In this study, resistance to RKN was examined in a mapping population consisting of 244 progenies derived from a cross (TB) between ‘Tanzania,’ a predominant African landrace cultivar with resistance to RKN, and ‘Beauregard,’ an RKN susceptible major cultivar in the USA. We performed quantitative trait loci (QTL) analysis using a random-effect QTL mapping model on the TB genetic map. An RKN bioassay incorporating potted cuttings of each genotype was conducted in the greenhouse and replicated five times over a period of 10 weeks. For each replication, each genotype was inoculated with ca. 20,000 RKN eggs, and root-knot galls were counted ~62 days after inoculation. Resistance to RKN in the progeny was highly skewed toward the resistant parent, exhibiting medium to high levels of resistance. We identified one major QTL on linkage group 7, dominant in nature, which explained 58.3% of the phenotypic variation in RKN counts. This work represents a significant step forward in our understanding of the genetic architecture of RKN resistance and sets the stage for future utilization of genomics-assisted breeding in sweetpotato breeding programs.}, number={7}, journal={Theoretical and Applied Genetics}, publisher={Springer Science and Business Media LLC}, author={Oloka, Bonny Michael and da Silva Pereira, Guilherme and Amankwaah, Victor A. and Mollinari, Marcelo and Pecota, Kenneth V. and Yada, Benard and Olukolu, Bode A. and Zeng, Zhao-Bang and Yencho, G. Craig}, year={2021}, month={Apr}, pages={1945–1955} }
 @article{soares_mollinari_oliveira_pereira_vieira_2021, title={Meiosis in Polyploids and Implications for Genetic Mapping: A Review}, volume={12}, ISSN={2073-4425}, url={http://dx.doi.org/10.3390/genes12101517}, DOI={10.3390/genes12101517}, abstractNote={Plant cytogenetic studies have provided essential knowledge on chromosome behavior during meiosis, contributing to our understanding of this complex process. In this review, we describe in detail the meiotic process in auto- and allopolyploids from the onset of prophase I through pairing, recombination, and bivalent formation, highlighting recent findings on the genetic control and mode of action of specific proteins that lead to diploid-like meiosis behavior in polyploid species. During the meiosis of newly formed polyploids, related chromosomes (homologous in autopolyploids; homologous and homoeologous in allopolyploids) can combine in complex structures called multivalents. These structures occur when multiple chromosomes simultaneously pair, synapse, and recombine. We discuss the effectiveness of crossover frequency in preventing multivalent formation and favoring regular meiosis. Homoeologous recombination in particular can generate new gene (locus) combinations and phenotypes, but it may destabilize the karyotype and lead to aberrant meiotic behavior, reducing fertility. In crop species, understanding the factors that control pairing and recombination has the potential to provide plant breeders with resources to make fuller use of available chromosome variations in number and structure. We focused on wheat and oilseed rape, since there is an abundance of elucidating studies on this subject, including the molecular characterization of the Ph1 (wheat) and PrBn (oilseed rape) loci, which are known to play a crucial role in regulating meiosis. Finally, we exploited the consequences of chromosome pairing and recombination for genetic map construction in polyploids, highlighting two case studies of complex genomes: (i) modern sugarcane, which has a man-made genome harboring two subgenomes with some recombinant chromosomes; and (ii) hexaploid sweet potato, a naturally occurring polyploid. The recent inclusion of allelic dosage information has improved linkage estimation in polyploids, allowing multilocus genetic maps to be constructed.}, number={10}, journal={Genes}, publisher={MDPI AG}, author={Soares, Nina Reis and Mollinari, Marcelo and Oliveira, Gleicy K. and Pereira, Guilherme S. and Vieira, Maria Lucia Carneiro}, year={2021}, month={Sep}, pages={1517} }
 @article{da silva pereira_mollinari_qu_thill_zeng_haynes_yencho_2021, title={Quantitative Trait Locus Mapping for Common Scab Resistance in a Tetraploid Potato Full-Sib Population}, volume={105}, ISSN={0191-2917 1943-7692}, url={http://dx.doi.org/10.1094/PDIS-10-20-2270-RE}, DOI={10.1094/PDIS-10-20-2270-RE}, abstractNote={ Despite the negative impact of common scab (Streptomyces spp.) on the potato industry, little is known about the genetic architecture of resistance to this bacterial disease in the crop. We evaluated a mapping population (∼150 full sibs) derived from a cross between two tetraploid potatoes (‘Atlantic’ × B1829-5) in three environments (MN11, PA11, ME12) under natural common scab pressure. Three measures to common scab reaction, namely percentage of scabby tubers and disease area and lesion indices, were found to be highly correlated (>0.76). Because of the large environmental effect, heritability values were zero for all three traits in MN11, but moderate to high in PA11 and ME12 (∼0.44 to 0.79). We identified a single quantitative trait locus (QTL) for lesion index in PA11, ME12, and joint analyses on linkage group 3, explaining ∼22 to 30% of the total variation. The identification of QTL haplotypes and candidate genes contributing to disease resistance can support genomics-assisted breeding approaches in the crop.  [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license . }, number={10}, journal={Plant Disease}, publisher={Scientific Societies}, author={da Silva Pereira, Guilherme and Mollinari, Marcelo and Qu, Xinshun and Thill, Christian and Zeng, Zhao-Bang and Haynes, Kathleen and Yencho, G. Craig}, year={2021}, month={Oct}, pages={3048–3054} }
 @article{da silva pereira_mollinari_schumann_clough_zeng_yencho_2021, title={The recombination landscape and multiple QTL mapping in a Solanum tuberosum cv. ‘Atlantic’-derived F1 population}, volume={126}, ISSN={0018-067X 1365-2540}, url={http://dx.doi.org/10.1038/s41437-021-00416-x}, DOI={10.1038/s41437-021-00416-x}, abstractNote={AbstractThere are many challenges involved with the genetic analyses of autopolyploid species, such as the tetraploid potato,Solanum tuberosum(2n = 4x = 48). The development of new analytical methods has made it valuable to re-analyze an F1population (n = 156) derived from a cross involving ‘Atlantic’, a widely grown chipping variety in the USA. A fully integrated genetic map with 4285 single nucleotide polymorphisms, spanning 1630 cM, was constructed with MAPpoly software. We observed that bivalent configurations were the most abundant ones (51.0~72.4% depending on parent and linkage group), though multivalent configurations were also observed (2.2~39.2%). Seven traits were evaluated over four years (2006–8 and 2014) and quantitative trait loci (QTL) mapping was carried out using QTLpoly software. Based on a multiple-QTL model approach, we detected 21 QTL for 15 out of 27 trait-year combination phenotypes. A hotspot on linkage group 5 was identified with co-located QTL for maturity, plant yield, specific gravity, and internal heat necrosis resistance evaluated over different years. Additional QTL for specific gravity and dry matter were detected with maturity-corrected phenotypes. Among the genes around QTL peaks, we found those on chromosome 5 that have been previously implicated in maturity (StCDF1) and tuber formation (POTH1). These analyses have the potential to provide insights into the biology and breeding of tetraploid potato and other autopolyploid species.}, number={5}, journal={Heredity}, publisher={Springer Science and Business Media LLC}, author={da Silva Pereira, Guilherme and Mollinari, Marcelo and Schumann, Mitchell J. and Clough, Mark E. and Zeng, Zhao-Bang and Yencho, G. Craig}, year={2021}, month={Mar}, pages={817–830} }
 @inproceedings{mollinari_bode_pereira_gemenet_khan_yencho_zeng_2020, title={Characterization of Sweetpotato Inheritance Using Ultradense Multilocus Genetic Map}, booktitle={International Plant & Animal Genome XXVIII Conference}, author={Mollinari, M. and Bode, A.O. and Pereira, G.S. and Gemenet, D.C. and Khan, A. and Yencho, Gc and Zeng, Z B}, year={2020} }
 @article{da silva pereira_gemenet_mollinari_olukolu_wood_diaz_mosquera_gruneberg_khan_buell_et al._2020, title={Multiple QTL Mapping in Autopolyploids: A Random-Effect Model Approach with Application in a Hexaploid Sweetpotato Full-Sib Population}, volume={215}, ISSN={1943-2631}, url={http://dx.doi.org/10.1534/genetics.120.303080}, DOI={10.1534/genetics.120.303080}, abstractNote={Abstract
               Genetic analysis in autopolyploids is a very complicated subject due to the enormous number of genotypes at a locus that needs to be considered. For instance, the number of...
               In developing countries, the sweetpotato, Ipomoea batatas (L.) Lam. (2n=6x=90), is an important autopolyploid species, both socially and economically. However, quantitative trait loci (QTL) mapping has remained limited due to its genetic complexity. Current fixed-effect models can fit only a single QTL and are generally hard to interpret. Here, we report the use of a random-effect model approach to map multiple QTL based on score statistics in a sweetpotato biparental population (‘Beauregard’ × ‘Tanzania’) with 315 full-sibs. Phenotypic data were collected for eight yield component traits in six environments in Peru, and jointly adjusted means were obtained using mixed-effect models. An integrated linkage map consisting of 30,684 markers distributed along 15 linkage groups (LGs) was used to obtain the genotype conditional probabilities of putative QTL at every centiMorgan position. Multiple interval mapping was performed using our R package QTLpoly and detected a total of 13 QTL, ranging from none to four QTL per trait, which explained up to 55% of the total variance. Some regions, such as those on LGs 3 and 15, were consistently detected among root number and yield traits, and provided a basis for candidate gene search. In addition, some QTL were found to affect commercial and noncommercial root traits distinctly. Further best linear unbiased predictions were decomposed into additive allele effects and were used to compute multiple QTL-based breeding values for selection. Together with quantitative genotyping and its appropriate usage in linkage analyses, this QTL mapping methodology will facilitate the use of genomic tools in sweetpotato breeding as well as in other autopolyploids.}, number={3}, journal={Genetics}, publisher={Oxford University Press (OUP)}, author={da Silva Pereira, Guilherme and Gemenet, Dorcus C and Mollinari, Marcelo and Olukolu, Bode A and Wood, Joshua C and Diaz, Federico and Mosquera, Veronica and Gruneberg, Wolfgang J and Khan, Awais and Buell, C Robin and et al.}, year={2020}, month={Jul}, pages={579–595} }
 @article{silva pereira_mollinari_qu_thill_zeng_haynes_yencho_2020, title={Quantitative trait locus mapping for common scab resistance in a tetraploid potato full-sib population}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85098810824&partnerID=MN8TOARS}, DOI={10.1101/2020.10.24.353557}, abstractNote={AbstractDespite the negative impact of common scab (Streptomyces spp.) to the potato industry, little is known about the genetic architecture of resistance to this bacterial disease in the crop. We evaluated a mapping population (~150 full-sibs) derived from a cross between two tetraploid potatoes (‘Atlantic’ × B1829-5) in three environments (MN11, PA11, ME12) under natural common scab pressure. Three measures to common scab reaction were assessed, namely percentage of scabby tubers, and disease area and lesion indices, which were highly correlated (>0.76). Due to large environmental effect, heritability values were zero for all three traits in MN11, but moderate to high in PA11 and ME12 (0.44~0.79). We identified a single quantitative trait locus (QTL) for lesion index in PA11, ME12 and joint analyses on linkage group 3, explaining 22~30% of the total variation. The identification of QTL haplotypes and candidate genes contributing to disease resistance can support genomics-assisted breeding approaches.}, journal={bioRxiv}, author={Silva Pereira, Guilherme and Mollinari, Marcelo and Qu, Xinshun and Thill, Christian and Zeng, Zhao-Bang and Haynes, Kathleen and Yencho, G. Craig}, year={2020} }
 @article{gemenet_lindqvist-kreuze_de boeck_da silva pereira_mollinari_zeng_craig yencho_campos_2020, title={Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops}, volume={133}, ISSN={0040-5752 1432-2242}, url={http://dx.doi.org/10.1007/s00122-020-03673-2}, DOI={10.1007/s00122-020-03673-2}, abstractNote={Key messagePolypoid crop breeders can balance resources between density and sequencing depth, dosage information and fewer highly informative SNPs recommended, non-additive models and QTL advantages on prediction dependent on trait architecture.AbstractThe autopolyploid nature of potato and sweetpotato ensures a wide range of meiotic configurations and linkage phases leading to complex gene-action and pose problems in genotype data quality and genomic selection analyses. We used a 315-progeny biparentalF1population of hexaploid sweetpotato and a diversity panel of 380 tetraploid potato, genotyped using different platforms to answer the following questions: (i) do polyploid crop breeders need to invest more for additional sequencing depth? (ii) how many markers are required to make selection decisions? (iii) does considering non-additive genetic effects improve predictive ability (PA)? (iv) does considering dosage or quantitative trait loci (QTL) offer significant improvement to PA? Our results show that only a small number of highly informative single nucleotide polymorphisms (SNPs; ≤ 1000) are adequate for prediction in the type of populations we analyzed. We also show that considering dosage information and models considering only additive effects had the best PA for most traits, while the comparative advantage of considering non-additive genetic effects and including known QTL in the predictive model depended on trait architecture. We conclude that genomic selection can help accelerate the rate of genetic gains in potato and sweetpotato. However, application of genomic selection should be considered as part of optimizing the entire breeding program. Additionally, since the predictions in the current study are based on single populations, further studies on the effects of haplotype structure and inheritance on PA should be studied in actual multi-generation breeding populations.}, number={12}, journal={Theoretical and Applied Genetics}, publisher={Springer Science and Business Media LLC}, author={Gemenet, Dorcus C. and Lindqvist-Kreuze, Hannele and De Boeck, Bert and da Silva Pereira, Guilherme and Mollinari, Marcelo and Zeng, Zhao-Bang and Craig Yencho, G. and Campos, Hugo}, year={2020}, month={Sep}, pages={3345–3363} }
 @article{gazaffi_amadeu_mollinari_rosa_taniguti_margarido_garcia_2020, title={fullsibQTL: An R package for QTL mapping in biparental populations of outcrossing species}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85099897031&partnerID=MN8TOARS}, DOI={10.1101/2020.12.04.412262}, abstractNote={ABSTRACTAccurate QTL mapping in outcrossing species requires software programs which consider genetic features of these populations, such as markers with different segregation patterns and different level of information. Although the available mapping procedures to date allow inferring QTL position and effects, they are mostly not based on multilocus genetic maps. Having a QTL analysis based in such maps is crucial since they allow informative markers to propagate their information to less informative intervals of the map. We developedfullsibQTL, a novel and freely availableRpackage to perform composite interval QTL mapping considering outcrossing populations and markers with different segregation patterns. It allows to estimate QTL position, effects, segregation patterns, and linkage phase with flanking markers. Additionally, several statistical and graphical tools are implemented, for straightforward analysis and interpretations.fullsibQTLis anRopen source package withCandRsource code (GPLv3). It is multiplatform and can be installed fromhttps://github.com/augusto-garcia/fullsibQTL.}, journal={bioRxiv}, author={Gazaffi, R. and Amadeu, R.R. and Mollinari, M. and Rosa, J.R.B.F. and Taniguti, C.H. and Margarido, G.R.A. and Garcia, A.A.F.}, year={2020} }
 @article{mollinari_garcia_2019, title={Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models}, volume={9}, ISSN={2160-1836}, url={http://dx.doi.org/10.1534/g3.119.400378}, DOI={10.1534/g3.119.400378}, abstractNote={AbstractModern SNP genotyping technologies allow measurement of the relative abundance of different alleles for a given locus and consequently estimation of their allele dosage, opening a new road for genetic studies in autopolyploids. Despite advances in genetic linkage analysis in autotetraploids, there is a lack of statistical models to perform linkage analysis in organisms with higher ploidy levels. In this paper, we present a statistical method to estimate recombination fractions and infer linkage phases in full-sib populations of autopolyploid species with even ploidy levels for a set of SNP markers using hidden Markov models. Our method uses efficient two-point procedures to reduce the search space for the best linkage phase configuration and reestimate the final parameters by maximizing the likelihood of the Markov chain. To evaluate the method, and demonstrate its properties, we rely on simulations of autotetraploid, autohexaploid and autooctaploid populations and on a real tetraploid potato data set. The results show the reliability of our approach, including situations with complex linkage phase scenarios in hexaploid and octaploid populations.}, number={10}, journal={G3&#58; Genes|Genomes|Genetics}, publisher={Genetics Society of America}, author={Mollinari, Marcelo and Garcia, Antonio Augusto Franco}, year={2019}, month={Aug}, pages={3297–3314} }
 @misc{silva pereira_gemenet_mollinari_olukolu_wood_diaz_mosquera_gruneberg_khan_buell_et al._2019, title={Multiple QTL mapping in autopolyploids: a random-effect model approach with application in a hexaploid sweetpotato full-sib population}, url={http://dx.doi.org/10.1101/622951}, DOI={10.1101/622951}, abstractNote={ABSTRACTIn developing countries, the sweetpotato,Ipomoea batatas(L.) Lam. (2n= 6x= 90), is an important autopolyploid species, both socially and economically. However, quantitative trait loci (QTL) mapping has remained limited due to its genetic complexity. Current fixed-effect models can only fit a single QTL and are generally hard to interpret. Here we report the use of a random-effect model approach to map multiple QTL based on score statistics in a sweetpotato bi-parental population (‘Beauregard’בTanzania’) with 315 full-sibs. Phenotypic data were collected for eight yield component traits in six environments in Peru, and jointly predicted means were obtained using mixed-effect models. An integrated linkage map consisting of 30,684 markers distributed along 15 linkage groups (LGs) was used to obtain the genotype conditional probabilities of putative QTL at every cM position. Multiple interval mapping was performed using our R package QTLPOLY and detected a total of 41 QTL, ranging from one to ten QTL per trait. Some regions, such as those on LGs 3 and 15, were consistently detected among root number and yield traits and provided basis for candidate gene search. In addition, some QTL were found to affect commercial and noncommercial root traits distinctly. Further best linear unbiased predictions allowed us to characterize additive allele effects as well as to compute QTL-based breeding values for selection. Together with quantitative genotyping and its appropriate usage in linkage analyses, this QTL mapping methodology will facilitate the use of genomic tools in sweetpotato breeding as well as in other autopolyploids.}, publisher={Cold Spring Harbor Laboratory}, author={Silva Pereira, Guilherme da and Gemenet, Dorcus C. and Mollinari, Marcelo and Olukolu, Bode A. and Wood, Joshua C. and Diaz, Federico and Mosquera, Veronica and Gruneberg, Wolfgang J. and Khan, Awais and Buell, C. Robin and et al.}, year={2019}, month={Apr} }
 @inproceedings{oloka_pereira_mollinari_gesteira_fraher_pecota_olukolu_yada_anyanga_chelangat_et al._2019, title={Progress in the Implementation of Genomic Selection and Marker-Assisted Breeding in Sweetpotato}, booktitle={International Plant & Animal Genome 30 Conference}, author={Oloka, B.M. and Pereira, G. da S. and Mollinari, M. and Gesteira, G.S. and Fraher, S. and Pecota, K. and Olukolu, B.A. and Yada, B. and Anyanga, M.O. and Chelangat, D. and et al.}, year={2019} }
 @article{gemenet_da silva pereira_de boeck_wood_mollinari_olukolu_diaz_mosquera_ssali_david_et al._2019, title={Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated β-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.]}, volume={133}, ISSN={0040-5752 1432-2242}, url={http://dx.doi.org/10.1007/s00122-019-03437-7}, DOI={10.1007/s00122-019-03437-7}, abstractNote={Abstract

Key message
β-Carotene content in sweetpotato is associated with the Orange and phytoene synthase genes; due to physical linkage of phytoene synthase with sucrose synthase, β-carotene and starch content are negatively correlated.


Abstract
In populations depending on sweetpotato for food security, starch is an important source of calories, while β-carotene is an important source of provitamin A. The negative association between the two traits contributes to the low nutritional quality of sweetpotato consumed, especially in sub-Saharan Africa. Using a biparental mapping population of 315 F1 progeny generated from a cross between an orange-fleshed and a non-orange-fleshed sweetpotato variety, we identified two major quantitative trait loci (QTL) on linkage group (LG) three (LG3) and twelve (LG12) affecting starch, β-carotene, and their correlated traits, dry matter and flesh color. Analysis of parental haplotypes indicated that these two regions acted pleiotropically to reduce starch content and increase β-carotene in genotypes carrying the orange-fleshed parental haplotype at the LG3 locus. Phytoene synthase and sucrose synthase, the rate-limiting and linked genes located within the QTL on LG3 involved in the carotenoid and starch biosynthesis, respectively, were differentially expressed in Beauregard versus Tanzania storage roots. The Orange gene, the molecular switch for chromoplast biogenesis, located within the QTL on LG12 while not differentially expressed was expressed in developing roots of the parental genotypes. We conclude that these two QTL regions act together in a cis and trans manner to inhibit starch biosynthesis in amyloplasts and enhance chromoplast biogenesis, carotenoid biosynthesis, and accumulation in orange-fleshed sweetpotato. Understanding the genetic basis of this negative association between starch and β-carotene will inform future sweetpotato breeding strategies targeting sweetpotato for food and nutritional security.
}, number={1}, journal={Theoretical and Applied Genetics}, publisher={Springer Science and Business Media LLC}, author={Gemenet, Dorcus C. and da Silva Pereira, Guilherme and De Boeck, Bert and Wood, Joshua C. and Mollinari, Marcelo and Olukolu, Bode A. and Diaz, Federico and Mosquera, Veronica and Ssali, Reuben T. and David, Maria and et al.}, year={2019}, month={Oct}, pages={23–36} }
 @article{mollinari_olukolu_pereira_khan_gemenet_yencho_zeng_2019, title={Unraveling the Hexaploid Sweetpotato Inheritance Using Ultra-Dense Multilocus Mapping}, volume={10}, ISSN={2160-1836}, url={http://dx.doi.org/10.1534/g3.119.400620}, DOI={10.1534/g3.119.400620}, abstractNote={AbstractThe hexaploid sweetpotato (Ipomoea batatas (L.) Lam., 2n = 6x = 90) is an important staple food crop worldwide and plays a vital role in alleviating famine in developing countries. Due to its high ploidy level, genetic studies in sweetpotato lag behind major diploid crops significantly. We built an ultra-dense multilocus integrated genetic map and characterized the inheritance system in a sweetpotato full-sib family using our newly developed software, MAPpoly. The resulting genetic map revealed 96.5% collinearity between I. batatas and its diploid relative I. trifida. We computed the genotypic probabilities across the whole genome for all individuals in the mapping population and inferred their complete hexaploid haplotypes. We provide evidence that most of the meiotic configurations (73.3%) were resolved in bivalents, although a small portion of multivalent signatures (15.7%), among other inconclusive configurations (11.0%), were also observed. Except for low levels of preferential pairing in linkage group 2, we observed a hexasomic inheritance mechanism in all linkage groups. We propose that the hexasomic-bivalent inheritance promotes stability to the allelic transmission in sweetpotato.}, number={1}, journal={G3&#58; Genes|Genomes|Genetics}, publisher={Genetics Society of America}, author={Mollinari, Marcelo and Olukolu, Bode A. and Pereira, Guilherme da S. and Khan, Awais and Gemenet, Dorcus and Yencho, G. Craig and Zeng, Zhao-Bang}, year={2019}, month={Nov}, pages={281–292} }
 @inproceedings{mollinari_bode_pereira_gemenet_khan_kitavi_ghislain_yencho_zeng_2018, title={B.Construction of an Ultradense Genetic Map in Hexaploid Sweetpotato}, booktitle={International Plant & Animal Genome XXVI Conference}, author={Mollinari, M. and Bode, Ao and Pereira, G.S. and Gemenet, D.C. and Khan, A. and Kitavi, M.N. and Ghislain, M and Yencho, G.C. and Zeng, Z}, year={2018} }
 @inproceedings{mollinari_pereira_shumann_yencho_zeng_garcia_2016, title={Construction of Genetic Maps in Complex Autopolyploids}, booktitle={International Conference in Quantitative Genetics 5}, author={Mollinari, M. and Pereira, G.S. and Shumann, M and Yencho, C and Zeng, Z.-B. and Garcia, A.A.F.}, year={2016} }
 @article{vigna_santos_jungmann_do valle_mollinari_pastina_pagliarini_garcia_souza_2016, title={Evidence of Allopolyploidy in Urochloa humidicola Based on Cytological Analysis and Genetic Linkage Mapping}, volume={11}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0153764}, DOI={10.1371/journal.pone.0153764}, abstractNote={The African species Urochloa humidicola (Rendle) Morrone & Zuloaga (syn. Brachiaria humidicola (Rendle) Schweick.) is an important perennial forage grass found throughout the tropics. This species is polyploid, ranging from tetra to nonaploid, and apomictic, which makes genetic studies challenging; therefore, the number of currently available genetic resources is limited. The genomic architecture and evolution of U. humidicola and the molecular markers linked to apomixis were investigated in a full-sib F1 population obtained by crossing the sexual accession H031 and the apomictic cultivar U. humidicola cv. BRS Tupi, both of which are hexaploid. A simple sequence repeat (SSR)-based linkage map was constructed for the species from 102 polymorphic and specific SSR markers based on simplex and double-simplex markers. The map consisted of 49 linkage groups (LGs) and had a total length of 1702.82 cM, with 89 microsatellite loci and an average map density of 10.6 cM. Eight homology groups (HGs) were formed, comprising 22 LGs, and the other LGs remained ungrouped. The locus that controls apospory (apo-locus) was mapped in LG02 and was located 19.4 cM from the locus Bh027.c.D2. In the cytological analyses of some hybrids, bi- to hexavalents at diakinesis were observed, as well as two nucleoli in some meiocytes, smaller chromosomes with preferential allocation within the first metaphase plate and asynchronous chromosome migration to the poles during anaphase. The linkage map and the meiocyte analyses confirm previous reports of hybridization and suggest an allopolyploid origin of the hexaploid U. humidicola. This is the first linkage map of an Urochloa species, and it will be useful for future quantitative trait locus (QTL) analysis after saturation of the map and for genome assembly and evolutionary studies in Urochloa spp. Moreover, the results of the apomixis mapping are consistent with previous reports and confirm the need for additional studies to search for a co-segregating marker.}, number={4}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Vigna, Bianca B. Z. and Santos, Jean C. S. and Jungmann, Leticia and do Valle, Cacilda B. and Mollinari, Marcelo and Pastina, Maria M. and Pagliarini, Maria Suely and Garcia, Antonio A. F. and Souza, Anete P.}, editor={Yin, TongmingEditor}, year={2016}, month={Apr}, pages={e0153764} }
 @article{costa_anoni_mancini_santos_marconi_gazaffi_pastina_perecin_mollinari_xavier_et al._2016, title={QTL mapping including codominant SNP markers with ploidy level information in a sugarcane progeny}, volume={211}, ISSN={0014-2336 1573-5060}, url={http://dx.doi.org/10.1007/s10681-016-1746-7}, DOI={10.1007/s10681-016-1746-7}, abstractNote={AbstractQuantitative trait locus (QTL) mapping contributes to sugarcane (Saccharum spp.) breeding programs by providing information about the genetic effects, positioning and number of QTLs. Combined with marker-assisted selection, it can help breeders reduce the time required to develop new sugarcane varieties. We performed a QTL mapping study for important agronomic traits in sugarcane using the composite interval mapping method for outcrossed species. A new approach allowing the 1:2:1 segregation ratio and different ploidy levels for SNP markers was used to construct an integrated genetic linkage map that also includes AFLP and SSR markers. Were used 688 molecular markers with 1:1, 3:1 and 1:2:1 segregation ratios. A total of 187 individuals from a bi-parental cross (IACSP95-3018 and IACSP93-3046) were assayed across multiple harvests from two locations. The evaluated yield components included stalk diameter (SD), stalk weight (SW), stalk height (SH), fiber percentage (Fiber), sucrose content (Pol) and soluble solid content (Brix). The genetic linkage map covered 4512.6 cM and had 118 linkage groups corresponding to 16 putative homology groups. A total of 25 QTL were detected for SD (six QTL), SW (five QTL), SH (four QTL), Fiber (five QTL), Pol (two QTL) and Brix (three QTL). The percentage of phenotypic variation explained by each QTL ranged from 0.069 to 3.87 %, with a low individual effect because of the high ploidy level. The mapping model provided estimates of the segregation ratio of each mapped QTL (1:2:1, 3:1 or 1:1). Our results provide information about the genetic organization of the sugarcane genome and constitute the first step toward a better dissection of complex traits.}, number={1}, journal={Euphytica}, publisher={Springer Science and Business Media LLC}, author={Costa, E. A. and Anoni, C. O. and Mancini, M. C. and Santos, F. R. C. and Marconi, T. G. and Gazaffi, R. and Pastina, M. M. and Perecin, D. and Mollinari, M. and Xavier, M. A. and et al.}, year={2016}, month={Jul}, pages={1–16} }
 @article{gazaffi_margarido_pastina_mollinari_garcia_2014, title={A model for quantitative trait loci mapping, linkage phase, and segregation pattern estimation for a full-sib progeny}, volume={10}, ISSN={1614-2942 1614-2950}, url={http://dx.doi.org/10.1007/s11295-013-0664-2}, DOI={10.1007/s11295-013-0664-2}, abstractNote={Quantitative trait loci (QTL) mapping is an important approach for the study of the genetic architecture of quantitative traits. For perennial species, inbred lines cannot be obtained due to inbreed depression and a long juvenile period. Instead, linkage mapping can be performed by using a full-sib progeny. This creates a complex scenario because both markers and QTL alleles can have different segregation patterns as well as different linkage phases between them. We present a two-step method for QTL mapping using full-sib progeny based on composite interval mapping (i.e., interval mapping with cofactors), considering an integrated genetic map with markers with different segregation patterns and conditional probabilities obtained by a multipoint approach. The model is based on three orthogonal contrasts to estimate the additive effect (one in each parent) and dominance effect. These estimatives are obtained using the EM algorithm. In the first step, the genome is scanned to detect QTL. After, segregation pattern and linkage phases between QTL and markers are estimated. A simulated example is presented to validate the methodology. In general, the new model is more effective than existing approaches, because it can reveal QTL present in a full-sib progeny that segregates in any pattern present and can also identify dominance effects. Also, the inclusion of cofactors provided more statistical power for QTL mapping.}, number={4}, journal={Tree Genetics & Genomes}, publisher={Springer Science and Business Media LLC}, author={Gazaffi, Rodrigo and Margarido, Gabriel R. A. and Pastina, Maria Marta and Mollinari, Marcelo and Garcia, Antonio Augusto F.}, year={2014}, month={Apr}, pages={791–801} }
 @inproceedings{mollinari_garcia_craig_doerge_2014, title={A new method to construct genetic maps in complex autopolyploids using quantitative SNP genotyping}, booktitle={Kansas State Conference on Applied Statistics in Agriculture}, author={Mollinari, M. and Garcia, A.A.F. and Craig, B. and Doerge, R.W.}, year={2014} }
 @inbook{mollinari_serang_2014, title={Quantitative SNP Genotyping of Polyploids with MassARRAY and Other Platforms}, volume={1245}, ISBN={9781493919659 9781493919666}, ISSN={1064-3745 1940-6029}, url={http://dx.doi.org/10.1007/978-1-4939-1966-6_17}, DOI={10.1007/978-1-4939-1966-6_17}, abstractNote={Accurate genotyping is essential for building genetic maps and performing genome assembly of polyploid species. Recent high-throughput techniques, such as Illumina GoldenGate™ and Sequenom iPLEX MassARRAY®, have made it possible to accurately estimate the relative abundances of different alleles even when the ploidy of the population is unknown. Here we describe the experimental methods for collecting these relative allele intensities and then demonstrate the practical concerns for inferring genotypes using Bayesian inference via the software package SuperMASSA.}, booktitle={Methods in Molecular Biology}, publisher={Springer New York}, author={Mollinari, Marcelo and Serang, Oliver}, year={2014}, month={Oct}, pages={215–241} }
 @article{garcia_mollinari_marconi_serang_silva_vieira_vicentini_costa_mancini_garcia_et al._2013, title={SNP genotyping allows an in-depth characterisation of the genome of sugarcane and other complex autopolyploids}, volume={3}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/srep03399}, DOI={10.1038/srep03399}, abstractNote={Many plant species of great economic value (e.g., potato, wheat, cotton and sugarcane) are polyploids. Despite the essential roles of autopolyploid plants in human activities, our genetic understanding of these species is still poor. Recent progress in instrumentation and biochemical manipulation has led to the accumulation of an incredible amount of genomic data. In this study, we demonstrate for the first time a successful genetic analysis in a highly polyploid genome (sugarcane) by the quantitative analysis of single-nucleotide polymorphism (SNP) allelic dosage and the application of a new data analysis framework. This study provides a better understanding of autopolyploid genomic structure and is a sound basis for genetic studies. The proposed methods can be employed to analyse the genome of any autopolyploid and will permit the future development of high-quality genetic maps to assist in the assembly of reference genome sequences for polyploid species.}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Garcia, Antonio A. F. and Mollinari, Marcelo and Marconi, Thiago G. and Serang, Oliver R. and Silva, Renato R. and Vieira, Maria L. C. and Vicentini, Renato and Costa, Estela A. and Mancini, Melina C. and Garcia, Melissa O. S. and et al.}, year={2013}, month={Dec} }
 @article{palhares_rodrigues-morais_van sluys_domingues_maccheroni_jordão_souza_marconi_mollinari_gazaffi_et al._2012, title={A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers}, volume={13}, ISSN={1471-2156}, url={http://dx.doi.org/10.1186/1471-2156-13-51}, DOI={10.1186/1471-2156-13-51}, abstractNote={Abstract
          
            Background
            The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily.
          
          
            Results
            The mapping population parents (‘IAC66-6’ and ‘TUC71-7’) contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56) were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization.
          
          
            Conclusions
            Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposon scIvana_1 (~60) copies in the sugarcane genome, confirming previously reported molecular results. In addition, this research possibly will have indirect implications in crop economics e.g., productivity enhancement via QTL studies, as the mapping population parents differ in response to an important fungal disease.
          }, number={1}, journal={BMC Genetics}, publisher={Springer Science and Business Media LLC}, author={Palhares, Alessandra C and Rodrigues-Morais, Taislene B and Van Sluys, Marie-Anne and Domingues, Douglas S and Maccheroni, Walter, Jr and Jordão, Hamilton, Jr and Souza, Anete P and Marconi, Thiago G and Mollinari, Marcelo and Gazaffi, Rodrigo and et al.}, year={2012}, month={Jun} }
 @inproceedings{mollinari_marconi_mancini_costa_pinto_souza_garcia_2012, title={A novel method to construct genetic linkage maps in high autopolyploid species using hidden Markov models, with applications in sugarcane}, booktitle={International Plant & Animal Genome XX Conference}, author={Mollinari, M. and Marconi, T.G. and Mancini, M.C. and Costa, E.A. and Pinto, L.R. and Souza, A.P. and Garcia, A.A.F.}, year={2012} }
 @article{serang_mollinari_garcia_2012, title={Efficient Exact Maximum a Posteriori Computation for Bayesian SNP Genotyping in Polyploids}, volume={7}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0030906}, DOI={10.1371/journal.pone.0030906}, abstractNote={The problem of genotyping polyploids is extremely important for the creation of genetic maps and assembly of complex plant genomes. Despite its significance, polyploid genotyping still remains largely unsolved and suffers from a lack of statistical formality. In this paper a graphical Bayesian model for SNP genotyping data is introduced. This model can infer genotypes even when the ploidy of the population is unknown. We also introduce an algorithm for finding the exact maximum a posteriori genotype configuration with this model. This algorithm is implemented in a freely available web-based software package SuperMASSA. We demonstrate the utility, efficiency, and flexibility of the model and algorithm by applying them to two different platforms, each of which is applied to a polyploid data set: Illumina GoldenGate data from potato and Sequenom MassARRAY data from sugarcane. Our method achieves state-of-the-art performance on both data sets and can be trivially adapted to use models that utilize prior information about any platform or species.}, number={2}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Serang, Oliver and Mollinari, Marcelo and Garcia, Antonio Augusto Franco}, editor={Rapallo, FabioEditor}, year={2012}, month={Feb}, pages={e30906} }
 @article{sabadin_malosetti_boer_tardin_santos_guimarães_gomide_andrade_albuquerque_caniato_et al._2012, title={Studying the genetic basis of drought tolerance in sorghum by managed stress trials and adjustments for phenological and plant height differences}, volume={124}, ISSN={0040-5752 1432-2242}, url={http://dx.doi.org/10.1007/s00122-012-1795-9}, DOI={10.1007/s00122-012-1795-9}, abstractNote={Managed environments in the form of well watered and water stressed trials were performed to study the genetic basis of grain yield and stay green in sorghum with the objective of validating previously detected QTL. As variations in phenology and plant height may influence QTL detection for the target traits, QTL for flowering time and plant height were introduced as cofactors in QTL analyses for yield and stay green. All but one of the flowering time QTL were detected near yield and stay green QTL. Similar co-localization was observed for two plant height QTL. QTL analysis for yield, using flowering time/plant height cofactors, led to yield QTL on chromosomes 2, 3, 6, 8 and 10. For stay green, QTL on chromosomes 3, 4, 8 and 10 were not related to differences in flowering time/plant height. The physical positions for markers in QTL regions projected on the sorghum genome suggest that the previously detected plant height QTL, Sb-HT9-1, and Dw2, in addition to the maturity gene, Ma5, had a major confounding impact on the expression of yield and stay green QTL. Co-localization between an apparently novel stay green QTL and a yield QTL on chromosome 3 suggests there is potential for indirect selection based on stay green to improve drought tolerance in sorghum. Our QTL study was carried out with a moderately sized population and spanned a limited geographic range, but still the results strongly emphasize the necessity of corrections for phenology in QTL mapping for drought tolerance traits in sorghum.}, number={8}, journal={Theoretical and Applied Genetics}, publisher={Springer Science and Business Media LLC}, author={Sabadin, P. K. and Malosetti, M. and Boer, M. P. and Tardin, F. D. and Santos, F. G. and Guimarães, C. T. and Gomide, R. L. and Andrade, C. L. T. and Albuquerque, P. E. P. and Caniato, F. F. and et al.}, year={2012}, month={Feb}, pages={1389–1402} }
 @article{pastina_malosetti_gazaffi_mollinari_margarido_oliveira_pinto_souza_van eeuwijk_garcia_2011, title={A mixed model QTL analysis for sugarcane multiple-harvest-location trial data}, volume={124}, ISSN={0040-5752 1432-2242}, url={http://dx.doi.org/10.1007/s00122-011-1748-8}, DOI={10.1007/s00122-011-1748-8}, abstractNote={Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic architecture of quantitative traits in sugarcane, and they may be used in marker-assisted selection to speed up artificial selection. Although the performance of sugarcane progenies in breeding programs are commonly evaluated across a range of locations and harvest years, many of the QTL detection methods ignore two- and three-way interactions between QTL, harvest, and location. In this work, a strategy for QTL detection in multi-harvest-location trial data, based on interval mapping and mixed models, is proposed and applied to map QTL effects on a segregating progeny from a biparental cross of pre-commercial Brazilian cultivars, evaluated at two locations and three consecutive harvest years for cane yield (tonnes per hectare), sugar yield (tonnes per hectare), fiber percent, and sucrose content. In the mixed model, we have included appropriate (co)variance structures for modeling heterogeneity and correlation of genetic effects and non-genetic residual effects. Forty-six QTLs were found: 13 QTLs for cane yield, 14 for sugar yield, 11 for fiber percent, and 8 for sucrose content. In addition, QTL by harvest, QTL by location, and QTL by harvest by location interaction effects were significant for all evaluated traits (30 QTLs showed some interaction, and 16 none). Our results contribute to a better understanding of the genetic architecture of complex traits related to biomass production and sucrose content in sugarcane.}, number={5}, journal={Theoretical and Applied Genetics}, publisher={Springer Science and Business Media LLC}, author={Pastina, M. M. and Malosetti, M. and Gazaffi, R. and Mollinari, M. and Margarido, G. R. A. and Oliveira, K. M. and Pinto, L. R. and Souza, A. P. and van Eeuwijk, F. A. and Garcia, A. A. F.}, year={2011}, month={Dec}, pages={835–849} }
 @article{marconi_costa_miranda_mancini_cardoso-silva_oliveira_pinto_mollinari_garcia_souza_2011, title={Functional markers for gene mapping and genetic diversity studies in sugarcane}, volume={4}, ISSN={1756-0500}, url={http://dx.doi.org/10.1186/1756-0500-4-264}, DOI={10.1186/1756-0500-4-264}, abstractNote={The database of sugarcane expressed sequence tags (EST) offers a great opportunity for developing molecular markers that are directly associated with important agronomic traits. The development of new EST-SSR markers represents an important tool for genetic analysis. In sugarcane breeding programs, functional markers can be used to accelerate the process and select important agronomic traits, especially in the mapping of quantitative traits loci (QTL) and plant resistant pathogens or qualitative resistance loci (QRL). The aim of this work was to develop new simple sequence repeat (SSR) markers in sugarcane using the sugarcane expressed sequence tag (SUCEST database).A total of 365 EST-SSR molecular markers with trinucleotide motifs were developed and evaluated in a collection of 18 genotypes of sugarcane (15 varieties and 3 species). In total, 287 of the EST-SSRs markers amplified fragments of the expected size and were polymorphic in the analyzed sugarcane varieties. The number of alleles ranged from 2-18, with an average of 6 alleles per locus, while polymorphism information content values ranged from 0.21-0.92, with an average of 0.69. The discrimination power was high for the majority of the EST-SSRs, with an average value of 0.80. Among the markers characterized in this study some have particular interest, those that are related to bacterial defense responses, generation of precursor metabolites and energy and those involved in carbohydrate metabolic process.These EST-SSR markers presented in this work can be efficiently used for genetic mapping studies of segregating sugarcane populations. The high Polymorphism Information Content (PIC) and Discriminant Power (DP) presented facilitate the QTL identification and marker-assisted selection due the association with functional regions of the genome became an important tool for the sugarcane breeding program.}, number={1}, journal={BMC Research Notes}, publisher={Springer Science and Business Media LLC}, author={Marconi, Thiago G and Costa, Estela A and Miranda, Hercília RCAN and Mancini, Melina C and Cardoso-Silva, Cláudio B and Oliveira, Karine M and Pinto, Luciana R and Mollinari, Marcelo and Garcia, Antônio AF and Souza, Anete P}, year={2011}, month={Jul} }
 @article{tarazi_sebbenn_mollinari_vencovsky_2010, title={Mendelian inheritance, linkage and linkage disequilibrium in microsatellite loci of Copaifera langsdorffii Desf.}, volume={2}, ISSN={1877-7252 1877-7260}, url={http://dx.doi.org/10.1007/s12686-010-9230-5}, DOI={10.1007/s12686-010-9230-5}, number={1}, journal={Conservation Genetics Resources}, publisher={Springer Science and Business Media LLC}, author={Tarazi, Roberto and Sebbenn, Alexandre Magno and Mollinari, Marcelo and Vencovsky, Roland}, year={2010}, month={Apr}, pages={201–204} }
 @article{hotta_lembke_domingues_ochoa_cruz_melotto-passarin_marconi_santos_mollinari_margarido_et al._2010, title={The Biotechnology Roadmap for Sugarcane Improvement}, volume={3}, ISSN={1935-9756 1935-9764}, url={http://dx.doi.org/10.1007/s12042-010-9050-5}, DOI={10.1007/s12042-010-9050-5}, number={2}, journal={Tropical Plant Biology}, publisher={Springer Science and Business Media LLC}, author={Hotta, Carlos T. and Lembke, Carolina G. and Domingues, Douglas S. and Ochoa, Edgar A. and Cruz, Guilherme M. Q. and Melotto-Passarin, Danila M. and Marconi, Thiago G. and Santos, Melissa O. and Mollinari, Marcelo and Margarido, Gabriel R. A. and et al.}, year={2010}, month={Apr}, pages={75–87} }
 @article{oliveira_pinto_marconi_mollinari_ulian_chabregas_falco_burnquist_garcia_souza_2009, title={Characterization of new polymorphic functional markers for sugarcane}, volume={52}, ISSN={0831-2796 1480-3321}, url={http://dx.doi.org/10.1139/G08-105}, DOI={10.1139/g08-105}, abstractNote={ Expressed sequence tags (ESTs) offer the opportunity to exploit single, low-copy, conserved sequence motifs for the development of simple sequence repeats (SSRs). The authors have examined the Sugarcane Expressed Sequence Tag database for the presence of SSRs. To test the utility of EST-derived SSR markers, a total of 342 EST–SSRs, which represent a subset of over 2005 SSR-containing sequences that were located in the sugarcane EST database, could be designed from the nonredundant SSR-positive ESTs for possible use as potential genic markers. These EST–SSR markers were used to screen 18 sugarcane ( Saccharum spp.) varieties. A high proportion (65.5%) of the above EST–SSRs, which gave amplified fragments of foreseen size, detected polymorphism. The number of alleles ranged from 2 to 24 with an average of 7.55 alleles per locus, while polymorphism information content values ranged from 0.16 to 0.94, with an average of 0.73. The ability of each set of EST–SSR markers to discriminate between varieties was generally higher than the polymorphism information content analysis. When tested for functionality, 82.1% of these 224 EST–SSRs were found to be functional, showing homology to known genes. As the EST–SSRs are within the expressed portion of the genome, they are likely to be associated to a particular gene of interest, improving their utility for genetic mapping; identification of quantitative trait loci, and comparative genomics studies of sugarcane. The development of new EST–SSR markers will have important implications for the genetic analysis and exploitation of the genetic resources of sugarcane and related species and will provide a more direct estimate of functional diversity. }, number={2}, journal={Genome}, publisher={Canadian Science Publishing}, author={Oliveira, K. M. and Pinto, L. R. and Marconi, T. G. and Mollinari, M. and Ulian, E. C. and Chabregas, S. M. and Falco, M. C. and Burnquist, W. and Garcia, A. A.F. and Souza, A. P.}, editor={Golding, BrianEditor}, year={2009}, month={Feb}, pages={191–209} }
 @article{mollinari_margarido_vencovsky_garcia_2009, title={Evaluation of algorithms used to order markers on genetic maps}, volume={103}, ISSN={0018-067X 1365-2540}, url={http://dx.doi.org/10.1038/hdy.2009.96}, DOI={10.1038/hdy.2009.96}, abstractNote={When building genetic maps, it is necessary to choose from several marker ordering algorithms and criteria, and the choice is not always simple. In this study, we evaluate the efficiency of algorithms try (TRY), seriation (SER), rapid chain delineation (RCD), recombination counting and ordering (RECORD) and unidirectional growth (UG), as well as the criteria PARF (product of adjacent recombination fractions), SARF (sum of adjacent recombination fractions), SALOD (sum of adjacent LOD scores) and LHMC (likelihood through hidden Markov chains), used with the RIPPLE algorithm for error verification, in the construction of genetic linkage maps. A linkage map of a hypothetical diploid and monoecious plant species was simulated containing one linkage group and 21 markers with fixed distance of 3 cM between them. In all, 700 F2 populations were randomly simulated with 100 and 400 individuals with different combinations of dominant and co-dominant markers, as well as 10 and 20% of missing data. The simulations showed that, in the presence of co-dominant markers only, any combination of algorithm and criteria may be used, even for a reduced population size. In the case of a smaller proportion of dominant markers, any of the algorithms and criteria (except SALOD) investigated may be used. In the presence of high proportions of dominant markers and smaller samples (around 100), the probability of repulsion linkage increases between them and, in this case, use of the algorithms TRY and SER associated to RIPPLE with criterion LHMC would provide better results.}, number={6}, journal={Heredity}, publisher={Springer Science and Business Media LLC}, author={Mollinari, M and Margarido, G R A and Vencovsky, R and Garcia, A A F}, year={2009}, month={Jul}, pages={494–502} }
 @article{mollinari_margarido_garcia_2008, title={Comparison of algorithms rapid chain delineation and seriation, for the construction of genetic linkage maps,Comparação dos algoritmos delineação rápida em cadeia e seriação, para a construção de mapas genéticos}, volume={43}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-45849149972&partnerID=MN8TOARS}, DOI={10.1590/S0100-204X2008000400009}, abstractNote={O objetivo deste trabalho foi avaliar a eficiência, na construção de mapas genéticos, dos algoritmos seriação e delineação rápida em cadeia, além dos critérios para avaliação de ordens: produto mínimo das frações de recombinação adjacentes, soma mínima das frações de recombinação adjacentes e soma máxima dos LOD Scores adjacentes, quando usados com o algoritmo de verificação de erros " ripple" . Foi simulado um mapa com 24 marcadores, posicionados aleatoriamente a distâncias variadas, com média 10 cM. Por meio do método Monte Carlo, foram obtidas 1.000 populações de retrocruzamento e 1.000 populações F2, com 200 indivíduos cada, e diferentes combinações de marcadores dominantes e co-dominantes (100% co-dominantes, 100% dominantes e mistura com 50% co-dominantes e 50% dominantes). Foi, também, simulada a perda de 25, 50 e 75% dos dados. Observou-se que os dois algoritmos avaliados tiveram desempenho semelhante e foram sensíveis à presença de dados perdidos e à presença de marcadores dominantes; esta última dificultou a obtenção de estimativas com boa acurácia, tanto da ordem quanto da distância. Além disso, observou-se que o algoritmo " ripple" geralmente aumenta o número de ordens corretas e pode ser combinado com os critérios soma mínima das frações de recombinação adjacentes e produto mínimo das frações de recombinação adjacentes.}, number={4}, journal={Pesquisa Agropecuaria Brasileira}, author={Mollinari, M. and Margarido, G.R.A. and Garcia, A.A.F.}, year={2008}, pages={505–512} }