@article{gesteiro_ordas_butron_fuente_jimenez-galindo_samayoa_cao_malvar_2023, title={Genomic versus phenotypic selection to improve corn borer resistance and grain yield in maize}, volume={14}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2023.1162440}, abstractNote={Introduction The study of yield and resistance/tolerance to pest are related traits fundamental for maize breeding programs. Genomic selection (GS), which uses all marker information to calculate genomic breeding values, is presented as an emerging alternative to phenotypic and marker-assisted selections for improving complex traits controlled by many genes with small effects. Therefore, although phenotypic selection (PS) has been effective for increasing resistance and yield under high infestation with maize stem borers, higher genetic gains are expected to be obtained through GS based on the complex architecture of both traits. Our objective was to test whether GS is more effective than PS for improving resistance and/or tolerance to maize stem borers and grain yield. Methods For this, we compared different selection programs based on phenotype and genotypic value for a single trait, resistance or yield, and for both traits together. Results and discussion We obtained that GS achieved the highest genetic gain for yield, meanwhile phenotypic selection for yield was the program that achieved the highest reduction of tunnel length, but was ineffective for increasing yield. However, phenotypic or genomic selection for increased resistance may be more effective in improving both traits together; although the gains per cycle would be small for both traits.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Gesteiro, Noemi and Ordas, Bernardo and Butron, Ana and Fuente, Maria and Jimenez-Galindo, Jose Cruz and Samayoa, Luis Fernando and Cao, Ana and Malvar, Rosa Ana}, year={2023}, month={Jul} }
 @article{samayoa_olukolu_yang_chen_stetter_york_sanchez-gonzalez_glaubitz_bradbury_romay_et al._2021, title={Domestication reshaped the genetic basis of inbreeding depression in a maize landrace compared to its wild relative, teosinte}, volume={17}, ISSN={["1553-7404"]}, DOI={10.1371/journal.pgen.1009797}, abstractNote={Inbreeding depression is the reduction in fitness and vigor resulting from mating of close relatives observed in many plant and animal species. The extent to which the genetic load of mutations contributing to inbreeding depression is due to rare large-effect variation versus potentially more common variants with very small individual effects is unknown and may be affected by population history. We compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte. Inbreeding depression was greater in maize than teosinte for 15 of 18 traits, congruent with the greater segregating genetic load predicted from sequence data in the maize population. For many traits - and more commonly in maize - genetic variation among selffertilized families was less than expected based on additive and dominance variance estimated in outcrossed families, suggesting that a negative covariance between additive and homozygous dominance effects limits the variation available to selection under partial inbreeding. We identified quantitative trait loci (QTL) representing large-effect rare variants carried by only a single parent, which were more important in teosinte than maize. Teosinte also carried more putative juvenile-acting lethal variants identified by segregation distortion. These results suggest a mixture of mostly polygenic, smalleffect recessive variation underlying inbreeding depression, with an additional contribution from rare larger-effect variants that was more important in teosinte but depleted in maize following to the domestication bottleneck. Purging associated with the maize domestication bottleneck may have selected against large effect variants, but polygenic load is harder to purge and segregating mutational burden increased in maize compared to teosinte.}, number={12}, journal={PLOS GENETICS}, author={Samayoa, Luis Fernando and Olukolu, Bode A. and Yang, Chin Jian and Chen, Qiuyue and Stetter, Markus G. and York, Alessandra M. and Sanchez-Gonzalez, Jose de Jesus and Glaubitz, Jeffrey C. and Bradbury, Peter J. and Romay, Maria Cinta and et al.}, year={2021}, month={Dec} }
 @article{stagnati_lanubile_samayoa_bragalanti_giorni_busconi_holland_marocco_2019, title={A Genome Wide Association Study Reveals Markers and Genes Associated with Resistance to Fusarium verticillioides Infection of Seedlings in a Maize Diversity Panel}, volume={9}, ISSN={["2160-1836"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85061232004&partnerID=MN8TOARS}, DOI={10.1534/g3.118.200916}, abstractNote={Abstract}, number={2}, journal={G3-GENES GENOMES GENETICS}, author={Stagnati, Lorenzo and Lanubile, Alessandra and Samayoa, Luis F. and Bragalanti, Mario and Giorni, Paola and Busconi, Matteo and Holland, James B. and Marocco, Adriano}, year={2019}, month={Feb}, pages={571–579} }
 @article{samayoa_cao_santiago_malvar_butron_2019, title={Genome-wide association analysis for fumonisin content in maize kernels}, volume={19}, ISSN={["1471-2229"]}, DOI={10.1186/s12870-019-1759-1}, abstractNote={Plant breeding has been proposed as one of the most effective and environmentally safe methods to control fungal infection and to reduce fumonisin accumulation. However, conventional breeding can be hampered by the complex genetic architecture of resistance to fumonisin accumulation and marker-assisted selection is proposed as an efficient alternative. In the current study, GWAS has been performed for the first time for detecting high-resolution QTL for resistance to fumonisin accumulation in maize kernels complementing published GWAS results for Fusarium ear rot.Thirty-nine SNPs significantly associated with resistance to fumonisin accumulation in maize kernels were found and clustered into 17 QTL. Novel QTLs for fumonisin content would be at bins 3.02, 5.02, 7.05 and 8.07. Genes with annotated functions probably implicated in resistance to pathogens based on previous studies have been highlighted.Breeding approaches to fix favorable functional variants for genes implicated in maize immune response signaling may be especially useful to reduce kernel contamination with fumonisins without significantly interfering in mycelia development and growth and, consequently, in the beneficial endophytic behavior of Fusarium verticillioides.}, journal={BMC PLANT BIOLOGY}, author={Samayoa, L. F. and Cao, A. and Santiago, R. and Malvar, R. A. and Butron, A.}, year={2019}, month={Apr} }
 @article{lopez-malvar_butron_samayoa_figueroa-garrido_malvar_santiago_2019, title={Genome-wide association analysis for maize stem Cell Wall-bound Hydroxycinnamates}, volume={19}, ISSN={["1471-2229"]}, DOI={10.1186/s12870-019-2135-x}, abstractNote={Abstract}, number={1}, journal={BMC PLANT BIOLOGY}, author={Lopez-Malvar, A. and Butron, A. and Samayoa, L. F. and Figueroa-Garrido, D. J. and Malvar, R. A. and Santiago, R.}, year={2019}, month={Nov} }
 @article{cruz jimenez-galindo_ana malvar_butron_santiago_fernando samayoa_caicedo_ordas_2019, title={Mapping of resistance to corn borers in a MAGIC population of maize}, volume={19}, ISSN={["1471-2229"]}, DOI={10.1186/s12870-019-2052-z}, abstractNote={Abstract}, number={1}, journal={BMC PLANT BIOLOGY}, author={Cruz Jimenez-Galindo, Jose and Ana Malvar, Rosa and Butron, Ana and Santiago, Rogelio and Fernando Samayoa, Luis and Caicedo, Marlon and Ordas, Bernardo}, year={2019}, month={Oct} }
 @article{butron_santiago_cao_samayoa_malvar_2019, title={QTLs for Resistance to Fusarium Ear Rot in a Multiparent Advanced Generation Intercross (MAGIC) Maize Population}, volume={103}, ISSN={["1943-7692"]}, DOI={10.1094/PDIS-09-18-1669-RE}, abstractNote={Alternative approaches to linkage and association mapping using inbred panels may allow further insights into loci involved in resistance to Fusarium ear rot and lead to the discovery of suitable markers for breeding programs. Here, the suitability of a maize multiparent advanced-generation intercross population for detecting quantitative trait loci (QTLs) associated with Fusarium ear rot resistance was evaluated and found to be valuable in uncovering genomic regions containing resistance-associated loci in temperate materials. In total, 13 putative minor QTLs were located over all of the chromosomes, except chromosome 5, and frequencies of favorable alleles for resistance to Fusarium ear rot were, in general, high. These findings corroborated the quantitative characteristic of resistance to Fusarium ear rot in which many loci have small additive effects. Present and previous results indicate that crucial regions such as 210 to 220 Mb in chromosome 3 and 166 to 173 Mb in chromosome 7 (B73-RefGen-v2) contain QTLs for Fusarium ear rot resistance and fumonisin content.}, number={5}, journal={PLANT DISEASE}, author={Butron, A. and Santiago, R. and Cao, A. and Samayoa, L. F. and Malvar, R. A.}, year={2019}, month={May}, pages={897–904} }
 @article{yang_samayoa_bradbury_olukolu_xue_york_tuholski_wang_daskalska_neumeyer_et al._2019, title={The genetic architecture of teosinte catalyzed and constrained maize domestication}, volume={116}, ISBN={0027-8424}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85063274624&partnerID=MN8TOARS}, DOI={10.1073/pnas.1820997116}, abstractNote={
            The process of evolution under domestication has been studied using phylogenetics, population genetics–genomics, quantitative trait locus (QTL) mapping, gene expression assays, and archaeology. Here, we apply an evolutionary quantitative genetic approach to understand the constraints imposed by the genetic architecture of trait variation in teosinte, the wild ancestor of maize, and the consequences of domestication on genetic architecture. Using modern teosinte and maize landrace populations as proxies for the ancestor and domesticate, respectively, we estimated heritabilities, additive and dominance genetic variances, genetic-by-environment variances, genetic correlations, and genetic covariances for 18 domestication-related traits using realized genomic relationships estimated from genome-wide markers. We found a reduction in heritabilities across most traits, and the reduction is stronger in reproductive traits (size and numbers of grains and ears) than vegetative traits. We observed larger depletion in additive genetic variance than dominance genetic variance. Selection intensities during domestication were weak for all traits, with reproductive traits showing the highest values. For 17 of 18 traits, neutral divergence is rejected, suggesting they were targets of selection during domestication. Yield (total grain weight) per plant is the sole trait that selection does not appear to have improved in maize relative to teosinte. From a multivariate evolution perspective, we identified a strong, nonneutral divergence between teosinte and maize landrace genetic variance–covariance matrices (
            
              
                G
              
            
            -matrices). While the structure of
            
              
                G
              
            
            -matrix in teosinte posed considerable genetic constraint on early domestication, the maize landrace
            
              
                G
              
            
            -matrix indicates that the degree of constraint is more unfavorable for further evolution along the same trajectory.
          }, number={12}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Yang, Chin Jian and Samayoa, Luis Fernando and Bradbury, Peter J. and Olukolu, Bode A. and Xue, Wei and York, Alessandra M. and Tuholski, Michael R. and Wang, Weidong and Daskalska, Lora L. and Neumeyer, Michael A. and et al.}, year={2019}, pages={5643–5652} }
 @article{samayoa_butron_malvar_2019, title={Usefulness of marker-assisted selection to improve maize for increased resistance to Sesamia nonagrioides attack with no detrimental effect on yield}, volume={174}, ISSN={["1744-7348"]}, DOI={10.1111/aab.12480}, abstractNote={Two decades of investigations on maize resistance to Mediterranean corn borer (Sesamia nonagrioides Lefebvre; MCB) have shown that breeding for increased resistance to stem tunnelling by MCB often resulted in reduced yield because significant genetic correlation between both traits exists in some backgrounds. Unlike phenotypic selection, marker‐assisted selection (MAS) could differentiate markers linked only to one trait from those linked simultaneously to yield potential and susceptibility to the pest. In the current study, the suitability of MAS for improving resistance to stem tunnelling without adverse effects on yield has been tested. The unfavourable genetic relationship between yield potential and susceptibility could be overcome using MAS. Gains obtained using MAS were weak, because genetic variance explained by the quantitative trait loci (QTL) was low but results encourage us to persevere in using marker information for simultaneous improvement of resistance and yield especially if genome‐wide approaches are applied. Approaches to detect QTL are widely used, but studies on the suitability of markers linked to QTL for performing MAS have been mostly neglected.}, number={2}, journal={ANNALS OF APPLIED BIOLOGY}, author={Samayoa, Luis F. and Butron, Ana and Malvar, Rosa A.}, year={2019}, month={Mar}, pages={219–222} }
 @article{andres_coneva_frank_tuttle_samayoa_han_kaur_zhu_fang_bowman_et al._2017, title={Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.)}, volume={114}, DOI={10.1101/062612}, abstractNote={Abstract}, number={1}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Andres, R. J. and Coneva, V. and Frank, M. H. and Tuttle, J. R. and Samayoa, L. F. and Han, S. W. and Kaur, B. and Zhu, L. L. and Fang, Hui and Bowman, D. T. and et al.}, year={2017}, pages={E57–66} }
 @article{jimenez-galindo_ordas_butron_samayoa_malvar_2017, title={QTL mapping for yield and resistance against Mediterranean corn borer in maize}, volume={8}, DOI={10.3389/fpls.2017.00698}, abstractNote={Introduction: The Mediterranean corn borer (MCB), Sesamia nonagrioides, is a major pest of maize, Zea mays, in Mediterranean countries, inflicting significant kernel yield losses. For that reason, it necessary to know the genetic mechanisms that regulate the agronomic and resistance traits. A quantitative trait loci (QTL) mapping study for yield, resistance against MCB attack, and other relevant agronomic traits was performed using a recombinant inbred line (RIL) population derived from the cross A637 × A509 that is expected to segregate for yield, and ear, and stalk resistance to MCB. 171 RILs were evaluated in 2014 and 2015 at Pontevedra, Spain, along with the two parental inbreds A637 and A509 using a 13 × 14 single lattice design with two replications. A genetic map with 285 SNP markers was used for QTL analysis. Our objectives were to detect QTL for resistance to MCB and tolerance-related agronomic traits, to gain insights on the genetic relationship between resistance to MCB attack and yield, and to establish the best way for simultaneously improving yield and resistance to MCB. Results: Twelve significant QTL were detected for agronomic and resistance traits. QTL at bins 1.10 and 5.04 were especially interesting because the same allelic variant at these QTL simultaneously improved yield and insect resistance. In contrast, in the region 8.04–8.05, QTL showed opposite effects for yield and resistance. Several QTL for indexes which combine yield and resistance traits were found especially in the region 10.02–10.03. Conclusions: Selecting genotypes with the favorable allele of QTL on chromosome 5 (bin 5.01) will decrease tunnel length without affect yield, silking and plant height and QTL on the region 5.04 could be used to improve stalk resistance and yield simultaneously. An allele of QTL on bin 9.07 will increase ear resistance to MCB attack but it could produce later varieties while favorable allele in region 1.10 could improve ear and stalk resistance and yield without secondary negative effects. The region 8.03–8.05 mainly but also the region 10.02–10.03 and 5.04 may play an important role to elucidate the association between yield, other agronomic traits and MCB resistance.}, journal={Frontiers in Plant Science}, author={Jimenez-Galindo, J. C. and Ordas, B. and Butron, A. and Samayoa, L. F. and Malvar, R. A.}, year={2017} }