@article{schoonmaker_hulse-kemp_youngblood_rahmat_iqbal_rahman_kochan_scheffler_scheffler_2023, title={Detecting Cotton Leaf Curl Virus Resistance Quantitative Trait Loci in Gossypium hirsutum and iCottonQTL a New R/Shiny App to Streamline Genetic Mapping}, volume={12}, ISSN={["2223-7747"]}, url={https://doi.org/10.3390/plants12051153}, DOI={10.3390/plants12051153}, abstractNote={Cotton leaf curl virus (CLCuV) causes devastating losses to fiber production in Central Asia. Viral spread across Asia in the last decade is causing concern that the virus will spread further before resistant varieties can be bred. Current development depends on screening each generation under disease pressure in a country where the disease is endemic. We utilized quantitative trait loci (QTL) mapping in four crosses with different sources of resistance to identify single nucleotide polymorphism (SNP) markers associated with the resistance trait to allow development of varieties without the need for field screening every generation. To assist in the analysis of multiple populations, a new publicly available R/Shiny App was developed to streamline genetic mapping using SNP arrays and to also provide an easy method to convert and deposit genetic data into the CottonGen database. Results identified several QTL from each cross, indicating possible multiple modes of resistance. Multiple sources of resistance would provide several genetic routes to combat the virus as it evolves over time. Kompetitive allele specific PCR (KASP) markers were developed and validated for a subset of QTL, which can be used in further development of CLCuV-resistant cotton lines.}, number={5}, journal={PLANTS-BASEL}, author={Schoonmaker, Ashley N. and Hulse-Kemp, Amanda M. and Youngblood, Ramey C. and Rahmat, Zainab and Iqbal, Muhammad Atif and Rahman, Mehboob-ur and Kochan, Kelli J. and Scheffler, Brian E. and Scheffler, Jodi A.}, year={2023}, month={Mar} }
 @article{delorean_youngblood_simpson_schoonmaker_scheffler_rutter_hulse-kemp_2023, title={Representing true plant genomes: haplotype-resolved hybrid pepper genome with trio-binning}, volume={14}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2023.1184112}, abstractNote={As sequencing costs decrease and availability of high fidelity long-read sequencing increases, generating experiment specific de novo genome assemblies becomes feasible. In many crop species, obtaining the genome of a hybrid or heterozygous individual is necessary for systems that do not tolerate inbreeding or for investigating important biological questions, such as hybrid vigor. However, most genome assembly methods that have been used in plants result in a merged single sequence representation that is not a true biologically accurate representation of either haplotype within a diploid individual. The resulting genome assembly is often fragmented and exhibits a mosaic of the two haplotypes, referred to as haplotype-switching. Important haplotype level information, such as causal mutations and structural variation is therefore lost causing difficulties in interpreting downstream analyses. To overcome this challenge, we have applied a method developed for animal genome assembly called trio-binning to an intra-specific hybrid of chili pepper (Capsicum annuum L. cv. HDA149 x Capsicum annuum L. cv. HDA330). We tested all currently available softwares for performing trio-binning, combined with multiple scaffolding technologies including Bionano to determine the optimal method of producing the best haplotype-resolved assembly. Ultimately, we produced highly contiguous biologically true haplotype-resolved genome assemblies for each parent, with scaffold N50s of 266.0 Mb and 281.3 Mb, with 99.6% and 99.8% positioned into chromosomes respectively. The assemblies captured 3.10 Gb and 3.12 Gb of the estimated 3.5 Gb chili pepper genome size. These assemblies represent the complete genome structure of the intraspecific hybrid, as well as the two parental genomes, and show measurable improvements over the currently available reference genomes. Our manuscript provides a valuable guide on how to apply trio-binning to other plant genomes.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Delorean, Emily E. and Youngblood, Ramey C. and Simpson, Sheron A. and Schoonmaker, Ashley N. and Scheffler, Brian E. and Rutter, William B. and Hulse-Kemp, Amanda M.}, year={2023}, month={Nov} }
 @article{yu_schoonmaker_yan_hulse-kemp_fontanier_martin_moss_wu_2022, title={Genetic variability and QTL mapping of winter survivability and leaf firing in African bermudagrass}, volume={10}, ISSN={["1435-0653"]}, DOI={10.1002/csc2.20849}, abstractNote={Abstract}, journal={CROP SCIENCE}, author={Yu, Shuhao and Schoonmaker, Ashley N. and Yan, Liuling and Hulse-Kemp, Amanda M. and Fontanier, Charles H. and Martin, Dennis L. and Moss, Justin Q. and Wu, Yanqi Q.}, year={2022}, month={Oct} }
 @article{schoonmaker_hao_bird_conant_2020, title={A Single, Shared Triploidy in Three Species of Parasitic Nematodes}, volume={10}, ISSN={["2160-1836"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85077664460&partnerID=MN8TOARS}, DOI={10.1534/g3.119.400650}, abstractNote={Abstract}, number={1}, journal={G3-GENES GENOMES GENETICS}, author={Schoonmaker, Ashley and Hao, Yue and Bird, David McK. and Conant, Gavin C.}, year={2020}, month={Jan}, pages={225–233} }