@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={AbstractTurf‐type bermudagrass is susceptible to winterkill when grown in transition zone climates. Minimizing water use in turfgrass management is of societal significance. African bermudagrass (Cynodon transvaalensis Burtt‐Davy) has been extensively used to cross with common bermudagrass (C. dactylon Pers. var. dactylon) in the creation of F1 hybrid cultivars. Little information regarding the molecular basis of winter survivability and drought resistance in African bermudagrass is available. Accordingly, the objectives of this study were to quantify genetic variability and identify quantitative trait loci (QTL) associated with winter survivability traits (spring greenup, SG; spring greenup percent green cover, SGPGC; winterkill, WK), and leaf firing (LF) in African bermudagrass. A total of 109 first‐generation self‐pollinated (S1) progeny of ‘OKC1163’ were evaluated in a field trial in a randomized complete block design with three replications for four seasons. Significant genetic variation existed for all the traits examined, and the broad‐sense heritability estimates ranged from .36 to .54 for the winter survivability traits and .80 for LF. Ten QTL were identified for winter survivability traits and two for LF based on a preexisting high‐density linkage map, which was aligned, reoriented, and renamed as to a recently published reference genome. Seven of 12 QTL were consistently identified at least in 2 yr. The colocation of two QTL, one for winter survivability and another for LF, suggests the possibility of improving both traits together. Findings provide new insights to genetic control of winter survivability traits and LF and contribute genetic resources for marker‐assisted selection in turf‐type bermudagrass improvement.}, 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
               The root-knot nematodes of the genus Meloidogyne are important and damaging parasites capable of infecting most flowering plants. Within this genus, several species of the Meloidogyne incognita group show evidence of paleopolyploidy in their genomes. We used our software tool POInT, the Polyploidy Orthology Inference Tool, to phylogenetically model the gene losses that followed that polyploidy. These models, and simulations based on them, show that three of these species (M. incognita, M. arenaria and M. javanica) descend from a single common hybridization event that yielded triplicated genomes with three distinguishable subgenomes. While one of the three subgenomes shows elevated gene loss rates relative to the other two, this subgenome does not show elevated sequence divergence. In all three species, ancestral loci where two of the three gene copies have been lost are less likely to have orthologs in Caenorhabditis elegans that are lethal when knocked down than are ancestral loci with surviving duplicate copies.}, 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} }