Article
Genetics & Heredity
Claudia E. Osorio, Nuan Wen, Jaime H. Mejias, Bao Liu, Stephen Reinbothe, Diter von Wettstein, Sachin Rustgi
FUNCTIONAL & INTEGRATIVE GENOMICS
(2019)
Review
Plant Sciences
Claudia E. Osorio
FRONTIERS IN PLANT SCIENCE
(2019)
Article
Genetics & Heredity
Corrinne E. Grover, Mi-Jeong Yoo, Meng Lin, Matthew D. Murphy, David B. Harker, Robert L. Byers, Alexander E. Lipka, Guanjing Hu, Daojun Yuan, Justin L. Conover, Joshua A. Udall, Andrew H. Paterson, Michael A. Gore, Jonathan F. Wendel
G3-GENES GENOMES GENETICS
(2020)
Article
Genetics & Heredity
Corrinne E. Grover, Mengqiao Pan, Daojun Yuan, Mark A. Arick, Guanjing Hu, Logan Brase, David M. Stelly, Zefu Lu, Robert J. Schmitz, Daniel G. Peterson, Jonathan F. Wendel, Joshua A. Udall
G3-GENES GENOMES GENETICS
(2020)
Article
Genetics & Heredity
Corrinne E. Grover, Daojun Yuan, Mark A. Arick, Emma R. Miller, Guanjing Hu, Daniel G. Peterson, Jonathan F. Wendel, Joshua A. Udall
Summary: Cotton, an important textile crop, has faced production challenges due to various diseases, leading breeding efforts to focus on introgressing wild, naturally resistant germplasm. Gossypium stocksii, a wild cotton species from Africa, could be a valuable reservoir of natural pest resistance, as suggested by pest resistance surveys and breeding efforts. The high-quality de novo genome sequence of G. stocksii provides insights into pest resistance in cotton, particularly resistance to cotton leaf curl virus, highlighting its utility in breeding programs.
G3-GENES GENOMES GENETICS
(2021)
Article
Chemistry, Multidisciplinary
Daojun Yuan, Corrinne E. Grover, Guanjing Hu, Mengqiao Pan, Emma R. Miller, Justin L. Conover, Spencer P. Hunt, Joshua A. Udall, Jonathan F. Wendel
Summary: Two cultivated allopolyploid cottons, G. hirsutum and G. barbadense, underwent parallel independent domestication processes, involving significant morphological transformations. Wild forms of both species were initially domesticated in the Yucatan Peninsula and NW South America, respectively, before spreading over 4000-8000 years to encompass most of the American tropics. Genome-wide bidirectional introgression occurred between the two co-resident genomes of these allopolyploids, revealing genetic asymmetries and regions targeted during domestication.
Article
Genetics & Heredity
Lindsey C. Perkin, Al Bell, Lori L. Hinze, Charles P-C Suh, Mark A. Arick, Daniel G. Peterson, Joshua A. Udall
Summary: Upland cotton is susceptible to damage by nematodes, causing significant yield losses annually in the US. Traditional methods like crop rotation and nematicides are effective but costly, making the use of resistant cultivars the most efficient and economical approach for managing nematodes in cotton. The genomes of nematode-resistant cotton lines BARBREN-713 and BAR 32-30 may facilitate the development of DNA markers for introducing nematode resistance into commercially valuable cotton lines.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
Corrinne E. Grover, Daojun Yuan, Mark A. Arick, Emma R. Miller, Guanjing Hu, Daniel G. Peterson, Jonathan F. Wendel, Joshua A. Udall
Summary: This study presents a high-quality de novo genome assembly of Gossypium anomalum, a wild African species with potential applications in cotton breeding and hybrid lethality research. By using synthetic allopolyploids, regions in the G. anomalum genome possibly involved in hybrid lethality were identified, shedding light on the genetic factors underlying this phenomenon.
G3-GENES GENOMES GENETICS
(2021)
Article
Plant Sciences
Stephen M. Parris, Steven N. Jeffers, James M. Olvey, James M. Olvey, Jeffrey W. Adelberg, Li Wen, Joshua A. Udall, Jeffrey J. Coleman, Don C. Jones, Christopher A. Saski
Summary: An in vitro coculture system using an inert polyphenolic foam substrate and liquid medium was designed to study the resistance of domesticated cotton to Fusarium oxysporum f. sp. vasinfectum race 4. The results showed that susceptible cultivars exhibited more severe disease symptoms and plant mortality, while resistant cultivars performed better.
Article
Plant Sciences
Jing Yu, Sook Jung, Chun-Huai Cheng, Taein Lee, Ping Zheng, Katheryn Buble, James Crabb, Jodi Humann, Heidi Hough, Don Jones, J. Todd Campbell, Josh Udall, Dorrie Main
Summary: Over the past eight years, the volume of data generated by the cotton research community has exponentially increased, leading to the creation of the CottonGen online community database which provides access to integrated genetic and breeding data and analysis tools. The data stored in CottonGen includes genes, genotypes, and phenotypes, and the platform facilitates utilization of these resources for research on cotton crop improvement through curation and online tools.
Article
Evolutionary Biology
Corrinne E. Grover, Mark A. Arick, Adam Thrash, Joel Sharbrough, Guanjing Hu, Daojun Yuan, Samantha Snodgrass, Emma R. Miller, Thiruvarangan Ramaraj, Daniel G. Peterson, Joshua A. Udall, Jonathan F. Wendel
Summary: This study provides insights into genome evolution and domestication in cultivated diploid cotton species, Gossypium herbaceum and Gossypium arboreum, showing their independent domestication and variable permeability to introgression among chromosomes. The findings establish a foundation for understanding the contribution of introgression and/or strong parallel selection to the extensive morphological similarities shared between these species.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Thiruvarangan Ramaraj, Corrinne E. Grover, Azalea C. Mendoza, Mark A. Arick II, Josef J. Jareczek, Alexis G. Leach, Daniel G. Peterson, Jonathan F. Wendel, Joshua A. Udall
Summary: In this study, the genome of G. herbaceum cv. Wagad, representing the first domesticated accession for this species, was sequenced and assembled. The genome of this cultivar was compared to wild G. herbaceum subspecies africanum to investigate changes in the G. herbaceum genome during domestication, and gene expression analysis was performed using RNA-seq. The results demonstrate the importance of studying the G. herbaceum cv. Wagad genome for understanding domestication in diploid species and guiding modern breeding programs.
G3-GENES GENOMES GENETICS
(2023)
Review
Plant Sciences
Karina Y. Morales, Aya H. Bridgeland, Kater D. Hake, Joshua A. Udall, Michael J. Thomson, John Z. Yu
Summary: This article reviews the biochemical modes of plant nuclear male sterility (NMS) and categorizes them into four groups. It analyzes and compares GMS genes in different plants and identifies potential candidate genes in the upland cotton genome for the development of new male sterile germplasm.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agricultural Engineering
Qingying Meng, Jiaqi Gu, Zhongping Xu, Jie Zhang, Jiwei Tang, Anzhou Wang, Ping Wang, Zhaowei Liu, Yuxuan Rong, Peihao Xie, Liuyang Hui, Joshua A. Udall, Corrinne E. Grover, Jonathan F. Wendel, Shuangxia Jin, Xianlong Zhang, Daojun Yuan
Summary: With advancements in sequencing technology and high-performance computing systems, sequencing and assembling complex genomes has become easier. However, the assembly quality of cotton genomes can vary, posing challenges when selecting appropriate genomes for genetic analysis and comparing results. This study comprehensively evaluates and compares the assembly accuracy, completeness, and contiguity of multiple versions of two cultivated cotton species. Structural errors introduced during genome assembly are identified, and gene relationships between annotations from multiple genomes are defined. The results and resources provided by this study contribute to the field of cotton genomics.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Agriculture, Multidisciplinary
Claudia E. Osorio, Gustavo del Canto, Annally Rupayan, Nicole Lichtin, Ivan J. Maureira-Butler
CIENCIA E INVESTIGACION AGRARIA
(2019)