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Restrepo-Montoya D, Hulse-Kemp AM, Scheffler JA, Haigler CH, Hinze LL, Love J, Percy RG, Jones DC, Frelichowski J. Leveraging National Germplasm Collections to Determine Significantly Associated Categorical Traits in Crops: Upland and Pima Cotton as a Case Study. Front Plant Sci 2022; 13:837038. [PMID: 35557715 PMCID: PMC9087864 DOI: 10.3389/fpls.2022.837038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/21/2022] [Indexed: 06/15/2023]
Abstract
Observable qualitative traits are relatively stable across environments and are commonly used to evaluate crop genetic diversity. Recently, molecular markers have largely superseded describing phenotypes in diversity surveys. However, qualitative descriptors are useful in cataloging germplasm collections and for describing new germplasm in patents, publications, and/or the Plant Variety Protection (PVP) system. This research focused on the comparative analysis of standardized cotton traits as represented within the National Cotton Germplasm Collection (NCGC). The cotton traits are named by 'descriptors' that have non-numerical sub-categories (descriptor states) reflecting the details of how each trait manifests or is absent in the plant. We statistically assessed selected accessions from three major groups of Gossypium as defined by the NCGC curator: (1) "Stoneville accessions (SA)," containing mainly Upland cotton (Gossypium hirsutum) cultivars; (2) "Texas accessions (TEX)," containing mainly G. hirsutum landraces; and (3) Gossypium barbadense (Gb), containing cultivars or landraces of Pima cotton (Gossypium barbadense). For 33 cotton descriptors we: (a) revealed distributions of character states for each descriptor within each group; (b) analyzed bivariate associations between paired descriptors; and (c) clustered accessions based on their descriptors. The fewest significant associations between descriptors occurred in the SA dataset, likely reflecting extensive breeding for cultivar development. In contrast, the TEX and Gb datasets showed a higher number of significant associations between descriptors, likely correlating with less impact from breeding efforts. Three significant bivariate associations were identified for all three groups, bract nectaries:boll nectaries, leaf hair:stem hair, and lint color:seed fuzz color. Unsupervised clustering analysis recapitulated the species labels for about 97% of the accessions. Unexpected clustering results indicated accessions that may benefit from potential further investigation. In the future, the significant associations between standardized descriptors can be used by curators to determine whether new exotic/unusual accessions most closely resemble Upland or Pima cotton. In addition, the study shows how existing descriptors for large germplasm datasets can be useful to inform downstream goals in breeding and research, such as identifying rare individuals with specific trait combinations and targeting breakdown of remaining trait associations through breeding, thus demonstrating the utility of the analytical methods employed in categorizing germplasm diversity within the collection.
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Affiliation(s)
- Daniel Restrepo-Montoya
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Amanda M. Hulse-Kemp
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
- Genomics and Bioinformatics Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Raleigh, NC, United States
| | - Jodi A. Scheffler
- Crop Genetics Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Stoneville, MS, United States
| | - Candace H. Haigler
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Lori L. Hinze
- Crop Germplasm Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), College Station, TX, United States
| | - Janna Love
- Crop Germplasm Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), College Station, TX, United States
| | - Richard G. Percy
- Crop Germplasm Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), College Station, TX, United States
| | | | - James Frelichowski
- Crop Germplasm Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), College Station, TX, United States
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Huang G, Wu Z, Percy RG, Bai M, Li Y, Frelichowski JE, Hu J, Wang K, Yu JZ, Zhu Y. Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution. Nat Genet 2020; 52:516-524. [PMID: 32284579 PMCID: PMC7203013 DOI: 10.1038/s41588-020-0607-4] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/04/2020] [Indexed: 12/13/2022]
Abstract
Upon assembling the first Gossypium herbaceum (A1) genome and substantially improving the existing Gossypium arboreum (A2) and Gossypium hirsutum ((AD)1) genomes, we showed that all existing A-genomes may have originated from a common ancestor, referred to here as A0, which was more phylogenetically related to A1 than A2. Further, allotetraploid formation was shown to have preceded the speciation of A1 and A2. Both A-genomes evolved independently, with no ancestor-progeny relationship. Gaussian probability density function analysis indicates that several long-terminal-repeat bursts that occurred from 5.7 million years ago to less than 0.61 million years ago contributed compellingly to A-genome size expansion, speciation and evolution. Abundant species-specific structural variations in genic regions changed the expression of many important genes, which may have led to fiber cell improvement in (AD)1. Our findings resolve existing controversial concepts surrounding A-genome origins and provide valuable genomic resources for cotton genetic improvement.
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Affiliation(s)
- Gai Huang
- Institute for Advanced Studies, Wuhan University, Wuhan, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Zhiguo Wu
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Richard G Percy
- Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, TX, USA
| | | | - Yang Li
- College of Life Sciences, Wuhan University, Wuhan, China
| | - James E Frelichowski
- Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, TX, USA
| | - Jiang Hu
- Nextomics Biosciences Institute, Wuhan, China
| | - Kun Wang
- College of Life Sciences, Wuhan University, Wuhan, China
| | - John Z Yu
- Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, TX, USA.
| | - Yuxian Zhu
- Institute for Advanced Studies, Wuhan University, Wuhan, China.
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Hinze LL, Hulse-Kemp AM, Wilson IW, Zhu QH, Llewellyn DJ, Taylor JM, Spriggs A, Fang DD, Ulloa M, Burke JJ, Giband M, Lacape JM, Van Deynze A, Udall JA, Scheffler JA, Hague S, Wendel JF, Pepper AE, Frelichowski J, Lawley CT, Jones DC, Percy RG, Stelly DM. Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array. BMC Plant Biol 2017; 17:37. [PMID: 28158969 PMCID: PMC5291959 DOI: 10.1186/s12870-017-0981-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 01/23/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits. RESULTS The SNP markers distinctly separated G. hirsutum from other Gossypium species and distinguished the wild from cultivated types of G. hirsutum. The markers also efficiently discerned differences among cultivars, which was the primary goal when designing the CottonSNP63K array. Population structure within the genus compared favorably with previous results obtained using SSR markers, and an association study identified loci linked to factors that affect cottonseed protein content. CONCLUSIONS Our results provide a large genome-wide variation data set for primarily cultivated cotton. Thousands of SNPs in representative cotton genotypes provide an opportunity to finely discriminate among cultivated cotton from around the world. The SNPs will be relevant as dense markers of genome variation for association mapping approaches aimed at correlating molecular polymorphisms with variation in phenotypic traits, as well as for molecular breeding approaches in cotton.
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Affiliation(s)
- Lori L. Hinze
- USDA-ARS, Crop Germplasm Research Unit, College Station, TX 77845 USA
| | - Amanda M. Hulse-Kemp
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA 95616 USA
| | - Iain W. Wilson
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Qian-Hao Zhu
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Danny J. Llewellyn
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Jen M. Taylor
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Andrew Spriggs
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - David D. Fang
- USDA-ARS, Cotton Fiber Bioscience Research Unit, New Orleans, LA 70124 USA
| | - Mauricio Ulloa
- USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX 79415 USA
| | - John J. Burke
- USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX 79415 USA
| | - Marc Giband
- CIRAD, UMR AGAP, Montpellier, F34398 France
- EMBRAPA, Algodão, Nucleo Cerrado, 75.375-000 Santo Antônio de Goias, GO Brazil
| | | | - Allen Van Deynze
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA 95616 USA
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602 USA
| | - Jodi A. Scheffler
- USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, MS 38776 USA
| | - Steve Hague
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011 USA
| | - Alan E. Pepper
- Department of Biology, Texas A&M University, College Station, TX 77843 USA
- Interdisciplinary Department of Genetics, Texas A&M University, College Station, TX 77843 USA
| | | | - Cindy T. Lawley
- Illumina Inc., 499 Illinois Street, San Francisco, CA 94158 USA
| | - Don C. Jones
- Cotton Incorporated, Agricultural Research, Cary, NC 27513 USA
| | - Richard G. Percy
- USDA-ARS, Crop Germplasm Research Unit, College Station, TX 77845 USA
| | - David M. Stelly
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843 USA
- Interdisciplinary Department of Genetics, Texas A&M University, College Station, TX 77843 USA
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Hinze LL, Gazave E, Gore MA, Fang DD, Scheffler BE, Yu JZ, Jones DC, Frelichowski J, Percy RG. Genetic Diversity of the Two Commercial Tetraploid Cotton Species in the Gossypium Diversity Reference Set. J Hered 2016; 107:274-86. [PMID: 26774060 DOI: 10.1093/jhered/esw004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 01/04/2016] [Indexed: 11/14/2022] Open
Abstract
A diversity reference set has been constructed for the Gossypium accessions in the US National Cotton Germplasm Collection to facilitate more extensive evaluation and utilization of accessions held in the Collection. A set of 105 mapped simple sequence repeat markers was used to study the allelic diversity of 1933 tetraploid Gossypium accessions representative of the range of diversity of the improved and wild accessions of G. hirsutum and G. barbadense. The reference set contained 410 G. barbadense accessions and 1523 G. hirsutum accessions. Observed numbers of polymorphic and private bands indicated a greater diversity in G. hirsutum as compared to G. barbadense as well as in wild-type accessions as compared to improved accessions in both species. The markers clearly differentiated the 2 species. Patterns of diversity within species were observed but not clearly delineated, with much overlap occurring between races and regions of origin for wild accessions and between historical and geographic breeding pools for cultivated accessions. Although the percentage of accessions showing introgression was higher among wild accessions than cultivars in both species, the average level of introgression within individual accessions, as indicated by species-specific bands, was much higher in wild accessions of G. hirsutum than in wild accessions of G. barbadense. The average level of introgression within individual accessions was higher in improved G. barbadense cultivars than in G. hirsutum cultivars. This molecular characterization reveals the levels and distributions of genetic diversity that will allow for better exploration and utilization of cotton genetic resources.
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Affiliation(s)
- Lori L Hinze
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones).
| | - Elodie Gazave
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
| | - Michael A Gore
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
| | - David D Fang
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
| | - Brian E Scheffler
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
| | - John Z Yu
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
| | - Don C Jones
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
| | - James Frelichowski
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
| | - Richard G Percy
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
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5
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Abdurakhmonov IY, Ayubov MS, Ubaydullaeva KA, Buriev ZT, Shermatov SE, Ruziboev HS, Shapulatov UM, Saha S, Ulloa M, Yu JZ, Percy RG, Devor EJ, Sharma GC, Sripathi VR, Kumpatla SP, van der Krol A, Kater HD, Khamidov K, Salikhov SI, Jenkins JN, Abdukarimov A, Pepper AE. RNA Interference for Functional Genomics and Improvement of Cotton (Gossypium sp.). Front Plant Sci 2016; 7:202. [PMID: 26941765 PMCID: PMC4762190 DOI: 10.3389/fpls.2016.00202] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 02/05/2016] [Indexed: 02/05/2023]
Abstract
RNA interference (RNAi), is a powerful new technology in the discovery of genetic sequence functions, and has become a valuable tool for functional genomics of cotton (Gossypium sp.). The rapid adoption of RNAi has replaced previous antisense technology. RNAi has aided in the discovery of function and biological roles of many key cotton genes involved in fiber development, fertility and somatic embryogenesis, resistance to important biotic and abiotic stresses, and oil and seed quality improvements as well as the key agronomic traits including yield and maturity. Here, we have comparatively reviewed seminal research efforts in previously used antisense approaches and currently applied breakthrough RNAi studies in cotton, analyzing developed RNAi methodologies, achievements, limitations, and future needs in functional characterizations of cotton genes. We also highlighted needed efforts in the development of RNAi-based cotton cultivars, and their safety and risk assessment, small and large-scale field trials, and commercialization.
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Affiliation(s)
- Ibrokhim Y. Abdurakhmonov
- Center of Genomics and Bioinformatics, Structural and Functional Genomics, Academy of Sciences the Republic of Uzbekistan, Ministry of Agriculture and Water Resources the Republic of Uzbekistan and “Uzpakhtasanoat” AssociationKibray, Uzbekistan
- *Correspondence: Ibrokhim Y. Abdurakhmonov,
| | - Mirzakamol S. Ayubov
- Center of Genomics and Bioinformatics, Structural and Functional Genomics, Academy of Sciences the Republic of Uzbekistan, Ministry of Agriculture and Water Resources the Republic of Uzbekistan and “Uzpakhtasanoat” AssociationKibray, Uzbekistan
| | - Khurshida A. Ubaydullaeva
- Center of Genomics and Bioinformatics, Structural and Functional Genomics, Academy of Sciences the Republic of Uzbekistan, Ministry of Agriculture and Water Resources the Republic of Uzbekistan and “Uzpakhtasanoat” AssociationKibray, Uzbekistan
| | - Zabardast T. Buriev
- Center of Genomics and Bioinformatics, Structural and Functional Genomics, Academy of Sciences the Republic of Uzbekistan, Ministry of Agriculture and Water Resources the Republic of Uzbekistan and “Uzpakhtasanoat” AssociationKibray, Uzbekistan
| | - Shukhrat E. Shermatov
- Center of Genomics and Bioinformatics, Structural and Functional Genomics, Academy of Sciences the Republic of Uzbekistan, Ministry of Agriculture and Water Resources the Republic of Uzbekistan and “Uzpakhtasanoat” AssociationKibray, Uzbekistan
| | - Haydarali S. Ruziboev
- Center of Genomics and Bioinformatics, Structural and Functional Genomics, Academy of Sciences the Republic of Uzbekistan, Ministry of Agriculture and Water Resources the Republic of Uzbekistan and “Uzpakhtasanoat” AssociationKibray, Uzbekistan
| | - Umid M. Shapulatov
- Center of Genomics and Bioinformatics, Structural and Functional Genomics, Academy of Sciences the Republic of Uzbekistan, Ministry of Agriculture and Water Resources the Republic of Uzbekistan and “Uzpakhtasanoat” AssociationKibray, Uzbekistan
- Laboratory of Plant Physiology, Wageningen UniversityWageningen, Netherlands
| | - Sukumar Saha
- Crop Science Research Laboratory, United States Department of Agriculture – Agricultural Research Service, StarkvilleMS, USA
| | - Mauricio Ulloa
- Plant Stress and Germplasm Development Research, United States Department of Agriculture – Agricultural Research Service, LubbockTX, USA
| | - John Z. Yu
- Crop Germplasm Research Unit, United States Department of Agriculture – Agricultural Research Service, College StationTX, USA
| | - Richard G. Percy
- Crop Germplasm Research Unit, United States Department of Agriculture – Agricultural Research Service, College StationTX, USA
| | - Eric J. Devor
- Department of Obstetrics and Gynecology, University of Iowa Carver College of Medicine, Iowa CityIA, USA
| | - Govind C. Sharma
- Department of Biological and Environmental Sciences, Alabama A&M University, NormalAL, USA
| | | | | | | | - Hake D. Kater
- Agricultural and Environmental Research, CaryNC, USA
| | - Khakimdjan Khamidov
- Center of Genomics and Bioinformatics, Structural and Functional Genomics, Academy of Sciences the Republic of Uzbekistan, Ministry of Agriculture and Water Resources the Republic of Uzbekistan and “Uzpakhtasanoat” AssociationKibray, Uzbekistan
| | - Shavkat I. Salikhov
- Center of Genomics and Bioinformatics, Structural and Functional Genomics, Academy of Sciences the Republic of Uzbekistan, Ministry of Agriculture and Water Resources the Republic of Uzbekistan and “Uzpakhtasanoat” AssociationKibray, Uzbekistan
| | - Johnie N. Jenkins
- Crop Science Research Laboratory, United States Department of Agriculture – Agricultural Research Service, StarkvilleMS, USA
| | - Abdusattor Abdukarimov
- Center of Genomics and Bioinformatics, Structural and Functional Genomics, Academy of Sciences the Republic of Uzbekistan, Ministry of Agriculture and Water Resources the Republic of Uzbekistan and “Uzpakhtasanoat” AssociationKibray, Uzbekistan
| | - Alan E. Pepper
- Department of Biology, Texas A&M University, Colleges StationTX, USA
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6
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Hulse-Kemp AM, Lemm J, Plieske J, Ashrafi H, Buyyarapu R, Fang DD, Frelichowski J, Giband M, Hague S, Hinze LL, Kochan KJ, Riggs PK, Scheffler JA, Udall JA, Ulloa M, Wang SS, Zhu QH, Bag SK, Bhardwaj A, Burke JJ, Byers RL, Claverie M, Gore MA, Harker DB, Islam MS, Jenkins JN, Jones DC, Lacape JM, Llewellyn DJ, Percy RG, Pepper AE, Poland JA, Mohan Rai K, Sawant SV, Singh SK, Spriggs A, Taylor JM, Wang F, Yourstone SM, Zheng X, Lawley CT, Ganal MW, Van Deynze A, Wilson IW, Stelly DM. Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp. G3 (Bethesda) 2015; 5:1187-209. [PMID: 25908569 PMCID: PMC4478548 DOI: 10.1534/g3.115.018416] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/11/2015] [Indexed: 11/18/2022]
Abstract
High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal × Seemann, G. mustelinum Miers × Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F2 mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community.
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Affiliation(s)
- Amanda M Hulse-Kemp
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843
| | - Jana Lemm
- TraitGenetics GmbH, 06466 Gatersleben, Germany
| | | | - Hamid Ashrafi
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, California 95616
| | - Ramesh Buyyarapu
- Dow AgroSciences, Trait Genetics and Technologies, Indianapolis, Indiana 46268
| | - David D Fang
- USDA-ARS-SRRC, Cotton Fiber Bioscience Research Unit, New Orleans, Louisiana 70124
| | - James Frelichowski
- USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845
| | - Marc Giband
- CIRAD, UMR AGAP, Montpellier, F34398, France EMBRAPA, Algodão, Nucleo Cerrado, 75.375-000 Santo Antônio de Goias, GO, Brazil
| | - Steve Hague
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843
| | - Lori L Hinze
- USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845
| | - Kelli J Kochan
- Department of Animal Science, Texas A&M University, College Station, Texas 77843
| | - Penny K Riggs
- Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843 Department of Animal Science, Texas A&M University, College Station, Texas 77843
| | - Jodi A Scheffler
- USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, Mississippi 38776
| | - Joshua A Udall
- Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602
| | - Mauricio Ulloa
- USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, Texas 79415
| | - Shirley S Wang
- USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845
| | - Qian-Hao Zhu
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - Sumit K Bag
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - Archana Bhardwaj
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - John J Burke
- USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, Texas 79415
| | - Robert L Byers
- Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602
| | | | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
| | - David B Harker
- Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602
| | - Md S Islam
- USDA-ARS-SRRC, Cotton Fiber Bioscience Research Unit, New Orleans, Louisiana 70124
| | - Johnie N Jenkins
- USDA-ARS, Genetics and Precision Agriculture Research, Mississippi State, Mississippi 39762
| | - Don C Jones
- Cotton Incorporated, Agricultural Research, Cary, North Carolina 27513
| | | | - Danny J Llewellyn
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - Richard G Percy
- USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845
| | - Alan E Pepper
- Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843 Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Jesse A Poland
- Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Kansas State University, Manhattan, Kansas 66506
| | - Krishan Mohan Rai
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - Samir V Sawant
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - Sunil Kumar Singh
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - Andrew Spriggs
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - Jen M Taylor
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - Fei Wang
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843
| | - Scott M Yourstone
- Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602
| | - Xiuting Zheng
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843
| | | | | | - Allen Van Deynze
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, California 95616
| | - Iain W Wilson
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - David M Stelly
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843
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7
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Li F, Fan G, Lu C, Xiao G, Zou C, Kohel RJ, Ma Z, Shang H, Ma X, Wu J, Liang X, Huang G, Percy RG, Liu K, Yang W, Chen W, Du X, Shi C, Yuan Y, Ye W, Liu X, Zhang X, Liu W, Wei H, Wei S, Huang G, Zhang X, Zhu S, Zhang H, Sun F, Wang X, Liang J, Wang J, He Q, Huang L, Wang J, Cui J, Song G, Wang K, Xu X, Yu JZ, Zhu Y, Yu S. Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nat Biotechnol 2015; 33:524-30. [PMID: 25893780 DOI: 10.1038/nbt.3208] [Citation(s) in RCA: 650] [Impact Index Per Article: 72.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 03/15/2015] [Indexed: 12/27/2022]
Abstract
Gossypium hirsutum has proven difficult to sequence owing to its complex allotetraploid (AtDt) genome. Here we produce a draft genome using 181-fold paired-end sequences assisted by fivefold BAC-to-BAC sequences and a high-resolution genetic map. In our assembly 88.5% of the 2,173-Mb scaffolds, which cover 89.6%∼96.7% of the AtDt genome, are anchored and oriented to 26 pseudochromosomes. Comparison of this G. hirsutum AtDt genome with the already sequenced diploid Gossypium arboreum (AA) and Gossypium raimondii (DD) genomes revealed conserved gene order. Repeated sequences account for 67.2% of the AtDt genome, and transposable elements (TEs) originating from Dt seem more active than from At. Reduction in the AtDt genome size occurred after allopolyploidization. The A or At genome may have undergone positive selection for fiber traits. Concerted evolution of different regulatory mechanisms for Cellulose synthase (CesA) and 1-Aminocyclopropane-1-carboxylic acid oxidase1 and 3 (ACO1,3) may be important for enhanced fiber production in G. hirsutum.
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Affiliation(s)
- Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | | | - Cairui Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Guanghui Xiao
- 1] State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China. [2] Institute for Advanced Studies and College of Life Sciences, Wuhan University, Wuhan, China
| | - Changsong Zou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Russell J Kohel
- Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, US Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, Texas, USA
| | - Zhiying Ma
- Key Laboratory for Crop Germplasm Resources of Hebei, Agricultural University of Hebei, Baoding, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiongfeng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jianyong Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | | | - Gai Huang
- 1] State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China. [2] Institute for Advanced Studies and College of Life Sciences, Wuhan University, Wuhan, China
| | - Richard G Percy
- Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, US Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, Texas, USA
| | - Kun Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Weihua Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | | | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | | | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Wuwei Ye
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, China
| | - Xueyan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | | | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shoujun Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | | | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Shuijin Zhu
- Department of Agronomy, Zhejiang University, Hangzhou, China
| | | | | | - Xingfen Wang
- Key Laboratory for Crop Germplasm Resources of Hebei, Agricultural University of Hebei, Baoding, China
| | | | | | | | | | | | - Jinjie Cui
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Guoli Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
| | - John Z Yu
- Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, US Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, Texas, USA
| | - Yuxian Zhu
- 1] State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China. [2] Institute for Advanced Studies and College of Life Sciences, Wuhan University, Wuhan, China
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
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8
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Xu Z, Yu J, Kohel RJ, Percy RG, Beavis WD, Main D, Yu JZ. Distribution and evolution of cotton fiber development genes in the fibreless Gossypium raimondii genome. Genomics 2015; 106:61-9. [PMID: 25796538 DOI: 10.1016/j.ygeno.2015.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 02/05/2015] [Accepted: 03/11/2015] [Indexed: 01/15/2023]
Abstract
Cotton fiber represents the largest single cell in plants and they serve as models to study cell development. This study investigated the distribution and evolution of fiber Unigenes anchored to recombination hotspots between tetraploid cotton (Gossypium hirsutum) At and Dt subgenomes, and within a parental diploid cotton (Gossypium raimondii) D genome. Comparative analysis of At vs D and Dt vs D showed that 1) the D genome provides many fiber genes after its merger with another parental diploid cotton (Gossypium arboreum) A genome although the D genome itself does not produce any spinnable fiber; 2) similarity of fiber genes is higher between At vs D than between Dt vs D genomic hotspots. This is the first report that fiber genes have higher similarity between At and D than between Dt and D. The finding provides new insights into cotton genomic regions that would facilitate genetic improvement of natural fiber properties.
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Affiliation(s)
- Zhanyou Xu
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, USA; Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - Jing Yu
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, USA; Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Russell J Kohel
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, USA
| | - Richard G Percy
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, USA
| | - William D Beavis
- Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - John Z Yu
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, USA.
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9
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Hinze LL, Horn PJ, Kothari N, Dever JK, Frelichowski J, Chapman KD, Percy RG. Nondestructive Measurements of Cottonseed Nutritional Trait Diversity in the U.S. National Cotton Germplasm Collection. Crop Sci 2015. [PMID: 0 DOI: 10.2135/cropsci2014.04.0318] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Affiliation(s)
- Lori L. Hinze
- USDA‐ARSSouthern Plains Agricultural Research Center2881 F&B Rd.College StationTX77845
| | - Patrick J. Horn
- Dep. of Biological SciencesCenter for Plant Lipid Research, Univ. of North Texas1511 W. SycamoreDentonTX76203
| | - Neha Kothari
- Dep. of Soil and Crop ScienceTexas AgriLife Research1102 East FM 1294LubbockTX79403
| | - Jane K. Dever
- Dep. of Soil and Crop ScienceTexas AgriLife Research1102 East FM 1294LubbockTX79403
| | - James Frelichowski
- USDA‐ARSSouthern Plains Agricultural Research Center2881 F&B Rd.College StationTX77845
| | - Kent D. Chapman
- Dep. of Biological SciencesCenter for Plant Lipid Research, Univ. of North Texas1511 W. SycamoreDentonTX76203
| | - Richard G. Percy
- USDA‐ARSSouthern Plains Agricultural Research Center2881 F&B Rd.College StationTX77845
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10
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Logan-Young CJ, Yu JZ, Verma SK, Percy RG, Pepper AE. SNP discovery in complex allotetraploid genomes (Gossypium spp., Malvaceae) using genotyping by sequencing. Appl Plant Sci 2015; 3:apps1400077. [PMID: 25798340 PMCID: PMC4356317 DOI: 10.3732/apps.1400077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 02/03/2015] [Indexed: 05/11/2023]
Abstract
PREMISE OF THE STUDY Single-nucleotide polymorphism (SNP) marker discovery in plants with complex allotetraploid genomes is often confounded by the presence of homeologous loci (along with paralogous and orthologous loci). Here we present a strategy to filter for SNPs representing orthologous loci. METHODS AND RESULTS Using Illumina next-generation sequencing, 54 million reads were collected from restriction enzyme-digested DNA libraries of a diversity of Gossypium taxa. Loci with one to three SNPs were discovered using the Stacks software package, yielding 25,529 new cotton SNP combinations, including those that are polymorphic at both interspecific and intraspecific levels. Frequencies of predicted dual-homozygous (aa/bb) marker polymorphisms ranged from 6.7-11.6% of total shared fragments in intraspecific comparisons and from 15.0-16.4% in interspecific comparisons. CONCLUSIONS This resource provides dual-homozygous (aa/bb) marker polymorphisms. Both in silico and experimental validation efforts demonstrated that these markers are enriched for single orthologous loci that are homozygous for alternative alleles.
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Affiliation(s)
| | - John Z. Yu
- USDA-ARS, Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, Texas 77845 USA
| | - Surender K. Verma
- Department of Biology, Texas A&M University, College Station, Texas 77843 USA
| | - Richard G. Percy
- USDA-ARS, Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, Texas 77845 USA
| | - Alan E. Pepper
- Department of Biology, Texas A&M University, College Station, Texas 77843 USA
- Author for correspondence:
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11
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Hinze LL, Fang DD, Gore MA, Scheffler BE, Yu JZ, Frelichowski J, Percy RG. Molecular characterization of the Gossypium Diversity Reference Set of the US National Cotton Germplasm Collection. Theor Appl Genet 2015; 128:313-327. [PMID: 25431191 DOI: 10.1007/s00122-014-2431-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 11/14/2014] [Indexed: 06/04/2023]
Abstract
A core marker set containing markers developed to be informative within a single commercial cotton species can elucidate diversity structure within a multi-species subset of the Gossypium germplasm collection. An understanding of the genetic diversity of cotton (Gossypium spp.) as represented in the US National Cotton Germplasm Collection is essential to develop strategies for collecting, conserving, and utilizing these germplasm resources. The US collection is one of the largest world collections and includes not only accessions with improved yield and fiber quality within cultivated species, but also accessions possessing sources of abiotic and biotic stress resistance often found in wild species. We evaluated the genetic diversity of a subset of 272 diploid and 1,984 tetraploid accessions in the collection (designated the Gossypium Diversity Reference Set) using a core set of 105 microsatellite markers. Utility of the core set of markers in differentiating intra-genome variation was much greater in commercial tetraploid genomes (99.7 % polymorphic bands) than in wild diploid genomes (72.7 % polymorphic bands), and may have been influenced by pre-selection of markers for effectiveness in the commercial species. Principal coordinate analyses revealed that the marker set differentiated interspecific variation among tetraploid species, but was only capable of partially differentiating among species and genomes of the wild diploids. Putative species-specific marker bands in G. hirsutum (73) and G. barbadense (81) were identified that could be used for qualitative identification of misclassifications, redundancies, and introgression within commercial tetraploid species. The results of this broad-scale molecular characterization are essential to the management and conservation of the collection and provide insight and guidance in the use of the collection by the cotton research community in their cotton improvement efforts.
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Affiliation(s)
- Lori L Hinze
- Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, USDA-ARS, College Station, TX, USA
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12
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Yu JZ, Ulloa M, Hoffman SM, Kohel RJ, Pepper AE, Fang DD, Percy RG, Burke JJ. Mapping genomic loci for cotton plant architecture, yield components, and fiber properties in an interspecific (Gossypium hirsutum L. × G. barbadense L.) RIL population. Mol Genet Genomics 2014; 289:1347-67. [PMID: 25314923 DOI: 10.1007/s00438-014-0930-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 09/20/2014] [Indexed: 12/27/2022]
Abstract
A quantitative trait locus (QTL) mapping was conducted to better understand the genetic control of plant architecture (PA), yield components (YC), and fiber properties (FP) in the two cultivated tetraploid species of cotton (Gossypium hirsutum L. and G. barbadense L.). One hundred and fifty-nine genomic regions were identified on a saturated genetic map of more than 2,500 SSR and SNP markers, constructed with an interspecific recombinant inbred line (RIL) population derived from the genetic standards of the respective cotton species (G. hirsutum acc. TM-1 × G. barbadense acc. 3-79). Using the single nonparametric and MQM QTL model mapping procedures, we detected 428 putative loci in the 159 genomic regions that confer 24 cotton traits in three diverse production environments [College Station F&B Road (FB), TX; Brazos Bottom (BB), TX; and Shafter (SH), CA]. These putative QTL loci included 25 loci for PA, 60 for YC, and 343 for FP, of which 3, 12, and 60, respectively, were strongly associated with the traits (LOD score ≥ 3.0). Approximately 17.7 % of the PA putative QTL, 32.9 % of the YC QTL, and 48.3 % of the FP QTL had trait associations under multiple environments. The At subgenome (chromosomes 1-13) contributed 72.7 % of loci for PA, 46.2 % for YC, and 50.4 % for FP while the Dt subgenome (chromosomes 14-26) contributed 27.3 % of loci for PA, 53.8 % for YC, and 49.6 % for FP. The data obtained from this study augment prior evidence of QTL clusters or gene islands for specific traits or biological functions existing in several non-homoeologous cotton chromosomes. DNA markers identified in the 159 genomic regions will facilitate further dissection of genetic factors underlying these important traits and marker-assisted selection in cotton.
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Affiliation(s)
- John Z Yu
- USDA-ARS, Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX, 77845, USA,
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13
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Li F, Fan G, Wang K, Sun F, Yuan Y, Song G, Li Q, Ma Z, Lu C, Zou C, Chen W, Liang X, Shang H, Liu W, Shi C, Xiao G, Gou C, Ye W, Xu X, Zhang X, Wei H, Li Z, Zhang G, Wang J, Liu K, Kohel RJ, Percy RG, Yu JZ, Zhu YX, Wang J, Yu S. Genome sequence of the cultivated cotton Gossypium arboreum. Nat Genet 2014; 46:567-72. [DOI: 10.1038/ng.2987] [Citation(s) in RCA: 634] [Impact Index Per Article: 63.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 04/24/2014] [Indexed: 01/05/2023]
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14
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Yu J, Jung S, Cheng CH, Ficklin SP, Lee T, Zheng P, Jones D, Percy RG, Main D. CottonGen: a genomics, genetics and breeding database for cotton research. Nucleic Acids Res 2013; 42:D1229-36. [PMID: 24203703 PMCID: PMC3964939 DOI: 10.1093/nar/gkt1064] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, visualization and data retrieval of cotton research data. CottonGen contains annotated whole genome sequences, unigenes from expressed sequence tags (ESTs), markers, trait loci, genetic maps, genes, taxonomy, germplasm, publications and communication resources for the cotton community. Annotated whole genome sequences of Gossypium raimondii are available with aligned genetic markers and transcripts. These whole genome data can be accessed through genome pages, search tools and GBrowse, a popular genome browser. Most of the published cotton genetic maps can be viewed and compared using CMap, a comparative map viewer, and are searchable via map search tools. Search tools also exist for markers, quantitative trait loci (QTLs), germplasm, publications and trait evaluation data. CottonGen also provides online analysis tools such as NCBI BLAST and Batch BLAST.
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Affiliation(s)
- Jing Yu
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA, Cotton Incorporated, Cary, NC 27513, USA and Crop Germplasm Research Unit, USDA-ARS-SPARC, College Station, TX 77845, USA
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15
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Buyyarapu R, Kantety RV, Yu JZ, Xu Z, Kohel RJ, Percy RG, Macmil S, Wiley GB, Roe BA, Sharma GC. BAC-pool sequencing and analysis of large segments of A12 and D12 homoeologous chromosomes in upland cotton. PLoS One 2013; 8:e76757. [PMID: 24116150 PMCID: PMC3792896 DOI: 10.1371/journal.pone.0076757] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 08/28/2013] [Indexed: 11/19/2022] Open
Abstract
Although new and emerging next-generation sequencing (NGS) technologies have reduced sequencing costs significantly, much work remains to implement them for de novo sequencing of complex and highly repetitive genomes such as the tetraploid genome of Upland cotton (Gossypium hirsutum L.). Herein we report the results from implementing a novel, hybrid Sanger/454-based BAC-pool sequencing strategy using minimum tiling path (MTP) BACs from Ctg-3301 and Ctg-465, two large genomic segments in A12 and D12 homoeologous chromosomes (Ctg). To enable generation of longer contig sequences in assembly, we implemented a hybrid assembly method to process ~35x data from 454 technology and 2.8-3x data from Sanger method. Hybrid assemblies offered higher sequence coverage and better sequence assemblies. Homology studies revealed the presence of retrotransposon regions like Copia and Gypsy elements in these contigs and also helped in identifying new genomic SSRs. Unigenes were anchored to the sequences in Ctg-3301 and Ctg-465 to support the physical map. Gene density, gene structure and protein sequence information derived from protein prediction programs were used to obtain the functional annotation of these genes. Comparative analysis of both contigs with Arabidopsis genome exhibited synteny and microcollinearity with a conserved gene order in both genomes. This study provides insight about use of MTP-based BAC-pool sequencing approach for sequencing complex polyploid genomes with limited constraints in generating better sequence assemblies to build reference scaffold sequences. Combining the utilities of MTP-based BAC-pool sequencing with current longer and short read NGS technologies in multiplexed format would provide a new direction to cost-effectively and precisely sequence complex plant genomes.
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Affiliation(s)
- Ramesh Buyyarapu
- Center for Molecular Biology, Department of Biological and Environmental Sciences, Alabama Agricultural & Mechanical University, Normal, Alabama, United States of America
| | - Ramesh V. Kantety
- Center for Molecular Biology, Department of Biological and Environmental Sciences, Alabama Agricultural & Mechanical University, Normal, Alabama, United States of America
| | - John Z. Yu
- United States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, Texas, United States of America
| | - Zhanyou Xu
- United States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, Texas, United States of America
| | - Russell J. Kohel
- United States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, Texas, United States of America
| | - Richard G. Percy
- United States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, Texas, United States of America
| | - Simone Macmil
- Gene Structure and Function Laboratory, University of Otago, Dunedin, New Zealand
| | - Graham B. Wiley
- Arthritis & Immunology Department, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Bruce A. Roe
- Advanced Center for Genome Technology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Govind C. Sharma
- Center for Molecular Biology, Department of Biological and Environmental Sciences, Alabama Agricultural & Mechanical University, Normal, Alabama, United States of America
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16
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Abstract
Cotton (Gossypium spp.) is an important crop plant that is widely grown to produce both natural textile fibers and cottonseed oil. Cotton fibers, the economically more important product of the cotton plant, are seed trichomes derived from individual cells of the epidermal layer of the seed coat. It has been known for a long time that large numbers of genes determine the development of cotton fiber, and more recently it has been determined that these genes are distributed across At and Dt subgenomes of tetraploid AD cottons. In the present study, the organization and evolution of the fiber development genes were investigated through the construction of an integrated genetic and physical map of fiber development genes whose functions have been verified and confirmed. A total of 535 cotton fiber development genes, including 103 fiber transcription factors, 259 fiber development genes, and 173 SSR-contained fiber ESTs, were analyzed at the subgenome level. A total of 499 fiber related contigs were selected and assembled. Together these contigs covered about 151 Mb in physical length, or about 6.7% of the tetraploid cotton genome. Among the 499 contigs, 397 were anchored onto individual chromosomes. Results from our studies on the distribution patterns of the fiber development genes and transcription factors between the At and Dt subgenomes showed that more transcription factors were from Dt subgenome than At, whereas more fiber development genes were from At subgenome than Dt. Combining our mapping results with previous reports that more fiber QTLs were mapped in Dt subgenome than At subgenome, the results suggested a new functional hypothesis for tetraploid cotton. After the merging of the two diploid Gossypium genomes, the At subgenome has provided most of the genes for fiber development, because it continues to function similar to its fiber producing diploid A genome ancestor. On the other hand, the Dt subgenome, with its non-fiber producing D genome ancestor, provides more transcription factors that regulate the expression of the fiber genes in the At subgenome. This hypothesis would explain previously published mapping results. At the same time, this integrated map of fiber development genes would provide a framework to clone individual full-length fiber genes, to elucidate the physiological mechanisms of the fiber differentiation, elongation, and maturation, and to systematically study the functional network of these genes that interact during the process of fiber development in the tetraploid cottons.
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Affiliation(s)
- Zhanyou Xu
- Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, Texas, United States of America
| | - John Z. Yu
- Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, Texas, United States of America
- * E-mail:
| | - Jaemin Cho
- Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, Texas, United States of America
| | - Jing Yu
- Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, Texas, United States of America
| | - Russell J. Kohel
- Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, Texas, United States of America
| | - Richard G. Percy
- Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, Texas, United States of America
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Saha S, Jenkins JN, Wu J, McCarty JC, Gutiérrez OA, Percy RG, Cantrell RG, Stelly DM. Effects of chromosome-specific introgression in upland cotton on fiber and agronomic traits. Genetics 2006; 172:1927-38. [PMID: 16387867 PMCID: PMC1456304 DOI: 10.1534/genetics.105.053371] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2005] [Accepted: 12/22/2005] [Indexed: 11/18/2022] Open
Abstract
Interspecific chromosome substitution is among the most powerful means of introgression and steps toward quantitative trait locus (QTL) identification. By reducing the genetic "noise" from other chromosomes, it greatly empowers the detection of genetic effects by specific chromosomes on quantitative traits. Here, we report on such results for 14 cotton lines (CS-B) with specific chromosomes or chromosome arms from G. barbadense L. substituted into G. hirsutum and chromosome-specific F2 families. Boll size, lint percentage, micronaire, 2.5% span length, elongation, strength, and yield were measured by replicated field experiments in five diverse environments and analyzed under an additive-dominance (AD) genetic model with genotype and environment interaction. Additive effects were significant for all traits and dominance effects were significant for all traits except 2.5% span length. CS-B25 had additive effects increasing fiber strength and fiber length and decreasing micronaire. CS-B16 and CS-B18 had additive effects related to reduced yields. The results point toward specific chromosomes of G. barbadense 3-79 as the probable locations of the genes that significantly affect quantitative traits of importance. Our results provided a scope to analyze individual chromosomes of the genome in homozygous and heterozygous conditions and thus detected novel effects of alleles controlling important QTL.
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Affiliation(s)
- Sukumar Saha
- United States Department of Agriculture-Agriculture Research Service, Crop Science Research Laboratory, Mississippi State, Mississippi 39762, USA.
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Radin JW, Lu Z, Percy RG, Zeiger E. Genetic variability for stomatal conductance in Pima cotton and its relation to improvements of heat adaptation. Proc Natl Acad Sci U S A 1994; 91:7217-21. [PMID: 11607487 PMCID: PMC44370 DOI: 10.1073/pnas.91.15.7217] [Citation(s) in RCA: 133] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Responses of stomata to environment have been intensively studied, but little is known of genetic effects on stomatal conductance or their consequences. In Pima cotton (Gossypium barbadense L.), a crop that is bred for irrigated production in very hot environments, stomatal conductance varies genetically over a wide range and has increased with each release of new higher-yielding cultivars. A cross between heat-adapted (high-yielding) and unadapted genotypes produced F2 progeny cosegregating for stomatal conductance and leaf temperature. Within segregating populations in the field, conductance was negatively correlated with foliar temperature because of evaporative cooling. Plants were selected from the F2 generation specifically and solely for differing stomatal conductance. Among F3 and F4 populations derived from these selections, conductance and leaf cooling were significantly correlated with fruiting prolificacy during the hottest period of the year and with yield. Conductance was not associated with other factors that might have affected yield potential (single-leaf photosynthetic rate, leaf water potential). As breeders have increased the yield of this crop, genetic variability for conductance has allowed inadvertent selection for "heat avoidance" (evaporative cooling) in a hot environment.
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Affiliation(s)
- J W Radin
- U.S. Department of Agriculture, Agricultural Research Service, Western Cotton Research Laboratory, Phoenix, AZ 85040, USA
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Percy RG, Wendel JF. Allozyme evidence for the origin and diversification of Gossypium barbadense L. Theor Appl Genet 1990; 79:529-42. [PMID: 24226459 DOI: 10.1007/bf00226164] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/1989] [Accepted: 11/09/1989] [Indexed: 05/23/2023]
Abstract
Gossypium barbadense L. is a commercially important cotton species of tropical South American origin presently grownin many regions of the world. The species is morphologically diverse, consisting of a wide range of wild (or feral), commensal, landrace, and highly improvedcommercial forms. We performed allozyme analysis on 153 accessions representing the spectrum of G. barbadense diversityto ascertain the geographic origin of the species, its patterns of diffusion subsequent to domestication, and to reveal infraspecific relationships. Levels ofgenetic variation in G. barbadense are moderate. Of 59 loci scored, 24 were polymorphic, with a mean number of alleles perlocus of 1.69 and an average panmictic heterozygosity of 0.062. Principal component analysis revealed geographic clustering of accessions into six relativelydiscrete regions. Gene frequencies at many loci are significantly heterogeneous among these regions, with an average G STof 0.272. Northwestern South America contains the greatest genetic variability; we suggest that this region is the ancestral home of the species. The data indicate separate diffusion pathways from this region into Argentina-Paraguay and into eastern and northern South America east of the Andes. Caribbean Island and Central American forms appear to be derived from the latter. These diffusion pathways are in accordance with morphological evidence and historical record. In contrast to expectations based on geographic proximity, Pacific Island forms have their closest affinity to accessions from eastern South America. Advanced cultivated stocks seem largely derived from western Andean material, but also contain introgressed G. hirsutum germ plasm. Introgression was relatively high (22%-50% of accessions) in commercial stocks and in forms from Argentina-Paraguay and various Pacific Islands, but was conspicuously low or absent in material from Central America and the Caribbean, where commensal and commercial forms of both species are sympatric.
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Affiliation(s)
- R G Percy
- USDA-ARS, in cooperation with the Arizona Agricultural Experiment Station, Maricopa Agricultural Center, 37860 W. Smith-Enke Rd., 85339, Maricopa, AZ, USA
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Wendel JF, Percy RG. Allozyme diversity and introgression in the Galapagos Islands endemic Gossypium darwinii and its relationship to continental G. barbadense. BIOCHEM SYST ECOL 1990. [DOI: 10.1016/0305-1978(90)90123-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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