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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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Hulse-Kemp AM, Ashrafi H, Plieske J, Lemm J, Stoffel K, Hill T, Luerssen H, Pethiyagoda CL, Lawley CT, Ganal MW, Van Deynze A. A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding. Hortic Res 2016; 3:16036. [PMID: 27602231 PMCID: PMC4962762 DOI: 10.1038/hortres.2016.36] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/06/2016] [Accepted: 07/08/2016] [Indexed: 05/18/2023]
Abstract
The Capsicum genus (Pepper) is a part of the Solanacae family. It has been important in many cultures worldwide for its key nutritional components and uses as spices, medicines, ornamentals and vegetables. Worldwide population growth is associated with demand for more nutritionally valuable vegetables while contending with decreasing resources and available land. These conditions require increased efficiency in pepper breeding to deal with these imminent challenges. Through resequencing of inbred lines we have completed a valuable haplotype map (HapMap) for the pepper genome based on single-nucleotide polymorphisms (SNP). The identified SNPs were annotated and classified based on their gene annotation in the pepper draft genome sequence and phenotype of the sequenced inbred lines. A selection of one marker per gene model was utilized to create the PepperSNP16K array, which simultaneously genotyped 16 405 SNPs, of which 90.7% were found to be informative. A set of 84 inbred and hybrid lines and a mapping population of 90 interspecific F2 individuals were utilized to validate the array. Diversity analysis of the inbred lines shows a distinct separation of bell versus chile/hot pepper types and separates them into five distinct germplasm groups. The interspecific population created between Tabasco (C. frutescens chile type) and P4 (C. annuum blocky type) produced a linkage map with 5546 markers separated into 1361 bins on twelve 12 linkage groups representing 1392.3 cM. This publically available genotyping platform can be used to rapidly assess a large number of markers in a reproducible high-throughput manner for pepper. As a standardized tool for genetic analyses, the PepperSNP16K can be used worldwide to share findings and analyze QTLs for important traits leading to continued improvement of pepper for consumers. Data and information on the array are available through the Solanaceae Genomics Network.
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Affiliation(s)
- Amanda M Hulse-Kemp
- Department of Plant Sciences, University of California-Davis, Davis, California 95616, USA
| | - Hamid Ashrafi
- Department of Plant Sciences, University of California-Davis, Davis, California 95616, USA
| | - Joerg Plieske
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, Gatersleben, Germany
| | - Jana Lemm
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, Gatersleben, Germany
| | - Kevin Stoffel
- Department of Plant Sciences, University of California-Davis, Davis, California 95616, USA
| | - Theresa Hill
- Department of Plant Sciences, University of California-Davis, Davis, California 95616, USA
| | - Hartmut Luerssen
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, Gatersleben, Germany
| | | | - Cindy T Lawley
- Illumina Incorporated, 5200 Illumina Way, San Diego, CA 92122, USA
| | - Martin W Ganal
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, Gatersleben, Germany
| | - Allen Van Deynze
- Department of Plant Sciences, University of California-Davis, Davis, California 95616, USA
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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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