title: Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.
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.
authors.affiliation: 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.
authors.forename: Amanda M
authors.identifier: http://orcid.org/0000-0001-9670-9433
authors.initials: AM
authors.lastname: Hulse-Kemp
authors.affiliation: TraitGenetics GmbH, 06466 Gatersleben, Germany.
authors.forename: Jana
authors.initials: J
authors.lastname: Lemm
authors.affiliation: TraitGenetics GmbH, 06466 Gatersleben, Germany.
authors.forename: Joerg
authors.initials: J
authors.lastname: Plieske
authors.affiliation: Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, California 95616.
authors.forename: Hamid
authors.identifier: http://orcid.org/0000-0002-2094-2367
authors.initials: H
authors.lastname: Ashrafi
authors.affiliation: Dow AgroSciences, Trait Genetics and Technologies, Indianapolis, Indiana 46268.
authors.forename: Ramesh
authors.identifier: http://orcid.org/0000-0002-5343-9960
authors.initials: R
authors.lastname: Buyyarapu
authors.affiliation: USDA-ARS-SRRC, Cotton Fiber Bioscience Research Unit, New Orleans, Louisiana 70124.
authors.forename: David D
authors.identifier: http://orcid.org/0000-0003-0036-5459
authors.initials: DD
authors.lastname: Fang
authors.affiliation: USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845.
authors.forename: James
authors.initials: J
authors.lastname: Frelichowski
authors.affiliation: CIRAD, UMR AGAP, Montpellier, F34398, France EMBRAPA, Algodão, Nucleo Cerrado, 75.375-000 Santo Antônio de Goias, GO, Brazil.
authors.forename: Marc
authors.initials: M
authors.lastname: Giband
authors.affiliation: Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843.
authors.forename: Steve
authors.initials: S
authors.lastname: Hague
authors.affiliation: USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845.
authors.forename: Lori L
authors.initials: LL
authors.lastname: Hinze
authors.affiliation: Department of Animal Science, Texas A&M University, College Station, Texas 77843.
authors.forename: Kelli J
authors.identifier: http://orcid.org/0000-0001-8124-8283
authors.initials: KJ
authors.lastname: Kochan
authors.affiliation: 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.
authors.forename: Penny K
authors.identifier: http://orcid.org/0000-0003-3296-320X
authors.initials: PK
authors.lastname: Riggs
authors.affiliation: USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, Mississippi 38776.
authors.forename: Jodi A
authors.identifier: http://orcid.org/0000-0001-7897-2916
authors.initials: JA
authors.lastname: Scheffler
authors.affiliation: Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602.
authors.forename: Joshua A
authors.initials: JA
authors.lastname: Udall
authors.affiliation: USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, Texas 79415.
authors.forename: Mauricio
authors.initials: M
authors.lastname: Ulloa
authors.affiliation: USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845.
authors.forename: Shirley S
authors.initials: SS
authors.lastname: Wang
authors.affiliation: CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia.
authors.forename: Qian-Hao
authors.identifier: http://orcid.org/0000-0002-6505-7417
authors.initials: QH
authors.lastname: Zhu
authors.affiliation: CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India.
authors.forename: Sumit K
authors.identifier: http://orcid.org/0000-0001-8907-2841
authors.initials: SK
authors.lastname: Bag
authors.affiliation: CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India.
authors.forename: Archana
authors.initials: A
authors.lastname: Bhardwaj
authors.affiliation: USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, Texas 79415.
authors.forename: John J
authors.initials: JJ
authors.lastname: Burke
authors.affiliation: Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Byers
authors.affiliation: CIRAD, UMR AGAP, Montpellier, F34398, France.
authors.forename: Michel
authors.initials: M
authors.lastname: Claverie
authors.affiliation: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853.
authors.forename: Michael A
authors.identifier: http://orcid.org/0000-0001-6896-8024
authors.initials: MA
authors.lastname: Gore
authors.affiliation: Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602.
authors.forename: David B
authors.initials: DB
authors.lastname: Harker
authors.affiliation: USDA-ARS-SRRC, Cotton Fiber Bioscience Research Unit, New Orleans, Louisiana 70124.
authors.forename: Md S
authors.initials: MS
authors.lastname: Islam
authors.affiliation: USDA-ARS, Genetics and Precision Agriculture Research, Mississippi State, Mississippi 39762.
authors.forename: Johnie N
authors.initials: JN
authors.lastname: Jenkins
authors.affiliation: Cotton Incorporated, Agricultural Research, Cary, North Carolina 27513.
authors.forename: Don C
authors.initials: DC
authors.lastname: Jones
authors.affiliation: CIRAD, UMR AGAP, Montpellier, F34398, France.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Lacape
authors.affiliation: CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia.
authors.forename: Danny J
authors.initials: DJ
authors.lastname: Llewellyn
authors.affiliation: USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845.
authors.forename: Richard G
authors.initials: RG
authors.lastname: Percy
authors.affiliation: Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843 Department of Biology, Texas A&M University, College Station, Texas 77843.
authors.forename: Alan E
authors.initials: AE
authors.lastname: Pepper
authors.affiliation: Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Kansas State University, Manhattan, Kansas 66506.
authors.forename: Jesse A
authors.initials: JA
authors.lastname: Poland
authors.affiliation: CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India.
authors.forename: Krishan
authors.initials: K
authors.lastname: Mohan Rai
authors.affiliation: CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India.
authors.forename: Samir V
authors.identifier: http://orcid.org/0000-0002-7635-5049
authors.initials: SV
authors.lastname: Sawant
authors.affiliation: CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India.
authors.forename: Sunil Kumar
authors.identifier: http://orcid.org/0000-0002-4897-8812
authors.initials: SK
authors.lastname: Singh
authors.affiliation: CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia.
authors.forename: Andrew
authors.initials: A
authors.lastname: Spriggs
authors.affiliation: CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia.
authors.forename: Jen M
authors.initials: JM
authors.lastname: Taylor
authors.affiliation: Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843.
authors.forename: Fei
authors.initials: F
authors.lastname: Wang
authors.affiliation: Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602.
authors.forename: Scott M
authors.initials: SM
authors.lastname: Yourstone
authors.affiliation: Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843.
authors.forename: Xiuting
authors.identifier: http://orcid.org/0000-0002-8574-4708
authors.initials: X
authors.lastname: Zheng
authors.affiliation: Illumina Inc., San Francisco, California 94158.
authors.forename: Cindy T
authors.initials: CT
authors.lastname: Lawley
authors.affiliation: TraitGenetics GmbH, 06466 Gatersleben, Germany.
authors.forename: Martin W
authors.initials: MW
authors.lastname: Ganal
authors.affiliation: Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, California 95616.
authors.forename: Allen
authors.identifier: http://orcid.org/0000-0002-2093-0577
authors.initials: A
authors.lastname: Van Deynze
authors.affiliation: CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia.
authors.forename: Iain W
authors.initials: IW
authors.lastname: Wilson
authors.affiliation: 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 stelly@tamu.edu.
authors.forename: David M
authors.identifier: http://orcid.org/0000-0002-3468-4119
authors.initials: DM
authors.lastname: Stelly
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D032461:Chromosomes, Plant / Q000235:genetics; D003434:Crossing Over, Genetic; D030541:Databases, Genetic; D005787:Gene Frequency / Q000235:genetics; D008040:Genetic Linkage; D005819:Genetic Markers; D005838:Genotype; D060005:Genotyping Techniques; D003368:Gossypium / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011123:Polyploidy; D015203:Reproducibility of Results; D013045:Species Specificity; D026801:Synteny / Q000235:genetics
chemical_list: D005819:Genetic Markers
keywords: breeding; interspecific SNPs; intraspecific SNPs; linkage analysis; recombination