Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array.
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.



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.



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.
USDA-ARS, Crop Germplasm Research Unit, College Station, TX, 77845, USA. Lori.Hinze@ars.usda.gov.
Lori L
LL
Hinze
Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA, 95616, USA.
Amanda M
AM
Hulse-Kemp
CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT, 2601, Australia.
Iain W
IW
Wilson
CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT, 2601, Australia.
Qian-Hao
QH
Zhu
CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT, 2601, Australia.
Danny J
DJ
Llewellyn
CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT, 2601, Australia.
Jen M
JM
Taylor
CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT, 2601, Australia.
Andrew
A
Spriggs
USDA-ARS, Cotton Fiber Bioscience Research Unit, New Orleans, LA, 70124, USA.
David D
DD
Fang
USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX, 79415, USA.
Mauricio
M
Ulloa
USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX, 79415, USA.
John J
JJ
Burke
CIRAD, UMR AGAP, Montpellier, F34398, France.|EMBRAPA, Algodão, Nucleo Cerrado, 75.375-000, Santo Antônio de Goias, GO, Brazil.
Marc
M
Giband
CIRAD, UMR AGAP, Montpellier, F34398, France.
Jean-Marc
JM
Lacape
Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA, 95616, USA.
Allen
A
Van Deynze
Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, USA.
Joshua A
JA
Udall
USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, MS, 38776, USA.
Jodi A
JA
Scheffler
Department of Soil & Crop Sciences, Texas A&M University, College Station, TX, 77843, USA.
Steve
S
Hague
Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA.
Jonathan F
JF
Wendel
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.
Alan E
AE
Pepper
USDA-ARS, Crop Germplasm Research Unit, College Station, TX, 77845, USA.
James
J
Frelichowski
Illumina Inc., 499 Illinois Street, San Francisco, CA, 94158, USA.
Cindy T
CT
Lawley
Cotton Incorporated, Agricultural Research, Cary, NC, 27513, USA.
Don C
DC
Jones
USDA-ARS, Crop Germplasm Research Unit, College Station, TX, 77845, USA.
Richard G
RG
Percy
Department of Soil & Crop Sciences, Texas A&M University, College Station, TX, 77843, USA. stelly@tamu.edu.|Interdisciplinary Department of Genetics, Texas A&M University, College Station, TX, 77843, USA. stelly@tamu.edu.
David M
DM
Stelly
D000483:Alleles; D005819:Genetic Markers; D014644:Genetic Variation; D018745:Genome, Plant; D005838:Genotype; D003368:Gossypium / Q000145:classification / Q000235:genetics*; D018895:Microsatellite Repeats; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D020641:Polymorphism, Single Nucleotide
D005819:Genetic Markers; D010940:Plant Proteins
Breeding; Cotton; Diversity analysis; Genome-wide association analysis; Germplasm collection; Molecular markers; Seed protein content