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Table 1 Measures of SNP-based genetic diversity within G. hirsutum germplasm groups

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

  

Average MAF

  

Group

N

Including monomorphic

Excluding monomorphic

Total polymorphic SNPs (proportion)

Genetic diversity (HE)

Gossypium spp.

390

0.184

0.213

33507 (0.86)

0.249

G. hirsutum

363

0.169

0.252

25829 (0.67)

0.225

G. hirsutum, improved

292

0.145

0.242

23145 (0.60)

0.195

G. hirsutum, wild

71

0.177

0.260

26299 (0.68)

0.232

G. hirsutum, improved, US

185

0.141

0.241

22626 (0.58)

0.190

G. hirsutum, improved, other countries

107

0.147

0.248

22961 (0.59)

0.197

G. hirsutum, improved, US, eastern

48

0.132

0.234

21810 (0.56)

0.177

G. hirsutum, improved, US, mid-south

48

0.111

0.222

19357 (0.50)

0.151

G. hirsutum, improved, US, plains

43

0.135

0.245

21350 (0.55)

0.183

G. hirsutum, improved, US, western

12

0.118

0.267

17093 (0.44)

0.157

G. hirsutum, improved, US, n/a

34

0.142

0.231

23851 (0.62)

0.193

  1. Number of polymorphic SNPs (MAF ≥ 0.01) was calculated out of 38,822 SNPs. N sample size, MAF minor allele frequency