Skip to main content

Table 2 Favorable SNP alleles, their phenotypic effects (ai), and representative accessions

From: Identification of favorable SNP alleles and candidate genes for traits related to early maturity via GWAS in upland cotton

Traits SNP Position Alleles Favorable alleles ai Accessions Representative accessionsa
WGP rs26538646 At3:26538646 A/G A −6.70** 59 zhongmiansuo74, xia25, zhong416
rs26538688 At3:26538688 G/T G −6.70** 59 zhongmiansuo74, xia25, zhong416
rs13562854 Dt3:13562854 A/G A −7.53** 66 zhongmiansuo74, xia25, zhong416
rs8917898 Dt3:8917898 A/G G −7.58** 49 zhong6426, zhong51822, xia13-7
rs13153008 Dt3:13153008 A/G A −7.76** 42 xia25, zhong416, baimian17
FT rs22465987 At4:22465987 A/G G −0.07 94 1476, zhongmiansuo74, xiaomian3
rs48627288 At12:48627288 A/G A −0.55 86 xia25, xiazao3, zhongmiansuo14
rs13562854 Dt3:13562854 A/G A −3.88** 66 xiazao2,zhongmiansuo74,xia25
rs8917898 Dt3:8917898 A/G G −3.69** 49 xia25, 1476, xiazao3
rs37255056 Dt3:37255056 A/G A −3.40** 56 xia25, 1476, xiazao3
FBP rs13153008 Dt3:13153008 A/G A −4.09** 42 zhong416, xia25, zhongmiansuo64
NFFB rs13562854 Dt3:13562854 A/G A −0.91** 66 xiaozao2, xiazao3, xia25
YPBF rs13562854 Dt3:13562854 A/G A 10.45** 66 zhongmiansuo74, xia25, xiazao3
  1. aRepresentative accessions consist of the top 3 entries for the target trait values of accessions with the corresponding favorable alleles; **highly favorable SNP alleles that exhibit significantly different traits compared with the unfavorable alleles (P < 0.01)