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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)