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Table 5 Four SNP loci significantly related to protein content as determined by genome-wide association analysis

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

SNP

Significance test

p-value

Genome sequence

Chromosome

Position

Marker

i28873Gh

Wald test

3.70E-06

G. raimondii v221

*

0

Group

TAMU

Likelihood Ratio Test

1.11E-05

G. arboreum v2

Ca13

41,692,946

Group_name

GH_TBb049I03r236

Score Test

4.81E-05

G. hirsutum NBI v1.1

NBI_A02

7,820,104

Sequence

TCGATATGAACGGAAAATGCTTGCTCGTCGGTTGGAAGGGGACGCCGATGYTTTCAATTTCGGTTTGGAA

ATTTCTATAAGCCAATGTCTAAATGTTACCA

Marker

i34975Gh

Wald test

3.70E-06

G. raimondii v221

Chr05

7,028,098

Group

TAMU

Likelihood Ratio Test

1.11E-05

G. arboreum v2

Ca13

41,671,786

Group_name

GH_TBb119J20f639

Score Test

4.81E-05

G. hirsutum NBI v1.1

NBI_A02

7,800,710

Sequence

ATGGATGACAGAAATAGGACTATGATCAATCCCATCCACCGCTACTCGGTMCCTGTGTATCCAGGTACC

CAACACAAAGCTAGCTAGCTATGACAGTAAAT

Marker

i20295Gh

Wald test

1.52E-05

G. raimondii v221

Chr13

30,556,525

Group

CSIRO

Likelihood Ratio Test

9.78E-04

G. arboreum v2

*

0

Group_name

Scaffold_13_30556525

Score Test

6.41E-03

G. hirsutum NBI v1.1

*

0

Sequence

AACGTACTAAATTCGTAGTTAGATAGTAGCCAAGGACTCACTTAAACCAACTAAAACATCAACCTATTCTAAGTTCTCATGTAACAAAAATTTAACATAAYAAACTTAGAATGCTTATAACTCGGTCTATGCTTAACCTTTTCACCTAAAACGAATTTTGTTCACCTATTTAGTCTTCTACGACTAATCATCAACCCTTAA

Marker

i22490Gh

Wald test

1.60E-05

G. raimondii v221

*

0

Group

USDA

Likelihood Ratio Test

1.03E-03

G. arboreum v2

*

0

Group_name

CFB2569

Score Test

6.41E-03

G. hirsutum NBI v1.1

NBI_D01

35,251,544

Sequence

TGCCGCATACTTGTGGACCACATARTCGTGTACAATTGGAAAATTAGGGATTTAGAGGAATTTTGGTGCC

ACACGACCGTGTGGCTGATT

  1. Information is provided on p-values associated with three significance tests, as well as known chromosomal locations in three available Gossypium genome sequences