Table 5.
Four SNP loci significantly related to protein content as determined by genome-wide association analysis
| 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 |
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| 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 |
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| 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 |
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Information is provided on p-values associated with three significance tests, as well as known chromosomal locations in three available Gossypium genome sequences