Table 4 List of SNPs significantly associated with the traits evaluated under salt tolerance in a MAGIC cowpea population, chromosome and physical position (bp) of each SNP, LOD (-log10(p-value)), minor allele frequency MAF (%), annotated genes found within the 20-kb region flanking each significant SNP, and functional annotations for each gene ID. LOD threshold was greater or equal to 3.5. If no SNPs were above the threshold, the top 3 SNPs with the highest LOD were listed in below table. The BLINK model does not compute R_square, so no R_square information is provided
Traits | SNP | Chr | Position (bp) | LOD | MAF(%) | Gene_ID | Functional_annotation |
|---|---|---|---|---|---|---|---|
DeadPlants | 2_26528 | 3 | 47,346,498 | 4.1 | 35.1 | Vigun03g290500.1 | Homeobox associated leucine zipper |
2_05819 | 3 | 47,359,021 | 4.1 | 35.1 | Vigun03g290600.1 | Xyloglucan:xyloglucosyl transferase | |
2_28348 | 3 | 47,394,698 | 3.7 | 35.7 | Vigun03g290800.1 | NA | |
2_25790 | 7 | 1,969,327 | 4.1 | 13.6 | Vigun07g023000.1 | RNA helicase | |
Vigun07g023100.1 | Leucine Rich repeat | ||||||
2_07660 | 7 | 3,048,839 | 3.7 | 11.6 | Vigun07g032400.1 | Calcium-dependent protein kinase 32 | |
Vigun07g032300.1 | Typa-like translation elongation factor SVR3-related | ||||||
2_02219 | 7 | 3,062,497 | 3.7 | 11.6 | Vigun07g032500.1 | Raffinose synthase or seed imbibition protein Sip1 | |
2_02220 | 7 | 3,063,296 | 3.7 | 11.6 | Vigun07g032500.1 | Raffinose synthase or seed imbibition protein Sip1 | |
Score | 2_13484 | 1 | 25,524,675 | 3.6 | 29.3 | Vigun01g093100.1 | Na+/Ca2+ K+ independent exchanger |
2_13485 | 1 | 25,525,542 | 3.6 | 29.3 | Vigun01g093100.1 | Na+/Ca2+ K+ independent exchanger | |
S_Chloro | 2_14317 | 3 | 43,217,726 | 3.7 | 38.0 | Vigun03g263100.1 | Mitochondrial folate transporter/carrier |
2_33024 | 3 | 43,218,173 | 4.2 | 49.6 | Vigun03g263100.1 | Mitochondrial folate transporter/carrier | |
2_45043 | 3 | 43,435,268 | 3.6 | 38.4 | Vigun03g264700.1 | NA | |
2_15070 | 3 | 43,489,540 | 3.6 | 38.8 | Vigun03g265200.1 | Auxilin/cyclin G-associated kinase-related | |
2_02054 | 3 | 43,739,483 | 3.9 | 48.8 | Vigun03g267000.1 | Clathrin coat assembly protein | |
Vigun03g267100.1 | Lysine methyltransferase | ||||||
Vigun03g266900.1 | Phytoene dehydrogenase | ||||||
2_29692 | 3 | 43,757,044 | 3.9 | 48.8 | Vigun03g267200.1 | Retinaldehyde binding protein-related | |
2_07148 | 3 | 43,786,460 | 3.7 | 49.2 | Vigun03g267400.1 | Succinate dehydrogenase flavoprotein subunit | |
2_46677 | 3 | 44,031,642 | 3.6 | 48.8 | NA | NA | |
2_47326 | 3 | 44,089,702 | 3.6 | 48.8 | NA | NA | |
2_31683 | 3 | 44,242,654 | 3.6 | 48.8 | Vigun03g269900.1 | Protein DA1-related | |
2_51323 | 3 | 44,389,344 | 3.7 | 49.6 | Vigun03g270400.1 | Cysteine-rich secretory protein family | |
Vigun03g270300.1 | NA | ||||||
2_20981 | 3 | 44,394,170 | 3.7 | 49.6 | Vigun03g270400.1 | Cysteine-rich secretory protein family | |
Vigun03g270300.1 | NA | ||||||
2_20980 | 3 | 44,394,695 | 3.7 | 49.6 | Vigun03g270400.1 | Cysteine-rich secretory protein family | |
Vigun03g270300.1 | NA | ||||||
2_51556 | 3 | 44,395,302 | 3.7 | 49.6 | Vigun03g270400.1 | Cysteine-rich secretory protein family | |
Vigun03g270300.1 | NA | ||||||
2_27478 | 3 | 44,562,081 | 3.7 | 48.8 | Vigun03g271300.1 | Vacuolar protein sorting-associated protein VPS13 | |
2_26528 | 3 | 47,346,498 | 4.1 | 35.1 | Vigun03g263000.1 | Alpha/beta hydrolase fold | |
2_05819 | 3 | 47,359,021 | 4.1 | 35.1 | Vigun03g290600.1 | Xyloglucan:xyloglucosyl transferase | |
2_28348 | 3 | 47,394,698 | 4.0 | 35.7 | Vigun03g290800.1 | NA | |
RTI_C | 2_14317 | 3 | 43,217,726 | 3.5 | 38.0 | Vigun03g263100.1 | Mitochondrial folate transporter/carrier |
2_33024 | 3 | 43,218,173 | 4.6 | 49.6 | Vigun03g263100.1 | Mitochondrial folate transporter/carrier | |
Vigun03g263000.1 | Alpha/beta hydrolase fold-containing protein | ||||||
2_15070 | 3 | 43,489,540 | 3.6 | 38.8 | Vigun03g265200.1 | Auxilin/cyclin G-associated kinase-related | |
2_02054 | 3 | 43,739,483 | 4.1 | 48.8 | Vigun03g267000.1 | Clathrin coat assembly protein | |
Vigun03g267100.1 | Lysine methyltransferase | ||||||
Vigun03g266900.1 | Phytoene dehydrogenase | ||||||
2_29692 | 3 | 43,757,044 | 4.1 | 48.8 | Vigun03g267200.1 | Retinaldehyde binding protein-related | |
2_07148 | 3 | 43,786,460 | 3.8 | 49.2 | Vigun03g267400.1 | Succinate dehydrogenase flavoprotein subunit | |
2_46677 | 3 | 44,031,642 | 3.9 | 48.8 | NA | NA | |
2_47326 | 3 | 44,089,702 | 3.9 | 48.8 | NA | NA | |
2_31683 | 3 | 44,242,654 | 3.9 | 48.8 | Vigun03g269900.1 | Protein DA1-related | |
2_51323 | 3 | 44,389,344 | 4.0 | 49.6 | Vigun03g270400.1 | Cysteine-rich secretory protein-related | |
Vigun03g270300.1 | NA | ||||||
2_20981 | 3 | 44,394,170 | 4.0 | 49.6 | Vigun03g270400.1 | Cysteine-rich secretory protein-related | |
Vigun03g270300.1 | NA | ||||||
2_20980 | 3 | 44,394,695 | 4.0 | 49.6 | Vigun03g270400.1 | Cysteine-rich secretory protein-related | |
Vigun03g270300.1 | NA | ||||||
2_51556 | 3 | 44,395,302 | 4.0 | 49.6 | Vigun03g270400.1 | Cysteine-rich secretory protein-related | |
Vigun03g270300.1 | NA | ||||||
2_27478 | 3 | 44,562,081 | 3.9 | 48.8 | Vigun03g271300.1 | Vacuolar protein sorting-associated protein VPS13 | |
2_26528 | 3 | 47,346,498 | 3.9 | 35.1 | Vigun03g290500.1 | Homeobox-leucine zipper protein HAT9 | |
2_05819 | 3 | 47,359,021 | 3.9 | 35.1 | Vigun03g290600.1 | Xyloglucan:xyloglucosyl transferase | |
2_28348 | 3 | 47,394,698 | 3.8 | 35.7 | Vigun03g290800.1 | NA | |
S_Leaf | 2_27478 | 3 | 44,562,081 | 3.0 | 48.8 | Vigun03g271300.1 | Na+/Ca2+ K+ independent exchanger |
2_28348 | 3 | 47,394,698 | 3.3 | 35.7 | Vigun03g290800.1 | NA | |
2_50921 | 7 | 16,162,316 | 3.1 | 24.3 | NA | NA | |
RTI_FL | 2_27478 | 3 | 44,562,081 | 3.9 | 48.8 | Vigun03g271300.1 | Vacuolar protein sorting-associated protein VPS13 |
2_28348 | 3 | 47,394,698 | 4.0 | 35.7 | Vigun03g290800.1 | NA | |
RTI_FS | 2_20734 | 4 | 40,193,498 | 3.4 | 10.3 | Vigun04g178400.1 | Glycosyltransferase 8 domain-containing protein |
Vigun04g178500.1 | NA | ||||||
Vigun04g178300.1 | CCR4-not transcription complex related | ||||||
2_13286 | 4 | 40,198,028 | 3.4 | 10.3 | Vigun04g178400.1 | Glycosyltransferase 8 domain-containing protein | |
Vigun04g178500.1 | NA | ||||||
2_13285 | 4 | 40,198,314 | 3.4 | 10.3 | Vigun04g178400.1 | Glycosyltransferase 8 domain-containing protein | |
Vigun04g178500.1 | NA | ||||||
2_44170 | 4 | 40,238,551 | 3.4 | 10.3 | Vigun04g178900.1 | Â H+/oligopeptide symporter | |
Vigun04g178800.1 | NA | ||||||
2_47221 | 4 | 40,244,092 | 3.4 | 10.3 | Vigun04g178900.1 | Â H+/oligopeptide symporter | |
Vigun04g179000.1 | Zinc finger FYVE domain containing protein | ||||||
RTI_FB | 2_33574 | 5 | 579,544 | 3.6 | 7.0 | Vigun05g006800.1 | Mannose-6-phosphate isomerase |
Vigun05g006700.1 | Alpha/beta hydrolase fold-containing protein | ||||||
Vigun05g006600.1 | NA | ||||||
Vigun05g006500.1 | Neoxanthin biosynthesis | ||||||
RTI_H | 2_26489 | 3 | 20,639,699 | 4.2 | 28.1 | Vigun03g171400.1 | O-methyltransferase-related |
1_0247 | 3 | 20,639,954 | 4.2 | 28.1 | Vigun03g171400.1 | O-methyltransferase-related | |
2_04756 | 3 | 20,640,004 | 4.2 | 28.1 | Vigun03g171400.1 | O-methyltransferase-related | |
2_34159 | 3 | 21,168,375 | 4.2 | 28.9 | Vigun03g172900.1 | Protein transport protein Sect. 23 | |
Vigun03g173100.1 | Peptidyl-prolyl cis-trans isomerase | ||||||
2_34562 | 3 | 21,184,999 | 4.2 | 29.0 | Vigun03g173200.1 | Cystatin-C | |
2_00955 | 3 | 21,195,566 | 4.2 | 28.9 | Vigun03g173300.1 | Phospholipases | |
2_52154 | 3 | 21,311,445 | 4.2 | 28.9 | Vigun03g173800.1 | Dolichol-phosphate mannosyltransferase | |
2_15515 | 3 | 21,332,934 | 4.2 | 28.9 | Vigun03g174100.1 | IQ-domain 9 protein | |
Vigun03g174000.1 | Mutt-nudix-related | ||||||
Vigun03g173900.1 | Magnesium chelatase subunit I | ||||||
2_06057 | 3 | 21,415,465 | 4.2 | 28.9 | Vigun03g174200.1 | Ionotropic glutamate receptor | |
Vigun03g174300.1 | Apoptosis inhibitor 5 | ||||||
2_03596 | 3 | 21,479,991 | 4.2 | 28.9 | Vigun03g174500.1 | NA | |
Vigun03g174400.1 | Peroxidase 19 | ||||||
2_45312 | 3 | 21,500,420 | 4.2 | 28.9 | Vigun03g174600.1 | Triacylglycerol degradation | |
2_39953 | 3 | 21,742,682 | 3.8 | 28.9 | NA | NA | |
2_30884 | 3 | 21,777,011 | 3.8 | 28.9 | Vigun03g175900.1 | Cytochrome P450 | |
2_37604 | 3 | 21,810,301 | 3.8 | 28.9 | NA | NA | |
2_32781 | 3 | 21,841,991 | 3.8 | 28.9 | Vigun03g176100.1 | Microfibril-associated protein | |
2_25800 | 3 | 21,872,524 | 3.8 | 28.9 | Vigun03g176300.1 | Suberin monomers biosynthesis | |
2_14391 | 3 | 21,913,428 | 3.8 | 28.9 | Vigun03g176400.1 | Homoserine dehydrogenase | |
2_14392 | 3 | 21,914,412 | 3.8 | 28.9 | Vigun03g176400.1 | Homoserine dehydrogenase | |
2_54159 | 3 | 22,010,385 | 3.8 | 28.9 | Vigun03g177000.1 | Beta-galactosidase 9 | |
Vigun03g177100.1 | Beta-galactosidase 9 | ||||||
2_52111 | 3 | 22,014,192 | 3.8 | 28.9 | Vigun03g177000.1 | Beta-galactosidase 9 | |
Vigun03g177100.1 | Beta-galactosidase 9 | ||||||
2_47286 | 3 | 22,025,277 | 3.8 | 28.9 | Vigun03g177100.1 | Beta-galactosidase 9 | |
2_49598 | 3 | 23,926,152 | 3.8 | 28.9 | NA | NA | |
2_15529 | 3 | 24,031,773 | 3.8 | 28.9 | Vigun03g184300.1 | NA |