Table 8 Annotation of genes harbouring the homolog trait-associated SNPs across all chromosomes in rice under salinity stress
Marker | Sequence | Trait | Ch. | Position (bp) | p-value | FDR | R2 (%) | Homolog gene ID in rice | Description |
|---|---|---|---|---|---|---|---|---|---|
rs15925 | TGCAGCAGAGAGGCGCGGAAACACGCGATCTCCGCACGCTGGGCCGCCCCAGTGGGCGGCGGTC | ELI | 1 | 38,144,793-38,146,141 | 0.000144354 | 0.999599159 | 7.27 | Os01g0878900 | Similar to 4,5-DOPA dioxygenase extradiol-like protein |
rs48518 | TGCAGGCGGTTGGACATGGGCATGCCCATCGACGATTCAGACGAATACGAGATCAACAAGATAT | SPAD | 11 | 4,522,342-4,557,911 | 0.00012878 | 0.567532444 | 8.44 | OsOSC7 Os11g0189600 | 2,3-oxidosqualene cyclase, Triterpene synthase, Parkeol synthas |
rs25433 | TGCAGAGTTATAGGGAAGAAGAAGAAGGCGTACGTGGAAAAAACGATTCGAGGAGCGCTCCCGT | SFW | 1 | 9,954,154-9,955,696 | 0.000150218 | 0.915267063 | 7.04 | Os01g0280200 | IQ motif, EF-hand binding site domain containing protein |
rs8636 | TGCAGATCGGGCTTCCCCCACTGGCTTTGCGTGCGGGCAGTTTTGGGTGGTGCTTGCTGGTGGC | SDW | 12 | 23,805,152-23,808,859 | 0.000177924 | 0.986473673 | 9.28 | OsPAP1d Os12g0576600 | Metallophosphoesterase domain containing protein |
rs54146 | TGCAGGTGGAAAATGGAATCGCTAGGCCGCCGCCGAGATCGGAAGAGCGGGATCACCGACTGCC | RWC | 2 | 15,310,546-15,324,161 | 0.000103142 | 0.998787304 | 10.33 | Os02g0458900 | Conserved hypothetical protein |
rs257 | TGCAGAAAAGTAAGAAATTTGAAGGAGTTTTGTTCAATCACCATTTTATTACGTGTCCTCCCGA | RFW | 12 | 23,810,618-23,814,363 | 0.000259648 | 0.972631462 | 17.48 | OsPAP1c Os12g0576700 | Similar to Diphosphonucleotide phosphatase 1 precursor |
rs37983 | TGCAGCTCTGACCGACTCCGCCTGAAGCCGCCATCGTTGCCACACAGGAGGACGACCTATTATT | RDW | 1 | 36,936,986-36,939,375 | 0.000119634 | 0.879468434 | 16.57 | Os01g0855400 | SANT domain, DNA binding domain containing protein |
rs18682 | TGCAGCAGTGGTGGTGTGCCCTTGGTCCATGCCATGTTTGTGTGCTCACCCTGTGGTTGTGGTG | RV | 9 | 17,024,575-17,028,546 | 0.000185224 | 0.961706611 | 10.14 | OsIDI4 Os09g0453800 | 1-aminocyclopropane-1-carboxylate synthase family protein |
rs55629 | TGCAGTAAACCAATCAAAATGCATGGAACTCGCAGCGCTGCTCCCGCTTGTTCCCTTCGCCG | SH | 6 | 5,060,664-5,064,952 | 0.000155318 | 0.863370079 | 22.64 | OsGPCR Os06g0199800 | cAMP-type GPCR family protein |
rs2368 | TGCAGAAGTGGAGCTAGTGCAGCACGTCCTAGGTGGGTCGGCCGACTTGTCGTGCTGCTGTCCG | RH | 1 | 689,788-693,923 | 0.000287879 | 0.948801211 | 5.86 | Os01g0112800 | Disease resistance protein domain containing protein |
rs34693 | TGCAGCTACGGCGACGGCGGATGGGGCCTTGTTGGTCACCCCACTGCGCGTCGCAGCGCCTAGG | Chl a | 2 | 3,353,590-3,358,320 | 0.000242824 | 0.999635105 | 7.06 | OsENODL6 Os02g0162200 | Similar to Early salt stress and cold acclimation-induced protein 2–3 |
rs53998 | TGCAGGTGCCTTGTTGCGTGATAGGCCGCCCCATCGGCTCCATGGGCAGCCAGCGATCCCTCCA | Chl b | 10 | 22,124,277-22,127,759 | 0.000115546 | 0.96757668 | 6.42 | Os10g0561300 | Similar to Monosaccharid transporter |
rs34693 | TGCAGCTACGGCGACGGCGGATGGGGCCTTGTTGGTCACCCCACTGCGCGTCGCAGCGCCTAGG | Total Chl | 2 | 3,353,590-3,358,320 | 0.000109509 | 0.997017439 | 7.48 | OsENODL6 Os02g0162200 | Similar to Early salt stress and cold acclimation-induced protein 2–3 |
rs59624 | TGCAGTCTGGCTGCGATGGTTTCCTCGCTTCCTCCACCTTCTTTAGAAAATAGAGACGGAGGCA | Car | 6 | 14,281,547-14,290,711 | 0.000121166 | 0.93879979 | 6.07 | OsGELP83 Os06g0351500 | Lipase, GDSL domain containing protein |
rs18946 | TGCAGCATAGGAAACAGAGAACAAGTTAAGGCTGGTTTTAATGGTGAGTATCATATACTATTAT | protein | 4 | 7,136,795-7,140,421 | 0.000114795 | 0.95311657 | 6.2 | Os04g0206200 | DNA helicase domain containing protein |
rs15183 | TGCAGCACGGCTCAATCTCCTCCTGGGACAAGATGCGCGACCGTGTTGTCGCCAACTTCTAGGG | proline | 7 | 23,965,804-23,970,059 | 0.000152893 | 0.92929063 | 23.21 | OsWD40–145 Os07g0588500 | WD40 repeat-like domain containing protein |
rs27492 | TGCAGCCTGTTCCTCAATCAGTGAAGGCGCGCTGCACTCCGAGATGATCTTCAATCTTCAAGAG | CAT | 5 | 1,199,358-1,201,038 | 0.000103556 | 0.989061867 | 5.49 | Os05g0121900 | Similar to Phosphate/phosphoenolpyruvate translocator protein-like |
rs61179 | TGCAGTGGAAGCGGATGGTTGAGGACCTGCTGGCGCTGGGCAAACTCAACAACTGCCTCGCCGT | GPX | 7 | 306,054-306,968 | 0.00017113 | 0.906304397 | 6.23 | Os07g0105600 | Photosystem II oxygen evolving complex protein PsbQ family protein |
rs10192 | TGCAGATTGAACCCATCCTATTCTTCTGATTGAATTCATCAGTTAATTAGAAGAAGGGAAATGG | MDA | 2 | 34,853,787-34,855,494 | 0.000141883 | 0.854263863 | 7.88 | Os02g0813600 | Thiolase-like, subgroup domain containing protein |
rs61025 | TGCAGTGCTAGCTGCATGCACGGGGGAGGCGATGCCATGGCATGGCGCGGCACGGGCACGGGCA | Na-s | 3 | 8,679,164-8,682,334 | 0.000122977 | 0.68045149 | 8.58 | Os03g0263900 | EF-HAND 2 domain containing protein |
rs3228 | TGCAGACACAAACGTCTCGTACCAGTGGAATGTGTAAAGAATAGTTGTTATATATCTTGCCATC | Na-r | 4 | 28,744,397-28,747,841 | 0.000128791 | 0.980216786 | 7.26 | OsRFPH2–14 Os04g0571200 | Similar to OSIGBa0111L12.9 protein |
rs63185 | TGCAGTTCCATATAGCCCAAAGTAATGCGCAAATTCCTATCTGAATATGTTCGGCAATAGCTGG | K-s | 1 | 41,251,235-41,272,093 | 0.000116307 | 0.562674471 | 11.67 | Os01g0939700 | Similar to Esterase D (EC 3.1.1.1) |
rs28569 | TGCAGCGACTCCAGCGTGTCCGACTTGTCGCCGTCCGTGGCCGCCGTGGCCGCGCGCACCACCA | K-r | 6 | 5,018,088-5,020,389 | 0.000136869 | 0.46984536 | 9.92 | OsRLCK202 Os06g0198900 | Tyrosine protein kinase domain containing protein |
rs10633 | TGCAGATTTTTTGATTTCAGAAGGCACTCGACAGCGGCACCGTGGAAGTCCATCAAACTGCCGA | K/Na-s | 8 | 19,382,952-19,386,574 | 0.000152288 | 0.959659751 | 8.67 | Os08g0405700 | Similar to Copper chaperone homolog CCH |
rs26891 | TGCAGCCTCGGCATCTCCCGTACTCGCTGCTCCCGAGATCGGAAGAGCGGGATCACCGACTGCC | K/Na-r | 2 | 15,310,546-15,324,161 | 0.000100334 | 0.40666194 | 8.74 | Os02g0458900 | Conserved hypothetical protein |