Table 3.
DEGs and reported yield related genes showing difference between the sequences of KMR3 and IL50-13.
| S. No | Category | Gene Name | Description | Gene length | KMR3 scaffold | Start position of scaffold | End position of scaffold | 50-13 scaffold | Start position of scaffold | End position of scaffold | Differences between KMR3 and 50-13 scaffolds |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | A28 | Os02t0589000-01 | Lecithin: cholesterol acyltransferase family protein | 10391 | scaffold9446_size10065 | 984 | 3580 | scaffold14856_size6220 | 1 | 2790 | SNPs + InDels |
| 2 | A61 | Os02t0626400-03 | Similar to Phenylalanine ammonia-lyase | 1589 | scaffold13385_size7025 | 3655 | 4920 | scaffold12144_size7524 | 3315 | 2050 | SNPs + InDels |
| 3 | A11 | Os02t0569800-00 | Hypothetical genes | 4024 | scaffold2303_size25555 | 19748 | 21711 | scaffold17631_size5156 | 2282 | 3988 | SNPs + InDels |
| 4 | A51 | Os02t0616600-01 | Conserved hypothetical protein | 3728 | scaffold15492_size5752 | 3500 | 5752 | scaffold26405_size2842 | 474 | 2842 | SNPs + InDels |
| 5 | A32 | Os02t0592000-00 | Similar to OSIGBa0106G07.8 protein | 9817 | scaffold8341_size11245 | 7965 | 10401 | scaffold17585_size5169 | 1236 | 2636 | SNPs + InDels |
| 6 | A16 | Os02t0574800-01 | Ethylene insensitive 3 domain containing protein | 739 | scaffold14052_size6604 | 4 | 276 | scaffold21804_size3915 | 3915 | 3667 | SNPs |
| 7 | A1 | Os02t0552500-00 | 1185 | scaffold23485_size2774 | 2774 | 1848 | scaffold30709_size2103 | 415 | 1 | SNPs | |
| 8 | A12 | Os02t0569900-01 | Cytochrome P450 family protein | 1657 | scaffold7129_size12786 | 9197 | 10493 | scaffold24827_size3169 | 3169 | 2828 | SNPs |
| 9 | A62 | Os02t0626400-01 | Phenylalanine ammonia-lyase (EC 4.3.1.5) | 2593 | scaffold13385_size7025 | 2826 | 4920 | scaffold12144_size7524 | 4141 | 2050 | SNPs + InDels |
| 10 | A63 | Os02t0627100-01 | Similar to Phenylalanine ammonia-lyase (EC 4.3.1.5) | 2405 | scaffold7515_size12279 | 1251 | 3210 | scaffold12144_size7524 | 4200 | 2051 | SNPs + InDels |
| 11 | B8 | Os08t0468100-03 | Similar to Nitrate reductase. | 2053 | scaffold32698_size2633 | 1589 | 1 | scaffold5531_size12871 | 3714 | 1775 | InDels |
| 12 | B21 | Os08t0487301-00 | - | 485 | scaffold243_size48649 | 4120 | 3822 | scaffold6702_size11543 | 11094 | 11491 | SNPs + InDels |
| 13 | B23 | Os08t0490100-01 | Similar to PBF protein | 1261 | scaffold8993_size10535 | 8750 | 9323 | scaffold3687_size21453 | 15734 | 15885 | SNPs + InDels |
| 14 | C1 | Os01t0314800-01 | Late embryogenesis abundant protein 3 family protein. | 731 | scaffold2182_size25019 | 20065 | 19335 | scaffold17822_size5094 | 3714 | 4149 | SNPs |
| 15 | C4 | Os02t0831500-01 | Similar to Sucrose synthase | 6271 | scaffold8577_size10987 | 1 | 2889 | scaffold5992_size12325 | 12325 | 9137 | SNPs |
| 16 | C10 | Os06t0229800-01 | Similar to Starch synthase IIA. | 4905 | scaffold1456_size29059 | 29059 | 24569 | scaffold8945_size9534 | 1 | 3623 | SNPs |
| 17 | D6 | Os03t0407400-00 | - | 945 | scaffold14776_size6169 | 2241 | 1683 | scaffold6119_size12184 | 6218 | 6724 | SNPs |
| 18 | D8 | Os03t0117900-01 | - | 955 | scaffold9265_size10248 | 5473 | 6424 | scaffold21042_size4123 | 1 | 446 | SNPs |
| 19 | D19 | Os08t0509600-01 | Rice squamosa promoter binding protein-like 14. | 4156 | scaffold3452_size19961 | 487 | 4642 | scaffold2693_size19548 | 108 | 3677 | SNPs |
Category A refers to genes within qyld2.1, B refers to genes within qyld8.2, C refers to genes showing high fold expression and D refers to reported yield related genes.