Table 2.
List of top suspect genes in the 12 selected genomic regions of Figure 6 that contain SNPs ranking 200 or less in the GWAS analyses of at least four traits. Genes in bold were characterized by qRT‐PCR for their response to the standard salinity treatment. Microarray data on gene expression under hydroponic salinity stress (up to 48 hr), drought stress, and seed desiccation were obtained from https://mtgea.noble.org/v3/index.php
| Gene | Start | End | Strand | Annotation (Mt. 4.0) | M. truncatula Microarray probeset | In M. truncatula, regulation under | |||
|---|---|---|---|---|---|---|---|---|---|
| salinity stress?a | drought in root?b | drought in shoot?b | seed desiccation?c | ||||||
| Medtr2g028730 | 10659792 | 10661824 | − | Trm112p‐like protein | Mtr.16016.1.S1_at | no | no | no | ** |
| Medtr2g028740 | 10664184 | 10664396 | − | hypothetical protein | none | ||||
| Medtr2g028750 | 10665954 | 10669267 | + | nonclathrin coat protein zeta1‐COP | Mtr.16017.1.S1_at | no | no | ** | no |
| Medtr2g028760 | 10669468 | 10669638 | − | hypothetical protein | none | ||||
| Medtr2g028770 | 10672439 | 10679871 | − | magnesium transporter CorA family protein | Mtr.52281.1.S1_at | ** | *** | *** | ** |
| Medtr2g028790 | 10690943 | 10695600 | + | synaptobrevin‐like protein | Mtr.16019.1.S1_at | no | ** | *** | *** |
| Medtr2g028795 | 10702242 | 10702842 | − | hypothetical protein | none | ||||
| Medtr2g048630 | 21440873 | 21453740 | + | regulator of nonsense transcripts‐like protein | Mtr.21538.1.S1_at | * | *** | ** | * |
| Medtr2g048635 | 21455804 | 21456661 | + | pentatricopeptide (PPR) repeat protein | none | ||||
| Medtr2g048680 | 21472115 | 21477040 | + | ankyrin repeat protein EMB506 | Mtr.42601.1.S1_at | no | ** | no | ** |
| Medtr2g048720 | 21491260 | 21497003 | − | inositol transporter 4 | Mtr.48631.1.S1_at | *** | *** | ** | *** |
| Medtr2g436900 | 14430380 | 14431772 | − | C2 domain protein | Mtr.12381.1.S1_at | ** | * | no | * |
| Medtr2g436910 | 14436094 | 14436501 | − | hypothetical protein | none | ||||
| Medtr2g436930 | 14442534 | 14448484 | + | substrate carrier family protein | Mtr.9356.1.S1_at | no | * | *** | ** |
| Medtr2g436940 | 14448712 | 14451781 | − | hypothetical protein | Mtr.41375.1.S1_at | no | *** | ** | *** |
| Medtr2g436960 | 14454918 | 14456001 | − | light‐harvesting complex I chlorophyll A/B‐binding protein | Mtr.15166.1.S1_at | * | * | no | * |
| Medtr2g437020 | 14472093 | 14476696 | − | mTERF protein | none | ||||
| Medtr2g437480 | 14725811 | 14732214 | + | chromatin remodeling complex subunit | none | ||||
| Medtr2g437490 | 14733099 | 14733710 | − | transmembrane protein, putative | Mtr.21581.1.S1_at | no | no | no | no |
| Medtr2g437500 | 14741244 | 14742166 | − | transcription factor GTE6, putative | none | ||||
| Medtr2g437520 | 14751210 | 14753146 | + | hypothetical protein | none | ||||
| Medtr2g437530 | 14754185 | 14756065 | − | DREPP plasma membrane protein | none | ||||
| Medtr3g009760 | 2151533 | 2153673 | + | FAD‐linked oxidoreductase | Mtr.13518.1.S1_at | no | no | ** | * |
| Medtr3g009820 | 2175256 | 2177107 | + | FAD‐linked oxidoreductase | none | ||||
| Medtr3g009850 | 2184364 | 2185062 | + | FAD‐linked oxidoreductase | none | ||||
| Medtr3g077360 | 34731943 | 34732457 | + | hypothetical protein | none | ||||
| Medtr3g077400 | 34742781 | 34744107 | − | hypothetical protein | none | ||||
| Medtr3g077410 | 34747003 | 34749760 | + | NAD(P)‐binding rossmann‐fold protein | Mtr.51752.1.S1_at | no | no | no | * |
| Medtr3g077420 | 34751208 | 34755524 | + | transcription factor, putative | Mtr.17177.1.S1_at | no | *** | ** | no |
| Medtr3g077430 | 34757686 | 34761543 | − | carboxyl‐terminal peptidase | Mtr.51747.1.S1_at | *** | *** | ** | * |
| Medtr3g077440 | 34767661 | 34777932 | + | modifier OF SNC1 1, putative | Mtr.29563.1.S1_at | no | ** | * | * |
| Medtr3g077450 | 34780007 | 34791257 | + | modifier OF SNC1 1, putative | Mtr.14802.1.S1_at | no | ** | no | * |
| Medtr3g077460 | 34792157 | 34793856 | − | cytochrome P450 family 71 protein | Mtr.51055.1.S1_at | no | no | no | *** |
| Medtr3g077490 | 34806841 | 34810528 | + | embryo defective 2759 protein | Mtr.14799.1.S1_at | no | *** | ** | ** |
| Medtr3g077500 | 34811954 | 34816546 | + | transmembrane protein, putative | Mtr.39510.1.S1_s_at | no | * | no | no |
| Medtr3g077620 | 34884550 | 34891032 | + | phox (PX) domain protein | Mtr.14792.1.S1_s_at | no | no | no | no |
| Medtr3g077630 | 34892075 | 34895483 | − | transmembrane protein, putative | Mtr.4339.1.S1_at | * | no | *** | ** |
| Medtr3g077640 | 34908806 | 34913845 | + | plastid phosphate translocator | none | ||||
| Medtr3g077650 | 34915543 | 34917386 | + | transcription factor MYB98 | Mtr.48147.1.S1_at | * | no | no | *** |
| Medtr3g077670 | 34923242 | 34928630 | − | boron transporter‐like protein | Mtr.48146.1.S1_s_at | no | ** | * | ** |
| Medtr3g093630 | 42788484 | 42790479 | + | hypothetical protein | none | ||||
| Medtr3g093660 | 42797203 | 42800974 | − | RING zinc finger protein, putative | none | ||||
| Medtr3g093690 | 42807993 | 42812754 | + | transmembrane protein, putative | Mtr.6105.1.S1_at | no | ** | * | no |
| Medtr3g093710 | 42814305 | 42818320 | + | receptor‐like kinase | Mtr.45101.1.S1_at | ** | * | ** | ** |
| Medtr3g093730 | 42821390 | 42825561 | − | methylesterase | none | ||||
| Medtr3g093780 | 42847107 | 42851695 | + | DUF3133 family protein | Mtr.33238.1.S1_at | no | no | no | no |
| Medtr3g093790 | 42851825 | 42855319 | − | nucleic acid‐binding, OB‐fold‐like protein | Mtr.12947.1.S1_at | no | no | ** | ** |
| Medtr3g093800 | 42857714 | 42860884 | − | transcription elongation factor S‐II, putative | Mtr.43413.1.S1_at | * | ** | * | no |
| Medtr3g093810 | 42862192 | 42865834 | − | ubiquinol‐cytochrome C reductase complex protein, putative | Mtr.37864.1.S1_at | no | *** | no | *** |
| Medtr3g093900 | 42905400 | 42907112 | + | MADS‐box transcription factor family protein, putative | none | ||||
| Medtr4g046713 | 16525346 | 16527516 | − | peroxidase family protein | Mtr.44569.1.S1_at | *** | *** | no | no |
| Medtr4g066280 | 25015686 | 25020396 | − | glycoside hydrolase family 1 protein | Mtr.47870.1.S1_at | * | no | no | no |
| Medtr4g066290 | 25022356 | 25022951 | + | Nodule Cysteine‐Rich (NCR) secreted peptide | none | ||||
| Medtr4g066310 | 25031757 | 25032810 | − | hypothetical protein | none | ||||
| Medtr4g066320 | 25032880 | 25034289 | + | hypothetical protein | none | ||||
| Medtr4g066330 | 25037019 | 25042115 | − | glycoside hydrolase family 1 protein | none | ||||
| Medtr4g066340 | 25044288 | 25047517 | − | cyanogenic beta‐glucosidase, putative | none | ||||
| Medtr4g066380 | 25062108 | 25065460 | − | basic helix loop helix (bHLH) DNA‐binding family protein | none | ||||
| Medtr7g081010 | 30882053 | 30887619 | − | archaeal/vacuolar‐type H + ‐ATPase subunit B | Mtr.12301.1.S1_at | *** | *** | ** | *** |
| Medtr7g081020 | 30892633 | 30894709 | + | protein phosphatase 2C family protein | Mtr.9338.1.S1_at | ** | *** | *** | *** |
| Medtr7g081040 | 30897385 | 30901657 | − | trafficking protein particle complex subunit‐like protein | Mtr.42623.1.S1_at | no | *** | ** | * |
| Medtr7g081070 | 30913276 | 30915702 | − | DUF1279 family protein | none | ||||
| Medtr7g081090 | 30923192 | 30923518 | + | transmembrane protein, putative | none | ||||
| Medtr7g081105 | 30927714 | 30927950 | + | Thionin related | none | ||||
| Medtr7g081120 | 30931309 | 30932323 | + | transmembrane protein, putative | none | ||||
| Medtr7g081140 | 30939953 | 30940153 | − | hypothetical protein | none | ||||
| Medtr7g082110 | 31436869 | 31439723 | + | receptor‐like kinase, putative | none | ||||
| Medtr7g082120 | 31448827 | 31449485 | − | hypothetical protein | none | ||||
| Medtr7g082130 | 31451724 | 31455731 | − | hypothetical protein | none | ||||
| Medtr7g082140 | 31460852 | 31465655 | − | peptidase M50B‐like protein | Mtr.44385.1.S1_at | no | *** | no | *** |
| Medtr7g082150 | 31467830 | 31471924 | − | U1 small nuclear ribonucleoprotein | Mtr.33442.1.S1_at | * | ** | * | no |
| Medtr7g082160 | 31473081 | 31475033 | − | PPR containing plant‐like protein | none | ||||
| Medtr7g082180 | 31482984 | 31485168 | + | hypothetical protein | Mtr.39860.1.S1_at | ** | no | ** | * |
| Medtr7g082190 | 31489286 | 31489554 | + | transmembrane protein, putative | none | ||||