Table 2.
Identification of genomic loci and candidate gene associated with the process of domestication, diversification and improvement
| Crop | Trait | Category | Gene | Reference |
|---|---|---|---|---|
| Soybean | Shattering | Domestication | GmSHAT1-5 | Dong et al. (2014) |
| Hard seededness | Domestication | GmHs1-1 | Sun et al. (2015) | |
| Determinate growth | Diversification | GmDt1/GmTFL1b | Liu et al. (2010), Tian et al. (2010), Zhou et al. (2015a) | |
| Semi-determinate growth | Diversification | GmDt2 | Ping et al. (2014) | |
| Flowering time | Diversification | GmCRY1a | Zhang et al. (2008), | |
| Flowering time | Diversification | GmTFL1a | Li et al. (2013) | |
| Flowering time | Diversification | GmCOL7a | Li et al. (2013) | |
| Flowering and maturity | Diversification/improvement | E1; E2 (GmGIa); E3 (GmPhyA3); E4 (GmPhyA2) | Watanabe et al. (2011), Langewisch et al. (2014) | |
| Seed coat color, hilum color | Diversification | I (GmCHS) | Tuteja et al. (2009), Zhou et al. (2015a) | |
| Flower color | Diversification | W1 (F3′5′H) | Zhou et al. (2015a) | |
| Pubescence | Diversification | T | Zhou et al. (2015a) | |
| Cyst nematode resistance | Improvement | Rhg1 | Cook et al. (2012), Zhou et al. (2015a) | |
| Pod color | Improvement | L1 (MYB) | He et al. (2015) | |
| Shattering | Improvement | GmPdh1 | Funatsuki et al. (2014) | |
| Leaf shape and four seed pod | Improvement | Ln | Zhou et al. (2015a) | |
| Oil content | Improvement | LPD1 | Qi et al. (2011), Zhou et al. (2015a) | |
| Structural diversity of glycosylation | Improvement | Sg-1 | Zhou et al. (2015a) | |
| Flowering and maturity | Improvement | Tof12 | Lu et al. (2020) | |
| Salt tolerance | Improvement | GmCHX1 | Qi et al. (2014) | |
| Common bean | Pod dehiscence | Domestication | PD; PvIND | Gioia et al. (2013), Parker et al. (2020) |
| Resistance and tolerance gene | Improvement | AN-Pv33, AN-Pv69, AN-DNAJ and Leg223 | Bitocchi et al. (2017) | |
| Photoperiodic response | Improvement | GIGANTEA (GI) | Bellucci et al. (2014) | |
| Vernalization | Diversification (Mesoamerican) | VRN1 (Phvul.003G033400) and VRN2 (Phvul.002G000500) | Schmutz et al. (2014) | |
| Diversification (Andean) | FRL1 (Phvul.006G053200) and TFL2 (Phvul.009G117500) | Schmutz et al. (2014) | ||
| Flowering | Diversification (Mesoamerican) | COP1 | Schmutz et al. (2014) | |
| Diversification (Andean) | CUL4 along with COP1 | Schmutz et al. (2014) | ||
| FUL and AGL42 | Schmutz et al. (2014) | |||
| Nitrogen metabolism (nitrate reductase) | Phvul.008G168000; Phvul.005 G132200 | Schmutz et al. (2014) | ||
| Nitrogen transporter | Phvul.002G242900 | Schmutz et al. (2014) | ||
| Chickpea | Vernalization | Diversification | VRN1 | Varshney et al. (2019) |
| Shattering | Domestication | Shatterproof2 | Varshney et al. (2021b) | |
| Flower development and reproductive phase transition of meristem | Diversification | FLP2 | Varshney et al. (2021b) | |
| Flowering time | Diversification | DTF3A | Ortega et al. 2019 | |
| Root growth | LRP1 | Varshney et al. (2021b) | ||
| Signaling pathways for survival and T cell metabolism | PIP5KL1 | Varshney et al. (2021b) | ||
| Flavonoid biosynthesis | MYB12 | Varshney et al. (2021b) | ||
| Groundnut | Seed size/weight | Domestication | TGA7, topless-related protein 2, IAA-amino acid hydrolase ILR1-like 5 and putative pentatricopeptide repeat-containing (PPR) protein | Li et al. (2021) |
| Lentil | Pod indehiscence | Domestication | Pi | Sonnante et al. (2009) |
| Growth habitat | Gh | Sonnante et al. (2009) | ||
| Cotyledon color | Improvement | Yc | Sonnante et al. (2009) | |
| Epicotyl color | Improvement | Gs | Sonnante et al. (2009) | |
| Seed coat spotting | Improvement | Scp | Sonnante et al. (2009) | |
| Seed ground color | Improvement | Ggc | Sonnante et al. (2009) | |
| Flower color | Improvement | W | Sonnante et al. (2009) | |
| Pea | Dehiscent pod | Domestication | Dpo | Blixt (1972), Hradilová et al. (2017) |
| Pigeonpea | Shattering | Domestication | SHATTERING1(C.cajan_24676) | Varshney et al. (2017), Ogutcen et al. (2018) |
| Flowering | Improvement | EARLY FLOWERING3 (ELF3)(C.cajan_22378), FLOWERING LOCUS C A10(C.cajan_18407), TERMINAL FLOWER1b(C.cajan_10074), FLOWERING TIME1(C.cajan_42877) | Varshney et al. (2017) | |
| Transparent testa | Improvement | C.cajan_01740 | Varshney et al. (2017) | |
| Seed-related features | Improvement | Granule bound starch synthase I (C.cajan_02047), AcruGRANULE BOUND STARCH SYNTHASE I(C.cajan_07051), FRUIT WEIGHT(C.cajan_15593), SUGARY1(C.cajan_2320) | Varshney et al. (2017) | |
| Semi-dwarf | Improvement | C.cajan_04115 | Varshney et al. (2017) | |
| Determinacy | Diversification | CcTFL1 | Mir et al. (2014) |