Table 3.
Some examples of WGRS‐based GWA studies in select crops
| Crop | Trait | MTA/QTL/candidate genes identified | SNP/indels | Number of genotypes | LGs/Chromosomes | References |
|---|---|---|---|---|---|---|
| Rice | Agronomic traits | 80 significant MTAs | 3.6 million SNPs | 517 | 1–12 | Huang et al. (2010) |
| Rice | Amylose content and seed length, pericarp colour | Os03g0407400, Os06g0133000, Os10g0536400 | 2.3 million SNPs | 203 | 6, 7, 10 | Wang et al. (2016) |
| Rice | Days to heading date, awn length, panicles per plant, plant height, panicle length, spikelet number per panicle, leaf blade width | LOC_Os01g62780, LOC_Os11g08410, LOC_Os04g52479, LOC_Os08g37890 | 426 337 SNPs, 67 544 indels | 176 | 1, 4, 6, 8, 11 | Yano et al. (2016) |
| Rice | Grain shape, length and width | GWi7.1, GWi7.2, GL3.1, GWi5.1, GWi11.1 | 2.9 million SNPs, 3.9 million indels | 591 | 3, 5, 7, 10, 11 | Misra et al. (2017) |
| Rice | Alkalinity | Eight QTLs | 788 396 SNPs | 295 | 3 | Li et al. (2019) |
| Rice | 17 mineral elements | 72 loci | 6.4 million SNPs | 529 | 1‐12 | Yang et al. (2018) |
| Rice | Heading date, grain mass, straw biomass, harvest index | 115 QTLs | ∼2 million SNPs | 266 | 1‐12 | Norton et al. (2018) |
| Rice | Pericarp colour, amylose content, protein content, panicle number | 2 046 529 SNPs | 137 | 2, 3, 5, 6,7, 9 | Kim et al. (2016) | |
| Rice | Grain width, grain length | MTAs coincided with GS3, GW5, and qGL7, OsFD | 223 743 SNPs | 3,010 | 1, 3, 5, 6, 7, 9, 11 | Wang et al. (2018) |
| Bacterial blight | Xa26 | 148 999 SNPs | ||||
| Rice | Seed coat colour, grain length | Rc locus, LONG KERNEL 3 gene | 889 903 SNPs | 365 | 7, 11 | Fuentes et al. (2019) |
| Soybean | Oil content, plant height, domestication traits, pubescence form, flower colour, cyst nematode tolerance, seed weight | – | 9 790 744 SNPs, 876 799 indels | 302 | – | Zhou et al. (2015) |
| Soybean | Salinity tolerance | 401 and 328 MTAs for leaf scorch score and leaf chlorophyll content, respectively | 5 million SNPs | 106 | – | Patil et al. (2016) |
| Soybean | 84 traits | 245 loci | 4 million SNPs | 809 | 1–20 | Fang et al. (2017) |
| Soybean | Salinity tolerance | 51 significant MTAs | 3.7 million SNPs | 234 | 1, 2, 3, 5, 6, 8, 14,15,16, 18, 19, 20 | Do et al. (2019) |
| Chickpea | Ascochyta blight | AB4.1 and 12 candidate genes and 20 significant SNPs | 144 000 SNPs | 132 | 4 | Li et al. (2017) |
| Chickpea | Yield‐related traits under drought stress | 38 significant SNPs | 144 777 SNPs | 132 | 3, 4, 5, 6 | Li et al. (2018) |
| Chickpea | Traits related to drought and heat stress | 262 MTAs and several candidate genes including TIC, REF6, aspartic protease, cc‐NBS‐LRR, RGA3, Ca_13671, Ca_13939 | 3.65 million SNPs | 429 | – | Varshney et al. (2019) |
| Pigeonpea | Agronomic traits | 241 MTAs, homologs of LIGULELESS1, SHATTERING1 and EARLY FLOWERING3 (ELF3) | 15.1 million SNPs, 2.1 million indels | 292 | 1–11 | Varshney et al. (2017) |
| Common bean | Phenological traits and yield and yield‐related traits, anthracnose resistance | 505 MTAs | 4.8 million SNPs | 683 | 1–11 | Wu et al. (2020) |
| Linseed | Seed size and seed weight | 13 candidate genes | 674 074 SNPs | 200 | 1, 4, 5, 6, 7, 9, 11, 12, 14, 15 | Guo et al. (2020) |
| Brassica napus | Seed yield, silique length, oil content and seed quality | 60 loci | 670 028 SNPs | 588 | A08, A02, A09, C02, C03, C07 | Lu et al. (2019) |
| Brassica napus | Flowering time | FLOWERING LOCUS T, FLOWERING LOCUS C | 2 753 575 SNPs | 991 | A02 | Wu et al. (2019) |