Table 1.
An overview of sequencing-based trait mapping efforts in chickpea
| S no | Sequencing technology | Mapping population | Trait mapping approach | Target trait(s) | Significant results | Reference |
|---|---|---|---|---|---|---|
| 1 | GBS | Amit x ICCV 96029 | Genetic mapping (3,430 SNPs) | Ascochyta blight resistance | QTLs for resistance on CaLG02, CaLG03, CaLG04, CaLG05 and CaLG06 explaining up to 40% of phenotypic variance (PVE) | Deokar et al. (2019a) |
| 2 | GBS | ICC 4567 × ICC 15614 | Genetic mapping (271 SNPs) | Heat tolerance | QTLs on CaLG05 and CaLG06 with a cumulative PVE of 51.89% and 25.84%, respectively | Paul et al. (2018) |
| 3 | GBS | SBD377 x BGD112 | Genetic mapping (3,228 SNPs) | Seed trait | QTLs explaining up to 29.71% PVE and candidate genes for seed traits | Verma et al. (2015) |
| 4 | GBS | ICC 4958 × ICC 1882 | Genetic mapping (743 SNPs) | Drought tolerance-related traits | Refined the "QTL-hotspot" region from ca. 29 cM to 14 cM and added 49 SNPs in the region | Jaganathan et al. (2015) |
| 5 | GBS | Cultivated and wild accessions | GWAS, genetic mapping | Photosynthetic efficiency and seed yield per plant | SNPs and candidate genes associated with photosynthetic efficiency and seed yield per plant | Basu et al. (2019) |
| 6 | GBS | Cultivated accessions | Genetic diversity (4,349 SNPs) | Seed yield per plant | A pentricopeptide repeat (PPR) gene associated with seed yield per plant | Basu et al. (2018) |
| 7 | GBS | Cultivated accessions | GWAS (16,591 SNPs) | Seed iron and zinc | Genomic loci/ genes (with 29% combined PVE) associated with seed-Fe and Zn concentrations | Upadhyaya et al. (2016) |
| 8 | GBS | Cultivated and wild accessions | Genetic diversity (82,489 SNPs) | NIL | Analysis of genetic diversity, population structure and linkage disequilibrium | Bajaj et al. (2015) |
| 9 | GBS | Cultivated and wild accessions | Genetic diversity (44,844 SNPs) | NIL | Revealed complex admixed domestication pattern, and extended LD decay | Kujur et al. (2015) |
| 10 | GBS | Cultivated accessions | Genetic diversity (3,187 SNPs) | NIL | Genetic cluster associated with black seeded genotypes | Pavan et al. (2017) |
| 11 | RAD-Seq | ICCV 96029 × CDC Frontier | Genetic mapping (604 bins) | NIL | High-density linkage map constructed | Deokar et al. (2014) |
| 12 | Axiom Array | ICC 4958 × ICC 1882 & ICC 283 × ICC 8261 | Genetic mapping (13,679 and 7,769 SNPs) | Drought tolerance-related traits | Main-effect QTLs for several drought component traits | Roorkiwal et al. (2018b) |
| 13 | WGRS | ICC 4958 × ICC 1882 | Genetic mapping | Drought tolerance-related traits | Delimited "QTL-hotspot" region to ~ 300 kb and identified 26 candidate genes | Kale et al. (2015) |
| 14 | WGRS | ICC 4958 × ICC 1882 | Genetic mapping | Plant vigour and canopy conductance | QTLs for plant vigour and canopy conductance traits on CaLG04 and CaLG03, respectively | Sivasakthi et al. (2018) |
| 15 | WGRS | ICCV 96029 × CDC Frontier and ICCV 96029 × Amit | QTL-seq | Ascochyta blight resistance | Candidate genes for ascochyta blight resistance | Deokar et al. (2019b) |
| 16 | WGRS | ICC 4958 × ICC 1882 | QTL-seq | 100-seed weight (100SDW) and root/total plant dry weight ratio (RTR) | Genomic regions on CaLG01 (1.08 Mb) and CaLG04 (2.7 Mb) linked with 100-seed weight. Two genes (Ca_04364 and Ca_04607) for 100SDW and one gene (Ca_04586) for RTR | Singh et al. (2016) |
| 17 | WGRS | ICC 7184 × ICC 15061 | QTL-seq | 100-seed weight | Genomic region on CaLG01 harbouring six candidate genes for 100-seed weight | Das et al. (2015) |
| 18 | WGRS | Released varieties and advanced breeding lines | GWAS (144,000 SNPs) | Drought tolerance | MTAs significantly associated with yield and yield-related traits under drought | Li et al. (2018) |
GBS Genotyping by sequencing, RAD-Seq restriction-site-associated sequencing, WGRS whole-genome re-sequencing