Table 1. Candidate genes harbouring major QTLs regulating PH identified by QTL mapping and genetic association analysis in chickpea.
| QTL mapping | Association mapping | SNPs tightly linkedto QTLs (trait-associated SNPs) | Structuralannotation | Functional annotation | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Linkagegroups(LGs) | QTLsidentities | Marker intervalswith geneticpositions (cM) | LOD | Phenotypicvariationexplained (PVE%)by QTLs | Additiveeffects | P | R2 (%) | |||
| Ca_Desi_LG01 | qPH1.1 | 0.239: Ca_Desi_SNP525 (56.984) to Ca_Desi_SNP528 (57.223) | 10.7 | 21.3 | 4.5 | 2.1 × 10−6 | 20.8 | Ca_Desi_SNP526 (A/G) | Ca19207 (URR) | Cytochrome C biosynthesis protein |
| Ca_Desi_LG02 | qPH2.1 | 0.356: Ca_DesiSNP848 (29.496) to Ca_Desi_SNP851 (29.852) | 8.6 | 15.9 | 3.9 | 4.2 × 10−6 | 17.9 | Ca_Desi_SNP849 (A/C) | Ca10330 (CDS-Syn) | Mitochondrial NAD-dependent malic enzyme (Malic oxidoreductase) |
| Ca_Desi_LG03 | qPH3.1 | 0.178: Ca_DesiSNP1251 (26.358) to Ca_Desi_SNP1253 (26.536) | 8.1 | 16.2 | 2.8 | 1.3 × 10−5 | 16.7 | Ca_Desi_SNP1252 (T/C) | Ca20411 (DRR) | NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 |
| Ca_Desi_LG04 | qPH4.1 | 0.058:Ca_Desi_SNP1805 (28.738) to Ca_Desi_SNP1807 (28.796) | 7.8 | 12.4 | 2.5 | 1.9 × 10−5 | 12.9 | Ca_Desi_SNP1806 (A/G) | Ca04741 (Intron) | Unknown expressed protein |
| Ca_Desi_LG07 | qPH7.1 | 0.393: Ca_Desi_SNP3314 (63.792) to Ca_Desi_SNP3316 (64.185) | 9.5 | 20.5 | 2.1 | 3.9 × 10−6 | 20.3 | Ca_Desi_SNP3315 (A/C) | Ca09193 (Intron) | Basic leucine zipper (bZIP) transcription factor 60 |
| Ca_Desi_LG08 | qPH8.1 | 0.688: Ca_Desi_SNP3491 (44.194) to Ca_Desi_SNP3493 (44.882) | 6.1 | 11.5 | 1.7 | 4.8 × 10−5 | – | Ca_Desi_SNP3492 (A/T) | Intergenic | – |