Table 3 Identification of SNPs in putative candidate genes for leaf shape.
From: QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea
Linkage group | Gene | Position | ICP 5529 allele | OLS allele | SNP index (OLS pool)a | LLS allele | SNP index (LLS Pool)b | Δ SNP-indexc | SNP Effect | Function |
|---|---|---|---|---|---|---|---|---|---|---|
CcLG08 | C.cajan_15985 | 6701814 | A | A | 0 | T | 1 | −1 | Intron | Beta-carotene hydroxylase 2 |
CcLG08 | C.cajan_15991 | 6764651 | T (Tgt)d | T (Tgt)d | 0 | C (Cgt)d | 1 | −1 | Exon (nsSNP) | Ac-like transposase |
CcLG08 | C.cajan_16002 | 6915910 | T (aTg)d | T (aTg)d | 0 | C (aCg)d | 1 | −1 | Exon (nsSNP) | Uncharacterized protein |
CcLG08 | C.cajan_16003 | 6921340 | A | A | 0 | G | 1 | −1 | Exon (sSNP) | Pro-Pol polyprotein |
CcLG08 | C.cajan_16003 | 6923929 | T | T | 0 | C | 1 | −1 | Intron | |
CcLG08 | C.cajan_16003 | 6924854 | A | A | 0 | G | 1 | −1 | Intron | |
CcLG08 | C.cajan_16003 | 6927480 | C | C | 0 | T | 1 | −1 | Intron | |
CcLG08 | C.cajan_16003 | 6927533 | A | A | 0 | G | 1 | −1 | Intron | |
CcLG08 | C.cajan_16003 | 6927560 | T | T | 0 | C | 1 | −1 | Intron | |
CcLG08 | C.cajan_16003 | 6927678 | T | T | 0 | C | 1 | −1 | Intron | |
CcLG08 | C.cajan_16012 | 7057478 | G (Gca)d | G (Gca)d | 0 | A (Aca)d | 1 | −1 | Exon (nsSNP) | F-box protein |
CcLG08 | C.cajan_16012 | 7059171 | T | T | 0 | C | 1 | −1 | Intron | |
CcLG08 | C.cajan_16013 | 7068488 | G | G | 0 | C | 1 | −1 | Intron | Uncharacterized protein |
CcLG08 | C.cajan_16013 | 7068679 | G | G | 0 | A | 1 | − | Intron | |
CcLG08 | C.cajan_16013 | 7070780 | C (cCt)d | C (cCt)d | 0 | T (cTt)d | 1 | −1 | Exon (nsSNP) | |
CcLG08 | C.cajan_16014 | 7083922 | T | T | 0 | A | 1 | −1 | Intron | Transcriptional corepressor |
CcLG08 | C.cajan_16014 | 7093751 | G | G | 0 | A | 1 | −1 | Intron | |
CcLG08 | C.cajan_16038 | 7456634 | T | T | 0 | C | 1 | −1 | Intron | Cytochrome P450 |
CcLG08 | C.cajan_16038 | 7456764 | A | A | 0 | G | 1 | −1 | Intron | |
CcLG08 | C.cajan_16038 | 7456831 | T | T | 0 | A | 1 | −1 | Intron | |
CcLG08 | C.cajan_16038 | 7456974 | A | A | 0 | G | 1 | −1 | Intron | |
CcLG08 | C.cajan_16038 | 7457844 | C | C | 0 | A | 1 | −1 | Intron | |
CcLG08 | C.cajan_16041 | 7486941 | A | A | 0 | G | 1 | −1 | Intron | Uncharacterized protein |
CcLG08 | C.cajan_16047 | 7606346 | T | T | 0 | A | 1 | −1 | Intron | Transposon Ty3-I |
CcLG08 | C.cajan_16049 | 7641790 | A | A | 0 | C | 1 | −1 | Intron | E3 ubiquitin-protein ligase |
CcLG08 | C.cajan_16049 | 7642733 | G | G | 0 | A | 1 | −1 | Intron | |
CcLG08 | C.cajan_16049 | 7643315 | A | A | 0 | C | 1 | −1 | Exon (sSNP) | |
CcLG08 | C.cajan_16051 | 7666784 | A | A | 0 | G | 1 | −1 | Intron | Protein ROOT PRIMORDIUM DEFECTIVE 1 |
CcLG08 | C.cajan_16051 | 7667174 | T | T | 0 | C | 1 | −1 | Intron | |
CcLG08 | C.cajan_16059 | 7780600 | A | A | 0 | T | 1 | −1 | Intron | Probable methyltransferase PMT16 |
CcLG08 | C.cajan_16061 | 7838639 | C | C | 0 | T | 1 | −1 | Exon (sSNP) | 1-aminocyclopropane-1-carboxylate oxidase homolog 1 |
CcLG08 | C.cajan_16062 | 7870949 | A | A | 0 | G | 1 | −1 | Intron | |
CcLG08 | C.cajan_16063 | 7888623 | G | G | 0 | A | 1 | −1 | Intron | 1-aminocyclopropane-1-carboxylate oxidase homolog 12 |
CcLG08 | C.cajan_16066 | 7940765 | C | C | 0 | G | 1 | −1 | Intron | Tripeptidyl-peptidase 2 |
CcLG08 | C.cajan_16066 | 7947009 | G | G | 0 | A | 1 | −1 | Intron | |
CcLG08 | C.cajan_16066 | 7950673 | A | A | 0 | C | 1 | −1 | Intron | |
CcLG08 | C.cajan_16068 | 8008253 | C | C | 0 | A | 1 | −1 | Intron | Cytochrome P450 |
CcLG08 | C.cajan_16074 | 8168767 | C | C | 0 | A | 1 | −1 | Intron | Type I inositol |
CcLG08 | C.cajan_16099 | 8666995 | T | T | 0 | C | 1 | −1 | Exon (sSNP) | - |
