Table 2.
Identification of SNPs in putative candidate genes for days to flowering.
| Linkage group | Gene | Position | ICP 5529 allele | LF allele | SNP index (LF pool)a | EF allele | SNP index (EF pool)b | Δ SNP-indexc | SNP effect | Function |
|---|---|---|---|---|---|---|---|---|---|---|
| CcLG03 | C.cajan_09900 | 19222701 | G (aCg)d | G (aCg)d | 0 | A (aTg)d | 1 | −1 | Exon (nsSNP) | Pentatricopeptide repeat-containing protein |
| CcLG03 | C.cajan_09938 | 19549631 | A | A | 0 | G | 1 | −1 | Intron | Chromodomain-helicase-DNA-binding protein 4 |
| CcLG03 | C.cajan_09958 | 19690312 | G | G | 0 | A | 1 | −1 | Intron | Maestro heat-like repeat-containing protein family |
| CcLG03 | C.cajan_09965 | 19763754 | C | C | 0 | T | 1 | −1 | Intron | Phosphatidylinositol 4-phosphate 5-kinase 9 |
| CcLG03 | C.cajan_10046 | 20439904 | G | G | 0 | C | 1 | −1 | Intron | 1,4-alpha-glucan-branching enzyme |
| CcLG03 | C.cajan_10067 | 20635496 | T | T | 0 | A | 1 | −1 | Intron | Uridine nucleosidase 1 |
| CcLG03 | C.cajan_10078 | 20745506 | G | G | 0 | T | 1 | −1 | Exon (sSNP) | Cell division protein |
| CcLG03 | C.cajan_10078 | 20745771 | A | A | 0 | G | 1 | −1 | Intron | |
| CcLG03 | C.cajan_10078 | 20747419 | C | C | 0 | T | 1 | −1 | Intron |
nsSNP non-synonymous SNPS, sSNP synonymous SNP.
aSNP-index of late flowering (LF) was calculated based on the allele calls and read depth in comparison to ICP 5529 reference assembly.
bSNP-index of early flowering (EF) bulk was calculated based on the allele calls and read depth in comparison to ICP 5529 reference assembly.
cΔ SNP-index of each SNP positions was calculated using following formula: Δ SNP-index = SNP-index of LF − SNP-index of EF.
dValue in parenthesis indicates the codon change due to SNP/Code for changed amino acids.