Table 3. Sixteen genes with SNPs regulating seed-Fe and Zn concentrations delineated by integrating GWAS and candidate gene-based association analysis with QTL mapping and expression profiling.
| SNP IDs | Kabulichromosomes | SNP physical positions (bp) | SNPs | Gene accession IDs | Structural annotation | Known/putative functions | Association analysis |
||
|---|---|---|---|---|---|---|---|---|---|
| P | R2 (%) | Traits associated | |||||||
| *,#CakSNP1426/SNP53 | Ca_Kabuli_Chr01 | 16379258 | [C/T] | Ca06927 | Intron | Ubiquitin-associated/translation elongation factor EF1B | 1.5 × 10−8 | 10 | Seed Fe concentration |
| *,#CakSNP1628/SNP55 | Ca_Kabuli_Chr01 | 24071014 | [T/G] | Ca19289 | Intron | AUX/IAA (auxin/indole-3-acetic acid) protein | 1.9 × 10−8 | 10 | Seed Fe concentration |
| *,#CakSNP14941/SNP110 | Ca_Kabuli_Chr02 | 96532 | [G/T] | Ca27126 | Intron | Vacuolar protein sorting-associated protein | 1.0 × 10−9 | 14 | Seed Zn concentration |
| *,#SNP159 | Ca_Kabuli_Chr03 | 20101590 | [G/A] | Ca09416 | URR | Ferritin 1 (FER1) | 2.0 × 10−8 | 10 | Seed Fe concentration |
| #CakSNP4409/ SNP186 | Ca_Kabuli_Chr03 | 30837284 | [C/T] | Ca12181 | CDS(Nsyn) | Domain of unknown function 828 (DUF828) | 1.2 × 10−7 | 6 | Seed Fe and Zn concentrations |
| *,#CakSNP4476/SNP208 | Ca_Kabuli_Chr03 | 31631451 | [A/C] | Ca12262 | CDS(Nsyn) | RNA recognition motif domain | 2.0 × 10−8 | 12 | Seed Zn concentration |
| #CakSNP4678/SNP216 | Ca_Kabuli_Chr03 | 36050319 | [T/C] | Ca00903 | CDS(Syn) | SWAP (suppressor-of-white-apricot)/Surp domain-containing protein | 1.2 × 10−7 | 9 | Seed Zn concentration |
| #CakSNP4740/SNP229 | Ca_Kabuli_Chr03 | 36387718 | [C/T] | Ca00947 | CDS(Syn) | WD40 [tryptophan-aspartic acid (W-D) dipeptide] repeat-containing protein | 1.0 × 10−7 | 8 | Seed Zn concentration |
| *,#SNP300 | Ca_Kabuli_Chr04 | 4138693 | [C/T] | Ca03842 | URR | Yellow stripe-like 1 (YSL1) | 1.0 × 10−9 | 12 | Seed Fe and Zn concentrations |
| *,#CakSNP6693/SNP315 | Ca_Kabuli_Chr04 | 30258596 | [G/C] | Ca14189 | CDS(Syn) | Late embryogenesis abundant (LEA) protein | 1.3 × 10−9 | 12 | Seed Fe concentration |
| *,#CakSNP7405/SNP317 | Ca_Kabuli_Chr04 | 44814982 | [A/G] | Ca09146 | Intron | IQ-domain like protein | 2.5 × 10−9 | 11 | Seed Fe concentration |
| #CakSNP15585/SNP380 | Ca_Kabuli_Chr05 | 43372 | [C/T] | Ca22196 | CDS(Syn) | Ubiquitin | 1.1 × 10−7 | 8 | Seed Zn concentration |
| #CakSNP15145/SNP396 | Ca_Kabuli_Chr05 | 82342 | [C/T] | Ca24399 | CDS(Nsyn) | Unknown expressed gene | 1.3 × 10−7 | 7 | Seed Zn concentration |
| *,#CakSNP9048/SNP413 | Ca_Kabuli_Chr05 | 41080035 | [C/T] | Ca07626 | CDS(Syn) | Zinc/iron permease (AtZIP1) | 1.0 × 10−8 | 11 | Seed Fe and Zn concentrations |
| *,#CakSNP11677/SNP471 | Ca_Kabuli_Chr07 | 781409 | [A/G] | Ca03400 | CDS(Nsyn) | Octicosapeptide/Phox/Bem1p (PB1) domain-containing protein | 3.2 × 10−7 | 6 | Seed Fe concentration |
| *,#SNP472 | Ca_Kabuli_Chr07 | 2515209 | [A/G] | Ca03227 | URR | Heavy metal ATPases 2/4 (HMA2/4) | 3.5 × 10−7 | 10 | Seed Fe and Zn concentrations |
*Validated by QTL mapping and
#differential expression profiling.