Table 1.
Functional significance of TFGMS and TFFDMS markers designed from the five TF genes showed association with seed and pod traits in chickpea
| TFs | Functional domains | TFGMS markers (NCBI PUIDs) | TFGMS repeat motifs | Association (P and R2 value) and differentially expressed (DE)/not differentially expressed (NDE) during seed development | TFFDMS markers (NCBI PUIDs) | TFFDMS repeat motifs | Association (P and R2 value) and differentially expressed (DE)/not differentially expressed (NDE) during seed development | SNP loci discovered | Sequenced gene amplicon size (bp) | Frequency (SNPs/bp) | Association (P and R2 value) | Associated seed and pod traits | Genetic position (cM) on the LGs |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Teosinte branched 1/cycloidea/proliferating cell factors (TCP) | TCP | TFGMS5 (16 584 978) |
(TCTCAT)4 | <0.046 0.19 NDE |
TFFDMS15-Type-I (16 586 183) |
(TCT)5 | <0.0034 0.31 NDE |
A/T, G/A, T/A, C/A, G/T, T/C |
1850 | 1/308.3 | <0.0026 0.40 |
Pod number per plant | LG1 55.4 |
| Squamosa-promoter-binding protein (SBP) | SBP | TFGMS21 (16 584 994) |
(CTC)4 | <0.014 0.25 NDE |
TFFDMS21-Type-Ia (16 586 189) |
(CAC)8 | <0.0019 0.38 NDE |
C/T, T/A, C/T, G/C, C/T, A/T, G/A, G/A, C/T, A/C, G/A |
3000 | 1/272.7 | <0.0012 0.45 |
Seed size/100-seed weight | LG1 74.5 |
| No apical meristem-arabidopsis transcription activation factor-cup shaped cotyledon (NAC) | NAM | TFGMS12 (16 584 985) |
(AATCCA)5 | <0.037 0.22 NDE |
TFFDMS18-Type-Ia 16 586 186 |
(GAT)6 | <0.0059 0.33 NDE |
A/G, T/C, G/C, T/A, G/A |
1400 | 1/280 | <0.0054 0.38 |
Seed size/100-seed weight Pod number per plant Seed number per plant |
LG1 73.9 |
| TFGMS17 (16 584 990) |
(CAA)5 | <0.032 0.25 NDE |
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| TFGMS3 (16 584 976) |
(TAA)5 | <0.049 0.18 NDE |
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| Domain of unknown function (DUF1635) | DUF1635 | TFGMS18a (16 584 991) |
(CTA)6 | <0.0024 0.31 DE |
TFFDMS16-Type-I (16 586 184) |
(CAA)6 | <0.047 0.23 NDE |
A/G, C/T, C/G, A/T, C/T, T/G |
2000 | 1/333.3 | <0.0046 0.43 |
Seed size/100-seed weight | LG1 73.5 |
| TFGMS1 (16 584 974) |
(GAA)6 | <0.043 0.18 NDE |
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| TFGMS4 (16 584 977) |
(AGA)8 | <0.041 0.19 NDE |
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| Domain of unknown function (DUF702) | DUF702 | TFGMS13 (16 584 986) |
(ACA)4 | <0.028 0.23 NDE |
TFFDMS20-Type-Ia (16 586 188) |
(ATA)5 | <0.0062 0.35 NDE |
C/T, G/A, A/C, G/C |
1100 | 1/275 | <0.0058 0.41 |
Seed size/100-seed weight Seed number per plant |
LG1 75.2 |
aValidated through traditional bi-parental genetic mapping.