| Literature DB >> 27148286 |
Deepak Bajaj1, Rishi Srivastava1, Manoj Nath2, Shailesh Tripathi3, Chellapilla Bharadwaj3, Hari D Upadhyaya4, Akhilesh K Tyagi1, Swarup K Parida1.
Abstract
The large-scale mining and high-throughput genotyping of novel gene-based allelic variants in natural mapping population are essential for association mapping to identify functionally relevant molecular tags governing useful agronomic traits in chickpea. The present study employs an alternative time-saving, non-laborious and economical pool-based EcoTILLING approach coupled with agarose gel detection assay to discover 1133 novel SNP allelic variants from diverse coding and regulatory sequence components of 1133 transcription factor (TF) genes by genotyping in 192 diverse desi and kabuli chickpea accessions constituting a seed weight association panel. Integrating these SNP genotyping data with seed weight field phenotypic information of 192 structured association panel identified eight SNP alleles in the eight TF genes regulating seed weight of chickpea. The associated individual and combination of all SNPs explained 10-15 and 31% phenotypic variation for seed weight, respectively. The EcoTILLING-based large-scale allele mining and genotyping strategy implemented for association mapping is found much effective for a diploid genome crop species like chickpea with narrow genetic base and low genetic polymorphism. This optimized approach thus can be deployed for various genomics-assisted breeding applications with optimal expense of resources in domesticated chickpea. The seed weight-associated natural allelic variants and candidate TF genes delineated have potential to accelerate marker-assisted genetic improvement of chickpea.Entities:
Keywords: EcoTILLING; SNP; allele; association mapping; chickpea; seed weight; transcription factor
Year: 2016 PMID: 27148286 PMCID: PMC4835497 DOI: 10.3389/fpls.2016.00450
Source DB: PubMed Journal: Front Plant Sci ISSN: 1664-462X Impact factor: 5.753
Figure 1Schematic depicting the major steps followed in an agarose gel-based EcoTILLING assay for efficient identification of functionally relevant molecular tags governing useful agronomic traits in chickpea. This strategy is optimized for successful large-scale mining of novel SNP allelic variants from the target genomic regions (genes) by genotyping in a constituted field-phenotyped association panel (desi and kabuli core/mini-core germplasm lines). A, Accessions; SP, Superpool; F, (Forward); and R, (Reverse) primers.
Figure 2Optimization and validation of pool-based EcoTILLING approach coupled with agarose gel detection assay for large-scale mining of novel allelic variants from diverse coding and regulatory sequence components of TF genes by genotyping in a 192 A representative gel illustrating the optimization followed by PCR amplification of seven primer-pairs (Pr1-Pr7) designed targeting various coding and regulatory regions of seven TF genes in the genomic DNA of a desi chickpea accession (ICC 4958) to produce single reproducible amplicons of each primer for EcoTILLING analysis. (B,C) The representative gels depicting the screening of allelic variants from the eight representative micropools (P1–P8) and two superpools (SP1 and SP2) made from the genomic DNA of 192 desi and kabuli germplasm lines (including ICC 4958 as control) employing an agarose gel-based EcoTILLING assay as defined in the Figure 1. The absence (B) and presence (C) of one non-synonymous SNP allelic variant in the pools and superpools based on cleavage/digestion patterns of 1500 bp fragments amplified from the target CDS region of a mTERF TF gene was apparent in 2.5% agarose gel. The occurrence of 1500 bp homoduplex uncut PCR amplicons as well as mismatch-specific CEL I cleavage of 1500 bp heteroduplex PCR amplified fragments into two varied amplicons of 760 and 740 bp fragment sizes due to the effect of single nucleotide polymorphism (SNP-allele) was observed in the four pools (P5–P8) and one superpool (SP2). M: 1 kb DNA ladder size standard. (D) The sequencing of 1500 bp amplified PCR product of an mTERF TF gene followed by multiple alignment of their high-quality sequences ascertained the presence of one coding SNP (C to G) exhibiting missense non-synonymous amino acid substitution [aspargine (AAC) to lysine (AAG)] in the four pools (P5–P8), one superpool (SP2) and seven individual desi and kabuli accessions as per expectation based on agarose gel-based EcoTILLING assay. The sequenced region carrying the non-synonymous SNP is indicated with a dotted box. The detail information of genes used for validation is mentioned in the Table S2.
Eight seed weight-associated SNP allelic variants of transcription factor genes delineated by EcoTILLING-based trait association mapping.
| SNP0018 | 12794147 | [G/T] | CDS-Non Syn | Basic-leucine zipper (bZIP) protein | 1.3 × 10−5 | 15 | ||
| SNP0361 | 26026817 | [C/T] | CDS-Syn | Squamosa promoter binding protein (SBP) | 2.1 × 10−4 | 10 | ||
| SNP0748 | 3778 | [C/T] | URR | Zinc finger-domain containing protein | 2.3 × 10−4 | 10 | ||
| SNP0777 | 16680465 | [T/C] | CDS-Non Syn | No apical meristem Arabidopsis transcription activation factor-cup shaped cotyledon (NAC) | 1.7 × 10−4 | 12 | ||
| SNP0790 | 46718906 | [C/G] | CDS-Non Syn | mitochondrial transcription termination factor (mTERF) | 1.9 × 10−4 | 11 | ||
| SNP0804 | 10330226 | [T/C] | CDS-Non Syn | Basic helix-loop-helix (bHLH) protein | 1.0 × 10−5 | 14 | ||
| SNP0875 | 39546588 | [G/A] | CDS-Non Syn | APETALA-2/ethylene response element binding protein (AP2-EREBP) | 1.5 × 10−4 | 13 | ||
| SNP0952 | 48384848 | [C/T] | CDS-Non Syn | ARF (auxin response factor) | 2.5 × 10−4 | 10 | ||
CDS, coding DNA sequence; Syn, synonymous; and NonSyn, non-synonymous.
Validated previously by seed weight QTL mapping.