title: Identification of Novel SNP in Promoter Sequence of TaGW2-6A Associated with Grain Weight and Other Agronomic Traits in Wheat (Triticum aestivum L.).
abstract: TaGW2 is an orthologue of rice gene OsGW2, which encodes E3 RING ubiquitin ligase and controls the grain size in rice. In wheat, three copies of TaGW2 have been identified and mapped on wheat homoeologous group 6 viz. TaGW2-6A, TaGW2-6B and TaGW2-6D. In the present study, using as many as 207 Indian wheat genotypes, we identified four SNPs including two novel SNPs (SNP-988 and SNP-494) in the promoter sequence of TaGW2-6A. All the four SNPs were G/A or A/G substitutions (transitions). Out of the four SNPs, SNP-494 was causal, since it was found associated with grain weight. The mean TGW (41.1 g) of genotypes with the allele SNP-494_A was significantly higher than mean TGW (38.6 g) of genotypes with the allele SNP-494_G. SNP-494 also regulates the expression of TaGW2-6A so that the wheat genotypes with SNP-494_G have higher expression and lower TGW and the genotypes with SNP-494_A have lower expression but higher TGW. Besides, SNP-494 was also found associated with grain length-width ratio, awn length, spike length, grain protein content, peduncle length and plant height. This suggested that gene TaGW2-6A not only controls grain size, but also controls other agronomic traits. In the promoter region, SNP-494 was present in 'CGCG' motif that plays an important role in Ca2+/calmodulin mediated regulation of genes. A user-friendly CAPS marker was also developed to identify the desirable allele of causal SNP (SNP-494) for use in marker-assisted selection for improvement of grain weight in wheat. Using four SNPs, five haplotypes were identified; of these, Hap_5 (G_A_G_A) was found to be a desirable haplotype having significantly higher grain weight (41.13g) relative to other four haplotypes (36.33-39.16 g).
authors.affiliation: Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India.
authors.forename: Vandana
authors.initials: V
authors.lastname: Jaiswal
authors.affiliation: Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India.
authors.forename: Vijay
authors.initials: V
authors.lastname: Gahlaut
authors.affiliation: Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi, India.
authors.forename: Saloni
authors.initials: S
authors.lastname: Mathur
authors.affiliation: Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India.
authors.forename: Priyanka
authors.initials: P
authors.lastname: Agarwal
authors.affiliation: Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi, India.
authors.forename: Manoj Kumar
authors.initials: MK
authors.lastname: Khandelwal
authors.affiliation: Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi, India; Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India.
authors.forename: Jitendra Paul
authors.initials: JP
authors.lastname: Khurana
authors.affiliation: National Institute of Plant Genome Research, New Delhi, India.
authors.forename: Akhilesh Kumar
authors.initials: AK
authors.lastname: Tyagi
authors.affiliation: Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India.
authors.forename: Harindra Singh
authors.initials: HS
authors.lastname: Balyan
authors.affiliation: Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India.
authors.forename: Pushpendra Kumar
authors.initials: PK
authors.lastname: Gupta
mesh_terms: D018506:Gene Expression Regulation, Plant; D005838:Genotype; D008957:Models, Genetic; D063245:Plant Development / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D014908:Triticum / Q000235:genetics* / Q000254:growth & development; D044767:Ubiquitin-Protein Ligases / Q000235:genetics*
chemical_list: D010940:Plant Proteins; D044767:Ubiquitin-Protein Ligases