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Identification of novel SNP in promoter sequence of TaGW2-6A associated with grain weight and other agronomic traits in wheat (Triticum aestivum L.)

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Title Identification of novel SNP in promoter sequence of TaGW2-6A associated with grain weight and other agronomic traits in wheat (Triticum aestivum L.)
 
Creator Jaiswal, Vandana
Gahlaut, Vijay
Mathur, Saloni
Agarwal, Priyanka
Khandelwal, Manoj Kumar
Khurana, Jitendra Paul
Tyagi, Akhilesh K.
Balyan, Harindra Singh
Gupta, Pushpendra Kumar
 
Subject Wheat
Triticum aestivum L.
Agronomic Traits
Grain Weight
TaGW2-6A
 
Description Accepted date: May 7, 2015
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).
Thanks are due to the Department of Biotechnology, New Delhi, Department of Science Technology (Funds for Improvement of Science and Technology infrastructure program), New Delhi and University Grants Commission (Special Assistance Program-Departmental Research Support Program), New Delhi for support which facilitated this study. PKG was awarded the position of NASI-Senior Scientist, VG was awarded SRF under the same program. CSIR awarded SRF to VJ.
 
Date 2016-01-05T10:29:50Z
2016-01-05T10:29:50Z
2015
 
Type Article
 
Identifier PLoS One, 10(6): e0129400
1932-6203
http://172.16.0.77:8080/jspui/handle/123456789/516
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0129400
10.1371/journal.pone.0129400
 
Language en_US
 
Publisher PLOS