Cloning and Characterization of TaTGW-7A Gene Associated with Grain Weight in Wheat via SLAF-seq-BSA

Abstract

Thousand-grain weight (TGW) of wheat (Triticum aestivum L.) contributes significantly to grain yield. In the present study, a candidate gene associated with TGW was identified through specific-locus amplified fragment sequencing (SLAF-seq) of DNA bulks of recombinant inbred lines (RIL) derived from the cross between Jing 411 and Hongmangchun 21. The gene was located on chromosome 7A, designated as TaTGW-7A with a complete genome sequence and an open reading frame (ORF). A single nucleotide polymorphism (SNP) was present in the first exon between two alleles at TaTGW-7A locus, resulting in a Val to Ala substitution, corresponding to a change from higher to lower TGW. Cleaved amplified polymorphic sequence (CAPS) (TGW7A) and InDel (TG9) markers were developed to discriminate the two alleles TaTGW-7Aa and TaTGW-7Ab for higher and lower TGW, respectively. A major QTL co-segregating with TaTGW-7A explained 21.7–27.1% of phenotypic variance for TGW in the RIL population across five environments. The association of TaTGW-7A with TGW was further validated in a natural population and Chinese mini-core collections. Quantitative real-time PCR revealed higher transcript levels of TaTGW-7Aa than those of TaTGW-7Ab during grain development. High frequencies of the superior allele TaTGW-7Aa for higher TGW in Chinese mini-core collections (65.0%) and 501 wheat varieties (86.0%) indicated a strong and positive selection of this allele in wheat breeding. The molecular markers TGW7A and TG9 can be used for improvement of TGW in breeding programs.

Toward Identification of Black Lemma and Pericarp Gene Blp1 in Barley Combining Bulked Segregant Analysis and Specific-Locus Amplified Fragment Sequencing

“…Specific-locus amplified fragment sequencing (SLAF-seq) is a newly efficient strategy for large-scale de novo SNP discovery and high-resolution genotyping ( Sun et al, 2013 ). Combining BSA and SLAF-seq technologies have been successfully proven to be a powerful method for identifying major QTLs or candidate gene isolation in maize ( Xia et al, 2015 ), rice ( Xu F. et al, 2015 ), cucumber ( Xu X. et al, 2015 ), barley ( Qin et al, 2015 ), wheat ( Hu et al, 2016 ), tomato ( Zhao et al, 2016 ), and pepper ( Xu et al, 2016 ).…”

SNP-based association study of kernel architecture in a worldwide collection of durum wheat germplasm

“…A stable QTL qKW-6A was detected in both RIL population and DH population, suggesting that qKW-6A plays an important role in kernel width of wheat [19]. TaTGW-7A, a major QTL explaining 21.7-27.1% of phenotypic variance for thousand-kernel weight contributed significantly to wheat grain yield [20]. A single nucleotide polymorphism (SNP) in the promoter region of 1-FEH w3 gene was identified to be associated with thousand-kernel weight under drought conditions [21].…”

Phenotypic and Genotypic Evaluation of Synthetic Hexaploid Wheat Lines (Aabbdd) for Grain Parameters Under the Conditions of Western Siberia

“…Оценка полиморфизма по локусам, отвечающим за размер и массу зерновки, с помощью 13 SNP маркеров выявила амплификацию 9 маркеров в генотипах синтетических форм. Частота встречаемости идентифицированных локусов у изученных синтетических линий была разной: для TaTTP6A (30). Однако эти локусы нельзя рассматривать как ключевые, поскольку требуется дальнейшее фенотипирование синтетических линий в конкретных почвенноклиматических условиях.…”