Abstract
Amylopectin concentration in barley endosperm has important effects on grain quality and end-use. In this study, quantitative trait locus (QTL) analysis together with genome-wide association studies (GWAS) were performed to identify markers linked to grain amylopectin content respectively using a doubled haploid (DH) population of 178 lines and a collection of 185 diverse barley germplasms both genotyped by genotyping-by-sequencing (GBS). A stable QTL on chromosome 7H and 11 associated single nucleotide polymorphisms (SNPs) were detected. In the co-localized region, the SSIIa (SSII-3) gene was predicted as the candidate gene. Then we isolated and characterized biparental SSIIa alleles of the DH population, investigated the expression pattern by quantitative real-time PCR (qRT-PCR), and revealed that a 33-bp deletion in exon 2 is responsible for reducing SSIIa transcript, thus resulting in a reduced amylopectin content. A sequence-based molecular marker was developed for the SSIIa allele and validated the effectivity, which would provide help for barley breeding.
Highlights
Barley (Hordeum vulgare L.) is the fourth largest cereal crop planted worldwide with the extensive utilization in various fields
It has been reported in the barley, wheat, rice and maize that the composition and content as well as properties of grain starch can be changed by the altered synthase IIa (SSIIa) (Yamamori et al, 2000; Umemoto et al, 2002; Morell et al, 2003; Zhang et al, 2004; Konik-Rose et al, 2007)
The results of this study reveal new genetic insights into grain amylopectin content in barley and provide the sequence-based marker for use in marker-assisted selection (MAS) for barley breeding
Summary
Barley (Hordeum vulgare L.) is the fourth largest cereal crop planted worldwide with the extensive utilization in various fields. Starch synthase IIa (SSIIa) encoded by SSIIa (SSII-3) gene is the one of a family enzymes that work progressively in the conversion of ADP-glucose to starch polymers by elongating short amylopectin chains which has the degree of polymerization (DP) ≤ 10 to intermediate chains of amylopectin (DP = 12∼24) in the cereal endosperm (Fontaine et al, 1993; Luo et al, 2015) It has been reported in the barley, wheat, rice and maize that the composition and content as well as properties of grain starch can be changed by the altered SSIIa (Yamamori et al, 2000; Umemoto et al, 2002; Morell et al, 2003; Zhang et al, 2004; Konik-Rose et al, 2007). The results of this study reveal new genetic insights into grain amylopectin content in barley and provide the sequence-based marker for use in marker-assisted selection (MAS) for barley breeding
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