AUTHOR=Fan Xiangyun , Zhu Juan , Dong Wenbin , Sun Yuandong , Lv Chao , Guo Baojian , Xu Rugen 

TITLE=Comparative Mapping and Candidate Gene Analysis of SSIIa Associated with Grain Amylopectin Content in Barley (Hordeum vulgare L.)

JOURNAL=Frontiers in Plant Science

VOLUME=8

YEAR=2017

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2017.01531

DOI=10.3389/fpls.2017.01531

ISSN=1664-462X

ABSTRACT=<p>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 <italic>SSIIa</italic> (<italic>SSII-3</italic>) gene was predicted as the candidate gene. Then we isolated and characterized biparental <italic>SSIIa</italic> 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 <italic>SSIIa</italic> transcript, thus resulting in a reduced amylopectin content. A sequence-based molecular marker was developed for the <italic>SSIIa</italic> allele and validated the effectivity, which would provide help for barley breeding.</p>