Identification of Multiple Grain Shape-Related Loci in Rice Using Bulked Segregant Analysis With High-Throughput Sequencing

• Published in: Frontiers in plant science Vol. 11; p. 303
• Main Authors: Wu, Lian, Cui, Yue, Xu, Zhengjin, Xu, Quan
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 03-04-2020
• Subjects: BSA; DEP1; grain shape; high-throughput sequence; Plant Science; rice; high-throughput sequence; BSA; grain shape; rice; DEP1
• ISSN: 1664-462X; 1664-462X
• DOI: 10.3389/fpls.2020.00303

Grain shape (GS) is an important agronomic trait that can improve rice breeding for optimal appearance quality, and it varies highly between
and
subspecies. In this study, we conducted a genome sequencing of a series of recombination inbred lines (RILs) derived from a cross between
variety Shennong265 (SN265) and
variety R99, and we successfully detected seven loci associated with GS. Subsequent analysis showed that a major quantitative trait locus (QTL) corresponded to the
. To identify a main-effect locus, we conducted bulked segregant analysis (BSA) in two F
populations. A 0.8-Mb region on chromosome 9 was identified as the candidate region of GS. There are 101 predicted genes in this region, and eight single nucleotide polymorphisms/insertions and deletions (SNPs/INDELs) caused frameshift. We found that a 637-bp stretch in exon 5 of the
(
) locus in SN265 was replaced by a 12-bp sequence. The two types of CRISPR/Cas9 gene-edited plants confirmed that
affected GS, and both Gγ and Cys-rich domains participated in this regulatory mechanism. These findings improve our understanding of the underlying mechanism of GS in rice and provide an effective and rapid strategy for the identification of main-effect loci of target traits.