Abstract
Grain shape (GS) is an important agronomic trait that can improve rice breeding for optimal appearance quality, and it varies highly between indica and japonica subspecies. In this study, we conducted a genome sequencing of a series of recombination inbred lines (RILs) derived from a cross between japonica variety Shennong265 (SN265) and indica variety R99, and we successfully detected seven loci associated with GS. Subsequent analysis showed that a major quantitative trait locus (QTL) corresponded to the qSW5/GW5. To identify a main-effect locus, we conducted bulked segregant analysis (BSA) in two F2 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 DENSE AND ERECT PANICLE 1 (DEP1) locus in SN265 was replaced by a 12-bp sequence. The two types of CRISPR/Cas9 gene-edited plants confirmed that DEP1 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.
Highlights
Rice, a staple food crop cultivated worldwide, feeds over 50% of the world’s population
Among the quantitative trait locus (QTL), one major locus qGS5 was co-located with GW5/GS5E, which has been reported to be related to rice grain width and grain weight
These results suggested that the truncated dep1 alleles generated an opposite phenotypic change on grain number per panicle under a different genetic background
Summary
A staple food crop cultivated worldwide, feeds over 50% of the world’s population. The indica and japonica rice varieties differ in term of GS, and this trait has undergone extensive selection during rice domestication and breeding. Recent studies have shown that GS is controlled by multiple signaling pathways, and advances in the functional genomics have facilitated the cloning of a series of loci that control grain size. QSW5/GW5 encodes a polyubiquitin-binding protein that is involved in the ubiquitin-proteasome pathway. This was shown to be a major loci of rice domestication and indica/japonica differentiation (Shomura et al, 2008; Weng et al, 2008). GL3.1 regulates cyclin-T1-38 to influence GS, and qGL3 encodes OsPPKL1phosphatase, which has been suggested to be involved in brassinosteroid
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