Abstract
BackgroundGrain appearance quality is a main determinant of market value in rice and one of the highly important traits requiring improvement in breeding programs. The genetic basis of grain shape and endosperm chalkiness have been given significant attention because of their importance in affecting grain quality. Meanwhile, the introduction of NGS (Next Generation Sequencing) has a significant part to play in the area of genomics, and offers the possibility for high-resolution genetic map construction, population genetics analysis and systematic expression profile study.ResultsA RIL population derived from an inter-subspecific cross between indica rice PYZX and japonica rice P02428 was generated, based on the significant variations for the grain morphology and cytological structure between these two parents. Using the Genotyping-By-Sequencing (GBS) approach, 2711 recombination bin markers with an average physical length of 137.68 kb were obtained, and a high-density genetic map was constructed. Global genetic mapping of QTLs affecting grain shape and chalkiness traits was performed across four environments and the newly identified stable loci were obtained. Twelve important QTL clusters were detected, four of which were coincident with the genomic regions of cloned genes or fine mapped QTL reported. Eight novel QTL clusters (including six for grain shape, one for chalkiness, and one for both grain shape and chalkiness) were firstly obtained and highlighted the value and reliability of the QTL analysis. The important QTL cluster on chromosome 5 affects multiple traits including circularity (CS), grain width (GW), area size of grain (AS), percentage of grains with chalkiness (PGWC) and degree of endosperm chalkiness (DEC), indicating some potentially pleiotropic effects. The transcriptome analysis demonstrated an available gene expression profile responsible for the development of chalkiness, and several DEGs (differentially expressed genes) were co-located nearby the three chalkiness-related QTL regions on chromosomes 5, 7, and 8. Candidate genes were extrapolated, which were suitable for functional validation and breeding utilization.ConclusionQTLs affecting grain shape (grain width, grain length, length-width ratio, circularity, area size of grain, and perimeter length of grain) and chalkiness traits (percentage of grains with chalkiness and degree of endosperm chalkiness) were mapped with the high-density GBS-SNP based markers. The important differentially expressed genes (DEGs) were co-located in the QTL cluster regions on chromosomes 5, 7 and 8 affecting PGWC and DEC parameters. Our research provides a crucial insight into the genetic architecture of rice grain shape and chalkiness, and acquired potential candidate loci for molecular cloning and grain quality improvement.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0121-6) contains supplementary material, which is available to authorized users.
Highlights
Grain appearance quality is a main determinant of market value in rice and one of the highly important traits requiring improvement in breeding programs
The grain appearance traits, including grain length, grain width, the ratio of grain length and width, circularity, area size of grain, and perimeter length of grain for grain shape parameters, and chalk property including percentage of grain with chalkiness and degree of endosperm chalkiness were examined under four environments (Table 1 and Additional file 1: Table S1)
The grain width (GW) and Grain length (GL) of PYZX were at an average of 2.26 mm and 12.17 mm, whereas averages were 3.75 mm and 7.16 mm respectively for P02428
Summary
Grain appearance quality is a main determinant of market value in rice and one of the highly important traits requiring improvement in breeding programs. The genetic basis of grain shape and endosperm chalkiness have been given significant attention because of their importance in affecting grain quality. Grain shape and chalkiness have attracted significant attention in rice genetic research, as a practical matter, grain appearance quality is mostly conditioned by quantitative trait locus QTL, representing a major problem for rice improvement programs and production. By using map-based cloning strategies, several valuable genes regulating grain shape have been isolated, including GS3 (Fan et al 2006), GW2 (Song et al 2007), GS5 (Weng et al 2008), qSW5 (Shomura et al 2008), OsSPL16 (Wang et al 2012), qGL3.1/qGL3 (Qi et al 2012; Zhang et al 2012), GS6 (Sun et al 2013), GW7 (Wang et al 2015a), SLG7 (Zhou et al 2015b) and GL7 (Wang et al 2015b), which have enhanced our knowledge of the molecular regulatory mechanisms responsible for grain shape and enables breeders to develop high-yield varieties with improved grain-quality (Wang et al 2015b)
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