Abstract
Rice grain size plays a crucial role in determining grain quality and yield. In this study, two multiparent advanced generation intercross (MAGIC) populations, DC1 and BIM, were evaluated for grain size across three environments and genotyped with 55K array-based SNP detection and genotype-by-sequencing (GBS), respectively, to identify QTLs and SNPs associated with grain length, grain width, grain length–width ratio, grain thickness, and thousand grain weight. A total of 18 QTLs were identified for the five grain size-related traits and explained 6.43–63.35% of the total phenotypic variance. Twelve of these QTLs colocalized with the cloned genes, GS3, GW5/qSW5, GW7/GL7/SLG7, and GW8/OsSPL16, of which the first two genes showed the strongest effect for grain length and grain width, respectively. Four potential new genes were also identified from the QTLs, which exhibited both genetic background independency and environment stability and could be validated in future studies. Moreover, the significant SNP markers identified are valuable for direct utilization in marker-assisted breeding to improve rice grain size.
Highlights
Grain size is one of the key agronomic traits that proceeded from unconscious selective pressure over the course of rice domestication
Two multiparent advanced generation intercross (MAGIC) populations developed at the International Rice Research Institute (IRRI) were used: (1) a four-parent MAGIC population, DC1, previously characterized by Meng et al (2016), and (2) an eight-parent MAGIC population reported by Bandillo et al (2013), which we referred to as Bandillo indica MAGIC (BIM) population in this study
Prominent data skewness was observed for grain width (GW) of DC1 and BIM populations tested in Hainan 2017 and Hainan 2018, respectively (Figure 1)
Summary
Grain size is one of the key agronomic traits that proceeded from unconscious selective pressure over the course of rice domestication. Rice grain size is characterized by a combination of grain length (GL), grain width (GW), and grain thickness (GT) (Tan et al, 2000; Xing et al, 2002). It is closely associated with grain weight, a major yield component along with the number of panicles per plant and the number of grains per panicle. Many QTL mapping studies using populations derived from various biparental crosses have been conducted. Recent advances in rice functional genomics facilitated the cloning and functional characterization of several genes that either positively or negatively regulates grain size. Given the tiny fraction of the total variation present, different biparental populations yield different QTLs and with varying effects due to epistasis, pleiotropy, and QTL-byenvironment interaction
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