Identifying QTLs for Grain Size in a Colossal Grain Rice (Oryza sativa L.) Line, and Analysis of Additive Effects of QTLs

Abstract

Grain size is an important component of quality and harvest traits in the field of rice breeding. Although numerous quantitative trait loci (QTLs) of grain size in rice have been reported, the molecular mechanisms of these QTLs remain poorly understood, and further research on QTL observation and candidate gene identification is warranted. In our research, we developed a suite of F2 intercross populations from a cross of 9311 and CG. These primary populations were used to map QTLs conferring grain size, evaluated across three environments, and then subjected to bulked-segregant analysis-seq (BSA-seq). In total, 4, 11, 12 and 14 QTLs for grain length (GL), grain width (GW), 1000-grain weight (TGW), and length/width ratio (LWR), respectively, were detected on the basis of a single-environment analysis. In particular, over 200 splicing-related sites were identified by whole-genome sequencing, including one splicing-site mutation with G>A at the beginning of intron 4 on Os03g0841800 (qGL3.3), producing a smaller open reading frame, without the third and fourth exons. A previous study revealed that the loss-of-function allele caused by this splicing site can negatively regulate rice grain length. Furthermore, qTGW2.1 and qGW2.3 were new QTLs for grain width. We used the near-isogenic lines (NILs) of these GW QTLs to study their genetic effects on individuals and pyramiding, and found that they have additive effects on GW. In summary, these discoveries provide a valuable genetic resource, which will facilitate further study of the genetic polymorphism of new rice varieties in rice breeding.

Identification of Elite R-Gene Combinations against Blast Disease in Geng Rice Varieties

“…However, due to the high variability of M. oryzae populations and the emergence of new virulent strains, many resistant varieties that contain the individual R gene may lose resistance after a period of large-scale cultivation [ 8 ]. Therefore, gene pyramiding using different R genes has been considered a more effective approach to preventing the loss of resistance in varieties and to breeding varieties with durable, broad-spectrum resistance [ 9 ]. For example, Wu et al (2019) used molecular-marker-assisted selection (MAS) to pyramid Pigm and Pi1 , Pi54 , and Pi33 , and the pyramiding lines showed stable broad-spectrum resistance under artificial inoculation at both seedling and booting stages [ 1 ].…”

Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics

“…Two research papers from this Special Issue focused on rice from Professor Ye’s laboratory [ 7 , 8 ], where findings may directly assist in strategies for rice yield or quality improvements. In the first paper, Professor Ye’s team studied the molecular effects of post-anthesis moderate soil drying (MD)n which is proven to be an effective method for promoting starch synthesis and inferior spikelet grain filling.…”