Fine Mapping Identifies a New QTL for Brown Rice Rate in Rice (Oryza Sativa L.)

BACKGROUND: High yield and quality determine the commercial potential of rice variety. Brown rice rate (BRR) is a key factor ensuring grain yield and quality in rice. So far, there were few reports about the genes that directly controlled the BRR in rice. Therefore, dissecting the genetic mechanism of the BRR genes can facilitate improving effective rice supply or edible grain yield. RESULTS: A double haploid population derived from the cross between Taichung Native 1 (TN1) (an indica variety) and Chunjiang 06 (CJ06) (a japonica variety) was used to investigate the genetic basis of grain milling and appearance traits affecting the BRR. By using a constructed molecular linkage map, four quantitative trait loci (QTLs) for the BRR were detected on chromosomes 1, 8, 9, and 10, respectively. In addition, three QTLs for appearance traits, including grain weight and grain length/width ratio, were detected on chromosomes 6, 9 and 10, respectively. Chromosome segment substitution lines (CSSLs) were established at the qBRR-10 locus. Finally, the qBRR-10 was narrowed to a 39.5 kb region on chromosome 10. In this region, two candidate genes, LOC_Os10g32124 and LOC_Os10g32190, showed significantly differential expression in TN1 and CSSL1-2 compared with CJ06. Histocytological analysis suggested that cell size and hull thickness may be important factors for the BRR. CONCLUSION: In the study, the qBRR-10 affected the BRR and was finally located to a region between two markers, P13 and P14. Two candidate genes were selected based on the expression difference between two parents, which facilitated the further cloning of the qBRR-10 gene and largely contributed to improve the grain yield and quality in rice. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12284-016-0076-7) contains supplementary material, which is available to authorized users.