Identify QTLs and candidate genes underlying source-, sink-, and grain yield-related traits in rice by integrated analysis of bi-parental and natural populations

• Published in: PloS one Vol. 15; no. 8; p. e0237774
• Main Authors: Wang, Yun, Wang, Junmin, Zhai, Laiyuan, Liang, Chengwei, Chen, Kai, Xu, Jianlong
• Format: Journal Article
• Language: English
• Published: San Francisco Public Library of Science 14.08.2020; Public Library of Science (PLoS)
• Subjects: Agricultural production; Agriculture; Annotations; Biology and Life Sciences; Crop science; Crop yield; Crop yields; Gene mapping; Genes; Genetic aspects; Genomes; Genomics; Genotype & phenotype; Grain size; Haplotypes; Identification and classification; Laboratories; Marker-assisted selection; Markers; Natural populations; Nucleotides; Physiological aspects; Plant ecophysiology; Polymorphism; Populations; Quantitative genetics; Quantitative trait loci; Research and Analysis Methods; Rice; Single-nucleotide polymorphism; Source-sink relationships; Source-sink relationships (Photosynthesis); Supervision; Traveling salesman problem; China; Beijing China
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0237774

The source-sink relationship determines the ultimate grain yield of rice. In this study, we used a set of reciprocal introgression lines (ILs) derived from Xuishui09 x IR2061 to map quantitative trait loci (QTLs) that were associated with sink-, source-, and grain yield-related traits. A total of 95 QTLs influencing eight measured traits were identified using 6181 high-quality single nucleotide polymorphism markers. Nine background-independent QTLs were consistently detected in seven chromosomal regions in different genetic backgrounds. Seven QTLs clusters simultaneously affected sink-, source-, and grain yield-related traits, probably due to the genetic basis of significant correlations of grain yield with source and sink traits. We selected 15 candidate genes in the four QTLs consistently identified in the two populations by performing gene-based association and haplotype analyses using 2288 accessions from the 3K project. Among these, LOC_Os03g48970 for qTSN3b, LOC_Os06g04710 for qFLL6a, and LOC_Os07g32510 for qTGW7 were considered as the most likely candidate genes based on functional annotations. These results provide a basis for further study of candidate genes and for the development of high-yield rice varieties by balancing source-sink relationships using marker-assisted selection.