Genome‐wide SNP discovery and QTL mapping for economic traits in a recombinant inbred line of Oryza sativa

• Published in: Food and energy security 2021-05, Vol.10 (2), p.313-328
• Main Authors: Li, Gengmi, Yang, Qianhua, Li, Deqiang, Zhang, Tao, Yang, Li, Qin, Jian, Tang, Bin, Guo, Xiaojiao, Cao, Yingjiang, You, Shumei, Li, Zhaoxiang, Luo, Jing, Wan, Xianqi, Liu, Ying, Huang, Fu, Guo, Longbiao, Jiang, Kaifeng, Zheng, Jiakui
• Format: Article
• Language: English
• Subjects: Agricultural production; Breeding; Crop yield; Cultivation; Distance; DNA methylation; DNA sequences; Economics; Enzymes; Gene mapping; Gene sequencing; genetic linkage map; Genomes; Genotyping; Grain cultivation; Identification; Inbreeding; Nitrogen; Population; Quantitative trait loci; recombinant inbred line; Recombinants; Rice; Seeds; Single-nucleotide polymorphism; Yields
• ISSN: 2048-3694; 2048-3694
• DOI: 10.1002/fes3.274

The objective of the study was to understand the genetic basis of eight traits conferring grain appearance and yield in a recombinant inbred line (RIL8) derived from a cross between cultivated Indica rice varieties Dexiang074B and Pujiang6. We conducted whole genome re‐sequencing for the two parental lines and genotyping by sequencing (GBS) for the RIL8 population. Next, we aligned the clean reads to the rice genome Nipponbare IRGSP 1.0, constructed the genetic linkage map (GLM), and performed the quantitative trait loci (QTL) analysis. In total, 2631 high‐quality markers were generated for 315 RIL8 samples. We identified a rice GLM containing 12 linkage groups (total map distance: 1946.71 cM; average map distance: 0.74 cM) and 98 QTLs related to the rice yield, including 31 high credible QTLs. In addition, 39 QTLs were identified to be associated with the G*E interaction. While most of the QTLs were co‐localized with previously reported rice QTLs, some novel QTLs were identified for the first time in this study. These findings provide a genetic basis for developing cultivated rice with good economic characteristics based on molecular breeding technologies. A total of 98 additive QTLs and 39 additive QTLs for environment interaction were detected in this research, including 5 new QTLs, found to be related to the grain width and thousand kernel weight.