Identify QTLs for grain size and weight in common wild rice using chromosome segment substitution lines across six environments.

Grain size and weight are important determinants of rice yield. The identification of beneficial genes from wild rice that have been lost or weakened in cultivated rice has become increasingly important for modern breeding strategies. In this study, we constructed a set of chromosome segment substitution lines (CSSLs) of wild rice, Oryza rufipogon with the indica cultivar 9311 genetic background. Four grain-related traits, i.e., grain length (GL), grain width (GW), length-width ratio (LWR), and thousand grain weight (TGW), were screened across six environments. A total of 37 quantitative trait loci (QTLs) were identified in these environments and mapped to 12 chromosomes. Sixteen QTLs were detected in at least two environments, and two QTL clusters were observed on Chr. 4 and Chr. 8. Based on a comparative analysis with QTLs identified in previous studies, the CSSLs between Oryza rufipogon accessions and 9311 had high genetic diversity. Among the sixteen stable QTLs, seven for TGW, LWR, GL, and GW were not previously identified, indicating potentially novel alleles from wild rice. These CSSLs provide powerful tools for functional studies and the cloning of essential genes in rice; furthermore, we identified elite germplasm for rice variety improvement.