Substitution mapping of yield-related traits utilizing three Cybonnet rice x wild introgression libraries

Improving rice (Oryza sativa L.) yields is a major objective of breeding programs worldwide. The Oryza rufipogon species complex (ORSC), which includes the rice ancestral species O. rufipogon Griff. and O. nivara S. D. Sharma & Shastry, is an underutilized resource. Using three phenotypically and genotypically diverse ORSC accessions identified as OrA, OrB, and OrC, three Cybonnet x ORSC chromosome segment substitution line (CSSL) libraries were developed to make this genepool more accessible to breeders. The objective was to characterize these libraries for 20 yield-related traits to discover genes not currently deployed for rice improvement. Cybonnet and 212 CSSLs from these libraries were evaluated for 2 years in field studies for six agronomic, six panicle architecture, and eight seed traits. Across the three libraries, 62 CSSLs were found to be significantly different from Cybonnet for one or more traits. Of these, 27 CSSLs were significantly different for seed size traits. To ascertain the chromosome region and underlying candidate gene(s) causing these differences, substitution mapping was performed with previously reported genotypes. Mapping with the CSSLs, which had delayed heading under long days, revealed five known genes associated with rice flowering time pathways. The OsMADS50, RFT1, HD3A, SE1, and GHD7 genes were mapped in the OrB and OrC derived CSSLs but only OsMADS50 mapped in the OrA derived CSSLs. Employing this approach for the other 19 traits revealed 28 total candidate genes. A total of 12 of these genes are currently not deployed for yield enhancement. The introgressed ORSC regions associated with these genes are potential sources of novel variation for rice improvement. Three Cybonnet rice x wild introgression line libraries were evaluated for 20 yield-related traits. Overall, 62 introgression lines were significantly different from Cybonnet for a yield-related trait(s). Substitution mapping narrowed the wild genome region to search for gene(s) affecting yield-related trait(s). Substitution mapping is demonstrated with the five genes affecting days to heading under long day conditions. Of the 28 candidate genes presumed to affect yield traits, 12 are not targeted for breeding, thus potentially novel.