Registration of six <i>Oryza rufipogon</i> species complex ( <i>ORSC</i> ) chromosome segment substitution line (CSSL) libraries in elite <i>Indica</i> and <i>Japonica</i> rice backgrounds

Abstract The two varietal groups of cultivated rice ( Oryza sativa ) are Indica and Japonica . Ancestral species O. rufipogon and O. nivara , collectively identified as the Oryza rufipogon species complex ( ORSC ), represent an underutilized resource for rice improvement. To make the ORSC genepool more accessible for breeding, three genotypically and phenotypically diverse ORSC accessions were selected as donors to develop chromosome segment substitution line (CSSL) libraries from crosses with IR64, an indica long grain grown in South and Southeast Asia, and Cybonnet, a U.S. tropical japonica long grain. The Cybonnet (Cyb) x OrA ( O. rufipogon , NIAS W1944) CSSL Library (Reg. no. MP‐11, NSL 551190 MAP) and IR64 x OrA ( O. rufipogon , NIAS W1944) CSSL Library (Reg. no. MP‐14, NSL 551377 MAP) used an ORSC donor from China, Cybonnet (Cyb) x OrB ( O. nivara , IRGC106148) CSSL Library (Reg. no. MP‐12, NSL 551297 MAP) and IR64 x OrB ( O. nivara , IRGC106148) CSSL Library (Reg. no. MP‐15, NSL 551378 MAP) an ORSC donor from Laos, and Cybonnet (Cyb) x OrC ( O. rufipogon , IRGC105567) CSSL Library (Reg. no. MP‐13, NSL 551376 MAP) and IR64 x OrC ( O. rufipogon , IRGC105567) CSSL Library (Reg. no. MP‐16, NSL 551379 MAP) an ORSC donor from Indonesia. The libraries were genotyped with an Infinium 7K array for rice. Previously, Cybonnet and 212 of the 216 Cybonnet CSSLs from the three libraries were evaluated in replicated field studies for six agronomic, six panicle architecture, and eight seed traits. Similarly, IR64 and 218 IR64 CSSLs from three libraries were grown in the greenhouse and characterized for six agronomic traits, panicle type and length, and four seed traits. Awn presence and culm color were noted for all CSSLs with three underlying genes identified. Of the 28 candidate genes identified by substitution mapping in the Cybonnet libraries, 11 were validated for the same traits phenotyped in the IR64 libraries. Phenotypes of CSSLs with ORSC introgressions that included the LK3 , Waxy , ALK , and Pita genes validated the ORSC allele for these genes. These six CSSL libraries are a unique resource for researchers to discover novel alleles in the ORSC donors for rice improvement.