Registration of six Oryza rufipogon Species Complex (ORSC) chromosome segment substitution sine (CSSL) libraries in elite Indica and Japonica rice backgrounds

Authors: Eizenga, Georgia; SINGH, NAMRATA - Cornell University; ALI, LIAKAT - University Of Arkansas; SHAKIBA, EHSAN - University Of Arkansas; AKTHER, KAZI - Cornell University; HARRINGTON, SANDRA - Cornell University; MCCOUCH, SUSAN - Cornell University

Submitted to: Journal of Plant Registrations
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/7/2025
Publication Date: N/A
Citation: N/A

Interpretive Summary: Rice is one of the two primary cereals in the human diet, highlighting the importance of exploring new avenues for improving rice yields and tolerance to diseases, insect pests, drought and heat stress. Cultivated rice has two varietal groups, Indica and Japonica which were identified in ancient times. The wild species that crop plants were domesticated from are a largely untapped reservoir of genetic variation available to plant breeders as they confront the challenges of a changing climate. The ancestral species of cultivated rice are Oryza rufipogon which is found throughout Asia and South America, and Oryza nivara which is limited to South and Southeast Asia. When considered together, these species are identified as the Oryza rufipogon species complex (ORSC). To enhance efforts to incorporate the genetic variation hidden in the ORSC, three genetically and phenotypically diverse accessions originating from China, Laos and Indonesia were crossed with IR64, an elite Indica variety developed by the International Rice Research Institute in the Philippines and grown throughout South and Southeast Asia, and Cybonnet, an elite Japonica variety developed in Arkansas for the US Mid-south. From crosses between these three ORSC accessions and the two varieties, six populations were developed which had small segments of the ORSC DNA in the background of either IR64 or Cybonnet. The 218 progeny lines comprising the three IR64 populations and the IR64 parent were characterized for 14 traits related to plant phenotype in the greenhouse in Arkansas. The traits evaluated included seven agronomic traits (days to heading, plant height, culm color and habit, leaf length and width, and number of tillers per plant), panicle type and length, awn presence and four seed size traits. The 216 progeny lines comprising the three Cybonnet populations and the Cybonnet parent were previously characterized for 22 yield-related over two field seasons in Arkansas. These traits included seven agronomic traits (days to heading, plant height, culm color and habit, leaf length and width, and number of panicles per plant), six traits related to panicle architecture, four seed size traits, four seed weight and awn presence. Analysis of the phenotypic data from the three Cybonnet populations revealed a total of 31 different genes attributed to the ORSC parents controlling the traits evaluated and 13 of these genes were validated in the three IR64 populations. Currently these six populations are distributed through the Genetic Stocks Oryza (GSOR) collection for rice researchers to identify traits in the ORSC donors that would enhance the resilience of the rice varieties currently grown.

Technical Abstract: The two varietal groups of cultivated rice (Oryza sativa) are Indica and Japonica. The rice ancestral species are O. rufipogon and O. nivara, collectively identified as the Oryza rufipogon species complex (ORSC) and are an underutilized resource for rice improvement. To make the ORSC genepool more accessible, three genotypically and phenotypically diverse ORSC accessions were selected as donors, OrA (W1944) from China, OrB (IRGC106148) from Laos and OrC (IRGC105567) from Indonesia, 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 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 the 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 LONG KERNEL 3 gene affecting grain length, WAXY gene affecting apparent amylose content, ALKALI DEGENERATION (ALK) gene affecting gelatinization temperature and Pita gene affecting blast resistance 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.