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

Authors: Eizenga, Georgia; Edwards, Jeremy; Jackson, Aaron; Huggins, Trevis

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/15/2024
Publication Date: 5/24/2024
Citation: Eizenga, G.C., Edwards, J., Jackson, A.K., Huggins, T.D. 2024. Substitution mapping of yield-related traits utilizing three cybonnet rice x wild introgression libraries. Crop Science. 64:2288-2304 https://doi.org/10.1002/csc2.21264.
DOI: https://doi.org/10.1002/csc2.21264

Interpretive Summary: Rice is a staple food for half the world’s population. Over 401 million tons of milled rice are consumed annually, highlighting the importance of improving rice yields to feed the increasing global population. 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 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 Cybonnet, an elite rice variety developed in Arkansas, USA. From these crosses, three populations were developed which had small segments of the ORSC DNA in the background of Cybonnet. The 212 progeny lines comprising these three populations and the Cybonnet parent were characterized for 20 traits related to yield over two field seasons in Arkansas. The traits evaluated included six agronomic traits (days to heading, plant height, tiller angle, leaf length and width, and number of panicles per plant), six traits related to panicle architecture, four traits for seed size and four traits for seed weight. From this evaluation, 62 progeny lines were significantly different from the Cybonnet parent for one or more yield related traits. The most notable differences were for seed size and weight, which directly relates to yield because increases in seed (grain) size would result in heavier seed (grains), thus higher yield. Examination of the chromosomal regions with the wild ORSC DNA in these 61 progeny lines for the genes controlling these yield-related traits, revealed 28 different genes. Sixteen of these genes are already being targeted by rice breeders for rice improvement but this study identified twelve other genes which potentially could enhance yield and should be explored in future studies.

Technical Abstract: Improving rice yields is a major objective of breeding programs worldwide. The Oryza rufipogon species complex (ORSC) includes the rice ancestral species, O. rufipogon and O. nivara, 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 rice breeders. The objective was to characterize these libraries for 20 yield-related traits to discover genes that are not currently deployed for rice improvement. Cybonnet and 212 CSSLs from these libraries were evaluated for two 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. Twenty of these 62 CSSLs were significantly different for seed traits. To ascertain the chromosome region(s) and underlying candidate gene(s) causing these differences, substitution mapping was performed with previously reported genotypes. Substitution mapping using 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 GW7 genes were mapped in the OrB and OrC derived CSSLs but only OsMADS50 mapped in OrA derived CSSLs. Employing the same approach for the other 19 traits, revealed 28 total candidate genes. Twelve of these genes are currently not deployed for rice improvement. The introgressed ORSC regions associated with these genes are potential sources of novel variation for rice improvement.