Phenotypic characterization of a suite of wild introgression lines in elite Indica and Japonica rice backgrounds

Authors: Eizenga, Georgia; SINGH, NAMRATA - Cornell University; HARRINGTON, SANDRA - Cornell University; AKTHER, KAZI - Cornell University; MCCOUCH, SUSAN - Cornell University

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 1/11/2023
Publication Date: 1/30/2024
Citation: Eizenga, G.C., Singh, N., Harrington, S., Akther, K., McCouch, S. 2024. Phenotypic characterization of a suite of wild introgression lines in elite Indica and Japonica rice backgrounds. Proceedings of 39th Rice Technical Working Group meeting, Hot Springs, Arkansas, Feb 20-23, 2023. p. 76-77.

Interpretive Summary:

Technical Abstract: Wild relatives of crop plants are a critical gene pool that can be used to expand the diversity of modern cultivars for improved yield and stress tolerance. Cultivated rice (Oryza sativa L.) has two widely diverged varietal groups, Japonica and Indica that were domesticated from the Oryza rufipogon Species Complex (ORSC). The ORSC includes accessions classified as O. rufipogon, O. nivara or Oryza spp. (mixed O. rufipogon/O. nivara and O. sativa ancestry). To exploit this gene pool for rice improvement, six libraries of wild introgression lines were developed by crossing three phenotypically and genotypically diverse wild donors originating from China, Laos and Indonesia to Japonica and Indica cultivated recurrent parents, Cybonnet, a tropical japonica long-grain variety from Arkansas, USA and IR64, an indica long-grain variety from the International Rice Research Institute in the Philippines. The libraries provide complete genome coverage of each of the three wild donors in the two recurrent parent backgrounds and were released as chromosome segment substitution lines (CSSLs). The six CSSL libraries were genotyped with 7,098 SNPs using the Cornell 7K SNP (C7AIR) array. Across the three Cybonnet libraries, the number of polymorphic SNPs ranged from 2,116 to 2,693 SNPs and the number of lines per library was 63 to 77 CSSLs. Across the three IR64 libraries, the number of polymorphic SNPs ranged from 1,596 to 2,962 SNPs with 68 to 81 CSSLs per library. Seed of the six CSSL libraries is currently available from the Genetic Stocks-Orzya Collection and the associated genotypic data is available at: http://cssl identifier.rcac.purdue.edu/. Greenhouse-grown plants of the CSSLs were characterized for flowering, shattering, bran (pericarp) color and pigmented hull. Recently, greenhouse plants of the three IR64 CSSL libraries were further characterized for plant height, culm color, culm habit, awn presence, seed length, seed width and seed length-to-width ratio, and mature plant architecture was documented with a digital image. Previous studies identified trait-enhancing QTLs associated with O. rufipogon introgressions in the U.S tropical japonica variety, Jefferson. One study documented eight Jefferson/O. rufipogon introgression lines (ILs) with grain yields 15.5 to 27.7% greater than the Jefferson recurrent parent, despite the poor agronomic traits of the wild donor. A subsequent study supported an additive model of transgressive variation, where the wild donor introgressions contributed to delayed growth rate, flag leaf length and panicle size in the Jefferson genetic background, resulting in increased grain yield. To determine whether introgressions from different ORSC donors in the same chromosomal regions also enhance yield and yield components in the Cybonnet background, plants of the three Cybonnet CSSL libraries were evaluated over two field seasons in Arkansas, USA. Evaluations included five agronomic traits (days to heading, plant height, culm habit, flag leaf length and width), six panicle architecture traits (panicle length, number of primary panicle branches, florets, seeds, and unfilled florets per panicle, and percent seed set), four seed traits (seed length, width, length-to-width ratio and 100-seed weight), grain yield per panicle and grain yield per plant. Additionally, culm color was recorded, and mature plant architecture was documented with a digital image. Preliminary results suggest that wild introgressions in the Cybonnet CSSLs do not enhance grain yield in the same way as in the Jefferson ILs. This may be because different wild ORSC donors were used to develop the Jefferson ILs and Cybonnet CSSLs. There also were substantially fewer background introgressions in the Cybonnet CSSLs as compared to the Jefferson ILs, suggesting that multiple, wild introgressions may be necessary to achieve the same level