A coordinated suite of wild-introgression lines in Indica and Japonica elite backgrounds

Authors: SINGH, NAMRATA - Cornell University; WANG, DIANE - Cornell University; Eizenga, Georgia; ALI, LIAKAT - University Of Arkansas; KIM, HYUNJUNG - Cornell University; AKTHER, KAZI - Cornell University; HARRINGTON, SANDRA - University Of Arkansas; KANG, JU-WON - Chungnam National University; SHAKIBA, EHSAN - University Of Arkansas; SHI, YUXIN - Cornell University; DECLERCK, GENEVIEVE - Cornell University; MEADOWS, BYRON - Cornell University; GOVINDARAJ, VISHNU - Cornell University; AHN, SANGNAG - Chungnam National University; MCCOUCH, SUSAN - Cornell University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/12/2020
Publication Date: 11/12/2020
Citation: Singh, N., Wang, D.R., Eizenga, G.C., Ali, L.M., Kim, H., Akther, K.M., Harrington, S.E., Kang, J., Shakiba, E., Shi, Y., Declerck, G., Meadows, B., Govindaraj, V., Ahn, S., McCouch, S.R. 2020. A coordinated suite of wild-introgression lines in Indica and Japonica elite backgrounds. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2020.564824.
DOI: https://doi.org/10.3389/fpls.2020.564824

Interpretive Summary: More than half of the world’s population depends on rice for more than 20% of their daily calories, thus it is critical that we expand the diversity in the rice gene pool to develop varieties that are adapted to extreme variations in climate including heat, cold, and drought, as well as, disease and insect pressure. Rice was domesticated from the wild ancestral species, O. rufipogon, which harbors a wealth of genes that were lost during the domestication process. Incorporating these “lost genes” back into cultivated rice may offer new opportunities for developing new varieties that are tolerant to biotic and abiotic stresses. Cultivated rice, O. sativa, as we know it today, has diverged into the two varietal groups, Indica and Japonica. Six different populations were developed from crosses between each of three diverse O. rufipogon accessions originating from China, Laos and Indonesia with a Japonica variety, Cybonnet, developed in the USA and an Indica variety, IR64, developed in the Philippines. Each population consists of progeny that possess small chromosome segments from the O. rufipogon donor parents in the background of the either Cybonnet or IR64, both of which are well adapted for production in the USA. These rice lines can be used by rice breeders to identify novel genetic variation from the wild ancestral species, O. rufipogon, and easily incorporate the desired gene(s) or trait(s) into locally adapted, elite germplasm for the development of new high yield, resilient rice varieties.

Technical Abstract: Rice, Oryza sativa L., is a cultivated, inbreeding species that serves as the staple food for the largest number of people on earth. It has two strongly diverged varietal groups, Indica and Japonica, which have resulted from a combination of natural and human selection. The genetic divergence of these groups reflects the underlying population structure of their wild ancestors and suggests that a breeding strategy designed to take advantage of existing genetic, geographic and ecological substructure may provide a rational approach to the utilization of crop wild ancestors in plant improvement. Here we describe the coordinated development of six introgression libraries (n= 63 to 81 lines per library) in both Indica (cultivar IR64 developed in the Philippines) and Japonica (cultivar Cybonnet developed in Arkansas, USA) backgrounds using three bio-geographically diverse wild donors representing the O. rufipogon Species Complex (ORSC) from China, Laos and Indonesia. The final libraries were genotyped using an Infinium 7K SNP rice array, identified as “C7AIR”, and analyzed for a set of morphological and physiological phenotypes including days to heading, shattering, hull color, phenol reaction of the grain, pericarp color and seed set. The mechanisms underlying these traits are discussed based on the introgressed wild donor segment(s). These six interspecific populations can be used as individual Chromosome Segment Substitution Line (CSSL) libraries and, when considered together, serve as a powerful genetic resource for systematic genetic dissection of agronomic, physiological and developmental traits in rice.