Pre-breeding studies focused on rice grown in temperate regions at the USDA-ARS Dale Bumpers National Rice Research Center

Authors: Eizenga, Georgia; Edwards, Jeremy; Huggins, Trevis; Pinson, Shannon; SCHLAPPI, MICHAEL - Marquette University; Rohila, Jai; Jia, Yulin

Submitted to: Temperate Rice Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 4/15/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: The USDA-ARS Dale Bumpers National Rice Research Center (DBNRRC) mission is to improve the competitiveness of the US rice industry in global and domestic markets through research and technology development that assures high yields, value-added grain quality, pest resistance, and stress tolerance. A key component for rice improvement is understanding the genes controlling desirable traits. Based on current resequencing data, rice (Oryza sativa L.) is composed of nine subpopulations with US rice mainly represented by the tropical japonica (TRJ) and temperate japonica (TEJ) subpopulations. Examination of the founders of US rice revealed short-grains are TEJ, medium-grains are admixtures of TEJ and TRJ and long-grains are TRJ with California cultivars having more TEJ than those grown in the Midsouth. Assembling a SNP database of private/nearly private alleles for each of the nine subpopulations from three resequencing studies revealed the US medium-grain cultivars were an admixture of TEJ and TRJ alleles with indica introgressions in chromosomes 1, 8, 9, 11 and 12. DBNRRC studies identified rice cultivars grown in temperate regions are a source of fissure resistance, cold tolerance and salt tolerance. Studies focused on fissure resistance determined resistance to kernel fissuring, first noted in the southern US cultivar Cypress (TRJ, long-grain), was also inherited by its progeny cultivar Cybonnet (TRJ, long-grain), and was attributed to three QTLs presumably inherited from the California long grain parent, L-202 (TRJ). The QTL with the largest individual effect explained from 10 to 30% of the total phenotypic variance in three mapping populations and was fine-mapped to a 1.28 Mb region approximately 8 cM distal to the semidwarf locus (sd1) on chromosome 1. Resistance to kernel fissuring is especially important and prevalent in California rice cultivars because the wide extremes between hot day and cool nighttime temperatures in California cause heavy dew to develop daily, which induces kernel fissuring due to pre-harvest rewetting of the mature grains. Evaluation of the Rice Minicore (RMC) composed of 202 O. sativa accessions, for cold tolerance at the germination and seedling stages revealed TEJ accessions (34) were the most cold-tolerant for the five traits measured and the aus accessions (38) and indica accessions (68) were the most cold-sensitive. To further dissect the QTL regions associated with seedling stage cold tolerance, two mapping populations were developed. Specifically, cold-tolerant TEJ accessions, Krasnodarskij 3352 and WIR911 were crossed with the cold-sensitive aus accession, Carolino 164. Mapping within these populations identified 25 candidate genes most of which were cold temperature regulated and had deleterious nucleotide variants in the Carolino 164 parent, which might contribute to its cold-sensitive phenotype. The functionality of two genes, OsFKBP13 and CYP59A, is currently being analyzed to determine if these genes belong to a new module regulating the trade-off between stress response, and growth and development. If confirmed, markers will be developed for use in marker-assisted breeding schemes to improve rice cold tolerance. The RMC also was evaluated for early seedling vigor under salt stress in the greenhouse to identify salt tolerant accessions. This study identified M-202, a California TEJ medium-grain, as extremely salt tolerant which was subsequently validated in a greenhouse study using salty Atlantic Ocean water. Currently, a M-202/Carolina Gold (TRJ, long-grain) mapping population is being developed to uncover the QTL for seedling stage salt tolerance and potentially develop markers for selected genes associated with salt tolerance to be used in marker-assisted breeding. Recently, Eclipse (PI 701081), a blast-resistant rice germplasm with the ‘Calrose’ type medium-grain quality was d