Identification of genetic diversity in the USDA-minicore and among selected Vietnamese rice accessions for seedling stage salt tolerance

Authors: Rohila, Jai; Edwards, Jeremy; GIOI, TRAN - Cuu Long Delta Rice Research Institute; Jackson, Aaron; McClung, Anna

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 9/3/2018
Publication Date: 10/14/2018
Citation: Rohila, J.S., Edwards, J., Gioi, T.D., McClung, A.M. 2018. Identification of genetic diversity in the USDA-minicore and among selected Vietnamese rice accessions for seedling stage salt tolerance. Meeting Abstract. 5th International Rice Congress, October 14-17, 2018, Marina Bay Sands, Singapore.

Interpretive Summary:

Technical Abstract: In the USA, salt tolerance in rice at the seedling stage is more critical than at the flowering stage. Currently, one effective QTL, Saltol, has been identified in rice but has had limited utilization in USA rice breeding programs. There is a strong need to discover additional QTL/genes for salt tolerance at the seedling stage for the rice breeding community. The USDA-minicore is a subset of approximately 19,000 global rice accessions that holds promise for identifying novel genes/alleles for salt tolerance. In this hydroponic greenhouse study, 164 lines consisting of 123 USDA-minicore accessions (30 aus, 59 indica, 5 TEJ, and 29 TRJs) along with 26 Vietnamese accessions and 15 various checks including Pokkali (resistant) and IR29 (sensitive) were subjected to salt stress at the three-to-four leaf seedling stage. A salt concentration of EC 6.0 dSm-1 was used as treatment with 3 replications in a randomized block design. Twelve variables associated with salt tolerance component traits were determined. Salt stress scoring followed the standard IRRI protocol at 10 and 16 days after exposure to salt. After 16 days of salt stress, 32.7% of lines were highly sensitive, 40.7% moderately sensitive, 21.6% moderately tolerant, and 5% as highly tolerant. Pokkali was the most tolerant and Nerica-6 was the most sensitive line among this set of 164 lines. Among 26 Vietnamese accessions, several, including Soc Nau, possessed salt tolerant traits. A set of 30 genome-wide SSR markers were used to genotype the Vietnamese accessions, and RM340 was found to be uniquely associated with visual tolerance ratings and shoot and root biomass. We implemented GWAS on the USDA-minicore accessions using over 3.3 million SNPs to detect genomic regions associated with salt tolerance at 10 and 16 days. Multiple genomic regions associated with moderate to high salt tolerance were identified in each treatment with the several segments common between 10 and 16 days treatments. These segments include novel loci, and previously reported genes such as: RICE SALT SENSITIVE3. Accessions identified as having novel alleles for salt tolerance will be further tested to assess their potential as new sources of salt tolerance in rice breeding programs.