Development and exploration of a global tropical japonica diversity panel

Authors: McClung, Anna; Huggins, Trevis; Edwards, Jeremy; Sells, Laduska - Laduska Simpson; Coral, Luis

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 1/11/2023
Publication Date: 1/30/2024
Citation: McClung, A.M., Huggins, T.D., Edwards, J., Sells, L.J., Coral, L.E. 2024. Development and exploration of a global tropical japonica diversity panel. Rice Technical Working Group Meeting Proceedings. Hot Springs, Arkansas, February 20-23, 2023.

Interpretive Summary:

Technical Abstract: Most of the rice grown in the USA is derived from the tropical japonica (TRJ) genepool but traces to very few progenitor parental lines. As a means to broaden the genepool for US breeders, a diversity panel of over 500 TRJ accessions from 60 countries was established to identify traits and marker linked alleles that may enhance rice breeding efforts. The panel was assembled using TRJ accessions sourced from other diversity panels such as RDP1, the USDA Core, and the Brazil Core as well as key US parental cultivars and 10 known check varieties of Indica, Temperate japonica, and Aus origin. In 2020 and 2021, the TRJ Core was grown at Stuttgart, AR in a flooded field trial with two replications for extensive phenotyping. Heading, height, panicle length, seed per panicle, seed weight per panicle, panicle primary and secondary branching, flag leaf length, width and pubescence, chlorophyl content (SPAD), awns, plant type, and hull color were among the traits measured. Initial findings from the 2021 study revealed that the TRJ Core contains accessions which exceed the best of the check varieties for panicle length, primary and secondary panicle branching, seed per panicle, chlorophyll content, and flag leaf size. Interestingly, secondary branching on the panicle was more strongly correlated than primary branching with seed number and seed weight per panicle. Traits that were measured over multiple time points, initial and final heading, and collar height over an 11-week period, were strongly correlated indicating that accession growth rates were consistent throughout the season. In addition, chlorophyll readings were negatively associated with plant height throughout the growth cycle. Flag leaf measurements were not correlated with any trait. Protocols are being developed for assessing several biotic and abiotic stress traits over the next few years. These protocols will be used to evaluate a TRJ micro-core which contains approximately 25% of the TRJ Core accessions. Currently, the TRJ micro-core has been evaluated for drought stress, submergence tolerance, and anaerobic germination. To conduct a genome-wide association study (GWAS) for a wide variety of agronomic, quality, and plant stress-related traits, tissue from each of the TRJ accessions is being genotyped by means of skim sequencing with a target read depth of approximately 1x. To increase marker density, SNP data obtained from skim sequencing will be imputed using data from the 3000 Rice Genomes (3KRG). The imputed SNPs will be used in GWAS to identify chromosomal regions associated with these traits. The SNP data will also be used in genomic prediction (GP) to train a GP model on TRJ micro-core phenotypes, which will then be applied across the whole TRJ Core to find accessions that have desirable predicted trait attributes and trait combinations. On the basis of the results of GWAS and GP, superior germplasm will be identified for use in complementary crossing to develop improved breeding lines for US programs. Initial findings from all completed studies will be presented.