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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #418005
Research Project: Broadening and Strengthening the Genetic Base of Rice for Adaptation to a Changing Climate, Crop Production Systems, and Markets

Location: Dale Bumpers National Rice Research Center

Title: Development, gene discovery and allele mining of a global tropical japonica core collection

Author
item Huggins, Trevis
item Edwards, Jeremy
item MCCLUNG, ANNA - Retired ARS Employee
item Jia, Yulin
item Jia, Melissa
item Jackson, Aaron
item Sells, Laduska - Laduska Simpson
item Lawrence, Brenda

Submitted to: Meeting Abstract
Publication Type: Proceedings
Publication Acceptance Date: 8/9/2024
Publication Date: 8/9/2024
Citation: Huggins, T.D., Edwards, J., Mcclung, A., Jia, Y., Jia, M.H., Jackson, A.K., Sells, L.J., Lawrence, B.S. 2024. Development, gene discovery and allele mining of a global tropical japonica core collection. Abstract. 2024 International Symposium on Rice Functional Genomics, September 9-11, 2024. Little Rock/Stuttgart, Arkansas.

Interpretive Summary:

Technical Abstract: Over the past 100 years, US rice variety development has focused on lines that trace back to about 40 founder parents, creating a lack of genetic diversity in modern US rice breeding programs. Most rice varieties grown in the Southern USA derive from the tropical japonica subpopulation, thus a tropical japonica Core (TRJ) panel was developed as a source of genetic diversity for improving, yield, quality, and sustainability of US rice. Accessions believed to be tropical japonica were selected from all available sources and subsequently genotyped with 13 molecular markers to verify subpopulation, resulting in a final panel of 529 accessions from 61 countries. From the TRJ panel, 398 accessions were sequenced with an average coverage of 3X, and single nucleotide polymorphisms (SNPs) were called using Google DeepVariant and GLnexus on the USDA-ARS SCINet HPC system. The TRJ Core was evaluated as single plots in a field experiment with two replications in 2021 and 2022. The accessions were evaluated for days to 50% heading, plant height, awns, leaf blade pubescence, lodging, growth rate, and flag leaf width and length. Additionally, yield components were measured including panicle length, seeds per panicle, seed weight per panicle, number of primary and secondary panicle branches, and grain dimensions. The panel was also scored for blast resistance under greenhouse conditions. Genome wide analyses were performed to discover associations between SNPs and the measured traits.