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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #411158
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: Establishing a global Tropical Japonica rice core collection for allele mining and gene discovery: construction, sequencing, and phenotyping

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: Abstract Only
Publication Acceptance Date: 12/19/2023
Publication Date: 1/16/2024
Citation: Huggins, T.D., Edwards, J., McClung, A., Jia, Y., Jia, M.H., Jackson, A.K., Sells, L.J., Lawrence, B.S. 2024. Establishing a global Tropical Japonica rice core collection for allele mining and gene discovery: construction, sequencing, and phenotyping. Plant and Animal Genome Conference January 12-17, 2024, San Diego, California. Meeting Abstract.

Interpretive Summary:

Technical Abstract: The US rice industry grows mostly varieties from the tropical japonica subpopulation, however, most of the developed varieties can be traced back to less than 40 founders for the past 100 years. To address the lack of genetic diversity in US rice breeding programs, 740 globally diverse cultivars, US pedigree cultivars and cultivars from diversity panels believed to be tropical japonica were selected to create a tropical japonica (TRJ) Core panel. After genetic marker analysis with 13 molecular markers to determine subpopulation, the final panel contained 529 accessions from 61 countries with three improvement levels, bred cultivar, landrace or uncertain. 398 accessions plus non TRJ controls were sequenced with an average coverage of 3X. Single nucleotide polymorphisms (SNP) calling was performed using Google DeepVariant and GLnexus on the USDA-ARS SCINet HPC system. After imputation and filtering,436,022 biallelic SNPs were identified. Neighbor joining analysis showed the tropical japonica accessions forming a clade that is distinct from the checks from other subpopulations, and the subclades formed within tropical japonica somewhat reflect country of origin. The TRJ Core was evaluated in the field in a replicated experiment for two years in single plots. Traits assessed include 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 (cm), number of seed per panicle, seed weight per panicle (g), and number of primary and secondary panicle branches, grain length and width and length/width ratio. The panel was also scored for various blast strain resistance under greenhouse conditions. Preliminary genome wide association analysis identified significant SNPs for some agronomic traits and panicle architecture traits. The TRJ core is an excellent resource for mining the allelic diversity of tropical japonica to identify superior germplasm with beneficial alleles for breeding improved tropical japonica rice.