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ARS Home » Pacific West Area » Davis, California » Crops Pathology and Genetics Research » Research » Publications at this Location » Publication #334297

Title: Identification of seedling vigor-associated quantitative trait loci in temperate japonica rice

item CORDERO-LARA, KARLA - University Of California
item KIM, HYUNJUNG - University Of California
item Tai, Thomas

Submitted to: Plant Breeding and Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/16/2016
Publication Date: 11/30/2016
Citation: Cordero-Lara, K.L., Kim, H., Tai, T. 2016. Identification of seedling vigor-associated quantitative trait loci in temperate japonica rice. Plant Breeding and Biotechnology. 4:426-440.

Interpretive Summary: Seedling vigor is an important trait for rice varieties grown in direct-seeded rice production systems used in the U.S. and several other countries around the world. Seedlings that grow vigorously are able to establish themselves quickly under adverse conditions (e.g. cool weather) in order to compete against weeds for nutrients. In this study, differences in seedling vigor between two California medium grain rice varieties were observed and investigated using a genetic approach called quantitative trait loci (QTL) analysis. Using a genetic mapping population generated from the two varieties, four major traits associated with seedling vigor (i.e. seedling height at early and late growth stage, growth rate, and fresh weight) were evaluated and a cutting edge molecular marker technology called genotyping by sequencing was employed to construct a genetic linkage map of the population. Eight significant QTL were detected. Most contributed minor effects (7 to 11% of the trait variation observed) as expected for quantitative, complex traits such as seedling vigor. However, one QTL identified on chromosome 1 contributed over 34% of the trait variation observed for seedling fresh weight. This QTL was located in the same position as a second QTL for early seedling height. The same gene or genes may be involved in both traits. Most genetic studies of seedling vigor in rice have been studied in populations derived by crossing very genetically distant varieties. In this study, we have used very closely related varieties which are currently in production or use in breeding so the results (i.e. markers, germplasm) are more likely to be transferable to breeding programs.

Technical Abstract: A quantitative trait loci (QTL) analysis of seedling vigor traits was conducted under dry-seeded conditions using 176 recombinant inbred lines developed from a cross of two California temperate japonica rice varieties M-203 and M-206. Height at early seedling (HES) and late seedling (HLS) stage, growth rate (GR), and fresh weight (FW) were evaluated in a growth chamber. Assessment of HES, HLS, and GR was also performed in outdoor basins in 2015 and 2016. M-203 was significantly better for all traits in the growth chamber, however, no significant differences were observed between the parents in the outdoor basins with the exception of HES in 2015. Genotyping by sequencing was used to construct a map of >6,000 single nucleotide polymorphisms. Six QTL were detected in the growth chamber, one each on chromosomes 2, 9, 10 and 12 and two at the same position on 1. qFW1 and qHES1 explain 34.6% and 8.7% of the phenotypic variation observed for their respective traits and correspond to previously reported QTL for shoot length. All positive effects were contributed by the M-203 allele except for the qHLS12. Two QTL, qHES8 (12.3%; M-206 allele) and qHES9 (9.4%; M-203 allele), were detected in the outdoor basin 2016, but none in 2015. RIL-187 was consistently among the highest vigor lines in all environments and additional evaluations confirmed this finding. The molecular and genetic resources developed here will facilitate further investigation of seedling vigor and breeding of enhanced temperate japonica rice varieties.