Skip to main content
ARS Home » Pacific West Area » Davis, California » Crops Pathology and Genetics Research » Research » Publications at this Location » Publication #356928

Research Project: Evaluation and Utilization of Novel Genetic Variation in Rice for the Enhancement of Agronomic Performance and Grain Quality

Location: Crops Pathology and Genetics Research

Title: Identification of QTL controlling seedling traits in temperate japonica rice under normal and reduced water availability conditions

item YUN, YEOTAE - Agricultural Research And Extension Service, Korea
item KIM, HYUNJUNG - University Of California, Davis
item Tai, Thomas

Submitted to: Plant Breeding and Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/7/2019
Publication Date: 6/1/2019
Citation: Yun, Y., Kim, H., Tai, T. 2019. Identification of QTL controlling seedling traits in temperate japonica rice under normal and reduced water availability conditions. Plant Breeding and Biotechnology. 7(2):106-122.

Interpretive Summary: Seedling vigor in rice is an important trait for direct-seeded production systems used in the U.S. and several other countries. Seedlings that grow vigorously under stress conditions (e.g., drought) are desirable. In this study, differences in seedling vigor under low water conditions between two California medium grain rice varieties were observed and investigated by quantitative trait loci (QTL) analysis. Four traits (shoot and root length, shoot and root dry weight) were examined and a number of QTL controlling these traits under normal and low water conditions were identified and found to correspond to previous reports. Lines exhibiting higher tolerance to low water conditions were identified. Together these genetic data (i.e., DNA markers) and rice germplasm represent useful resources relevant to breeding seedling vigor in temperate japonica rice prevalent in the U.S. and other temperate rice growing countries.

Technical Abstract: The objective of this study was to detect QTL for rice seedling traits under normal water (control) and low water conditions (drought stress). Ninety-eight recombinant inbred lines (RILs) from a cross between closely-related japonica cultivars, M-203 and M-206 were grown under both low water and normal water conditions. QTL for morphological traits were investigated at seedling stage using 5,164 single nucleotide polymorphisms via genotyping-by-sequencing. Twenty-three QTL were associated with four seedling traits: shoot length (SL), root length (RL), shoot dry weight (SW) and root dry weight (RW), were detected and most QTL were clustered on chromosome 1, 6, 7 and 11. Under normal water conditions, nine QTL for seedling traits were detected and M-203 alleles increased all the values. The locations of most QTL were consistent with genes that regulate or respond to auxin and gibberellin. For drought tolerance, fourteen QTL were detected including seven for drought stress conditions and seven for relative performance (values from drought stress conditions/normal water conditions). Five QTL for relative performance were identified in the similar region as the QTL detected under normal water conditions and showed the opposite direction of additive effect, suggesting that genes show different responses depending on the conditions such as genotype-by-environment interaction. Seven QTL from drought stress conditions coincided with the loci of previously identified drought tolerance genes. Based on the shoot and root length under drought stress conditions, five lines exhibiting the highest values in common were selected as a drought tolerance group. Those lines exhibited better growth than the parents under drought stress conditions and had QTL alleles for drought tolerance detected in this study. QTL information and selected lines may be used for improving seedling vigor and drought tolerance of rice in breeding programs.