Abstract
BackgroundDrought tolerance is a major challenge in breeding rice for unfavorable environments. In this study, we used a panel of 180 Vietnamese rice landraces genotyped with 21,623 single-nucleotide polymorphism markers to perform a genome-wide association study (GWAS) for different drought response and recovery traits during the vegetative stage. These landraces originate from different geographical locations and are adapted to different agrosystems characterized by contrasted water regimes. Vietnamese landraces are often underrepresented in international panels used for GWAS, but they can contain original genetic determinants related to drought resistance.ResultsThe panel of 180 rice varieties was phenotyped under greenhouse conditions for several drought-related traits in an experimental design with 3 replicates. Plants were grown in pots for 4 weeks and drought-stressed by stopping irrigation for an additional 4 weeks. Drought sensitivity scores and leaf relative water content were measured throughout the drought stress. The recovery capacity was measured 2 weeks after plant rewatering. Several QTLs associated with these drought tolerance traits were identified by GWAS using a mixed model with control of structure and kinship. The number of detected QTLs consisted of 14 for leaf relative water content, 9 for slope of relative water content, 12 for drought sensitivity score, 3 for recovery ability and 1 for relative crop growth rate. This set of 39 QTLs actually corresponded to a total of 17 different QTLs because 9 were simultaneously associated with two or more traits, which indicates that these common loci may have pleiotropic effects on drought-related traits. No QTL was found in association with the same traits in both the indica and japonica subpanels. The possible candidate genes underlying the quantitative trait loci are reviewed.ConclusionsSome of the identified QTLs contain promising candidate genes with a function related to drought tolerance by osmotic stress adjustment.
Highlights
Drought tolerance is a major challenge in breeding rice for unfavorable environments
A genome-wide association study (GWAS) was carried out on a natural population consisting of 529 worldwide rice accessions for dissecting the genetic basis controlling 21 root traits under normal and drought stress conditions at the maturation stage (Li et al 2017)
Vietnamese landraces are often underrepresented in panels used for GWAS, even in the fully sequenced 3 K genomes-panel (Li et al 2014), while they can contain original genetic determinants related to drought resistance (Nguyen et al 2006)
Summary
Phenotypic Variation and Heritability Analysis Showed that the Panel Globally Presented an Homogeneous Response to Drought and Exhibited Variability at the Genotype Level To assess the severity level of the stress in our trial, we analyzed the variation of the average RWC and Score of the panel over time (from T1 after 1 week of stress to T4 after 4 weeks of stress). In addition to the co-locations with QTLs deriving from mapping populations, we observed overlaps between the associations from our study and the associations for drought-related traits detected using genome-wide association mapping (Courtois et al 2013; Muthukumar et al 2015; Al-Shugeairy et al 2015; Swamy et al 2017, Guo et al 2018) It found only 58 overlaps in a total of 1889 GWAS sites collected, in which there are 31 associations from the present study underlying the QTLs q1, q4, q5, q7, q9, q11, q13, and q14 (Additional file 1: Table S9). The genes in the QTL regions were investigated by using the Oryza sativa reference
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