Genome-wide Association Study of a Panel of Vietnamese Rice Landraces Reveals New QTLs for Tolerance to Water Deficit During the Vegetative Phase

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.Electronic supplementary materialThe online version of this article (10.1186/s12284-018-0258-6) contains supplementary material, which is available to authorized users.

QTL Mapping and Identification of Candidate Genes for Heat Tolerance at the Flowering Stage in Rice

“…This analysis identi ed 10 annotated genes that were potential candidate genes for heat stress tolerance during the owering stage in rice. Out of 10, six genes are related to drought tolerance in rice, namely LOC_Os08g06430, LOC_Os08g06500, LOC_Os08g06630, LOC_Os08g07060, LOC_Os08g07440 and LOC_Os08g07760 [38,39,[41][42][43]46]. It has been reported that gene expression might play the same role under different stress conditions.…”

“…The qHTT8 QTL harbored 53 genes that were annotated in the GO database. A sum of 119 GO terms were grouped to the three categories, within which genes corresponding to molecular function (39) and biological process (46) were the most abundant. Signi cantly enriched GO terms were associated with all of the three categories, including proteolysis involved in cellular protein catabolic process (GO:0051603), serine-type carboxypeptidase activity (GO:0004185), molecular_function (GO:0003674) and integral component of membrane (GO: 0016021) ( Fig.…”

“…To further analyze the candidate genes in the chromosome region containing qHTT8, we predicted 65 putative genes in the Nipponbare genome using the Rice Genome Annotation Project database (RGAP http://rice.plantbiology.msu.edu/) (Supplementary Table 3). Among these genes, 10 genes that are located within the mapped region have been reported to be involved in abiotic stress tolerance, such as high night temperature, drought, cold, salinity and saline-alkaline (Table 4) [38][39][40][41][42][43][44][45][46][47].…”

Genome-wide association study for yield and yield related traits under reproductive stage drought in a diverse indica-aus rice panel

“…Recently, GWAS studies conducted on 180 Vietnamese rice landraces identi ed a total of 17 QTLs associated with vegetative stage drought tolerance under greenhouse conditions (Hoang et al 2019). Different signi cant MTAs in the two subpanels of the study, indica and japonica were detected using mixed model approach with structure control and kinship among the studied landraces.…”

Genome-wide association study for yield and yield related traits under reproductive stage drought in a diverse indica-aus rice panel

“…Recently, GWAS studies conducted on 180 Vietnamese rice landraces identified a total of 17 QTLs associated with vegetative stage drought tolerance under greenhouse conditions (Hoang et al 2019).…”