Abstract
BackgroundSalt stress, a major plant environmental stress, is a critical constraint for rice productivity. Dissecting the genetic loci controlling salt tolerance in rice for improving productivity, especially at the flowering stage, remains challenging. Here, we conducted a genome-wide association study (GWAS) of salt tolerance based on exome sequencing of the Thai rice accessions.ResultsPhotosynthetic parameters and cell membrane stability under salt stress at the flowering stage; and yield-related traits of 104 Thai rice (Oryza sativa L.) accessions belonging to the indica subspecies were evaluated. The rice accessions were subjected to exome sequencing, resulting in 112,565 single nucleotide polymorphisms (SNPs) called with a minor allele frequency of at least 5%. LD decay analysis of the panel indicates that the average LD for SNPs at 20 kb distance from each other was 0.34 (r2), which decayed to its half value (~ 0.17) at around 80 kb. By GWAS performed using mixed linear model, two hundred loci containing 448 SNPs on exons were identified based on the salt susceptibility index of the net photosynthetic rate at day 6 after salt stress; and the number of panicles, filled grains and unfilled grains per plant. One hundred and forty six genes, which accounted for 73% of the identified loci, co-localized with the previously reported salt quantitative trait loci (QTLs). The top four regions that contained a high number of significant SNPs were found on chromosome 8, 12, 1 and 2. While many are novel, their annotation is consistent with potential involvement in plant salt tolerance and in related agronomic traits. These significant SNPs greatly help narrow down the region within these QTLs where the likely underlying candidate genes can be identified.ConclusionsInsight into the contribution of potential genes controlling salt tolerance from this GWAS provides further understanding of salt tolerance mechanisms of rice at the flowering stage, which can help improve yield productivity under salinity via gene cloning and genomic selection.
Highlights
Salt stress, a major plant environmental stress, is a critical constraint for rice productivity
Phenotypic variation among Thai rice accessions under salt effect We evaluated photosynthetic parameters and cell membrane stability on 104 rice accessions individually at the flowering stage after salt stress for 3, 6 and 9 days and analyzed yield-related traits at harvesting time
The highest reduction of phenotypic traits was observed at day 9 after salt stress: photosynthetic rate, PN (− 49%); stomatal conductance, gs (− 50%); transpiration rate, E (− 43%), and cell membrane stability, CMS (− 18%) when compared with the control condition (Table 1)
Summary
A major plant environmental stress, is a critical constraint for rice productivity. Plant breeders are Lekklar et al BMC Genomics (2019) 20:76 continuously improving salt tolerant rice cultivars to increase yield productivity [11]. To fill the knowledge gap between genotypes and phenotypes of the salt stress response in rice, forward and reverse genetics have been performed to identify salt-responsive loci/genes such as genetic mapping of quantitative trait loci (QTLs) using cross population; screening of mutants generated by chemical- or irradiation-induced mutagenesis; and transgenic approach [15, 16]. To identify salt-responsive genes using cross population, a number of mapping studies have identified QTLs of physiological traits related to salinity tolerance in economic crops such as soybean, barley and rice [17,18,19]. The genotyping by SSR markers, which is usually based on polymerase chain reaction (PCR), is limiting to examining the kinds of variations, and laborious and time-consuming when high-density genotyping is needed for a large number of individuals [22]
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