Genome-wide association study for salinity tolerance at the flowering stage in a panel of rice accessions from Thailand

- 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..
- LD decay analysis of the panel indicates that the average LD for SNPs at 20 kb distance from each other was 0.34 (r 2.
- 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.
- 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).
- Stress caused by salinity is one of the most serious environ- mental factors, which inhibits plant growth and decreases crop productivity worldwide [1].
- one of the world’s most important cereal crops, is classified as a salinity sensitive crop [1, 8]..
- Full list of author information is available at the end of the article.
- 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0.
- 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-re- sponsive loci/genes such as genetic mapping of quantita- tive trait loci (QTLs) using cross population.
- Although QTL mapping is a powerful and popular method to tag the salt tolerance region in plants, the examination of the variation is one of the limitation because QTL map- ping can identify only allelic diversity that segregates be- tween the parents of a particular F 2 cross or within recombinant inbred lines and the mapping resolution is limited by the amount of the genetic recombination event occurring in the mapping populations [20, 21].
- GWAS, which is the analysis of the statistical asso- ciation between genetic variants and traits on the whole genome scale in a large number of individuals within an organism, has been employed to identify causal genetic variability for target traits, including those in Arabidopsis and crop species .
- GWAS in rice was performed for agronomic traits such as tiller number, grain width, grain length and spikelet number in the indica subspecies based on SNPs identified by whole-genome sequencing..
- Forty-six significant loci were identified and Ghd7 was highlighted as a major locus for the natural variation of the chlorophyll content [30].
- [37] studies GWAS on germination stage of salt-treated rice using SNPs, 11 loci containing 22 significant SNPs responsible for stress-susceptibility indices of the vigor index and ger- mination time were identified.
- However, GWAS has not been applied for the analysis of photosynthetic and yield-related traits in rice exposed to salt stress at the flowering stage, which is a highly salt-sensitive stage.
- According to the limitation of the time-consuming process of data collection, the experiment was performed in three separate sets of experiments.
- transpiration rate (E), and intercellular CO 2 concentration (C i ) were measured during the same period a.m.) by the LI-6400 XT portable photosynthesis system (LI-COR, Lincoln, NE) on the middle portion of the 2nd leaf (penul- timate leaf) of the main tiller on days 0, 3, 6 and 9 after salt stress treatment.
- One gram of the 2nd leaf was cut into segments of 2 mm in length and put into 10 ml of deionized water in a test tube and left at room temperature for 2 h.
- Each of the unique DNA barcodes (Bioo Scientific, Austin, TX) was joined to DNA in each library using DNA ligase (New England Biolabs).
- Pre-capture libraries were hybridized with the capture probes of the rice exome region, which were de- signed based on the O.
- Variants were filtered if they fitted the following criteria: to be called heterozygous, minimum coverage and minimum percentage of each of the two observed major basecalls were 5 and 20, respect- ively and minimum total coverage was 10.
- the phenotypic and genomic data, analysis of the popula- tion structure within the rice population was performed using EIGENSOFT version 6.0.1, which used principal component analysis (PCA) to model ancestry differences in a population [47, 48].
- 40% of the varieties.
- Genome-wide association (GWA) mapping was con- ducted using GEMMA software based on the SNP data and the phenotypic data [51, 52].
- The relationships of the salt stability index of all parameters were determined by Pearson’s correlation r (Additional file 4: Table S3).
- In total, 190 rice accessions were used for exome-sequencing, with the capture probes designed to cover about 50 Mb of the nucleotide target covering all 12 chromosomes of rice..
- of our population were removed to decrease overesti- mation of the effect of low-MAF SNPs.
- The median of each trait is shown as a horizontal bar in the box, and the upper and lower sides of a box represent the first and third quartile values of the distribution, respectively.
- For LD decay analysis of the panel, the binned r 2 values were mapped against the physical distance and the distance at which the average of r 2 dropped to half of the maximum value was described as LD decay.
- Genome-wide association mapping and candidate loci associated with salt tolerance at flowering stage.
- Figure S3a and b show the regions containing those significant SNPs with the shade color in the blue bar representing the pair-wise LD indicated by r 2 value for the SNP of the lowest p-value in that region..
- Comparison of the GWAS prediction and previously reported QTLs.
- of the significant SNPs (33 SNPs) was located in qGY12.1 (RM519-RM1103) on chromosome 12, which associated with grain yield (GY) of rice under salt stress at reproduct- ive stage.
- Variations of the salt tolerance of rice at the flowering stage.
- Salt-tolerance of rice is a dynamic trait affected by grow- ing stage and genotype [59, 60].
- salt stress at the reproductive stage of rice [61].
- Previous studies used SNP array to identify SNP markers for GWAS in rice.
- The present study, however, focused on exonic regions, which are specific sequences in the genome while accounting for only one-sixth of the rice genome, resulted in more than 100,000 SNPs.
- Candidate genes associated with salt tolerance of rice at the flowering stage.
- Functional annotation of the 200 identified genes revealed a number of plausible candidates.
- The pair-wise LD for the SNP of the lowest p-value (red letters) is indicated as r 2 values, where the markers were divided into bins of 5 kb and the r 2 values were averaged and shown as blue bars.
- Note that the diagram of r 2 values represents all neighboring SNPs present in that region, while it is not proportional to the physical distance of the chromosome.
- in rice and other crop species such as maize or sorghum [70, 71], as well as Arabidopsis [72].
- The nature of the candidate genes indi- cates that different molecular and cellular strategies have evolved to favor survival during salt stress [81]..
- The positions of the QTL regions correspond to Table 3.
- Additionally, ectopic expression of the P450 gene PtCYP714A3 from Populus trichocarpa was studied in rice.
- A conserved N-terminal F-box domain (40 – 50 amino acids), is a component of the multi-subunit of ubiquitin E3 ligase, an enzyme in the last step of the ubiquitination pathway [98, 99].
- In fact, USP genes are widely distributed across many organisms including plant, which encode a protein containing the 140–160 highly conserved residues of the Universal Stress Protein A domain (USPA, Pfam accession number PF00582).
- Furthermore, the role of the USP protein (At3g53990: AtUsp) in enhancing oxidative stress has been reported in the plant model Arabidopsis [105]..
- of the candidate genes controlling salt tolerance identified in our GWAS overlap with the salt QTLs.
- Pearson ’ s correlation coefficients of the phenotypic traits measured in 104 rice accessions.
- Population structure of 190 rice association panels, which consisted mostly of the indica accessions.
- The pair-wise LD for the SNP of the lowest p-value (red letters) is indi- cated as r2 values, where the markers were divided into binds of 5 kb and the r2 values were averaged and shown as blue bars.
- Note that the diagram of r2 values represents all neighboring SNPs present in that region, while it is not proportional to the physical distance of the chromosome.
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