Comparative Genomic Analysis of Rice with Contrasting Photosynthesis and Grain Production under Salt Stress.

Unfavourable environmental conditions, including soil salinity, lead to decreased rice (Oryza sativa L.) productivity, especially at the reproductive stage. In this study, we examined 30 rice varieties, which revealed significant differences in the photosynthetic performance responses under salt stress conditions during the reproductive stage, which ultimately affected yield components after recovery. In rice with a correlation between net photosynthetic rate (PN) and intercellular CO2 concentration (Ci) under salt stress, PN was found to be negatively correlated with filled grain number after recovery. Applying stringent criteria, we identified 130,317 SNPs and 15,396 InDels between two "high-yield rice" varieties and two "low-yield rice" varieties with contrasting photosynthesis and grain yield characteristics. A total of 2,089 genes containing high- and moderate-impact SNPs or InDels were evaluated by gene ontology (GO) enrichment analysis, resulting in over-represented terms in the apoptotic process and kinase activity. Among these genes, 262 were highly expressed in reproductive tissues, and most were annotated as receptor-like protein kinases. These findings highlight the importance of variations in signaling components in the genome and these loci can serve as potential genes in rice breeding to produce a variety with salt avoidance that leads to increased yield in saline soil

Identification of nutrients limiting rice growth in soils of northeast Thailand under water-limiting and non-limiting conditions

Glasshouse nutrient omission trials are useful in identifying nurient limitations for plant growth in soils under the same environmental conditions.Soils of low fertility are commonly used for production of rainfed lowland rice(Oryza sative L.), and the crop often encounters water stress.Nutrient requirements may be modified when standing water disappears from the field.Two experiments with rice seedlings were conducted in a glasshouse at Ubon Rice Research Center, Thailand to identify the untrients which limit rice growth in soils of Northeast Thailand, and to determine whether nutrient limitations are affected by water availability.In Experiment l, rice was grown on two soils(Roi et and Ubon series)under well-watered and water-limiting conditions, and 15 nutrient treatments were imposed.In Experiment 2, six soils from Northeast Thailand were examined using the same 15 nutrient treatments.The nutrients which clearly limited the growth of rice plants in soils of Northeast Thailand were nitrogen(N)and phosphorus(P).In some cases, potassium(K)and sulfur(S)also limited growth, and in one soil zinc(Zn)and boron(B)also limited growth.A shortage of N was the most important limitation for plant growth in all soils except one in which P was more important.The low supply of P decreased plant height and leaf area development during early growth ; low N supply had a greater effect later during growth.The omission of P has a larger detrimental effect on growth when water supply was limited.In the Roi et soil, the omission of S had a large effect on leaf area and total dry matter production only under water stress conditions, but this was not found in the other soils examined.These results from glasshouse studies show that the nutrients limiting rice growth depend on soil type and water availability in soils of Northeast Thailand

Comparative Genomic Analysis of Rice with Contrasting Photosynthesis and Grain Production under Salt Stress.

Unfavourable environmental conditions, including soil salinity, lead to decreased rice (Oryza sativa L.) productivity, especially at the reproductive stage. In this study, we examined 30 rice varieties, which revealed significant differences in the photosynthetic performance responses under salt stress conditions during the reproductive stage, which ultimately affected yield components after recovery. In rice with a correlation between net photosynthetic rate (PN) and intercellular CO2 concentration (Ci) under salt stress, PN was found to be negatively correlated with filled grain number after recovery. Applying stringent criteria, we identified 130,317 SNPs and 15,396 InDels between two "high-yield rice" varieties and two "low-yield rice" varieties with contrasting photosynthesis and grain yield characteristics. A total of 2,089 genes containing high- and moderate-impact SNPs or InDels were evaluated by gene ontology (GO) enrichment analysis, resulting in over-represented terms in the apoptotic process and kinase activity. Among these genes, 262 were highly expressed in reproductive tissues, and most were annotated as receptor-like protein kinases. These findings highlight the importance of variations in signaling components in the genome and these loci can serve as potential genes in rice breeding to produce a variety with salt avoidance that leads to increased yield in saline soil

Identification of a Negative Regulator for Salt Tolerance at Seedling Stage via a Genome-Wide Association Study of Thai Rice Populations

Salt stress is a major limiting factor in crop production and yield in many regions of the world. The objective of this study was to identify the genes responsible for salt tolerance in Thai rice populations. We performed a genome-wide association study with growth traits, relative water content, and cell membrane stability at the seedling stage, and predicted 25 putative genes. Eleven of them were located within previously reported salt-tolerant QTLs (ST-QTLs). OsCRN, located outside the ST-QTLs, was selected for gene characterization using the Arabidopsis mutant line with T-DNA insertion in the orthologous gene. Mutations in the AtCRN gene led to the enhancement of salt tolerance by increasing the ability to maintain photosynthetic pigment content and relative water content, while the complemented lines with ectopic expression of OsCRN showed more susceptibility to salt stress detected by photosynthesis performance. Moreover, the salt-tolerant rice varieties showed lower expression of this gene than the susceptible rice varieties under salt stress conditions. The study concludes that by acting as a negative regulator, OsCRN plays an important role in salt tolerance in rice

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

Abstract Background Salt 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. Results Photosynthetic 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 (r 2), 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. Conclusions Insight 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