Genome-wide association study to identify candidate loci and genes for Mn toxicity tolerance in rice.
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ABSTRACT:
SUBMITTER: Shrestha A
PROVIDER: S-EPMC5806864 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Alkalinity stress is a major hindrance to enhancing rice production globally due to its damaging effect on plants' growth and development compared with salinity stress. However, understanding of the physiological and molecular mechanisms of alkalinity tolerance is limited. Therefore, a panel of indica and japonica rice genotypes was evaluated for alkalinity tolerance at the seedling stage in a genome-wide association study to identify tolerant genotypes and candidate genes. Principal component analysis revealed that traits such as alkalinity tolerance score, shoot dry weight, and shoot fresh weight had the highest contribution to variations in tolerance, while shoot Na+ concentration, shoot Na+:K+ ratio, and root-to-shoot ratio had moderate contributions. Phenotypic clustering and population structure analysis grouped the genotypes into five subgroups. Several salt-susceptible genotypes such as IR29, Cocodrie, and Cheniere placed in the highly tolerant cluster suggesting different underlying tolerance mechanisms for salinity and alkalinity tolerance. Twenty-nine significant SNPs associated with alkalinity tolerance were identified. In addition to three alkalinity tolerance QTLs, qSNK4, qSNC9, and qSKC10, which co-localized with the earlier reported QTLs, a novel QTL, qSNC7, was identified. Six candidate genes that were differentially expressed between tolerant and susceptible genotypes were selected: LOC_Os04g50090 (Helix-loop-helix DNA-binding protein), LOC_Os08g23440 (amino acid permease family protein), LOC_Os09g32972 (MYB protein), LOC_Os08g25480 (Cytochrome P450), LOC_Os08g25390 (Bifunctional homoserine dehydrogenase), and LOC_Os09g38340 (C2H2 zinc finger protein). The genomic and genetic resources such as tolerant genotypes and candidate genes would be valuable for investigating the alkalinity tolerance mechanisms and for marker-assisted pyramiding of the favorable alleles for improving alkalinity tolerance at the seedling stage in rice.
| S-EPMC10255560 | biostudies-literature
Project description:Mining salt tolerance genes is significant for breeding high-quality salt-tolerant rice varieties in order to improve the utilization of saline-alkaline land. In this study, 173 rice accessions were measured for their germination potential (GP), germination rate (GR), seedling length (SL), root length (RL), germination potential relative to salt damage rate (GPR), germination rate relative to salt damage rate (GRR), seedling length relative to salt damage rate (SLR), relative salt damage rate at the germination stage (RSD) and comprehensive relative salt damage rate in the early seedling stage (CRS) under normal and salt stress conditions. Genome-wide association analysis was performed with 1,322,884 high-quality SNPs obtained by resequencing. Eight quantitative trait loci (QTLs) related to salt tolerance traits at the germination stage were detected in 2020 and 2021. They were related to the GPR (qGPR2) and SLR (qSLR9), which were newly discovered in this study. Three genes were predicted as salt tolerance candidate genes: LOC_Os02g40664, LOC_Os02g40810, and LOC_Os09g28310. At present, marker-assisted selection (MAS) and gene-edited breeding are becoming more widespread. Our discovery of candidate genes provides a reference for research in this field. The elite alleles identified in this study may provide a molecular basis for cultivating salt-tolerant rice varieties.
| S-EPMC10255615 | biostudies-literature
Project description:BackgroundRice is considered as a salt-sensitive plant, particularly at early vegetative stage, and its production is suffered from salinity due to expansion of salt affected land in areas under cultivation. Hence, significant increase of rice productivity on salinized lands is really necessary. Today genome-wide association study (GWAS) is a method of choice for fine mapping of QTLs involved in plant responses to abiotic stresses including salinity stress at early vegetative stage. In this study using >?33,000 SNP markers we identified rice genomic regions associated to early stage salinity tolerance. Eight salinity-related traits including shoot length (SL), root length (RL), root dry weight (RDW), root fresh weight (RFW), shoot fresh weight (SFW), shoot dry weight (SDW), relative water content (RWC) and TW, and 4 derived traits including SL-R, RL-R, RDW-R and RFW-R in a diverse panel of rice were evaluated under salinity (100?mM NaCl) and normal conditions in growth chamber. Genome-wide association study (GWAS) was applied based on MLM(+Q?+?K) model.ResultsUnder stress conditions 151 trait-marker associations were identified that were scattered on 10 chromosomes of rice that arranged in 29 genomic regions. A genomic region on chromosome 1 (11.26 Mbp) was identified which co-located with a known QTL region SalTol1 for salinity tolerance at vegetative stage. A candidate gene (Os01g0304100) was identified in this region which encodes a cation chloride cotransporter. Furthermore, on this chromosome two other candidate genes, Os01g0624700 (24.95 Mbp) and Os01g0812000 (34.51 Mbp), were identified that encode a WRKY transcription factor (WRKY 12) and a transcriptional activator of gibberellin-dependent alpha-amylase expression (GAMyb), respectively. Also, a narrow interval on the same chromosome (40.79-42.98 Mbp) carries 12 candidate genes, some of them were not so far reported for salinity tolerance at seedling stage. Two of more interesting genes are Os01g0966000 and Os01g0963000, encoding a plasma membrane (PM) H+-ATPase and a peroxidase BP1 protein. A candidate gene was identified on chromosome 2 (Os02g0730300 at 30.4 Mbp) encoding a high affinity K+ transporter (HAK). On chromosome 6 a DnaJ-encoding gene and pseudouridine synthase gene were identified. Two novel genes on chromosome 8 including the ABI/VP1 transcription factor and retinoblastoma-related protein (RBR), and 3 novel genes on chromosome 11 including a Lox, F-box and Na+/H+ antiporter, were also identified.ConclusionKnown or novel candidate genes in this research were identified that can be used for improvement of salinity tolerance in molecular breeding programmes of rice. Further study and identification of effective genes on salinity tolerance by the use of candidate gene-association analysis can help to precisely uncover the mechanisms of salinity tolerance at molecular level. A time dependent relationship between salt tolerance and expression level of candidate genes could be recognized.
| S-EPMC7797017 | biostudies-literature
Project description:Lodging reduces rice yield, but increasing lodging resistance (LR) usually limits yield potential. Stem strength and leaf type are major traits related to LR and yield, respectively. Hence, understanding the genetic basis of stem strength and leaf type is of help to reduce lodging and increase yield in LR breeding. Here, we carried out an association analysis to identify quantitative trait locus (QTLs) affecting stem strength-related traits (internode length/IL, stem wall thickness/SWT, stem outer diameter/SOD, and stem inner diameter/SID) and leaf type-associated traits (Flag leaf length/FLL, Flag leaf angle/FLA, Flag leaf width/FLW, leaf-rolling/LFR and SPAD/Soil, and plant analyzer development) using a diverse panel of 550 accessions and evaluated over two years. Genome-wide association study (GWAS) using 4,076,837 high-quality single-nucleotide polymorphisms (SNPs) identified 89 QTLs for the nine traits. Next, through "gene-based association analysis, haplotype analysis, and functional annotation", the scope was narrowed down step by step. Finally, we identified 21 candidate genes in 9 important QTLs that included four reported genes (TUT1, OsCCC1, CFL1, and ACL-D), and seventeen novel candidate genes. Introgression of alleles, which are beneficial for both stem strength and leaf type, or pyramiding stem strength alleles and leaf type alleles, can be employed for LR breeding. All in all, the experimental data and the identified candidate genes in this study provide a useful reference for the genetic improvement of rice LR.
| S-EPMC8151605 | biostudies-literature
Project description:Low temperature significantly affects rice growth and yield. Temperatures lower than 15°C are generally detrimental for germination and uniform seedling stand. To investigate the genetic architecture underlying cold tolerance during germination in rice, we conducted a genome-wide association study using a novel diversity panel of 257 rice accessions from around the world and the 7K SNP marker array. Phenotyping was conducted in controlled growth chambers under dark conditions at 13°C. The rice accessions were measured for low-temperature germinability, germination index, coleoptile length under cold stress, plumule length at 4-day recovery, and plumule length recovery rate. A total of 51 QTLs were identified at p < 0.001 and 17 QTLs were identified using an FDR < 0.05 across the different chilling indices with the whole panel of accessions. At the threshold of p < 0.001, a total of 20 QTLs were identified in the subset of japonica accessions, while 9 QTLs were identified in the subset of indica accessions. Considering the recurring SNPs and linked SNPs across different chilling indices, we identified 31 distinct QTL regions in the whole panel, 13 QTL regions in the japonica subset, and 7 distinct QTL regions in the indica subset. Among these QTL regions, three regions were common between the whole panel and japonica, three regions were common between the whole panel and indica, and one region was common between indica and japonica. A subset of QTL regions was potentially colocalized with previously identified genes and QTLs, including 10 from the japonica subset, 4 from the indica subset, and 6 from the whole panel. On the other hand, a total of 21 potentially novel QTL regions from the whole panel, 10 from the japonica subset, and 1 from the indica subset were identified. The results of our study provide useful information on the genetic architecture underlying cold tolerance during germination in rice, which in turn can be used for further molecular study and crop improvement for low-temperature stressed environments.
| S-EPMC7047875 | biostudies-literature
Project description:Salinity-alkalinity stress is one of the main abiotic factors limiting rice production worldwide. With the widespread use of rice direct seeding technology, it has become increasingly important to improve the tolerance to salinity-alkalinity of rice varieties at the germination stage. Although we have a more comprehensive understanding of salt tolerance in rice, the genetic basis of alkali tolerance in rice is still poorly understood. In this study, we measured seven germination-related traits under alkali stress and control conditions using 428 diverse rice accessions. The alkali tolerance levels of rice germplasms varied considerably during germination. Xian/indica accessions had generally higher tolerance to alkali stress than Geng/japonica accessions at the germination stage. Using genome-wide association analysis, 90 loci were identified as significantly associated with alkali tolerance. Eight genes (LOC_Os01g12000, LOC_Os03g60240, LOC_Os03g08960, LOC_Os04g41410, LOC_Os09g25060, LOC_Os11g35350, LOC_Os12g09350, and LOC_Os12g13300) were selected as important candidate genes for alkali tolerance based on the gene functional annotation and gene-CDS-haplotype analysis. According to the expression levels of LOC_Os09g25060 (OsWRKY76), it is likely to play a negative regulatory role in alkali tolerance during rice germination. An effective strategy for improving rice alkali tolerance may be to pyramid alkali-tolerant haplotypes of multiple candidate genes to obtain the optimal haplotype combination. Our findings may provide valuable genetic information and expand the use of alkali tolerance germplasm resources in rice molecular breeding to improve the alkali tolerance at the germination stage.
| S-EPMC9033254 | biostudies-literature
Project description:Aluminum (Al) stress is becoming the major limiting factor in crop production in acidic soils. Rice has been reported as the most Al-tolerant crop and the capacity of Al toxicity tolerance is generally evaluated by comparing root growth under Al stress. Here, we performed an association mapping of Al toxicity tolerance using a core collection of 211 indica rice accessions with 700 K high quality SNP data. A total of 21 putative QTL affecting shoot height (SH), root length (RL), shoot fresh weight (SFW), shoot dry weight (SDW), root dry weight (RDW) and shoot water content (SWC) were identified at seedling stage, including three QTL detected only under control condition, eight detected only under Al stress condition, ten simultaneously detected in both control and Al stress conditions, and seven were identified by stress tolerance index of their corresponding traits. Total of 21 candidate genes for 7 important QTL regions associated with Al toxicity tolerance were identified based on combined haplotype analysis and functional annotation, and the most likely candidate gene(s) for each important QTL were also discussed. Also a candidate gene Nrat1 on chromosome 2 was further fine-mapped using BSA-seq and linkage analysis in the F2 population derived from the cross of Al tolerant accession CC105 and super susceptible accession CC180. A new non-synonymous SNP variation was observed at Nrat1 between CC105 and CC180, which resulted in an amino-acid substitution from Ala (A) in CC105 to Asp (D) in CC180. Haplotype analysis of Nrat1 using 327 3K RGP accessions indicated that minor allele variations in aus and indica subpopulations decreased Al toxicity tolerance in rice. The candidate genes identified in this study provide valuable information for improvement of Al toxicity tolerance in rice. Our research indicated that minor alleles are important for QTL mapping and its application in rice breeding when natural gene resources are used.
| S-EPMC5997306 | biostudies-literature
Project description:IntroductionRice (Oryza sativa L.) production is being challenged by global warming. Identifying new loci and favorable alleles associated with heat tolerance is crucial to developing rice heat-tolerant varieties.MethodsWe evaluated the heat tolerance at the seedling stage using 620 diverse rice accessions. A total of six loci associated with heat tolerance were identified by a genome-wide association study (GWAS) with ~2.8 million single nucleotide polymorphisms (SNPs).ResultsAmong the six detected loci, qHT7 harbored the strongest association signal and the most associated SNPs. By comparing the transcriptomes of two representative accessions with contrasting heat tolerance, LOC_Os07g48710 (OsVQ30) was selected as a promising candidate gene in qHT7 due to the significant difference in its expression level between the two accessions. Haplotype 4 (Hap4) of LOC_Os07g48710 was determined as the favorable haplotype for heat tolerance via the gene-based haplotype analysis. The heat-tolerant haplotype LOC_Os07g48710Hap4 is highly enriched in the tropical Geng/Japonica accessions, and its frequency has decreased significantly during the improvement process of rice varieties.DiscussionBased on the GWAS and transcriptomics integrated results, a hypothetical model modulated by qHT7 in response to heat stress was proposed. Our results provide valuable candidate genes for improving rice heat tolerance through molecular breeding.
| S-EPMC9868562 | biostudies-literature
Project description:BackgroundIn Asian rice production, an increasing number of countries now choose the direct seeding mode because of rising costs, labour shortages and water shortages. The ability of rice seeds to undergo anaerobic germination (AG) plays an important role in the success of direct seeding.ResultsIn this study, we used 2,123,725 single nucleotide polymorphism (SNP) markers based on resequencing to conduct a dynamic genome-wide association study (GWAS) of coleoptile length (CL) and coleoptile diameter (CD) in 209 natural rice populations. A total of 26 SNP loci were detected in these two phenotypes, of which 5 overlapped with previously reported loci (S1_ 39674301, S6_ 20797781, S7_ 18722403, S8_ 9946213, S11_ 19165397), and two sites were detected repeatedly at different time points (S3_ 24689629 and S5_ 27918754). We suggest that these 7 loci (-log10 (P) value > 7.3271) are the key sites that affect AG tolerance. To screen the candidate genes more effectively, we sequenced the transcriptome of the flooding-tolerant variety R151 in six key stages, including anaerobic (AN) and the oxygen conversion point (AN-A), and obtained high-quality differential expression profiles. Four reliable candidate genes were identified: Os01g0911700 (OsVP1), Os05g0560900 (OsGA2ox8), Os05g0562200 (OsDi19-1) and Os06g0548200. Then qRT-PCR and LC-MS/ MS targeting metabolite detection technology were used to further verify that the up-regulated expression of these four candidate genes was closely related to AG.ConclusionThe four novel candidate genes were associated with gibberellin (GA) and abscisic acid (ABA) regulation and cell wall metabolism under oxygen-deficiency conditions and promoted coleoptile elongation while avoiding adverse effects, allowing the coleoptile to obtain oxygen, escape the low-oxygen environment and germinate rapidly. The results of this study improve our understanding of the genetic basis of AG in rice seeds, which is conducive to the selection of flooding-tolerant varieties suitable for direct seeding.
| S-EPMC7788155 | biostudies-literature
Project description:In this study, relative germination percentage (RGP) and delayed mean germination time (DMGT) were measured in various rice accessions at the germination stage and carried out association analysis to identify candidate genes related to low temperature germination (LTG) using a natural population comprising 137 rice cultivars and inbred lines selected from the Korean rice core set. Genome-wide association study using ~ 1.44 million high-quality SNPs, which were identified by re-sequencing all rice collections, revealed 48 candidate genes on chromosome 10 and 55 candidate genes on chromosome 11 in the high peak SNP sites of associated loci for RGP and DMGT, respectively. By detecting highly associated variations located inside genic regions and performing functional annotation of the genes, we detected 23 candidate genes for RGP and 18 genes for DMGT for LTG. In addition, the haplotype and sequence analysis of the candidate gene (Os10g0371100) with RGP trait and the candidate gene (Os11t0104240-00) with DMGT revealed correlation between sequences of functional variations and phenotypes. Several novel LTG-related candidate genes previously were known for the function during rice germination and uncovered their substantial natural variations. These candidate genes represent valuable resources for molecular breeding and genetic improvement of cold tolerance during rice germination.
| S-EPMC5928009 | biostudies-literature