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Genome-Wide Association Mapping for Heat Stress Responsive Traits in Field Pea.

ABSTRACT: Environmental stress hampers pea productivity. To understand the genetic basis of heat resistance, a genome-wide association study (GWAS) was conducted on six stress responsive traits of physiological and agronomic importance in pea, with an objective to identify the genetic loci associated with these traits. One hundred and thirty-five genetically diverse pea accessions from major pea growing areas of the world were phenotyped in field trials across five environments, under generally ambient (control) and heat stress conditions. Statistical analysis of phenotype indicated significant effects of genotype (G), environment (E), and G × E interaction for all traits. A total of 16,877 known high-quality SNPs were used for association analysis to determine marker-trait associations (MTA). We identified 32 MTAs that were consistent in at least three environments for association with the traits of stress resistance: six for chlorophyll concentration measured by a soil plant analysis development meter; two each for photochemical reflectance index and canopy temperature; seven for reproductive stem length; six for internode length; and nine for pod number. Forty-eight candidate genes were identified within 15 kb distance of these markers. The identified markers and candidate genes have potential for marker-assisted selection towards the development of heat resistant pea cultivars.

SUBMITTER: Tafesse EG

PROVIDER: S-EPMC7139655 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Genome-Wide Association Mapping for Heat Stress Responsive Traits in Field Pea.

Tafesse Endale G EG Gali Krishna K KK Lachagari V B Reddy VBR Bueckert Rosalind R Warkentin Thomas D TD

International journal of molecular sciences 20200317 6

Environmental stress hampers pea productivity. To understand the genetic basis of heat resistance, a genome-wide association study (GWAS) was conducted on six stress responsive traits of physiological and agronomic importance in pea, with an objective to identify the genetic loci associated with these traits. One hundred and thirty-five genetically diverse pea accessions from major pea growing areas of the world were phenotyped in field trials across five environments, under generally ambient (c ...[more]

PMID: 32192061

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Project description:Heat stress during the seedling stage of early-planted winter wheat (Triticum aestivum L.) is one of the most abiotic stresses of the crop restricting forage and grain production in the Southern Plains of the United States. To map quantitative trait loci (QTLs) and identify single-nucleotide polymorphism (SNP) markers associated with seedling heat tolerance, a genome-wide association mapping study (GWAS) was conducted using 200 diverse representative lines of the hard red winter wheat association mapping panel, which was established by the Triticeae Coordinated Agricultural Project (TCAP) and genotyped with the wheat iSelect 90K SNP array. The plants were initially planted under optimal temperature conditions in two growth chambers. At the three-leaf stage, one chamber was set to 40/35°C day/night as heat stress treatment, while the other chamber was kept at optimal temperature (25/20°C day/night) as control for 14 days. Data were collected on leaf chlorophyll content, shoot length, number of leaves per seedling, and seedling recovery after removal of heat stress treatment. Phenotypic variability for seedling heat tolerance among wheat lines was observed in this study. Using the mixed linear model (MLM), we detected multiple significant QTLs for seedling heat tolerance on different chromosomes. Some of the QTLs were detected on chromosomes that were previously reported to harbor QTLs for heat tolerance during the flowering stage of wheat. These results suggest that some heat tolerance QTLs are effective from the seedling to reproductive stages in wheat. However, new QTLs that have never been reported at the reproductive stage were found responding to seedling heat stress in the present study. Candidate gene analysis revealed high sequence similarities of some significant loci with candidate genes involved in plant stress responses including heat, drought, and salt stress. This study provides valuable information about the genetic basis of seedling heat tolerance in wheat. To the best of our knowledge, this is the first GWAS to map QTLs associated with seedling heat tolerance targeting early planting of dual-purpose winter wheat. The SNP markers identified in this study will be used for marker-assisted selection (MAS) of seedling heat tolerance during dual-purpose wheat breeding.

Project description:BackgroundHeat tolerance is becoming increasingly important where maize is grown under spring season in India which coincide with grain filling stage of crop resulting in tassel blast, reduced pollen viability, pollination failure and barren ears that causes devastating yield losses. So, there is need to identify the genomic regions associated with heat tolerance component traits which could be further employed in maize breeding program.ResultsAn association mapping panel, consisting of 662 doubled haploid (DH) lines, was evaluated for yield contributing traits under normal and natural heat stress conditions. Genome wide association studies (GWAS) carried out using 187,000 SNPs and 130 SNPs significantly associated for grain yield (GY), days to 50% anthesis (AD), days to 50% silking (SD), anthesis-silking interval (ASI), plant height (PH), ear height (EH) and ear position (EPO) were identified under normal conditions. A total of 46 SNPs strongly associated with GY, ASI, EH and EPO were detected under heat stress conditions. Fifteen of the SNPs was found to have common association with more than one trait such as two SNPs viz. S10_1,905,273 and S10_1,905,274 showed colocalization with GY, PH and EH whereas S10_7,132,845 SNP associated with GY, AD and SD under normal conditions. No such colocalization of SNP markers with multiple traits was observed under heat stress conditions. Haplotypes trend regression analysis revealed 122 and 85 haplotype blocks, out of which, 20 and 6 haplotype blocks were associated with more than one trait under normal and heat stress conditions, respectively. Based on SNP association and haplotype mapping, nine and seven candidate genes were identified respectively, which belongs to different gene models having different biological functions in stress biology.ConclusionsThe present study identified significant SNPs and haplotype blocks associated with yield contributing traits that help in selection of donor lines with favorable alleles for multiple traits. These results provided insights of genetics of heat stress tolerance. The genomic regions detected in the present study need further validation before being applied in the breeding pipelines.

Dataset Information

Genome-Wide Association Mapping for Heat Stress Responsive Traits in Field Pea.

Publications

Genome-Wide Association Mapping for Heat Stress Responsive Traits in Field Pea.

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