Next-Generation Sequencing Enabled Genetics in Hexaploid Wheat

Gardiner, Laura‐Jayne; Joynson, Ryan; Hall, Anthony

doi:10.1016/b978-0-08-102163-7.00003-x

Cited by 5 publications

(3 citation statements)

References 44 publications

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“…Genotyping-by-sequencing (GBS) is an NGS-based genotyping technology that dramatically decreases genotyping costs and improves genotyping efficiency (Gardiner et al, 2019a). A protocol for the construction of wheat GBS libraries using two restriction enzymes and a pipeline for SNP calling have been developed (Poland et al, 2012;Alipour et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

High-Resolution Genome-wide Association Study Identifies Genomic Regions and Candidate Genes for Important Agronomic Traits in Wheat

et al. 2020

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Wheat (Triticum aestivum) is a major staple food crop worldwide. Genetic dissection of important agronomic traits is essential for continuous improvement of wheat yield to meet the demand of the world's growing population. We conducted a large-scale genome-wide association study (GWAS) using a panel of 768 wheat cultivars that were genotyped with 327 609 single-nucleotide polymorphisms generated by genotyping-by-sequencing and detected 395 quantitative trait loci (QTLs) for 12 traits under 7 environments. Among them, 273 QTLs were delimited to %1.0-Mb intervals and 7 of them are either known genes (Rht-D, Vrn-B1, and Vrn-D1) that have been cloned or known QTLs (TaGA2ox8, APO1, TaSus1-7B, and Rht12) that were previously mapped. Eight putative candidate genes were identified for three QTLs that enhance spike seed setting and grain size using gene expression data and were validated in three biparental populations. Protein sequence analysis identified 33 putative wheat orthologs that have high identity with rice genes in QTLs affecting similar traits. Large r 2 values for additive effects observed among the QTLs for most traits indicated that the phenotypes of these identified QTLs were highly predictable. Results from this study demonstrated that significantly increasing GWAS population size and marker density greatly improves detection and identification of candidate genes underlying a QTL, solidifying the foundation for large-scale QTL fine mapping, candidate gene validation, and developing functional markers for genomics-based breeding in wheat.

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Section: Introductionmentioning

confidence: 99%

High-Resolution Genome-wide Association Study Identifies Genomic Regions and Candidate Genes for Important Agronomic Traits in Wheat

et al. 2020

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“…The value of this approach in breeding efforts is starting to be more widely recognised. In conjunction with high throughput phenotyping methods 42 , high density, unbiased markers can be leveraged to discover MTAs or to narrow pre-existing QTL intervals to provide more robust markers for global breeding programs 43,44 . Using these methods, we have identified alleles at three pleiotropic MTAs on chromosomes 1B, 2B and 6D that when stacked increase yield by 56.5% and reduce canopy temperature by 1.97 °C/2.37 °C under heat stress conditions when compared to lines containing the three major alleles at these positions (Fig.…”

Section: Discussionmentioning

confidence: 99%

Exotic alleles contribute to heat tolerance in wheat under field conditions

et al. 2023

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Global warming poses a major threat to food security and necessitates the development of crop varieties that are resilient to future climatic instability. By evaluating 149 spring wheat lines in the field under yield potential and heat stressed conditions, we demonstrate how strategic integration of exotic material significantly increases yield under heat stress compared to elite lines, with no significant yield penalty under favourable conditions. Genetic analyses reveal three exotic-derived genetic loci underlying this heat tolerance which together increase yield by over 50% and reduce canopy temperature by approximately 2 °C. We identified an Ae. tauschii introgression underlying the most significant of these associations and extracted the introgressed Ae. tauschii genes, revealing candidates for further dissection. Incorporating these exotic alleles into breeding programmes could serve as a pre-emptive strategy to produce high yielding wheat cultivars that are resilient to the effects of future climatic uncertainty.

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“…The value of de novo SNP discovery through sequencing in breeding efforts is starting to be more widely recognised. In conjunction with high throughput phenotyping methods (36), high density, unbiased markers can be leveraged to discover novel MTAs or to narrow pre-existing QTL intervals to provide more robust markers for global breeding programs (37, 38). Using these methods, we have identified three pleiotropic markers on chromosomes 1B, 2B and 6D that when stacked increase yield by 56.5% and reduce canopy temperature by 1.97°C/2.37°C under heat stress conditions when compared to lines containing the three major alleles at these positions ( Fig.…”

Section: Discussionmentioning

confidence: 99%

Exotic alleles contribute to heat tolerance in wheat under field conditions

Molero

Coombes

Joynson

et al. 2022

Preprint

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Global warming is one of the most significant threats to food security. With temperatures predicted to rise and extreme weather events becoming more common we must safeguard food production by developing crop varieties that are more tolerant to heat stress without compromising yield under favourable conditions. By evaluating 149 spring wheat lines in the field under yield potential and heat stressed conditions, we demonstrate how strategic integration of exotic material significantly increases yield under heat stress compared to elite lines, with no significant yield penalty under favourable conditions. Genome-wide association analysis revealed three marker trait associations, which together increase yield under heat stress by over 50% compared to lines without the advantageous alleles and was associated with approximately 2°C lower canopy temperature. We identified an Aegilops tauschii introgression underlying the most significant of these associations. By comparing overlapping recombination of this introgressed segment between lines, we identified a 1.49Mbp region of the introgression responsible for this association that increases yield under heat stress by 32.4%. The genes within this region were extracted from diverse Ae. tauschii genomes, revealing a novel Ae. tauschii MAPK gene, a SOC1 orthologue and a pair of type-B two-component response regulators. Incorporating these exotic alleles into breeding programmes could serve as a pre-emptive strategy to produce high yielding wheat cultivars that are resilient to the effects of future climate uncertainty with no yield penalty under favourable conditions.

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Next-Generation Sequencing Enabled Genetics in Hexaploid Wheat

Cited by 5 publications

References 44 publications

High-Resolution Genome-wide Association Study Identifies Genomic Regions and Candidate Genes for Important Agronomic Traits in Wheat

High-Resolution Genome-wide Association Study Identifies Genomic Regions and Candidate Genes for Important Agronomic Traits in Wheat

Exotic alleles contribute to heat tolerance in wheat under field conditions

Exotic alleles contribute to heat tolerance in wheat under field conditions

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