A wheat chromosome segment substitution line series supports characterization and use of progenitor genetic variation

Horsnell, Richard; Leigh, Fiona; Wright, Tally I.C.; Burridge, Amanda J.; Ligeza, Aleksander; Przewieslik-Allen, Alexandra M.; Howell, Phil; Uauy, Cristóbal; Edwards, Keith J.; Bentley, Alison R.

doi:10.1002/tpg2.20288

Cited by 8 publications

(4 citation statements)

References 107 publications

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“…Introgression lines, established through several generations of crossing and/or backcrossing with the aid of marker‐assisted selection, serve as a stable genetic resource. Horsnell et al (2023) detailed the development of chromosome segment substitution lines in spring wheat, aiming to comprehensively capture genetic variation from tetraploid ( Triticum turgidum ssp. dicoccoides ) and diploid ( Aegilops tauschii ) progenitor species.…”

Section: Genetic Diversity and Stress Tolerancementioning

confidence: 99%

Exploring the genomics of abiotic stress tolerance and crop resilience to climate change

Varshney,

Barmukh,

Bentley

et al. 2024

The Plant Genome

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Abiotic stresses have a detrimental impact on crop production globally. The escalating frequency and intensity of these stresses, driven by rapid changes in climatic conditions, pose significant challenges to agriculture. This situation is worsened by the burgeoning human population that is projected to heighten the demand for food in the coming years, emphasizing the need for further agricultural innovations. Addressing these challenges and steering agriculture toward sustainability requires concerted research efforts to mitigate the adverse effects of climate change-induced abiotic stresses. One of the most logical and cost-effective strategies on a global scale is the development and utilization of crop varieties endowed with increased tolerance to different abiotic stresses.Conventional breeding has played a key role in developing crops resilient to abiotic stress; however, recent advancements in genomics technologies have expedited these efforts. The development and public availability of multiple crop genomes, coupled with improvements in genome assembly quality and the emergence of pangenome and super-pangenome, signify a substantial leap forward. Highquality reference genomes, whole-genome resequencing, and pangenome approaches have enabled the mapping of allelic variants, discovery of candidate genes, development of molecular markers, and the introgression of traits related to abiotic stress tolerance. This wealth of genomic data, complemented by other omics datasets such as transcriptomics, proteomics, metabolomics, and phenomics, has effectively bridged the genotype-phenotype gap (Varshney, Bohra et al., 2021). This integration is crucial for gene mapping and marker-assistedThis is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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Section: Genetic Diversity and Stress Tolerancementioning

confidence: 99%

Exploring the genomics of abiotic stress tolerance and crop resilience to climate change

Varshney,

Barmukh,

Bentley

et al. 2024

The Plant Genome

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“…The bread wheat genome already contains significant genetic variation, and much work is being done to enhance the germplasm with novel alleles from wide crosses. The previous 35k Breeders array had previously been used with wheat wild relative material in a pre-breeding context (Horsnell et al, 2023;Kumar et al, 2020;Wright et al, 2023) and for elite durum wheat cultivars (Ganugi et al, 2021;Kabbaj et al, 2017;Shewry et al, 2023). The genotype calls generated on the TaNG v1.1 array across a diverse set of wheat relative material here (Data S4) illustrate that secondary and tertiary gene pool material may also be genotyped alongside T. aestivum accessions.…”

Section: Supporting Genotype and Marker Datamentioning

confidence: 99%

Development of a next generation SNP genotyping array for wheat

Burridge,

Winfield,

Przewieslik‐Allen

et al. 2024

Plant Biotechnology Journal

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SummaryHigh‐throughput genotyping arrays have provided a cost‐effective, reliable and interoperable system for genotyping hexaploid wheat and its relatives. Existing, highly cited arrays including our 35K Wheat Breeder's array and the Illumina 90K array were designed based on a limited amount of varietal sequence diversity and with imperfect knowledge of SNP positions. Recent progress in wheat sequencing has given us access to a vast pool of SNP diversity, whilst technological improvements have allowed us to fit significantly more probes onto a 384‐well format Axiom array than previously possible. Here we describe a novel Axiom genotyping array, the ‘Triticum aestivum Next Generation’ array (TaNG), largely derived from whole genome skim sequencing of 204 elite wheat lines and 111 wheat landraces taken from the Watkins ‘Core Collection’. We used a novel haplotype optimization approach to select SNPs with the highest combined varietal discrimination and a design iteration step to test and replace SNPs which failed to convert to reliable markers. The final design with 43 372 SNPs contains a combination of haplotype‐optimized novel SNPs and legacy cross‐platform markers. We show that this design has an improved distribution of SNPs compared to previous arrays and can be used to generate genetic maps with a significantly higher number of distinct bins than our previous array. We also demonstrate the improved performance of TaNGv1.1 for Genome‐wide association studies (GWAS) and its utility for Copy Number Variation (CNV) analysis. The array is commercially available with supporting marker annotations and initial genotyping results freely available.

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“…This can be overcome by back-crossing into adapted and elite wheat backgrounds. Furthermore, back-crossing can be targeted such that introgressions from SHW are transferred into speci c genomic regions of elite wheat cultivars (Horsnell et al, 2023). Here, we report the creation of a large winter wheat NAM resource, called the NIAB_WW_SHW_NAM population.…”

Section: Introductionmentioning

confidence: 99%

“…Further investigation is needed into the underlying, and potentially, useful novel haplotypes at the QTLs and major gene loci that have been mapped here. Introgression libraries, such as chromosome segment substitution lines (CSSLs;Horsnell et al, 2023), that incorporate speci c introgressions from Ae. tauschii accessions across the bread wheat genome, could subsequently be used to better understand the function of these potentially novel haplotypes.…”

mentioning

confidence: 99%

A new winter wheat genetic resource harbours untapped diversity from synthetic hexaploid wheat.

Wright,

Horsnell,

Love

et al. 2023

Preprint

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The allelic richness harboured in progenitors of hexaploid bread wheat (Triticum aestivum L.) is a useful resource for addressing the genetic diversity bottleneck in modern cultivars. Synthetic Hexaploid Wheat (SHW) is created through resynthesis of the hybridisation events between the tetraploid (Triticum turgidum subsp. durum) and diploid (Aegilops tauschii) bread wheat progenitors. We developed a large and diverse winter wheat Nested Association Mapping (NAM) population (termed the NIAB_WW_SHW_NAM) consisting of 3241 genotypes derived from 54 nested back-cross 1 (BC1) populations, each formed via back-crossing a different primary SHW into the UK winter wheat cultivar ‘Robigus’. The primary SHW accessions were created using 15 T. durum donors and 47 Ae. tauschii accessions that spanned the lineages and geographical range of the species. Primary SHW parents were typically earlier flowering, taller and showed better resistance to yellow rust infection (Yr) than ‘Robigus’. The NIAB_WW_SHW_NAM population was genotyped using a single nucleotide polymorphism (SNP) array and 27 Quantitative Trait Loci (QTLs) were detected for flowering time, plant height and Yr resistance. Across multiple field trials, a QTL for Yr resistance was found on chromosome 4D that corresponded to the Yr28 resistance gene previously reported in other SHW accessions. These findings highlight the value of the NIAB_WW_SHW_NAM population for genetic mapping and provide the first evidence of Yr28 working in current UK environments and genetic backgrounds. These examples, coupled with the evidence of commercial wheat breeders selecting promising genotypes, highlights the potential value of the NIAB_WW_SHW_NAM to variety improvement.

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A wheat chromosome segment substitution line series supports characterization and use of progenitor genetic variation

Cited by 8 publications

References 107 publications

Exploring the genomics of abiotic stress tolerance and crop resilience to climate change

Exploring the genomics of abiotic stress tolerance and crop resilience to climate change

Development of a next generation SNP genotyping array for wheat

A new winter wheat genetic resource harbours untapped diversity from synthetic hexaploid wheat.

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