Wheat Landrace Genome Diversity

Wingen, Luzie U.; West, Claire; Leverington-Waite, Michelle; Collier, Sarah; Orford, Simon; Goram, Richard; Yang, Caiyun; King, Julie; Allen, Alexandra M.; Burridge, Amanda J.; Edwards, Keith J.; Griffiths, Simon

doi:10.1534/genetics.116.194688

Cited by 78 publications

(77 citation statements)

References 62 publications

(86 reference statements)

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“…Here, we developed a spring wheat NAM population and used it to dissect the genetic architecture of recombination rate variation, and to study the relationship between recombination, genetic variation, and deleterious SNPs in an allopolyploid crop with a large, highly repetitive genome. This NAM population further expands the number of multi‐parent mapping populations available to the wheat community for studying the genetic architecture of complex traits (Cavanagh et al ., ; Bajgain et al ., ; Gardner et al ., ; Wingen et al ., ).…”

Section: Discussionmentioning

confidence: 99%

“…While these findings hold great promise for plant breeding, their practical applications are hindered by the limited understanding of the genetics of recombination rate control in specific crops that may differ in genomic organization, genome size, or ploidy level from those of the model species (Mercier et al ., ). For example, some of the most important agricultural crops, like wheat, maize, or barley contain large regions of the genome comprised of transposable elements, preferentially located in the pericentromeric regions, in which recombination is severely suppressed (Akhunov et al ., ; Saintenac et al ., ; Choulet et al ., ; Wingen et al ., ). Due to the reduced efficiency of background selection, these genomes were shown to be enriched for SNPs with possible deleterious effects (Mezmouk and Ross‐Ibarra, ; Liu et al ., ).…”

Section: Introductionmentioning

confidence: 99%

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The genetic architecture of genome‐wide recombination rate variation in allopolyploid wheat revealed by nested association mapping

et al. 2018

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SummaryRecombination affects the fate of alleles in populations by imposing constraints on the reshuffling of genetic information. Understanding the genetic basis of these constraints is critical for manipulating the recombination process to improve the resolution of genetic mapping, and reducing the negative effects of linkage drag and deleterious genetic load in breeding. Using sequence‐based genotyping of a wheat nested association mapping (NAM) population of 2,100 recombinant inbred lines created by crossing 29 diverse lines, we mapped QTL affecting the distribution and frequency of 102 000 crossovers (CO). Genome‐wide recombination rate variation was mostly defined by rare alleles with small effects together explaining up to 48.6% of variation. Most QTL were additive and showed predominantly trans‐acting effects. The QTL affecting the proximal COs also acted additively without increasing the frequency of distal COs. We showed that the regions with decreased recombination carry more single nucleotide polymorphisms (SNPs) with possible deleterious effects than the regions with a high recombination rate. Therefore, our study offers insights into the genetic basis of recombination rate variation in wheat and its effect on the distribution of deleterious SNPs across the genome. The identified trans‐acting additive QTL can be utilized to manipulate CO frequency and distribution in the large polyploid wheat genome opening the possibility to improve the efficiency of gene pyramiding and reducing the deleterious genetic load in the low‐recombining pericentromeric regions of chromosomes.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The genetic architecture of genome‐wide recombination rate variation in allopolyploid wheat revealed by nested association mapping

et al. 2018

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“…In this manner, rather than phenotyping a large diversity collection for many traits, the phenotypic value of different haplotype blocks across a specific interval could be examined in further detail. The Watkins nested association mapping populations offer a valuable resource to this effect as the landrace haplotypes can be directly evaluated within available mapping populations (Wingen et al ., ). As breeding programs increasingly look to combine genotypic and phenotypic data, the availability of haplotype data for wild relatives, landrace collections and elite wheat cultivars with their associated phenotypic value has the potential to shape the way in which breeding programs are structured.…”

Section: Moving From Snps To Haplotypes In Breedingmentioning

confidence: 97%

Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat

2018

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Summary Improving traits in wheat has historically been challenging due to its large and polyploid genome, limited genetic diversity and in‐field phenotyping constraints. However, within recent years many of these barriers have been lowered. The availability of a chromosome‐level assembly of the wheat genome now facilitates a step‐change in wheat genetics and provides a common platform for resources, including variation data, gene expression data and genetic markers. The development of sequenced mutant populations and gene‐editing techniques now enables the rapid assessment of gene function in wheat directly. The ability to alter gene function in a targeted manner will unmask the effects of homoeolog redundancy and allow the hidden potential of this polyploid genome to be discovered. New techniques to identify and exploit the genetic diversity within wheat wild relatives now enable wheat breeders to take advantage of these additional sources of variation to address challenges facing food production. Finally, advances in phenomics have unlocked rapid screening of populations for many traits of interest both in greenhouses and in the field. Looking forwards, integrating diverse data types, including genomic, epigenetic and phenomics data, will take advantage of big data approaches including machine learning to understand trait biology in wheat in unprecedented detail.

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“…Recent genetic studies have shown the potential for these wild species to provide useful genetic variation for grain weight that could possibly have been excluded from the gene pool during domestication (Golan et al ; Arora et al ; Avni et al ). The genome sequences and other genomic resources now available for many of these progenitor species and landraces will aid the identification of these novel genes and alleles (Avni et al ; Luo et al ; Wingen et al ).…”

Section: Interactionsmentioning

confidence: 99%

A reductionist approach to dissecting grain weight and yield in wheat

Brinton

Uauy

2019

JIPB

122

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Grain yield is a highly polygenic trait that is influenced by the environment and integrates events throughout the life cycle of a plant. In wheat, the major grain yield components often present compensatory effects among them, which alongside the polyploid nature of wheat, makes their genetic and physiological study challenging. We propose a reductionist and systematic approach as an initial step to understand the gene networks regulating each individual yield component. Here, we focus on grain weight and discuss the importance of examining individual sub‐components, not only to help in their genetic dissection, but also to inform our mechanistic understanding of how they interrelate. This knowledge should allow the development of novel combinations, across homoeologs and between complementary modes of action, thereby advancing towards a more integrated strategy for yield improvement. We argue that this will break barriers in terms of phenotypic variation, enhance our understanding of the physiology of yield, and potentially deliver improved on‐farm yield.

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Wheat Landrace Genome Diversity

Abstract: Understanding the genomic complexity of bread wheat is important for unraveling domestication processes, environmental adaptation, and for future of...

Cited by 78 publications

References 62 publications

The genetic architecture of genome‐wide recombination rate variation in allopolyploid wheat revealed by nested association mapping

The genetic architecture of genome‐wide recombination rate variation in allopolyploid wheat revealed by nested association mapping

Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat

A reductionist approach to dissecting grain weight and yield in wheat

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