Conversion of array-based single nucleotide polymorphic markers for use in targeted genotyping by sequencing in hexaploid wheat (<i>Triticum aestivum</i>)

Burridge, Amanda J.; Wilkinson, Paul; Winfield, Mark O.; Barker, Gary L A; Allen, Alexandra M.; Coghill, Jane A.; Waterfall, Christy; Edwards, Keith J.

doi:10.1111/pbi.12834

Cited by 22 publications

(52 citation statements)

References 36 publications

(52 reference statements)

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“…We could directly associate on average 95.7% of our previously defined GCs with GC events in the sequencing data that were on average 29,992,400 bp in length with 61.2% of events < 20 Mbp (Table 1). Furthermore, on average, we could validate 83.0% of the specific array SNP alleles that were used to define GCs and given the reported agreement rates of 85.7% for SNP arrays when compared to sequencing data by Burridge et al [5]; this is in line with expectations. Using the array, the reason for our ability to identify GCs in low-resolution genotyping data is that we typically detect the larger GC events whereas whole genome sequencing gives the ability to robustly detect shorter GC events across the genome.…”

Section: Resultssupporting

confidence: 85%

Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency

et al. 2019

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Background Sequence exchange between homologous chromosomes through crossing over and gene conversion is highly conserved among eukaryotes, contributing to genome stability and genetic diversity. A lack of recombination limits breeding efforts in crops; therefore, increasing recombination rates can reduce linkage drag and generate new genetic combinations. Results We use computational analysis of 13 recombinant inbred mapping populations to assess crossover and gene conversion frequency in the hexaploid genome of wheat ( Triticum aestivum ). We observe that high-frequency crossover sites are shared between populations and that closely related parents lead to populations with more similar crossover patterns. We demonstrate that gene conversion is more prevalent and covers more of the genome in wheat than in other plants, making it a critical process in the generation of new haplotypes, particularly in centromeric regions where crossovers are rare. We identify quantitative trait loci for altered gene conversion and crossover frequency and confirm functionality for a novel RecQ helicase gene that belongs to an ancient clade that is missing in some plant lineages including Arabidopsis. Conclusions This is the first gene to be demonstrated to be involved in gene conversion in wheat. Harnessing the RecQ helicase has the potential to break linkage drag utilizing widespread gene conversions. Electronic supplementary material The online version of this article (10.1186/s13059-019-1675-6) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 85%

Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency

et al. 2019

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“…We could directly associate on average 95.7% of our previously defined GCs with GC events in the sequencing data that were on average 29,992,400bp in length with 61.2% of events <20Mbp ( Table 2). Furthermore on average we could validate 83.0% of the specific array SNP alleles that were used to define GCs and given the reported agreement rates of 85.7% for SNP arrays when compared to sequencing data by Burridge et al (2017), this is in line with expectations. Using the array, the reason for our ability to identify GCs in low-resolution genotyping data is that we typically detect the larger GC events whereas whole genome sequencing gives the ability to robustly detect shorter GC events across the genome.…”

Section: Using Whole Genome Sequencing To Validate Our Array Based Cosupporting

confidence: 80%

Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency

Gardiner

Wingen

Bailey

et al. 2019

Preprint

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Sequence exchange between homologous chromosomes through crossing over and gene conversion is highly conserved among eukaryotes, contributing to genome stability and genetic diversity. Lack of recombination limits breeding efforts in crops, therefore increasing recombination rates can reduce linkage-drag and generate new genetic combinations. We use computational analysis of 13 recombinant inbred mapping populations to assess crossover and gene conversion frequency in the hexaploid genome of wheat (Triticum aestivum). We observe that high frequency crossover sites are shared between populations and that closely related parental founders lead to populations with more similar crossover patterns. We demonstrate that gene conversion is more prevalent and covers more of the genome in wheat than in other plants, making it a critical process in the generation of new haplotypes, particularly in centromeric regions where crossovers are rare. We have identified QTL for altered gene conversion and crossover frequency and confirm functionality for a novel RecQ helicase gene that belongs to an ancient clade that is missing in some plant lineages including Arabidopsis. This is the first gene to be demonstrated to be involved in gene conversion in wheat. Harnessing the RecQ helicase has the potential to break linkage-drag utilizing widespread gene conversions. Main Text:There is an evolutionary requirement for genetic diversity across a species. Shuffling of material between homologous chromosomes, or genetic recombination, breaks linkage between genes resulting in offspring that have combinations of alleles that differ from those found in either of the parents. During meiosis, double-strand breaks (DSBs) can generate sequence variation in gametes via the DSB repair model (Szostak et al., 1983). DSBs are resolved either by homologous recombination as crossovers (COs) i.e. the reciprocal exchange of large regions between chromosomes, or otherwise as non-crossovers (NCOs). A minimum of one CO per chromosome during meiosis is a requirement for proper chromosome segregation (Pardo-Manuel De Villena and Sapienza, 2001). When both COs and NCOs are resolved, they can also give rise to gene conversions (GCs) as a mechanism of DSB repair involving the non-reciprocal transfer of short DNA segments between homologous non-sister chromatids (Sun et al., 2012;Halldorsson et al., 2016). GCs can be

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“…Leaf tissue was harvested 4 weeks after germination, frozen in liquid nitrogen and stored at −20°C prior to nucleic acid extraction. Genomic DNA was prepared using a phenol–chloroform extraction method (Burridge et al, 2017), treated with RNase-A (QIAGEN Ltd., Manchester, UK) according to the manufacturer's instructions and purified using the QiaQuick PCR purification kit (QIAGEN Ltd).…”

Section: Methodsmentioning

confidence: 99%

Developing a High-Throughput SNP-Based Marker System to Facilitate the Introgression of Traits From Aegilops Species Into Bread Wheat (Triticum aestivum)

Przewieslik-Allen¹,

Burridge²,

Wilkinson³

et al. 2019

Front. Plant Sci.

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The genus Aegilops contains a diverse collection of wild species exhibiting variation in geographical distribution, ecological adaptation, ploidy and genome organization. Aegilops is the most closely related genus to Triticum which includes cultivated wheat, a globally important crop that has a limited gene pool for modern breeding. Aegilops species are a potential future resource for wheat breeding for traits, such as adaptation to different ecological conditions and pest and disease resistance. This study describes the development and application of the first high-throughput genotyping platform specifically designed for screening wheat relative species. The platform was used to screen multiple accessions representing all species in the genus Aegilops. Firstly, the data was demonstrated to be useful for screening diversity and examining relationships within and between Aegilops species. Secondly, markers able to characterize and track introgressions from Aegilops species in hexaploid wheat were identified and validated using two different approaches.

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Conversion of array-based single nucleotide polymorphic markers for use in targeted genotyping by sequencing in hexaploid wheat (Triticum aestivum)

Cited by 22 publications

References 36 publications

Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency

Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency

Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency

Developing a High-Throughput SNP-Based Marker System to Facilitate the Introgression of Traits From Aegilops Species Into Bread Wheat (Triticum aestivum)

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