High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus

Bayer, Philipp E.; Ruperao, Pradeep; Mason, Annaliese S.; Stiller, Jiri; Chan, Chon‐Kit Kenneth; Hayashi, Satomi; Long, Yan; Meng, Jinling; Sutton, Tim; Visendi, Paul; Varshney, Rajeev K.; Batley, Jacqueline; Edwards, David

doi:10.1007/s00122-015-2488-y

Cited by 69 publications

(51 citation statements)

References 43 publications

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“…Genomic reads from parental individuals are mapped to the reference genome and SNPs are predicted. Reads from the progeny are then mapped to the same reference and comparison with the parental SNP file enables the calling of SNPs in the progeny of one or other of the parental genotypes (Bayer et al, 2015). Associated genetic markers can be causal for the trait of interest or in linkage disequilibrium with a causal locus (Rafalski, 2010).…”

Section: Introductionmentioning

confidence: 99%

“…The aim of the present study was to perform GWAS association mapping using whole genome SkimGBS (Bayer et al, 2015) to identify allelic variation that affects fatty acid composition in progeny seeds from 60 B. napus doubled haploid (DH) lines. This novel approach led to identification of a genomic hotspot of candidate regulatory genes on chromosome A05 of winter type oilseed rape.…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Association Study of Genetic Control of Seed Fatty Acid Biosynthesis in Brassica napus

et al. 2017

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Fatty acids and their composition in seeds determine oil value for nutritional or industrial purposes and also affect seed germination as well as seedling establishment. To better understand the genetic basis of seed fatty acid biosynthesis in oilseed rape (Brassica napus L.) we applied a genome-wide association study, using 91,205 single nucleotide polymorphisms (SNPs) characterized across a mapping population with high-resolution skim genotyping by sequencing (SkimGBS). We identified a cluster of loci on chromosome A05 associated with oleic and linoleic seed fatty acids. The delineated genomic region contained orthologs of the Arabidopsis thaliana genes known to play a role in regulation of seed fatty acid biosynthesis such as Fatty acyl-ACP thioesterase B (FATB) and Fatty Acid Desaturase (FAD5). This approach allowed us to identify potential functional genes regulating fatty acid composition in this important oil producing crop and demonstrates that this approach can be used as a powerful tool for dissecting complex traits for B. napus improvement programs.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Study of Genetic Control of Seed Fatty Acid Biosynthesis in Brassica napus

et al. 2017

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“…This approach works best with biparental populations, where the two parent genotypes can be sequenced with higher read coverage and missing haplotype data imputed in the population based on these parent data. Skim genotyping-bysequencing in B. napus was used to identify the frequency of gene conversion events and homologous recombination in a mapping population (Bayer et al 2015), with a range of future applications including marker discovery, as well as conventional linkage mapping, QTL identification, genome-wide association studies and genomic selection . In particular, genotyping-by-sequencing approaches provide an opportunity for detection and primary characterisation of de novo variation derived from interspecific hybrids.…”

Section: Proximity To Model Plant a Thalianamentioning

confidence: 99%

Oilseed rape: learning about ancient and recent polyploid evolution from a recent crop species

Mason

Snowdon

2016

Plant Biol J

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Oilseed rape (Brassica napus) is one of our youngest crop species, arising several times under cultivation in the last few thousand years and completely unknown in the wild. Oilseed rape originated from hybridisation events between progenitor diploid species B. rapa and B. oleracea, both important vegetable species. The diploid progenitors are also ancient polyploids, with remnants of two previous polyploidisation events evident in the triplicated genome structure. This history of polyploid evolution and human agricultural selection makes B. napus an excellent model with which to investigate processes of genomic evolution and selection in polyploid crops. The ease of de novo interspecific hybridisation, responsiveness to tissue culture, and the close relationship of oilseed rape to the model plant Arabidopsis thaliana, coupled with the recent availability of reference genome sequences and suites of molecular cytogenetic and high-throughput genotyping tools, allow detailed dissection of genetic, genomic and phenotypic interactions in this crop. In this review we discuss the past and present uses of B. napus as a model for polyploid speciation and evolution in crop species, along with current and developing analysis tools and resources. We further outline unanswered questions that may now be tractable to investigation.

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“…A similar number of crossovers and gene conversions were also seen in B. napus (Bayer et al, 2015b). Chromosome wide recombinations on Ca1 before and after filtering were shown in Figure Brassica A and C genomes may have high mis-assemblies than release kabuli reference genome (Bayer et al, 2015b). Compared to kabuli, desi reference genome is of poor quality (Chapter 2) and can be expect to have higher error rate than Brassica species.…”

Section: Gene Predictionsmentioning

confidence: 76%

“…A custom script 'snp_genotyping_all.pl (Bayer et al, 2015a) was used to call genotypes from each individual of population as explained in chapter 3.…”

Section: Validation Of Snps Using Skim Genotyping By Sequencingmentioning

confidence: 99%

Analysis of the Chickpea genome using next generation sequencing data

Ruperao¹

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Chickpea is an annual, self-pollinating, diploid (2n=2x=16) and the second most important food legume crop with major production areas in the Indian sub-continent, West Asia and North Africa. Australia is the largest exporter of chickpea and yield for 2015 has been forecasted at 990,000 tonnes (http://www.agriculture.gov.au/abares/media-releases/2015). The main constraint for increasing yield is the susceptibility of the plant to foliar disease, ascochyta blight, fusarium wilt. Chickpea breeding aims at high yielding cultivars that combine longlasting resistance against both biotic and abiotic stress. Emerging sequencing technologies have enhanced the availability of crop genomic resources. Analysis of huge amounts of genomic data comes with major computational challenges.This thesis describes a new method for assessing the quality of reference genome assembly by flow sorting and isolating chromosomes based on size. This chromosomal DNA was sequenced and mapped to the reference genome assembly.This approach will reduce the genome DNA complexity to a chromosome level and is expect to correspond to only one chromosome assembly. Appling this approach on both released desi and kabuli reference genomes has shown miss-assembly. The desi genome was of poor quality compared to the kabuli genome. To fix these misassemblies, we developed a novel method called skimGBS for rearranging the fragmented sequences. In this approach, genotypes were called from population individuals to construct haplotype blocks. Based on the haplotype block signature, contigs/fragmented sequences were reordered as new assemblies. Using this approach, both desi and kabuli genomes were improved by placing unplaced contig sequences into chromosomes. Furthermore, these improved reference assemblieswere assessed and annotated.This thesis also reports identification of more than 800,000 high quality SNPs by sequencing 69 diverse Australian chickpea accessions. Gene loss, genetic relatedness, population structure and diversity analysis was also performed. The public accessibility of the data and above results provides a valuable resource to support chickpea research.iiThe developed methodology can also apply to other genomics studies, and will therefore be a valuable approach to assist crop improvement and further breeding approaches.iii

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High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus

Cited by 69 publications

References 43 publications

Genome-Wide Association Study of Genetic Control of Seed Fatty Acid Biosynthesis in Brassica napus

Genome-Wide Association Study of Genetic Control of Seed Fatty Acid Biosynthesis in Brassica napus

Oilseed rape: learning about ancient and recent polyploid evolution from a recent crop species

Analysis of the Chickpea genome using next generation sequencing data

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