WGVD: an integrated web-database for wheat genome variation and selective signatures

Abstract Bread wheat is one of the most important crops worldwide. With the release of the complete wheat reference genome and the development of next-generation sequencing technology, a mass of genomic data from bread wheat and its progenitors has been yield and has provided genomic resources for wheat genetics research. To conveniently and effectively access and use these data, we established Wheat Genome Variation Database, an integrated web-database including genomic variations from whole-genome resequencing and exome-capture data for bread wheat and its progenitors, as well as selective signatures during the process of wheat domestication and improvement. In this version, WGVD contains 7 346 814 single nucleotide polymorphisms (SNPs) and 1 044 400 indels focusing on genic regions and upstream or downstream regions. We provide allele frequency distribution patterns of these variations for 5 ploidy wheat groups or 17 worldwide bread wheat groups, the annotation of the variant types and the genotypes of all individuals for 2 versions of bread wheat reference genome (IWGSC RefSeq v1.0 and IWGSC RefSeq v2.0). Selective footprints for Aegilops tauschii, wild emmer, domesticated emmer, bread wheat landrace and bread wheat variety are evaluated with two statistical tests (FST and Pi) based on SNPs from whole-genome resequencing data. In addition, we provide the Genome Browser to visualize the genomic variations, the selective footprints, the genotype patterns and the read coverage depth, and the alignment tool Blast to search the homologous regions between sequences. All of these features of WGVD will promote wheat functional studies and wheat breeding. Database URL http://animal.nwsuaf.edu.cn/code/index.php/Wheat

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The fate of deleterious variants in a barley genomic prediction population

10.1101/442020 ◽

2018 ◽

Cited By ~ 2

Author(s):

TJY Kono ◽

C Liu ◽

EE Vonderharr ◽

D Koenig ◽

JC Fay ◽

...

Keyword(s):

Genomic Prediction ◽

Genetic Variants ◽

Recombination Rate ◽

Exome Capture ◽

Whole Genome ◽

Genome Resequencing ◽

Initial Frequency ◽

A Genome ◽

Hordeum Murinum ◽

Whole Genome Resequencing

AbstractTargeted identification and purging of deleterious genetic variants has been proposed as a novel approach to animal and plant breeding. This strategy is motivated, in part, by the observation that demographic events and strong selection associated with cultivated species pose a “cost of domestication.” This includes an increase in the proportion of genetic variants where a mutation is likely to reduce fitness. Recent advances in DNA resequencing and sequence constraint-based approaches to predict the functional impact of a mutation permit the identification of putatively deleterious SNPs (dSNPs) on a genome-wide scale. Using exome capture resequencing of 21 barley 6-row spring breeding lines, we identify 3,855 dSNPs among 497,754 total SNPs. In order to polarize SNPs as ancestral versus derived, we generated whole genome resequencing data of Hordeum murinum ssp. glaucum as a phylogenetic outgroup. The dSNPs occur at higher density in portions of the genome with a higher recombination rate than in pericentromeric regions with lower recombination rate and gene density. Using 5,215 progeny from a genomic prediction experiment, we examine the fate of dSNPs over three breeding cycles. Average derived allele frequency is lower for dSNPs than any other class of variants. Adjusting for initial frequency, derived alleles at dSNPs reduce in frequency or are lost more often than other classes of SNPs. The highest yielding lines in the experiment, as chosen by standard genomic prediction approaches, carry fewer homozygous dSNPs than randomly sampled lines from the same progeny cycle. In the final cycle of the experiment, progeny selected by genomic prediction have a mean of 5.6% fewer homozygous dSNPs relative to randomly chosen progeny from the same cycle.Author SummaryThe nature of genetic variants underlying complex trait variation has been the source of debate in evolutionary biology. Here, we provide evidence that agronomically important phenotypes are influenced by rare, putatively deleterious variants. We use exome capture resequencing and a hypothesis-based test for codon conservation to predict deleterious SNPs (dSNPS) in the parents of a multi-parent barley breeding population. We also generated whole-genome resequencing data of Hordeum murinum, a phylogenetic outgroup to barley, to polarize dSNPs by ancestral versus derived state. dSNPs occur disproportionately in the gene-rich chromosome arms, rather than in the recombination-poor pericentromeric regions. They also decrease in frequency more often than other variants at the same initial frequency during recurrent selection for grain yield and disease resistance. Finally, we identify a region on chromosome 4H that strongly associated with agronomic phenotypes in which dSNPs appear to be hitchhiking with favorable variants. Our results show that targeted identification and removal of dSNPs from breeding programs is a viable strategy for crop improvement, and that standard genomic prediction approaches may already contain some information about unobserved segregating dSNPs.

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Rice Chloroplast Genome Variation Architecture and Phylogenetic Dissection in Diverse Oryza Species Assessed by Whole-Genome Resequencing

Rice ◽

10.1186/s12284-016-0129-y ◽

2016 ◽

Vol 9 (1) ◽

Cited By ~ 26

Author(s):

Wei Tong ◽

Tae-Sung Kim ◽

Yong-Jin Park

Keyword(s):

Chloroplast Genome ◽

Oryza Species ◽

Whole Genome ◽

Genome Resequencing ◽

Genome Variation ◽

Whole Genome Resequencing

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Discovery of genomic variations by whole-genome resequencing of the North American Araucana chicken

PLoS ONE ◽

10.1371/journal.pone.0225834 ◽

2019 ◽

Vol 14 (12) ◽

pp. e0225834

Author(s):

Rooksana E. Noorai ◽

Vijay Shankar ◽

Nowlan H. Freese ◽

Christopher M. Gregorski ◽

Susan C. Chapman

Keyword(s):

North American ◽

Whole Genome ◽

Genome Resequencing ◽

Genomic Variations ◽

The North ◽

Whole Genome Resequencing

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Seeing the Forest through the (Phylogenetic) Trees: Functional Characterisation of Grapevine Terpene Synthase (VviTPS) Paralogues and Orthologues

Plants ◽

10.3390/plants10081520 ◽

2021 ◽

Vol 10 (8) ◽

pp. 1520

Author(s):

Samuel J. Smit ◽

Melané A. Vivier ◽

Philip R. Young

Keyword(s):

Phylogenetic Trees ◽

Reference Genome ◽

Gene Isolation ◽

Terpene Synthase ◽

Sequence Information ◽

Whole Genome ◽

Genome Resequencing ◽

Volatile Analysis ◽

Functional Characterisation ◽

Whole Genome Resequencing

Gene families involved in specialised metabolism play a key role in a myriad of ecophysiological and biochemical functions. The Vitis vinifera sesquiterpene synthases represent the largest subfamily of grapevine terpene synthase (VviTPS) genes and are important volatile metabolites for wine flavour and aroma, as well as ecophysiological interactions. The functional characterisation of VviTPS genes is complicated by a reliance on a single reference genome that greatly underrepresents this large gene family, exacerbated by extensive duplications and paralogy. The recent release of multiple phased diploid grapevine genomes, as well as extensive whole-genome resequencing efforts, provide a wealth of new sequence information that can be utilised to overcome the limitations of the reference genome. A large cluster of sesquiterpene synthases, localised to chromosome 18, was explored by means of comparative sequence analyses using the publicly available grapevine reference genome, three PacBio phased diploid genomes and whole-genome resequencing data from multiple genotypes. Two genes, VviTPS04 and -10, were identified as putative paralogues and/or allelic variants. Subsequent gene isolation from multiple grapevine genotypes and characterisation by means of a heterologous in planta expression and volatile analysis resulted in the identification of genotype-specific structural variations and polymorphisms that impact the gene function. These results present novel insight into how grapevine domestication likely shaped the VviTPS landscape to result in genotype-specific functions.

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Genome-wide variations analysis of special waxy sorghum cultivar Hongyingzi for brewing Moutai liquor

10.1101/810580 ◽

2019 ◽

Author(s):

Can Wang ◽

Lingbo Zhou ◽

Xu Gao ◽

Yanqing Ding ◽

Bin Cheng ◽

...

Keyword(s):

Chalcone Synthase ◽

Reference Genome ◽

Copy Number Variations ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Structural Variations ◽

Genome Resequencing ◽

Single Nucleotide ◽

Genome Wide ◽

Whole Genome Resequencing

AbstractsHongyingzi is a special waxy sorghum (Sorghum bicolor L. Moench) cultivar for brewing Moutai liquor. For an overall understanding of the whole genome of Hongyingzi, we performed whole-genome resequencing technology with 56.10 X depth to reveal its comprehensive variations. Compared with the BTx623 reference genome, 2.48% of genome sequences were altered in the Hongyingzi genome. Among these alterations, there were 1885774 single nucleotide polymorphisms (SNPs), 309381 small fragments insertions and deletions (Indels), 31966 structural variations (SVs), and 217273 copy number variations (CNVs). These alterations conferred 29614 genes variations. It was also predicted that 35 genes variations were related to the multidrug and toxic efflux (MATE) transporter, chalcone synthase (CHS), ATPase isoform 10 (AHA10) transporter, dihydroflavonol-4-reductase (DFR), the laccase 15 (LAC15), flavonol 3′-hydroxylase (F3′H), flavanone 3-hydroxylase (F3H), O-methyltransferase (OMT), flavonoid 3′5′ hydroxylase (F3′5′H), UDP-glucose:sterol-glucosyltransferase (SGT), flavonol synthase (FLS), and chalcone isomerase (CHI) involved in the tannin synthesis. These results would provide theoretical supports for the molecular markers developments and gene function studies related to the liquor-making traits, and the genetic improvement of waxy sorghum based on the genome editing technology.

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Genetic diversity and population structure of Tibetan sheep breeds determined by whole genome resequencing

Tropical Animal Health and Production ◽

10.1007/s11250-021-02605-6 ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Lei-Lei Li ◽

Shi-Ke Ma ◽

Wei Peng ◽

You-Gui Fang ◽

Hai-Rui Duo ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Whole Genome ◽

Genome Resequencing ◽

Sheep Breeds ◽

Tibetan Sheep ◽

Whole Genome Resequencing

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Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)

Scientific Reports ◽

10.1038/s41598-021-87445-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Luciano Calderón ◽

Nuria Mauri ◽

Claudio Muñoz ◽

Pablo Carbonell-Bejerano ◽

Laura Bree ◽

...

Keyword(s):

Genetic Diversity ◽

Somatic Mutations ◽

Clonal Propagation ◽

Variant Calling ◽

Vitis Vinifera L ◽

Whole Genome ◽

Single Nucleotide Variants ◽

Genome Resequencing ◽

Diversity Pattern ◽

Whole Genome Resequencing

AbstractGrapevine cultivars are clonally propagated to preserve their varietal attributes. However, genetic variations accumulate due to the occurrence of somatic mutations. This process is anthropically influenced through plant transportation, clonal propagation and selection. Malbec is a cultivar that is well-appreciated for the elaboration of red wine. It originated in Southwestern France and was introduced in Argentina during the 1850s. In order to study the clonal genetic diversity of Malbec grapevines, we generated whole-genome resequencing data for four accessions with different clonal propagation records. A stringent variant calling procedure was established to identify reliable polymorphisms among the analyzed accessions. The latter procedure retrieved 941 single nucleotide variants (SNVs). A reduced set of the detected SNVs was corroborated through Sanger sequencing, and employed to custom-design a genotyping experiment. We successfully genotyped 214 Malbec accessions using 41 SNVs, and identified 14 genotypes that clustered in two genetically divergent clonal lineages. These lineages were associated with the time span of clonal propagation of the analyzed accessions in Argentina and Europe. Our results show the usefulness of this approach for the study of the scarce intra-cultivar genetic diversity in grapevines. We also provide evidence on how human actions might have driven the accumulation of different somatic mutations, ultimately shaping the Malbec genetic diversity pattern.

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