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

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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Clonal propagation history shapes the intra-cultivar genetic diversity in ‘Malbec’ grapevines

10.1101/2020.10.27.356790 ◽

2020 ◽

Author(s):

Luciano Calderón ◽

Nuria Mauri ◽

Claudio Muñoz ◽

Pablo Carbonell-Bejerano ◽

Laura Bree ◽

...

Keyword(s):

Genetic Diversity ◽

Clonal Propagation ◽

Variant Calling ◽

Red Wines ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Diversity Pattern ◽

History Of ◽

Potential Impact ◽

Whole Genome Resequencing

AbstractGrapevine (Vitis vinifera L.) cultivars are clonally propagated to preserve their varietal attributes. However, novel genetic variation still accumulates due to somatic mutations. Aiming to study the potential impact of clonal propagation history on grapevines intra-cultivar genetic diversity, we have focused on ‘Malbec’. This cultivar is appreciated for red wines elaboration, it was originated in Southwestern France and introduced into Argentina during the 1850s. Here, we generated whole-genome resequencing data for four ‘Malbec’ clones with different historical backgrounds. A stringent variant calling procedure was established to identify reliable clonal polymorphisms, additionally corroborated by Sanger sequencing. This analysis retrieved 941 single nucleotide variants (SNVs), occurring among the analyzed clones. Based on a set of validated SNVs, a genotyping experiment was custom-designed to survey ‘Malbec’ genetic diversity. We successfully genotyped 214 samples and identified 14 different clonal genotypes, that clustered into two genetically divergent groups. Group-Ar was driven by clones with a long history of clonal propagation in Argentina, while Group-Fr was driven by clones that have longer remained in Europe. Findings show the ability of such approaches for clonal genotypes identification in grapevines. In particular, we provide evidence on how human actions may have shaped ‘Malbec’ extant genetic diversity pattern.

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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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164 Single nucleotide variants and indels identified from whole-genome resequencing of Gyr, Girolando, and Holstein cattle breeds

Journal of Animal Science ◽

10.2527/asasann.2017.164 ◽

2017 ◽

Vol 95 (suppl_4) ◽

pp. 80-81

Author(s):

N. B. Stafuzza ◽

A. Zerlotini ◽

F. P. Lobo ◽

M. E. B. Yamagishi ◽

T. C. S. Chud ◽

...

Keyword(s):

Holstein Cattle ◽

Whole Genome ◽

Single Nucleotide Variants ◽

Genome Resequencing ◽

Single Nucleotide ◽

Cattle Breeds ◽

Whole Genome Resequencing

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Variant Calling Using Whole Genome Resequencing and Sequence Capture for Population and Evolutionary Genomic Inferences in Norway Spruce (Picea Abies)

Compendium of Plant Genomes - The Spruce Genome ◽

10.1007/978-3-030-21001-4_2 ◽

2020 ◽

pp. 9-36 ◽

Cited By ~ 1

Author(s):

Carolina Bernhardsson ◽

Xi Wang ◽

Helena Eklöf ◽

Pär K. Ingvarsson

Keyword(s):

Picea Abies ◽

Norway Spruce ◽

Variant Calling ◽

Whole Genome ◽

Genome Resequencing ◽

Sequence Capture ◽

Evolutionary Genomic ◽

Whole Genome Resequencing

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Genetic diversity analysis of Chinese plum (Prunus salicina L.) based on whole-genome resequencing

Tree Genetics & Genomes ◽

10.1007/s11295-021-01506-x ◽

2021 ◽

Vol 17 (3) ◽

Author(s):

Xiao Wei ◽

Fei Shen ◽

Qiuping Zhang ◽

Ning Liu ◽

Yuping Zhang ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Principal Component ◽

Private Allele ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Genome Resequencing ◽

Cultivar Group ◽

Prunus Salicina ◽

Whole Genome Resequencing

AbstractChinese plum (Prunus salicina L.), also known as Japanese plum, is gaining importance because of its extensive genetic diversity and nutritional attributes that are beneficial for human health. Single-nucleotide polymorphisms (SNPs) are the most abundant form of genomic polymorphisms and are widely used in population genetics research. In this study, we constructed high-quality SNPs through whole-genome resequencing of 67 Prunus accessions with a depth of ~20× to evaluate the genome-level diversity and population structure. Phylogenetic analysis, principal component analysis, and population structure profiling indicated that the 67 plum accessions could be classified into four groups corresponding to their origin location, the southern cultivar group (SCG), the northern cultivar group (NCG), the foreign cultivar group (FG), and the mixed cultivar group (MG). Some cultivars from South China clustered with the other three groups. The genetic diversity indices including private allele number, observed heterozygosity, expected heterozygosity, and the nucleotide diversity of the SCG were higher than those of the NCG. Gene flow from the SCG to FG was also detected. Based on the distribution of wild resources, we concluded that the domestication center of origin of the Chinese plum was southwestern China. This study also provided genetic variation features and the population structure of Chinese plum cultivars, laying a foundation for breeders to use diverse germplasm and allelic variants to improve Chinese plum varieties.

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Genetic diversity and natural selection in wild fruit flies revealed by whole-genome resequencing

Genomics ◽

10.1016/j.ygeno.2017.12.002 ◽

2018 ◽

Vol 110 (5) ◽

pp. 304-309 ◽

Cited By ~ 1

Author(s):

Ting Lian ◽

Diyan Li ◽

Xinxin Tan ◽

Tiandong Che ◽

Zhongxian Xu ◽

...

Keyword(s):

Genetic Diversity ◽

Natural Selection ◽

Fruit Flies ◽

Whole Genome ◽

Genome Resequencing ◽

Wild Fruit ◽

Whole Genome Resequencing

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Revealing Distinctions in Genetic Diversity and Adaptive Evolution Between Two Varieties of Camellia sinensis by Whole-Genome Resequencing

Frontiers in Plant Science ◽

10.3389/fpls.2020.603819 ◽

2020 ◽

Vol 11 ◽

Author(s):

Yanlin An ◽

Xiaozeng Mi ◽

Shiqi Zhao ◽

Rui Guo ◽

Xiaobo Xia ◽

...

Keyword(s):

Genetic Diversity ◽

Adaptive Evolution ◽

Camellia Sinensis ◽

Balancing Selection ◽

Genetic Research ◽

Whole Genome ◽

Genome Resequencing ◽

Synonymous Mutations ◽

Indel Markers ◽

Whole Genome Resequencing

Camellia sinensis var. sinensis (CSS) and C. sinensis var. assamica (CSA) are the two most economically important tea varieties. They have different characteristics and geographical distribution. Their genetic diversity and differentiation are unclear. Here, we identified 18,903,625 single nucleotide polymorphisms (SNPs) and 7,314,133 insertion–deletion mutations (indels) by whole-genome resequencing of 30 cultivated and three wild related species. Population structure and phylogenetic tree analyses divided the cultivated accessions into CSS and CSA containing 6,440,419 and 6,176,510 unique variations, respectively. The CSS subgroup possessed higher genetic diversity and was enriched for rare alleles. The CSA subgroup had more non-synonymous mutations and might have experienced a greater degree of balancing selection. The evolution rate (dN/dS) and KEGG enrichment indicated that genes involved in the synthesis and metabolism of flavor substances were positively selected in both CSS and CSA subpopulations. However, there are extensive genome differentiation regions (2959 bins and approximately 148 M in size) between the two subgroups. Compared with CSA (141 selected regions containing 124 genes), the CSS subgroup (830 selected regions containing 687 genes) displayed more selection regions potentially related to environmental adaptability. Fifty-three pairs of polymorphic indel markers were developed. Some markers were located in hormone-related genes with distinct alleles in the two cultivated subgroups. These identified variations and selected regions provide clues for the differentiation and adaptive evolution of tea varieties. The newly developed indel markers will be valuable in further genetic research on tea plants.

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Whole-genome resequencing reveals genetic characteristics of different duck breeds from the Guangxi region in China

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab054 ◽

2021 ◽

Author(s):

Ran Wang ◽

Junli Sun ◽

Hu Han ◽

Yingfei Huang ◽

Tao Chen ◽

...

Keyword(s):

Genetic Diversity ◽

Environmental Variability ◽

Small Body ◽

Indigenous Populations ◽

Whole Genome ◽

Genome Resequencing ◽

Component Structure ◽

Genetic Characteristics ◽

Whole Genome Resequencing ◽

Meat Type

Abstract Distinctive indigenous duck (Anas platyrhynchos) populations of Guangxi, China evolved due to the geographical, cultural, and environmental variability of this region. To investigate the genetic diversity and population structure of the indigenous ducks of Guangxi, 78 individuals from eight populations were collected and sequenced by whole-genome resequencing with an average depth of ∼9.40×. The eight indigenous duck populations included four breeds and four resource populations. Moreover, the genome data of 47 individuals from two typical meat-type breeds and two native egg-type breeds were obtained from a public database. Calculation of heterozygosity (Hp), nucleotide diversity (π), Tajima’s D, and FST indicated that the Guangxi populations were characterized by higher genetic diversity and lower differentiation than meat-type breeds. The highest diversity was observed in the Xilin-Ma ducks. Principal component, structure, and phylogenetic tree analyses revealed the relationship between the indigenous duck populations of Guangxi. A mild degree of differentiation was observed among the Guangxi populations, although three populations were closer to the meat or egg breeds. Indigenous populations are famous for their special flavor, small body size, and slow growth rates. Selective sweep analysis revealed the candidate genes and pathways associated with these growth traits. Our findings provide a valuable source of information regarding genetic diversity, population conservation, and genome-associated breeding of ducks.

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Genetic diversity analysis of Chinese plum (Prunus salicina L.) based on whole-genome resequencing

10.1101/2020.08.28.271411 ◽

2020 ◽

Author(s):

Xiao Wei ◽

Fei Shen ◽

Qiuping Zhang ◽

Ning Liu ◽

Yuping Zhang ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

South China ◽

Yangtze River Basin ◽

Private Allele ◽

Whole Genome ◽

Genome Resequencing ◽

Cultivar Group ◽

Prunus Salicina ◽

Whole Genome Resequencing

AbstractChinese plum (Prunus salicina L.), also known as Japanese plum, is gaining importance due to their extensive genetic diversity and nutritional attributes beneficial for human health. Single-nucleotide polymorphisms (SNPs) are the most abundant form of genomic polymorphisms and are widely used in population genetics research. Here, we construed high-density haplotype map by whole-genome resequencing of 67 Prunus accessions with a depth of ~20× to evaluate the genome-level diversity and population structure. The phylogenetic analysis, the principal component analysis, and the population structure profiling, indicated that the 67 plum accessions could be classified into four groups corresponding to their origin location, the southern cultivar group (SCG), the northern cultivar group (NCG), the foreign cultivar group (FG), and the mixed cultivar group (MG). Some cultivars from South China were clustered with the other three groups. The genetic diversity indices including the private allele number, the observed heterozygosity, the expected heterozygosity, and the nucleotide diversity of the SCG were higher than those of the NCG. The gene flow from the SCG to the FG was detected as well. We concluded that the origin center of Chinese plum was at the Yangtze River Basin in South China. This study provided genetic variation features and population structure of Chinese plum cultivars, laying a foundation for breeders to use diverse germplasm and allelic variants for improving Chinese plum varieties.

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