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

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

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

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.

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

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.

scholarly journals Whole Genome Sequencing of 5 Tibetan Sheep Breeds Identifies Selective Signatures to Adaptability at Different High-Altitude Areas in Qinghai-Tibetan Plateau

2020 ◽  
Author(s):  
Lei-Lei Li ◽  
Shi-Ke Ma ◽  
Wei Peng ◽  
You-Gui Fang ◽  
Hong-Yun Fu ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Plateau Region ◽  
Sheep Breeds ◽  
Wool Growth ◽  
Tibetan Sheep ◽  
Whole Genome Resequencing ◽  
Close Genetic Relationship

ABSTRACTTibetan sheep is one of primitive Chinese sheep breeds, which achieved the divergence about 2500 years ago in Qinghai plateau region. According to different geographic conditions, especially altitudes, Tibetan sheep evolved into different breeds. In this study, we performed pooled whole genome resequencing of 125 individuals from 5 representative Tibetan sheep breeds. Comparative genomic analysis showed that they can be divided into different clades with a close genetic relationship. However, some genes with common selective regions were enriched for hypoxic adaptability in different breeds living at higher altitude, including GHR, BMP15 and CPLANE1. Furthermore, breed-specific selective regions about physical characteristics, especially wool growth, were found in genes such as BSND, USP24, NCAPG and LCORL. This study could contribute to our understanding about trait formation and offer a reference for breeding of Tibetan sheep.

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

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.

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

Genomics ◽  
2018 ◽  
Vol 110 (5) ◽  
pp. 304-309 ◽  
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

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

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.

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

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.

scholarly journals Analysis of Whole Genome Resequencing Datasets from a Worldwide Sample of Sheep Breeds to Identify Potential Causal Mutations Influencing Milk Composition Traits

Animals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1542
Author(s):  
Héctor Marina ◽  
Beatriz Gutiérrez-Gil ◽  
Cristina Esteban-Blanco ◽  
Aroa Suárez-Vega ◽  
Rocío Pelayo ◽  
...  
Keyword(s):  
Milk Composition ◽  
Future Research ◽  
Domestic Sheep ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Phenotypic Effect ◽  
Milk Fatty Acids ◽  
Cheese Making ◽  
Sheep Breeds ◽  
Whole Genome Resequencing

Different studies have shown that polymorphisms in the sequence of genes coding for the milk proteins and milk fatty acids are associated with milk composition traits as well as with cheese-making traits. However, the lack of coincident results across sheep populations has prevented the use of this information in sheep breeding programs. The main objective of this study was to exploit the information derived from a total of 175 whole genome resequencing (WGR) datasets from 43 domestic sheep breeds and three wild sheep to evaluate the genetic diversity of 24 candidate genes for milk composition and identify genetic variants with a potential phenotypic effect. The functional annotation of the identified variants highlighted five single nucleotide polymorphisms (SNPs) predicted to have a high impact on the protein function and 42 missense SNPs with a putative deleterious effect. When comparing the allelic frequencies at these 47 polymorphisms with relevant functional effects between the genomes of Assaf and Churra sheep breeds, two missense deleterious variants were identified as potential markers associated to the milk composition differences found between the Churra and Assaf: XDH:92215727C>T and LALBA:137390760T>C. Future research is required to confirm the effect of the potential functionally relevant variants identified in the present study on milk composition and cheese-making traits.

scholarly journals Genotyping and Whole-Genome Resequencing of Welsh Sheep Breeds Reveal Candidate Genes and Variants for Adaptation to Local Environment and Socioeconomic Traits

2021 ◽  
Vol 12 ◽  
Author(s):  
James Sweet-Jones ◽  
Vasileios Panagiotis Lenis ◽  
Andrey A. Yurchenko ◽  
Nikolay S. Yudin ◽  
Martin Swain ◽  
...  
Keyword(s):  
Coat Color ◽  
Local Environment ◽  
Meat Production ◽  
Whole Genome ◽  
Missense Mutations ◽  
Genome Resequencing ◽  
Sheep Breeds ◽  
Livestock Breeding ◽  
Whole Genome Resequencing ◽  
Upland Pasture

BackgroundAdvances in genetic tools applied to livestock breeding has prompted research into the previously neglected breeds adapted to harsh local environments. One such group is the Welsh mountain sheep breeds, which can be farmed at altitudes of 300 m above sea level but are considered to have a low productive value because of their poor wool quality and small carcass size. This is contrary to the lowland breeds which are more suited to wool and meat production qualities, but do not fare well on upland pasture. Herein, medium-density genotyping data from 317 individuals representing 15 Welsh sheep breeds were used alongside the whole-genome resequencing data of 14 breeds from the same set to scan for the signatures of selection and candidate genetic variants using haplotype- and SNP-based approaches.ResultsHaplotype-based selection scan performed on the genotyping data pointed to a strong selection in the regions of GBA3, PPARGC1A, APOB, and PPP1R16B genes in the upland breeds, and RNF24, PANK2, and MUC15 in the lowland breeds. SNP-based selection scan performed on the resequencing data pointed to the missense mutations under putative selection relating to a local adaptation in the upland breeds with functions such as angiogenesis (VASH1), anti-oxidation (RWDD1), cell stress (HSPA5), membrane transport (ABCA13 and SLC22A7), and insulin signaling (PTPN1 and GIGFY1). By contrast, genes containing candidate missense mutations in the lowland breeds are related to cell cycle (CDK5RAP2), cell adhesion (CDHR3), and coat color (MC1R).ConclusionWe found new variants in genes with potentially functional consequences to the adaptation of local sheep to their environments in Wales. Knowledge of these variations is important for improving the adaptative qualities of UK and world sheep breeds through a marker-assisted selection.

scholarly journals Genetic Diversity, Molecular Phylogeny, and Selection Evidence of Jinchuan Yak Revealed by Whole-Genome Resequencing

2018 ◽  
Vol 8 (3) ◽  
pp. 945-952 ◽  
Author(s):  
Daoliang Lan ◽  
Xianrong Xiong ◽  
Tserang-Donko Mipam ◽  
Changxiu Fu ◽  
Qiang Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Phylogeny ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Whole Genome Resequencing
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