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 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 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 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

scholarly journals The Genotypes of Polymorphic Simple Sequence Repeat Loci Revealed by Whole-genome Resequencing Data of 30 Pyrus Accessions

2019 ◽  
Vol 144 (5) ◽  
pp. 321-328
Author(s):  
Shuang Jiang ◽  
Haishan An ◽  
Xiaoqing Wang ◽  
Chunhui Shi ◽  
Jun Luo ◽  
...  
Keyword(s):  
Population Structure ◽  
Molecular Marker ◽  
Whole Genome ◽  
Marker Assisted Breeding ◽  
Genome Resequencing ◽  
Polymorphic Ssrs ◽  
Ssr Loci ◽  
Whole Genome Resequencing ◽  
Wild Accessions ◽  
Simple Sequence

Simple sequence repeats (SSRs) are widely used in cultivar identification, genetic relationship analysis, and quantitative trait locus mapping. Currently, the selection of hybrid progeny plants in molecular marker-assisted breeding mostly relies on SSR markers because of their ease of operation. In Pyrus, a large number of SSR markers have been developed previously. The method to identify polymorphic SSRs quickly is still lacking in cultivated as well as wild pear species. We present a large number of polymorphic SSRs identified using a quick in silico approach applied across 30 cultivated and wild accessions from Pyrus species. A total of 49,147 SSR loci were identified in Pyrus, and their genotypes were evaluated by whole-genome resequencing data of 30 Pyrus accessions. The results show that most SSR loci were dinucleotide repeat motifs located in intergenic regions. The genotypes of all SSR loci were revealed in all accessions. A total of 23,209 loci were detected, with more than one genotype in all Pyrus accessions. We selected 702 highly polymorphic SSR loci to characterize the pear accessions with an average polymorphism information content value of 0.67, suggesting that these SSR loci were highly polymorphic. The genetic relationship of Pyrus species in the neighbor-joining (NJ) tree and population structure showed a clear division between the oriental and occidental accessions. The population structure split all oriental pears into two groups: cultivars and wild accessions. These new findings of the polymorphic SSR loci in this study are valuable for selecting appropriate markers in molecular marker-assisted breeding in Pyrus.

scholarly journals Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tetsuo Kon ◽  
Liyi Pei ◽  
Ryota Ichikawa ◽  
Chunyan Chen ◽  
Ping Wang ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Genomics ◽  
Living Environment ◽  
Large Yellow Croaker ◽  
Whole Genome ◽  
Effective Population ◽  
Genome Resequencing ◽  
Genetic Population ◽  
Whole Genome Resequencing ◽  
Sea Area

AbstractLarge yellow croaker is an economically important fish in China and East Asia. Despite its economic importance, genome-wide adaptions of domesticated large yellow croaker are largely unknown. Here, we performed whole-genome resequencing of 198 individuals of large yellow croaker obtained in the sea or from farmers in Zhoushan or Ningde. Population genomics analyses revealed the genetic population structure of our samples, reflecting the living environment. Each effective population size is estimated to be declining over generations. Moreover, we identified genetically differentiated genomic regions between the sea-captured population in the Zhoushan Sea area and that of the Ningde Sea area or between the sea-captured population and the farmed population in either area. Gene ontology analyses revealed the gene groups under selective sweep for the adaptation to the domesticated environment. All these results suggest that individuals of the large yellow croaker populations show genomic signatures of adaptation to different living environments.

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