Population structure and genetic diversity of 25 Russian sheep breeds based on whole-genome genotyping

AbstractThe freshwater true bug Aphelocheirus aestivalis (Aphelocheiridae) is widely distributed in Europe but occurs rather locally and often in isolated populations. Moreover, it is threatened with extinction in parts of its range. Unfortunately, little is known about the genetic diversity and population structure due to the lack of molecular tools for this species. Thus, to overcome the limitations, a whole-genome sequencing has been performed to identify polymorphic microsatellite markers for A. aestivalis. The whole-genome sequencing has been performed with the Illumina MiSeq platform. Obtained paired-end reads were processed and overlapped into 2,378,426 sequences, and the subset of 267 sequences containing microsatellite motifs were then used for in silico primer designing. Finally, 56 microsatellite markers were determined and 34 of them were polymorphic. Analyses performed in two samples (collected from Drawa and Gowienica rivers, respectively) showed that the number of alleles per locus ranged from 2 to 21, and the observed and expected heterozygosity varied from 0 to 0.933 and 0.064 to 0.931, respectively. The microsatellite markers developed in the present study provide new suitable tools available for the scientific community to study A. aestivalis population dynamics. The assessment of its genetic diversity and population structure will provide important data, that can be used in population management and conservation efforts, elucidating the broad- and fine-scale population genetic structure of A. aestivalis.

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Genetic diversity and population structure among six cattle breeds in South Africa using a whole genome SNP panel

Frontiers in Genetics ◽

10.3389/fgene.2014.00333 ◽

2014 ◽

Vol 5 ◽

Cited By ~ 42

Author(s):

Sithembile O. Makina ◽

Farai C. Muchadeyi ◽

Este van Marle-KÃ¶ster ◽

Michael D. MacNeil ◽

Azwihangwisi Maiwashe

Keyword(s):

South Africa ◽

Genetic Diversity ◽

Population Structure ◽

Whole Genome ◽

Cattle Breeds ◽

Snp Panel

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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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Genomic Uniqueness of Local Sheep Breeds From Morocco

Frontiers in Genetics ◽

10.3389/fgene.2021.723599 ◽

2021 ◽

Vol 12 ◽

Author(s):

Abdessamad Ouhrouch ◽

Simon Boitard ◽

Frédéric Boyer ◽

Bertrand Servin ◽

Anne Da Silva ◽

...

Keyword(s):

Genetic Diversity ◽

Demographic History ◽

Large Set ◽

Whole Genome ◽

Selection Signatures ◽

Effective Population ◽

High Genetic Diversity ◽

Sheep Breeds ◽

Genome Data ◽

Genomic Regions

Sheep farming is a major source of meat in Morocco and plays a key role in the country’s agriculture. This study aims at characterizing the whole-genome diversity and demographic history of the main Moroccan sheep breeds, as well as to identify selection signatures within and between breeds. Whole genome data from 87 individuals representing the five predominant local breeds were used to estimate their level of neutral genetic diversity and to infer the variation of their effective population size over time. In addition, we used two methods to detect selection signatures: either for detecting selective sweeps within each breed separately or by detecting differentially selected regions by contrasting different breeds. We identified hundreds of genomic regions putatively under selection, which related to several biological terms involved in local adaptation or the expression of zootechnical performances such as Growth, UV protection, Cell maturation or Feeding behavior. The results of this study revealed selection signatures in genes that have an important role in traits of interest and increased our understanding of how genetic diversity is distributed in these local breeds. Thus, Moroccan local sheep breeds exhibit both a high genetic diversity and a large set of adaptive variations, and therefore, represent a valuable genetic resource for the conservation of sheep in the context of climate change.

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Development and Validation of Polymorphic Microsatellite Loci for the NA2 Lineage of Phytophthora ramorum from Whole Genome Sequence Data

Plant Disease ◽

10.1094/pdis-11-16-1586-re ◽

2017 ◽

Vol 101 (5) ◽

pp. 666-673 ◽

Cited By ~ 10

Author(s):

Marie-Claude Gagnon ◽

Nicolas Feau ◽

Angela L. Dale ◽

Braham Dhillon ◽

Richard C. Hamelin ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genome Sequence ◽

Sequence Data ◽

Ornamental Plants ◽

Phytophthora Ramorum ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequence Data ◽

And Migration

Phytophthora ramorum is the causal agent of sudden oak death and sudden larch death, and is also responsible for causing ramorum blight on woody ornamental plants. Many microsatellite markers are available to characterize the genetic diversity and population structure of P. ramorum. However, only two markers are polymorphic in the NA2 lineage, which is predominant in Canadian nurseries. Microsatellite motifs were mined from whole-genome sequence data of six P. ramorum NA2 isolates. Of the 43 microsatellite primer pairs selected, 13 loci displayed different allele sizes among the four P. ramorum lineages, 10 loci displayed intralineage variation in the EU1, EU2, and/or NA1 lineages, and 12 microsatellites displayed polymorphism in the NA2 lineage. Genotyping of 272 P. ramorum NA2 isolates collected in nurseries in British Columbia, Canada, from 2004 to 2013 revealed 12 multilocus genotypes (MLGs). One MLG was dominant when examined over time and across sampling locations, and only a few mutations separated the 12 MLGs. The NA2 population observed in Canadian nurseries also showed no signs of sexual recombination, similar to what has been observed in previous studies. The markers developed in this study can be used to assess P. ramorum inter- and intralineage genetic diversity and generate a better understanding of the population structure and migration patterns of this important plant pathogen, especially for the lesser-characterized NA2 lineage.

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