Whole-Genome Resequencing Reveals Genetic Structure and Introgression in Chinese Pudong White Pigs

Abstract Background: Pudong white (PDW) pigs originating from Shanghai, are the only Chinese indigenous pigs with white coat color except Rongchang (RC) pigs. However, there is limited information about its overall genetic structure, relationship with other breeds especially the East Chinese (ECN) and European pig due to the white coat of PDW. Whole-genome sequencing provides the effective approach to get the unique information of genome. The high-depth whole-genome sequencing data of 26 global pig breeds, European Wild boars (EWB), Chinese Wild boars (CWB) and out group (OUT) were implemented to detect the genetic structure, signature of selection and potential exotic introgression in PDW pigs.Results: The PDW pigs belonging to ECN pigs based on genetic relationship, and harbor lower genetic diversity and higher inbreeding coefficient compared to other Chinese indigenous pigs. Both the f3 and D-statistics analysis demonstrated that PDW pigs shared apparent alleles with Large White (LW) pigs. Then, two statistics, haplotype heat-map, copy number variation (CNV) and rIBD analysis further revealed that PDW pigs carry the same KIT genotype and share haplotypes at PARG-MARCHF8 locus with LW pigs, suggesting that the lineage of European (EUR) pigs in PDW originated from LW pigs. After detecting the KIT mutations in different pig breeds, PDW was confirmed to be same with LW at DUP1, DUP2 and the splicing mutation on intron 17 of KIT which determine the white coat color phenotype in European white pigs.Conclusions: This study shows that ECN pigs crossed with LW pigs after introduced to China about 110-164 years ago, where the offspring carrying KIT genotype that caused white coat color phenotype, and then were selected due to the rare white coat color in Chinese indigenous pigs, gradually forming PDW pig breed. To our knowledge, this study gives the first thorough description of the genetic structure of PDW pig via whole-genome resequencing data. This study not only advances our understanding of genetic structure, molecular phylogeny, and molecular origin of PDW pigs, but also provides a basis for facilitating the development of a national project for the conservation and utilization of this unique Chinese local population.

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Whole genome resequencing data for rock pigeon (Columba livia)

BMC Research Notes ◽

10.1186/s13104-021-05718-1 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Ali Esmailizadeh ◽

Hamed Kharrati-Koopaee ◽

Hojjat Assadoullahpour Nanaei

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Columba Livia ◽

Homing Pigeon ◽

Genetic Mechanism ◽

Whole Genome ◽

Genome Resequencing ◽

Homing Pigeons ◽

Rock Pigeon ◽

Whole Genome Resequencing

Abstract Objective Navigation is the most important feature of homing pigeons, however no integrated response to genetic mechanism of navigation has been reported. The generated data herein represent whole-genome resequencing data for homing pigeon and three other breeds of rock pigeons. Selective sweep analysis between homing pigeon and other breeds of rock pigeon can provide new insight about identification of candidate genes and biological pathways for homing pigeon ability. Data description Whole-genomes sequence data related to 95 birds from four breeds of rock pigeons including, 29 feral pigeons, 24 Shiraz tumblers, 24 Persian high flyers and 18 homing pigeons were provided. More than 6.94 billion short reads with coverage (average ≈7.50 x) and 407.1 Gb data were produced. Whole genome sequencing was carried out on the Illumina Hiseq 2000 platform using a 350 bp library size and 150 bp paired-end read lengths. The whole genome sequencing data have been submitted at the NCBI SRA Database (PRJNA532675). The presented data set can provide useful genomic information to explain the genetic mechanism of navigation ability of homing pigeons and also testing other genetic hypothesis by genomic analysis.

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Whole-genome resequencing reveals genetic structure and introgression in Pudong White pigs

animal ◽

10.1016/j.animal.2021.100354 ◽

2021 ◽

Vol 15 (10) ◽

pp. 100354

Author(s):

M. Huang ◽

H. Zhang ◽

Z.P. Wu ◽

X.P. Wang ◽

D.S. Li ◽

...

Keyword(s):

Genetic Structure ◽

Whole Genome ◽

Genome Resequencing ◽

Whole Genome Resequencing

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Whole-Genome Resequencing Identifies KIT New Alleles That Affect Coat Color Phenotypes in Pigs

Frontiers in Genetics ◽

10.3389/fgene.2019.00218 ◽

2019 ◽

Vol 10 ◽

Author(s):

Zhongping Wu ◽

Zheng Deng ◽

Min Huang ◽

Yong Hou ◽

Hui Zhang ◽

...

Keyword(s):

Coat Color ◽

Whole Genome ◽

Genome Resequencing ◽

Whole Genome Resequencing ◽

New Alleles

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Fine Mapping and Whole-Genome Resequencing Identify the Seed Coat Color Gene in Brassica rapa

PLoS ONE ◽

10.1371/journal.pone.0166464 ◽

2016 ◽

Vol 11 (11) ◽

pp. e0166464 ◽

Cited By ~ 19

Author(s):

Yanhua Wang ◽

Lu Xiao ◽

Shaomin Guo ◽

Fengyun An ◽

Dezhi Du

Keyword(s):

Brassica Rapa ◽

Fine Mapping ◽

Seed Coat ◽

Coat Color ◽

Whole Genome ◽

Seed Coat Color ◽

Genome Resequencing ◽

Whole Genome Resequencing ◽

Coat Color Gene ◽

Color Gene

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

Frontiers in Genetics ◽

10.3389/fgene.2021.612492 ◽

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.

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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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