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

animal ◽  
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

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

2021 ◽  
Author(s):  
Min Huang ◽  
Zhongping Wu ◽  
Xiaopeng Wang ◽  
Desen Li ◽  
Shaojuan Liu ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Genome Sequencing ◽  
Coat Color ◽  
White Coat ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Indigenous Pigs ◽  
Whole Genome Resequencing ◽  
Color Phenotype ◽  
Coat Color Phenotype

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.

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.

scholarly journals Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery

BMC Genomics ◽  
2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Paul Stothard ◽  
Jung-Woo Choi ◽  
Urmila Basu ◽  
Jennifer M Sumner-Thomson ◽  
Yan Meng ◽  
...  
Keyword(s):  
Holstein Cattle ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Whole Genome Resequencing

scholarly journals Whole-Genome Resequencing Points to Candidate DNA Loci Affecting Body Temperature under Cold Stress in Siberian Cattle Populations

Life ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 959
Author(s):  
Alexander Igoshin ◽  
Nikolay Yudin ◽  
Ruslan Aitnazarov ◽  
Andrey A. Yurchenko ◽  
Denis M. Larkin
Keyword(s):  
Body Temperature ◽  
Cold Stress ◽  
Candidate Snps ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Functional Annotations ◽  
Cold Environments ◽  
Cold Tolerant ◽  
Cold Sensitive ◽  
Whole Genome Resequencing

Despite the economic importance of creating cold resilient cattle breeds, our knowledge of the genetic basis of adaptation to cold environments in cattle is still scarce compared to information on other economically important traits. Herein, using whole-genome resequencing of animals showing contrasting phenotypes on temperature maintenance under acute cold stress combined with the existing SNP (single nucleotide polymorphism) functional annotations, we report chromosomal regions and candidate SNPs controlling body temperature in the Siberian cattle populations. The SNP ranking procedure based on regional FST calculations, functional annotations, and the allele frequency difference between cold-tolerant and cold-sensitive groups of animals pointed to multiple candidate genes. Among these, GRIA4, COX17, MAATS1, UPK1B, IFNGR1, DDX23, PPT1, THBS1, CCL5, ATF1, PLA1A, PRKAG1, and NR1I2 were previously related to thermal adaptations in cattle. Other genes, for example KMT2D and SNRPA1, are known to be related to thermogenesis in mice and cold adaptation in common carp, respectively. This work could be useful for cattle breeding strategies in countries with harsh climates, including the Russian Federation.

scholarly journals High-Density Genetic Linkage Map Construction Using Whole-Genome Resequencing for Mapping Qtls of Resistance to Aspergillus Flavus Infection in Peanut

2021 ◽  
Author(s):  
Yifei Jiang ◽  
Huaiyong Luo ◽  
Bolun Yu ◽  
Yingbin Ding ◽  
Yanping Kang ◽  
...  
Keyword(s):  
Linkage Map ◽  
Aspergillus Flavus ◽  
Genetic Linkage ◽  
Genetic Basis ◽  
Genetic Linkage Map ◽  
Aflatoxin Contamination ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Favorable Alleles ◽  
Whole Genome Resequencing

Abstract Cultivated peanut (Arachis hypogaea L.) is rich in edible oil and protein, which is widely planted around the world as an oil and cash crop. However, aflatoxin contamination seriously affects the quality safety of peanut, hindering the development of peanut industry and threatening consumers’ health. Breeding peanut varieties with resistance to Aspergillus flavus infection is important for control the aflatoxin contamination, and understanding of the genetic basis of resistance is vital to its genetic enhancement. In this study, we report the QTL mapping of resistance to A. flavus infection of a well-known resistant variety J11. A recombination inbred line (RIL) population was constructed by crossing a susceptible variety Zhonghua 16 and J11. Through whole-genome resequencing, a genetic linkage map was constructed with 2,802 recombination bins and an average inter-bin distance of 0.58 cM. Combined with phenotypic data of infection index in four consecutive years, six novel resistant QTLs were identified and they explained 5.03-10.87% phenotypic variances. The favorable alleles of five QTLs were from J11 while that of one QTL were from Zhonghua 16. The pyramiding of these favorable alleles significantly improved the resistance to A. flavus infection. These results could contribute greatly to understanding of genetic basis of A. flavus resistance and could be meaningful in further resistance improvement in peanut.

Sign in / Sign up

Export Citation Format

Share Document