Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
3.1
2.4
Journals
Diversity
Special Issues
Genetic Diversity, Population Structure, and Ancestral Origin of Livestock
share announcement

Genetic Diversity, Population Structure, and Ancestral Origin of Livestock

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Phylogeny and Evolution".

Deadline for manuscript submissions: closed (15 November 2022) | Viewed by 11046

Special Issue Editor

Dr. Tatiana Deniskova

E-Mail Website
Guest Editor
L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, 142132 Podolsk, Russia
Interests: livestock genomics; genetic diversity; phylogenetic studies; DNA markers

Special Issue Information

Dear Colleagues,

Genomes of modern livestock species have been shaped by two powerful driving forces of evolution, including natural selection and breeding. Thus, the majority of livestock species significantly differ from their ancestors and wild relatives, whose genetic variations have predominantly been caused by environmental changes of different nature (climatic, earth axis shift, anthropomorphic, etc.).

The deepening knowledge and elucidation of new insights into “wild” genetic origin of domestic animal species and populations expand our understanding of the directions of evolution under various circumstances and contribute to unlocking genetic mechanisms, which underlie the amazing resilience and adaptions of these species. In addition, timely tracing of the genetic interactions between domestic species and their wild relatives sharing habitats might indicate future population changes to prevent negative consequences for both species.

This Special Issue on “Genetic Diversity, Population Structure, and Ancestral Origin of Livestock” aims to embrace any aspects of origin of livestock species regarding their links to wild relatives and highlight their shared ancestral genome components based on using molecular markers.

Dr. Tatiana Deniskova
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diversity is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • origin
  • wild and domestic species
  • single nucleotide polymorphisms
  • microsatellites
  • mtDNA
  • genetic diversity

Published Papers (5 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

12 pages, 5055 KiB  
Article
Runs of Homozygosity and Gene Identification in Pelibuey Sheep Using Genomic Data
by Wilber Hernández-Montiel, Nubia Noemi Cob-Calan, Lilia E. Cahuich-Tzuc, José A. Rueda, Jorge Quiroz-Valiente, Víctor Meza-Villalvazo and Roberto Zamora-Bustillos
Diversity 2022, 14(7), 522; https://doi.org/10.3390/d14070522 - 28 Jun 2022
Viewed by 1720
Abstract
The runs of homozygosity (ROHs), the inbreeding coefficient, and the effective population size (Ne) in Pelibuey sheep were analyzed in 24 Pelibuey ewes from two lambs at parturition and 24 ewes that gave birth to a single lamb using the Ilumina [...] Read more.
The runs of homozygosity (ROHs), the inbreeding coefficient, and the effective population size (Ne) in Pelibuey sheep were analyzed in 24 Pelibuey ewes from two lambs at parturition and 24 ewes that gave birth to a single lamb using the Ilumina OvineSNP50 BeadChip. The Ne decreased from 535 to 192 in the first ten generations. A total of 2194 ROHs were identified on the basis of single nucleotide polymorphisms (SNPs), were identified in the prolific group and 2185 SNPs in ROH in the non-prolific group. The distribution of the lengths of the ROH, considering both groups, were found to be: 4065 less than 6 Mb, 213 between 6 and 12 Mb, 72 between 12 and 24 Mb, twenty between 24 and 48 Mb and 8 greater than 48 Mb. In prolific sheep, the ROH associated with prolificacy were identified near the LINGO2, FLRT2, ADGRB3 genes, related to “positive regulation of synapse assembly”; and the DGKG, DGKE, DGKB and DGKI genes, related to “protein kinase C-activating G-protein coupled receptor signaling pathway”. The present work present genes that can function as signal mediators or have activity in embryonic development, which is relevant to the economic activity of this species. Full article
(This article belongs to the Special Issue Genetic Diversity, Population Structure, and Ancestral Origin of Livestock)
►▼ Show Figures

Figure 1

11 pages, 2083 KiB  
Communication
A Search for Eurasian Sheep Relationships: Genomic Assessment of the Autochthonous Sheep Breeds in Russia and the Persian Plateau
by Tatiana Deniskova, Ali Esmailizadeh, Arsen Dotsev, Olga Koshkina, Mohammad Ali Farahvashi, Mortaza Mokhtari, Mozhdeh Moosanezhad Khabisi, Feng-Hua Lv and Natalia Zinovieva
Diversity 2022, 14(6), 445; https://doi.org/10.3390/d14060445 - 02 Jun 2022
Cited by 1 | Viewed by 2048
Abstract
Genomic assessment of local sheep breeds is relevant to the reconstruction of post-domestication migrations and to filling in gaps in the developmental history and contemporary phylogeographic-differentiation patterns in Eurasia. In this study, we aimed to reveal possible genetic relationships between local sheep breeds [...] Read more.
Genomic assessment of local sheep breeds is relevant to the reconstruction of post-domestication migrations and to filling in gaps in the developmental history and contemporary phylogeographic-differentiation patterns in Eurasia. In this study, we aimed to reveal possible genetic relationships between local sheep breeds in Russia and the Persian Highlands (Iran) based on high-density SNP genotypes. All samples (n = 395) from 11 Iranian and 10 Russian sheep breeds were genotyped by using the Ovine Infinium HD BeadChip (Illumina, San Diego, CA, USA). Principal Component Analysis, maximum-likelihood assessment, and Neighbor-Net graph analysis demonstrated a clear differentiation between Russian sheep breeds of European ancestry from the Iranian local cluster and Russian breeds of Asian origin. Admixture analysis revealed a shared ancestral background, which was detected in several Iranian-local and Russian-local fat-tailed coarse-wool sheep breeds. Our findings contribute to a better understanding of the pattern of historic admixture, which is present in the genomes of many Eurasian sheep breeds. Full article
(This article belongs to the Special Issue Genetic Diversity, Population Structure, and Ancestral Origin of Livestock)
►▼ Show Figures

Graphical abstract

19 pages, 2841 KiB  
Article
Genetic and Population Structure of Croatian Local Donkey Breeds
by Ante Ivanković, Giovanni Bittante, Gordan Šubara, Edmondo Šuran, Zdenko Ivkić, Mateja Pećina, Miljenko Konjačić, Ivica Kos, Nikolina Kelava Ugarković and Jelena Ramljak
Diversity 2022, 14(5), 322; https://doi.org/10.3390/d14050322 - 21 Apr 2022
Cited by 2 | Viewed by 2305
Abstract
The two native Croatian donkey breeds (Littoral-Dinaric donkey and Istrian donkey) were marginalized in the second half of the 20th century and were on the verge of biological extinction. The aim of this study was to analyze the demographic and genetic status of [...] Read more.
The two native Croatian donkey breeds (Littoral-Dinaric donkey and Istrian donkey) were marginalized in the second half of the 20th century and were on the verge of biological extinction. The aim of this study was to analyze the demographic and genetic status of two donkey breeds, two decades after the start of protection by analyzing their pedigrees and genetic structure. The average generation interval was higher for the Istrian donkey (7.73) than for the Littoral-Dinaric donkey (7.27). The rate of the effective number of founders compared with the effective number of ancestors in the Littoral-Dinaric donkey (1.03; 325/316) and in the Istrian donkey (1.08; 70/65) revealed no evidence of a genetic bottleneck. The inbreeding coefficient (F) and the average relatedness coefficient (AR) was lower in the Littoral-Dinaric donkey population (0.99%; 0.13%) than in the Istrian donkey population (1.77%; 1.10%). Genetic microsatellite analysis showed relatively high genetic diversity in Littoral-Dinaric donkey and Istrian donkey breeds, expressed by mean allele number (5.92; 5.85) and expected heterozygosity (0.650; 0.653). Genetic differentiation between the Littoral-Dinaric donkey and the Istrian donkey has not significantly increased in the last two decades (FST = 0.028). Genetic analysis also showed no evidence of high inbreeding or genetic bottleneck in both breeds. A total of 11 haplotypes including 28 polymorphic sites were found in 30 samples. Analysis of mtDNA has shown that the Littoral-Dinaric donkey and Istrian donkey breeds belong to the Equus asinus africanus group. The study confirms the need to use different analytical approaches to get a regular and complete insight into the situation and trends within and between breeds, so that the existing diversity can be fully preserved. Full article
(This article belongs to the Special Issue Genetic Diversity, Population Structure, and Ancestral Origin of Livestock)
►▼ Show Figures

Graphical abstract

12 pages, 650 KiB  
Article
Comparative Analysis of the Polymorphism of the Casein Genes in Camels Bred in Kazakhstan
by Makpal Amandykova, Kairat Dossybayev, Aizhan Mussayeva, Bakytzhan Bekmanov and Naruya Saitou
Diversity 2022, 14(4), 285; https://doi.org/10.3390/d14040285 - 11 Apr 2022
Cited by 4 | Viewed by 1953
Abstract
Caseins play an important role in determining the technological properties and quantitative characteristics of camel milk. To date, only a few studies on the genetic polymorphism of casein genes have been reported in the camel populations of Kazakhstan. Therefore, this work aimed to [...] Read more.
Caseins play an important role in determining the technological properties and quantitative characteristics of camel milk. To date, only a few studies on the genetic polymorphism of casein genes have been reported in the camel populations of Kazakhstan. Therefore, this work aimed to identify the genetic polymorphism level of casein genes among camel populations of the Almaty region of Kazakhstan. The PCR-RFLP method was used for this purpose and the following genotypes were revealed as a result: CSN3 gene—CC, CT, TT, where the T allele predominated in all populations, with a frequency of 0.60; CSN2 gene—AA, AG, GG, with the predomination of A allele (0.64); and CSN1S1 gene—GG and GT, with the predomination of G allele (0.94). Statistical analysis was carried out using the POPGENE and GenAlEx software. The χ2 values were equal to 12.1 (CSN3), 8.6 (CSN2), and 14.5 (CSN1S1). As a result, three out of 53 animals were designated as the “core” of the population—animals with the desired genotypes: CC genotype for the CSN3 gene and AA genotype for the CSN2 gene. Such animals can be selected for further use with an increase in the number of livestock with high productivity rates. Full article
(This article belongs to the Special Issue Genetic Diversity, Population Structure, and Ancestral Origin of Livestock)
►▼ Show Figures

Figure 1

11 pages, 973 KiB  
Article
Distribution of Homozygosity Regions in the Genome of Kazakh Cattle Breeds
by Indira Beishova, Kairat Dossybayev, Alzhan Shamshidin, Alena Belaya, Anuarbek Bissembayev, Kadyrzhan Khamzin, Alexandr Kovalchuk and Askar Nametov
Diversity 2022, 14(4), 279; https://doi.org/10.3390/d14040279 - 08 Apr 2022
Cited by 1 | Viewed by 2018
Abstract
Runs of homozygosity (ROH) are contiguous stretches of homozygous genotypes that are passed from parents to their offspring. ROHs are suitable for determining population history, inbreeding rates, and the genetic relationships between individuals in the populations, as well as to detect candidate genes [...] Read more.
Runs of homozygosity (ROH) are contiguous stretches of homozygous genotypes that are passed from parents to their offspring. ROHs are suitable for determining population history, inbreeding rates, and the genetic relationships between individuals in the populations, as well as to detect candidate genes responsible for economic traits in farm animals. In this study, we observed that the Kazakh white-headed (KWh) cattle breed (ROH n = 55,976) had a higher number of ROH compared to the Auliekol (AK) breed (ROH n = 13,137). When calculating the mean length of ROH, there were considerable differences between Kazakh white-headed (211.59 ± 92.98 Mb) and Auliekol (99.62 ± 46.48 Mb) populations. The maximum length of ROH was higher in Auliekol cattle (510.25 Mb) than in Kazakh white-headed cattle (498.91 Mb). The average inbreeding coefficient rate was equal to 0.084 ± 0.037 in Kazakh white-headed cattle and 0.039 ± 0.018 in Auliekol cattle. The high frequency of genomic regions showed that the strongest patterns were observed on chromosomes 2, 6, and 26 for KWh and 1, 5, and 14 for AK. The estimation of ROH numbers per animal showed that the number of ROH decreased with increasing ROH length in both populations. The genomic inbreeding coefficient of both cattle breeds was calculated based on the ROH, and ancient inbreeding was observed. The harbored genes within ROH islands were associated with meat growth and milk production. Full article
(This article belongs to the Special Issue Genetic Diversity, Population Structure, and Ancestral Origin of Livestock)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-5
Back to TopTop