Unraveling the Genetic Diversity and Population Structure of Bangladeshi Indigenous Cattle Populations Using 50K SNP Markers.
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ABSTRACT:
SUBMITTER: Bhuiyan MSA
PROVIDER: S-EPMC8388693 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundThe indigenous cattle populations from Greece and Cyprus have decreased to small numbers and are currently at risk of extinction due to socio-economic reasons, geographic isolation and crossbreeding with commercial breeds. This study represents the first comprehensive genome-wide analysis of 10 indigenous cattle populations from continental Greece and the Greek islands, and one from Cyprus, and compares them with 104 international breeds using more than 46,000 single nucleotide polymorphisms (SNPs).ResultsWe estimated several parameters of genetic diversity (e.g. heterozygosity and allelic diversity) that indicated a severe loss of genetic diversity for the island populations compared to the mainland populations, which is mainly due to the declining size of their population in recent years and subsequent inbreeding. This high inbreeding status also resulted in higher genetic differentiation within the Greek and Cyprus cattle group compared to the remaining geographical breed groups. Supervised and unsupervised cluster analyses revealed that the phylogenetic patterns in the indigenous Greek breeds were consistent with their geographical origin and historical information regarding crosses with breeds of Anatolian or Balkan origin. Cyprus cattle showed a relatively high indicine ancestry. Greek island populations are placed close to the root of the tree as defined by Gir and the outgroup Yak, whereas the mainland breeds share a common historical origin with Buša. Unsupervised clustering and D-statistics analyses provided strong support for Bos indicus introgression in almost all the investigated local cattle breeds along the route from Anatolia up to the southern foothills of the Alps, as well as in most cattle breeds along the Apennine peninsula to the southern foothills of the Alps.ConclusionsAll investigated Cyprus and Greek breeds present complex mosaic genomes as a result of historical and recent admixture events between neighbor and well-separated breeds. While the contribution of some mainland breeds to the genetic diversity pool seems important, some island and fragmented mainland breeds suffer from a severe decline of population size and loss of alleles due to genetic drift. Conservation programs that are a compromise between what is feasible and what is desirable should focus not only on the still highly diverse mainland breeds but also promote and explore the conservation possibilities for island breeds.
| S-EPMC7391618 | biostudies-literature
Project description:Inferring the effective population size and the pattern of selection signatures is of interest both from an evolutionary perspective and to improve models for mapping of quantitative trait genes. We used DNA samples of 61 sires and 486 progeny of the Hanwoo, genotyped by the Illumina Bovine SNP50 BeadChip, to analyze the genetic structure. Our study showed a persistent decline in effective population size throughout the period considered, but suggested a marked decline at one distinctive time point (100th generation) and two sharp decline intervals (50th-25th generation and 25th-10th generation). This pattern can be explained by Hanwoo formation and the modern breeding program. Our results revealed 95 regions exhibiting the footprint of recent positive selection at a threshold level of 0.01. We found an overlap of the 11 core regions presenting top P-values and those that had previously been identified as harboring quantitative trait loci from other breeds. The information generated from this study can be used to better understand the mechanism of selection in Hanwoo breeding, and provide important implications for the design and application of association studies in the Hanwoo population.
| S-EPMC4498654 | biostudies-literature
Project description:The Dwarf Lagune and the Savannah Somba cattle in Benin are typical representatives of the endangered West African indigenous Shorthorn taurine. The Lagune was previously exported to African and European countries and bred as Dahomey cattle, whereas the Somba contributed to the formation of two indigenous hybrids known as Borgou and Pabli cattle. These breeds are affected by demographic, economic, and environmental pressures in local production systems. Considering current and historical genomic data, we applied a formal test of admixture, estimated admixture proportions, and computed genomic inbreeding coefficients to characterize the five breeds. Subsequently, we unraveled the most recent selection signatures using the cross-population extended haplotype homozygosity approach, based on the current and historical genotypes. Results from principal component analyses and high proportion of Lagune ancestry confirm the Lagune origin of the European Dahomey cattle. Moreover, the Dahomey cattle displayed neither indicine nor European taurine (EUT) background, but they shared on average 40% of autozygosity from common ancestors, dated approximately eight generations ago. The Lagune cattle presented inbreeding coefficients larger than 0.13; however, the Somba and the hybrids (Borgou and Pabli) were less inbred (≤0.08). We detected evidence of admixture in the Somba and Lagune cattle, but they exhibited a similar African taurine (AFT) ancestral proportion (≥96%) to historical populations, respectively. A moderate and stable AFT ancestral proportion (62%) was also inferred for less admixed hybrid cattle including the Pabli. In contrast, the current Borgou samples displayed a lower AFT ancestral proportion (47%) than historical samples (63%). Irrespective of the admixture proportions, the hybrid populations displayed more selection signatures related to economic traits (reproduction, growth, and milk) than the taurine. In contrast, the taurine, especially the Somba, presented several regions known to be associated with adaptive traits (immunity and feed efficiency). The identified subregion of bovine leukocyte antigen (BoLA) class IIb (including DSB and BOLA-DYA) in Somba cattle is interestingly uncommon in other African breeds, suggesting further investigations to understand its association with specific adaptation to endemic diseases in Benin. Overall, our study provides deeper insights into recent evolutionary processes in the Beninese indigenous cattle and their aptitude for conservation and genetic improvement.
| S-EPMC8694269 | biostudies-literature
Project description:Sheep in Ethiopia are adapted to a wide range of environments, including extreme habitats. Elucidating their genetic diversity is critical for improving breeding strategies and mapping quantitative trait loci associated with productivity. To this end, the present study investigated the genetic diversity and population structure of five Ethiopian sheep populations exhibiting distinct phenotypes and sampled from distinct production environments, including arid lowlands and highlands. To investigate the genetic relationships in greater detail and infer population structure of Ethiopian sheep breeds at the continental and global levels, we analyzed genotypic data of selected sheep breeds from the Ovine SNP50K HapMap dataset. All Ethiopian sheep samples were genotyped with Ovine Infinium HD SNP BeadChip (600K). Mean genetic diversity ranged from 0.29 in Arsi-Bale to 0.32 in Menz sheep, while estimates of genetic differentiation among populations ranged from 0.02 to 0.07, indicating low to moderate differentiation. An analysis of molecular variance revealed that 94.62 and 5.38% of the genetic variation was attributable to differences within and among populations, respectively. Our population structure analysis revealed clustering of five Ethiopian sheep populations according to tail phenotype and geographic origin-i.e., short fat-tailed (very cool high-altitude), long fat-tailed (mid to high-altitude), and fat-rumped (arid low-altitude), with clear evidence of admixture between long fat-tailed populations. North African sheep breeds showed higher levels of within-breed diversity, but were less differentiated than breeds from Eastern and Southern Africa. When African breeds were grouped according to geographic origin (North, South, and East), statistically significant differences were detected among groups (regions). A comparison of population structure between Ethiopian and global sheep breeds showed that fat-tailed breeds from Eastern and Southern Africa clustered together, suggesting that these breeds were introduced to the African continent via the Horn and migrated further south.
| S-EPMC5744078 | biostudies-literature
Project description:ObjectiveEuropean pigs have been imported to improve the economically important traits of Thai pigs by crossbreeding and was finally completely replaced. Currently Thai indigenous pigs are particularly kept in a small population. Therefore, indigenous pigs risk losing their genetic diversity and identity. Thus, this study was conducted to perform large-scale genetic diversity and phylogenetic analyses on the many pig breeds available in Thailand.MethodsGenetic diversity and phylogenetics analyses of 222 pigs belonging to Thai native pigs (TNP), Thai wild boars (TWB), European commercial pigs, commercial crossbred pigs, and Chinese indigenous pigs were investigated by genotyping using 26 microsatellite markers.ResultsThe results showed that Thai pig populations had a high genetic diversity with mean total (TNA) and effective (Ne) number of alleles of 14.59 and 3.71, respectively, and expected heterozygosity (He) across loci (0.710). The polymorphic information content (PIC) per locus ranged between 0.651 and 0.914 leading to an average value above all loci of 0.789, and private alleles were found in six populations. The higher He compared to Ho in TNP, TWB, and the commercial pigs indicated some inbreeding within a population. The Nei's genetic distance, mean FST estimates, neighbour-joining tree of populations and individual, as well as multidimensional analysis indicated close genetic relationship between Thai indigenous pigs and some Chinese pigs, and they are distinctly different from European pigs.ConclusionOur study reveals a close genetic relationship between Thai native pigs and Chinese pigs. The genetic introgression from European breeds is found in some Thai native pig populations, and signs of genetic erosion are shown. Private alleles found in this study should be taken into consideration for the breeding program. The genetic information from this study will be a benefit for both conservation and utilization of Thai pig genetic resources.
| S-EPMC6718910 | biostudies-literature
Project description:Indigenous cattle in Sichuan Province, southwestern China, provide abundant genetic resources. However, their genetic diversity and population structure remain largely unknown, especially on the genome-wide scale. In the present study, we successfully employed the restriction site-associated DNA sequencing approach (RADseq) to explore genome-wide SNPs among six breeds of Sichuan cattle. A total of 238,725 high-confidence SNPs were finally obtained with a mean distance of 11,140 bp between two adjacent sites, and 43.4% were revealed to be novel in comparison with a public reference database of genetic variants. The mean nucleotide diversity and polymorphism information content (PIC) among all six breeds were 0.1878 and 0.1555, respectively. Pingwu and Ganzi cattle showed the highest and lowest genetic diversity, respectively. The inter-breed comparisons revealed that Ganzi and Ebian cattle were obviously separate from the others. Our reference set of genome-wide SNPs specific to indigenous cattle in Sichuan is the first of its kind. Moreover, our set can be used to investigate the genetic diversity and population structure and for genome-wide association studies.
| S-EPMC6082554 | biostudies-literature
Project description:Transitioning from traditional to new genotyping technologies requires the development of bridging methodologies to avoid extra genotyping costs. This study aims to identify the optimum number of single nucleotide polymorphisms (SNPs) necessary to accurately impute microsatellite markers to develop a low-density SNP chip for parentage verification in the Assaf sheep breed. The accuracy of microsatellite marker imputation was assessed with three metrics: genotype concordance (C), genotype dosage (length r2), and allelic dosage (allelic r2), for all imputation scenarios tested (0.5-10 Mb microsatellite flanking SNP windows). The imputation accuracy for the three metrics analyzed for all haplotype lengths tested was higher than 0.90 (C), 0.80 (length r2), and 0.75 (allelic r2), indicating strong genotype concordance. The window with 2 Mb length provides the best accuracy for the imputation procedure and the design of an affordable low-density SNP chip for parentage testing. We additionally evaluated imputation performance under two null models, naive (imputing the most common allele) and random (imputing by randomly selecting the allele), which in comparison showed weak genotype concordances (0.41 and 0.15, respectively). Therefore, we describe a precise methodology in the present article to impute multiallelic microsatellite genotypes from a low-density SNP chip in sheep and solve the problem of parentage verification when different genotyping platforms have been used across generations.
| S-EPMC7824810 | biostudies-literature
Project description:The classical MHC class I and class II molecules play key roles in determining the antigenic-specificity of CD8+ and CD4+ T-cell responses-as such characterisation of the repertoire of MHCI and MHCII allelic diversity is fundamental to our ability to understand, and potentially, exploit how genetic diversity influences the outcome of immune responses. Cattle remain one of the most economically livestock species, with particular importance to many small-holder farmers in low-and-middle income countries (LMICs). However, our knowledge of MHC (BoLA) diversity in the indigenous breeds that form the mainstay of cattle populations in many LMICs remains very limited. In this study we develop a MiSeq-based platform to enable the rapid analysis of BoLA-DQA and BoLA-DQB, and combine this with similar platforms to analyse BoLA-I and BoLA-DRB repertoires, to study a large cohort of cattle (~800 animals) representing the 3 major indigenous breeds (Angoni, Barotse, Tonga) in Zambia. The data presented confirms the capacity of this high-throughput and high-resolution approach to provide a full characterisation of the MHCI-MHCII genotypes of cattle for which little previous MHC sequence data has been obtained. The cattle in Zambia were found to express a diverse range of MHCI, MHCII and extended MHCI-MHCII haplotypes. The combined MHCI-MHCII genotyping now possible opens new opportunities to rapidly expand our knowledge of MHC diversity in cattle that could find applications in a related translational disciplines such as vaccine development.
| S-EPMC10952738 | biostudies-literature
Project description:Levels of inbreeding in cattle populations have increased in the past due to the use of a limited number of bulls for artificial insemination. High levels of inbreeding lead to reduced genetic diversity and inbreeding depression. Various estimators based on different sources, e.g., pedigree or genomic data, have been used to estimate inbreeding coefficients in cattle populations. However, the comparative advantage of using full sequence data to assess inbreeding is unknown. We used pedigree and genomic data at different densities from 50k to full sequence variants to compare how different methods performed for the estimation of inbreeding levels in three different cattle breeds.Five different estimates for inbreeding were calculated and compared in this study: pedigree based inbreeding coefficient (F(PED)); run of homozygosity (ROH)-based inbreeding coefficients (F(ROH)); genomic relationship matrix (GRM)-based inbreeding coefficients (F(GRM)); inbreeding coefficients based on excess of homozygosity (F(HOM)) and correlation of uniting gametes (F(UNI)). Estimates using ROH provided the direct estimated levels of autozygosity in the current populations and are free effects of allele frequencies and incomplete pedigrees which may increase in inaccuracy in estimation of inbreeding. The highest correlations were observed between F(ROH) estimated from the full sequence variants and the F(ROH) estimated from 50k SNP (single nucleotide polymorphism) genotypes. The estimator based on the correlation between uniting gametes (F(UNI)) using full genome sequences was also strongly correlated with F(ROH) detected from sequence data.Estimates based on ROH directly reflected levels of homozygosity and were not influenced by allele frequencies, unlike the three other estimates evaluated (F(GRM), F(HOM) and FU(NI)), which depended on estimated allele frequencies. F(PED) suffered from limited pedigree depth. Marker density affects ROH estimation. Detecting ROH based on 50k chip data was observed to give estimates similar to ROH from sequence data. In the absence of full sequence data ROH based on 50k can be used to access homozygosity levels in individuals. However, genotypes denser than 50k are required to accurately detect short ROH that are most likely identical by descent (IBD).
| S-EPMC4509611 | biostudies-literature
Project description:Rwanda has about 4.5 million of indigenous chicken (IC) that are very low in productivity. To initiate any genetic improvement programme, IC needs to be accurately characterized. The key purpose of this study was to ascertain the genetic diversity of IC in Rwanda using microsatellite markers. Blood samples of IC sampled from 5 agro-ecological zones were collected from which DNA was extracted, amplified by PCR and genotyped using 28 microsatellite markers. A total of 325 (313 indigenous and 12 exotic) chickens were genotyped and revealed a total number of 305 alleles varying between 2 and 22 with a mean of 10.89 per locus. One hundred eighty-six (186) distinct alleles and 60 private alleles were also observed. The frequency of private alleles was highest in samples from the Eastern region, whereas those from the North West had the lowest. The influx of genes was lower in the Eastern agro-ecological zone than the North West. The mean observed heterozygosity was 0.6155, whereas the average expected heterozygosity was 0.688. The overall inbreeding coefficient among the population was 0.040. Divergence from the Hardy-Weinberg equilibrium was significant (p<0.05) in 90% of loci in all the populations. The analysis of molecular variance revealed that about 92% of the total variation originated from variation within populations. Additionally, the study demonstrated that IC in Rwanda could be clustered into four gene groups. In conclusion, there was considerable genetic diversity in IC in Rwanda, which represents a crucial genetic resource that can be conserved or optimized through genetic improvement.
| S-EPMC7117670 | biostudies-literature