Genetic Diversity and Population Structure of Ethiopian Sheep Populations Revealed by High-Density SNP Markers

Edea, Zewdu; Dessie, Tadelle; Dadi, Hailu; Do, Kyoung-Tag; Kim, Kwan‐Suk

doi:10.3389/fgene.2017.00218

Cited by 51 publications

(46 citation statements)

References 61 publications

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Section: Discussionsupporting

confidence: 93%

“…Perhaps this is because these animals are the result of and representative of the breeding strategies of purebred flocks. Other work in 97 sheep breeds across the world including Ethiopian sheep reported inbreeding coefficients between À0.07 and 0.16 and observed heterozygosity between 0.061 and 0.343, which are similar to our results (Edea et al 2017;Zhang et al 2018). Despite similarity in inbreeding coefficient and heterozygosity estimates, Western Suffolk shows moderate differentiation from Suffolk whereas Hampshire, Oxford, Shropshire and Suffolk show little to moderate differentiation from each other.…”

Section: Discussionsupporting

confidence: 89%

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Genetic structure and admixture in sheep from terminal breeds in the United States

Davenport

Hiemke²,

McKay

et al. 2020

Animal Genetics

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Summary Selection for performance in diverse production settings has resulted in variation across sheep breeds worldwide. Although sheep are an important species to the United States, the current genetic relationship among many terminal sire breeds is not well characterized. Suffolk, Hampshire, Shropshire and Oxford (terminal) and Rambouillet (dual purpose) sheep (n = 248) sampled from different flocks were genotyped using the Applied Biosystems Axiom Ovine Genotyping Array (50K), and additional Shropshire sheep (n = 26) using the Illumina Ovine SNP50 BeadChip. Relationships were investigated by calculating observed heterozygosity, inbreeding coefficients, eigenvalues, pairwise Wright’s FST estimates and an identity by state matrix. The mean observed heterozygosity for each breed ranged from 0.30 to 0.35 and was consistent with data reported in other US and Australian sheep. Suffolk from two different regions of the United States (Midwest and West) clustered separately in eigenvalue plots and the rectangular cladogram. Further, divergence was detected between Suffolk from different regions with Wright’s FST estimate. Shropshire animals showed the greatest divergence from other terminal breeds in this study. Admixture between breeds was examined using admixture, and based on cross‐validation estimates, the best fit number of populations (clusters) was K = 6. The greatest admixture was observed within Hampshire, Suffolk, and Shropshire breeds. When plotting eigenvalues, US terminal breeds clustered separately in comparison with sheep from other locations of the world. Understanding the genetic relationships between terminal sire breeds in sheep will inform us about the potential applicability of markers derived in one breed to other breeds based on relatedness.

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Section: Discussionsupporting

confidence: 93%

Section: Discussionsupporting

confidence: 89%

Genetic structure and admixture in sheep from terminal breeds in the United States

Davenport

Hiemke²,

McKay

et al. 2020

Animal Genetics

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“…), the vast exchange of domestic animals was inevitable (Boivin, 2017;Taylor et al, 2018). To date, large amounts of SNP genotyping data have been generated from worldwide popular sheep breeds (Kijas et al, 2012;Ciani et al, 2015) and local populations including Welsh (Beynon et al, 2015), Ethiopian (Edea et al, 2017), Chinese (Zhao et al, 2017), and Russian sheep (Deniskova et al, 2018). Analysis of whole genome data on the Kyrgyz sheep breeds including available SNP profiles of the European and Asian sheep populations might be useful to establish probable admixture patterns that resulted from ancient trade interactions.…”

Section: Introductionmentioning

confidence: 99%

Population Structure and Genetic Diversity of Sheep Breeds in the Kyrgyzstan

et al. 2019

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Sheep are a main livestock species of Kyrgyzstan, a Central Asian country with predominating mountain terrain. The current gene pool of local sheep resources has been forming under diverse climate conditions from the era of the trading caravans of the Great Silk Road, through the Soviet period of large-scale livestock improvements, which was followed by the deep crisis at the end of the 20th century, up to now. However, not much is known about the genetic background and variability of the local sheep populations. Therefore, our aims were to provide a characterization of the population structure and genetic relations within the Kyrgyz sheep breeds and to study their genetic connections with the global sheep breeds using SNP analysis. Samples of the Alai (n = 31), Gissar (n = 30), Kyrgyz coarse wool (n = 13), Aykol (n = 31), and Tien-Shan (n = 24) breeds were genotyped with the OvineSNP50 BeadChip or the Ovine Infinium HD BeadChip (Illumina Inc., USA). The measure of inbreeding based on runs of homozygosity showed a minimum value in the Aykol breed (F ROH = 0.034), while the maximum was found in the Alai breed (F ROH = 0.071). Short ROH segments (ROH ≤ 4 Mb) were predominant in all breeds. Long ROH segments (ROH > 16 Mb) were absent in the Gissar breed. The Gissar and Aykol breeds had the highest values of the effective population sizes estimated for five generations ago (Ne 5 = 660 and 563), whereas the Alai and Kyrgyz coarse wool displayed lower values (Ne 5 = 176 and 128, respectively). The synthetic origin of the Aykol breed was clearly evidenced by all analyses applied. Based on the network and admixture analyses of the Kyrgyz and global sheep breeds, the Tien-Shan and the Russian semi-fine wool breeds demonstrated a common ancestry that most likely is due to a contribution of the Lincoln breed. The Gissar, Aykol, and Kyrgyz coarse wool breeds showed a genetic background predominating in sheep populations from Iran and China whereas the Alai demonstrated the different ancestry type. The revealed admixture patterns probably resulted from the exchange and trade during the era of the Great Silk Road, which partly overlapped with historical and archeological findings.

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“…Single-nucleotide polymorphism (SNP) markers have been widely utilized in recent years due to their high abundance in the genome and the improved resolution they provide for populations (Carvalho et al, 2017;Edea et al, 2017;Fischer et al, 2017). With the development of next-generation sequencing (NGS), it is increasingly feasible to develop and genotype SNP markers across whole genomes rather than targeting specific regions.…”

Section: Introductionmentioning

confidence: 99%

Organellar Genome Variation and Genetic Diversity of Chinese Pyropia yezoensis

Tang

et al. 2019

Front. Mar. Sci.

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Pyropia yezoensis is an economically important marine algae crop that, due to its large economic value, has generated considerable interest in the development of breeding programs to improve its production rates. Here, we sequenced the complete mitochondrial and plastid genomes of the P. yezoensis strain RZ-58 using the PacBio RS II sequencing technology. The mitochondrial genome (mtDNA) is 41,692 bp in size with an overall guanine-cytosine (GC) content of 32.72%, and the plastid genome (ptDNA) is 191,977 bp with a GC content of 33.09%. The complete mitochondrial and plastid genomes of 53 individuals from three geographical populations were then resequenced using the next-generation sequencing (NGS) technology to characterize their molecular features. When compared, the plastid genomes displayed similar genomic lengths and conserved gene synteny. However, mitochondrial genomes were quite different in length, which was mainly due to the different patterns of intron distributions. Single-nucleotide polymorphisms (SNPs) were examined to evaluate the genetic diversity of different geographical populations. High diversity was observed across the whole collection with moderate genetic variation between populations. In total, there were 463 and 366 highquality SNPs detected in the mtDNA and ptDNA, respectively. The Qingdao wild group has the highest diversity with a mean pi of 0.00348 for mtDNA and 0.000388 for ptDNA, while the Yantai group had the lowest diversity. Cluster-based grouping and principal component analysis revealed three subpopulations in the whole collections. However, a genetic break of organellar DNA was observed in populations at sympatric localities, which was inferred as the result of historic biogeographic events. Our findings provide important information to guide marker-assisted selective breeding of Chinese P. yezoensis in the future.

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Genetic Diversity and Population Structure of Ethiopian Sheep Populations Revealed by High-Density SNP Markers

Cited by 51 publications

References 61 publications

Genetic structure and admixture in sheep from terminal breeds in the United States

Genetic structure and admixture in sheep from terminal breeds in the United States

Population Structure and Genetic Diversity of Sheep Breeds in the Kyrgyzstan

Organellar Genome Variation and Genetic Diversity of Chinese Pyropia yezoensis

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