Accurate Estimation of Effective Population Size in the Korean Dairy Cattle Based on Linkage Disequilibrium Corrected by Genomic Relationship Matrix

Shin, Donghyun; Cho, Kwang-Hyun; Park, Kyoung-Do; Lee, Hyun-Jeong; Kim, Heebal

doi:10.5713/ajas.2013.13320

Cited by 23 publications

(36 citation statements)

References 33 publications

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“…Generally, as the distance among markers increase, the LD among them decreases. This trend was previously detected in goats [56], sheep [57], cattle [58] and pigs [46]. Additionally, the LD patterns have shown clear differences among species.…”

Section: Linkage Disequilibrium: Understanding the Demographic Historsupporting

confidence: 72%

Genomic Tools for Effective Conservation of Livestock Breed Diversity

2019

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Human concern about the status of genetic diversity in livestock breeds and their conservation has increased, as intense selection and reduced population sizes in many breeds has caused losses on the global livestock genetic biodiversity. Traditionally, pedigree data provided by the breeders were used to estimate genetic diversity parameters, but over the past decades, technology has made possible the development of genomic markers. The result has been new opportunities to estimate genetic diversity in more detail, and to improve selection as well as prioritizing animals for conservation of genetic resources. The aim of the review is to summarize the evolution of livestock genomic markers and to explore the potential of the newest high-throughput technologies for estimation and conservation of livestock genetic diversity. More accurate diversity parameters are observed when genomic information is used for selection decisions instead of the traditional estimates using pedigree data. It is also possible to estimate additional parameters such as linkage disequilibrium to calculate effective population size or to minimize the genetic relatedness among the selected individuals based on runs of homozygosity. For long-term perspectives, new methods on genome editing are considered as new perspectives to reach a genetic diversity balance.

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Section: Linkage Disequilibrium: Understanding the Demographic Historsupporting

confidence: 72%

Genomic Tools for Effective Conservation of Livestock Breed Diversity

2019

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“…The second approach is based on the average r 2 over different bins of genetical distance [26,47], which has been already mentioned earlier in the discussion. It aims at estimating population size on a much larger time scale and has been extensively applied in cattle [41,57,58] and other livestock species [59]. Indeed, a very large number of animals have been genotyped using SNP chips in these species, sometimes for other purposes, such as QTL detection, and used for LD estimation.…”

Section: Contribution To the Demographic History Of Cattlementioning

confidence: 99%

Inferring population size history from large samples of genome wide molecular data - an approximate Bayesian computation approach

Boitard

Rodríguez

Jay

et al. 2016

Preprint

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Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins ofNC 4.0 International license peer-reviewed) is the author/funder. It is made available under aThe copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/036178 doi: bioRxiv preprint first posted online Jan. 7, 2016; physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey), PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles.

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“…The presence of the extent of an effective population size (Ne), is an important population genetic parameter that has recently received a great deal of research attention [64], determining population demographic development [12] and demographic processes such as migration and admixture [45], and having profound implications for understanding the architecture of the animal genome [27,3]. In addition, Ne is widely regarded as one of the most critical population parameters because it measures the rates of genetic drift and inbreeding as well as affects the e cacy of systematic evolutionary forces such as mutation, selection, and migration [56]. It also helps to discover population demographic history and allows for the prediction of the behaviour of genetic diversity through time.…”

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confidence: 99%

“…Length and frequency of ROHs may also be used to distinguish distant from more recent inbreeding since the length of IBD segments follows an inverse exponential distribution with a mean of 1/2 g Morgans, where g is the number of generations from a common ancestor [23]. Effective populations (Ne) and ROH have been studied in humans [20], cattle [31,15,34], pigs [56,1] sheep [33] but less comprehensively in other livestock species, such as goats for designing conservation strategies especially on the communal indigenous goats of South Africa. The objective of this study was to determine the conservation status and historical relatedness of South African communal indigenous goat populations using genome-wide SNP markers.…”

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confidence: 99%

Conservation Status and Historical Relatedness of South African Communal Indigenous Goat Populations Using Genome-Wide Snp Marker

Chokoe¹,

Hadebe

Muchadeyi

et al. 2020

Preprint

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Background: Indigenous goats forms the majority of populations in smallholder; low input, low output production systems and are considered an important genetic resource due to their adaptability to different production environments and support communal farming. Effective population size (Ne), inbreeding levels, and the runs of homozygosity (ROHs) are effective tools for exploring the genetic diversity and understanding the demographic history in efforts to support breeding strategies to use and conserve genetic resources. Results: Across populations, the current Ne of Gauteng was the lowest at 371 animals, while the historical Ne across populations suggests that the ancestor Ne has decreased by 53.86%, 44.58%, 42.16% and 41.16% in Free State (FS), North West (NW), Limpopo (LP) and Gauteng (GP), respectively, over the last 971 generations. Genomic inbreeding levels related to ancient kinship (FROH >5Mb) was highest in FS (0.08±0.09) and lowest for Eastern Cape (EC) (0.02±0.02). A total of 871 ROH island regions which include important environmental adaptation and hermo-tolerance genes such as IL10RB, IL23A, FGF9, IGF1, EGR1, MTOR and MAPK3 were identified (occurring in over 20% of the samples) in FS (n = 37), GP (n = 42), NW (n = 2) populations only. The mean length of ROH across populations was 7.76Mb and ranged from 1.61Mb KwaZulu-Natal (KZN) to 98.05Mb (GP and NW). Distribution of ROH according to their size showed that the majority (n = 1949) of the detected ROH were >5Mb in length than the other categories. Assuming two hypothetical ancestral populations, the population from KZN and LP are revealed, supporting PC 1. The genomes of KZN and LP shared an origin but have substantial admixture from the EC and NW populations.Conclusions: These findings indicated a greater negative impact of inbreeding in recent times which is important for planning conservation strategies. It was revealed that the occurrence of high Ne and autozygosity varied largely across breeds in communal indigenous goat populations at different recent and ancient events when a genome-wide SNP marker was used.

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Accurate Estimation of Effective Population Size in the Korean Dairy Cattle Based on Linkage Disequilibrium Corrected by Genomic Relationship Matrix

Cited by 23 publications

References 33 publications

Genomic Tools for Effective Conservation of Livestock Breed Diversity

Genomic Tools for Effective Conservation of Livestock Breed Diversity

Inferring population size history from large samples of genome wide molecular data - an approximate Bayesian computation approach

Conservation Status and Historical Relatedness of South African Communal Indigenous Goat Populations Using Genome-Wide Snp Marker

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