Estimation of Linkage Disequilibrium, Effective Population Size, and Genetic Parameters of Phenotypic Traits in Dabieshan Cattle

Jin, Hai; Zhao, Shuaiyang; Jia, Yutang; Liu, Xu

doi:10.3390/genes14010107

Cited by 5 publications

(7 citation statements)

References 39 publications

(54 reference statements)

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“…The method of Santiago et al (2020) has now been applied to different species, particularly in the last year, including insects, such as honeybees (Sang et al, 2022); birds, such as Black Robin (von Seth et al, 2022); fishes, such as turbot, seabream and seabass (Saura et al, 2021), Baltic herring (Atmore et al, 2022), pikeperch (De Los Ríos-Pérez et al, 2022, coho salmon (Martinez et al, 2022), catfish (Coimbra et al, 2023) and sailfish (Ferrette et al, 2023); wild mammals, such as grey wolf (Pacheco et al, 2022), killer whales (Kardos et al, 2023), sika deer (Iijima et al, 2023), scimitar-horned oryx (Humble et al, 2023) and gorilla (Alvarez-Estape et al, 2023); humans (Bird et al, 2023); domestic species, such as pigs (Krupa et al, 2022), cattle (Jin et al, 2022;Magnier et al, 2022), sheep (Djokic et al, 2023;Drzaic et al, 2022), horse (Criscione et al, 2022) and chicken (Gao et al, 2023;Liu et al, 2023); plants, such as walnut (Ding et al, 2022); crustaceans, such as Daphnia (Wersebe & Weider, 2023) and fungi (Singh et al, 2021). As suggested by Santiago et al (2020), the method is generally reliable for about 200 generations in the past, although…”

Section: Discussionmentioning

confidence: 99%

An empirical test of the estimation of historical effective population size using Drosophila melanogaster

Novo

Pérez‐Pereira

Santiago

et al. 2023

Molecular Ecology Resources

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The availability of a large number of high‐density markers (SNPs) allows the estimation of historical effective population size (Ne) from linkage disequilibrium between loci. A recent refinement of methods to estimate historical Ne from the recent past has been shown to be rather accurate with simulation data. The method has also been applied to real data for numerous species. However, the simulation data cannot encompass all the complexities of real genomes, and the performance of any estimation method with real data is always uncertain, as the true demography of the populations is not known. Here, we carried out an experimental design with Drosophila melanogaster to test the method with real data following a known demographic history. We used a population maintained in the laboratory with a constant census size of about 2800 individuals and subjected the population to a drastic decline to a size of 100 individuals. After a few generations, the population was expanded back to the previous size and after a few further generations again expanded to twice the initial size. Estimates of historical Ne were obtained with the software GONE both for autosomal and X chromosomes from samples of 17 individuals sequenced for the whole genome. Estimates of the historical effective size were able to infer the patterns of changes that occurred in the populations showing generally good performance of the method. We discuss the limitations of the method and the application of the software carried out so far.

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Section: Discussionmentioning

confidence: 99%

An empirical test of the estimation of historical effective population size using Drosophila melanogaster

Novo

Pérez‐Pereira

Santiago

et al. 2023

Molecular Ecology Resources

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“…This approach on which SNeP relies for estimation of the historical N e is limited to the assumption of linear or steady population. Under this recently developed GONE software has been demonstrated with the ability to discern significant shifts in the historical N e [38][39][40][41][42]. A simulation study concluded that the N e derived using GONE reflects genuine demographic changes across generations and is not significantly impacted by selection or the heterogeneity in recombination rate across the genome [39].…”

Section: Discussionmentioning

confidence: 99%

“…Because of this, it is challenging to forecast with accuracy how drift will affect LD cumulatively over generations, especially when the recombination rate is low [14]. The GONE software has also been reported to work well with a small sample size [38]. When measuring the effective population sizes in turbot, seabream, European seabass, and common carp species of fish using GONE [40] discovered a similar pattern of drastic reduction of N e between the five to nine generations, and these declines might be related to the mixing, founder effect, and artificial selection.…”

Section: Discussionmentioning

confidence: 99%

Comparative assessment of the effective population size and linkage disequilibrium of Karan Fries cattle revealed viable population dynamics

Bhardwaj,

Togla,

Mumtaz

et al. 2024

Anim Biosci

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Objective: Karan Fries (KF), a high-producing composite cattle was developed through crossing indicine Tharparkar cows with taurine bulls (Holstein Friesian, Brown Swiss, and Jersey), to increase the milk yield across India. This composite cattle population must maintain sufficient genetic diversity for long-term development and breed improvement in the coming years. The level of linkage disequilibrium (LD) measures the influence of population genetic forces on the genomic structure and provides insights into the evolutionary history of populations, while the decay of LD is important in understanding the limits of genome-wide association studies for a population. Effective population size (Ne) which is genomically based on LD accumulated over the course of previous generations, is a valuable tool for e valuation of the genetic diversity and level of inbreeding. The present study was undertaken to understand KF population dynamics through the estimation of Ne and LD for the longterm sustainability of these breeds.Methods: The present study included 96 KF samples genotyped using Illumina HDBovine array to estimate the effective population and examine the LD pattern. The genotype data were also obtained for other crossbreds (Santa Gertrudis, Brangus, and Beefmaster) and Holstein Friesian cattle for comparison purposes.Results: The average LD between single nucleotide polymorphisms (SNPs) was r2 = 0.13 in the present study. LD decay (r2 = 0.2) was observed at 40 kb inter-marker distance, indicating a panel with 62,765 SNPs was sufficient for genomic breeding value estimation in KF cattle. The pedigree-based Ne of KF was determined to be 78, while the Ne estimates obtained using LD-based methods were 52 (SNeP) and 219 (genetic optimization for Ne estimation), respectively.Conclusion: KF cattle have an Ne exceeding the FAO's minimum recommended level of 50, which was desirable. The study also revealed significant population dynamics of KF cattle and increased our understanding of devising suitable breeding strategies for longterm sustainable development.

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“…Nevertheless, these results were similar to those estimated for indigenous cattle breeds from India (Strucken et al, 2021; N e = 13, 30 and 43), Bangladesh (Bhuiyan et al, 2021; N e = 26.02-108.29 until five generations ago), Korea (Sudrajad et al, 2016; N e = 53-60 11 generations ago), China and Japan ; N e = 27, 34 and 14 for South and North Chinese cattle, and Black Japanese breed, respectively) and South Africa (Dlamini et al, 2022; N e = 56-99 for five generations ago). Other native breeds such as Dabieshan Chinese cattle (Jin et al, 2022; N e = 86 for one generation ago) and Indian native cattle (Strucken et al, 2021; N e = 399 for one generation ago) exhibited higher values. The significant decrease of N e in recent generations in Creole cattle populations agrees with the high contribution of large segments of F ROH to the inbreeding values.…”

Section: Sc Usmentioning

confidence: 98%

Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America

Marcuzzi,

Calcaterra,

Loza Vega

et al. 2024

Animal Genetics

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The conservation of animal genetic resources refers to measures taken to prevent the loss of genetic diversity in livestock populations, including the protection of breeds from extinction. Creole cattle populations have suffered a drastic reduction in recent decades owing to absorbent crosses or replacement with commercial breeds of European or Indian origin. Genetic characterization can serve as a source of information for conservation strategies to maintain genetic variation. The objective of this work was to evaluate the levels of inbreeding and kinship through the use of genomic information. A total of 903 DNAs from 13 cattle populations from Argentina, Bolivia and Uruguay were genotyped using an SNP panel of 48 K. Also, a dataset of 76 K SNPs from Peruvian Creole was included. Two inbreeding indices (FROH and Fhat2) and kinship relationships were calculated. In addition, effective population size (Ne), linkage disequilibrium, population composition and phylogenetic relationships were estimated. In Creole cattle, FROH ranged from 0.14 to 0.03, and Fhat2 was close to zero. The inferred Ne trends exhibited a decline toward the present for all populations, whereas Creole cattle presented a lower magnitude of Ne than foreign breeds. Cluster analysis clearly differentiated the taurine and Zebu components (K2) and showed that Bolivian Creole cattle presented Zebu gene introgression. Despite the population reduction, Creole populations did not present extreme values of consanguinity and kinship and maintain high levels of genetic diversity. The information obtained in this work may be useful for planning conservation programmes for these valuable local animal genetic resources.

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Estimation of Linkage Disequilibrium, Effective Population Size, and Genetic Parameters of Phenotypic Traits in Dabieshan Cattle

Cited by 5 publications

References 39 publications

An empirical test of the estimation of historical effective population size using Drosophila melanogaster

An empirical test of the estimation of historical effective population size using Drosophila melanogaster

Comparative assessment of the effective population size and linkage disequilibrium of Karan Fries cattle revealed viable population dynamics

Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America

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