A genetically unique Chinese cattle population shows evidence of common ancestry with wild species when analysed with a reduced ascertainment bias SNP panel

Barbato, Mario; Reichel, Michael P.; Passamonti, Matilde Maria; Low, Wai Yee; Colli, Licia; Tearle, Rick; Williams, J. L.; Marsan, P. Ajmone

doi:10.1371/journal.pone.0231162

Cited by 9 publications

(11 citation statements)

References 47 publications

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“…The results point to the fact that the Limousine was involved in the formation of Blonde d'Aquitaine and have common historical ancestors. As expected, the Angus and Red Angus are more genetically linked together and appeared on the same branch as the Hereford breed similarly as reported by Barbato et al (2020). The Charolais breed is separated from other breeds under consideration.…”

Section: Resultssupporting

confidence: 85%

Evaluation of Genetic Diversity in Selected Beef Breeds

Lehocká

Kasarda

Olšanská

et al. 2020

AGR

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The aim of the study was to estimate genetic drift and gene flow related to population structure and genetic diversity in selected beef cattle. For the evaluation of the genetic drift and gene flow among analysed populations, the Bayesian Population Structure Analysis and software Treemix were used. The genetic analysis included two cattle breeds bred in Slovakia (Charolais and Limousine). In addition to the Limousine and Charolais breeds, other beef cattle (Angus N = 90, Belgian Blue N = 4, Blonde d'Aquitaine N= 5, Hereford N = 98 and Red Angus N = 15) were analysed. The 50k Bead chip was used; the dataset consisted of 34,834 SNPs. To avoid detection bias, SNPs with high linkage disequilibrium (r2 = 0.05) were pruned from the database; the final data set consisted of 296 animals and 2,539 SNP markers. Our results reflected four modes of gene flow between Angus, Red Angus, Charolais, Limousine and Hereford. Analysed breeds were not confirmed to influence genetic make-up of Belgian Blue and Blonde d'Aquitaine populations. All migration edges reached weight values below 0.2. The only two migration edges higher in weight was observed, first between the ancestor of Limousine breed into Blond d'Aquitaine, and second among historical ancestor of Hereford breed into Red Angus. Our results reflect that the donor population has made a significant contribution to the recipient population.

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Section: Resultssupporting

confidence: 85%

Evaluation of Genetic Diversity in Selected Beef Breeds

Lehocká

Kasarda

Olšanská

et al. 2020

AGR

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“…in [ 29 ] the observed heterozygosities for indicine breeds were lower than 0.21 and those for taurine breeds were higher than 0.3. However, a deeper analysis detected an ascertainment bias that explained this difference since the SNP array chips were predominantly based on taurine breeds [ 30 , 33 , 34 ]. A number of later studies (including the 1000 bull genomes project) based on whole-genome sequencing data showed that indicine breeds had an almost two-fold higher nucleotide diversity, i.e.…”

Section: Discussionmentioning

confidence: 99%

Deleterious protein-coding variants in diverse cattle breeds of the world

Subramanian

2021

Genet Sel Evol

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The domestication of wild animals has resulted in a reduction in effective population sizes, which can affect the deleterious mutation load of domesticated breeds. In addition, artificial selection contributes to the accumulation of deleterious mutations because of an increased rate of inbreeding among domesticated animals. Since founder population sizes and artificial selection differ between cattle breeds, their deleterious mutation load can vary. We investigated this question by using whole-genome data from 432 animals belonging to 54 worldwide cattle breeds. Our analysis revealed a negative correlation between genomic heterozygosity and nonsynonymous-to-silent diversity ratio, which suggests a higher proportion of single nucleotide variants (SNVs) affecting proteins in low-diversity breeds. Our results also showed that low-diversity breeds had a larger number of high-frequency (derived allele frequency (DAF) > 0.51) deleterious SNVs than high-diversity breeds. An opposite trend was observed for the low-frequency (DAF ≤ 0.51) deleterious SNVs. Overall, the number of high-frequency deleterious SNVs was larger in the genomes of taurine cattle breeds than of indicine breeds, whereas the number of low-frequency deleterious SNVs was larger in the genomes of indicine cattle than in those of taurine cattle. Furthermore, we observed significant variation in the counts of deleterious SNVs within taurine breeds. The variations in deleterious mutation load between taurine and indicine breeds could be attributed to the population sizes of the wild progenitors before domestication, whereas the variations observed within taurine breeds could be due to differences in inbreeding level, strength of artificial selection, and/or founding population size. Our findings imply that the incidence of genetic diseases can vary between cattle breeds.

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“…Hong Kong cattle show heterogeneous morphology, both in body type, size and coat colour. A recent analysis of the genotype showed that Hong Kong feral cattle have relatively high levels of genetic distinctiveness and stressed the conservation value of this population [ 36 ]. In this context, GonaCon could be used to increase time between births, with most cattle contributing to the population’s gene pool.…”

Section: Discussionmentioning

confidence: 99%

Long-term effect of a GnRH-based immunocontraceptive on feral cattle in Hong Kong

Pinkham

Koon

et al. 2022

PLoS ONE

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Increasing human-wildlife conflicts worldwide are driving the need for multiple solutions to reducing “problem” wildlife and their impacts. Fertility control is advocated as a non-lethal tool to manage free-living wildlife and in particular to control iconic species. Injectable immunocontraceptives, such as GonaCon, stimulate the immune system to produce antibodies against the gonadotrophin-releasing hormone (GnRH), which in turn affects the release of reproductive hormones in mammals. Feral cattle (Bos indicus or Bos taurus) in Hong Kong are an iconic species whose numbers and impacts on human activities have increased over the last decade. Previous studies have proven that a primer vaccination and booster dose of GonaCon in female cattle are safe and effective in reducing pregnancy levels one year post-treatment. The aims of this project were 1. to evaluate the longevity of the effect of GonaCon in feral cattle up to four years post-vaccination; and 2. to assess if a second booster dose of GonaCon, administered at either two or four years post-vaccination, extends the contraceptive effect in this species. Vaccination with GonaCon, administered as a primer and booster dose, was effective in causing significant infertility in free-living cattle for at least three years post-vaccination, with the percentage of pregnant animals in the vaccinated group decreasing from 76% at vaccination to 35%, 19% and 7% in years 2, 3 and 4 post-vaccination, compared with 67% at vaccination to 50%, 57% and 14% respectively in the control group. A second booster dose of GonaCon administered either 2 or 4 years after vaccination rendered 100% of the Treated cattle infertile for at least another year. These results suggested that vaccination with GonaCon can reduce feral cattle population growth and that a second booster dose can extend the longevity of the contraceptive effect.

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A genetically unique Chinese cattle population shows evidence of common ancestry with wild species when analysed with a reduced ascertainment bias SNP panel

Cited by 9 publications

References 47 publications

Evaluation of Genetic Diversity in Selected Beef Breeds

Evaluation of Genetic Diversity in Selected Beef Breeds

Deleterious protein-coding variants in diverse cattle breeds of the world

Long-term effect of a GnRH-based immunocontraceptive on feral cattle in Hong Kong

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