Genetic characterization of a herd of the endangered Danish Jutland cattle

Pertoldi, Cino; Purfield, D. C.; Berg, Peer; Jensen, Trine Hammer; Bach, O. S.; Vingborg, R. K. K.; Kristensen, Torsten Nygaard

doi:10.2527/jas.2013-7206

Cited by 20 publications

(20 citation statements)

References 22 publications

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“…The results presented in this study also provide insight for conserving livestock breeds, an internationally recognized issue of concern (Pertoldi et al 2014;FAO 2013;Welsh et al 2010). These results suggest that endangered breeds can be hybridized in an effort to maintain viable populations capable of improving productivity.…”

Section: Discussionmentioning

confidence: 56%

Dynamics of genomic architecture during composite breed development in cattle

et al. 2020

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Summary Some livestock breeds face the challenge of reduced genetic variation, increased inbreeding depression owing to genetic drift and selection. Hybridization can reverse these processes and increase levels of productivity and adaptation to various environmental stressors. Samples from American Brangus were used to evaluate the indicine/taurine composition through nine generations (~45 years) after the hybridization process was completed. The purpose was to determine how hybridization alters allelic combinations of a breed over time when genetic factors such as selection and drift are operating. Furthermore, we explored genomic regions with deviations from the expected composition from the progenitor breeds and related these regions to traits under selection. The Brangus composition deviated from the theoretical expectation, defined by the breed association, of 62.5% taurine, showing taurine composition to be 70.4 ± 0.6%. Taurine and indicine proportion were not consistent across chromosomes. Furthermore, these non‐uniform areas were found to be associated with traits that were probably under selection such as intermuscular fat and average daily gain. Interestingly, the sex chromosomes were predominantly taurine, which could be due to the composite being formed particularly in the final cross that resulted in progeny designated as purebred Brangus. This work demonstrated the process of new breed formation on a genomic level. It suggests that factors like genetic drift, selection and complementarity shift the genetic architecture into a uniquely different population. These findings are important to better understand how hybridization and crossbreeding systems shape the genetic architecture of composite populations.

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Section: Discussionmentioning

confidence: 56%

Dynamics of genomic architecture during composite breed development in cattle

et al. 2020

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“…Among the 16 Chillingham cattle, 9.1% of the SNP loci on the HD SNP panel exhibit allelic polymorphism, compared with the estimated 62-90% polymorphic loci found in 14 taurine and indicine breeds (Ramey et al 2013;Pertoldi et al 2014;Porto-Neto et al 2014); these studies had sample sizes ranging from 39 to 262 individuals and applied no filter on low MAF SNPs (except for Pertoldi et al 2014 BTA1 for the Chillingham and three other cattle breeds (one dairy, two beef white breeds -Holstein-Friesian, Chianina, and Romagnola) is shown in Fig. 3.…”

Section: Discussionmentioning

confidence: 99%

Inbreeding and purging at the genomic Level: the Chillingham cattle reveal extensive, non‐random SNP heterozygosity

et al. 2015

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SummaryLocal breeds of livestock are of conservation significance as components of global biodiversity and as reservoirs of genetic variation relevant to the future sustainability of agriculture. One such rare historic breed, the Chillingham cattle of northern England, has a 350-year history of isolation and inbreeding yet shows no diminution of viability or fertility. The Chillingham cattle have not been subjected to selective breeding. It has been suggested previously that the herd has minimal genetic variation. In this study, high-density SNP genotyping with the 777K SNP chip showed that 9.1% of loci on the chip are polymorphic in the herd, compared with 62-90% seen in commercial cattle breeds. Instead of being homogeneously distributed along the genome, these loci are clustered at specific chromosomal locations. A high proportion of the Chillingham individuals examined were heterozygous at many of these polymorphic loci, suggesting that some loci are under balancing selection. Some of these frequently heterozygous loci have been implicated as sites of recessive lethal mutations in cattle. Linkage disequilibrium equal or close to 100% was found to span up to 1350 kb, and LD was above r 2 = 0.25 up to more than 5000 kb. This strong LD is consistent with the lack of polymorphic loci in the herd. The heterozygous regions in the Chillingham cattle may be the locations of genes relevant to fitness or survival, which may help elucidate the biology of local adaptation in traditional breeds and facilitate selection for such traits in commercial cattle.

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“…Therefore, estimate of F using ROH is particularly appealing as the number of generations of inbreeding and the history of recent selection events can be inferred from the extend and frequency of ROH regions (Purfield et al, 2012). Although ROH from high-throughput genotyping analyses have been studied extensively in humans, these estimates are rare in cattle, particular in local breeds, and in other livestock species (Purfield et al, 2012;Ferenčaković et al, 2013a;Silió et al, 2013;Pertoldi et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

Mastrangelo

Tolone

Gerlando

et al. 2016

Animal

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128

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In the local breeds with small population size, one of the most important problems is the increase of inbreeding coefficient ( F). High levels of inbreeding lead to reduced genetic diversity and inbreeding depression. The availability of high-density single nucleotide polymorphism (SNP) arrays has facilitated the quantification of F by genomic markers in farm animals. Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes and represent an estimate of the degree of autozygosity at genome-wide level. The current study aims to quantify the genomic F derived from ROH ( F ROH ) in three local dairy cattle breeds. F ROH values were compared with F estimated from the genomic relationship matrix ( F GRM ), based on the difference between observed v. expected number of homozygous genotypes ( F HOM ) and the genomic homozygosity of individual i ( F MOL i ). The molecular coancestry coefficient ( f MOL ij ) between individuals i and j was also estimated. Individuals of Cinisara (71), Modicana (72) and Reggiana (168) were genotyped with the 50K v2 Illumina BeadChip. Genotypes from 96 animals of Italian Holstein cattle breed were also included in the analysis. We used a definition of ROH as tracts of homozygous genotypes that were >4 Mb. Among breeds, 3661 ROH were identified. Modicana showed the highest mean number of ROH per individual and the highest value of F ROH , whereas Reggiana showed the lowest ones. Differences among breeds existed for the ROH lengths. The individuals of Italian Holstein showed high number of short ROH segments, related to ancient consanguinity. Similar results showed the Reggiana with some extreme animals with segments covering 400 Mb and more of genome. Modicana and Cinisara showed similar results between them with the total length of ROH characterized by the presence of large segments. High correlation was found between F HOM and F ROH ranged from 0.83 in Reggiana to 0.95 in Cinisara and Modicana. The correlations among F ROH and other estimated F coefficients were generally lower ranged from 0.45 ( F MOL i − F ROH ) in Cinisara to 0.17 ( F GRM − F ROH ) in Modicana. On the basis of our results, recent inbreeding was observed in local breeds, considering that 16 Mb segments are expected to present inbreeding up to three generations ago. Our results showed the necessity of implementing conservation programs to control the rise of inbreeding and coancestry in the three Italian local dairy cattle breeds.Keywords: genomic inbreeding, local cattle breeds, runs of homozygosity ImplicationsIn the local breeds with small population size, one of the most important problems is the increase of inbreeding that leads to different negative effects as a reduction in phenotypic values. The current study aims to quantify the genomic inbreeding derived from runs of homozygosity (ROH) (F ROH ) in three Italian local dairy cattle breeds. According to ROH results, recent inbreeding was well detected in the investigated local dairy cattle breeds. Our results showed the necessity of implementing co...

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Genetic characterization of a herd of the endangered Danish Jutland cattle

Cited by 20 publications

References 22 publications

Dynamics of genomic architecture during composite breed development in cattle

Dynamics of genomic architecture during composite breed development in cattle

Inbreeding and purging at the genomic Level: the Chillingham cattle reveal extensive, non‐random SNP heterozygosity

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

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