Consequences for diversity when animals are prioritized for conservation of the whole genome or of one specific allele

Engelsma, K.A.; Veerkamp, R.F.; Calus, M.P.L.; Windig, J.J.

doi:10.1111/jbg.12052

Cited by 9 publications

(10 citation statements)

References 22 publications

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“…They furthermore showed that restricting the increase in similarity at specific regions would result in an increase in similarity for the rest of the genome. This was also described by Engelsma et al [296] and Roughsedge et al [297]. By including a constraint on the increase in similarity for the rest of the genome, this increase could be limited, although it was still higher than when no region-specific management was applied [82].…”

Section: Region-specific Diversity Managementsupporting

confidence: 53%

“…Various studies have stressed the potential benefit of maintaining diversity in specific regions of the genome, such as the Major Histocompatibility Complex (MHC) or regions associated with inbreeding depression [82,295,296]. With an approach like SDP, it is technically possible to perform region-specific diversity management.…”

Section: Region-specific Diversity Managementmentioning

confidence: 99%

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Genomic characterization and conservation of genetic diversity in cattle

Doekes¹

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Genetic diversity in livestock populations is important, because it forms the basis for these populations to adapt to changing environments and human demands. Traditionally, livestock genetic diversity has been characterized and conserved with pedigree-based measures of inbreeding and kinship. Thanks to the increasing availability of genomic information, in particular single nucleotide polymorphism (SNP) data, we now have additional opportunities to better manage genetic diversity. In this thesis, I utilized SNP data to characterize and conserve genetic diversity in Dutch cattle, both in in situ populations and ex situ gene bank collections. The Holstein Friesian (HF) breed was the main breed of interest, because of its importance in the Dutch and global dairy cattle sector. First, it was demonstrated how changes in breeding practices in the past have been accompanied by changes in genetic diversity trends in the Dutch-Flemish HF breeding program. Among others, it was shown that the introduction of genomic selection has been accompanied by an increase in pedigree-based and SNP-based rates of inbreeding and kinship. Second, the negative effects of inbreeding on performance ("inbreeding depression") were quantified for yield, fertility and udder health traits of Dutch HF cows. It was shown that recent inbreeding may be more harmful than ancient inbreeding, although results were mixed. It was also shown that, based on SNP data, the negative effects of inbreeding are quite equally distributed across the genome and well captured by genome-wide homozygosity. Third, the value of the Dutch cattle gene bank collection was demonstrated. It was shown that old HF gene bank bulls can be used in the current or future HF breeding program to increase (or recover) genetic diversity, or to improve genetic merit given a certain level of diversity. It was also shown that Dutch native breeds in the gene bank collection harbor genetic diversity, both within and across breeds, although some breeds showed substantial overlap. Last, it was discussed how genomic information (in particular SNP data) can be used to maintain genetic diversity in livestock populations. Based on our current knowledge and the availability of SNP data, I recommend to limit the increase in SNP-by-SNP similarity (and, thus, homozygosity) while performing selection. For gene bank collections, I envision a transition towards bio-digital resource centers, in which large amounts of genomic and phenotypic data are stored in addition to physical germplasm material. Overall, the findings of this thesis improve our understanding of (conservation of) genetic diversity in livestock and, thereby, contribute to sustainable livestock production.

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Section: Region-specific Diversity Managementsupporting

confidence: 53%

Section: Region-specific Diversity Managementmentioning

confidence: 99%

Genomic characterization and conservation of genetic diversity in cattle

Doekes¹

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“…Selection may directly cause changes in the frequency of major and minor alleles. Significance of frequencies of such alleles in the assessment of genetic diversity has been the object of various studies (Kaur et al, 2014;Engelsma et al, 2013), because they are an indicator of genetic variability and polymorphism in the observed locus (Singh et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

Genetic variability and biodiversity of Ukrainian Gray cattle by the BoLA-DRB3 gene

Suprovych¹,

Suprovych²,

Mokhnachova³

et al. 2021

Regul. Mech. Biosyst.

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At the current stage of genetic studies of cattle, more and more attention is being drawn to autochthonous breeds. Native cattle have a number of prominent phenotypic traits and have preserved unique genes and their combinations lost by modern commercial breeds, which would be valuable to use in selective programs. We surveyed polymorphism of the Ukrainian autochthonous Gray breed according to alleles of exon 2 of the BoLA-DRB3 gene. The uniqueness of the gene lies in the broad variability of its allele variants. Significant informativeness at DNA level is quite important for genetic studies. We surveyed allele polymorphism using the PCR-RLFP method on DNA isolated from 88 samples of blood of cows and 5 samples of sperm. We identified 28 alleles, of which 23 variants were nomenclature ones and 5 (jba, *jab, *jbb, *nad and *nda) were “without established nomenclature”, their share accounting for 8.9%. Four alleles *06, *12, *16 and *jba had a frequency above 5% and occupied 69.9% of the breed’s allele fund overall. The commonest allele was BoLA-DRB3.2*16 (44.1%). In total, we found 40 genotypes. Considering the significant dominance of variant *16, as expected, 5 genotypes with its inclusion occurred: *16/*16, *12/*16, *06/*16, *16/*24 and *jba/*16. It was present in the genotype of two out three studied animals. Parameters of heterozygosity, effective number of alleles, Shannon and Pielou indices indicate that Ukrainian Gray cattle are characterized by lowest level of genetic variability and biodiversity according to the BoLA-DRB3 gene compared with other breeds. Due to significant dominance of allele *16, the breed has no inbred motifs. We noted deviation toward increase in homozygosity without deviations from the norm of the distribution according to Hardy-Weinberg equilibrium. The obtained results will be used for genetic-populational programs with the purpose of improving the genetic potential of cattle breeds in terms of economically beneficial traits and diseases of cattle.

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“…In the cases of adaptively neutral loci, genetic drift has a significant role on the distribution of allelic frequencies. The importance of major and minor allele frequencies in genetic diversity estimation were subjects of various studies (De la Cruz & Raska, 2014; Kaur et al, 2014;Engelsma et al, 2013).…”

mentioning

confidence: 99%

iMAF - INDEX OF MAJOR ALLELE FREQUENCY

Pojskić

2018

GenApp

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Consequences for diversity when animals are prioritized for conservation of the whole genome or of one specific allele

Cited by 9 publications

References 22 publications

Genomic characterization and conservation of genetic diversity in cattle

Genomic characterization and conservation of genetic diversity in cattle

Genetic variability and biodiversity of Ukrainian Gray cattle by the BoLA-DRB3 gene

iMAF - INDEX OF MAJOR ALLELE FREQUENCY

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