Use of High-density SNP analyses to develop a long-term strategy for conventional populations to prevent loss of diversity - review

Article Details: Received: 2020-09-10 | Accepted: 2020-10-30 | Available online: 2020-12-31 https://doi.org/10.15414/afz.2020.23.04.236-240 The aim was to review obtained results related to molecular-genetic analyses by high-density SNP chips and mtDNA in farm and wild populations within the project APVV-17-0060 Genomic Indicators of extranuclear DNA as a source of Diversity for Animal Breeding. Continuous human activity and subsequent socioeconomic and climatic changes of the environment significantly affect the genetic diversity of livestock on both intra- and inter-population levels. Concerning the conservation of local livestock populations and thus animal genetic resources (AnGR) for future generations is, therefore, necessary to monitor and look for new “more precise“ tools to measure the amount of genetic diversity. The expected result will be the identification of SNP markers and spot mutations with a significant effect on the process of development resp. variability of traits. In the case of the dog, identification of regions related to fitness, health, and trainability will be the primary objective. Keywords: Genetic diversity, economically important breeds, Animal genetic resources, Slovakia References CURIK, I., FERENČAKOVIĆ, M. and SÖLKNER, J. (2014). Inbreeding and runs of homozygosity: a possible solution to an old problem. Livestock Science, 166, 26–34. ENGELSMA, K.A., VEERKAMP, R.F., CALUS, M.P., BIJMA, P. and WINDIG, J.J. (2012). Pedigree and marker-based methods in the estimation of genetic diversity in small groups of Holstein cattle. Journal of Animal Breeding and Genetics, 129, 195–205. FERENČAKOVIĆ, M., BANADINOVIĆ, M., MERCVAJLER, M., KHAYATZADEH, N., MÉSZÁROS, G., CUBRIC-CURIK, V., CURIK, I. and SÖLKNER, J. (2016) Mapping of heterozygosity rich regions in Austrian Pinzgauer cattle. Acta argiculturae Slovenica, Supplement 5, 41–44. KASARDA, R., KADLEČÍK, O., TRAKOVICKÁ, A. and MORAVČÍKOVÁ, N. (2019d). Genomic and pedigree-based inbreeding in Slovak Spotted cattle. In AGROFOR, 4(1), 102–110. KASARDA, R., Kadlečík, O., Trakovická, A. and Moravčíková, N. (2019f). Genomic and pedigree-based inbreeding in Slovak spotted cattle. In AGROFOR International Journal. KASARDA, R., MORAVČÍKOVÁ, N., HALO, M., HORNÝ, M., LEHOCKÁ, K., OLŠANSKÁ, B., BUJKO, J. and CANDRÁK, J. (2019a). Trend vývoja genomického inbrídingu v populácii plemena lipican. In Aktuálne smerovanie v chove koní. Nitra : Slovenská poľnohospodárska univerzita, p. 32–36. KASARDA, R., MORAVČÍKOVÁ, N., KADLEČÍK, O., TRAKOVICKÁ, A., HALO, M. and CANDRÁK, J. (2019b). Level of inbreeding in Norik of Muran horse: pedigree vs. genomic data. Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis, 67(6), 1457–1463. KASARDA, R., MORAVČÍKOVÁ, N., KADLEČÍK, O., TRAKOVICKÁ, A., ŽITNÝ, J., TERPAJ, V. P., MINDEKOVÁ, S. and MLYNEKOVÁ, L. (2019c). Common origin of local cattle breeds in western region of Carpathians. Danubian animal genetic resources, 4, 84–90. KASARDA, R., MORAVČÍKOVÁ, N., ŽIDEK, R., TRAKOVICKÁ, A. and KADLEČÍK, O. (2019e). Gene flow and diversity in local red deer populations. In 15th International Arctic Ungulate conference. 1st ed. 83 p. Arctic Ungulate conference. Uppsala : Swedish University of Agricultural Sciences, pp. 61. KASARDA, R., MORAVČÍKOVÁ, N., TRAKOVICKÁ, A., KRUPOVÁ, Z. and KADLEČÍK, O. (2017) Genomic variation across cervid species in respect to the estimation of Red deer diversity. Acta Veterinaria, 67(1), 43–56. KASARDA, R., MORAVČÍKOVÁ, N., ŽIDEK, R., MÉSZÁROS, G., KADLEČÍK, O., TRAKOVICKÁ, A. and POKORÁDI, J. (2015) Investigation of the genetic distances of bovids and cervids using BovineSNP50k BeadChip. Archiv Tierzucht, 58, 57–63. KASARDA, R., MORAVČÍKOVÁ, N., KUKUČKOVÁ, V., KADLEČÍK, O., TRAKOVICKÁ, A. and MÉSZÁROS, G. (2016). Evidence of selective sweeps through haplotype structure of Pinzgau cattle. Acta agriculturae Slovenica, 107(Suppl. 5), 160–164. KUKUČKOVÁ, V., MORAVČÍKOVÁ, N., CURIK, I., SIMČIČ, M., MÉSZÁROS, G. and KASARDA, R. (2018). Genetic diversity of local cattle. Acta Biochimica Polonica, 65(3), 421–424. KUKUČKOVÁ, V., MORAVČÍKOVÁ, N., FERENČAKOVIĆ, M., SIMČIČ, M., MÉSZÁROS, G., SÖLKNER, J., TRAKOVICKÁ, A., KADLEČÍK, O., CURIK, I. and KASARDA, R. (2017). Genomic characterization of Pinzgau cattle: genetic conservation and breeding perspectives. Conservation Genetics, 18(4), 893–910. LEHOCKÁ, K., KASARDA, R., TRAKOVICKÁ, A., KADLEČÍK, O. and MORAVČÍKOVÁ, N. (2019). Genomic diversity and level of admixture in the Slovak Spotted cattle. In AgroSym 2019. AgroSym. Bosna : University of East Sarajevo, pp. 1607–1612. LU, D. (2012) Applications of the Illumina BovineSNP50 BeadChip in Genetic Improvement of Beef Cattle. Guelph, Ontario, Canada, 1. MILUCHOVÁ, M., GÁBOR, M., CANDRÁK, J. and TRAKOVICKÁ, A. (2018). Bovine beta-casein and complex traits – The impact of the A2 variant of the CSN2 gene in the Slovak Holstein cow population on production traits. 2 THETA : Český Tešín. 96 p. MORAVČÍKOVÁ, N., KADLEČÍK, O., TRAKOVICKÁ, A. and KASARDA, R. (2018b). Autozygosity island resulting from artificial selection in slovak spotted cattle. In Agriculture & Forestry, 64(4), 21–28. MORAVČÍKOVÁ, N., KASARDA, R., HALO, M., KADLEČÍK, O., TRAKOVICKÁ, A., LEHOCKÁ, K., OLŠANSKÁ, B. and CANDRÁK, J. (2020a). Genome-wide distribution of autozygosity islands in Slovak Warmblood horse. In AGROFOR. in press. MORAVČÍKOVÁ, N., KASARDA, R., HALO, M., LEHOCKÁ, K., OLŠANSKÁ, B. and CANDRÁK, J. (2019b). Vplyv selekcie na genóm slovenského teplokrvníka. In Aktuálne smerovanie v chove koní. Nitra : Slovenská poľnohospodárska univerzita, p. 48–52. MORAVČÍKOVÁ, N., KASARDA, R., KADLEČÍK, O., TRAKOVICKÁ, A., HALO, M. and CANDRÁK, J. (2019c). Runs of homozygosity as footprints of selection in the norik of muran horse genome. Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis, 67(5), 1165–1170. MORAVČÍKOVÁ, N., KASARDA, R., VOSTRÝ, L., KRUPOVÁ, Z., KRUPA, E., LEHOCKÁ, K., OLŠANSKÁ, B., TRAKOVICKÁ, A., NÁDASKÝ, R., ŽIDEK, R., BELEJ, Ľ. and GOLIAN, J. (2019a). Analysis of selection signatures in the beef cattle genome. Czech journal of animal science, 64(12), 491–503. MORAVČÍKOVÁ, N., KASARDA, R., ŽIDEK, R., TRAKOVICKÁ, A. and KADLEČÍK, O. (2019e). Genetic variation of family Cervidae based on cross-species SNPs genotyping. In 15th International Arctic Ungulate conference. 1st ed. 83 p. Arctic Ungulate conference. Uppsala : Swedish University of Agricultural Sciences, pp. 60. MORAVČÍKOVÁ, N., KASARDA, R., ŽITNÝ, J., TRAKOVICKÁ, A. and KADLEČÍK, O. (2018a). Validation of bovine 50k SNP chip transferability into non-model wild animals. Slovak Journal of Animal Science, 51(4), 180. MORAVČÍKOVÁ, N., SIMONOVÁ, D. and KASARDA, R. (2019d). Traces of Carpathanian wolf in genome of dogs. In Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science. Annual meeting of the European federation of animal science. Wageningen : Wageningen Academic Publishers, pp. 462. MORAVČÍKOVÁ, N., KASARDA, R. and KADLEČÍK, O. (2017) The degree of genetic admixture within species from genus cervus. Agriculture and Forestry, 63(1), 137–143. MORAVČÍKOVÁ, N., KASARDA, R., KUKUČKOVÁ, V., VOSTRÝ, L. and KADLEČÍK, O. (2016) Genetic diverzity of old Kladruber and Nonius horse populations through microsatellite variation analysis. Acta agriculturae Slovenica, 107, 45–49. MORAVČÍKOVÁ, N., TRAKOVICKÁ, A., KADLEČÍK, O. and KASARDA, R. (2019f). Genomic signatures of selection in cattle throught variation of allele frequencies and linkage disequilibrium. Journal of Central European Agriculture, 20(2), 576–580. MORAVČÍKOVÁ, N., ŽIDEK, R., KASARDA, R., JAKABOVÁ, D., GENČÍK, M., POKORÁDI, J. and FERIANCOVÁ, E. (2020b). Identification of genetic families based on mitochondrial D-loop sequence in population of the Tatra chamois (Rupicapra rupicapra tatrica). Biologia, 75(1), 121–128. TRAKOVICKÁ, A., LEHOCKÁ, K., KASARDA, R., KADLEČÍK, O. and MORAVČÍKOVÁ, N. (2019). Effective population size and genomic inbreeding of Slovak Spotted cattle. In Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science. Annual meeting of the European federation of animal science. Wageningen : Wageningen Academic Publishers, pp. 112.

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