Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

Abstract

Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses—calculation of fixation index (FST) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals—were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were elucidated. Only two of the selected regions (localised on BTA 14 at 24.4–25.1 Mbp and on BTA 16 at 42.5–43.5 Mb) overlapped in Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74–5.36 Mbp, BTA 15 at 17.80–18.77 Mbp, and BTA 17 at 45.59–45.61 Mbp) and Kholmogor breeds (BTA 12 at 82.40–81.69 Mbp, BTA 15 at 16.04–16.62 Mbp, and BTA 18 at 0.19–1.46 Mbp) by using at least two of the above-mentioned methods. We expanded the list of candidate genes associated with the selected genomic regions and performed their functional annotation. We discussed the possible involvement of the identified candidate genes in artificial selection in connection with the origin and development of the breeds. Our findings on the Yaroslavl and Kholmogor breeds obtained using high-density SNP genotyping and three different statistical methods allowed the detection of novel putative genomic regions and candidate genes that might be under selection. These results might be useful for the sustainable development and conservation of these two oldest Russian native cattle breeds.

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

“…Methods used for defining signatures of selection: 3 F ST , top 0.1% SNPs by F ST value at pairwise population comparison; 4 hapFLK, regions identified by hapFLK analysis at p < 0.01; and 5 ROH50, ROH segments distributed in more than 50% of animals within each breed. Studied populations: 6 RW/WC comparison, 7 RW, and 8 WC.…”

“…Many native breeds are now at the risk of being lost, while potentially harboring significant historical footprints of selection for economically important phenotypes in their genomes. Conservation and molecular genetic characterization of biodiversity among domestic animal and poultry species used for food production are two of the key objectives to ensure the sustainability of local and regional agricultural production systems [1][2][3][4][5][6][7]. Genomic tools and resources for poultry-related research have advanced and been immensely enriched since the time of the first chicken reference genome sequence publication [8].…”

Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle

“…SERGEF is also among the 48 differentially expressed genes from two breeds of chicken showing extreme differences in hypoxic adaptation reared in Tibet ( Hu et al, 2020 ), whereas NDUFV2 has been identified as a candidate gene possibly involved in pulmonary hypertension in Black Angus cattle ( Newman et al, 2011 ). The NDUFV2 gene has been also detected under selection pressure for lipid metabolism in Yaroslavl cattle, and related with local adaptation to survive under poor nutrition conditions in winter ( Zinovieva et al, 2020 ). Additional genes located in the candidate regions on BTA15 ( HSPA8 , SCN3B ) and BTA19 ( LAMA1 ) point toward other aspects of environmental adaptation of Maremmana: HSPA8 plays a role in thermoregulatory protective mechanisms in cattle and buffalo under tropical environments ( Kumar et al, 2015 ), and associated with cellular response to heat stress in goats ( Mohanarao et al, 2014 ); SCN3B is involved in positive regulation of heart rate (GO:0010460) and sensory perception of pain (GO:0019233).…”

Тhe Population-Genetic Structure of Native Tagil Cattle by STR- And SNP-Markers

“…С помощью STR (short tandem repeat) маркеров изучали генетическую структуру популяций местных пород индийских зебу -онголе, деони, гир, канкрей (6), мексиканского скота криолло (7), а также красной степной (8), суксунской, истобенской, ярославской, холмогорской, серой украинской и холмогорской (печорский тип) пород КРС (9). Полногеномный SNP скрининг использовали для установления генетического разнообразия и межпородной дифференциации аборигенного южноафриканского скота (африканер, дракенсбергер, нгуни) (10), пяти местных пород КРС в Бангладеш (читагонгская красная, пабна и зебу муншигандж, северный бенгальский серый, деши) (11), шести пород скота из провинции Сычуань в Китае (башаньский, сюаньханьский, пингву, саньцзянский, ганзи, ляншаньский) (12), ирландской породы керри (13) и российских стародавних пород -бестужевской, холмогорской, костромской, красной горбатовской и ярославской (14,15).…”