Whole-genome SNP analysis elucidates the genetic structure of Russian cattle and its relationship with Eurasian taurine breeds

Abstract

BackgroundThe origin of native and locally developed Russian cattle breeds is linked to the historical, social, cultural, and climatic features of the diverse geographical regions of Russia. In the present study, we investigated the population structure of nine Russian cattle breeds and their relations to the cattle breeds from around the world to elucidate their origin. Genotyping of single nucleotide polymorphisms (SNPs) in Bestuzhev (n = 26), Russian Black-and-White (n = 21), Kalmyk (n = 14), Kholmogor (n = 25), Kostromsky (n = 20), Red Gorbatov (n = 23), Suksun (n = 20), Yakut (n = 25), and Yaroslavl cattle breeds (n = 21) was done using the Bovine SNP50 BeadChip. SNP profiles from an additional 70 breeds were included in the analysis as references.ResultsThe observed heterozygosity levels were quite similar in eight of the nine studied breeds (HO = 0.337–0.363) except for Yakut (Ho = 0.279). The inbreeding coefficients FIS ranged from -0.028 for Kalmyk to 0.036 for Russian Black-and-White and were comparable to those of the European breeds. The nine studied Russian breeds exhibited taurine ancestry along the C1 axis of the multidimensional scaling (MDS)-plot, but Yakut was clearly separated from the European taurine breeds on the C2 axis. Neighbor-Net and admixture analyses, discriminated three groups among the studied Russian breeds. Yakut and Kalmyk were assigned to a separate group because of their Turano-Mongolian origin. Russian Black-and-White, Kostromsky and Suksun showed transboundary European ancestry, which originated from the Holstein, Brown Swiss, and Danish Red breeds, respectively. The lowest level of introgression of transboundary breeds was recorded for the Kholmogor, Yaroslavl, Red Gorbatov and Bestuzhev breeds, which can be considered as an authentic genetic resource.ConclusionsWhole-genome SNP analysis revealed that Russian native and locally developed breeds have conserved authentic genetic patterns in spite of the considerable influence of Eurasian taurine cattle. In this paper, we provide fundamental genomic information that will contribute to the development of more accurate breed conservation programs and genetic improvement strategies.Electronic supplementary materialThe online version of this article (10.1186/s12711-018-0408-8) contains supplementary material, which is available to authorized users.

Adaptive introgression from indicine cattle into white cattle breeds from Central Italy

“…We identified eight regions of indicine-derived ancestry shared by the Central Italian white-cattle breeds within the top 5% of the genome-wide CIWI scores ( Supplementary Table S1). Within these genomic regions, we identified 25 genes spread across seven chromosomes (1,5,7,13,15,18, and 24; Table 2). More stringently, 24 of these genes were found within the top 1% of CIWI scores in at least one of the three breeds, but none of them shared by all the three breeds ( Table 2).…”

Whole genome studies of origin, selection and adaptation of the Russian cattle breeds

“…Исследование генетических профилей пяти молочных пород (бестужевской, холмогорской, костромской, красной горбатовской и ярославской) показало, с одной стороны, их обособленность от европейской голштино-фризской популяции, а с другой -значительную интрогрессию голштинского скота в генофонд бестужевской породы (Зи новьева и др., 2016). По результатам анализа SNP маркеров девять российских пород и 45 пород Евразии были сгруппированы по генетическому сходству в три кластера (Sermyagin et al, 2018). Первый кластер состоял из турано-монгольских пород (якутской и калмыцкой), которые оказались наиболее удаленными от всех остальных пород.…”

Genetic Relationship Between Bos Taurus and Bos Indicus

“…É ‡flÎ˚ fl‚-Îfl˛ÚÒfl ˆÂÌÌ˚ÏË ÊË‚ÓÚÌ˚ÏË ‰Îfl ÒÍ¢˂ ‡ÌËfl Ò ÏÂÒÚÌ˚Ï ÒÍÓÚÓÏ, Ì ‡ÔËÏÂ, Ò B. indicus ‚ ‚ÓÒ-ÚÓ˜ÌÓÈ ˜ ‡ÒÚË ÅÛÚ ‡Ì ‡ Ë ÄÛÌ ‡˜ ‡Î è ‡‰Â¯ ‡. ÉË•-ˉ˚ ÔÂ‚Ó"Ó ÔÓÍÓÎÂÌËfl, ÔÓÎÛ˜ÂÌÌ˚Â Ò Û˜ ‡ÒÚËÂÏ ÏÂÒÚÌ˚ı ÔÓÓ‰, ËÁ‚ÂÒÚÌ˚ Í ‡Í flÚ¯ ‡ (Jatsha -ÏÛÊ-ÒÍÓÈ) Ë flÚ¯ ‡Ï (Jatsham -ÊÂÌÒÍËÈ ÔÓÎ èÓÒΉÌË ‰ ‡ÌÌ˚ ÔÓÎÌÓ"ÂÌÓÏÌÓ"Ó ÒÂÍ‚ÂÌË-Ó‚ ‡ÌËfl ÁÌ ‡˜ËÚÂθÌÓ ÛÎÛ˜¯ËÎË Ô‰ÒÚ ‡‚ÎÂÌËfl ˝‚Ó-βˆËË ˝ÚËı ÍÛÔÌ˚ı ÍÓÔ˚ÚÌ˚ı Ë ÔÓÏÓ"ÎË ÔÓ-ÎËÚ¸ Ò‚ÂÚ Ì ‡ ÒÎÓÊÌ˚È ÔÓˆÂÒÒ Ó‰ÓÏ ‡¯ÌË‚ ‡ÌËfl Ë ‡‰ ‡ÔÚ ‡ˆËË ˝ÚËı ‚ˉӂ, "ÂÌÂÚ˘ÂÒÍËı ÔÓÚÓÍÓ‚ ÔË ÙÓÏËÓ‚ ‡ÌËË  ‡ÁÌ˚ı ÔÓÓ‰ ÍÛÔÌÓ"Ó Ó" ‡ÚÓ"Ó ÒÍÓÚ ‡, ÚÂÒÌÓ"Ó Û˜ ‡ÒÚËfl, ‚ ˜ ‡ÒÚÌÓÒÚË, Á•ۂˉÌÓ"Ó ÒÍÓÚ ‡ ‚ ÙÓÏËÓ‚ ‡ÌËË fl‰ ‡ ‚ÓÔÂÈÒÍËı ÔÓÓ‰ [11,16,25,26,27]. Ç ÚÓ Ê ‚ÂÏfl, ÏÌÓ"Ë ‡ÒÔÂÍÚ˚ "ÂÌÂÚ˘ÂÒÍËı ‚Á ‡ËÏÓÓÚÌÓ¯ÂÌËÈ ÏÂÊ‰Û Ô‰ÒÚ ‡‚ËÚÂÎflÏË Ó‰ ‡ «Ì ‡ÒÚÓfl˘Ëı» •˚ÍÓ‚ ‰Ó ÒËı ÔÓ ÓÒÚ ‡˛ÚÒfl ‰ÓÒÚ ‡ÚÓ˜-ÌÓ ÔÓÚË‚Ó˜˂˚ÏË.…”

“…éˆÂÌÍ ‡ ÒÂÚ‚˚ı ‚Á ‡ËÏÓÓÚÌÓ¯ÂÌËÈ ÏÂÊ‰Û ‚Ë-‰ ‡ÏË ˝ÚÓ"Ó Ó‰ ‡, ÓÒÌÓ‚ ‡ÌÌ ‡fl Ì ‡ ÂÁÛÎ¸Ú ‡Ú ‡ı ÔÓÎ-ÌÓ"ÂÌÓÏÌÓ"Ó ÒÂÍ‚ÂÌËÓ‚ ‡ÌËfl, ÔÓÁ‚ÓÎËÎ ‡ ÔÓÎÛ˜ËÚ‰ ‡ÌÌ˚Â, ҂ˉÂÚÂθÒÚ‚Û˛˘ËÂ Ó Ì ‡Î˘ËË ÏÂʂˉÓ-‚ÓÈ ËÌÚÓ"ÂÒÒËË "ÂÌÂÚ˘ÂÒÍÓ"Ó Ï ‡ÚÂË ‡Î ‡ Û  ‡Á-Ì˚ı ‚ˉӂ. èÓÍ ‡Á ‡ÌÓ, ˜ÚÓ Û  ‡ÁÌ˚ı Ô‰ÒÚ ‡‚ËÚÂ-ÎÂÈ Ó‰ ‡ Bos Ì ‡•Î˛‰ ‡ÂÚÒfl ‚˚ ‡ÊÂÌÌ ‡fl ËÌÚÓ"ÂÒ-ÒËfl Ë ˜ÚÓ ÓÌ ‡ ‚Ó ÏÌÓ"Ëı ÒÎÛ˜ ‡flı Ò‚flÁ ‡Ì ‡ Ò "ÂÌ ‡ÏË, Ëϲ˘ËÏË ÒÛ˘ÂÒÚ‚ÂÌÌÓ ‡‰ ‡ÔÚË‚ÌÓ ÁÌ ‡˜ÂÌË [25]. èÓÎÛ˜ÂÌÌ˚ ÂÁÛÎ¸Ú ‡Ú˚ ËÎβÒÚËÛ˛Ú ‚ ‡ÊÌÓÒÚȨ ÌÚÓ"ÂÒÒËË Í ‡Í ËÒÚÓ˜ÌËÍ ‡ ‡‰ ‡ÔÚË‚ÌÓÈ ËÁÏÂÌ-Ë‚ÓÒÚË Ë ‚ ÔÓˆÂÒÒ ӉÓÏ ‡¯ÌË‚ ‡ÌËfl, ‡ Ú ‡ÍÊ Ô‰ÔÓÎ ‡" ‡˛Ú, ˜ÚÓ Ó‰ Bos  ‡Á‚Ë‚ ‡ÂÚÒfl Í ‡Í ÍÓÏ-ÔÎÂÍÒ "ÂÌÂÚ˘ÂÒÍË ‚Á ‡ËÏÓÒ‚flÁ ‡ÌÌ˚ı ‚ˉӂ Ò Ó•-ËÏË ˝‚ÓβˆËÓÌÌ˚ÏË Ú ‡ÂÍÚÓËflÏË.…”