Population structure and genetic diversity of Russian native cattle breeds.

Conservation of native cattle populations' biodiversity is a crucial element in breeding selection programs. Reduction of local and improved livestock gene pool leads to the loss of valuable alleles for adaptation to specific environments. In our work, we investigated the genetic structure of the most essential native cattle breeds in Russia. Using Illumina Bovine 50K BeadChip, we genotyped nine breeds: Bestuzhev (BEST, n = 26), Black and White (BLWT, n = 21), Kalmyk (KALM, n = 14), Kholmogor (KHLM, n = 25), Kostroma (KSTR, n = 20), Red Gorbatov (RGBT, n = 23), Suksun (SKSN, n = 20), Yakut (YAKT, n = 25), and Yaroslavl (YRSL, n = 21). Statistical analysis was performed with PLINK 1.07, Admixture 1.3 software, and R packages "diveRsity" and "adegenet." Multi-dimensional scaling (MDS) analysis showed that all of the breeds formed their own clusters. The YAKT cluster was completely separated on the first component (C1) and was most distant from all other populations. KALM also separated on C1 but was much closer to the other clusters. Both of these breeds are of Asian origin. The other seven breeds, which are of European origin, separated from one another mostly on the second component (C2). Admixture analysis showed that the most probable number of populations (K) was 8. At K = 2, YAKT was separated from the other populations. Considerable admixture of YAKT was only found in the KALM cluster (from K = 2 to K = 8). At K = 8, all of the breeds but KALM formed their own clusters. KALM was combined from the seven other breed fragments (all but SKSN). Pairwise genetic distances (FST) values were higher for YAKT (from 0.126 with KALM to 0.187 with RGBT). Fst values between the other breeds ranged from 0.036 (BLWT and SKSN) to 0.103 (KSTR and RGBT). The lowest rarified allelic richness value was observed for YAKT (1.781 ± 0.002). For all of the other breeds, it ranged from 1.919 ± 0.001 for KSTR to 1.958 ± 0.001 for KALM. Expected heterozygosity was the lowest in YAKT (0.273 ± 0.001) while in all of the other breeds it ranged from 0.329 ± 0.001 in KSTR and RGBT to 0.352 ± 0.001 in BEST. Inbreeding coefficient (FIS) values in all of the breeds were close to zero (from -0.05 to 0.01). Our study revealed that all of the evaluated Russian breeds were structured, and only KALM had a more complex admixture. The most diverged, indigenous YAKT breed had a lower genetic diversity than all of the other breeds. The study was supported by the Russian Science Foundation within Project no.14-36-00039. [ABSTRACT FROM AUTHOR]