Study of the genetic structure of domestic and wild reindeer in the Republic of Sakha (Yakutia) using STR analysis

Abstract

Aim: evaluation of the current state of the genetic and allelic diversity of domestic and wild reindeer populations inhabiting the territory of the Republic of Sakha (Yakutia), using STR markers.Materials and methods. The sample of the domestic reindeer included animals from Even (EVN, n=33), Evenk (EVK, n=31), and Chukchi (Khargin) breeds (KH, n=33). The sample of wild reindeer comprised representatives of the tundra (WLD_TUN, n=119) and taiga (WLD_TGA, n=14) populations.Polymorphism analysis of 14 STR loci including NVHRT21, NVHRT24, NVHRT76, RT1, RT6, RT7, RT9, RT27, RT30, RT25, RT13, NV03, RT5, and NV73 was performed using proprietary methods on ABI3130xl genetic analyzer (Applied Biosystems, USA).Allelic and genetic diversity parameters were calculated using GenAlEx software (ver. 6.5.1) and R package “diveRsity”.To address the genetic structure, Principal Component Analysis (PCA) was performed using the R package adegenet and visualized in the R package gglot2.The genetic differentiation of reindeer populations was performed based on a matrix of pairwise FST values and visualized as a phylogenetic tree using the Neighbor-Net algorithm in the SplitsTree 4.14.5 program.Results. Analysis of genetic diversity parameters showed that the observed heterozygosity was the lowest in WLD_TGA (HO = 0.520) among all studied groups and varied from 0.615 in KH to 0.691 in EVK. All reindeer groups were characterized by a heterozygote deficit, as evidenced by the positive values of the inbreeding coefficient: from UFIS = 0.101 in EVK to UFIS = 0.372 in WLD_TGA. The mean number of alleles per locus varied from 7.1 in EVN to 12.4 in WLD_TUN. Wild reindeer had higher allelic richness (AR = 7.8–8.6 and AR = 6.2–6.8, respectively) and number of effective alleles per locus (NE = 5.3–6, 9 and NE = 4.1 – 4.5, respectively) in comparison with their domestic relatives. Principal Component Analysis showed that the first Principal Component separated wild reindeer from the domestic reindeer. Analyzing pairwise FST values, we found that the KH was the most genetically distant from domestic reindeer breeds (FST = 0.072 between KH and EVN, and FST = 0.065 between KH and EVK) and from wild reindeer populations (FST = 0.076 between KH and WLD_TGA, and FST = 0.06 between KH and WLD_TUN). Pairs EVN and EVK (FST = 0.047), as well as WLD_TUN and WLD_TGA (FST = 0.008) were characterized by insignificant genetic differentiation. Neighbor Net graph showed the formation of two clusters including wild and domestic reindeer populationsConclusion. The results may be useful for development of breeding programs for breeds of domestic reindeer and conservation programs for wild reindeer.