Genetic Contribution of Indigenous Yakutian Cattle to Two Hybrid Populations, Revealed by Microsatellite Variation

Abstract

Indigenous Yakutian cattle's adaptation to the hardest subarctic conditions makes them a valuable genetic resource for cattle breeding in the Siberian area. Since early last century, crossbreeding between native Yakutian cattle and imported Simmental and Kholmogory breeds has been widely adopted. In this study, variations at 22 polymorphic microsatellite loci in 5 populations of Yakutian, Kholmogory, Simmental, Yakutian-Kholmogory and Yakutian-Simmental cattle were analysed to estimate the genetic contribution of Yakutian cattle to the two hybrid populations. Three statistical approaches were used: the weighted least-squares (WLS) method which considers all allele frequencies; a recently developed implementation of a Markov chain Monte Carlo (MCMC) method called likelihood-based estimation of admixture (LEA); and a model-based Bayesian admixture analysis method (STRUCTURE). At population-level admixture analyses, the estimate based on the LEA was consistent with that obtained by the WLS method. Both methods showed that the genetic contribution of the indigenous Yakutian cattle in Yakutian-Kholmogory was small (9.6% by the LEA and 14.2% by the WLS method). In the Yakutian-Simmental population, the genetic contribution of the indigenous Yakutian cattle was considerably higher (62.8% by the LEA and 56.9% by the WLS method). Individual-level admixture analyses using STRUCTURE proved to be more informative than the multidimensional scaling analysis (MDSA) based on individual-based genetic distances. Of the 9 Yakutian-Simmental animals studied, 8 showed admixed origin, whereas of the 14 studied Yakutian-Kholmogory animals only 2 showed Yakutian ancestry (>5%). The mean posterior distributions of individual admixture coefficient ( qˆ) varied greatly among the samples in both hybrid populations. This study revealed a minor existing contribution of the Yakutian cattle in the Yakutian-Kholmogory hybrid population, but in the Yakutian-Simmental hybrid population, a major genetic contribution of the Yakutian cattle was seen. The results reflect the different crossbreeding patterns used in the development of the two hybrid populations. Additionally, molecular evidence for differences among individual admixture proportions was seen in both hybrid populations, resulting from the stochastic process in crossing over generations.

Molecular characterization of breeds and its use in conservation

“…Three programs are available: STRUCTURE (Pritchard et al, 2000), PARTITION (Dawson and Belkhir, 2001), and BAPS (Corander et al, 2004), and their differences are summarised by Pearse and Crandall (2004). This approach was first applied by Rosenberg et al (2001) to 20 chicken breeds and later to pigs (Fabuel et al, 2004;García et al, 2006;Alves et al, 2006b), cattle (Kumar et al, 2003;Li et al, 2005), sheep (Álvarez et al, 2004;Tapio et al, 2005), and horses . Interestingly, cluster analysis provides an alternative method of estimating genetic distances that does not assume isolation .…”

Characterization of rare migratory cattle and evaluation of its phylogeny using short-tandem-repeat-based markers

“…They are neutral markers and have high variability, widespread distribution throughout the genome and have shown a co-dominant inheritance. Microsatellites are best suited to evaluate genetic diversity (Metta et al 2004;Li et al 2005;Yoon et al 2005;Sodhi et al 2005Sodhi et al , 2006Pandey, Rekha, Singh, et al 2006, Pandey, Rekha, Yatender, et al 2006Sharma et al 2013) and relationships among cattle populations from Africa, Europe and Asia (Moazami-Goudarzi et al 1997;Machugh et al 1998;Martín-Burriel et al 1999;Mommens et al 1999;Beja-Pereira et al 2003;Jordana et al 2003). Using a set of bovine-specific microsatellite markers, Mukesh et al (2004) studied the genetic diversity (both within and between) and relationship among the three important Indian cattle breeds, namely Sahiwal, Hariana and Deoni.…”

Study on polymorphisms of microsatellite DNA of six Chinese indigenous sheep and goat breeds

“…They are widely used for DNA fingerprinting, paternity testing, construction of linkage maps, population genetic studies (Li et al 2005;Osma et al, 2005), individual identification, heterosis analysis, genetic bottleneck analysis, estimation of cultivative power of discrimination (Olowofeso et al, 2005;Pandy et al, 2005;Zhang et al, 2005) and marker-assisted selection (Casacuberta et al, 2000).…”