Study of population structure and stratification two ecotypes buffalo with dense single nucleotide polymorphism markers using Admixture, MDS, PCA and GC methods

Abstract

In applications of population genetics, classification of individuals in a sample into populations is important. With the development of high throughput genotyping technologies many markers such as SNPs are available which useful in the study of genetic diversity and structure population. The purpose of this research was to study of population structure and stratification buffaloes from different areas of the two ecotypes (Azari and North) using data SNPChip 90K. A total of 258 buffalo from Ardabil, West Azarbaijan, East Azarbaijan and Guilan provinces were sampled and genotyped. The result showed weak population stratification with λ =1.056 for GC method. Also the plots obtained from PCA and MDS showed separation of different provinces based on genetic distance and these animals have closed genetic relationship. Admixture method represents same results and admixture between individual from different provinces of two ecotypes and k=3 have low error cross validation. These methods are generally able to separate the animals. The results showed the close genetic relationship between two ecotypes from 4 different provinces.

Keywords

• population stratification
• buffalo
• snpchip 90k
• mds
• pca