PSX-17 Genome-wide diversity and demographic history of Russian native goat breeds

Abstract

Abstract Specific environmental conditions and local livestock management systems resulted in creation of valuable native breeds. The timely monitoring of genetic diversity within native breeds based on using high-throughput DNA arrays will prevent their irreparable loss. In this regard, we aimed to assess genome-wide diversity and to study demographic history of Russian native goat breeds (Altai Mountain, Orenburg, Soviet Mohair, Dagestan Milk, Dagestan Local, Dagestan Fluff and Karachaev) based on SNP-data. A total of 200 goats were genotyped using Goat 50K SNP BeadChip (Illumina, USA). Quality control and SNP-filtering were performed in PLINKv1.9. R package ‘diveRsity’ was used to calculate observed heterozygosity (Ho), expected heterozygosity (He), and inbreeding coefficient (Fis). Effective population sizes (Ne) were estimated in SneP software. Observed heterozygosity was high and exceeded 0.402 in five out of seven breeds. Orenburg, Soviet Mohair, Dagestan Milk, and Karachaev breeds showed slight excess of heterozygotes varied from 0.6% (Fis= -0.015) in Orenburg to 1.7% (Fis= -0.04) in Karachaev breed. The traces of insignificant inbreeding were found in Dagestan Local (Fis=0.005) and Dagestan Fluff (Fis= 0.01) breeds. The recent effective population sizes estimated for four generations ago varied from 140 in Karachaev to 472 in Orenburg breed. Analysis of historical trends in effective population sizes estimated for sixty generations ago revealed obvious decrease ranging from 10.25% in Dagestan Local to 34.65% in Orenburg breed. However, recent effective sizes in Russian native goats are higher than critical threshold (Ne= 100) that is essential to breed maintenance in the future. Our research findings provide an evidence that Russian native goat breeds are not in endangered status, but development of the effective utilization programs is highly recommended. The genotyping of 96 goats was funded by RSF No. 19-76-20006. The reported study was funded by RFBR according to the research project № 18-316-20006.