Conservation Assessment of the State Goat Farms by Using SNP Genotyping Data

Rabiul Islam; Zhangfa Liu; Yefang Li; Lin Jiang; Yuehui Ma

doi:10.3390/genes11060652

Conservation Assessment of the State Goat Farms by Using SNP Genotyping Data

Genes (Basel). 2020 Jun 13;11(6):652. doi: 10.3390/genes11060652.

Authors

Rabiul Islam^{1

2}, Zhangfa Liu³, Yefang Li¹, Lin Jiang¹, Yuehui Ma¹

Affiliations

¹ National Germplasm Center of Domestic Animal Resources, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Rd., Haidian, Beijing 100193, China.
² Department of Livestock Services of Ministry of Fisheries and Livestock, Farmgate, Dhaka 1215, Bangladesh.
³ The National conservation farm of Ningxia Zhongwei goats, Zhongwei, Ningxia 755006, China.

Abstract

Conservation of genetic resources is of great concern globally to maintain genetic diversity for sustainable food security. Comprehensive identification of the breed composition, estimation of inbreeding and effective population size are essential for the effective management of farm animal genetic resources and to prevent the animals from genetic erosion. The Zhongwei male (ZWM), Arbas Cashmere male (ACM) and Jining Grey male (JGM) goats are conserved in three different state goat farms in China but their family information, level of inbreeding and effective population size are unknown. We investigated the genomic relationship, inbreeding coefficient and effective population size in these three breeds from three state goat farms using the Illumina goat SNP50 BeadChip. Genomic relationships and phylogenetic analysis revealed that the breeds are clearly separated and formed separate clusters based on their genetic relationship. We obtained a high proportion of informative SNPs, ranging from 91.8% in the Arbas Cashmere male to 96.2% in the Jining Grey male goat breeds with an average mean of 96.8%. Inbreeding, as measured by F_ROH, ranged from 1.79% in ZWM to 8.62% in ACM goat populations. High F_ROH values, elevated genomic coverage of very long ROH (>30 Mb) and severe decline in effective population size were recorded in ACM goat farm. The existence of a high correlation between F_HOM and F_ROH indicates that F_ROH can be used as an alternative to inbreeding estimates in the absence of pedigree records. The N_e estimates 13 generations ago were 166, 69 and 79 for ZWM, ACM and JGM goat farm, respectively indicating that these goat breeds were strongly affected by selection pressure or genetic drift. This study provides insight into the genomic relationship, levels of inbreeding and effective population size in the studied goat populations conserved in the state goat farms which will be valuable in prioritizing populations for conservation and for developing suitable management practices for further genetic improvement of these Chinese male goats.

Keywords: Ne; SNP; genome coverage; inbreeding coefficient; runs of homozygosity.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Breeding
China
Farms
Genetic Variation / genetics*
Genome / genetics
Genotype*
Goats / genetics*
Inbreeding
Pedigree
Polymorphism, Single Nucleotide / genetics*
Population Density