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

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

doi:10.3390/genes11060652

Rabiul Islam, Lin Jiang + Show 3 more

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https://doi.org/10.3390/genes11060652

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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 FROH, ranged from 1.79% in ZWM to 8.62% in ACM goat populations. High FROH 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 FHOM and FROH indicates that FROH can be used as an alternative to inbreeding estimates in the absence of pedigree records. The Ne 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.

Highlights

In order to preserve animal genetic resources and promote sustainable livestock improvement in changing environmental conditions and demands, it is critical to assess the conservation status of genetic resources
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 pedigree information, level of inbreeding and effective population size are unknown
53,347 single nucleotide polymorphism (SNP) were considered before quality control

Summary

Introduction

In order to preserve animal genetic resources and promote sustainable livestock improvement in changing environmental conditions and demands, it is critical to assess the conservation status of genetic resources. 30% of the world’s farm animal breeds are at risk of extinction due to a lack of conservation policies [1]. Conservation policies of native goat breeds largely depend on the extent of knowledge about history and degree of genetic relationships within and across breeds, inbreeding status of a population, effective population size and characterization of breeds. Genes 2020, 11, 652 assessment of conservation parameters, reliable pedigree data is required. Pedigree data is difficult to record or sometimes unavailable due to error in recording and might not reflect the real relationship. In particular, single nucleotide polymorphism (SNP) markers are more effective in the assessment of breed composition than pedigree data [2]

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