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Open AccessArticle

Genome-Wide Runs of Homozygosity, Effective Population Size, and Detection of Positive Selection Signatures in Six Chinese Goat Breeds

1
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
Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 75002, Ningxia, China
*
Authors to whom correspondence should be addressed.
Genes 2019, 10(11), 938; https://doi.org/10.3390/genes10110938
Received: 21 October 2019 / Revised: 9 November 2019 / Accepted: 13 November 2019 / Published: 17 November 2019
(This article belongs to the Special Issue Genomics of Sexual Development and Reproduction in Mammals)
Detection of selection footprints provides insight into the evolution process and the underlying mechanisms controlling the phenotypic diversity of traits that have been exposed to selection. Selection focused on certain characters, mapping certain genomic regions often shows a loss of genetic diversity with an increased level of homozygosity. Therefore, the runs of homozygosity (ROHs), homozygosity by descent (HBD), and effective population size (Ne) are effective tools for exploring the genetic diversity, understanding the demographic history, foretelling the signature of directional selection, and improving the breeding strategies to use and conserve genetic resources. We characterized the ROH, HBD, Ne, and signature of selection of six Chinese goat populations using single nucleotide polymorphism (SNP) 50K Illumina beadchips. Our results show an inverse relationship between the length and frequency of ROH. A long ROH length, higher level of inbreeding, long HBD segment, and smaller Ne in Guangfeng (GF) goats suggested intensive selection pressure and recent inbreeding in this breed. We identified six reproduction-related genes within the genomic regions with a high ROH frequency, of which two genes overlapped with a putative selection signature. The estimated pair-wise genetic differentiation (FST) among the populations is 9.60% and the inter- and intra-population molecular variations are 9.68% and 89.6%, respectively, indicating low to moderate genetic differentiation. Our selection signatures analysis revealed 54 loci harboring 86 putative candidate genes, with a strong signature of selection. Further analysis showed that several candidate genes, including MARF1, SYCP2, TMEM200C, SF1, ADCY1, and BMP5, are involved in goat fecundity. We identified 11 candidate genes by using cross-population extended haplotype homozygosity (XP-EHH) estimates, of which MARF1 and SF1 are under strong positive selection, as they are differentiated in high and low reproduction groups according to the three approaches used. Gene ontology enrichment analysis revealed that different biological pathways could be involved in the variation of fecundity in female goats. This study provides a new insight into the ROHs patterns for maintenance of within breed diversity and suggests a role of positive selection for genetic variation influencing fecundity in Chinese goat. View Full-Text
Keywords: SNP; Chinese goat; genetic diversity; selection of signature; fecundity SNP; Chinese goat; genetic diversity; selection of signature; fecundity
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MDPI and ACS Style

Islam, R.; Li, Y.; Liu, X.; Berihulay, H.; Abied, A.; Gebreselassie, G.; Ma, Q.; Ma, Y. Genome-Wide Runs of Homozygosity, Effective Population Size, and Detection of Positive Selection Signatures in Six Chinese Goat Breeds. Genes 2019, 10, 938.

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