Abstract
Maximizing the number of offspring born per female is a key functionality trait in commercial- and/or subsistence-oriented livestock enterprises. Although the number of offspring born is closely associated with female fertility and reproductive success, the genetic control of these traits remains poorly understood in sub-Saharan Africa livestock. Using selection signature analysis performed on Ovine HD BeadChip data from the prolific Bonga sheep in Ethiopia, 41 candidate regions under selection were identified. The analysis revealed one strong selection signature on a candidate region on chromosome X spanning BMP15, suggesting this to be the primary candidate prolificacy gene in the breed. The analysis also identified several candidate regions spanning genes not reported before in prolific sheep but underlying fertility and reproduction in other species. The genes associated with female reproduction traits included SPOCK1 (age at first oestrus), GPR173 (mediator of ovarian cyclicity), HB-EGF (signalling early pregnancy success) and SMARCAL1 and HMGN3a (regulate gene expression during embryogenesis). The genes involved in male reproduction were FOXJ1 (sperm function and successful fertilization) and NME5 (spermatogenesis). We also observed genes such as PKD2L2, MAGED1 and KDM3B, which have been associated with diverse fertility traits in both sexes of other species. The results confirm the complexity of the genetic mechanisms underlying reproduction while suggesting that prolificacy in the Bonga sheep, and possibly African indigenous sheep is partly under the control of BMP15 while other genes that enhance male and female fertility are essential for reproductive fitness.
Highlights
The evolution of novel traits is underpinned by genetic changes encoding new phenotypes
The phenotypic dataset consisted of 98 litter size records of Bonga sheep, a non-seasonal breeder, that were collected between 2009 and 2018 from farmers flocks participating in a community-based breeding programme (CBBP)
XP-EHH detects long-range haplotypes or recent positive selection, where the selected loci are close to fixation in one population but remain polymorphic in another based on the relationship between an allele and its surrounding linkage disequilibrium (LD)
Summary
The evolution of novel traits is underpinned by genetic changes encoding new phenotypes. Little remains known on the genetic control of complex traits, which have proven challenging to study using traditional approaches. Recent developments in next-generation sequencing and associated techniques (single-nucleotide polymorphism (SNP) genotyping arrays and bioinformatics pipelines) have provided a unique opportunity to examine genes, and gene networks, encoding complex phenotypes in domestic animals (Andersson and Georges 2004; Gouivea et al 2014). Diverse geographic adaptation and selection pressure have resulted in shared and population-specific phenotypes in many livestock species (Xu et al 2015). Prolificacy is one such phenotype that has been observed in several
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