Cattle are central to the lives and diverse cultures of African people. It has played a crucial role in providing valuable protein for billions of households and sources of income and employment for producers and other actors in the livestock value chains. The long-term natural selection of African cattle typically signals signatures in the genome, contributes to high genetic differentiations across breeds. This has enabled them to develop unique adaptive traits to cope with inadequate feed supply, high temperatures, high internal and external parasites, and diseases. However, these unique cattle genetic resources are threatened by indiscriminate cross-breeding, breed replacements with exotic cosmopolitan breeds, and climate change pressures. Although there are no functional genomics studies, recent advancements in genotyping and sequencing technologies have identified and annotated limited functional genes and causal variants associated with unique adaptive and economical traits of African cattle populations. These genome-wide variants serve as candidates for breed improvement and support conservation efforts for endangered cattle breeds against future climate changes. Therefore, this review plans to collate comprehensive information on the identified selection footprints to support genomic studies in African cattle to confirm the validity of the results and provide a framework for further genetic association and QTL fine mapping studies.

The growth and development of skeletal muscle also determine the meat production of yak, ultimately affecting the economic benefits.  Hence, improving growth performance is a top priority in the yak industry.  Skeletal muscle development is a complex process involving the regulation of several genes, including microRNAs (miRNAs).  However, the transcription of miRNAs in yak skeletal muscle during prenatal to postnatal stages is unknown.  We used small RNA sequencing (small RNA-Seq) to determine the global miRNAs of longissimus dorsi muscle from yak (the samples were collected from three fetuses and three adults).  Totally 264 differently expressed miRNAs (|log₂(fold change)|>1 and P-value≤0.05) were detected between the two groups.  Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that differently expressed miRNAs-targeted genes participated in pathways associated with muscle development, such as MAPK, PI3K-Akt, and Hippo signaling pathways, etc.  MiR-652, which was up-regulated in the fetal group, was transfected into C2C12 myoblasts to examine its role.  miR-652 promoted (P≤0.05) proliferation and differentiation, but inhibited (P≤0.001) apoptosis at early period.  Furthermore, miR-652 reduced (P≤0.001) the proportion of C2C12 myoblasts in the G1 phase while increasing (P≤0.01) the proportion of cells in the S and G2 phases.  Dual-luciferase reporter assays indicated that ISL1 served as a target of miR-652.  In general, these findings expand our understanding of yak skeletal muscle miRNAs, and suggested that miR-652 probably regulated myogenesis by regulating ISL1.

Genetic diversity, population structure, and population expansion of goats worldwide (4 165 individuals from 196 breeds) were analyzed using published mitochondrial DNA (mtDNA) D_loop hypervariable region sequences. Results showed that 2 409 haplotypes and 301 polymorphic sites were present within the 401-bp length D_loop region, the nucleotide diversity (Pi) was 0.03471, and the haplotype diversity (Hd) was 0.9983. Phylogenetic analysis revealed that 98.92% of haplotypes were divided into six obvious clusters, consistent with the classification of the known mitochondrial haplogroups of goats. Haplogroup A accounted for the largest proportion (86%). Interestingly, two unknown divisions (Unknown I and Unknown II) were discovered from goats in Southwest China, suggesting that Southwest China has unique maternal haplogroups. Analysis of molecular variance (AMOVA) and the average number of pairwise differences between populations (PiXY) indicated that geographical variation was small but significant. Neutrality tests (Tajima’s D and Fu’s F_S tests) and mismatch distribution showed that haplogroups B, C, and G had expansion histories. In addition, the phylogenetic relationship between domestic and wild goats suggested that Capra aegagrus is the most likely wild ancestor and may have participated in the domestication of ancestral populations of A, B, C, and F haplogroups. A meta-analysis on the mtDNA sequences of goats from international databases was conducted to analyze goats’ genetic diversity, population structure, and matrilineal system evolution worldwide. The results may help further understand the domestication history and gene flow of goats worldwide.

Endothelial PAS domain protein 1 gene (EPAS1) is a key transcription factor that activates the expression of oxygen-regulated genes. In this study, in order to better understand the effects of EPAS1 gene on hematologic parameters in yak, we firstly quantified the tissue expression patterns for EPAS1 mRNA of yak, identified polymorphism in this gene and evaluated its association with hematologic parameters. Expression of EPAS1 mRNA was detected in all eight tissues (heart, liver, lung, spleen, pancreas, kidney, muscles and ovary). The expressions of EPAS1 in lung and pancreas were extremely higher than other tissues examined. Three novel single nucleotide polymorphisms (SNPs) (g.83052 C>T, g.83065 G>A and g.83067 C>A) within the EPAS1 were identified and genotyped in Pali (PL), Gannan (GN) and Tianzhu White (TZW) yak breeds. Significant higher frequencies of the AA and GA genotypes and A allele of the g.83065 G>A were observed in the PL and GN breeds than that in the TZW breed (P<0.01). Association analysis of the PL breed indicated that the g.83065 G>A polymorphism was significantly associated with hemoglobin (HGB) concentration in yaks (P<0.05). Individuals with genotype AA had significantly higher HGB concentration (P<0.05) than those with genotype GA and GG. All these results will help our further understanding of biological functional of yak EPAS1 gene in responding to hypoxia and also indicate EPAS1 might contribute to the hypoxia adaptation of the yak.

In the present study we studied the genetic structure of five Chinese sheep populations of Hu sheep, Tong sheep, SmalltailedHan sheep, Tan sheep, and Wadi (WD) sheep using 15 microsatellite loci. The results showed that the FIT, FST, andFIS statistics computed for the complete dataset had the following values, 0.523±0.140, 0.363±0.131 and 0.263±0.092,respectively. All loci were significantly contributed to the genetic differentiation among population (P<0.001). There is norelationship between the scatter of pairwise FST geographical distance points as geographical distance increases betweenthe five populations. Membership probabilities and genetic structure of sheep populations were estimated when K=2, thepopulations were classified into Hu, Tong, Han and WD, and Tan sheep group. However, when K=3, the populations wereclassified into Hu and Tong, Han and WD, and Tan sheep group. The findings supported the previous literatures thatthese populations are originated on different time stages from the primogenitor population and communicated geneticallywith each other by natural and artificial selection in different ecological environment.

Research on the identity of genes and their relationship with traits of economic importance in farm animals could assist in the selection of livestock. In this study, the polymorphisms of insulin-like growth factor 1 (IGF1) gene in 561 goats of ten breeds were detected by polymerase chain reaction (PCR)-single strand conformation polymorphism (SSCP) and their association with litter size and birth weight in three breeds were investigated. The effects of IGF1 polymorphisms on the breeding value for litter size and birth weight were examined using least square methods. Two deletions (CA) were detected in the microsatellite and two mutations (A1637G, T1640C) were found in 5´-flanking regulatory region. No significant association between the polymorphisms in 5´-flanking region of IGF1 and birth weight was found in the three breeds of goats. In Gulin Ma goats, two polymorphisms were found to affect litter size traits. In Chuandong White goats and Guizhou White goats, no significant difference (P<0.05) in litter size between goats carrying different genotypes was observed. Further evaluation and confirmation studies in more goat populations with larger sample sizes are necessary.