BackgroundSheep is important in the socio-economic lives of people around the world. It is estimated that more than half of our once common livestock breeds are now endangered. Since genetic characterization of Nigerian sheep is still lacking, we analyzed ten morphological traits on 402 animals and 15 microsatellite DNA markers in 384 animals of the 4 Nigerian sheep breeds to better understand genetic diversity for breeding management and germplasm conservation.ResultsMorphological traits of Uda and Balami were significantly (P < 0.05) higher than Yankasa, which were both higher than West African Dwarf (WAD) sheep. Stepwise discriminant analysis showed tail length, rump height, chest girth, ear length and chest depth as the most discriminating variables for classification. Mahalanobis distances show the least differentiation between Uda and Balami and the largest between WAD and Balami sheep. While 93.3% of WAD sheep were correctly assigned to their source genetic group, 63.9% of Yankasa, 61.2% of Balami and 45.2% of Uda were classified correctly by nearest neighbour discriminant analysis. The overall high Polymorphism Information Content (PIC) of all microsatellite markers ranged from 0.751 to 0.927 supporting their use in genetic characterization. Expected heterozygosity was high for all loci (0.783 to 0.93). Mean heterozygote deficiency across all populations (0.171 to 0.534) possibly indicate significant inbreeding (P < 0.05). Mean values for FST, FIT and FIS statistics across all loci were 0.088, 0.394 and 0.336 respectively. Yankasa and Balami are the most closely related breeds (DA = 0.184) while WAD and Balami are the farthest apart breeds (DA = 0.665), which is coincident with distance based on morphological analysis and population structure assessed by STRUCTURE.ConclusionsThese results suggest that within-breed genetic variation in Nigerian sheep is higher than between-breeds and may be a valuable tool for genetic improvement and conservation. The higher genetic variability in Yankasa suggests the presence of unique ancestral alleles reflecting the presence of certain functional genes which may result in better adaptability in more agro-ecological zones of Nigeria. These genetic characteristics are potentially useful in planning improvement and conservation strategies in Nigerian indigenous sheep.

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Multivariate analysis of phenotypic differentiation in Bunaji and Sokoto Gudali cattle The study aimed at examining morphometric differentiation in two Nigerian breeds of cattle using multifactorial discriminant analyses. Ten morphological traits (withers height, rump height,chest circumference, body length, face length, tail length, rump length, head width, rump width and shoulder width) of 224 Bunaji and 87 Sokoto Gudali cattle were measured. The animals, which were aged 2.5−3.6 years, were subjected to extensive management system. The linear type traits of Sokoto Gudali cattle were significantly (P < 0.05) higher than those of their Bunaji counterparts, with the exception of body length and face length respectively. The stepwise discriminant analysis gave a better resolution as only three variables, rump width, withers height and face length were more discriminating in separating the two cattle breeds. The Mahalanobis distance (7.19) between the two cattle populations was high and significant, which is an indication that they belong to genetically different groups. This was complemented by the result of the Nearest Neighbour Discriminant Analysis, where 85.48% of Bunaji cattle were classified into their source population while 96.55% of their Sokoto Gudali counterparts were correctly assigned into their source genetic group. The present phenotypic information will be the basis for the establishment of further characterization, conservation and selection strategies for the two Nigerian breeds of cattle. Key words: cattle / breeds / morphological traits / discriminant analysis / characterization / Nigeria Multivariatna analiza fenotipskih razlik med "Bunaji" in "Sokoto Gudali" govedom V študiji smo z multivariatno diskriminantno analizo proučevali morfometrične razlike med dvema nigerijskima pasmama goveda. Merili smo deset morfoloških lastnosti (višina vihra, višina trupa, obseg prsi, dolžina telesa, dolžina glave, dolžina repa, dolžina trupa, širina glave, širina trupa in širina pleč) pri 224 živalih pasme "Bunaji" in 87 živalih pasme "Sokoto Gudali". Živali so bile v ekstenzivni reji, stare med 2,5 ter 3,6 leti. Izmerjene vrednosti za linearne lastnosti živali pasme "Sokoto Gudali" so bile statistično značilno večje (P < 0,05) kot pri živalih pasme "Bunaji", izjema sta bila le dolžina telesa in dolžina glave. Za doseganje boljše resolucije smo uporabili postopno diskriminantno analizo, ker so le tri spremenljivke, širina telesa, višina vihra in dolžina glave, omogočile zanesljivo ločevanje obeh pasem. Mahalanobijeva distanca (7,19) med obema pasmama je bila visoko statistično značilna, kar nakazuje, da populaciji pripadata različnim pasemskim skupinam. Te rezultate potrjuje tudi diskriminantna analiza najbližjih sosedov, kjer je bilo 85,48% "Bunaji" goveda razvrščenega v izvorno populacijo, medtem, ko je bil ta odstotek pri "Sokoto Gudali" pasmi še višji (96,55). Tako pridobljene fenotipske informacije bomo uporabili za še natančnejši opis , zaščito in oblikovanje rejske strategije obeh nigerijskih pasem gove...

The DQB1 locus is located in the major histocompatibility complex (MHC) class II region and involved in immune response. We identified 20 polymorphic sites in a 228 bp fragment of exon 2, one of the most critical regions of the MHC DQB1 gene, in 60 Nigerian goats. Four sites are located in the peptide binding region, and 10 amino acid substitutions are peculiar to Nigerian goats, compared with published sequences. A significantly higher ratio of nonsynonymous/synonymous substitutions (dN/dS) suggests that allelic sequence evolution is driven by balancing selection (P < 0.01). In silico functional analysis using PANTHER predicted that substitution P56R, with a subPSEC score of -4.00629 (Pdeleterious = 0.73229), is harmful to protein function. The phylogenetic tree from consensus sequences placed the two northern breeds closer to each other than either was to the southern goats. This first report of sequence diversity at the DQB1 locus for any African goat breed may be useful in the search for disease-resistant genotypes.

The agouti-signaling protein (ASIP) plays a major role in mammalian pigmentation as an antagonist to melanocortin-1 receptor gene to stimulate pheomelanin synthesis, a major pigment conferring mammalian coat color. We sequenced a 352 bp fragment of ASIP gene spanning part of exon 2 and part of intron 2 in 215 animals representing six goat breeds from Nigeria and the United States: West African Dwarf, predominantly black; Red Sokoto, mostly red; and Sahel, mostly white from Nigeria; black and white Alpine, brown and white Spanish and white Saanen from the US. Twenty haplotypes from nine mutations representing three intronic, one silent and five missense (p.S19R, p.N35K, p.L36V, p.M42L and p.L45W) mutations were identified in Nigerian goats. Approximately 89 % of Nigerian goats carry haplotype 1 (TGCCATCCG) which seems to be the wild type configuration of mutations in this region of the gene. Although we found no association between these polymorphisms in the ASIP gene and coat color in Nigerian goats, in-silico functional analysis predicts putative deleterious functional impact of the p.L45W mutation on the basic amino-terminal domain of ASIP. In the American goats, two intronic mutations, g.293G>A and g.327C>A, were identified in the Alpine breed, although the g.293G>A mutation is common to American and Nigerian goat populations. All Sannen and Sahel goats in this study belong to haplotypes 1 of both populations which seem to be the wild-type composite ASIP haplotype. Overall, there was no clear association of this portion of the ASIP gene interrogated in this study with coat color variation. Therefore, additional genomic analyses of promoter sequence, the entire coding and non-coding regions of the ASIP gene will be required to obtain a definite conclusion.