Sunday O. Peters

Genetic diversity analysis of the mitochondrial D-loop of Nigerian indigenous sheep

Los recursos ganaderos autoctonos son de caracter estrategico en los aspectos socioeconomicos de los sistemas agricolas para garantizar la seguridad alimentaria en los paises de escasos recursos. Por lo tanto, conocer mejor la importancia de la variabilidad genetica es vital para su futura utilizacion, por medio de la conservacion. Se presenta el primer analisis de la diversidad genetica en ovejas de Nigeria basado en la region de control (D-loop) del Ovis aries del genoma mitocondrial, utilizando 1.179 bases entre las posiciones 15.437 y 16.616 de pares de bases. Una muestra de 290 animales, compuesta por las razas Balami, West African Dwarf (WAD), Uda y Yankasa, fue tomada al azar de toda Nigeria. Se observaron noventa y seis (96) haplotipos, con una alta diversidad media en cuanto anestos de 0,899 ± 0,148. La diversidad genetica fue mayor en la raza Uda (0,921 ± 0,021) y menor en la raza WAD (0,852 ± 0,061). Los indices de poblacion especificos FST variaron de 0.00133 en la raza Uda a 0,00335 en la razaWAD. La raza Yankasa presento el mayor numero de posiciones polimorficas (201), mientras que el menor lo mostro la raza Uda (96). Analisis de la varianza molecular revelo que 0,23% de la variacion se encuentra entre las poblaciones, en comparacion con el 99,77% de variacion que se encuentra dentro de las poblaciones. El arbol filogenetico indica que los linajes mitocondriales de las razas ovinas partieron de un origen comun en conformidadncon la primera divergencia de la raza Yankasa, seguida por WAD, mientras que las razas Balami y Uda se encuentran mas estrechamente relacionadas. Estos resultados demuestran que la divergencia evolutiva de las poblaciones ovinas de Nigeria, basados en el ADN mitocondrial de la region control, puede coincidir con la distribucion geografica en Nigeria e indican una tasa importante de cruzamiento entre ellas. Esto podria tener ventajas desde el punto de vista de la gestion de la mejora y las estrategias de conservacion y preservacion a largo plazo de las ovejas autoctonas de Nigeria.

Use of discriminant analysis for the evaluation of coccidiosis resistance parameters in chickens raised in hot humid tropical environment

Coccidiosis endemicity remains a major challenge in poultry production in the tropics and all over the world. In order to develop predictive tool for identification of chickens that are at risk of coccidiosis among Nigerian indigenous chickens, body weight gain (BWG) and hematological variables were determined for chickens infected with Eimeria tenella (femaleu2009=u200960, maleu2009=u200963) and uninfected (femaleu2009=u200951, maleu2009=u200945). The hematological variables analyzed include the following: packed cell volume (PCV, %), white blood cells (WBC, ×u2009106/μl), and red blood cells (RBC, ×u2009106/μl), as well as differential leucocyte percentages of neutrophils, lymphocytes, monocytes, and eosinophils. Body weight gain was determined at days 3, 6, 9, 12, and 15. Of the 12 variables analyzed, BWG at day 3, monocyte, PCV, and WBC in males and BWG at days 6, 9, and 12, PCV, and WBC in female chickens showed significant (Pu2009≤u20090.01) difference between the infected and uninfected. Stepwise discriminant analysis evolved a model that could distinguish uninfected from Eimeria-infected chickens. Packed cell volume, WBC, BWG at day 3, and lymphocytes emerged the most discriminant between uninfected and Eimeria-infected chickens in male chickens. In female chickens, PCV, RBC, and BWG at day 3 were identified as most discriminant variables in separating the uninfected from Eimeria-infected chickens. Therefore, this study suggests that routine blood test and estimates of body weight gain could serve as a useful tool for identifying chickens that may be at risk of coccidiosis, enabling improvement of preventive measures.

Genetic Diversity of Bovine Major Histocompatibility Complex Class II DRB3 locus in cattle breeds from Asia compared to those from Africa and America

Genetic polymorphisms and diversity of BoLA-DRB3.2 are essential because of DRB3 genes function in innate immunity and its association with infectious diseases resistance or tolerance in cattle. The present study was aimed at assessing the level of genetic diversity of DRB3 in the exon 2 (BoLA-DRB3.2) region in African, American and Asian cattle breeds. Amplification of exon 2 in 174 cattle revealed 15 haplotypes. The breeds with the highest number of haplotypes were Brangus (10), Sokoto Gudali (10) and Dajal (9), while the lowest number of haplotypes were found in Holstein and Sahiwal with 4 haplotypes each. Medium Joining network obtained from haplotypic data showed that all haplotypes condensed around a centric area and each sequence (except in H-3, H-51 and H-106) representing almost a specific haplotype. The BoLA-DRB3.2 sequence analyses revealed a non-significant higher rate of non-synonymous (dN) compared to synonymous substitutions (dS). The ratio of dN/dS substitution across the breeds were observed to be greater than one suggesting that variation at the antigen-binding sites is under positive selection; thus increasing the chances of these breeds to respond to wide array of pathogenic attacks. An analysis of molecular variance revealed that 94.01 and 5.99% of the genetic variation was attributable to differences within and among populations, respectively. Generally, results obtained suggest that within breed genetic variation across breeds is higher than between breeds. This genetic information will be important for investigating the relationship between BoLADRB3.2 and diseases in various cattle breeds studied with attendant implication on designing breeding programs that will aim at selecting individual cattle that carry resistant alleles.

Genetic variation in N- and C-terminal regions of bovine DNAJA1 heat shock protein gene in African, Asian and American cattle

DNAJA1 or heat shock protein 40 (Hsp40) is associated with heat adaptation in various organisms. We amplified and sequenced a total of 1,142 bp of bovine Hsp40 gene representing the critical N-terminal (NTR) and C-terminal (CTR) regions in representative samples of African, Asian and American cattle breeds. Eleven and 9 different haplotypes were observed in the NTR in Asian and African breeds respectively while in American Brangus, only two mutations were observed resulting in two haplotypes. The CTR appears to be highly conserved between cattle and yak. In-silico functional analysis with PANTHER predicted putative deleterious functional impact of c.161 T>A; p. V54Q while alignment of bovine and human NTR-J domains revealed that p.Q19H, p.E20Q and p. E21X mutations occurred in helix 2 and p.V54Q missense mutation occurred in helix 3 respectively. The 124 bp insertion found in the yak DNAJA1 ortholog may have significant functional relevance warranting further investigation. Our results suggest that these genetic differences may be concomitant with population genetic history and possible functional consequences for climate adaptation in bovidae.

Genetic diversity among Trypanosoma vivax strains detected in naturally infected cattle in Nigeria based on ITS1 of rDNA and diagnostic antigen gene sequences

Trypanosoma vivax (sub-genus Duttonella) is largely responsible for non profitable livestock production in sub-Sahara Africa. In Nigeria, no study has addressed the molecular characteristic of T. vivax except Y486. Hence, we characterized and assessed the genetic diversity among T. vivax detected in naturally infected cattle in Nigeria using internal transcribed spacer 1 (ITS1) of ribosoma DNA (rDNA) and diagnostic antigen gene (DAG) sequences. The length of ITS1 and DAG sequences range from 215–220 to 257–338xa0bp, respectively and the mean G–C contents were 60 and 61.5xa0%. Homology search revealed 93–99 and 95–100xa0% homologies to T. vivax DAG and ITS1 sequences from GenBank. Aligned sequences revealed both ITS1 rDNA and DAG to be less polymorphic but DAG sequences of the Y486 strain and its clone showed marked variation from autochthonous strains. Phylogenetic analysis yielded tree that grouped T. vivax ITS1rDNA gene and DAG sequences into two main clades each. Considering the ITI1 rDNA sequences, clade A contained autochthonous T. vivax within which the South American sequences clustered, clade B contained the sequences of T. vivax from East Africa. Analysis of DAG revealed that the clade A contains autochthonous T. vivax sequences but clade B contained the Y486 and its clones. In conclusion, the diagnostic antigen gene sequences of the T. vivax detected in this study may have undergone considerable gene recombination through time and suggests that more than one strain of T. vivax exist among cattle population in Nigeria.

Mitochondrial DNA hypervariable region 1 diversity in Nigerian goats – CORRIGENDUM

Moses Okpeku, Sunday O. Peters, Ikhide G. Imumorin, Kyle C. Caires, Varun K. Sharma, Mathew Wheto, Rakesh Tamang, Adeyemi S. Adenaike, Michael O. Ozoje and Kumarasamy Thangaraj doi: 10.1017/S2078633616000102, Published by Cambridge University Press, 3 January 2017 In the above publication (Okpeku, 2017) the incorrect affiliation was given for Kyle Caires. The correct affiliation is: Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaì i at M anoa, Honolulu, HI 96822, USA

Mitochondrial DNA hypervariable region 1 diversity in Nigerian goats

espanolLas cabras constituyen el mayor grupo de ganado rumiante en Nigeria y desempenan un papel estrategico en el aporte de proteina animal y en la mejora de la economia de los hogares rurales. Se investigo acerca de la region hipervariable 1 (HVR1) del genoma mitocondrial caprino con el fin de comprender mejor la importancia de la diversidad genetica para mejorar la seleccion en los programas de mejora y conservacion animal. Se secuencio y se analizo la region hipervariable 1 del ADN mitocondrial (HVR1) en 291 cabras autoctonas de Nigeria no relacionadas (Enana de Africa Occidental (EAO), Roja de Sokoto (RS) y Sahel (S)), seleccionadas aleatoriamente a lo largo del pais y comparadas con las secuencias HVR1 de 336 cabras indias y con otras 12 secuencias de 5 especies diferentes del generoCapra (C. falconeri, C. ibex nubiana, C. aegagrus, C. cylindricornis yC. sibirica). Un total de 139 sitios polimorficos de 291 individuos se concentraron en 204 haplotipos. La variacion intra- e interpoblacional fue de 77,25 por ciento y de 22,74 por ciento, respectivamente. Las cabras nigerianas mostraron una elevada diversidad genetica (0,87) y unos valores de FST elevados, distintos de los de las cabras indias y de los de las otras especies salvajes. De acuerdo con los haplogrupos, la cabra EAO se desliga de poblaciones concomitantes de RS y S con una historia demografica diferente. Se identifico una estructura genetica clara entre las razas caprinas de Nigeria, con una variacion apreciable en la region HVR1 del ADN mitocondrial. Este estudio agrupo las razas caprinas nigerianas en dos grupos principales, sugiriendo asi dos origenes demograficos distintos para las razas septentrionales y meridionales. El alto grado de mezcla genetica denota origenes maternos distintos, a diferencia de lo observado en cabras del Levante y Asia Central, donde se domesticaron originalmente las cabras. Palabras clave: diversidad genetica, cabras, region hipervariable, ADN mitocondrial, Nigeria EnglishGoats make up the largest group of ruminant livestock in Nigeria and are strategic in bridging animal protein supply gap and improving the economy of rural households. The hypervariable region 1 (HVR1) of the caprine mitochondrial genome was investigated to better understand genetic diversity important for improving selection for animal breeding and conservation programs. We sequenced and analysed the mitochondrial DNA (mtDNA) HVR1 in 291 unrelated indigenous Nigerian goats (West African Dwarf (WAD), Red Sokoto (RSO) and Sahel (SAH)), randomly sampled from around the country, and compared them with the HVR1 sequences of 336 Indian goats and 12 other sequences in five different species in the genusCapra (C. falconeri, C. ibex nubiana, C. aegagrus, C. cylindricornis andC. sibirica). A total of 139 polymorphic sites from 291 individuals were captured in 204 haplotypes. Within and among population variations were 77.25 and 22.74 percent, respectively. Nigerian goats showed high genetic diversity (0.87) and high FST values, and separate from Indian goats and other wild species. Haplogroups in WAD separates it from RSO and SAH concomitant with a differentdemographic history. Clear genetic structure was found among Nigerian goat breeds with appreciable variation in mtDNA HVR1 region. This study grouped Nigerian goat breeds into two major groups suggesting two different demographic origins for Northern and Southern breeds. High genetic admixing denotes different maternal origins and in contrast to evidence from goats from Levant and Central Asia, where goats were originally domesticated. Keywords: genetic diversity, goats, hypervariable region, mitochondrial DNA, Nigeria francaisLes caprins constituent le plus grand groupe de ruminants domestiques au Nigeria et jouent un role strategique dans l’approvisionnement en proteines animales et dans l’amelioration de l’economie des menages ruraux. Une recherche a ete menee a propos de la region hypervariable 1 (HVR1) du genome mitochondrial caprin dans le but de mieux comprendre l’importance de la diversite genetique pour ameliorer la selection dans les programmes d’amelioration genetique et de conservation des animaux. La region hypervariable 1 de l’ADN mitochondrial (HVR1) a ete sequencee et analysee chez 291 chevres indigenes du Nigeria, sans rapport entre elles (Naine d’Afrique Occidentale (NAO), Rouge de Sokoto (RS) et Sahel (S)), echantillonnees de maniere aleatoire a travers le pays et comparees avec les sequences HVR1 de 336 chevres indiennes et avec 12 autres sequences de 5 especes differentes du genre Capra (C. falconeri, C. ibex nubiana, C. aegagrus, C. cylindricornis et C. sibirica). Un total de 139 sites polymorphes de 291 individus a ete rassemble en 204 haplotypes. La variation intra- et inter-populationnelle a ete de 77,25 pour cent et de 22,74 pour cent, respectivement. Les caprins nigerians ont montre une grande diversite genetique (0,87) et des valeurs de FST elevees et differentes de celles des chevres indiennes et de celles des autres especes sauvages. D’apres les haplogroupes, la chevre NAO serait a separer des populations concomitantes de RS et S avec une histoire demographique differente. Une structure genetique claire a ete decelee entre les races caprines du Nigeria, avec une variation substantielle dans la region HVR1 de l’ADN mitochondrial. Cette etude a regroupe les races caprines nigerianes en deux groupes principaux, ce qui suggere deux origines demographiques differentes pour les races du Nord et du Sud. Le fort degre de melange genetique denote des origines maternelles differentes, contrairement a ce qui a ete observe chez les chevres du Levant et d’Asie Centrale, ou les caprins furent d’abord domestiques. Mots-cles: diversite genetique, caprins, region hypervariable, ADN mitochondrial, Nigeria