Genetic diversity and structure of domestic cavy (Cavia porcellus) populations from smallholder farms in southern Cameroon

Abstract

Abstract. Although domestic cavies are widely used in sub-Saharan Africa as a source of meat and income, there are only a few studies of their population structure and genetic relatedness. This seminal study was designed with the main objective to assess the genetic diversity and determine the population structure of cavy populations from Cameroon to guide the development of a cavy improvement program. Sixteen microsatellite markers were used to genotype 109 individuals from five cavy populations (Wouri, Moungo and Nkongsamba in the Littoral region, and Mémé and Fako in the Southwest region of Cameroon). Twelve markers worked in the five populations with a total of 17 alleles identified, with a range of 2.9 to 4.0 alleles per locus. Observed heterozygosity (from 0.022 to 0.277) among populations was lower than expected heterozygosity (from 0.42 to 0.54). Inbreeding rates between individuals of the populations and between individuals in each population were 59.3% and 57.2%, respectively, against a moderate differentiation rate of 4.9%. All the tested loci deviated from Hardy-Weinberg equilibrium, except for locus 3. Genetic distances between populations were small (from 0.008 to 0.277), with a high rate of variability among individuals within each population (54.4%). Three distinct genetic groups were structured. This study has shown that microsatellites are useful for the genetic characterization of cavy populations in Cameroon and that the populations investigated have sufficient genetic diversity that can be used to be deployed as a basis for weight, prolificacy and disease resistance improvement. The genetic of diversity in Southern Cameroon is wide and constitute an opportunity for cavy breeding program. Keywords: guinea pig; microsatellites; genetic diversity; small stock; sub-Saharan Africa Abstrak. Marmut banyak diternakkan di daerah sub-Sahara Afrika sebagai sumber daging dan pendapatan, namun studi tentang struktur populasi dan hubungan genetik pada marmut masih terbatas. Tujuan penelitian ini adalah untuk mengetahui keragaman genetik dan struktur populasi marmut di Kamerun sebagai panduan dalam pengembangan populasi marmut. Sebanyak 16 penanda mikrosatelit digunakan untuk mengidentifikasi genotip dari 109 individu di lima daerah (Wouri, Moungo dan Nkongsamba di Littoral region, dan Mémé serta Fako di daerah Baratdaya Kamerun). Sebanyak 12 marker dapat digunakan untuk mengidentifikasi 17 allel di lima daerah populasi dengan kisaran 2,9 sampai 4,0 allel per lokus. Heterozigositas yang diamati dalam populasi (0,022 sampai 0,277) ternyata lebih rendah daripada yang diharapkan (0,42 sampai 0,54). Laju inbreeding antar individu dalam populasi dan antar individu di masing-masing populasi berturut-turut adalah 59,3% dan 57,2%, dengan laju perbedaan yang sedang yakni 4,9%. Semua loci yang diuji memiliki deviasi dari keseimbangan Hardy-Weinberg, kecuali pada lokus 3. Jarak genetik antar populasi menunjukkan jarak yang kecil (0,008 sampai 0,277), dengan variasi yang tinggi antar individu di tiap populasi (54,4%)....

Variabilidad genética de dos subpoblaciones de Cuyes (Cavia porcellus) nativos del sur del Ecuador

“…Todos los marcadores amplificaron exitosamente en los C ecuatorianos, excepto el locus MS II que no logró amplificar. La población de animales nativos mostró un número de alelos considerable, con un promedio de 9,8 ± 3,6, oscilando dichos valores entre 7 y 16 en los loci MS III y MS IV, respectivamente, diferenciándose marcadamente este último de los otros cuatro El número de alelos encontrado en los diferentes locus, se ubican en un rango de 7 a 9 excepto en el MS IV que es mucho mayor; el valor promedio 9,8 obtenido, resultó menor a lo reportado para una muestra de animales nativos del altiplano de Ecuador, investigación que tomó en cuenta un mayor número de microsatélites incluidos dos de los estudiados [5], aunque fue superior a lo encontrado en C nativos colombianos [7] y muy superior a lo encontrado en las poblaciones de C estudiadas en Camerún [6] y Costa de Marfil [14], posiblemente estos dos últimos estuvieron bajo efecto de posibles apareamientos consanguineos. La no amplificacion del marcador MSII pudo deberse a que se trabajó con una especie diferente para la que originalmente fue diseñado (C. aperea), aspecto encontrado también por Burgos y col. [7], confirmándose que dicho marcador no debe ser usado para estudios en C. porcellus.…”

“…Número total de alelos observados;2 Rango de alelos observados (pb);3 Promedio de heterocigosis esperada población total; 4 Promedio heterocigosis esperada;5 Coeficiente de diferenciación;6 Equilibrio Hardy-Weinberg;7 Contenido de información polimórfica;8 Probabilidad de no exclusión (padre) TABLA II Número total y rango de alelos observados, media de heterocigosis Ht y He, coeficiente de diferenciación GST, H-W, PIC y PNE de la población total de Cuyes nativos ecuatorianos ___________________________________________________________Revista Cientifica, FCV-LUZ / Vol. XXXI, N°3, 107 -113, 2021…”

Phenotypic variability and typology of cavy (Cavia porcellus) production in the Democratic Republic of Congo (DRC)

“…The farm management system variations, as well as a variability of environmental conditions alongside genetic diversity, are all reasons that may explain this variability (Ayagiwe et al, 2015). Several genetic diversity assessment studies for cavy populations in sub-Saharan Africa (Kouakou et al, 2015a, Ayagirwe et al, 2017 and South America (Burgos-Paz et al, 2011, Aviles et al, 2015 have demonstrated the existence of great genetic variability. In this study, cavy weighted on average 577.29g; Metre (2012) reported 540 g in South Kivu for 24 weeks old cavies.…”

Genotyping‐by‐sequencing reveals a high number and quality of single nucleotide polymorphisms in guinea pigs (Cavia porcellus) from the Peruvian Andes

“…The observed heterozygosity ( H o ) was 0.31, the expected heterozygosity ( H e ) was 0.35 and the F‐ value was 0.1. Previous microsatellite‐based studies showed an H o value lower than H e in guinea pigs in Cameroon ( H o = 0.02–0.27; H e = 0.42–0.54) (Ayagirwe et al, 2017) and in Colombia ( H o = 0.34–0.61; H e = 0.67–0.76) (Burgos‐Paz et al, 2011). Genetic population studies in Peruvian guinea pigs revealed higher heterozygosity, specifically in Huancavelica and Junin ( H e = 0.54–0.91) (Chumbe, 2020) and Puno and Cuzco ( H e = 0.764) populations (Valladares, 2019).…”

“…The population genetics of guinea pigs in Peru has been described in the past by microsatellite‐based studies (Avilés‐Esquivel et al, 2018; Ayagirwe et al, 2017; Burgos‐Paz et al, 2011; Chumbe, 2020; Valladares, 2019). Despite their advantages, microsatellites have been progressively replaced by high‐throughput SNP technologies owing to their higher genotyping power, even in small populations with low to moderate diversity levels (Lemopoulos et al, 2019).…”