Genetic diversity and population structure of Nigerian indigenous goat using DNA microsatellite markers

Twenty-nine microsatellite markers were used to evaluate genetic diversity and rela- tionships among three Nigerian goat breeds and to compare with one South African and one European goat breeds as outgroups. A total of 244 goats from the Sahel (47), Maradi (47), and West African Dwarf (67) breeds; and as outgroup: Kalahari (47) and Saanen (36) breeds were included. DNA was extracted from blood preserved on FTA Classic cards according to manufacturer’s protocol. The microsatellite regions were amplified using thermal cycler. Mean number of allele (MNA), expected and observed Heterozygousities (He and Ho, respectively), Hardy-Weinberg Equilibrium (HWE) and genetic distances between populations were calculated. A dendogram was constructed to reveal evolutionary trend in the studied breeds. A genetic structure of the populations was performed using STRUCTURE. Genetic diversity was high with MNA per locus ranging from 6.69 to 8.79 for Kalahari and West African Dwarf, respectively. Ho values ranged from 59 % for West African Dwarf to 64.9 % for Saanen. The highest He estimates were observed in the West African Dwarf (70 %). The lowest He (66.5 %) was observed in Saanen population. The Mean Fis values for the studied populations ranged from 0.055 to 0.148 for Kalahari and West Africa Dwarf, respectively. Genetic distances between populations revealed the least genetic relationship between Saanen and Maradi (0.386) and highest between Maradi and Sahel (0.025). The HWE test revealed eighteen, seventeen, thirteen, twenty-three, and twenty-one loci were in HWE (p>0.05) in Maradi, West African Dwarf, Sahel, Saanen, and Kalahari, respectively. A gra- phic representation of the STRUCTURE analysis revealed that Nigerian goats descended from a common ancestor different from South African and European breeds used as outgroups.Se analizaron 29 microsatélites para evaluar la diversidad genética de tres razas capri- nas Nigerianas y establecer las relaciones genéticas entre ellas utilizando las razas Saanen y Kalahari como poblaciones outgroup. Se analizaron 244 distribuidas de la siguiente manera: en Sahel (47), Maradi (47) y WestAfrican Dwarf (67), Kalahari (47) y Saanen (36). El ADN se extrajo a partir de sangre conservada en tarjetas FTA Classic siguiendo las instrucciones del fabricante y se amplificaron los microsatélites mediante PCR. Se calcularon el número medio de alelos (MNA), las heterocigocidades observada (Ho) y esperada (He) y las distancias genéticas entre pares de poblaciones. Se hizo una prueba de equilibrio Hardy-Weinberg (HWE) y un análisis de la estructura genética de las poblaciones mediante el programa STRUCTURE. La diversidad genética encontrada fue alta con valores de MNA entre 6,69 y 8,79 para Kalahari y West African Dwarf, respectivamente. Los valores de Ho oscilaron entre un 59 % para West African Dwarf y un 64,9 % para Saanen. La He más alta se encontró en la raza West African Dwarf (70 %), mientras que el valor más bajo se observó en la raza Saanen (He= 66,5 %). Los valores medios de Fis para las poblaciones estudiadas variaron entre 0,055 en Kalahari y 0,148 en West African Dwarf. La distancia genética más elevada fué la encontrada entre Saanen y Maradi (0,386) y la menor entre Maradi y Sahel (0,025). La prueba de equilibrio de HWE reveló que dieciocho, diecisiete, trece, veintitrés y veintiún loci estaban en equilibrio HWE (p>0,05) en las razas Maradi, West African Dwarf, Sahel, Saanen y Kalahari, respectivamente. Una representación gráfica del análisis de estructura genética reveló que las cabras de Nigeria descienden de un ancestro común diferente de las razas sudafricanas y europeas que fueron utilizadas como grupos externos