Genetic variation of Nigerian cattle inferred from maternal and paternal genetic markers

Abstract

The African cattle provide unique genetic resources shaped up by both diverse tropical environmental conditions and human activities, the assessment of their genetic diversity will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the genetic diversity of cattle samples from Nigeria using both maternal and paternal DNA markers. Nigerian cattle can be assigned to 80 haplotypes based on the mitochondrial DNA (mtDNA) D-loop sequences and haplotype diversity was 0.985 + 0.005. The network showed two major matrilineal clustering: the dominant cluster constituting the Nigerian cattle together with other African cattle while the other clustered Eurasian cattle. Paternal analysis indicates only zebu haplogroup in Nigerian cattle with high genetic diversity 1.000 ± 0.016 compared to other cattle. There was no signal of maternal genetic structure in Nigerian cattle population, which may suggest an extensive genetic intermixing within the country. The absence of Bos indicus maternal signal in Nigerian cattle is attributable to vulnerability bottleneck of mtDNA lineages and concordance with the view of male zebu genetic introgression in African cattle. Our study shades light on the current genetic diversity in Nigerian cattle and population history in West Africa.

Keywords: Genetic diversity; Nigerian cattle; West Africa; Y-chromosome; mtDNA.

Figure 1. Sampling locations of cattle in Nigeria and the network of 420 cattle samples based on 636 bp of the mtDNA D-loop region.

(A) Map of cattle sampling locations in Nigeria (Zamfara, Kano, Katsina, Kaduna and Sokoto from North West; Taraba and Plateau from North East/Central; and Oyo from the West) and the haplogroup distribution based on mtDNA across Africa . The maps of Africa and Nigeria were generated by an online version of the SmartDraw 2012 software (https://cloud.smartdraw.com/editor.aspx?templateId=3a99cb96-00dd-4767-bca6-61a59bd9ad60&flags=128). (B) Median-joining network of 420 cattle samples constructed by using NETWORK v 4.6 ( Bandelt, Forster & Rohl, 1999). Reference sequences used for haplotype network analysis included: Europe, n = 76 (Loftus et al., 1994a; Lai et al., 2006; Achilli et al., 2008; Hiendleder, Lewalski & Janke, 2008; Bonfiglio et al., 2012b and AF034438–AF034446 were retrieved from the GenBank); West Asia, n = 16 (Achilli et al., 2008); Egypt, n = 31 (Bonfiglio et al., 2012b; Olivieri et al., 2015); Ethiopia, n = 126 (Dadi et al., 2009; Bonfiglio et al., 2012b); Mozambique, n = 16 (JQ684029–JQ684045 were retrieved from the GenBank), South Africa, n = 34 (Horsburgh et al., 2013) and two additional Nigerian samples mined from GenBank (Accession no. L27731 and L27730). Sizes of the circles are proportional to haplotype frequencies. m, refers to number of mutation steps and those not indicated are just one step mutation. Colours indicate the geographical distribution of the sampling locations across Africa, Europe and West Asia as shown by the legend in (B).

Figure 2. The network of 28 cattle samples based on 286 bp of the ZFY Y-chromosome region.

Sizes of the circles are proportional to haplotype frequencies and the number of mutation steps in each branch are given. Colours indicate the geographical distribution of the samples as follows: dark green, Nigeria; orange, Asia; and blue, Europe. The source of the data for the Y haplogroups was retrieved from Nijman et al. (2008), Ginja, Telo da Gama & Penedo (2009), MF683853, MF683854 were retrieved from the GenBank.