Genetic Evidences of Adaptive and Productive Features in the West African Indigenous Cattle Population in Benin

Abstract

The lack of proper genetic characterization of the West African cattle genetic resources is a major limitation for their sustainable management and the improvement of cattle production in this region. The current study examines the genetic background of adaptive and productive features in the indigenous cattle breeds kept in Benin. For this purpose, different approaches, including up-to-date genomic methodologies such as selection signature analysis, genome-wide association study (GWAS), and next generation sequencing were applied to genetically characterize the Beninese indigenous taurines (Lagune, Somba) and crossbreeds (Borgou, Pabli), as representatives of West African cattle genetic resources. Publication 1 provides an overview of the production systems and current institutional management of cattle breeds in Benin and summarizes the existing challenges to promote animal genetic resources and to sustain cattle production. Next, strategies for genetic evaluation and breed selection were explored with respect to the breeding goals and the traits (e.g., robustness) valued by smallholders, for efficient and durable improvements of farmer management practices and animal performances. In Publication 2, genotype data were generated with medium-density single nucleotide polymorphism (SNP) panels from current Dahomey cattle samples (30 animals) and current Beninese indigenous cattle samples (449 animals from four breeds: Lagune, Somba, Borgou and Pabli). These genotype data were contrasted with available historical genotypes from Beninese, other West African, Asian and European cattle, to test for admixture, to compute admixture proportions and genomic inbreeding, and to identify selection signatures. The findings substantiated the high genetic proximity of Dahomey cattle to the Lagune, in contrast to the European taurine. However, high inbreeding rate in the Dahomey cattle population suggested imperative strategies (including exchange of breeding stock) to increase diversity in the breed. Moreover, evidence of admixture with Zebu cattle was observed in the local cattle breeds sampled in Benin, especially the Borgou. The latter breed displayed an important reduction of African taurine (AFT) ancestral proportion, in comparison with historical data. Nevertheless, the most recent selection signatures identified in the investigated breeds were associated with economic traits (reproduction, growth, milk) and adaptive traits (immunity, feed efficiency), irrespective of the admixture proportions. More interestingly, specific genomic footprints (rarely reported in other African breeds), and hosting genes related to disease resistance (e.g., DSB, BOLA-DYA) were detected in the Somba. Furthermore, multi-breed genetic parameter estimations and GWAS were performed for six morphometric measurements (height at withers, HAW, sacrum height, SH, heart girth, HG, hip width, HW, body length, BL and ear length, EL), considering the genotype and the fixed effects (age, sex, agro-ecological zones) of the 449 current Beninese indigenous cattle samples (Publication 3). The estimated SNP-based heritabilities for the morphometric traits ranged between 0.46 ± 0.14 (HG) and 0.74 ± 0.13 (HW). Phenotypic and genetic correlations ranged from 0.25 ± 0.05 (HW-BL) to 0.89 ± 0.01 (HAW-SH), and from 0.14 ± 0.10 (HW-BL) to 0.85 ± 0.02 (HAW-SH), respectively. A total of 28 SNP showed significant associations with the investigated traits. The SNP were located in close proximity (± 25kb) to 15 genes related to height or body size (e.g. PIK3R6, PIK3R1), conformation, growth or carcass traits (VEPH1, CNTNAP5, GYPC), and stress or immune response (PTAFR, PBRM1, ADAMTS12). Six milk protein genes CSN1S1, CSN2, CSN1S2, CSN3, LALBA, and LGB were targeted in Publication 4 to study their polymorphisms, and casein haplotypes in Beninese indigenous cattle. Next generation sequencing of the genes’ exons, flanking intron regions and parts of the 5′-upstream regions, applied on 67 Beninese indigenous cattle, revealed a total of 1058 genetic variants with 731 previously undescribed. Within the identified genetic variants, 12 polymorphisms determined 17 milk protein variants, including two for CSN1S1 (B, C), three for CSN2 (A1, A2, L), two for CSN1S2 (A, B), three for CSN3 (A, B, K), four for LALBA (A, B, E, F), and three for LGB (B, B1, K). In this regard, the characterization of four novel milk protein variants (CSN3K, LALBAF, LGBB1 and LGBK) in the Beninese cattle breeds confirms their rich and unique genetic diversity. Additionally, five main haplotypes were constructed based on variants within the casein genes (CSN1S1-CSN2-CSN1S2-CSN3), but the haplotypes B-A1-A-B, B-A1-A-A and C-A2-A-B were the most frequent. Finally, Publication 5 reports the agricultural and ecological utilization or importance of the Dahomey cattle in European countries. The breed corresponds to the Beninese Lagune cattle breed, which was introduced to Europe in the early 1990’s. A web-based open-closed questionnaire was used to investigate the motivations and management practices of farmers keeping the Dahomey cattle in Germany, Switzerland and Austria. The results revealed increasing interests in the Dahomey cattle, which were mainly kept in small herds (seven animals on average) for landscape maintenance and meat production or breeding stock. Farmers appreciated various features (e.g., resistance to disease, calving ease, low feeding requirement) in the Dahomey cattle, and were dedicated to the promotion of the breed. Overall, this study evidenced a high genetic correlation between adaptive and productive features in the West African indigenous cattle in Benin. The current findings corroborate previous knowledge on West African or other African indigenous cattle. Their implications for the sustainable management of the breeds are discussed in chapter 7. Further investigations to consolidate these results and improve the management of West African cattle genetic resources are also suggested.