Phenotypic and whole-genome single nucleotide polymorphisms (SNP) characterization of Mozambican indigenous cattle breeds

Abstract

Mozambican (MZ) indigenous cattle are generally reared in resource-poor management systems and are well adapted to harsh environments. Despite their significance in food security and improved livelihoods, a limited number of studies have attempted to investigate the genetic variation of these genetic resources or their genetic relationships with other cattle breeds and ecotypes in the region. The current study aimed to characterize three Mozambican indigenous cattle breeds on both phenotypic and genomic levels, in four provinces of Mozambique, namely Maputo, Gaza, Inhambane, and Tete. Firstly, a total of 614 cattle from three indigenous populations including Angone (n=140), Landim (n=292), and Tete (n=182), were sampled in twenty-three villages in four provinces to collect body measurements and qualitative data. Findings showed significant morphological differentiation between the populations. Landim males and females were significantly (p<0.05) heavier than their Tete and Angone counterparts. A combination of six morphometric traits (Body length, horn length, rump width, height at withers, height at the rump, and top-line length) could be used for an individual assignment using discriminant function analysis of SPSS, with a success rate exceeding 70% for both Angone and Landim cattle. Tail hair samples from 228 animals (consisting of the three indigenous populations) were genotyped using the International Dairy and Beef SNP BeadChip array (IDBV3). Population genetic parameters showed a moderate level of variation, with estimates of expected heterozygosities ranging between 0.304 ± 0.166 (Angone) to 0.329 ± 0.148 (Tete). The three indigenous populations all had low positive (across-population average of 0.065±0.109) inbreeding rates. Both principal component (PCA) and admixture analyses indicated poor between-breed differentiation. A downward trend was observed in the effective population sizes of all three populations over time, indicating a narrowing genetic pool for the genetic resources. South African genotypes which included SA Nguni (n=150), SA Tuli (n=150), and SA Boran (n=150) were included in a between-population analysis. These genotypes were generated using the GeneSeek Genomic Profiler (GGP) 80K panel and compared with the Mozambican Nguni (MZ Nguni) cattle. Medium levels of genetic diversity, measured as expected heterozygosity, were observed, ranging from 0.284±0.158 (SA Boran) to 0.324±0.153 (SA Tuli). Runs of homozygosity (ROH) analysis revealed low inbreeding rates with the average FROH ranging from 0.003 (SA Nguni) to 0.006 (SA Tuli). A high frequency of short (ROH ≤ 5Mb) ROH segments suggested ancient inbreeding in all populations. PCA and Admixture analyses revealed a tight cluster of the two Nguni populations, while SA Tuli and SA Boran diverged, as expected, into two distinct clusters. Genome-wide FST and Rsb analyses identified 229 differentiated SNP potentially under selection in the MZ Nguni cattle breed compared to SA cattle populations. These regions were enriched with genes implicated in several metabolic processes essential for adaptation and production traits. This study indicate that Mozambican indigenous cattle populations have a high level of genetic diversity; and Mozambican Nguni and South African Nguni have similar genetic ancestry. A joint regional strategy for the preservation and sustainable use of indigenous animal resources will improve regional food security and the livelihood of farming communities.