Biology subjects

Houaga, I.

Publications and source records attributed to Houaga, I..

4 recordsLinked to original sources

bioRxiv2025

Genomic diversity, population structure and admixture in native cattle breeds of Benin

This study investigates the genetic diversity, population structure, and admixture patterns of indigenous cattle breeds in Benin, shedding light on their evolutionary relationships and adaptation to the West African environment. A total of 348 cattle from eight indigenous breeds of Benin, including taurine (Lagune, Borgou, Pabli, and Somba), zebu (Gudali, Zebu Peuhl, and Yakana) and one crossbred (Bourgou X Zebu) cattle were genotyped along with a reference dataset of cattle from Europe, Asia, and West Africa. After quality control, 28.591 SNPs from 838 cattle were analyzed for genetic diversity, differentiation, and admixture. Pairwise FST values revealed significant genetic differentiation between local taurine and zebu breeds (FST = 0.05 - 0.15), with some populations showing close genetic relationships, while others, such as the Borgou and NDama breeds, exhibiting relatively more divergence. The admixture analysis indicated significant gene flow from zebu cattle into local taurine breeds, suggesting adaptive introgression driven by factors such as heat tolerance and disease resistance. Additionally, the effective population size (Ne) was relatively higher in Benins taurine breeds as compared to zebu, likely attributable to traditional open communal mating practices. The genetic structure also reflected the influence of both historical and ongoing introgression from Asian zebu cattle. The results highlight the importance of maintaining genetic diversity through regional breeding strategies that consider environmental and adaptive pressures. The results of the present study will serve as a basis for the development of Community Based Breeding Programs (CBBPs) for Beninese cattle adapted to local contexts, integrating information on admixture levels, breeders preferences, production performance, and the conservation of local genetic diversity.

genomics↗

bioRxiv2025

High quality genome assemblies of African cattle breeds using PacBio HiFi sequencing

Africa has a uniquely rich cattle diversity of [~]150 breeds comprising the Bos taurus indicus sub-species, Bos taurus taurus, and their crosses. These represent [~]23% of the global cattle population. However, high quality, representative assemblies are limited for African cattle and especially for indicine breeds. Here we built high quality de novo assemblies for five important African indigenous cattle breeds using PacBio HiFi sequencing: Lagune (Bos taurus taurus), Gudali, Iringa Red and Singida White (Bos taurus indicus), and Mpwapwa (Bos taurus taurus x Bos taurus indicus). These new assemblies are the most contiguous and complete African cattle assemblies produced so far, with genome sizes of 3.25 - 3.36Gb, contiguity N50s ranging from 83.59Mb to 97.87Mb and scaffold N50s from 100.30Mb to 113.37Mb. BUSCO genome completeness scores were also higher than 99.68%, indicative of highly contiguous assemblies. These improved and highly contiguous genome assemblies are consequently a valuable resource for future African and global livestock genomic studies.

genomics↗

bioRxiv2025

Spatial modelling improves genomic evaluation in Tanzanian smallholder admixed dairy cattle

BackgroundSmallholder dairy production systems in low-and middle-income countries are characterised by large phenotypic variance due to diverse environmental effects, farming practices, and crossbreeding. Furthermore, small herds, low genetic connectedness, and limited data recording challenge accurate separation of environmental and genetic effect in such settings, limiting genetic improvement. Here, we evaluated the impact of modelling spatial variation between herds to address these challenges and improve the accuracy of genomic evaluation for Tanzanian smallholder dairy cattle. ResultsWe analysed 19,375 test-day milk yield records of 1894 dairy cows from 1386 herds across four distinct geographical regions in Tanzania. The cows had 664,822 SNP marker genotypes after quality control and were highly admixed. We fitted a series of GBLUP models to evaluate the impact of modelling the herd effect and the spatial effect on. The herd effect was fitted as an independent random effect, while the spatial effect was fitted as a random effect with Euclidean distance-based Matern covariance function. The models were compared based on: model fit; estimates of variance components and breeding values; correlations between the estimated contribution of breeding values, herd effect, and spatial effect to phenotype values; and the accuracy of phenotype prediction in cross-validation and forward validation. The results showed large differences in milk yield between and within regions, as well as significant variation due to the spatial effect, which were not fully captured by modelling the herd effect. The results also strongly indicate that a model with just the herd effect underestimated breeding values of animals in less favourable environments and overestimated breeding values of animals in more favourable environments. ConclusionsThis study demonstrated the challenge of achieving accurate genomic evaluation in smallholder settings. By leveraging spatial modelling we maximised the use of available data and improved the separation of genetic and environmental effects. Further work is required to improve smallholder genetic evaluations by understanding environmental and genetic processes that drive the large phenotypic variance in African smallholder setting.

genomics↗

bioRxiv2024

Accurate determination of breed origin of alleles in a simulated smallholder crossbred dairy cattle population

BackgroundAccurate assignment of breed origin of alleles at a heterozygote locus may help to introduce a resilient or adaptive haplotype in crossbreeding. In this study, we developed and tested a method to assign breed of origin for individual alleles in crossbred dairy cattle. After generations of mating within and between local breeds as well as the importation of exotic bulls, five rounds of selected crossbred cows were simulated to mimic a dairy breeding programme in the low- and middle-income countries (LMICs). In each round of selection, the alleles of those crossbred animals were phased and assigned to their breed of origin (being either local or exotic). ResultsAcross all core lengths and modes of phasing (with offset or no), the average percentage of alleles correctly assigned a breed origin was 95.76%, with only 1.39% incorrectly assigned and 2.85% missing or unassigned. On consensus, the average percentage of alleles correctly assigned a breed origin was 93.21%, with only 0.46% incorrectly assigned and 6.33% missing or unassigned. This high proportion of alleles correctly assigned a breed origin resulted in a high core-based mean accuracy of 0.99 and a very high consensus-based mean accuracy of 1.00. The algorithms assignment yield and accuracy were affected by the choice of threshold levels for the best match of assignments. The threshold level had the opposite effect on assignment yield and assignment accuracy. A less stringent threshold generated higher assignment yields and lower assignment accuracy. ConclusionsWe developed an algorithm that accurately assigns a breed origin to alleles of crossbred animals designed to represent breeding programmes in the LMICs. The developed algorithm is straightforward in its application and does not require prior knowledge of pedigree, which makes it more relevant and applicable in LMICs breeding programmes.

genetics↗