Biology subjects

Djikeng, A.

Publications and source records attributed to Djikeng, A..

4 recordsLinked to original sources

bioRxiv2025

A chromosome-level genome assembly of the South African indigenous, Kolbroek pig, Sus scrofa domesticus

The Kolbroek pig is indigenous to South Africa and a breed of choice for smallholder farmers. This is mainly due to its characteristics, such as disease resistance and adaptability to tropical agroecological environments. Despite these desirable traits, the genomic architecture of this breed has not been explored. In this study, we report a high-quality genome assembly of the South African Kolbroek pig sequenced at 31 x coverage through a combination of PacBio Sequel IIe HiFi and Illumina Novaseq 6000 Omni-C sequencing. The assembled genome resulted in a length of 2.6 Gb in size, including 83 Scaffolds, which consist of 19 chromosome-size scaffolds with 138.7 Mb/48.5 Mb for scaffold/contig N50 respectively. The BUSCO completeness at 95.5 %. Genome annotation and structure prediction identified 22,025 genes with protein-coding potential. The genome provides an opportunity to investigate genetic variation across multiple pig breeds and serves as a genetic resource to develop breeding programs for the conservation and improvement of the Kolbroek pig.

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↗

bioRxiv2019

A mini-atlas of gene expression for the domestic goat (Capra hircus) reveals transcriptional differences in immune signatures between sheep and goats

Goats (Capra hircus) are an economically important livestock species providing meat and milk across the globe. They are of particular importance in tropical agri-systems contributing to sustainable agriculture, alleviation of poverty, social cohesion and utilisation of marginal grazing. There are excellent genetic and genomic resources available for goats, including a highly contiguous reference genome (ARS1). However, gene expression information is limited in comparison to other ruminants. To support functional annotation of the genome and comparative transcriptomics we created a mini-atlas of gene expression for the domestic goat. RNA-Seq analysis of 22 transcriptionally rich tissues and cell-types detected the majority (90%) of predicted protein-coding transcripts and assigned informative gene names to more than 1000 previously unannotated protein-coding genes in the current reference genome for goat (ARS1). Using network-based cluster analysis we grouped genes according to their expression patterns and assigned those groups of co-expressed genes to specific cell populations or pathways. We describe clusters of genes expressed in the gastro-intestinal tract and provide the expression profiles across tissues of a subset of genes associated with functional traits. Comparative analysis of the goat atlas with the larger sheep gene expression atlas dataset revealed transcriptional differences between the two species in macrophage-associated signatures. The goat transcriptomic resource complements the large gene expression dataset we have generated for sheep and contributes to the available genomic resources for interpretation of the relationship between genotype and phenotype in small ruminants.

genomics↗