Effectiveness of DArTseq markers application in genetic diversity and population structure of indigenous chickens in Eastern Province of Rwanda.

BACKGROUND: The application of biotechnologies which make use of genetic markers in chicken breeding is developing rapidly. Diversity Array Technology (DArT) is one of the current Genotyping-By-Sequencing techniques allowing the discovery of whole genome sequencing. In livestock, DArT has been applied in cattle, sheep, and horses. Currently, there is no study on the application of DArT markers in chickens. The aim was to study the effectiveness of DArTSeq markers in the genetic diversity and population structure of indigenous chickens (IC) and SASSO in the Eastern Province of Rwanda. METHODS: In total 87 blood samples were randomly collected from 37 males and 40 females of indigenous chickens and 10 females of SASSO chickens purposively selected from 5 sites located in two districts of the Eastern Province of Rwanda. Genotyping by Sequencing (GBS) using DArTseq technology was employed. This involved the complexity reduction method through digestion of genomic DNA and ligation of barcoded adapters followed by PCR amplification of adapter-ligated fragments. RESULTS: From 45,677 DArTseq SNPs and 25,444 SilicoDArTs generated, only 8,715 and 6,817 respectively remained for further analysis after quality control. The average call rates observed, 0.99 and 0.98 for DArTseq SNPs and SilicoDArTs respectively were quite similar. The polymorphic information content (PIC) from SilicoDArTs (0.33) was higher than that from DArTseq SNPs (0.22). DArTseq SNPs and SilicoDArTs had 34.4% and 34% of the loci respectively mapped on chromosome 1. DArTseq SNPs revealed distance averages of 0.17 and 0.15 within IC and SASSO chickens respectively while the respective averages observed with SilicoDArTs were 0.42 and 0.36. The average genetic distance between IC and SASSO chickens was moderate for SilicoDArTs (0.120) compared to that of DArTseq SNPs (0.048). The PCoA and population structure clustered the chicken samples into two subpopulations (1 and 2); 1 is composed of IC and 2 by SASSO chickens. An admixture was observed in subpopulation 2 with 12 chickens from subpopulation 1. CONCLUSIONS: The application of DArTseq markers have been proven to be effective and efficient for genetic relationship between IC and separated IC from exotic breed used which indicate their suitability in genomic studies. However, further studies using all chicken genetic resources available and large big sample sizes are required.

Local chickens in East African region: their production and potential.

Indigenous chickens (IC) contribute socioeconomically to household food security in the region of East Africa. However, their potential and improvement are not well documented. This review is aimed at exploring the production and potential of indigenous chickens in East Africa. The various tools for literature search such as google search and Google scholars, agricultural journals, animal sciences and health journals, poultry related journals, and country online databases were used to gather information. IC were primarily reared by women and were kept predominantly under scavenging systems where the conditions of management (feeding, housing, and health care) are poor. They presented a high variation in their reproduction and production characteristics. The products (meat and eggs) were of good quality and preferred by the local consumers. Despite the variation and potential of IC, improvements in the village system were constrained by diseases and loss due to Newcastle, Gumboro, and Ecto-endo parasites and predators. Farmers primarily used traditional methods to control the diseases, and some used conventional medications and vaccines. Due to the potential of IC, the exploration of various strategies for improvement supported by the details of their genetic variability and adaptation as well as different management conditions was a goal of this review.