ArticleBMC genomics2024
Effectiveness of DArTseq markers application in genetic diversity and population structure of indigenous chickens in Eastern Province of Rwanda.
Article in BMC genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed, 5 citations in OpenAlex.
- Rapid turnover of sex chromosomes is associated with speciation in Neotropical armored catfish Harttia (Siluriformes, Loricariidae).Biology direct · 2026Article
- Genome-wide characterization of genetic diversity and population structure of the Chilean Mapuche fowl using DArTseq SNP markers.Poultry science · 2026Article
- Genetic variants associated with reduced body size in indigenous chickens of Eritrea: A genome-wide association study.Poultry science · 2026Article
- Genetic diversity and relationship of Bugesera and Rwamagana indigenous chicken populations with SASSO chickens using DArTseq SNPs.PloS one · 2025Article
- Genome-wide association mapping in safflower (Carthamus tinctorius L.) for genetic dissection of drought tolerance using DArTseq markers.Scientific reports · 2024Article
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3 authors at 2 institutions in 2 countries.
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Abstract
backgroundThe 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.
methodsIn 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.
resultsFrom 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.
conclusionsThe 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.
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