NGS allele counts versus called genotypes for testing genetic association

Silos, Rosa González; Fischer, Christine; Bermejo, Justo Lorenzo

doi:10.1016/j.csbj.2022.07.016

Cited by 1 publication

(2 citation statements)

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“…It was revealed that there was no difference between the two dataset markers as the median of 21 alternative alleles per locus was similar. It means that both markers have a similar ability to be used for further genetic association studies between alternative allele counts and phenotypes for a given trait of economic importance [ 37 , 38 ] in chickens. Some studies confirmed this association.…”

Section: Discussionmentioning

confidence: 99%

“…Some studies confirmed this association. The study by [ 38 ] tested the association between the ratio of alternative allele counts of the ASIP gene and Yoruba descent ancestry using linear regression to study the relationship between the genetic variability of this gene region and Yoruba ancestry. The authors observed the higher statistical power when the relationship between the genetic variability at a given region of the genome and phenotypes is tested by the association between alternative allele counts phenotypes.…”

Section: Discussionmentioning

confidence: 99%

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

Mujyambere,

Adomako,

Olympio

2024

BMC Genomics

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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.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%