Traditionally, genome-wide association studies (GWAS) require maximum numbers of genotyped and phenotyped animals to efficiently detect marker-trait associations. Under financial constraints, alternative solutions should be envisaged such that of performing GWAS with fractioned samples of the population. In the present study, we investigated the potential of using random and extreme phenotype samples of a population including 6,700 broilers in detecting significant markers and candidate genes for a typical complex trait (body weight at 35 days). We also explored the utility of using continuous vs. dichotomized phenotypes to detect marker-trait associations. Present results revealed that extreme phenotype samples were superior to random samples while detection efficacy was higher on the continuous over the dichotomous phenotype scale. Furthermore, the use of 50% extreme phenotype samples resulted in detection of 8 out of the 10 markers identified in whole population sampling. Putative causative variants identified in 50% extreme phenotype samples resided in genomic regions harboring 10 growth-related QTLs (e.g. breast muscle percentage, abdominal fat weight etc.) and 6 growth related genes (CACNB1, MYOM2, SLC20A1, ANXA4, FBXO32, SLAIN2). Current findings proposed the use of 50% extreme phenotype sampling as the optimal sampling strategy when performing a cost-effective GWAS.
Published in | International Journal of Genetics and Genomics (Volume 8, Issue 1) |
DOI | 10.11648/j.ijgg.20200801.14 |
Page(s) | 29-40 |
Creative Commons |
This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited. |
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Copyright © The Author(s), 2020. Published by Science Publishing Group |
Body Weight, Broilers, Extreme Phenotypes
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APA Style
Eirini Tarsani, Georgios Theodorou, Irida Palamidi, Antonios Kominakis. (2020). Identification of Candidate Genes for Body Weight in Broilers Using Extreme-Phenotype Genome-Wide Association Study. International Journal of Genetics and Genomics, 8(1), 29-40. https://doi.org/10.11648/j.ijgg.20200801.14
ACS Style
Eirini Tarsani; Georgios Theodorou; Irida Palamidi; Antonios Kominakis. Identification of Candidate Genes for Body Weight in Broilers Using Extreme-Phenotype Genome-Wide Association Study. Int. J. Genet. Genomics 2020, 8(1), 29-40. doi: 10.11648/j.ijgg.20200801.14
AMA Style
Eirini Tarsani, Georgios Theodorou, Irida Palamidi, Antonios Kominakis. Identification of Candidate Genes for Body Weight in Broilers Using Extreme-Phenotype Genome-Wide Association Study. Int J Genet Genomics. 2020;8(1):29-40. doi: 10.11648/j.ijgg.20200801.14
@article{10.11648/j.ijgg.20200801.14, author = {Eirini Tarsani and Georgios Theodorou and Irida Palamidi and Antonios Kominakis}, title = {Identification of Candidate Genes for Body Weight in Broilers Using Extreme-Phenotype Genome-Wide Association Study}, journal = {International Journal of Genetics and Genomics}, volume = {8}, number = {1}, pages = {29-40}, doi = {10.11648/j.ijgg.20200801.14}, url = {https://doi.org/10.11648/j.ijgg.20200801.14}, eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijgg.20200801.14}, abstract = {Traditionally, genome-wide association studies (GWAS) require maximum numbers of genotyped and phenotyped animals to efficiently detect marker-trait associations. Under financial constraints, alternative solutions should be envisaged such that of performing GWAS with fractioned samples of the population. In the present study, we investigated the potential of using random and extreme phenotype samples of a population including 6,700 broilers in detecting significant markers and candidate genes for a typical complex trait (body weight at 35 days). We also explored the utility of using continuous vs. dichotomized phenotypes to detect marker-trait associations. Present results revealed that extreme phenotype samples were superior to random samples while detection efficacy was higher on the continuous over the dichotomous phenotype scale. Furthermore, the use of 50% extreme phenotype samples resulted in detection of 8 out of the 10 markers identified in whole population sampling. Putative causative variants identified in 50% extreme phenotype samples resided in genomic regions harboring 10 growth-related QTLs (e.g. breast muscle percentage, abdominal fat weight etc.) and 6 growth related genes (CACNB1, MYOM2, SLC20A1, ANXA4, FBXO32, SLAIN2). Current findings proposed the use of 50% extreme phenotype sampling as the optimal sampling strategy when performing a cost-effective GWAS.}, year = {2020} }
TY - JOUR T1 - Identification of Candidate Genes for Body Weight in Broilers Using Extreme-Phenotype Genome-Wide Association Study AU - Eirini Tarsani AU - Georgios Theodorou AU - Irida Palamidi AU - Antonios Kominakis Y1 - 2020/01/31 PY - 2020 N1 - https://doi.org/10.11648/j.ijgg.20200801.14 DO - 10.11648/j.ijgg.20200801.14 T2 - International Journal of Genetics and Genomics JF - International Journal of Genetics and Genomics JO - International Journal of Genetics and Genomics SP - 29 EP - 40 PB - Science Publishing Group SN - 2376-7359 UR - https://doi.org/10.11648/j.ijgg.20200801.14 AB - Traditionally, genome-wide association studies (GWAS) require maximum numbers of genotyped and phenotyped animals to efficiently detect marker-trait associations. Under financial constraints, alternative solutions should be envisaged such that of performing GWAS with fractioned samples of the population. In the present study, we investigated the potential of using random and extreme phenotype samples of a population including 6,700 broilers in detecting significant markers and candidate genes for a typical complex trait (body weight at 35 days). We also explored the utility of using continuous vs. dichotomized phenotypes to detect marker-trait associations. Present results revealed that extreme phenotype samples were superior to random samples while detection efficacy was higher on the continuous over the dichotomous phenotype scale. Furthermore, the use of 50% extreme phenotype samples resulted in detection of 8 out of the 10 markers identified in whole population sampling. Putative causative variants identified in 50% extreme phenotype samples resided in genomic regions harboring 10 growth-related QTLs (e.g. breast muscle percentage, abdominal fat weight etc.) and 6 growth related genes (CACNB1, MYOM2, SLC20A1, ANXA4, FBXO32, SLAIN2). Current findings proposed the use of 50% extreme phenotype sampling as the optimal sampling strategy when performing a cost-effective GWAS. VL - 8 IS - 1 ER -