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Whole-Genome Sequencing

Genome-Wide Association Study of Body Size Traits in Luning Chickens Using Whole-Genome Sequencing



Chickens are one of the most economically important animals in the world with a population of over 34.4 billion in 2023 according to Food and Agriculture Organization (FAO) statistics. The broiler industry has evolved significantly over the past century, with a focus on rapid growth rates, efficient feed conversion, and high meat yield. Chicken is the second most numerous meat product in China, and mainly comes from white-feather and yellow-feather chickens. 

With the development of breeding technology, marker-assisted selection (MAS) and genomic selection (GS) have been increasingly utilized in the broiler industry to improve breeding efficiency and enhance target traits. Single-nucleotide polymorphisms (SNPs) and causal genes across the genome can be utilized to accurately estimate each chicken’s genetic potential for specific traits. Therefore, the identification of candidate genetic markers and genes would allow for more accurate and efficient selection of breeding stock, leading to faster genetic improvement and ultimately enhancing the quality and yield of broiler meat for consumers.

Chicken growth traits are well known for their genetic architectural complexity. Currently, there are 5339 chicken quantitative trait loci (QTL) related to the growth traits in the Animal QTL Database (https://www.animalgenome.org/cgi-bin/QTLdb/index, accessed on 24 April 2024). The accuracy and precision of locating QTL depends, in part, on the density of the linkage map created. Unfortunately, the denser the map, the more likely that false positive QTL will be detected with linkage map-based QTL methods. A more precise mapping of traits is possible with newly available genome sequences and genome-wide association studies (GWASs).

The GWAS is a powerful study design that can identify associations between genome-wide sets of genetic variations and a specific trait using genome resequencing or high-density chip technology. This methodology has generated a myriad of robust associations for a range of traits and diseases, and the number of associated variants is expected to grow steadily as GWAS sample sizes increase. With the development of modern breeding technology, GWASs have also been implemented in domestic animals to identify the genetic factors associated with important economic traits. Most of these GWASs were carried out using SNP chips due to high sequencing costs. Whole-genome sequencing (WGS) is a more efficient technology that can detect rare and undiscovered variants. It was more appropriate to explore genomic variation information by WGS with reduced costs.

Luning chickens are mainly located in Mianning County, Sichuan Province, China. As a well-known native breed, Luning chickens have a large body size, and exhibit well-developed chest and leg muscles, high muscle quality, high suitability, and resistance to disease. The increasing market demand has driven the price of Luning chickens to more than 10 times that of ordinary broilers. All the yellow feather broilers used in production are developed from local chicken breeds. Luning chickens are an underutilized genetic resource which needs a systematic evaluation. We aim to cultivate new genetic materials that meet market and industry development needs.

Down syndrome, cystic fibrosis, Huntington's disease, Tay-Sachs disease, Duchenne muscular dystrophy, fragile X syndrome, sickle cell anemia, hemophilia, thalassemia, Marfan syndrome, Turner syndrome, Klinefelter syndrome, phenylketonuria (PKU), neurofibromatosis, spinal muscular atrophy, Prader-Willi syndrome, Angelman syndrome, Rett syndrome, Wilson's disease,

#GeneticDisorders, #DNA, #GeneMutation, #RareDiseases, #DownSyndrome, #CysticFibrosis, #HuntingtonsDisease, #SickleCell, #Thalassemia, #MarfanSyndrome, #PKU, #TurnerSyndrome, #FragileX, #Hemophilia, #MuscularDystrophy, #Neurogenetics, #Genomics, #InheritedDisorders, #MolecularBiology, #PrecisionMedicine

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