Large-scale genomic and transcriptomic analyses elucidate the genetic basis of high meat yield in chickens

Self Cite

Exploring the genetic loci underlying economic traits is foundational for innovation in modern animal breeding technology. Genome‐wide association studies (GWAS) have been valid and commonly used tools to dissect the genomic variants associated with phenotypes for the past ∼20 years and have contributed to our understanding of genetic and molecular bases of various traits. Here, we comprehensively review the recent research progress on GWAS methods. We highlight the methodological advancements enabled by the combination of new proteome, transcriptome, epigenome, and metagenome information and multi‐omics analysis algorithms. The advances in GWAS investigations of chickens, pigs, cattle, and other animals during the last 5 years are also described. Finally, we discuss the current applications of GWAS in cutting‐edge breeding technologies and overall future perspectives of the post‐GWAS era.

Section: Mendelian Randomizationmentioning

confidence: 97%

Section: Experimental Populations and Data Resourcementioning

confidence: 99%

Section: Chickenmentioning

confidence: 99%

Section: Advantages and Limitations Of Gwasmentioning

confidence: 99%

Section: Gwas Combination With Other Technologiesmentioning

confidence: 99%

See 3 more Smart Citations

Research progress and applications of genome‐wide association study in farm animals

Tan

Fahey

et al. 2023

Self Cite

Designing and evaluating a cost‐effective single nucleotide polymorphism liquid array for Chinese native chickens

Liu,

Shan,

et al. 2023

Genotyping plays an important role in breeding and population studies. Currently available genotyping technologies, including solid‐phase chips and sequencing, often have several limitations in their application to local chickens in China, including high costs, insufficient diversity, and poor universality. In the present study, we developed a chicken 5 K single nucleotide polymorphism (SNP) array suitable for breeding and genetic analysis using genotyping by targeted sequencing technology. The chip design was based on genomic data from 33 local breeds, and 5847 SNPs were selected for the final chip design. Among these SNPs, 3427 sites were associated with economic traits in broiler chickens. Our chip contained 25,000 high‐quality SNP markers captured from 5 K regions with highly efficient target site capture. Population analyses of the eight breeds showed high detection rates and minor allele frequencies for SNP markers on the array, enabling clear differentiation of different populations and families within populations. The genetic diversity trend obtained using the chip was consistent with the results obtained from microsatellite analyses. Additionally, the 5 K array was applied to a genome‐wide association study of broilers, resulting in the identification of several growth‐ and meat quality‐related loci. Therefore, the newly developed chip is efficient, cost‐effective, and well suited for application in local Chinese chickens, which will accelerate poultry breeding improvements and enhance conservation efforts.

The Duck 1000 Genomes Project: Achievements and perspectives

Fan,

Hou,

Zhou

2024

The duck (Anas platyrhynchos) is not only a vital farm animal but also an excellent model for genetic dissection of economic traits. The integration of multiomics data provides a powerful approach to elucidate the genetic basis of domestication and phenotype variation. Since its inception in 2014, the Duck 1000 Genomes Project has aimed to uncover the genetic foundation of key economic traits in ducks by combining multiomics data including genomic, transcriptomic, and metabolomic from various natural and segregating populations. This paper summarizes the strategies and achievements of the Duck 1000 Genomes Project, highlighting the reference genome assembly, genome evolution analysis, and the identification of genes and causative mutations responsible for key economic traits in ducks. We also discuss perspectives and potential challenges in functional genomic studies that could further accelerate duck molecular breeding.