Large-scale transcriptome sequencing in broiler chickens to identify candidate genes for breast muscle weight and intramuscular fat content

Abstract

Background In broiler production, breast muscle weight and intramuscular fat (IMF) content are important economic traits. Understanding the genetic mechanisms that underlie these traits is essential to implement effective genetic improvement programs. To date, genome-wide association studies (GWAS) and gene expression analyses have been performed to identify candidate genes for these traits. However, GWAS mainly detect associations at the DNA level, while differential expression analyses usually have low power because they are typically based on small sample sizes. To detect candidate genes for breast muscle weight and IMF contents (intramuscular fat percentage and relative content of triglycerides, cholesterol, and phospholipids), we performed association analyses based on breast muscle transcriptomic data on approximately 400 Tiannong partridge chickens at slaughter age. Results First, by performing an extensive simulation study, we evaluated the statistical properties of association analyses of gene expression levels and traits based on the linear mixed model (LMM) and three regularized linear regression models, i.e., least absolute shrinkage and selection operator (LASSO), ridge regression (RR), and elastic net (EN). The results show that LMM, LASSO and EN with tuning parameters that are determined based on the one standard error rule exhibited the lowest type I error rates. Using results from all three models, we detected 43 candidate genes with expression levels that were associated with breast muscle weight. In addition, candidate genes were detected for intramuscular fat percentage (1), triglyceride content (2), cholesterol content (1), and phospholipid content (1). Many of the identified genes have been demonstrated to play roles in the development and metabolism of skeletal muscle or adipocyte. Moreover, weighted gene co-expression network analyses revealed that many candidate genes were harbored by gene co-expression modules, which were also significantly correlated with the traits of interest. The results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that these modules are involved in muscle development and contraction, and in lipid metabolism. Conclusions Our study provides valuable insight into the transcriptomic bases of breast muscle weight and IMF contents in Chinese indigenous yellow broilers. Our findings could be useful for the genetic improvement of these traits in broiler chickens.

Large-Scale Whole Genome Sequencing Study Reveals Genetic Architecture and Key Variants for Breast Muscle Weight in Native Chickens

“…For indigenous chicken, meat production, especially BrW, is the cardinal breeding index. In this study, a significant increase in BrW (about 12 g) was found in the IMF selected population, which was consistent with a previous report that a mild correlation was found between chicken IMF and BrW [ 11 ]. Herein, we used this ideal chicken model to investigate genetic markers associated with BrW.…”

“…Significant phenotypic enhancement and a discrete genetic architecture were identified for this selected line in previous reports [ 9 , 10 ]. Given that IMF and BrW are related, BrW could be enhanced significantly along with the selection of high IMF in chicken [ 9 , 11 ]. Therefore, comparison of the original line and the selected line is an excellent means by which to dissect genetic architecture and explore the genes affecting BrW.…”

“…For BrW trait, Liu et al identified a significant genomic region (chr3: 61.82–68.57 Mb) affecting BrW in Beijing You chickens, with NCO17 , TPD52L1 , FABP7 , CJA1 , and ASF1A identified as candidate genes regulating BrW [ 15 ]. Kang et al identified 43 genes that were correlated with BrW in transcriptional level for Tiannong partridge chickens [ 11 ]. Liu et al reported chromosome 4 and 27 had BrW associated SNPs and genes ( LCORL and MAPT ), and both of these two genes were expressed at significantly higher levels in chickens with larger breast muscle [ 16 ].…”

The SLC27A1 Gene and Its Enriched PPAR Pathway Are Involved in the Regulation of Flavor Compound Hexanal Content in Chinese Native Chickens

“…The RNA purity was determined using a NanoPhotometer ® -Spectrophotometer (IMPLEN Inc., West Lake Village, CA, USA) and RNA integrity and concentration were measured using the RNA Nano 6000 Assay Kit for the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). RNA-sequencing was performed on an Illumina NovaSeq 6000 S2 (Illumina Inc., San Diego, CA, USA) and 150-bp paired-end reads were generated [ 13 ]. We then performed quality control on the RNA data using tools Trimmomatic (v0.32) and FastQC (v0.11.7), including removal of low-quality reads (read quality < 30).…”

Identification of New Genes and Genetic Variant Loci Associated with Breast Muscle Development in the Mini-Cobb F2 Chicken Population Using a Genome-Wide Association Study

“…This technology has been widely used to explore the mechanisms of complex traits, including human diseases [ 5 , 6 , 7 ], plant development or disease resistance [ 8 , 9 ], as well as animal growth and reproductive capacity [ 10 , 11 ] in past years. Similarly, a GWAS has also been applied to the study of chicken development, especially breast muscle development and some significant candidate genes or genomic regions have been identified [ 12 , 13 , 14 ]. Interestingly, genetic variants within the genome significantly associated with breast muscle development appear to be diverse and are often associated with other traits, such as body weight, full evisceration weight, and so on [ 15 ].…”