title: RNA-seq analysis reveals new candidate genes for drip loss in a Pietrain × Duroc × Landrace × Yorkshire population.
abstract: Drip loss, one of the most important meat quality traits, is characterized by low heritability. To date, the genetic factors affecting the drip loss trait have not been clearly elucidated. The objective of this study was to identify critical candidate genes affecting drip loss. First, we generated a Pietrain × Duroc × Landrace × Yorkshire commercial pig population and obtained phenotypic values for the drip loss trait. Furthermore, we constructed two RNA libraries from pooled samples of longissimus dorsi muscles with the highest (H group) and lowest (L group) drip loss and identified the differentially expressed genes (DEGs) between these extreme phenotypes using RNA-seq technology. In total, 25 883 genes were detected in the H and L group libraries, and none was specifically expressed in only one library. Comparative analysis of gene expression levels found that 150 genes were differentially expressed, of which 127 were upregulated and 23 were downregulated in the H group relative to the L group. In addition, 68 drip loss quantitative trait loci (QTL) overlapping with 63 DEGs were identified, and these QTL were distributed mainly on chromosomes 1, 2, 5 and 6. Interestingly, the triadin (TRDN) gene, which is involved in muscle contraction and fat deposition, and the myostatin (MSTN) gene, which has a role in muscle growth, were localized to more than two drip loss QTL, suggesting that both are critical candidate genes responsible for drip loss.
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Bojiang
authors.initials: B
authors.lastname: Li
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Kaiqing
authors.initials: K
authors.lastname: Liu
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Qiannan
authors.initials: Q
authors.lastname: Weng
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Pinghua
authors.initials: P
authors.lastname: Li
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Wei
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Qifa
authors.initials: Q
authors.lastname: Li
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Chen
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Ruihua
authors.initials: R
authors.lastname: Huang
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Wangjun
authors.initials: W
authors.lastname: Wu
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Honglin
authors.initials: H
authors.lastname: Liu
mesh_terms: D000818:Animals; D001947:Breeding; D002352:Carrier Proteins / Q000235:genetics; D005260:Female; D015870:Gene Expression; D015723:Gene Library; D008297:Male; D008460:Meat; D009119:Muscle Contraction / Q000235:genetics; D009124:Muscle Proteins / Q000235:genetics; D055435:Myostatin / Q000235:genetics; D010641:Phenotype; D040641:Quantitative Trait Loci; D017423:Sequence Analysis, RNA; D013552:Swine / Q000235:genetics*
chemical_list: D002352:Carrier Proteins; D009124:Muscle Proteins; D055435:Myostatin; C070048:triadin
keywords: meat quality; pig; pork; sequencing; water holding capacity