1
|
Niu G, Yang Y, Zhang Y, Hua C, Wang Z, Tang Z, Li K. Identifying suitable reference genes for gene expression analysis in developing skeletal muscle in pigs. PeerJ 2016; 4:e2428. [PMID: 27994956 PMCID: PMC5157201 DOI: 10.7717/peerj.2428] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/11/2016] [Indexed: 11/20/2022] Open
Abstract
The selection of suitable reference genes is crucial to accurately evaluate and normalize the relative expression level of target genes for gene function analysis. However, commonly used reference genes have variable expression levels in developing skeletal muscle. There are few reports that systematically evaluate the expression stability of reference genes across prenatal and postnatal developing skeletal muscle in mammals. Here, we used quantitative PCR to examine the expression levels of 15 candidate reference genes (ACTB, GAPDH, RNF7, RHOA, RPS18, RPL32, PPIA, H3F3, API5, B2M, AP1S1, DRAP1, TBP, WSB, and VAPB) in porcine skeletal muscle at 26 different developmental stages (15 prenatal and 11 postnatal periods). We evaluated gene expression stability using the computer algorithms geNorm, NormFinder, and BestKeeper. Our results indicated that GAPDH and ACTB had the greatest variability among the candidate genes across prenatal and postnatal stages of skeletal muscle development. RPS18, API5, and VAPB had stable expression levels in prenatal stages, whereas API5, RPS18, RPL32, and H3F3 had stable expression levels in postnatal stages. API5 and H3F3 expression levels had the greatest stability in all tested prenatal and postnatal stages, and were the most appropriate reference genes for gene expression normalization in developing skeletal muscle. Our data provide valuable information for gene expression analysis during different stages of skeletal muscle development in mammals. This information can provide a valuable guide for the analysis of human diseases.
Collapse
Affiliation(s)
- Guanglin Niu
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yalan Yang
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - YuanYuan Zhang
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaoju Hua
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zishuai Wang
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhonglin Tang
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Kui Li
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| |
Collapse
|
2
|
Chen R, Yu S, Ren F, Lv XY, Pan CY. Detection of one large insertion/deletion (indel) and two novel SNPs within the <i>SPEF2</i> gene and their associations with male piglet reproduction traits. Arch Anim Breed 2016. [DOI: 10.5194/aab-59-275-2016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract. The sperm flagella 2 (SPEF2) gene is essential for normal sperm tail development and male fertility. To fully characterize the structure of the mutation and to further study the function of the pig SPEF2 gene, we explored the insertion/deletion (indel) and novel single-nucleotide polymorphisms (SNPs) within the pig SPEF2 gene, and tested their associations with the testicular sizes in male Large White (LW) and Landrace (LD) pigs from China. Herein, a large insertion located at the SPEF2 gene in chromosome 16 was found, and two alleles of "I" (insertion) and "D" (deletion) were designated. Allele "D" was dominant in all analyzed pigs. Two novel SNPs (namely (NC_010458) g.19642G > A, resulting in AfaI aCRS PCR–PFLP, and g.19886C > G, resulting in EcoRI aCRS PCR–PFLP) were found in LW and LD pigs. Association testing revealed that g.19886C > G was significantly associated with the testis long circumference (TLC) in LW pigs (P < 0.05), suggesting that this SNP would be the DNA marker for the marker-assisted selection (MAS) in reproduction traits. This preliminary result indicates that the pig SPEF2 gene had significant effects on male reproduction traits. These findings could not only extend the spectrum of genetic variations in the pig SPEF2 gene but also contribute to implementing MAS in genetics and breeding in pigs.
Collapse
|