Porcine LEM domain-containing 3: Molecular cloning, functional characterization, and polymorphism associated with ear size

doi:10.1016/S2095-3119(15)61173-X

Journal of Integrative Agriculture ›› 2016, Vol. 15 ›› Issue (06): 1321-1229.DOI: 10.1016/S2095-3119(15)61173-X

Porcine LEM domain-containing 3: Molecular cloning, functional characterization, and polymorphism associated with ear size

收稿日期:2015-03-30 出版日期:2016-06-01 发布日期:2016-06-06

Porcine LEM domain-containing 3: Molecular cloning, functional characterization, and polymorphism associated with ear size

LIANG Jing^1*, LI Na^{1, 2*}, ZHANG Long-chao¹, WANG Li-gang¹, LIU Xin¹, ZHAO Ke-bin¹, YAN Hua¹, PU Lei¹, ZHANG Yue-bo¹, SHI Hui-bi¹, ZHANG Qin², WANG Li-xian¹

¹Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation, Ministry of Agriculture/Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
² Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture/College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R.China

Received:2015-03-30 Online:2016-06-01 Published:2016-06-06
Contact: WANG Li-xian, Fax: +86-10-62818771, E-mail: iaswlx@263.net; ZHANG Qin, E-mail: qzhang@cau.edu.cn
About author:LIANG Jing, E-mail: jing_224@126.com
Supported by:
This research was supported by the Agricultural Science and Technology Innovation Program, China (ASTIP-IAS02), the National Key Technology R&D Program of China (2011BAD28B01), the Earmarked Fund for Modern Agro-Industry Technology Research System of China, and foundation from Chinese Academy of Agricultural Sciences (2014ZL006).

摘要/Abstract

Abstract: Ear size exhibits remarkable diversity in pig breeds. LEM domain-containing 3 (LEMD3) on chromosome 5 is considered as an important candidate for porcine ear size. This is the first study on cloning and characterization of LEMD3 cDNA. The complete cDNA contains 4 843 bp, including a 2 736-bp open reading frame (ORF), a 37-bp 5´-untranslated region (UTR) and a 2 070-bp 3´-UTR. The complete LEMD3 gene is 126 241-bp and contains 13 exons and 12 introns. The ORF encodes a deduced LEMD3 protein of 911 amino acids, which shares 82–94% nucleic acid and 51–96% amino acid identity with other species. A phylogenetic tree constructed based on the amino acid sequences revealed that the porcine LEMD3 protein was closely related with cattle LEMD3. Resequencing of the ORF and promoter of LEMD3 from Minzhu pig and Large White revealed three single nucleotide polymorphisms (SNPs): L964C>A in the complete coding region, L4625A>G in the 3´ UTR, and L-394T>C in the promoter region. Genome-wide association study (GWAS) revealed that all of SNPs were shown significant association with ear size in Large White×Minzhu pig intercross population. With conditional GWAS, –log₁₀(P-value) decreased by more than 80% when each of three SNPs was included as a fixed effect. These results suggested direct involvement of LEMD3 or close linkage to the causative mutation for ear size. The findings of this study might form the basis for understanding the genetic mechanism of ear size variation in pigs and provide potential molecular markers for screening ear size diversity in pig breeds.

Key words: association analysis , ear size , LEMD3 , molecular cloning, pig

LIANG Jing, LI Na, ZHANG Long-chao, WANG Li-gang, LIU Xin, ZHAO Ke-bin, YAN Hua, PU Lei, ZHANG Yue-bo, SHI Hui-bi, ZHANG Qin, WANG Li-xian. Porcine LEM domain-containing 3: Molecular cloning, functional characterization, and polymorphism associated with ear size[J]. Journal of Integrative Agriculture, 2016, 15(06): 1321-1229.

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Porcine LEM domain-containing 3: Molecular cloning, functional characterization, and polymorphism associated with ear size

Porcine LEM domain-containing 3: Molecular cloning, functional characterization, and polymorphism associated with ear size

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