Novel Haplotype in the HHEX Gene Promoter Associated with Body Length in Pigs

Yabiao Luo; Qiao Xu; Mingming Xue; Yubei Wang; Xiaoyang Yang; Shuheng Chan; Qiguo Tang; Feng Wang; Ruiping Sun; Zhe Chao; Meiying Fang

doi:10.3390/genes14020511

Novel Haplotype in the HHEX Gene Promoter Associated with Body Length in Pigs

Genes (Basel). 2023 Feb 17;14(2):511. doi: 10.3390/genes14020511.

Authors

Yabiao Luo¹, Qiao Xu^{1

2}, Mingming Xue¹, Yubei Wang¹, Xiaoyang Yang¹, Shuheng Chan¹, Qiguo Tang¹, Feng Wang³, Ruiping Sun³, Zhe Chao³, Meiying Fang^{1

4}

Affiliations

¹ Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
² Jiang Xi Province Key Lab of Genetic Improvement of Indigenous Chicken Breeds, Institution of Biological Technology, Nanchang Normal University, Nanchang 330029, China.
³ Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Science, Haikou 571100, China.
⁴ Sanya Institute of China Agricultural University, Sanya 572025, China.

Abstract

The screening of important candidate genes and the identification of genetic markers are important for molecular selection in the pig industry. The hematopoietically expressed homeobox (HHEX) gene plays an important role in embryonic development and organogenesis; however, the genetic variation and expression pattern of the porcine HHEX gene remains to be clarified. In this study, semiquantitative RT-PCR and immunohistochemistry results showed the specific expression of the HHEX gene in porcine cartilage tissues. A novel haplotype consisting of two SNPs rs80901185 (T > C) and rs80934526 (A > G) was detected in the promoter region of the HHEX gene. The expression of the HHEX gene was significantly higher in Yorkshire pigs (TA haplotype) than in Wuzhishan pigs (CG haplotype), and a population analysis showed that this haplotype was significantly associated with body length. An analysis subsequently revealed that the -586 to -1 bp region of the HHEX gene promoter showed the highest activity. Furthermore, we found that the activity of the TA haplotype was significantly higher than that of the CG haplotype by changing the potential binding of transcription factors YY1 and HDAC2. In summary, we conclude that the porcine HHEX gene may contribute to the breeding of pigs for body length traits.

Keywords: HHEX; body length; expression pattern; gene polymorphism; promoter activity.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Female
Genes, Homeobox*
Haplotypes
Homeodomain Proteins* / genetics
Polymorphism, Single Nucleotide
Pregnancy
Promoter Regions, Genetic
Swine*

Substances

Homeodomain Proteins

Grants and funding

This research was supported by the Zaozhuang Talent Program Funding to MYF, the National Natural Science Foundation of China (32072700 and U22A20508), the 2020 Research Program of Sanya Yazhou Bay Science and Technology City (Grant No. SKJC-2020-02-007), and the China Agriculture Research System of MOF and MARA (CARS-35).