Bovine HOXA11 Gene Identified from RNA-Seq: mRNA Profile Analysis and Genetic Variation Detection Using ME Method and Their Associations with Carcass Traits

Yangming Huang; Kejing Zhang; Yafang Li; Sihuan Zhang; Zhanerke Akhatayeva; Fugui Jiang; Enliang Song; Xianyong Lan

doi:10.3390/cells12040539

Bovine HOXA11 Gene Identified from RNA-Seq: mRNA Profile Analysis and Genetic Variation Detection Using ME Method and Their Associations with Carcass Traits

Cells. 2023 Feb 8;12(4):539. doi: 10.3390/cells12040539.

Authors

Yangming Huang¹, Kejing Zhang¹, Yafang Li¹, Sihuan Zhang^{1

2}, Zhanerke Akhatayeva¹, Fugui Jiang³, Enliang Song³, Xianyong Lan¹

Affiliations

¹ College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China.
² College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China.
³ Institute of Animal Science and Veterinary, Shandong Academy of Agriculture Science, Jinan 250100, China.

Abstract

The Homeobox A11 (HOXA11) gene regulates limb skeletal development and muscle growth, thus, it was selected as a candidate gene for bovine carcass traits. In this study, we analyzed the mRNA expression level of HOXA11 in various tissues and cells, and determined the genetic variations in the HOXA11 gene, which might be used as molecular markers for cattle breeding. The mRNA expression profiles of HOXA11 in bovine different tissues showed that HOXA11 was highly expressed in both fat and muscle. The gene expression trend of HOXA11 in myoblasts and adipocytes indicated that HOXA11 might be involved in the differentiation of bovine myoblasts and adipocytes. The data in the Ensembl database showed that there are two putative insertion/deletion (InDel) polymorphisms in the bovine HOXA11 gene. The insertion site (rs515880802) was located in the upstream region (NC_037331.1: g. 68853364-68853365) and named as P1-Ins-4-bp, and the deletion site (rs517582703) was located in the intronic region (NC_037331.1: g. 68859510-68859517) and named as P2-Del-8-bp. These polymorphisms within the HOXA11 gene were identified and genotyped by PCR amplification, agarose gel electrophoresis and DNA sequencing in the 640 Shandong Black Cattle Genetic Resource (SDBCGR) population. Moreover, the mutation frequency was very low after detection, so the mathematical expectation (ME) method was used for detection. Statistical analysis demonstrated that P1-Ins-4-bp was significantly correlated with the beef shoulder (p = 0.012) and tongue root (p = 0.004). Meanwhile, P2-Del-8-bp displayed a significant correlation with the back tendon (p = 0.008), money tendon (p = 2.84 × 10^-4), thick flank (p = 0.034), beef shin (p = 9.09 × 10^-7), triangle thick flank (p = 0.04), triangle flank (p = 1.00 × 10^-6), rump (p = 0.018) and small tenderloin (p = 0.043) in the female SDBCGR population. In summary, these outcomes may provide a new perspective for accelerating the molecular breeding of cattle through marker-assisted selection (MAS) strategies.

Keywords: HOXA11; carcass traits; cattle; insertion/deletion (InDel); marker-assisted selection (MAS); mathematical expectation (ME).

Publication types

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

MeSH terms

Animals
Cattle
Female
Genes, Homeobox*
Phenotype
Polymorphism, Single Nucleotide*
RNA, Messenger
RNA-Seq

Substances

RNA, Messenger

Grants and funding

This work was supported by the Agricultural Improved Seed Project of Shandong Province (No. 2020LZGC014) and the National Sci-Tech Innovation Project for Undergraduate of Northwest A&F University (No. 202210712103).