Exploring genotype–phenotype relationships of the LHX3 gene on growth traits in beef cattle

• The LHX3 plays an essential role in pituitary gland and nervous system development.
• 17 or 18 haplotypes were revealed and linkage disequilibrium was assessed in 802 cattle.
• SNPs 1–6 are associated with the body weight at 6, 12 and 18 months in NY cattle.
• A new field of study and extend the spectrum of genetic variation of the LHX3 gene.

The LIM-homeobox gene 3 (LHX3) plays an essential role in pituitary gland and nervous system development. Sequence variants (SVs) in coding and non-coding regions of LHX3 gene have an impact on LHX3 transcription and growth traits in cattle. Previously, we have identified 3 single nucleotide polymorphisms (SNPs: 1–3) in all exons and intron 2 regions of the LHX3 gene in cattle. Here, 7 novel SNPs (SNPs: 4-10) were identified by DNA sequencing and polymerase chain reaction single-stranded conformational polymorphism (PCR-SSCP) methods. In the present study, a total of 10 SNPs were assessed linkage disequilibrium (LD) in 802 cows representing four main cattle breeds from China (Nanyang, Qinchuan, Jiaxian, and Chinese Holstein). The assessment results demonstrated that 17 haplotypes and 18 diplotypes were revealed in these cattle populations. Moreover, association analysis indicated that the genotypes of SNPs 1–6 are associated with the body weight at 6, 12 and 18 months of age in Nanyang cattle (P < 0.01 or P < 0.05), whereas no significant association was found between the 18 diplotypes and growth traits. Our results provide evidence that some SNPs in LHX3 gene may be associated with body weight at certain age, and LHX3 gene may be used as candidate gene for marker-assisted selection (MAS) in beef cattle breeding.