Linkage disequilibrium and haplotype distribution of the bovine LHX4 gene in relation to growth

• The LHX4 involved in pituitary gland and nervous system development
• 31 haplotypes were revealed and linkage disequilibrium was assessed in 871 cattle.
• SNP1–5, and 6 are associated with the growth traits at 18 and 6 months in NY cattle.
• Bovine LHX4 gene may be utilized as genetic marker in MAS for beef cattle breeding.

LIM homeobox transcription factor 4 (LHX4) is a LIM homeodomain transcription factor involved in pituitary gland and nervous system development. The aim of this study was to examine the association of the LHX4 polymorphisms with growth traits in beef cattle breed. A total of 7 single nucleotide polymorphyisms (SNPs) have been identified in the coding region and noncoding region of the bovine LHX4 by sequencing pooled DNA samples (Pool-Seq) and PCR-single strand conformation polymorphism (PCR-SSCP) methods. The linkage disequilibrium was assessed in 871 individuals representing four main cattle breeds from China. The SNPs 2–5 and 7–8 were found to be in complete linkage disequilibrium, respectively. The result of haplotype analysis of 13 SNPs showed that 31 haplotypes were found in four Chinese cattle breeds, and 20 genotypes were only found in Nanyang cattle. The statistical analyses indicated that the SNP1–5, and 6 are associated with the body weight at 18, and 6 months of age in Nanyang cattle population (P < 0.05), but no significant associations between their twenty combined genotypes. Our results provide evidence that some polymorphisms in LHX4 are associated with growth traits at certain ages, and may be used as candidates for marker-assisted selection and management in cattle.