Identification of a novel 24 bp insertion–deletion (indel) of the androgen receptor gene and its association with growth traits in four indigenous cattle breeds

Abstract. During the past decades, insertions and deletions (indels) have become increasingly popular in animal breeding for understanding the relationship between genotypes and phenotypes. The androgen receptor (AR) plays the vital role of a bridge on the function of the androgen and has sexual size dimorphism. For this reason, the objective of this study was to explore the novel indel variants within the cattle AR gene and to detect their effects on growth traits in four breeds of Chinese yellow cattle. Herein, we first confirmed a novel 24 bp indel (AC_000187.1g.4187270-4187293delAATTTATTGGGAGATTATTGAATT) within the intron of the cattle AR gene. This is consistent with the results predicted from the NCBI SNP database. The distribution of the indel genotypes of four Chinese yellow cattle were significantly different from each other (P < 0.01). After significant correlation analysis, many remarkable phenotypic differences among the three genotypes were found (P < 0.05). In conclusion, a novel 24 bp indel within the AR gene significantly affected growth traits, suggesting that this indel may be a useful DNA marker for the elimination or selection of excellent individuals for cattle breeding.

A novel 12 bp deletion within goat <i>LHX4</i> gene significantly affected litter size

Abstract. The LIM homeobox transcription factor 4 (LHX4) gene plays a critical role in regulating the development of the pituitary and the secretion of growth hormone (GH) and prolactin (PRL) associated with reproduction. Thus this gene may affect litter size. Herein, the aim of this study is to detect the novel insertion/deletion (indel) within the LHX4 gene as well as to test its association with litter size in 1149 Shaanbei white cashmere goats. Herein, a novel 12 bp indel (NC_030823.1:g.60001011_60001022delGGGGAGGAGGGG) was firstly found, which was located in the first intron. Meanwhile, three genotypes were detected in Shaanbei white cashmere goats, and the allelic frequencies of I and D were 0.593 and 0.407, respectively. Interestingly, the genotype distributions between mothers of single-lamb (n = 895) and multi-lamb (n = 254) groups within Shaanbei white cashmere goats were significantly different, implying that the 12 bp indel might affect the litter size. Furthermore, the association analysis was carried out to find out that the 12 bp indel was significantly associated with litter size in the analyzed goat population (P  <  0.05). The litter sizes of genotype DD and ID individuals were superior to those of genotype II (P  <  0.05). These findings suggest that this locus could be considered as a genetic marker for goat breeding, enriching the research category of functional genome of goats.

A novel 29 bp insertion/deletion (indel) variant of the <i>LHX3</i> gene and its influence on growth traits in four sheep breeds of various fecundity

Abstract. Belonging to the same LIM homeobox (LHX) family, LHX3 and LHX4 are key transcription factors in animal growth and reproduction. Insertion/deletion (indel) is a relatively simple and effective DNA marker. Therefore, four sheep breeds of various fecundity were used to explore the novel indel variants within the sheep LHX3 and LHX4 gene, as well as to evaluate their effects on growth traits. Herein, only one novel 29 bp indel (NC_019460.2:g.3107494-3107522delGGCCTGGACTGTGATGGGCACCCTCCGGG) within the sheep LHX3 gene was found, and three genotypes were detected. Interestingly, the increasing trends of II (insertion/insertion) genotype frequency and I allelic frequency were the same as the growth of the fertility character. Genotypic frequency and allelic frequency distributions were significantly different between the high-fecundity breeds (HS, STHS and LFTS) and low-fecundity breed (TS) based on a χ2 test (P < 0.05). Association analyses showed that body length was significantly different in female TS and STHS and that chest width was significantly different for the female TS and male STHS (P < 0.05). These findings suggested that the 29 bp indel could extend the spectrum of genetic variations of the LHX3 gene in sheep and provide a valuable theoretical basis for the marker-assisted selection (MAS) in sheep breeding and genetics.