Detection of InDel variations within seven candidate genes and their associations with phenotypic traits in three cattle breeds

Detection of key gene InDels in JAK/STAT pathway and their associations with growth traits in four Chinese sheep breeds

OBJECTIVE

The Janus kinase/signal transducer and transporter activator (JAK/STAT) signaling pathway plays crucial roles in lipid metabolism, glucose metabolism and cell senescence, suggesting that they are potential candidate genes affecting growth traits in animals. The present study aimed to evaluate the association between InDels in the JAK/STAT pathway and growth traits of four Chinese sheep breeds, including Tong sheep, Hu sheep, Small-tailed Han sheep and Lanzhou fat-tailed sheep.

RESULTS

Seventy-six indel loci of 11 genes in JAK/STAT were detected, and three genotypes were selected at four loci by PCR amplification, electrophoresis and sequencing, including one locus in STAT3, one locus in STAT5A, and two loci in JAK1. The Correlation analysis indicated that there was no significant correlation between STAT3 and growth traits in four sheep breeds (P > 0.05); STAT5A was significantly associated with body height, rump width and tube circumference in Hu sheep and body length in Tong sheep (P < 0.05); JAK1 was significantly correlated with body height, body oblique length, cross height and tube circumference in Hu sheep (P < 0.05) and body oblique length, cross height and tube circumference in small-tailed Han sheep (P < 0.05).

CONCLUSION

Overall, our results indicated a potential association between the growth traits of sheep and the InDels of JAK1 and STAT5A.

Association of pleomorphic adenoma gene 1 with body weight and measurement of Bali cattle (Bos javanicus)

Background and Aim:

Pleomorphic adenoma gene 1 (PLAG1) encodes a multifunctional transcription factor that controls many genes and pathways and is associated with cattle body weight and measurements. This study aimed to evaluate the association between PLAG1 polymorphisms with body weight and measurements in Bali cattle.

Materials and Methods:

A total of 87 Bali cattle, consisting of 48 bulls and 39 heifers at the Breeding Center for Bali Cattle, were used as the population in this study. Cattle were 2 years old and kept semi-intensively in the pasture. Phenotype data consisting of body weight, withers height, body length, chest girth, waist height, and chest depth were measured. Birth weight data were obtained from birth records, and weight gain, adjusted weaning weight, and yearling weight were calculated using formulas. Blood samples were taken from the jugular vein as much as 5 mL, and genomic DNA was isolated using the salting-out method. Polymerase chain reaction (PCR) was performed to amplify three target polymorphisms, namely, g.48308 C>T, g.32212 (19 bp indel), and g.45233 T>C. The presence of a 19 bp indel was determined by direct observation of the PCR product on a 2% agarose gel. Two other polymorphisms were detected by PCR-restriction fragment length polymorphism using the restriction endonuclease enzymes SacII and BclI. PLAG1 genotype and phenotype associations were analyzed using a general linear model.

Results:

The results showed that two of the target polymorphisms in PLAG1 did not vary. The DD genotype indicated by 123 bp of PCR product was the only genotype identified for g.32212 19 bp indel, and TT genotype was the only genotype found for g.45233 T>C single-nucleotide polymorphism (SNP). Conversely, g.48308 C>T SNP was found to be polymorphic. In addition, the g.48308 C>T polymorphism of PLAG1 was significantly associated with body length of Bali cattle. Cattle with the CC genotype had a greater body length than the other two genotypes.

Conclusion:

The g.48308 C>T SNP in PLAG1 was associated with Bali cattle body length characteristics. This finding could be used as a basis for selecting Bali cattle based on body length characteristics.

Determination of genetic variation within the DYRK2 gene and its associations with milk traits in cattle

To speed up the progress of marker-assisted selection (MAS) in cattle breeding, the dual-specificity tyrosine phosphorylation-regulated kinase 2 (DYRK2), cadherin 2 (CDH2), and kinesin family member 1A (KIF1A) genes were chosen based on our pervious genome-wide association study (GWAS) analysis results. DYRK2 is a kinase that may participate in cell growth and/or development; it shows phosphorylation activity toward serine, threonine, and tyrosine fragments of proteins, and it is different from other protein kinases. The CDH2 gene encodes a classic cadherin, which is a member of the cadherin superfamily. The protein encoded by KIF1A is a member of the kinesin family and plays a role in the transportation of membrane organelles along axon microtubules. We detected insertion/deletion (InDel) variation in these three candidate genes in 438 individual cattle (Xinjiang Brown cattle and Wagyu × Luxi crossbreed cattle). Only DYRK2-P3-11 bp was polymorphic and genotyped. The polymorphism information content of DYRK2-P3-11 bp was 0.336. Correlation analyses showed that InDel polymorphism was significantly associated with six different milk traits. These findings may aid future analyses of InDel genotypes in cattle breeds, and speed up the progress of MAS in cattle breeding.