Haplotype combination of the caprine PC1 gene sequence variants and association with growth traits in Chinese Haimen breed

Genetic effects of MOGAT1 gene SNP in growth traits of Chinese cattle

Single nucleotide polymorphism (SNP) has recently become one of the ideal genetic markers. SNP refers to the DNA sequence polymorphism caused by double nucleotide variation in the genome, including the conversion or transversion of segmented bases. The synthesis and metabolism of triglycerides are related to the changes of energy in the body of livestock, which in turn affects their growth and development. Studies have shown that MOGAT1 gene plays a role in the route of triglyceride synthesis. PCR-RFLP and agarose gel electrophoresis technology were used to type the SNP site of MOGAT1 gene at g.25940T > C in this study. Association analysis between typing results and growth trait data was detected by SPSS 20.0 software. Results show that MOGAT1 gene was in a low level of heterozygosity in Xianan, Qinchuan and Pinan cattle population (0 < PIC < 0.25), and in middle level of heterozygosity in YL cattle population(0.25 < PIC < 0.5). And genotype 'AA' was dominant gene in Chinese cattle population. In QC and XN cattle, genotype of GG possess advantage on Body weight (P < 0.05); in YL cattle, individuals with genotype of homozygous mutation decreased significantly on Chest depth (P < 0.05). The purpose of this research is to provide theoretical materials for molecular breeding of yellow cattle and to promote the process of improving the growth traits of Chinese local yellow cattle.

Distribution and association study of PLAG1 gene between copy number variation and Chinese cattle populations

Copy number variation mainly refers to the copy number change of DNA fragments from 1 to 5 Mb. The deletion, duplication, inversion and ectopic of these fragments are collectively referred to as CNV. Numerous studies have shown that transfer factors play a vital role in regulating the growth and development of the body, for example the pleomorphic adenoma gene (PLAG). However, there is no study of CNV in PLAG1 gene. We qualified copy numbers within PLAG1 gene in 8 cattle breeds (Qinchuan, Qaidamu, Jinjiang, Guangfeng, Ji'an, Jiaxian, Pinan and Xianan cattle) by quantitative PCR, and explored their impacts on CNV of PLAG1 gene and phenotypic traits in Xianan cattle. We defined Deletion into CN = 0, Normal into CN = 1 and Duplication into CN = 2. The results showed that the individual with type of CN = 1 has a significant better effect on heart girth in JA cattle population (p < 0.01); the individual with type of CN = 1 and CN = 0 has a better effect on Rump length in JX cattle population (p < 0.05); the individual with type of CN = 0 has a better effect on cannon bone circumference in XN cattle population (p < 0.05). Association analysis showed that in JA cattle, the number of CN = 2 is great in JA cattle population, and the performance of CN = 2 in heart girth is better than CN = 1; in JX cattle, the rump length of CN = 2 is less than individual with CN = 0 and CN = 1; in XN cattle, individuals with CN = 0 have a better performance on cannon bone circumference than others. The results can provide a theoretical basis for molecular breeding of Chinese cattle, molecular mark-assist selection (MAS) of growth traits of Chinese cattle, and rapidly establish a Chinese cattle population with excellent genetic resources. Simple summaryWith the living standards rising, people's demand for beef is getting higher and higher, and there is a great significance to improve the growth performance of cattle. We measured body size data and detected copy number type of different cattle breeds (Xianan cattle, Ji'an cattle and Jiaxian cattle), and analyzed the correlation between the two object. We found that copy number variation of PLAG1 gene significantly affected some growth traits of XN cattle, JA cattle, and JX cattle. This may provide the basic material for molecular marker-assisted selection breeding of Chinese cattle breeds.

Copy Number Variation of the PIGY Gene in Sheep and Its Association Analysis with Growth Traits

Simple Summary

The PIGY (phosphatidylinositol glycan anchor biosynthesis class Y) gene is a member of the PIG gene family and encodes the glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex. It initiates the biosynthesis of GPI and plays an important role in cell–cell interactions. Sequencing has revealed a 3600 bp copy number variation (CNV) in exon 2 of the PIGY gene in sheep, potentially altering a functional part of the protein. The CNV overlaps 28 quantitative trait loci that are relevant to some economic traits like muscle density and carcass weight. We screened for this CNV of the PIGY gene in 569 individuals, namely, 240 Chaka sheep (CKS), 168 Hu sheep (HS), and 161 small-tailed Han sheep (STHS), and analyzed the association between the presence of this CNV and sheep body size traits. The results showed that the loss-type CNV was more prevalent than other types in these three breeds, and there were significant effects of the PIGY gene CNV on body weight, chest circumference, and circumference of cannon bone of sheep. The results showed that sheep with gain-type CNV had better growth traits than those with other types. The findings reveal the relationship between the CNV of the PIGY gene and growth traits of sheep, suggesting that CNV could be utilized for improved molecular breeding of sheep.

Abstract

Copy number variation (CNV) is a type of genomic variation with an important effect on animal phenotype. We found that the PIGY gene contains a 3600 bp copy number variation (CNV) region located in chromosome 6 of sheep (Oar_v4.0 36,121,601–36,125,200 bp). This region overlaps with multiple quantitative trait loci related to phenotypes like muscle density and carcass weight. Therefore, in this study, the copy number variation of the PIGY gene was screened in three Chinese sheep breeds, namely, Chaka sheep (CKS, May of 2018, Wulan County, Qinghai Province, China), Hu sheep (HS, May of 2015, Mengjin County, Henan Province, China), and small-tailed Han sheep (STHS, May of 2016, Yongjing, Gansu Province, China). Association analyses were performed on the presence of CNV and sheep body size traits. We used real-time quantitative PCR (qPCR) to detect the CNV for association analysis. According to the results, the loss-type CNV was more common than other types in the three breeds (global average: loss = 61.5%, normal = 17.5%, and gain = 21.0%). The association analysis also showed significant effects of the PIGY gene CNV on body weight, chest circumference, and circumference of the cannon bone of sheep. Sheep with gain-type CNV had better growth traits than those with other types. The results indicate a clear relationship between the PIGY gene CNV and growth traits of sheep, suggesting the use of CNV as a new molecular breeding marker.

Copy number variation (CNV) in the IGF1R gene across four cattle breeds and its association with economic traits

The insulin-like growth factor 1 receptor (IGF1R) plays a vital role in immunomodulation and muscle and bone growth. The copy number variation (CNV) is believed to the reason for many complex phenotypic variations. In this paper, we statistically analyzed the copy number and the expression profiling in different tissue types of the IGF1R gene using the 422 samples from four Chinese beef cattle breeds, and the mRNA of IGF1R was widely expressed in nine tissue types of adult cattle (heart, liver, kidney, muscle, fat, stomach, spleen, lung and testis). Results of CNV and growth traits indicated that the IGF1R CNV was significantly associated with body weight and body height of Jinnan (JN) cattle and was significantly associated with body height and hucklebone width of Qinchuan (QC) cattle, making IGF1R CNV a promising molecular marker to improve meat production in beef cattle breeding. Bioinformatics predictions show that the CNV region is highly similar to the human genome, and there are a large number of transcription factors, DNase I hypersensitive sites, and high levels of histone acetylation, suggesting that this region may play a role in transcriptional regulation, providing directions for further study of the role of bovine CNV and economic traits.