Massively parallel reporter assay: a novel technique for analyzing the regulation of gene expression.

Massively parallel reporter assay (MPRA) is a high-throughput analysis method that can simultaneously investigate the activity of thousands of regulatory elements in the genome. MPRA introduces a uniquely identified barcode on a conventional luciferase reporter gene vector, sequences the DNA barcode before transfection and the mRNA barcode after transfection by next-generation sequencing technology, and uses the ratio of mRNA and DNA barcode reads to analyze the activity of cis-regulatory elements. Since MPRA was proposed, it has been widely used in the identification of genomic cis-regulatory elements and functional variants, the effect of post-transcriptional regulation on phenotypes and so on.

A Study of Combined Genotype Effects of SHCBP1 on Wool Quality Traits in Chinese Merino.

SHCBP1 (Shc SH2-domain binding protein 1) is a member of the Src and collagen homolog (Shc) protein family and is closely associated with multiple signaling pathways that play important roles during hair follicle induction, morphogenesis, and cycling. The purpose of this study was to investigate SHCBP1 gene expression, polymorphisms, and the association between SHCBP1 and wool quality traits in Chinese Merino sheep. The SHCBP1 gene was shown, by qPCR, to be ubiquitously expressed in sheep tissues and differentially expressed in the adult skin of Chinese Merino and Suffolk sheep.

A phenome database (NEAUHLFPD) designed and constructed for broiler lines divergently selected for abdominal fat content.

Effective management and analysis of precisely recorded phenotypic traits are important components of the selection and breeding of superior livestocks. Over two decades, we divergently selected chicken lines for abdominal fat content at Northeast Agricultural University (Northeast Agricultural University High and Low Fat, NEAUHLF), and collected large volume of phenotypic data related to the investigation on molecular genetic basis of adipose tissue deposition in broilers. To effectively and systematically store, manage and analyze phenotypic data, we built the NEAUHLF Phenome Database (NEAUHLFPD).

TCF21 is related to testis growth and development in broiler chickens.

Background: Large amounts of fat deposition often lead to loss of reproductive efficiency in humans and animals. We used broiler chickens as a model species to conduct a two-directional selection for and against abdominal fat over 19 generations, which resulted in a lean and a fat line. Direct selection for abdominal fat content also indirectly resulted in significant differences (P < 0.

Detection of genome-wide copy number variations in two chicken lines divergently selected for abdominal fat content.

Background: The chicken (Gallus gallus) is an important model organism that bridges the evolutionary gap between mammals and other vertebrates. Copy number variations (CNVs) are a form of genomic structural variation widely distributed in the genome. CNV analysis has recently gained greater attention and momentum, as the identification of CNVs can contribute to a better understanding of traits important to both humans and other animals.

A genome-wide scan of selective sweeps in two broiler chicken lines divergently selected for abdominal fat content.

Background: Genomic regions controlling abdominal fatness (AF) were studied in the Northeast Agricultural University broiler line divergently selected for AF. In this study, the chicken 60KSNP chip and extended haplotype homozygosity (EHH) test were used to detect genome-wide signatures of AF.

Results: A total of 5357 and 5593 core regions were detected in the lean and fat lines, and 51 and 57 reached a significant level (P<0.

[Association of single nucleotide polymorphism of RB1 gene with body weight traits in chicken].

The Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF) were used in the current study to investigate the effects of Retinoblastoma1 (RB1) gene on chicken body weight (BW). The single nucleotide polymorphisms (SNPs) of the individuals were detected by MALDI-TOF-MS and PCR-RFLP methods and the genotypes of 27 SNPs were obtained. Haplotypes were constructed by liding window approach.

[Research advances on RB1 gene].

The retinoblastoma1 (RB1) gene is the first cloned tumor suppressor gene. As a negative regulator of the cell cycle, RB1 gene could maintain a balance between cell growth and development through binding to transcription factors and regulating the expression of genes involved in cell proliferation and differentiation. Thus, it is involved in cell cycle, cell senescence, growth arrest, apoptosis and differentiation.

[Association between chicken A-FABP gene polymorphisms and growth and body composition traits].

This experiment was designed to study the effects of polymorphism of A-FABP gene on growth and body composition traits in chicken. The 10th generation broiler population, derived from the Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF) was used. Polymorphism among individuals was detected by DNA sequencing, PCR-RFLP, PCR-LP, and DHPLC.

[Genetic analysis of epistatic effects between ApoB and UCP on abdominal fat trait in chicken].

It has been found that epistasis for selective response plays an indispensible role in animal genetics and breeding. In this study, the polymorphisms of T123G in apoliprotein B (ApoB) and C1197A in uncoupling protein (UCP) among individuals from the 8th to the 10th generation populations of the Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHFL) were detected, and genetic analysis of the epistatic effects between the two SNPs on abdominal fat percentage (AFP) was performed using Natural and Orthogonal InterActions (NOIA) model. According to these assays, we concluded that at least one out of four epistatic components between these two SNPs was significantly associated with AFP (Plt;0.

[A genetic linkage map of chicken chromosome 1 in an F2 resource population].

Three hundred and sixty-nine F2 individuals produced from Northeast Agricultural University Resource Population (NEAURP) were genotyped by 23 fluorescent microsatellite markers on chromosome 1. The characterization of these microsatellites was moderate or high polymorphic except marker MCW0058 which was low polymorphic. The length of the sex averaged linkage map was 637.

Profiling of chicken adipose tissue gene expression by genome array.

Background: Excessive accumulation of lipids in the adipose tissue is a major problem in the present-day broiler industry. However, few studies have analyzed the expression of adipose tissue genes that are involved in pathways and mechanisms leading to adiposity in chickens. Gene expression profiling of chicken adipose tissue could provide key information about the ontogenesis of fatness and clarify the molecular mechanisms underlying obesity.