Copy number variation identification and analysis of the chicken genome using a 60K SNP BeadChip

Zhang

J Animal Breeding Genetics

2019

Copy number variation (CNV) is an important source of genetic variability in human or animal genomes and play key roles in phenotypic diversity and disease susceptibility. In the present study, we performed a genome‐wide analysis for CNV detection using SNP genotyping data of 857 Large White pigs. A total of 312 CNV regions (CNVRs) were detected with the PennCNV algorithm, which covered 57.76 Mb of the pig genome and correspond to 2.36% of the genome sequence. The length of the CNVRs on autosomes ranged from 1.77 Kb to 1.76 Mb with an average of 185.11 Kb. Of these, 220 completely or partially overlapped with 1,092 annotated genes, which enriched a wide variety of biological processes. Comparisons with previously reported pig CNVR revealed 92 (29.49%) novel CNVRs. Experimentally, 80% of CNVRs selected randomly were validated by quantitative PCR (qPCR). We also performed an association analysis between some of the CNVRs and reproductive traits, with results demonstrating the potential importance of CNVR61 and CNVR283 associated with litter sizes. Notably, the GPER1 gene located in CNVR61 plays a key role in reproduction. Our study is an important complement to the CNV map in the pig genome and provides valuable information for investigating the association between genomic variation and economic traits.

Section: Discussionmentioning

confidence: 92%

Detection and analysis of genome‐wide copy number variation in the pig genome using an 80 K SNP Beadchip

Zhang

J Animal Breeding Genetics

2019

“…CNVs that encompass coding regions have the potential to alter gene expression [24], with a concomitant impact on phenotypic traits. Multiple studies have already identified CNVs in diverse chicken breeds [8,11,16,25,26]. Here we aimed to compare CNVs across our three lines to identify loci with the potential to contribute to phenotypic changes in commercial broilers.…”

Section: Genome Sequencing Reveals the Modern Broiler To Be Closely Rmentioning

confidence: 99%

Accumulation of genetic variants associated with immunity in the selective breeding of broilers

et al. 2020

Background: To satisfy an increasing demand for dietary protein, the poultry industry has employed genetic selection to increase the growth rate of broilers by over 400% in the past 50 years. Although modern broilers reach a marketable weight of~2 kg in a short span of 35 days, a speed twice as fast as a broiler 50 years ago, the expedited growth has been associated with several negative detrimental consequences. Aside from heart and musculoskeletal problems, which are direct consequences of additional weight, the immune response is also thought to be altered in modern broilers. Results: Given that identifying the underlying genetic basis responsible for a less sensitive innate immune response would be economically beneficial for poultry breeding, we decided to compare the genomes of two unselected meat control strains that are representative of broilers from 1957 and 1978, and a current commercial broiler line. Through analysis of genetic variants, we developed a custom prioritization strategy to identify genes and pathways that have accumulated genetic changes and are biologically relevant to immune response and growth performance. Our results highlight two genes, TLR3 and PLIN3, with genetic variants that are predicted to enhance growth performance at the expense of immune function. Conclusions: Placing these new genomes in the context of other chicken lines, reveal genetic changes that have specifically arisen in selective breeding programs that were implemented in the last 50 years.

“…CNVs that encompass coding regions have the potential to alter gene expression [22], with a concomitant impact on phenotypic traits. Multiple studies have already identified CNVs in diverse chicken breeds [8,11,16,[23][24][25]. Here we aimed to compare CNVs across our three lines to identify loci with the potential to contribute to phenotypic changes in commercial broilers.…”

Section: Genome Sequencing Reveals the Modern Broiler To Be Closely Rmentioning

confidence: 99%

Accumulation of genetic variants associated with immunity in the selective breeding of broilers

Zou

Nadeau

et al. 2019

Preprint

To satisfy an increasing demand for dietary protein, the poultry industry has employed genetic selection to increase the growth rate of broilers by over 400% in the past 50 years.Although modern broilers reach a marketable weight of ~2 kg in a short span of 35 days, a speed twice as fast as a broiler 50 years ago, the expedited growth has been associated with several negative detrimental consequences. Aside from heart and musculoskeletal problems, which are direct consequences of additional weight, the immune response is also thought to be altered in modern broilers. Given that identifying the underlying genetic basis responsible for a less sensitive innate immune response would be economically beneficial for poultry breeding, we decided to compare the genomes of two unselected meat control strains that are representative of broilers from 1957 and 1978, and a current commercial broiler line. Through analysis of genetic variants, we developed a custom prioritization strategy to identify genes and pathways that have accumulated genetic changes and are biologically relevant to immune response and growth performance. Our results highlight two genes, TLR3 and PLIN3, with genetic variants that are predicted to enhance growth performance at the expense of immune function. Placing these new genomes in the context of other chicken lines, reveal genetic changes that have specifically arisen in selective breeding programs that were implemented in the last 50 years. Obese Low growth Defense response (GO: 0006952) Defense response to other organism (GO: 0098542) Multi-organism process (GO: 0051704) BMP signaling pathway (GO: 0030509) Cellular response to BMP stimulus (GO: 0071773) Response to BMP (GO: 0071772) Herpes simplex infection (KEGG: 05168) Intestinal immune network for IgA production (KEGG: 04672) Phagosome (KEGG: 04145) Cytokine-cytokine receptor interaction (KEGG: 04060) Cell adhesion molecules (GO: 0007155) Extracellular region (GO: 0005576) Homologous recombination (GO: 0035825) Response to biotic stimulus (GO: 0009607) Response to stress (GO: 0033554) Defense response to bacterium (GO: 0042742) Chromosomal region (GO: 0000775)