Expression of multiple delta-protocadherins during feather bud formation

Dissecting Selective Signatures and Candidate Genes in Grandparent Lines Subject to High Selection Pressure for Broiler Production and in a Local Russian Chicken Breed of Ushanka

Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact of artificial selection on genomic architecture and the genetic markers sought remains a key area of research. Here, we used whole-genome resequencing data to analyze the genomic architecture, diversity, and selective sweeps in Cornish White (CRW) and Plymouth Rock White (PRW) transboundary breeds selected for meat production and, comparatively, in an aboriginal Russian breed of Ushanka (USH). Reads were aligned to the reference genome bGalGal1.mat.broiler.GRCg7b and filtered to remove PCR duplicates and low-quality reads using BWA-MEM2 and bcftools software; 12,563,892 SNPs were produced for subsequent analyses. Compared to CRW and PRW, USH had a lower diversity and a higher genetic distinctiveness. Selective sweep regions and corresponding candidate genes were examined based on ZFST, hapFLK, and ROH assessment procedures. Twenty-seven prioritized chicken genes and the functional projection from human homologs suggest their importance for selection signals in the studied breeds. These genes have a functional relationship with such trait categories as body weight, muscles, fat metabolism and deposition, reproduction, etc., mainly aligned with the QTLs in the sweep regions. This information is pivotal for further executing genomic selection to enhance phenotypic traits.

Comparative population genomics analysis uncovers genomic footprints and genes influencing body weight trait in Chinese indigenous chicken

Body weight of chicken is a typical quantitative trait, which shows phenotypic variations due to selective breeding. Despite some QTL loci have been obtained, the body weight of native chicken breeds in different geographic regions varies greatly, its genetic basis remains unresolved questions. To address this issue, we analyzed 117 Chinese indigenous chickens from 10 breeds (Huiyang Bearded, Xinhua, Hotan Black, Baicheng You, Liyang, Yunyang Da, Jining Bairi, Lindian, Beijing You, Tibetan). We applied fixation index (FST) analysis to find selected genomic regions and genes associated with body weight traits. Our study suggests that NELL1, XYLT1, and NCAPG/LCORL genes are strongly selected in the body weight trait of Chinese indigenous chicken breeds. In addition, the IL1RAPL1 gene was strongly selected in large body weight chickens, while the PCDH17 and CADM2 genes were strongly selected in small body weight chickens. This result suggests that the patterns of genetic variation of native chicken and commercial chicken, and/or distinct local chicken breeds may follow different evolutionary mechanisms.

Genomic diversity and signals of selection processes in wild and farm-reared red-legged partridges (Alectoris rufa)

The genetic dynamics of wild populations with releases of farm-reared reinforcements are very complex. These releases can endanger wild populations through genetic swamping or by displacing them. We assessed the genomic differences between wild and farm-reared red-legged partridges (Alectoris rufa) and described differential selection signals between both populations. We sequenced the whole genome of 30 wild and 30 farm-reared partridges. Both partridges had similar nucleotide diversity (π). Farm-reared partridges had a more negative Tajima's D and more and longer regions of extended haplotype homozygosity than wild partridges. We observed higher inbreeding coefficients (F_IS and F_ROH) in wild partridges. Selective sweeps (Rsb) were enriched with genes that contribute to the reproductive, skin and feather colouring, and behavioural differences between wild and farm-reared partridges. The analysis of genomic diversity should inform future decisions for the preservation of wild populations.

Comparative genomics reveal shared genomic changes in syngnathid fishes and signatures of genetic convergence with placental mammals

Syngnathids (seahorses, pipefishes and seadragons) exhibit an array of morphological innovations including loss of pelvic fins, a toothless tubular mouth and male pregnancy. They comprise two subfamilies: Syngnathinae and Nerophinae. Genomes of three Syngnathinae members have been analyzed previously. In this study, we have sequenced the genome of a Nerophinae member, the Manado pipefish (Microphis manadensis), which has a semi-enclosed brood pouch. Comparative genomic analysis revealed that the molecular evolutionary rate of the four syngnathids is higher than that of other teleosts. The loss of all but one P/Q-rich SCPP gene in the syngnathids suggests a role for the lost genes in dentin and enameloid formation in teleosts. Genome-wide comparison identified a set of 118 genes with parallel identical amino acid substitutions in syngnathids and placental mammals. Association of some of these genes with placental and embryonic development in mammals suggests a role for them in syngnathid pregnancy.

Genetic Mapping in Mice Reveals the Involvement of Pcdh9 in Long-Term Social and Object Recognition and Sensorimotor Development

BACKGROUND

Quantitative genetic analysis of basic mouse behaviors is a powerful tool to identify novel genetic phenotypes contributing to neurobehavioral disorders. Here, we analyzed genetic contributions to single-trial, long-term social and nonsocial recognition and subsequently studied the functional impact of an identified candidate gene on behavioral development.

METHODS

Genetic mapping of single-trial social recognition was performed in chromosome substitution strains, a sophisticated tool for detecting quantitative trait loci (QTL) of complex traits. Follow-up occurred by generating and testing knockout (KO) mice of a selected QTL candidate gene. Functional characterization of these mice was performed through behavioral and neurological assessments across developmental stages and analyses of gene expression and brain morphology.

RESULTS

Chromosome substitution strain 14 mapping studies revealed an overlapping QTL related to long-term social and object recognition harboring Pcdh9, a cell-adhesion gene previously associated with autism spectrum disorder. Specific long-term social and object recognition deficits were confirmed in homozygous (KO) Pcdh9-deficient mice, while heterozygous mice only showed long-term social recognition impairment. The recognition deficits in KO mice were not associated with alterations in perception, multi-trial discrimination learning, sociability, behavioral flexibility, or fear memory. Rather, KO mice showed additional impairments in sensorimotor development reflected by early touch-evoked biting, rotarod performance, and sensory gating deficits. This profile emerged with structural changes in deep layers of sensory cortices, where Pcdh9 is selectively expressed.

CONCLUSIONS

This behavior-to-gene study implicates Pcdh9 in cognitive functions required for long-term social and nonsocial recognition. This role is supported by the involvement of Pcdh9 in sensory cortex development and sensorimotor phenotypes.

MicroRNA-429 functions as a regulator of epithelial-mesenchymal transition by targeting Pcdh8 during murine embryo implantation

STUDY QUESTION

What is the role of miR-429 in murine embryo implantation?

SUMMARY ANSWER

miR-429 functions as a suppressor of epithelial-mesenchymal transition (EMT) during the process of embryo implantation by reverse regulation of Pcdh8.

WHAT IS KNOWN ALREADY

MicroRNAs (miRNAs) may serve as promising regulators of embryo implantation. miR-429 was recently found to be down-regulated during embryo implantation period in a microarray analysis.

STUDY DESIGN, SIZE, DURATION

The expression profile of miR-429 was clarified in a series of models, and the target gene was confirmed. The in vivo and in vitro effect of miR-429 on embryo implantation was examined.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Pregnancy was produced by natural mating between female C57BL6/J mice and male mice, and a series of models, including pseudopregnancy, delayed implantation and artificial decidualization, were established. The expression profile of miR-429 during the embryo implantation period was clarified in these models. Candidate target genes of miR-429 were predicted by bioinformatic analysis and tested by luciferase activity assay. The in vivo effects of miR-429 on embryo implantation were also examined. The in vitro effects of miR-429 on EMT were studied by examining migratory and invasive capacities by transwell assay and expression profiles of cadherin family members by western blotting and qRT-PCR.

MAIN RESULTS AND THE ROLE OF CHANCE

The expression profile of miR-429 in animal models suggested its down-regulation should be dependent on the presence and status of blastocysts and on endometrial decidualization. The luciferase activity assay showed that Pcdh8, a member of cadherin gene family, was the target gene of miR-429, and miR-429 suppressed the expression of Pcdh8 mRNA and protein. Gain-of-function of miR-429 in vivo resulted in a significant reduction of the number of implantation sites, but had little effect on fertilization. Up-regulation of miR-429 in vitro led to suppression of mesenchymal marker genes Vim, Cdh2, Zeb1 and Zeb2, and activation of epithelial marker gene Cdh1, resulting in suppression of the migratory and invasive capacities of cells. miR-429 also partially abrogated TGF-beta-induced EMT. The dysregulated expression profiles of EMT markers during embryo implantation period could be partially reversed by gain-of-function of miR-429 in vivo.

LIMITATIONS, REASONS FOR CAUTION

The association of miR-429 with other members of the miR-200 family in embryo implantation remains to be determined. The relationship between miR-429 and the cadherin family needs more intensive description and the detailed mechanism of miR-429 in regulating the cadherin family needs to be elucidated.

WIDER IMPLICATIONS OF THE FINDINGS

Our findings indicate that miR-429 plays a major role in embryo implantation as a suppressor of EMT by targeting Pcdh8. This information could contribute to a better understanding of the mechanisms involved in the miRNA-mediated regulation of embryo implantation, and subsequently improve treatments for infertility. The findings are consistent with that from previous research of the other members in miR-200 family in embryo implantation and in the EMT.

STUDY FUNDING/COMPETING INTERESTS

This study was supported by the Natural Science Foundation of China (Grant number: 81170592), and Special Fund from National Excellent Doctoral Dissertation (Grant number: 201079). There was no conflict of interest.