A genome-wide study to identify genes responsible for oviduct development in chickens

Age-dependent genetic architectures of chicken body weight explored by multidimensional GWAS and molQTL analyses

Chicken body weight (BW) is a critical trait in breeding. Although genetic variants associated with BW have been investigated by genome-wide association studies (GWAS), the contributions of causal variants and their molecular mechanisms remain largely unclear in chickens. In this study, we construct a comprehensive genetic atlas of chicken BW by integrative analysis of 30 age points and 5 quantitative trait loci (QTL) across 27 tissues. We find that chicken growth is a cumulative non-linear process, which can be divided into three distinct stages. Our GWAS analysis reveals that BW-related genetic variations show ordered patterns in these three stages. Genetic variations in chromosome 1 may regulate the overall growth process, likely by modulating the hypothalamus-specific expression of SLC25A30 and retina-specific expression of NEK3. Moreover, genetic variations in chromosome 4 and chromosome 27 may play dominant roles in regulating BW during Stage 2 (8-22 weeks) and Stage 3 (23-72 weeks), respectively. In summary, our study presents a comprehensive genetic atlas regulating developmental stage-specific changes in chicken BW, thus providing important resources for genomic selection in breeding programs.

Integration of GWAS and transcriptomic analyses reveal candidate genes for duck gonadal development during puberty onset

BACKGROUND

Puberty onset signifies the beginning of sexual maturation and reproductive phase in poultry indeed, and plays an essential role in genetics and breeding. Studying gonadal development is one of the important approaches to exploring the genetic mechanism of puberty onset.

RESULT

In our study, the phenotype data of the testes and ovaries of the 120-day-old Nonghua duck showed a large coefficient of variation, indicating that their gonads were in different developmental states. The CNV-based GWAS results for 358 Nonghua ducks showed two deleted-type CNVRs were associated with testicular weight (TW) and testicular percentage (TP), namely CNVR492 (Chr2: 59473501-59478500 bp) and CNVR494 (Chr2: 59514001-59517000 bp). Additionally, two both-type CNVRs were associated with ovarian weight (OW) and ovarian percentage (OP), namely CNVR557 (Chr2: 99951001-99956500 bp) and CNVR891 (Chr7: 39115001-39122500 bp). RNA-seq analysis showed 6228 and 1070 differentially expressed genes (DEGs) related to the TW and OW. These DEGs were mainly enriched in the MAPK signaling pathway, cytokine-cytokine receptor interaction, and focal adhesion, which were reported to affect gonadal development. Further, by joint analysis of CNV-based GWAS and RNA-seq data, 3 genes, including LOC106019197, CDH19 (LOC101793040), and TYW5 were identified as potential candidate genes for TW and OW. LOC106019197 and CDH19 were down-regulated in the heavier-testes group (> 5 g), while TYW5 was also down-regulated in the heavier-ovaries group (> 3 g). The qRT-PCR revealed that LOC106019197 and CDH19 exhibited higher expression levels in the wild/CN0 and CN0/CN0 genotypes compared to the wild/wild genotype. TYW5 showed the highest expression level in the wild/CN0 genotype and the lowest in the CN2/CN2 genotype. In addition, the expression levels of LOC106019197 and CDH19 were significantly higher at 0w than at 8w and 24w.

CONCLUSION

Our results revealed that LOC106019197 and CDH19 may act as inhibitors of duck testicular development. TYW5 may play a role in delaying ovarian development. These findings provide new insights into the mechanism of puberty onset in ducks.

Major regulatory factors for reproductive performances of female chickens

The reproductive performance of female chickens is critical for determining the efficiency of production and productivity and thus profitability. Studies have shown that the reproductive performance of female chickens is mainly regulated by the feed, hormones, genes, and light conditions. Herein, we review the major factors regulating female chicken reproductive performance and assess the reproductive organs and their functions. In the current review, we highlight how the interconnections of hormones, candidate genes, and photo-stimulation regulate female chicken reproductive hormones and thus regulate the reproductive organ performance. In this regard, the roles of main hormones [gonadotropinreleasing hormone (GnRH) and genes (GnRH-I)] in regulating sexual maturation and ovarian development and maintenance by influencing the survival and function of follicular granulosa cells were also reviewed. In addition, the current review also highlights how feeding female chickens with diets and artificial light-emitting diodes (LEDs) support the effective functioning of their reproductive capacity through the stimulation of sexual maturity at an appropriate age and regeneration of aged reproductive organs.

Elucidation of the genetic determination of clutch traits in Chinese local chickens of the Laiwu Black breed

BACKGROUND

Egg laying rate (LR) is associated with a clutch, which is defined as consecutive days of oviposition. The clutch trait can be used as a selection indicator to improve egg production in poultry breeding. However, little is known about the genetic basis of clutch traits. In this study, our aim was to estimate genetic parameters and identify quantitative trait single nucleotide polymorphisms for clutch traits in 399 purebred Laiwu Black chickens (a native Chinese breed) using a genome-wide association study (GWAS).

METHODS

In this work, after estimating the genetic parameters of age at first egg, body weight at first egg, LR, longest clutch until 52 week of age, first week when the longest clutch starts, last week when the longest clutch ends, number of clutches, and longest number of days without egg-laying until 52 week of age, we identified single nucleotide polymorphisms (SNPs) and potential candidate genes associated with clutch traits in Laiwu Black chickens. The restricted maximum likelihood method was used to estimate genetic parameters of clutch pattern in 399 Laiwu Black hens, using the GCTA software.

RESULTS

The results showed that SNP-based heritability estimates of clutch traits ranged from 0.06 to 0.59. Genotyping data were obtained from whole genome re-sequencing data. After quality control, a total of 10,810,544 SNPs remained to be analyzed. The GWAS revealed that 421 significant SNPs responsible for clutch traits were scattered on chicken chromosomes 1-14, 17-19, 21-25, 28 and Z. Among the annotated genes, NELL2, SMYD9, SPTLC2, SMYD3 and PLCL1 were the most promising candidates for clutch traits in Laiwu Black chickens.

CONCLUSION

The findings of this research provide critical insight into the genetic basis of clutch traits. These results contribute to the identification of candidate genes and variants. Genes and SNPs potentially provide new avenues for further research and would help to establish a framework for new methods of genomic prediction, and increase the accuracy of estimated genetic merit for egg production and clutch traits.

Disentangling clustering configuration intricacies for divergently selected chicken breeds

Divergently selected chicken breeds are of great interest not only from an economic point of view, but also in terms of sustaining diversity of the global poultry gene pool. In this regard, it is essential to evaluate the classification (clustering) of varied chicken breeds using methods and models based on phenotypic and genotypic breed differences. It is also important to implement new mathematical indicators and approaches. Accordingly, we set the objectives to test and improve clustering algorithms and models to discriminate between various chicken breeds. A representative portion of the global chicken gene pool including 39 different breeds was examined in terms of an integral performance index, i.e., specific egg mass yield relative to body weight of females. The generated dataset was evaluated within the traditional, phenotypic and genotypic classification/clustering models using the k-means method, inflection points clustering, and admixture analysis. The latter embraced SNP genotype datasets including a specific one focused on the performance-associated NCAPG-LCORL locus. The k-means and inflection points analyses showed certain discrepancies between the tested models/submodels and flaws in the produced cluster configurations. On the other hand, 11 core breeds were identified that were shared between the examined models and demonstrated more adequate clustering and admixture patterns. These findings will lay the foundation for future research to improve methods for clustering as well as genome- and phenome-wide association/mediation analyses.

Identification of Key Candidate Genes in Runs of Homozygosity of the Genome of Two Chicken Breeds, Associated with Cold Adaptation

Simple Summary

The search for genomic regions related to adaptive abilities preserved in the chicken gene pool of two breeds, which have not been under intensive selection pressure, is of great importance for breeding in the future. This study aimed to identify key candidate genes associated with the adaptation of chickens to cold environments (using the example of the Russian White breed) by using molecular genetic methods. A total of 12 key genes on breed-specific ROH (runs of homozygosity) islands were identified, which may be potential candidate genes associated with the high level of adaptability of chickens to cold environments in the early postnatal period. These genes were associated with lipid metabolism, maintaining body temperature in cold environments, non-shivering thermogenesis and muscle development and are perspectives for further research.

Abstract

It is well known that the chicken gene pools have high adaptive abilities, including adaptation to cold environments. This research aimed to study the genomic distribution of runs of homozygosity (ROH) in a population of Russian White (RW) chickens as a result of selection for adaptation to cold environments in the early postnatal period, to perform a structural annotation of the discovered breed-specific regions of the genome (compared to chickens of the Amroks breed) and to suggest key candidate genes associated with the adaptation of RW chickens to cold environments. Genotyping of individual samples was performed using Illumina Chicken 60K SNP BeadChip^® chips. The search for homozygous regions by individual chromosomes was carried out using the PLINK 1.9 program and the detectRuns R package. Twelve key genes on breed-specific ROH islands were identified. They may be considered as potential candidate genes associated with the high adaptive ability of chickens in cold environments in the early postnatal period. Genes associated with lipid metabolism (SOCS3, NDUFA4, TXNRD2, IGFBP 1, IGFBP 3), maintaining body temperature in cold environments (ADIPOQ, GCGR, TRPM2), non-shivering thermogenesis (RYR2, CAMK2G, STK25) and muscle development (METTL21C) are perspectives for further research. This study contributes to our understanding of the mechanisms of adaptation to cold environments in chickens and provides a molecular basis for selection work.

Long noncoding RNAs profiling in ovary during laying and nesting in Muscovy ducks (Cairina moschata)

There are recent reports of the important functions of long noncoding RNAs (lncRNAs) in female reproductive and ovarian development. Studies in which there was characterization of lncRNAs in the ovaries of laying compared with nesting poultry, however, are limited. In this study, RNA libraries were constructed by obtaining sequencing data of ovarian tissues from laying and nesting Muscovy ducks. In the ovarian tissues of Muscovy ducks, a total of 334 differentially abundant mRNA transcripts (DEGs) and 36 differentially abundant lncRNA transcripts were identified in the nesting period, when compared with during the laying period. These results were subsequently validated by qRT-PCR using nine randomly-selected lncRNAs and six randomly-selected DAMTs. Furthermore, the cis- and trans-regulatory target genes of differentially abundant lncRNA transcripts were identified, and lncRNA-gene interaction networks of 34 differentially abundant lncRNAs and 263 DEGs were constructed. A total of 7601 lncRNAs neighboring 10,542 protein-coding genes were identified and found to be enriched in the Wnt signaling pathway and oocyte meiosis pathways associated with follicular development. Overall, only 11 cis-targets and 57 mRNA-mRNA except trans-targets were involved in the lncRNA-gene interaction networks. Based on the interaction networks, nine DEGs were trans-regulated by differentially abundant lncRNAs and 20 differentially abundant lncRNAs were hypothesized to have important functions in the regulation of broodiness in Muscovy ducks. In this study, a predicted interaction network of differentially abundant lncRNAs and DEGs in Muscovy ducks was constructed for the first time leading to an enhanced understanding of lncRNA and gene interactions regulating broodiness.

Effect of very low-protein diets supplemented with branched-chain amino acids on energy balance, plasma metabolomics and fecal microbiome of pigs

Feeding pigs with very-low protein (VLP) diets while supplemented with limiting amino acids (AA) results in decreased growth. The objective of this study was to determine if supplementing VLP diets with branched-chain AA (BCAA) would reverse the negative effects of these diets on growth and whether this is associated with alterations in energy balance, blood metabolomics and fecal microbiota composition. Twenty-four nursery pigs were weight-matched, individually housed and allotted into following treatments (n = 8/group): control (CON), low protein (LP) and LP supplemented with BCAA (LP + BCAA) for 4 weeks. Relative to CON, pigs fed with LP had lower feed intake (FI) and body weight (BW) throughout the study, but those fed with LP + BCAA improved overall FI computed for 4 weeks, tended to increase the overall average daily gain, delayed the FI and BW depression for ~ 2 weeks and had transiently higher energy expenditure. Feeding pigs with LP + BCAA impacted the phenylalanine and protein metabolism and fatty acids synthesis pathways. Compared to CON, the LP + BCAA group had higher abundance of Paludibacteraceae and Synergistaceae and reduced populations of Streptococcaceae, Oxyphotobacteria_unclassified, Pseudomonadaceae and Shewanellaceae in their feces. Thus, supplementing VLP diets with BCAA temporarily annuls the adverse effects of these diets on growth, which is linked with alterations in energy balance and metabolic and gut microbiome profile.

A Map of Racial and Ethnic Disparities in Influenza Vaccine Uptake in the Medicare Fee-for-Service Program

INTRODUCTION

Despite improved understanding of the risks of influenza and better vaccines for older patients, influenza vaccination rates remain subpar, including in high-risk groups such as older adults, and demonstrate significant racial and ethnic disparities.

METHODS

This study considers demographic, clinical, and geographic correlates of influenza vaccination among Medicare Fee-for-Service (FFS) beneficiaries in 2015-2016 and maps the data on a geographic information system (GIS) at the zip code level.

RESULTS

Analyses confirm that only half of the senior beneficiaries evidenced a claim for receiving an inactivated influenza vaccine (IIV), with significant disparities observed among black, Hispanic, rural, and poorer beneficiaries. More extensive disparities were observed for the high-dose (HD) vaccine, with its added protection for older populations and confirmed economic benefit. Most white beneficiaries received HD; no non-white subgroup did so. Mapping of the data confirmed subpar vaccination in vulnerable populations with wide variations at the zip code level.

CONCLUSION

Urgent and targeted efforts are needed to equitably increase IIV rates, thus protecting the most vulnerable populations from the negative health impact of influenza as well as the tax-paying public from the Medicare costs from failing to do so.

Transcriptome analysis reveals differentially expressed genes and pathways for oviduct development and defense in prelaying and laying hens

PROBLEM

The oviduct plays an indispensable role in the formation of eggs, especially the magnum and uterus. The identification of oviduct development in different stages will help to target candidate genes and pathways in regulation of albumen and eggshell formation, as well as defense mechanism in oviduct and egg.

METHODS

To identify the function differences and the molecular defense mechanism of the oviduct and egg, we performed transcriptome sequencing analysis of the magnum and uterus in 120-d-old and 300-d-old Lohmann layers, three birds in each group.

RESULTS

With fold changes (log2 ratio) ≥ 2 and false discovery rate (FDR) < 0.01, RNA-Seq revealed 1,040 genes expressed differentially in the magnum and 595 genes in the uterus. By combining GO enrichment and KEGG pathway analysis, it served to show that gene activities of the magnum and uterus in prelaying chickens were more likely to concentrate on growth and development, and after egg-laying, they were mainly inclined to enhance the substances transmembrane transport and secretion activities. We further characterized 1579 new genes, while only 803 of them were functionally annotated. A complex mixture of proteins related to defense was measured in this study. A subset of avian β-defensins (AvBDs) and ovodefensins (OvoDs), that is, AvBD12, AvBD11, AvBD10, OvoDA1, OvoDB1, OvoDA2, OvoDA3, and OvoDBβ, was detected to express in the magnum of laying hens at high levels.

CONCLUSION

Collectively, the identification and functional analysis of these differentially expressed genes (DEGs), as well as specific expression of avian defensins, may contribute to understand the development and defense mechanisms of oviduct and eggs.

Gene expression variation and parental allele inheritance in a Xiphophorus interspecies hybridization model

Understanding the genetic mechanisms underlying segregation of phenotypic variation through successive generations is important for understanding physiological changes and disease risk. Tracing the etiology of variation in gene expression enables identification of genetic interactions, and may uncover molecular mechanisms leading to the phenotypic expression of a trait, especially when utilizing model organisms that have well-defined genetic lineages. There are a plethora of studies that describe relationships between gene expression and genotype, however, the idea that global variations in gene expression are also controlled by genotype remains novel. Despite the identification of loci that control gene expression variation, the global understanding of how genome constitution affects trait variability is unknown. To study this question, we utilized Xiphophorus fish of different, but tractable genetic backgrounds (inbred, F₁ interspecies hybrids, and backcross hybrid progeny), and measured each individual’s gene expression concurrent with the degrees of inter-individual expression variation. We found, (a) F₁ interspecies hybrids exhibited less variability than inbred animals, indicting gene expression variation is not affected by the fraction of heterozygous loci within an individual genome, and (b), that mixing genotypes in backcross populations led to higher levels of gene expression variability, supporting the idea that expression variability is caused by heterogeneity of genotypes of cis or trans loci. In conclusion, heterogeneity of genotype, introduced by inheritance of different alleles, accounts for the largest effects on global phenotypical variability.

Phenotypical variability is a multi-factorial phenomenon. Although it has been shown that inheriting certain gene is associated with lower phenotypical variability, how genome complexity affect phenotypical variability is still unclear. To study this question, we used inbred Xiphophorus fish, backcross interspecies hybrids, and F₁ interspecies hybrids between select Xiphophorus species to model genetic composition with minimum, medium, and maximum heterozygosity respectively, and measured their global gene expression variability. We found gene expression variation is not affected by the percentage of heterozygous loci in individual genome, but instead related to heterogeneity of genotype at local or remote loci.

Genetic architecture and candidate genes detected for chicken internal organ weight with a 600 K single nucleotide polymorphism array

Objective

Internal organs indirectly affect economic performance and well-being of animals. Study of internal organs during later layer period will allow full utilization of layer hens. Hence, we conducted a genome-wide association study (GWAS) to identify potential quantitative trait loci or genes that potentially contribute to internal organ weight.

Methods

A total of 1,512 chickens originating from White Leghorn and Dongxiang Blue-Shelled chickens were genotyped using high-density Affymetrix 600 K single nucleotide polymorphism (SNP) array. We conducted a GWAS, linkage disequilibrium analysis, and heritability estimated based on SNP information by using GEMMA, Haploview and GCTA software.

Results

Our results displayed that internal organ weights show moderate to high (0.283 to 0.640) heritability. Variance partitioned across chromosomes and chromosome lengths had a linear relationship for liver weight and gizzard weight (R² = 0.493, 0.753). A total of 23 highly significant SNPs that associated with all internal organ weights were mainly located on Gallus gallus autosome (GGA) 1 and GGA4. Six SNPs on GGA2 affected heart weight. After the final analysis, five top SNPs were in or near genes 5-Hydroxytryptamine receptor 2A, general transcription factor IIF polypeptide 2, WD repeat and FYVE domain containing 2, non-SMC condensin I complex subunit G, and sonic hedgehog, which were considered as candidate genes having a pervasive role in internal organ weights.

Conclusion

Our findings provide an understanding of the underlying genetic architecture of internal organs and are beneficial in the selection of chickens.