Genomic Analysis Reveals Candidate Genes Underlying Sex-Linked Eyelid Coloboma, Feather Color Traits, and Climatic Adaptation in Huoyan Geese.

Driven by natural and artificial selection, the domestic Huoyan geese from Northern China have gradually generated specific phenotypes and climatic adaptations. To understand the genetic basis of the two specific phenotypes that are sex linked, including upper eyelid coloboma and gosling feather color, as well as the climatic adaptations of the Huoyan goose, which can contribute to the artificial selection and breeding of geese. We selected Huoyan geese and nine Southern Chinese goose breeds and identified their divergence on the genomic level. Using selective sweep analysis, we found that PTPRM on chromosome Z influences the upper eyelid coloboma phenotype of the Huoyan goose, and TYRP1 is a plausible candidate gene for the Huoyan gosling feather color. We obtained a number of genes related to cold adaptation in Huoyan geese, mainly involved in physiological functions such as metabolism, angiogenesis contraction and circulatory system, apoptosis, immunity, stress, and neural system. The most interesting candidates for cold adaptation are PIP5K1B and NMNAT3 that are associated with energy metabolism and stress. We also obtained some genes related to heat adaptation, including AGTPBP1, associated with neurology; GDA, associated with skin pigmentation; and NAA35, associated with apoptosis. These findings deepen our understanding of the genetics of specific phenotypes and climate adaptation in local geese and provide insights for the selection of goose breeds.

Evolution, Inheritance, and Strata Formation of the W Chromosome in Duck (Anas platyrhynchos).

The nonrecombining female-limited W chromosome is predicted to experience unique evolutionary processes. Difficulties in assembling W chromosome sequences have hindered the identification of duck W-linked sequences and their evolutionary footprint. To address this, we conducted three initial contig-level genome assemblies and developed a rigorous pipeline by which to successfully expand the W-linked data set, including 11 known genes and 24 newly identified genes. Our results indicate that the W chromosome expression may not be subject to female-specific selection; a significant convergent pattern of upregulation associated with increased female-specific selection was not detected. The genetic stability of the W chromosome is also reflected in the strong evolutionary correlation between it and the mitochondria; the complete consistency of the cladogram topology constructed from their gene sequences proves the shared maternal coevolution. By detecting the evolutionary trajectories of W-linked sequences, we have found that recombination suppression started in four distinct strata, of which three were conserved across Neognathae. Taken together, our results have revealed a unique evolutionary pattern and an independent stratum evolutionary pattern for sex chromosomes.

Domestication affects sex-biased gene expression evolution in the duck.

Genes with sex-biased expression are thought to underlie sexually dimorphic phenotypes and are therefore subject to different selection pressures in males and females. Many authors have proposed that sexual conflict leads to the evolution of sex-biased expression, which allows males and females to reach separate phenotypic and fitness optima. The selection pressures associated with domestication may cause changes in population architectures and mating systems, which in turn can alter their direction and strength. We compared sex-biased expression and genetic signatures in wild and domestic ducks (Anas platyrhynchos), and observed changes of sexual selection and identified the genomic divergence affected by selection forces. The extent of sex-biased expression in both sexes is positively correlated with the level of both d N /d S and nucleotide diversity. This observed changing pattern may mainly be owing to relaxed genetic constraints. We also demonstrate a clear link between domestication and sex-biased evolutionary rate in a comparative framework. Decreased polymorphism and evolutionary rate in domesticated populations generally matched life-history phenotypes known to experience artificial selection. Taken together, our work suggests the important implications of domestication in sex-biased evolution and the roles of artificial selection and sexual selection for shaping the diversity and evolutionary rate of the genome.

RNA-Seq Analysis Reveals Expression Regulatory Divergence of W-Linked Genes between Two Contrasting Chicken Breeds.

The regulation of gene expression is a complex process involving organism function and phenotypic diversity, and is caused by cis- and trans- regulation. While prior studies identified the regulatory pattern of the autosome rewiring in hybrids, the role of gene regulation in W sex chromosomes is not clear due to their degradation and sex-limit expression. Here, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornish Game, which exhibited broad differences in gender-related traits, and assessed the expression of the genes on the W chromosome to disentangle the contribution of cis- and trans-factors to expression divergence. We found that female-specific selection does not have a significant effect on W chromosome gene-expression patterns. For different tissues, there were most parental divergence expression genes in muscle, and also more heterosis compared with two other tissues. Notably, a broader pattern of trans regulation in the W chromosome was observed, which is consistent with autosomes. Taken together, this work describes the regulatory divergence of W-linked genes between two contrasting breeds and indicates sex chromosomes have a unique regulation and expression mechanism.

Transcriptome-Wide Analyses Identify Dominant as the Predominantly Non-Conservative Alternative Splicing Inheritance Patterns in F1 Chickens.

Transcriptome analysis has been used to investigate many economically traits in chickens; however, alternative splicing still lacks a systematic method of study that is able to promote proteome diversity, and fine-tune expression dynamics. Hybridization has been widely utilized in chicken breeding due to the resulting heterosis, but the dynamic changes in alternative splicing during this process are significant yet unclear. In this study, we performed a reciprocal crossing experiment involving the White Leghorn and Cornish Game chicken breeds which exhibit major differences in body size and reproductive traits, and conducted RNA sequencing of the brain, muscle, and liver tissues to identify the inheritance patterns. A total of 40 515 and 42 612 events were respectively detected in the brain and muscle tissues, with 39 843 observed in the liver; 2807, 4242, and 4538 events significantly different between two breeds were identified in the brain, muscle, and liver tissues, respectively. The hierarchical cluster of tissues from different tissues from all crosses, based on the alternative splicing profiles, suggests high tissue and strain specificity. Furthermore, a comparison between parental strains and hybrid crosses indicated that over one third of alternative splicing genes showed conserved patterns in all three tissues, while the second prevalent pattern was non-additive, which included both dominant and transgressive patterns; this meant that the dominant pattern plays a more important role than suppression. Our study provides an overview of the inheritance patterns of alternative splicing in layer and broiler chickens, to better understand post-transcriptional regulation during hybridization.

RNA-seq reveals plant virus composition and diversity in alfalfa, thrips, and aphids in Beijing, China.

Viruses are widespread in alfalfa (Medicago sativa L.), representing a key limitation to the production of this important forage plant. Understanding the diversity of plant viruses in alfalfa and their potential vectors will play an important role in management to minimize the emergence, transmission, and impact of viruses. Next-generation sequencing (NGS) targeting the transcriptome was applied to monitor the virus communities in alfalfa and its two main pests, thrips (Odontothrips loti Haliday and Frankliniella intonsa Trybom) and aphids (Acyrthosiphon pisum Mordvilko and Therioaphis trifolii Monell). A comparison of transcriptome datasets with reference databases revealed the presence of eight candidate viruses. Five out of the eight viruses, alfalfa mosaic virus (AMV), Medicago sativa alphapartitivirus 1 (MsAPV1), Medicago sativa deltapartitivirus 1 (MsDPV1), Medicago sativa amalgavirus 1 (MsAV1), and bean yellow mosaic virus (BYMV), were confirmed by RT-PCR. We identified and determined the presence of four RNA viruses from alfalfa samples, two viruses (AMV and MsAPV1) from thrips samples, and one virus (BYMV) from T. trifolii. All sequences isolated from the insect samples were more than 95% identical to the sequences from the alfalfa samples or to sequences from the National Center for Biotechnology Information (NCBI) reference database. The RNA-seq results of this study suggest that AMV and MsAPV1 are the predominant RNA plant viruses infecting alfalfa and that they are carried by the major pests. This lays the foundation for future research on the vectors and transmission of these viruses. In addition, the sequence data have enabled the assembly of the first complete genome sequence of MsDPV1 from alfalfa.

Publisher Correction: Inheritance patterns of the transcriptome in hybrid chickens and their parents revealed by expression analysis.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Inheritance patterns of the transcriptome in hybrid chickens and their parents revealed by expression analysis.

Although many phenotypic traits of chickens have been well documented, the genetic patterns of gene expression levels in chickens remain to be determined. In the present study, we crossed two chicken breeds, White Leghorn (WL) and Cornish (Cor), which have been selected for egg and meat production, respectively, for a few hundred years. We evaluated transcriptome abundance in the brain, muscle, and liver from the day-old progenies of pure-bred WL and Cor, and the hybrids of these two breeds, by RNA-Seq in order to determine the inheritance patterns of gene expression. Comparison among expression levels in the different groups revealed that most of the genes showed conserved expression patterns in all three examined tissues and that brain had the highest number of conserved genes, which indicates that conserved genes are predominantly important compared to others. On the basis of allelic expression analysis, in addition to the conserved genes, we identified the extensive presence of additive, dominant (Cor dominant and WL dominant), over-dominant, and under-dominant genes in all three tissues in hybrids. Our study is the first to provide an overview of inheritance patterns of the transcriptome in layers and broilers, and we also provide insights into the genetics of chickens at the gene expression level.