Genetic characteristics of Jiaji Duck by whole genome re-sequencing

Whole-genome sequencing identifies potential candidate genes for egg production traits in laying ducks (Anas platyrhynchos)

Egg production traits are economically important in laying ducks. Genetic molecular mechanisms and candidate genes underlying these traits remain unclear. In this study, whole genome variants were identified through whole-genome resequencing using three high-egg producing (HEN) and three low-egg producing (LEN) laying ducks. The gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genome (KEGG) pathways for the genes of common differential variants between HEN and LEN ducks were determined. Frizzled class receptor 6 (FZD6) was further genotyped using the Sequenom MassARRAY iPLEX platform. The association of FZD6 gene polymorphisms with 73 egg production and weight traits in 329 female ducks were estimated. A total of 65,535 single nucleotide polymorphisms (SNPs) and 4,702 indels were identified across the genome. Fourteen GO terms and 14 KEGG pathways were determined for the genes of common differential variants, including MAPK signaling, Wnt signaling, melanogenesis and calcium signaling pathways, which are key functional pathways for poultry egg production reported in previous reports. Further analysis showed that 27 SNPs of FZD6 were associated with three early egg production of duck and egg weight traits, including egg production at 17 weeks (EP17), 18 weeks (EP18) and 19 weeks (EP19) and egg weight at 59 weeks (EW59). The FZD6 should be considered a novel candidate gene for egg production traits in laying ducks.

The study of candidate genes in the improvement of egg production in ducks – a review

Duck is the second-largest poultry species aside from chicken. The rate of egg production is a major determinant of the economic income of poultry farmers. Among the reproductive organs, the ovary is a major part of the female reproductive system which is highly important for egg production. Based on the importance of this organ, several studies have been carried out to identify candidate genes at the transcriptome level, and also the expression level of these genes at different tissues or egg-laying conditions, and single nucleotide polymorphism (SNPs) of genes associated with egg production in duck. In this review, expression profile and association study analyses at SNPs level of different candidate genes with egg production traits of duck were highlighted. Furthermore, different studies on transcriptome analysis, Quantitative Trait Loci (QTL) mapping, and Genome Wide Association Study (GWAS) approach used to identify potential candidate genes for egg production in ducks were reported. This review would widen our knowledge on molecular markers that are associated or have a positive correlation to improving egg production in ducks, for the increasing world populace.

Using Extract From the Stems and Leaves of Yizhi (Alpiniae oxyphyllae) as Feed Additive Increases Meat Quality and Intestinal Health in Ducks

Yizhi (Alpiniae Oxyphyllae, A. oxyphylla) has been widely used as an important traditional Chinese medicinal herb for centuries. Existing studies have shown that A. oxyphylla has numerous benefits in human and animal health. We hypothesized that extract from the stems and leaves of A. oxyphylla (AOE) as a feed additive may have positive effects on animal health and products. Thus, this study was conducted to evaluate the effects of AOE as a feed additive on growth performance, serum biochemical parameters, intestinal morphology, microbial composition, and meat quality in Jiaji ducks. A total of 240 Jiaji ducks of 42 days old (1675.8 ± 44.2 g, male: female ratio = 1:1) were blocked based on body weight and randomly allocated into four dietary treatments with three replicates that each had 20 duck individuals. The dietary treatments included: basal diet, control group (CK); basal diet supplementation with 30 mg/kg (Y1), 80 mg/kg (Y2), and 130 mg/kg (Y3) AOE, respectively, and lasted for 49 days. The results showed that average daily feed intake from day 42 to day 60 was decreased with the increasing level of AOE (P < 0.05). Compared with the CK group, the groups with AOE supplementation decreased serum LDL-C level (P < 0.05), the addition of 30 mg/kg AOE increased total amino acids, essential amino acids, branched-chain amino acids, nonessential amino acids, and umami taste amino acids (P < 0.05), but decreased selenium and zinc concentrations in breast muscle (P < 0.05). In addition, the supplementation of 30 or 130 mg/kg AOE significantly increased jejunal villus height (P < 0.05) and tended to increase the ratio of villus height to crypt depth in the jejunum (P = 0.092) compared to the CK group. Moreover, the addition of 30 mg/kg AOE showed a higher abundance of genus unclassified Bacteroidales and genus unclassified Ruminococcaceae than the CK group (P < 0.05). Therefore, dietary supplementation with 30 mg/kg AOE increased meat nutrition profile and flavor through promoting amino acid contents in breast muscle, as well as maintained intestine integrity and modulated the microbial composition. In conclusion, AOE as an antibiotic alternative displayed potential in maintaining intestinal health and improving meat quality.

A chromosome-level genome assembly of Cairina moschata and comparative genomic analyses

Background

The Muscovy duck (Cairina moschata) is an economically important duck species, with favourable growth and carcass composition parameters in comparison to other ducks. However, limited genomic resources for Muscovy duck hinder our understanding of its evolution and genetic diversity.

Results

We combined linked-reads sequencing technology and reference-guided methods for de novo genome assembly. The final draft assembly was 1.12 Gbp with 29 autosomes, one sex chromosome and 4,583 unlocalized scaffolds with an N50 size of 77.35 Mb. Based on universal single-copy orthologues (BUSCO), the draft genome assembly completeness was estimated to be 93.30 %. Genome annotation identified 15,580 genes, with 15,537 (99.72 %) genes annotated in public databases. We conducted comparative genomic analyses and found that species-specific and rapidly expanding gene families (compared to other birds) in Muscovy duck are mainly involved in Calcium signaling, Adrenergic signaling in cardiomyocytes, and GnRH signaling pathways. In comparison to the common domestic duck (Anas platyrhynchos), we identified 104 genes exhibiting strong signals of adaptive evolution (Ka/Ks > 1). Most of these genes were associated with immune defence pathways (e.g. IFNAR1 and TLR5). This is indicative of the existence of differences in the immune responses between the two species. Additionally, we combined divergence and polymorphism data to demonstrate the “faster-Z effect” of chromosome evolution.

Conclusions

The chromosome-level genome assembly of Muscovy duck and comparative genomic analyses provide valuable resources for future molecular ecology studies, as well as the evolutionary arms race between the host and influenza viruses.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07897-4.

Whole-genome resequencing reveals genetic characteristics of different duck breeds from the Guangxi region in China

Distinctive indigenous duck (Anas platyrhynchos) populations of Guangxi, China, evolved due to the geographical, cultural, and environmental variability of this region. To investigate the genetic diversity and population structure of the indigenous ducks of Guangxi, 78 individuals from eight populations were collected and sequenced by whole-genome resequencing with an average depth of ∼9.40×. The eight indigenous duck populations included four breeds and four resource populations. Moreover, the genome data of 47 individuals from two typical meat-type breeds and two native egg-type breeds were obtained from a public database. Calculation of heterozygosity, nucleotide diversity (π), Tajima’s D, and F_ST indicated that the Guangxi populations were characterized by higher genetic diversity and lower differentiation than meat-type breeds. The highest diversity was observed in the Xilin-Ma ducks. Principal component, structure, and phylogenetic tree analyses revealed the relationship between the indigenous duck populations of Guangxi. A mild degree of differentiation was observed among the Guangxi populations, although three populations were closer to the meat or egg breeds. Indigenous populations are famous for their special flavor, small body size, and slow growth rates. Selective sweep analysis revealed the candidate genes and pathways associated with these growth traits. Our findings provide a valuable source of information regarding genetic diversity, population conservation, and genome-associated breeding of ducks.

The population genomics of adaptive loss of function

Discoveries of adaptive gene knockouts and widespread losses of complete genes have in recent years led to a major rethink of the early view that loss-of-function alleles are almost always deleterious. Today, surveys of population genomic diversity are revealing extensive loss-of-function and gene content variation, yet the adaptive significance of much of this variation remains unknown. Here we examine the evolutionary dynamics of adaptive loss of function through the lens of population genomics and consider the challenges and opportunities of studying adaptive loss-of-function alleles using population genetics models. We discuss how the theoretically expected existence of allelic heterogeneity, defined as multiple functionally analogous mutations at the same locus, has proven consistent with empirical evidence and why this impedes both the detection of selection and causal relationships with phenotypes. We then review technical progress towards new functionally explicit population genomic tools and genotype-phenotype methods to overcome these limitations. More broadly, we discuss how the challenges of studying adaptive loss of function highlight the value of classifying genomic variation in a way consistent with the functional concept of an allele from classical population genetics.

Genomic characteristics of four different geese populations in China

It is well known that many Chinese goose breeds differ substantially in economic performance, but the genetic changes involved are still poorly understood. This study sequenced 35 individuals from four goose breeds namely Shitou, Zhedong White, Taihu, and Zi with an average sequencing depth of 10× for each individual. Among these populations, SNPs were identified, which clustered the individuals into four distinct genetic groups in accordance with the four breeds. Genomic comparisons among the four goose breeds revealed many candidate genes, as well as pathways that may be associated with meat yield in Shitou geese and laying traits in Zi geese. These findings will enable a better understanding of the artificial selection history of Chinese local geese and provide a valuable resource for future research on the breeding of geese for the economic traits of meat and egg production.