Genomic insights into local adaptation and phenotypic diversity of Wenchang chickens.

Wenchang chicken, a prized local breed in Hainan Province of China renowned for its exceptional adaptability to tropical environments and good meat quality, is deeply favored by the public. However, an insufficient understanding of its population architecture and the unclear genetic basis that governs its typical attributes have posed challenges in the protection and breeding of this precious breed. To address these gaps, we conducted whole-genome resequencing on 200 Wenchang chicken samples derived from 10 distinct strains, and we gathered data on an array of 21 phenotype traits. Population genomics analysis unveiled distinctive population structures in Wenchang chickens, primarily attributed to strong artificial selection for different feather colors. Selection sweep analysis identified a group of candidate genes, including PCDH9, DPF3, CDIN1, and SUGCT, closely linked to adaptations that enhance resilience in tropical island habitats. Genome-wide association studies (GWAS) highlighted potential candidate genes associated with diverse feather color traits, encompassing TYR, RAB38, TRPM1, GABARAPL2, CDH1, ZMIZ1, LYST, MC1R, and SASH1. Through the comprehensive analysis of high-quality genomic and phenotypic data across diverse Wenchang chicken resource groups, this study unveils the intricate genetic backgrounds and population structures of Wenchang chickens. Additionally, it identifies multiple candidate genes linked to environmental adaptation, feather color variations, and production traits. These insights not only provide genetic reference for the purification and breeding of Wenchang chickens but also broaden our understanding of the genetic basis of phenotypic diversity in chickens.

Putrescine promotes MMP9-induced angiogenesis in skeletal muscle through hydrogen peroxide/METTL3 pathway.

Blood vessels play a crucial role in the development of skeletal muscle, ensuring the supply of nutrients and oxygen. Putrescine, an essential polyamine for eukaryotic cells, has an unclear impact on skeletal muscle angiogenesis. In this study, we observed lower vessel density and reduced putrescine level in the muscle of low-birth-weight piglet models, and identified a positive correlation between putrescine content and muscle vessel density. Furthermore, putrescine was found to promote angiogenesis in skeletal muscle both in vitro and in vivo by targeting matrix metalloproteinase 9 (MMP9). On a mechanistic level, putrescine augmented the expression of methyltransferase like 3 (METTL3) by attenuating hydrogen peroxide production, thereby increasing the level of N6-methyladenosine (m6A)-modified MMP9 mRNA. This m6A-modified MMP9 mRNA was subsequently recognized and bound by the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), enhancing the stability of MMP9 mRNA and its protein expression, consequently accelerating angiogenesis in skeletal muscle. In summary, our findings suggest that putrescine enhances MMP9-mediated angiogenesis in skeletal muscle via the hydrogen peroxide/METTL3 pathway.

DUOX2-Induced Oxidative Stress Inhibits Intestinal Angiogenesis through MMP3 in a Low-Birth-Weight Piglet Model.

Intestinal vessels play a critical role in nutrient absorption, whereas the effect and mechanism of low birth weight (LBW) on its formation remain unclear. Here, twenty newborn piglets were assigned to the control (CON) group (1162 ± 98 g) and LBW group (724 ± 31 g) according to their birth weight. Results showed that the villus height and the activity of maltase in the jejunum were lower in the LBW group than in the CON group. LBW group exhibited a higher oxidative stress level and impaired mitochondrial function in the jejunum and was lower than the CON group in the intestinal vascular density. To investigate the role of oxidative stress in intestinal angiogenesis, H2O2 was employed to induce oxidative stress in porcine intestinal epithelial cells (IPEC-J2). The results showed that the conditioned media from IPEC-J2 with H2O2 treatment decreased the angiogenesis of porcine vascular endothelial cells (PVEC). Transcriptome analysis revealed that a higher expression level of dual oxidase 2 (DUOX2) was found in the intestine of LBW piglets. Knockdown of DUOX2 in IPEC-J2 increased the proliferation and decreased the oxidative stress level. In addition, conditioned media from IPEC-J2 with DUOX2-knockdown was demonstrated to promote the angiogenesis of PVEC. Mechanistically, the knockdown of DUOX2 decreased the reactive oxygen species (ROS) level, thus increasing the angiogenesis in a matrix metalloproteinase 3 (MMP3) dependent manner. Conclusively, our results indicated that DUOX2-induced oxidative stress inhibited intestinal angiogenesis through MMP3 in a LBW piglet model.

Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment.

BACKGROUND: Structural variations (SVs) in individual genomes are major determinants of complex traits, including adaptability to environmental variables. The Mongolian and Hainan cattle breeds in East Asia are of taurine and indicine origins that have evolved to adapt to cold and hot environments, respectively. However, few studies have investigated SVs in East Asian cattle genomes and their roles in environmental adaptation, and little is known about adaptively introgressed SVs in East Asian cattle. RESULTS: In this study, we examine the roles of SVs in the climate adaptation of these two cattle lineages by generating highly contiguous chromosome-scale genome assemblies. Comparison of the two assemblies along with 18 Mongolian and Hainan cattle genomes obtained by long-read sequencing data provides a catalog of 123,898 nonredundant SVs. Several SVs detected from long reads are in exons of genes associated with epidermal differentiation, skin barrier, and bovine tuberculosis resistance. Functional investigations show that a 108-bp exonic insertion in SPN may affect the uptake of Mycobacterium tuberculosis by macrophages, which might contribute to the low susceptibility of Hainan cattle to bovine tuberculosis. Genotyping of 373 whole genomes from 39 breeds identifies 2610 SVs that are differentiated along a "north-south" gradient in China and overlap with 862 related genes that are enriched in pathways related to environmental adaptation. We identify 1457 Chinese indicine-stratified SVs that possibly originate from banteng and are frequent in Chinese indicine cattle. CONCLUSIONS: Our findings highlight the unique contribution of SVs in East Asian cattle to environmental adaptation and disease resistance.

Supplementation of dietary areca nut extract modulates the growth performance, cecal microbiota composition, and immune function in Wenchang chickens.

Introduction: The study was aimed at evaluating the effects of areca nut extract (ANE) on the growth performance, cecal microbiota, and immunity of Wenchang chickens. Methods: For this study, 42-day-old healthy Wenchang chickens (n = 450) with similar body weight were chosen. The animals were randomly divided into five groups, with six replicates per group and 15 chickens per replicate. One group was fed a basal diet (control; CCK). The remaining four groups were fed a basal diet supplemented with varying ANE concentrations: 0.038, 0.063, 0.100, and 0.151 g/kg, with the groups denoted as CNT1, CNT2, CNT3, and CNT4, respectively. The feeding experiment lasted 35 days. The ligated cecum segments of the control and experimental groups were collected for metabolomic and metagenomic analysis, while the bone marrow samples were extracted for tandem mass tag (TMT)-based proteomic analysis. Results: All the experimental groups exhibited significantly higher average daily gain (ADG) and significantly lower feed-to-weight (F/G) ratios than CCK. Metabolomic screening of the cecum contents revealed the presence of 544 differential metabolites, including several gut health-related metabolites, such as xanthine, hydroxy hypoxanthine, 2,5-dimethylhydrazine, ganoderic acid, and 2-aminohexanoic acid. Metagenomic analysis of the cecum contents showed an upregulation in the abundance of Prevotella spp. in the experimental groups. However, we observed no significant differences in the abundances of other cecal microbes at phylum and genus levels. Furthermore, we observed significant associations between Prevotella spp. and the differentially abundant metabolites, such as cherubins, thiaburimamide, and 3,4-dihydroxy-L-phenylalanine, (r)-mevalonate, 5-O-methylalloptaeroxylin, nalidixic acid, and deoxyloganin (p < 0.05). Proteomic analysis revealed that the differentially expressed proteins (such as interferon-induced protein with tetratricopeptide repeats 5 (IFIT5), MHC-BF1, and death domain-associated protein (Daxx)) in the bone marrow of the chickens were primarily enriched in the immune network for IgA production and B cell receptor signaling pathway. Conclusion: In conclusion, dietary ANE supplementation was found to enhance metabolic activity and energy utilization, improve growth performance, modulate cecal microbiota, and strengthen the immunity of Wenchang chickens.

m6A and miRNA jointly regulate the development of breast muscles in duck embryonic stages.

N6-methyladenosine (m6A) is an abundant internal mRNA modification and plays a crucial regulatory role in animal growth and development. In recent years, m6A modification has been found to play a key role in skeletal muscles. However, whether m6A modification contributes to embryonic breast muscle development of Pekin ducks has not been explored. To explore the role of m6A in embryonic breast muscle development of ducks, we performed m6A sequencing and miRNA sequencing for the breast muscle of duck embryos on the 19th (E19) and 27th (E27) days. A total of 12,717 m6A peaks were identified at E19, representing a total of 7,438 gene transcripts. A total of 14,703 m6A peaks were identified, which overlapped with the transcripts of 7,753 genes at E27. Comparing E19 and E27, we identified 2,347 differential m6A peaks, which overlapped with 1,605 m6A-modified genes (MMGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that MMGs were enriched in multiple muscle- or fat-related pathways, which was also revealed from our analysis of differentially expressed genes (DEGs). Conjoint analysis of m6A-seq and RNA-seq data showed that pathways related to ß-oxidation of fatty acids and skeletal muscle development were significantly enriched, suggesting that m6A modification is involved in the regulation of fat deposition and skeletal muscle development. There were 90 upregulated and 102 downregulated miRNAs identified between the E19 and E27 stages. Through overlapping analysis of genes shared by MMGs and DEGs and the targets of differentially expressed miRNAs (DEMs), we identified six m6A-mRNA-regulated miRNAs. Finally, we found that m6A modification can regulate fat deposition and skeletal muscle development. In conclusion, our results suggest that m6A modification is a key regulator for embryonic breast muscle development and fat deposition of ducks by affecting expressions of mRNAs and miRNAs. This is the first study to comprehensively characterize the m6A patterns in the duck transcriptome. These data provide a solid basis for future work aimed at determining the potential functional roles of m6A modification in adipose deposition and muscle growth.

Chromosome-level genome assembly of the Muscovy duck provides insight into fatty liver susceptibility.

The Muscovy duck (Cairina moschata) is an economically important poultry species, which is susceptible to fatty liver. Thus, the Muscovy duck may serve as an excellent candidate animal model of non-alcoholic fatty liver disease. However, the mechanisms underlying fatty liver development in this species are poorly understood. In this study, we report a chromosome-level genome assembly of the Muscovy duck, with a contig N50 of 11.8 Mb and scaffold N50 of 83.16 Mb. The susceptibility of Muscovy duck to fatty liver was mainly attributed to weak lipid catabolism capabilities (fatty acid ß-oxidation and lipolysis). Furthermore, conserved noncoding elements (CNEs) showing accelerated evolution contributed to fatty liver formation by down-regulating the expression of genes involved in hepatic lipid catabolism. We propose that the susceptibility of Muscovy duck to fatty liver is an evolutionary by-product. In conclusion, this study revealed the potential mechanisms underlying the susceptibility of Muscovy duck to fatty liver.

Integrated analysis of lncRNA and gene expression in longissimus dorsi muscle at two developmental stages of Hainan black goats.

It is deemed that meat quality of kids' is better than that of adults' for Hainan black goat. Generally, meat quality is affected by many indicators, such as intramuscular fat (IMF) content, muscle fiber diameter and shear force. It is indicated that long non-coding RNAs (lncRNAs) play essential roles in meat quality of goats. However, it is unclear whether and how lncRNAs and genes play their roles in meat quality of Hainan Black goats. Here, we firstly compared the meat quality between two-month-old kids (kids) and adult goats (adults). Then, the lncRNA-seq and RNA-seq data were integrated and analyzed to explore the potential functions of lncRNAs and genes. The results showed that adults' IMF content and muscle fiber diameter were extremely significantly higher than that of kids (P<0.01). For the sequenced data, average 84,970,398, and 83,691,250 clean reads were obtained respectively for Kids and adults, among which ~96% were mapped to the reference genome of goats. Through analyzing, 18,242 goat annotated genes, 1,429 goat annotated lncRNAs and 2,967 novel lncRNAs were obtained. Analysis of differential expression genes (DEGs) and lncRNAs (DELs) showed that 328 DEGs and 98 DELs existed between kids and adults. Furthermore, functional enrichment analysis revealed that a number of DEGs and DELs were mainly associated with IMF. Primarily, DGAT2 expressed higher in adults than that in kids and CPT1A expressed higher in kids than that in adults. Both of them were overlapped by DEGs and targets of DELs, suggesting the two DEGs and the DELs targeted by the two DEGs might be the potential regulators of goat IMF deposition. Taken together, our results provide basic support for further understanding the function and mechanism of lncRNAs and genes in meat quality of Hainan black goats.

Transcriptome-wide study revealed m6A and miRNA regulation of embryonic breast muscle development in Wenchang chickens.

N 6-Methyladenosine (m6A) modification has been shown to play important role in skeletal muscle development. Wenchang chickens are commonly used as a high-quality animal model in researching meat quality. However, there have been no previous reports regarding the profile of m6A and its function in the embryonic breast muscle development of Wenchang chickens. In this paper, we identified different developmental stages of breast muscle in Wenchang chickens and performed m6A sequencing and miRNA sequencing in the breast muscle of embryos. Embryo breast muscles were weighed and stained with hematoxylin-eosin after hatching. We found that myofibers grew fast on the 10th day after hatching (E10) and seldom proliferated beyond the 19th day after hatching (E19). A total of 6,774 differentially methylated genes (DMGs) were identified between E10 and E19. For RNA-seq data, we found 5,586 differentially expressed genes (DEGs). After overlapping DEGs and DMGs, we recorded 651 shared genes (DEMGs). Subsequently, we performed miRNA-seq analysis and obtained 495 differentially expressed miRNAs (DEMs). Then, we overlapped DEMGs and the target genes of DEMs and obtained 72 overlapped genes (called miRNA-m6A-genes in this study). GO and KEGG results showed DEMGs enriched in many muscle development-related pathways. Furthermore, we chose WNT7B, a key regulator of skeletal muscle development, to perform IGV visualization analysis and found that the m6A levels on the WNT7B gene between E10 and E19 were significantly different. In conclusion, we found that miRNAs, in conjunction with m6A modification, played a key role in the embryonic breast muscle development of Wenchang chickens. The results of this paper offer a theoretical basis for the study of m6A function in muscle development and fat deposition of Wenchang chickens.

Effect of Lycopene on the Growth Performance, Antioxidant Enzyme Activity, and Expression of Gene in the Keap1-Nrf2 Signaling Pathway of Arbor Acres Broilers.

The objective of this study was to determine the effect of dietary lycopene supplementation on the growth performance, antioxidant enzyme activity of serum and liver, and gene expressions associated with Kelch-like ech-associated protein-1 (Keap1)/Nuclear Factor E2-related factor 2 (Nrf2) pathway in liver of Arbor Acres broilers. A total of 288 1-day-old male broilers were randomly divided into 4 treatments with 6 replicates and 12 chickens for each replicate. The control group was fed with the basal diet, while the treated groups were fed with the basal diet with 10, 20, and 30 mg/kg lycopene in powder. Feed and water were provided ad libitum for 42 days. Compared with the control group, (a) the average daily gain increased (p = 0.002 vs. p = 0.001) and the feed conversion ratio decreased (p = 0.017 vs. p = 0.023) in groups treated with lycopene in the grower and whole phases, and the average daily feed intake was quadratically affected (p = 0.043) by lycopene in the grower phase; (b) the serum superoxide dismutase content was linearly affected (p = 0.035) by lycopene at 21 days; (c) the serum glutathione peroxidase content, superoxide dismutase content, and total antioxidant capability were higher (p = 0.014, p = 0.003, and p = 0.016, respectively) in the 30 mg/kg lycopene group at 42 days; (d) the liver glutathione peroxidase and superoxide dismutase contents in groups treated with lycopene were higher (p ≤ 0.001 vs. p ≤ 0.001) at 21 days; (e) the liver glutathione peroxidase content was higher (p ≤ 0.001) in the 20 and 30 mg/kg lycopene groups, at 42 days; (f) the mRNA expression levels of Nrf2, superoxide dismutase 2, NAD(P)H quinone dehydrogenase 1, and heme oxygenase 1 genes were higher (21 days: p = 0.042, p = 0.021, p = 0.035, and p = 0.043, respectively; 42 days: p = 0.038, p = 0.025, p = 0.034, and p = 0.043, respectively) in the 20 and 30 mg/kg lycopene groups at 21 and 42 days. The 30 mg/kg lycopene concentration improved the growth performance, antioxidant enzyme activity in serum and liver, and gene expression in the Keap1-Nrf2 signaling pathway of Arbor Acres broilers.

Effects of Hydroxylated Lecithin on Growth Performance, Serum Enzyme Activity, Hormone Levels Related to Lipid Metabolism and Meat Quality in Jiangnan White Goslings.

The objective of the present study was to evaluate the effects of hydroxylated lecithin on growth performance, serum enzyme activity, hormone levels related to lipid metabolism and meat quality in Jiangnan White goslings. Six hundred 1-day-old goslings were randomly divided into five treatments with six replicates and 20 for each replicate. The control group (CG) was fed the basal diet, while the experimental group was fed the basal diet with 50, 100, 200 mg/kg hydroxylated lecithin and 100 mg/kg soy lecithin (HLG50, HLG100, HLG200, and LG100, respectively) in the form of powder. Feed and water were provided ad libitum for 32 days. Compared with the CG, (a) the average daily feed intake was higher (P < 0.05) in HLG100, the final body weight and average daily gain were higher (P < 0.05), and the feed conversion ratio was lower in the HLG200; (b) the alanine aminotransferase, malate dehydrogenase, leptin, glucagon, thyroid hormone, Triiodothyronine contents in the HLG200 were lower (P < 0.05); (c) The breast muscle water holding capacity was higher (P < 0.05) in groups with hydroxylated lecithin, the breast muscle shear force and fiber diameter were lower (P < 0.05) in the HLG100; (d) the inositic acid, intramuscular fat, phospholipid contents were higher (P < 0.05), the triglyceride content was lower (P < 0.05) in HLG100 of the breast muscle; (e) the relative expression of sterol regulatory element-binding protein-1 genes were higher (P < 0.05) in the treated groups of muscles, the phosphorylase kinase gamma subunit 1 gene expression was shown an opposite trend. In comparison with LG100, (a) the feed conversion ratio was lower (P < 0.05) in HLG200; (b) the alanine aminotransferase and adiponectin contents were higher (P < 0.05), the malondialdehyde and free fatty acid contents were lower (P < 0.05) in HLG200; (c) the water holding capacity and intramuscular fat contents in the breast and leg muscles were higher (P < 0.05) in HLG200. The hydroxylated lecithin concentration of 200 mg/kg improved the growth performance, serum enzyme activity, hormone levels related to lipid metabolism, and the meat quality of Jiangnan White goslings.

Dietary Supplementation With Didancao (Elephantopus scaber L.) Improves Meat Quality and Intestinal Development in Jiaji Ducks.

Didancao (Elephantopus scaber L.) has been used as a traditional herbal medicine and has exhibited a beneficial role in animal health. This study aimed to investigate the effects of dietary supplementation with E. scaber on growth performance, meat quality, intestinal morphology, and microbiota composition in ducks. A total of 480 Jiaji ducks (42 days old, male:female ratio = 1:1) were randomly assigned to one of four treatments. There were six replicates per treatment, with 20 ducks per replicate. The ducks in the control group (Con) were fed a basal diet; the three experimental groups were fed a basal diet supplementation with 30 (T1), 80 (T2), and 130 mg/kg (T3) of E. scaber. After a 48-day period of supplementation, growth performance, meat quality, intestinal morphology, and microbiota composition were evaluated. The results showed that no differences were observed in the final body weight, average daily feed intake, and average daily gain among the four groups. Compared with that in the Con group, the feed conversion in the T1 and T2 groups was increased significantly; the T2 group was shown to decrease the concentration of alanine aminotransferase in serum; the T3 group was lower than the Con group in the concentration of aspartate aminotransferase and was higher than the Con group in the concentration of high-density lipoprotein-cholesterol. The highest concentration of creatinine was observed in the T1 group. The T2 group was higher than the Con group in the contents of Phe, Ala, Gly, Glu, Arg, Lys, Tyr, Leu, Ser, Thr, Asp, and total amino acids in the breast muscle. Moreover, the T2 group was higher than the Con group in the contents of meat C18:2n-6 and polyunsaturated fatty acid. The concentration of inosinic acid in the T1, T2, and T3 groups was significantly higher than that in the Con group. However, the Con group was higher than the T2 or T3 group in the Zn content. The T2 group was lower than the Con group in the jejunal crypt depth. The T3 group was higher than the Con group in the ileal villus height and the ratio of villus height to crypt depth. In addition, the T3 group had a trend to significantly increase the abundance of Fusobacteria. Compared with the Con group, the T1 and T2 groups displayed a higher abundance of Subdoligranulum. Collectively, dietary supplementation with 80 mg/kg of E. scaber improves meat quality and intestinal development in ducks.

Transcriptome-wide study revealed m6A regulation of embryonic muscle development in Dingan goose (Anser cygnoides orientalis).

BACKGROUND: The number of myofiber is determined during the embryonic stage and does not increase during the postnatal period for birds, including goose. Thus, muscle production of adult goose is pre-determined during embryogenesis. Previous studies show N6-methyladenosine (m6A) is an important regulator for skeletal muscle development of birds and miRNAs play as a co-regulator for the skeletal muscle development in birds. Herein, we sequenced m6A and miRNA transcriptomes to investigate the profiles of m6A and their potential mechanism of regulating breast muscle development in Dingan Goose. RESULTS: We selected embryonic 21th day (E21) and embryonic 30th day (E30) to investigate the roles of transcriptome-wide m6A modification combining with mRNAs and miRNAs in goose breast muscle development. In this study, m6A peaks were mainly enriched in coding sequence (CDS) and start codon and397 genes were identified as differentially methylated genes (DMGs). GO and KEGG analysis showed that DMGs were highly related to cellular and metabolic process and that most DMGs were enriched in muscle-related pathways including Wnt signaling pathway, mTOR signaling and FoxO signaling pathway. Interestingly, a negative correlation between m6A methylation level and mRNA abundance was found through the analysis of m6A-RNA and RNA-seq data. Besides, we found 26 muscle-related genes in 397 DMGs. We also detected 228 differentially expressed miRNAs (DEMs), and further found 329 genes shared by the target genes of DEMs and DMGs (m6A-miRNA-genes), suggesting a tightly relationship between DEMs and DMGs. Among the m6A-miRNA-genes, we found 10 genes are related to breast muscle development. We further picked out an m6A-miRNA-gene, PDK3, from the 10 genes to visualize it and the result showed differentially methylated peaks on the mRNA transcript consistent with our m6A-seq results. CONCLUSION: GO and KEGG of DMGs between E21 and E30 showed most DMGs were muscle-related. In total, 228 DEMs were found, and the majority of DMGs were overlapped with the targets of DEGs. The differentially methylated peaks along with an m6A-miRNA-gene, PDK3, showed the similar results with m6A-seq results. Taken together, the results presented here provide a reference for further investigation of embryonic skeletal muscle development mechanism in goose.

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.

Effects of cassava foliage on feed digestion, meat quality, and antioxidative status of geese.

As the by-product of cassava, cassava foliage (CF) has been widely used in livestock feed. However, little information is available on its utilization for geese. In this study, we aimed to investigate the effects of CF on the feed digestion, meat quality, and antioxidative status of geese. A total of 108 male Hainan indigenous geese (28-days-old) with similar body weight were randomly and evenly divided into 3 groups, and the geese were fed for 42 D on either the control diet (CON) consisting of ground maize, soybean meal, and wheat bran, or the experimental diet composed of ground maize, soybean meal, and wheat bran supplemented with 5% (CF1) or 10% (CF2) CF. Dietary nutrient digestibility, physicochemical properties, amino acid and fatty acid composition of meat, and antioxidative status of geese were evaluated. The results showed that supplementation of CF in goose diets enhanced the feed digestion and affected the meat quality. In addition, supplementation of CF had beneficial effects on the regulation of amino acid and fatty acid profiles in muscle tissues. Moreover, such supplementation had no significant effect on antioxidative status. Taken together, goose diet containing 5% CF was recommended based on feed efficiency and meat quality.

Genetic characteristics of Jiaji Duck by whole genome re-sequencing.

Jiaji Duck (JJ) is a Muscovy duck species that possesses many superior characteristics, and it has become an important genetic resource in China. However, to date, its genetic characteristics and genetic relationship with other duck breeds have not been explored yet, which greatly limits the utilization of JJ. In the present study, we investigated the genome sequences of 15 individual ducks representing five different duck populations, including JJ, French Muscovy duck (FF), mallard (YD), hong duck (HD) and Beijing duck (BD). Moreover, we investigated the characteristics of JJ-specific single nucleotide polymorphisms (SNPs) and compared the genome sequences of JJ vs. YD and JJ vs. BD using integrated strategies, including mutation detection, selective screening, and Gene Ontology (GO) analysis. More than 40 Gb of clean data were obtained for each population (mean coverage of 13.46 Gb per individual). A total number of 22,481,367 SNPs and 4,156,829 small insertion-deletions (Indels) were identified for the five duck populations, which could be used as molecular markers in breeding and utilization of JJ. Moreover, we identified 1,447,932 JJ-specific SNPs, and found that genes covering at least one JJ-specific SNP mainly involved in protein phosphorylation and dephosphorylation, as well as DNA modification. Phylogenetic tree and principal components analysis (PCA) revealed that the genetic relationship of JJ was closest to FF, while it was farthest to BD. A total of 120 and 111 genes were identified as positive selection genes for JJ vs. BD and JJ vs. YD, respectively. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the positive selection genes for JJ vs. BD ducks mainly involved in pigmentation, muscle contraction and stretch, gland secretion, and immunology, while the positive selection genes obtained from JJ vs. YD ducks mainly involved in embryo development, muscle contraction and stretch, and gland secretion. Taken together, our findings enabled us to better understand the characteristics of JJ and provided a molecular basis for the breeding and hybrid utilization of JJ in the future.

Correction: Analysis of Anasplatyrhynchos genome resequencing data reveals genetic signatures of artificial selection.

[This corrects the article DOI: 10.1371/journal.pone.0211908.].

Analysis of Anasplatyrhynchos genome resequencing data reveals genetic signatures of artificial selection.

Three artificially selected duck populations (AS), higher lean meat ratios (LTPD), higher fat ratios (FTPD) and higher quality meat (CMD), have been developed in China, providing excellent populations for investigation of artificial selection effects. However, the genetic signatures of artificial selection are unclear. In this study, we sequenced the genome sequences of these three artificially selected populations and their ancestral population (mallard, M). We then compared the genome sequences between AS and M and between LTPD and FTPD using integrated strategies such as anchoring scaffolds to pseudo-chromosomes, mutation detection, selective screening, GO analysis, qRT-PCR, and protein multiple sequences alignment to uncover genetic signatures of selection. We anchored duck scaffolds to pseudo-chromosomes and obtained 28 pseudo-chromosomes, accounting for 84% of duck genome in length. Totally 78 and 99 genes were found to be under selection between AS and M and between LTPD and FTPD. Genes under selection between AS and M mainly involved in pigmentation and heart rates, while genes under selection between LTPD and FTPD involved in muscle development and fat deposition. A heart rate regulator (HCN1), the strongest selected gene between AS and M, harbored a GC deletion in AS and displayed higher mRNA expression level in M than in AS. IGF2R, a regulator of skeletal muscle mass, was found to be under selection between FTPD and LTPD. We also found two nonsynonymous substitutions in IGF2R, which might lead to higher IGF2R mRNA expression level in FTPD than LTPD, indicating the two nonsynonymous substitutions might play a key role for the regulation of duck skeletal muscle mass. Taken together, these results of this study provide valuable insight for the genetic basis of duck artificial selection.

Effect of cassava foliage on the performance, carcass characteristics and gastrointestinal tract development of geese.

Cassava foliage is a by-product of cassava and has been widely used in animal feed. However, little information is available on its utilization for geese. In this study, we investigated the effects of cassava foliage on the performance, carcass characteristics, and gastrointestinal tract development of geese. A total of 108 28-day-old Hainan indigenous male geese with similar body weight were randomly divided into 3 groups with 6 pens of 6 geese per group and fed for 42 D on either the control diet of ground maize, soybean meal, and wheat bran or the experimental diet of ground maize, soybean meal, and wheat bran supplemented with 5% or 10% cassava foliage, respectively. On day 70, their body weight (BW), average daily gain (ADG), average daily feed intake (ADFI), feed conversion ratio (FCR), carcass characteristics, and gastrointestinal tract development were compared. The results showed that cassava foliage diet significantly improved goose's BW (P < 0.05), ADG (P < 0.05), and ADFI (P < 0.05), affected carcass characteristics such as relative meat content (P < 0.05) and abdominal fat content (P < 0.05), and facilitated goose's gastrointestinal tract development. These findings suggested that incorporating cassava foliage into the diet of geese (day 28-70) could have positive effects, and supplementing 5% cassava foliage was more beneficial than 10%.