A comparative analysis reveals the genomic diversity among eight Muscovy duck populations.

The Muscovy duck (Cairina moschata) is a waterfowl indigenous to the neotropical regions of Central and South America. It has low demand for concentrated feed and strong adaptability to different rearing conditions. After being introduced to China through Eurasian commercial trade, Muscovy ducks have a domestication history of around 300 years in the Fujian Province of China. In the 1990s, the commodity Muscovy duck breed "Crimo", cultivated in Europe, entered the Chinese market for consumption and breeding purposes. Due to the different selective breeding processes, Muscovy ducks have various populational traits and lack transparency of their genetic background. To remove this burden in Muscovy duck breeding process, we analyzed genomic data from 8 populations totaling 83 individuals. We identify 11.24 million single nucleotide polymorphisms (SNPs) and categorized these individuals into the Fujian-bred and the Crimo populations according to phylogenetic analyses. We then delved deeper into their evolutionary relationships through assessing population structure, calculating fixation index (FST) values, as well as measuring genetic distances. Our exploration of runs of homozygosity (ROH) and homozygous-by-descent (HBD) uncovered genomic regions enriched for genes implicated in fatty acid metabolism, development and immunity pathways. Selective sweep analyses further indicated strong selective pressures exerted on genes including TECR, STAT2 and TRAF5. These findings provide insights into genetic variations of Muscovy ducks, thus offering valuable information regarding genetic diversity, population conservation, and genome-associated for the breeding of Muscovy ducks.

Using multiomics to explore the weight differences between genders in Muscovy ducks.

Sexual dimorphism in poultry, especially in Muscovy ducks, is a proven phenomenon characterized by significant differences in body weight, growth patterns, and gene expression between male and female individuals. However, there is a dearth of research on the candidate genes and mechanisms underlying these weight differences. We selected 301 Muscovy ducks and recorded their weekly body weights from birth. We utilized 3 non-linear growth models (Logistic, Bertalanffy, and Gompertz) to fit the growth curve of Muscovy ducks, it was found that the logistic model was the most suitable model for describing the growth curve of Muscovy ducks. The results from the logistic model showed that the inflection point of male Muscovy ducks occurred at a later age, and they had a heavier mature body weight than female Muscovy ducks. At 10 wk of age, we collected Muscovy duck breast muscle tissues for transcriptome sequencing (RNA-seq). To exclude the impact of weight difference, 185 differentially expressed genes (DEGs), such as PPAR, FABP3, PLIN1, and FOXO1, were screened. These DEGs were predominantly enriched in terms related to mitochondria, lipids, and nucleic acids. In addition, the gut microbiota has the ability to influence host physiology through the regulation of multiple processes, including playing a crucial role in host muscle growth and development. We randomly selected male and female Muscovy ducks for 16S rRNA sequencing analysis of their cecal microbiota. The results showed that there were significant differences in the composition of cecal microbiota between male and female Muscovy ducks. At the genus level, the relative abundance of Enterenecus and CAG_269 were lower in males compared to females, while Lawsonibacter, Parabacteroides_B, Streptococcus, UBA2658, Caccousia, and Butyricimonas were higher in males than in females. In summary, this study provides a scientific theoretical basis for revealing the different growth patterns of male and female Muscovy ducks, and offers explanations from both the molecular level and microbiological perspectives.

TAT gene polymorphism and its relationship with production traits in Muscovy ducks (Cairina Moschata).

In a previous study, the laying pattern of Muscovy duck was explored by macro-fitting the laying curve of Muscovy duck, and transcriptome sequencing technique of the ovarian tissues was used to screen the egg-related gene "TAT." Moreover, recent results have shown that TAT is expressed in organs such as oviduct, ovary, and testis. The objective of this study is to examine the effect of TAT gene on egg production traits of Muscovy ducks. First, the expression levels of TAT gene in highest producing (HP) and lowest producing (LP) in 3 tissues related to reproduction were examined, and the results indicated that the expression of TAT gene in hypothalamus was significantly different between HP and LP groups. Then, 6 SNP loci (g. 120G>T, g, 122G>A, g, 254G> A, g. 270C >T, g, 312G>A, and g. 341C>A) were detected in TAT gene. Further, association analysis between the six SNP loci of TAT gene and egg production traits of 652 individual Muscovy ducks was done. The results showed that g. 254G>A and g. 270C>T were significantly correlated (P < 0.05 or 0.001) with the egg production traits of Muscovy ducks. This study elucidated the molecular mechanism that TAT gene might be regulating the egg production traits of Muscovy ducks.

Research Note: Association of single nucleotide polymorphism of AKT3 with egg production traits in White Muscovy ducks (Cairina moschata).

Prior studies on transcriptomes of hypothalamus and ovary revealed that AKT3 is one of the candidate genes that might affect egg production in White Muscovy ducks. The role of AKT3 in the uterus during reproductive processes cannot be overemphasized. However, functional role of this gene in the tissues and on egg production traits of Muscovy ducks remains unknown. To identify the relationship between AKT3 and egg production traits in ducks, relative expression profile was first examined prior to identifying the variants within AKT3 that may underscore egg production traits [age at first egg (AFE), number of eggs at 300 d (N300D), and number of eggs at 59 wk (N59W)] in 549 ducks. The mRNA expression of AKT3 gene in high producing (HP) ducks was significantly higher than low producing (LP) ducks in the ovary, oviduct, and hypothalamus (P < 0.05 or 0.001). Three variants in AKT3 (C-3631A, C-3766T, and C-3953T) and high linkage block between C-3766T and C-3953T which are significantly (P < 0.05) associated with N300D and N59W were discovered. This study elucidates novel knowledge on the molecular mechanism of AKT3 that might be regulating egg production traits in Muscovy ducks.

Hypothalamic and ovarian transcriptome profiling reveals potential candidate genes in low and high egg production of white Muscovy ducks (Cairina moschata).

In China, the low egg production rate is a major challenge to Muscovy duck farmers. Hypothalamus and ovary play essential role in egg production of birds. However, there are little or no reports from these tissues to identify potential candidate genes responsible for egg production in White Muscovy ducks. A total of 1,537 laying ducks were raised; the egg production traits which include age at first egg (days), number of eggs at 300 d, and number of eggs at 59 wk were recorded. Moreover, 4 lowest (LP) and 4 highest producing (HP) were selected at 59 wk of age, respectively. To understand the mechanism of egg laying regulation, we sequenced the hypothalamus and ovary transcriptome profiles in LP and HP using RNA-Seq. The results showed that the number of eggs at 300 d and number of eggs at 59 wk in the HP were significantly more (P < 0.001) than the LP ducks. In total, 106.98G clean bases were generated from 16 libraries with an average of 6.68G clean bases for each library. Further analysis showed 569 and 2,259 differentially expressed genes (DEGs) were identified in the hypothalamus and ovary between LP and HP, respectively. The KEGG pathway enrichment analysis revealed 114 and 139 pathways in the hypothalamus and ovary, respectively which includes Calcium signaling pathway, ECM-receptor interaction, Focal adhesion, MAPK signaling pathway, Apoptosis and Apelin signaling pathways that are involved in egg production. Based on the GO terms and KEGG pathways results, 10 potential candidate genes (P2RX1, LPAR2, ADORA1, FN1, AKT3, ADCY5, ADCY8, MAP3K8, PXN, and PTTG1) were identified to be responsible for egg production. Further, protein-protein interaction was analyzed to show the relationship between these candidate genes. Therefore, this study provides useful information on transcriptome of hypothalamus and ovary of LP and HP Muscovy ducks.

Polymorphisms of AMY1A gene and their association with growth, carcass traits and feed intake efficiency in chickens.

Investigations on the association between chicken traits and genetic variations can provide basic information to improve production performance in chickens. In our previous work, we genotyped 450 male chickens with a 600 K SNP array [1] and found that several SNPs in the genomic regions of the amylase alpha 1A (AMY1A) gene were significantly associated with feed intake efficiency and carcass traits. Given the lower accuracy of the SNP array, we performed direct sequencing with male and female chickens to further test chicken AMY1A polymorphisms and investigate their association with 17 traits in chickens. The results showed that 7 SNPs in the 5' flanking region, exon, intron and 3' UTR (3' untranslated region) of AMY1A, were significantly associated with daily gain (DG), average daily feed intake (ADFI), leg muscle weight (LMW) and abdominal fat (AF) (p < 0.05). Additionally, the haplotypes based on three SNPs, rs15910189, rs314354067 and rs316026696, showed significant associations with DG (p < 0.01), ADFI and AF (p < 0.05). To better understand the transcriptional regulation of AMY1A, we cloned its 5' flanking region and found that the SNPs rs316436216 and rs314213090 which might change the transcriptional regulator binding sites, were in the suppressor and enhancer regions, respectively. In addition, luciferase assays revealed that the SNP rs314613110 in the 3' UTR influenced the binding of the miRNA gga-miR-1764-3p. To validate whether there is any copy number variation in AMY1A in our population, we performed a genome-wide assessment of CNVs through whole-genome resequencing data. However, no CNV was found in AMY1A in our population, which is different from the increased copy number of AMY1A found in humans who consume a high-starch diet. Therefore, the present study provides substantial evidence for the association of AMY1A polymorphisms with growth traits and feed intake efficiency, which might contribute to chicken breeding programs.

Efficacy of Fecal Sampling as a Gut Proxy in the Study of Chicken Gut Microbiota.

Despite the convenience and non-invasiveness of fecal sampling, the fecal microbiota does not fully represent that of the gastrointestinal (GI) tract, and the efficacy of fecal sampling to accurately represent the gut microbiota in birds is poorly understood. In this study, we aim to identify the efficacy of feces as a gut proxy in birds using chickens as a model. We collected 1,026 samples from 206 chickens, including duodenum, jejunum, ileum, cecum, and feces samples, for 16S rRNA amplicon sequencing analyses. In this study, the efficacy of feces as a gut proxy was partitioned to microbial community membership and community structure. Most taxa in the small intestine (84.11-87.28%) and ceca (99.39%) could be identified in feces. Microbial community membership was reflected with a gut anatomic feature, but community structure was not. Excluding shared microbes, the small intestine and ceca contributed 34.12 and 5.83% of the total fecal members, respectively. The composition of Firmicutes members in the small intestine and that of Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria members in the ceca could be well mirrored by the observations in fecal samples (ρ = 0.54-0.71 and 0.71-0.78, respectively, P < 0.001). However, there were few significant correlations for each genus between feces and each of the four gut segments, and these correlations were not high (ρ = -0.2-0.4, P < 0.05) for most genera. Our results suggest that fecal microbial community has a good potential to identify most taxa in the chicken gut and could moderately mirror the microbial structure in the intestine at the microbial population level with phylum specificity. However, it should be interpreted with caution by using feces as a proxy to study associations for microbial structure at individual microorganism level.

The gut microbiota is largely independent of host genetics in regulating fat deposition in chickens.

The gut microbiota has an important role in animal health and performance, but its contribution is difficult to determine, in particular given the effects of host genetic factors. Here, whole-genome sequencing of the hosts and 16S rRNA gene sequencing of the microbiota were performed to separate the effects between host genetics and the microbiota in the duodenum, jejunum, ileum, caecum and faeces on fat deposition in 206 yellow broilers reared under identical conditions. Despite the notable spatial variation in the diversity, composition and potential function of the gut microbiota, host genetics exerted limited effects on the gut microbial community. The duodenal and caecal microbiota made greater contributions to fat deposition and could separately account for 24% and 21% of the variance in the abdominal fat mass after correcting for host genetic effects. We further identified two caecal microbial taxa, Methanobrevibacter and Mucispirillum schaedleri, which were significantly correlated with fat deposition. Chickens with a lower Methanobrevibacter abundance had significantly lower abdominal fat content than those with a higher abundance of Methanobrevibacter (35.51 vs. 55.59 g), and the body weights of these chickens did not notably differ. Chickens with a higher M. schaedleri abundance exhibited lower abdominal fat accumulation (39.88 vs. 55.06 g) and body weight (2.23 vs. 2.41 kg) than those with a lower abundance of this species. These findings may aid the development of strategies for altering the gut microbiota to control fat deposition during broiler production.

Relationships between feeding behaviors and performance traits in slow-growing yellow broilers.

This study was conducted to investigate the feeding behaviors of slow-growing yellow broilers and the relationships of feeding behaviors with performance traits. With the help of automatic recording systems in floor houses, feeding events from a pure line of slow-growing yellow broilers were recorded from 57 to 77 d of age. After data quality control, a total of 116,477 feeding records from 319 birds were used for analyses. Feeding behaviors including number of visits per day (18.74), feeding duration per day (71.17 min/d), feeding duration per visit (262.00 s/visit), feeding rate (2.19 g/min), and feed intake per visit (8.52 g/visit) were calculated according to feeding records. Correlation analyses and comparisons between divergent efficiency groups were performed to examine the relationships between feed efficiency and feeding behaviors. Absolute correlations between residual feed intake (RFI) and feeding behaviors (except for feed intake per visit) were significant but weak (r = 0.18 to 0.34, P < 0.05), whereas feed conversion ratio (FCR) was not significantly correlated with any feeding behaviors. All of the weight-associated traits were positively correlated with feeding rate and feed intake per visit (r = 0.19 to 0.25, P < 0.05). Compared with the inefficient birds with the 20% highest RFI or FCR (HRFI or HFCR), the efficient ones with the 20% lowest RFI or FCR (LRFI or LFCR) ate faster (P < 0.05), spent shorter eating duration (P < 0.05) and had similar feed intakes per visit (P > 0.05). However, number of visits per day and the feeding duration per day were lower in the LRFI group than in the HRFI group (P < 0.05) but were not significantly different between the LFCR and HFCR groups (P > 0.05). In summary, this study shows the feeding behaviors of group-housed slow-growing yellow broilers and observed that RFI has closer relationships with feeding behaviors than FCR does, and the selection for birds with improved RFI may result in fewer visits, shorter duration and faster feeding rate.

Feed conversion ratio, residual feed intake and cholecystokinin type A receptor gene polymorphisms are associated with feed intake and average daily gain in a Chinese local chicken population.

BACKGROUND: The feed conversion ratio (FCR) and residual feed intake (RFI) are common indexes in measuring feed efficiency for livestock. RFI is a feed intake adjusted for requirements for maintenance and production so these two traits are related. Similarly, FCR is related to feed intake and weight gain because it is their ratio. Cholecystokinin type A receptor (CCKAR) plays an important role in animal digestive process. We examined the interplay of these three parameters in a local Chinese chicken population. RESULTS: The feed intake (FI) and body weights (BW) of 1,841 individuals were monitored on a daily basis from 56 to 105 d of age. There was a strong correlation between RFI and average daily feed intake (ADFI) and a negative correlation between the FCR and daily gain (rg = - 0.710). Furthermore, we identified 51 single nucleotide polymorphisms (SNPs) in the CCKAR and 4 of these resulted in amino acid mutations. The C334A mutation was specifically associated with FI and the expected feed intake (EFI) (P <  0.01) and significantly associated with the average daily gain (ADG) (P <  0.05). G1290A was significantly associated with FI and EFI (P < 0.05). CONCLUSION: FCR is apply to weight selecting, and RFI is more appropriate if the breeding focus is feed intake. And C334A and G1290A of the CCKAR gene can be deemed as candidate markers for feed intake and weight gain.

Feed efficiency measures and their relationships with production and meat quality traits in slower growing broilers.

Feed consumption accounts for the major cost of broiler production. Improving the efficiency of feed utilization is a primary goal in breeding strategies, although few studies have focused on slower growing broilers. Here, we recorded the feed intake (FI) during the fast-growing period (d 56 to 76) and measured the live weight, body measurements, carcass characteristics, and intramuscular fat (IMF) content of Chinese yellow broilers. Then, the residual feed intake (RFI) and feed conversion ratio (FCR) were calculated for each individual. Pair-wise phenotypic correlations were subsequently calculated between feed efficiency traits and others. Finally, we separately selected the more efficient individuals based on RFI and FCR values to evaluate the impacts on the traits of FI, growth, carcass characteristics, and meat quality. The results showed higher correlations between FCR and production traits than with RFI, while RFI showed a moderate and positive phenotypic correlation with abdominal fat. FCR was weakly correlated with FI and slightly positively correlated with IMF content. The correlation coefficient between RFI and FI was 0.62, and that between RFI and IMF content was close to zero. Without increasing FI, decreasing FCR could effectively enhance the growth rate and market weight with no adverse effect on meat quality. In contrast, by improving RFI, FI and abdominal fat mass were significantly reduced and thus increased the yield with no unfavorable effects on meat quality. In consideration of consumer preference and overall economical benefits, RFI is a more suitable index to improve feed efficiency in slower growing broilers.

Combination analysis of genome-wide association and transcriptome sequencing of residual feed intake in quality chickens.

BACKGROUND: Residual feed intake (RFI) is a powerful indicator for energy utilization efficiency and responds to selection. Low RFI selection enables a reduction in feed intake without affecting growth performance. However, the effective variants or major genes dedicated to phenotypic differences in RFI in quality chickens are unclear. Therefore, a genome-wide association study (GWAS) and RNA sequencing were performed on RFI to identify genetic variants and potential candidate genes associated with energy improvement. RESULTS: A lower average daily feed intake was found in low-RFI birds compared to high-RFI birds. The heritability of RFI measured from 44 to 83 d of age was 0.35. GWAS showed that 32 of the significant single nucleotide polymorphisms (SNPs) associated with the RFI (P < 10(-4)) accounted for 53.01 % of the additive genetic variance. More than half of the effective SNPs were located in a 1 Mb region (16.3-17.3 Mb) of chicken (Gallus gallus) chromosome (GGA) 12. Thus, focusing on this region should enable a deeper understanding of energy utilization. RNA sequencing was performed to profile the liver transcriptomes of four male chickens selected from the high and low tails of the RFI. One hundred and sixteen unique genes were identified as differentially expressed genes (DEGs). Some of these genes were relevant to appetite, cell activities, and fat metabolism, such as CCKAR, HSP90B1, and PCK1. Some potential genes within the 500 Kb flanking region of the significant RFI-related SNPs detected in GWAS (i.e., MGP, HIST1H110, HIST1H2A4L3, OC3, NR0B2, PER2, ST6GALNAC2, and G0S2) were also identified as DEGs in chickens with divergent RFIs. CONCLUSIONS: The GWAS findings showed that the 1 Mb narrow region of GGA12 should be important because it contained genes involved in energy-consuming processes, such as lipogenesis, social behavior, and immunity. Similar results were obtained in the transcriptome sequencing experiments. In general, low-RFI birds seemed to optimize energy employment by reducing energy expenditure in cell activities, immune responses, and physical activity compared to eating.

[Gene expression profiling of three tissues of chicken after heat stress treatment by microarray technique].

In the present study, tissue samples were collected from the cerebrum, liver, and leg muscle of 8-day-old dwarf chicks that were exposed to a 3 h treatment of 28℃± 1℃ (control group) or 40℃± 1℃ (treatment group). Differentially expressed (DE) genes in these samples were detected using whole-genome microarray chips, and their functions were.

Association of leptin receptor gene polymorphisms with growth and feed efficiency in meat-type chickens.

Many genetic factors influence the growth and feed intake of birds. In the current study, we evaluated the association of 8 previously reported SNP in the chicken leptin receptor (LEPR) gene with BW, BW gain (BWG), feed intake (FI), and feed conversion ratio (FCR). Four SNP with a very low minor allele frequency were removed by genotype quality control. The experimental population consisted of 796 pedigreed males from 2 genetically unrelated yellow meat-type chicken strains, 335 chickens from N202, and 461 chickens from N301. The BW at 49 (BW49) and 70 d of age (BW70) and FI (from 49 to 70 d of age) were measured individually. The BWG and FCR were calculated based on BW and FI in the interval between 49 to 70 d. The results indicated that rs14657336, rs13684613, rs13684615, and rs13684616 were found in strong linkage disequilibrium. This linkage disequilibrium block was significantly associated with BW49 (P < 0.05), BW70 (P < 0.05), and FI (P < 0.05) in the N202 strain, and FCR (P < 0.01) in the N301 strain, respectively. In addition, the GTACGTAC diplotype had the highest BWG and FI in both strains. The association revealed in this study suggests the need for further functional study on the role of LEPR gene in regulating feed intake and FCR of chickens.

Polymorphisms in the transforming growth factor ß3 gene and their associations with feed efficiency in chickens.

Growth and feeding traits such as BW, BW gain (BWG), feed intake (FI), and feed conversion ratio (FCR) are of economic importance in poultry production. In this study, 8 SNP of the transforming growth factor ß3 (TGF-ß3) gene, which are located in the proximity of quantitative trait loci affecting BW and FCR, were selected to be genotyped by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in 2 yellow meat-type chicken populations with 724 birds in total. Body weights at 49 (BW49) and 70 (BW70) d of age and FI in the interval were recorded, and respective BWG and FCR were calculated for each bird. Two SNP with a very low minor allele frequency (<1%) were discarded from further analysis. The results showed that both rs13586818 and rs14535174 had significant effects (P < 0.05) on BWG and FCR, and that rs14535177 was significantly (P < 0.05) associated with BW49, BW70, and FI. Furthermore, birds with the GA genotype of rs13586818 showed strongly higher FCR and lower BWG (P < 0.05) compared with AA individuals. The TT birds had significantly larger BWG (P < 0.05) than GT birds in rs14535174, whereas FCR was the opposite. Individuals with the GC genotype of rs14535177 had significantly higher BW49, BW70, FCR, and FI (P < 0.05) than those with the GG genotype. Additionally, haplotypes based on 3 SNP of rs13586818, rs14535174, and rs14535177 were significantly associated with FCR (P < 0.05). The SNP and analyzed haplotypes identified in this study might be used as potential genetic markers in meat-type chicken breeding.

[Isothermal unidirectional elongation method of gene synthesis].

Gene synthesis is gaining popularity as a versatile means of cloning genes. The prevailing synthesis methods are PCR-based and ligase-based gene synthesis. Both of them are not independent of the sequence content of the target gene. In the present study, a new gene synthesis method-isothermal unidirectional elongation method (IUEM) is proposed, which involves the cooperation of three enzymes, and is independent or partially independent of the target gene sequence by the specially designed oligonucleotides that form hairpins. The synthesis process is isothermal and serial in IUEM. Several factors that affect the elongation were studied, and two DNA segments of length 254 bp and 300 bp were synthesized with IUEM. The synthesized segments could work as building blocks for the synthesis of longer DNA sequences.

[Correlation between adenylosuccinate lyase (ADSL) gene polymorphism and inosine monophosphate acid (IMP) content in domestic fowl and genetic relationship between red jungle fowl and domestic fowl].

This study investigates single nucleotide polymorphism (SNP) of the adenylosuccinate lyase(ADSL) gene in variety chicken breeds, including Recessive White chickens, Silkies chickens, Baier chickens, Tibetan chickens and two red jungle fowls. Primers for exon 2 in ADSL gene were designed based on the chicken genomic sequence and a SNP(C/T at 3484) was detected by PCR-SSCP and DNA sequencing. Three genotypes within all breeds were found and least square analysis showed that TT genotype birds had a significant higher inosine monophosphate acid (IMP) content than TC (P < 0.01) and CC (P < 0.05) genotype birds, TC genotype birds had a little higher IMP content than CC genotype birds, but the difference was not significant. We proposed this SNP site correlated with IMP content in chickens. A neighbour-joining dendrogram was constructed based on the Nei's genentic distance. The genetic relationship between Chinese red jungle fowl and Tibetan chickens was the nearest, whereas Baier chickens were more closer to Silkies chickens. The Chinese red jungle fowls were relatively closer to the domestic fowls, whereas Thailand red jungle fowls were relatively diverging to the Chinese native breeds. These results supported the theory concerning the independent origins of Chinese native fowl breeds.

[Advances on melatonin receptor gene].

Melatonin exerts its biological effects through pharmacological specific, high affinity G protein-coupled receptors. This review introduced the structure, function, and regulation of melatonin receptor,the cloning and structure, developmental expression, mapping and polymorphism of melatonin receptor gene. The relationship between melatonin receptor gene and reproductive seasonality was also discussed.