Are the two polymorphic sites of anti-Marek’s disease in White Leghorn chickens also suitable for Partridge Shank chickens?

Background:The selection of Marek’s disease(MD)-resistant breeds in Partridge Shank chicken,a popular local chicken breed in Henan Province of China,has practical value.We hypothesized that the two polymorphic sites(rs14527240 located in SMOC1 and GGaluGA156129 located in PTPN3)related to MD resistance in White Leghorn chickens are also applicable to Partridge Shank chickens.Methods:In this experiment,we screened 10 live hens and 2 live roosters with the double GG genotype by genotyping the two sites from 6500 Partridge Shank chickens.Nineteen one-day-old chicks with the double GG genotype were obtained by artificial insemination.Seventy-two one-day-old chickens(19 from the population expansion test and 53 randomly selected from chicken farms)were injected with 2000 plaque-forming units of the Md5 virus strain.After 100 days of infection,all chickens were examined by pathological anatomical examination,histological sectioning,genotyping,and a quantitative polymerase chain reaction of SMOC1 and PTPN3.Results:There was only one site(rs14527240 located in SMOC1)associated with MD in Partridge Shank chickens(p<0.05),but the GG genotype of SMOC1 in Partridge Shank chickens indicated susceptibility to MD.SMOC1 expression in MD-susceptible chickens was also significantly higher than that in MDresistant chickens(p<0.05).Conclusion:Therefore,the MD resistance sites selected from White Leghorn chickens were not completely suitable for Partridge Shank chickens,but they can be used as a reference.This study indicated that SMOC1 plays an important role in screening for MD resistance in poultry.

Multilocus phylogeography and ecological niche modeling suggest speciation with gene flow between the two Bamboo Partridges

Background:Understanding how species diversify is a long-standing question in biology.The allopatric speciation model is a classic hypothesis to explain the speciation process.This model supposes that there is no gene flow during the divergence process of geographically isolated populations.On the contrary,the speciation with gene flow model supposes that gene flow does occur during the speciation process.Whether allopatric species have gene flow during the speciation process is still an open question.Methods:We used the genetic information from 31 loci of 24 Chinese Bamboo Partridges(Bambusicola thoracicus)and 23 Taiwan Bamboo Partridges(B.sonorivox)to infer the gene flow model of the two species,using the approxi-mate Bayesian computation(ABC)model.The ecological niche model was used to infer the paleo-distribution during the glacial period.We also tested whether the two species had a conserved ecological niche by means of a back-ground similarity test.Results:The genetic data suggested that the post-divergence gene flow between the two species was terminated before the mid-Pleistocene.Furthermore,our ecological niche modeling suggested that their ecological niches were highly conserved,and that they shared an overlapping potential distribution range in the last glacial maximum.Conclusions:The allopatric speciation model cannot explain the speciation process of the two Bamboo Partridges.The results of this study supported a scenario in which speciation with gene flow occurring between the allopatric species and have contributed to our understanding of the speciation process.

First complete genome sequence in Arborophila and comparative genomics reveals the evolutionary adaptation of Hainan Partridge(Arborophila ardens)

Background:The Hainan Partridge(Arborophila ardens,Phasianidae,Galliformes) is an endemic species of Hainan Island,China,and it is classified as globally vulnerable species.There are at least 16 species in genus Arborophila and no genome sequence is available.Methods:The whole genome of Hainan Partridge was de novo sequenced(with shotgun approach on the Illumina 2000 platform) and assembled.Results:The genome size of Arborophila ardens is about 1.05 Gb with a high N50 scaffold length of 8.28 Mb and it is the first high quality genome announced in Arborophila genus.About 9.19% of the genome was identified as repeat sequences and about 5.88 million heterozygous SNPs were detected.A total of 17,376 protein-coding genes were predicted and their functions were annotated.The genome comparison between Hainan Partridge and Red Junglefowl(Gallus gallus) demonstrated a conserved genome structure.The phylogenetic analysis indicated that the Hainan Partridge possessed a basal phylogenetic position in Phasianidae and it was most likely derived from a common ancestor approximately 36.8 million years ago(Mya).We found that the Hainan Partridge population had experienced bottleneck and its effective population decreased from about 1,040,000 individuals 1.5 Mya to about 200,000 individuals 0.2 Mya,and then recovered to about 460,000 individuals.The number of 1:1 orthologous genes that were predicted to have undergone positive selection in the Hainan Partridge was 504 and some environmental adaptation related categories,such as response to ultraviolet radiation were represented in GO distribution analysis.Conclusions:We announced the first high quality genome in Arborophila genus and it will be a valuable genomic resource for the further studies such as evolution,adaption,conservation,not only on Hainan Partridge but also on Arborophila or Phasianidae species.

Effect of Three Feed Antibiotics Substitutes on Growth Performance and Apparent Nutrient Digesti- bility of Guangxi Jinling Partridge

Totally 150 individuals of 1-day-old Guangxi Jinling partridges were randomly divided into five groups, 30 chickens each group. Chickens in control group were fed with basal diet, while chickens in experimental groups were fed with the diet containing antibiotics, Chinese herbal medicine, probiotics and acidifi- er. The entire trial lasted 50 d, and growth performance and apparent nutrient digestibility of tested chickens were observed and measured. Compared with control group, the feed gain ratio in experimental groups significantly decreased （P 〈 0.05 ）, while that in probiotics group was the lowest. The average daily gain in pmbi- otics group was significantly higher than that in control group or other experimental groups （P 〈 0.05）. The apparent digestibility of crude protein, crude fat and energy in probiotics group were significantly higher than that in control group or other experimental groups （P 〈 0.05 ）. The apparent digestibility of phosphorus, crude fat, crude fiber, calcium and crude protein in antibiotics group were significantly higher than that in control group （P 〈 0.05 ）. The apparent digestibility of crude protein, crude fiber and phosphorus in Chinese herbal medicine group were significantly higher than that in control group （P 〈 0.05 ）. The apparent digesti- bility of nutrient in acidifier group were significantly lower than that in control group or other experimental groups （ P 〈 0.05 ）. Therefore, pmbiotics had better effects on growth performance and apparent nutrient digestibility of chickens than antibiotics, while Chinese herbal medicine and acidifier had inferior effect than an- tibiotics.

Effects of Herba Picriae Extract on Growth Performance and Immune Organ Index of Guangxi Partridge Chickens

[Objectives]The purpose of this experiment was to study the effects of dietary supplementation of Herba Picriae extract on the growth performance and immune organ index of Guangxi partridge chickens.[Methods]A total of 500 one-day-old Guangxi partridge chickens were selected and randomly divided into five groups,five replicates for each group and 20 chickens for each replicate.Groups A,B and C were treatment groups,in which 0.70%,0.35%and 0.175%of Herba Picriae extract was added to the basal diet,respectively.Group D was a positive drug control group,in which 0.01%colistin sulfate premix was supplemented.Group E was a blank control group,in which the chickens were fed the basal diet.The experimental period was 105 d.During the experiment,five chickens were randomly selected from each group on days 21,35 and 49,respectively for the measurement of immune organ index.[Results]When the chickens were fed basal diet supplemented with 0.175%of Herba Picriae extract,their daily body weight gain increased significantly from day 22 to day 35 and from day 71 to day 105 and tended to increase from day 1 to day 21,from day 36 to day 49,and from day 50 to day 70,with a range of 7.37%-8.72%.Dietary supplementation of 0.70%and 0.175%of Herba Picriae extract significantly promoted the growth and development of Fabricius bursae in the experimental chickens.[Conclusions]Dietary supplementation of 0.175%of Herba Picriae extract improved the growth performance and feed intake,as well as 21-d-old bursal index of the experimental chickens.

First evidence of heteroplasmy in Grey Partridge(Perdix perdix)

We report for the first time the occurrence of heteroplasmy in Grey Partridge(Perdix perdix)revealed by means of two mitochondrial fragments.The possible serious biological and management implications of this exception to unilateral inheritance of mtDNA were underlined.

Effects of Dietary Picria felterrae Lour Extracts on Serum Biochemical Indexes and Immune Function of Guangxi Partridge Chickens

[Objective] This trial was to investigate the effect of dietary Picria felterrae Lour extracts on serum biochemical indexes and immune function of Guangxi Partridge chickens. [Method] Totally 500 individuals of 1-day-old Guangxi Partridge chickens were randomly divided into five groups, five replicates each group and 20 chicks each replicate. Groups A, B and C were treatment groups supplemented with 0.70%, 0.35% and0.175% P. felterrae extracts in the basal diet, respectively; group D was a medical control group supplemented with 0.01% colistin sulfate premix in the basal diet; and group E was a control group with basal diet. Serum samples were collected from 10 chickens in each group at 21, 35 and 49 days of age, to analyze the biochemical and immune indexes. [Result] It had no significant impact on serum TP and GLU contents of chickens by adding different levels of P. felterrae extracts in the basal diet（P 〉0.05）. However, at 21 and 35 days of age, the TBILI content of chickens in groups A, B and C were extremely lower or significantly lower than that in group E（ P〈0.01; P〈0.05）. At 35 days of age, the serum AKP activities in groups A, B and C were extremely higher than that in group E（P〈0.01）, and the serum GOT activities at 21 and 35 days of age in group C were significantly higher than that in group E（P〈0.05）. At 49 days of age, the serum Ig G content in groups A, B and C and the IL-2 content in group B and group C were significantly lower or extremely lower than that in group E（ P〈0.05; P〈0.01）; the T-AOC content in group B was significantly higher than that in group E（P〈0.05）; the GSH content in groups A, B and C were significantly higher than that in group E（ P〈0.05）. Adding different levels of P. felterrae extracts in the diet significantly decreased the TBILI content, reduced the Ig G, IL-2 and IL-6 contents, and improved the AKP and GOT activities and the T-AOC and GSH contents of Guangxi Partridge chicken. [Conclusion] Adding 0.35% P. felterrae extracts in the basal diet received the best effort.

Asymmetrical introgression patterns between rusty-necklaced partridge (Alectoris magna) and chukar partridge (Alectoris chukar) in China

The rusty-necklaced partridge(Alectoris magna)and the chukar partridge(Alectoris chukar)are the most com­mon gamebirds in northern China.Previous comparisons of mitochondrial DNA(mtDNA)have revealed an in­trogression phenomenon between 2 species of partridge in the Liupan Mountain region of China.mtDNA is ma­ternally inherited,making it difficult to determine the origin of parental genes.We assessed the genetic variation and gene flow between these 2 species of partridges using 8 microsatellite loci as neutral diagnostic markers in 171 samples from the hybrid zone.Our data revealed an extensive divergence of genetic structure between populations of rusty-necklaced partridges and chukar partridges.In this study,we found that 19 samples had been previously morphologically identified as rusty-necklaced partridge were genetically identified as hybrids through Bayesian analysis using STRUCTURE analysis.These hybrids exhibited a mosaic of alleles that were derived from both parental lineages.However,chukar partridges did not present the genotype of the rusty-neck­laced partridge.Thus,our findings demonstrate that the hybridization between the 2 species was the result of asymmetrical introgression,with gene flow occurring only from the chukar partridge to the rusty-necklaced par­tridge.In addition,we also note the high linkage disequilibrium in populations of the rusty-necklaced partridge.These results indicate that although unidirectional introgression did not reduce genetic diversity of the Alectoris partridges,it affected the balance of gene flow between populations.The data from microsatellite DNA prompt­ed our concern about the genetic integrity of the rusty-necklaced partridge.

Inter-glacial isolation caused divergence of cold-adapted species:the case of the snow partridge

Deciphering the role of climatic oscillations in species divergence helps us understand the mechanisms that shape global biodiversity.The coldadapted species may have expanded their distribution with the development of glaciers during glacial period.With the retreat of glaciers,these species were discontinuously distributed in the high-altitude mountains and isolated by geographical barriers.However,the study that focuses on the speciation process of cold-adapted species is scant.To fill this gap,we combined population genetic data and ecological niche models(ENMs)to explore divergence process of snow partridge(Lerwa lerwa).Lerwa lerwa is a cold-adapted bird that is distributed from 4,000 to 5,500 m.We found 2 genetic populations within L.lerwa,and they diverged from each other at about 0.40–0.44 million years ago(inter-glacial period after Zhongliangan glaciation).The ENMs suggested that L.lerwa expanded to the low elevations of the Himalayas and Hengduan mountains during glacial period,whereas it contracted to the high elevations,southern of Himalayas,and Hengduan mountains during inter-glacial periods.Effective population size trajectory also suggested that L.lerwa expanded its population size during the glacial period.Consistent with our expectation,the results support that inter-glacial isolation contributed to the divergence of cold-adapted L.lerwa on Qinghai-Tibetan Plateau.This study deepens our understanding of how climatic oscillations have driven divergence process of cold-adapted Phasianidae species distributed on mountains.

HACCP在淮北麻鸡宰杀及冷藏中的应用研究

该研究在淮北麻鸡宰杀及冷藏工艺过程微生物分析的基础上进行危害性分析,确定关键控制点。结果表明,应用HACCP理论指导生产,在生产过程通过控制车间环境卫生、加强操作人员卫生管理、严格工艺流程管理及监控、控制冷链温度等措施,可以减少鸡肉微生物初始污染,保证原料肉的质量安全。关键题:淮北麻鸡;宰杀;冷藏;

Effect of grassland mosaic structure and dynamism on the reproductive habitat suitability for Alectoris graeca in central Apennines

Over the last several decades,the Mediterranean region has been subjected to mountain abandonment and farming cessation,leading to changes in vegetation and coenological features of grasslands,contextually to the strong decline of the rock partridge(Alectoris graeca).Our hypothesis was that the ongoing dynamic processes leading to the compositional changes of grasslands in central Apennines affect the habitat suitability for the singing male(territorial male defending its reproductive site).In 2015,we defined the presence/absence of spring territorial singing males in seven sites(1,250-2,400 m a.s.l.),by the census in 74 playback stations,distributed along 15 transects.We characterized the topography and the vegetation mosaic of such sites according to the collected topographic and vegetation cover data in 59 randomly selected plots(100 m×100 m)along the transects.To understand the relations among the environmental variables and the effect of the composition and dynamism of the vegetation mosaics on the presence/absence of the singing male,we used principal components analysis and generalized linear mixed-effect modelling.Our results emphasized the marked overlap between the general environmental conditions,which proved to define the habitat suitability for A.graeca,and the characteristics of the site chosen by the singing male for starting the reproductive activities.Moreover,we found that the site suitability for the singing male decreases when the vegetation recovery processes are ongoing,because of the spread of coarse tall grassesdominated communities and/or grassland types with dense turf.Tall grass-dominated communities and thick-turf grasslands exert their negative effect decreasing the habitat suitability for the singing male starting from low cover values.Therefore,it is conceivable that singing male’s suitable habitat will be dramatically restricted to the steepest south-facing slopes,where topographic and soil conditions do not allow the spread of grasslands with dense turf and of invasive/dominant tall grasses,increasing the threat to the species due to the effect of climate change on the vegetation features.

The SNPs C.513A>T in the MHC B-F gene and rs15001532 in the SPOCK1 gene are associated with Salmonella pullorum disease resistance in chickens

supported by the Earmarked Fund for the Modern Agroindustry Technology Research System, China （CARS-41）;the National High Technology Research and Development Program of China （2011AA100301）

Metabarcoding of fecal DNA reveals the broad and flexible diet of a globally endangered bird

Knowing the diet of endangered wild animals is a prerequisite for species-specific conservation and habitat management.The Sichuan partridge Arborophila rufipectus is a globally endangered Galliformes species endemic to the mountains of southwest China.Existing information on the diet of this species is biased and fragmented owing to traditional observation methods.Little is known about their dietary composition or how they respond to temporal variations in food resources throughout the year.In this study,a dietary analysis was performed on 6o fecal samples using DNA Metabarcoding of invertebrates and plants to determine the primary animal and plant components of the diet across 3 critical periods of adult life history(breeding,postbreeding wandering,and overwintering).Preys from the dipteran order,followed by the lepidopteran and ara-neaen spp.,were the predominant,animal-derived foods.Symplocos,Rubus,Celastrus,Holboellia,and Actinidia spp.supply a large abundance of fruits and seeds for this omnivorous bird.Substantial temporal dietary changes among the 3 periods and a general shift toward lower dietary diversity during the breeding season were observed,suggesting that the Sichuan partridge can adjust their diet according to the availability of food resources and their own needs.Characterizing the composition and seasonal changes in Sichuan partridge diets informs the habitat management of native flora(the plant taxa that can generate berries and seeds,such as Symplocos,Rubus,Celastrus,and Holboellia,which are likely of conservation interest)to achieve full life-cycle conservation.