Genome-wide investigation to assess copy number variants in the Italian local chicken population

Background Copy number variants(CNV)hold significant functional and evolutionary importance.Numerous ongoing CNV studies aim to elucidate the etiology of human diseases and gain insights into the population structure of livestock.High-density chips have enabled the detection of CNV with increased resolution,leading to the identification of even small CNV.This study aimed to identify CNV in local Italian chicken breeds and investigate their distribution across the genome.Results Copy number variants were mainly distributed across the first six chromosomes and primarily associated with loss type CNV.The majority of CNV in the investigated breeds were of types 0 and 1,and the minimum length of CNV was significantly larger than that reported in previous studies.Interestingly,a high proportion of the length of chromosome 16 was covered by copy number variation regions(CNVR),with the major histocompatibility complex being the likely cause.Among the genes identified within CNVR,only those present in at least five animals across breeds(n=95)were discussed to reduce the focus on redundant CNV.Some of these genes have been associated to functional traits in chickens.Notably,several CNVR on different chromosomes harbor genes related to muscle development,tissue-specific biological processes,heat stress resistance,and immune response.Quantitative trait loci(QTL)were also analyzed to investigate potential overlapping with the identified CNVR:54 out of the 95 gene-containing regions overlapped with 428 QTL associated to body weight and size,carcass characteristics,egg production,egg components,fat deposition,and feed intake.Conclusions The genomic phenomena reported in this study that can cause changes in the distribution of CNV within the genome over time and the comparison of these differences in CNVR of the local chicken breeds could help in preserving these genetic resources.

Growth Efficiency of Local Chickens Using Sweet Potato Vine with Concentration Feed as a Basal Diet

The experiment was conducted at the animal experimental station of the Faculty of Animal Sciences,Royal University of Agriculture,commenced from 10 January to 14 March,2022.The CRD(Completely Randomized Design)was used with 5 treatments and 4 replications.The 500 chicks at one-day-old,local bread,were purchased from farmers who run their small scale hatchery farm.The chicks were kept together till 21 days old,and then were allocated randomly into in five diets(treatments),25 chicks per replication.The feed formulas for this study were designed and calculated to maintain a protein content of approximately 17%,dividing into 5 feed formulas(Treatments),such as concentrated feed only(control treatment:T0),plus 10%of fresh sweet potato vine(T1),plus 20%of fresh sweet potato vine(T2),plus 30%of fresh sweet potato vine(T3)and plus 20%of sweet potato vine meal(T4).The results showed that the treatment T1,had a similar final weight with the treatment T4,but was slightly lower than the treatment T0 which used concentrated feed alone.Feed intake and FCR(Feed Conversion Ratio)were not significantly different among those treatments.In conclusion,the average daily weight gain of chickens seemed to decrease with increasing the level of fresh sweet potato vine.Thus,the optimum level of fresh sweet potato vine was 10%,which may have little effect on the growth performance of local chickens.In addition,it was not far different from the positive control treatment and the treatment using sweet potato vine meal.However,the producers can increase the amount of sweet potato vine in feed formula by processing it into meal and mixing with concentrated feed or using as feed ingredients.

Application of Gaussian Weight to Improve Perturbation Features of Convection-Permitting Ensemble Forecast Based on Local Breeding of Growing Modes

Local breeding of growing modes(LBGM)is a method used to generate initial condition perturbation(ICP)for convection-permitting ensemble forecasts.Equal weights(EWs)are usually presumed in LBGM during the localization of ICP,without considering different contributions of the grid points within the local radius.To address this problem,Gaussian weights(GWs)are proposed in this study,which can accommodate the varied influences of the grids inside the local radius on the central grid through a Gaussian function.Specifically,two convection-permitting ensemble forecast experiments based on LBGM with GWs and EWs are compared and analyzed respectively for two squall line cases.The results showed that the use of the GWs intensified the local characteristics of the ICP and made the distribution of the ICP fields more flow-dependent.Kinetic energy spectrum of the ICP indicated that there could be more large-scale information in the ICP by using the GWs.In addition,mesoscale information also improved slightly.For forecast of nonprecipitation variables,GWs improved the relationship between the root-mean-square error and the spread and contributed to the forecasting accuracy of wind,temperature,geopotential height,and humidity.For the precipitation forecast,GWs simulated the precipitation structure successfully and provided better probability forecasting during the evolution of the two squall line processes than the EWs.

Algorithm based on local breeding of growing modes for convection-allowing ensemble forecasting

We propose a method based on the local breeding of growing modes(LBGM) considering strong local weather characteristics for convection-allowing ensemble forecasting. The impact radius was introduced in the breeding of growing modes to develop the LBGM method. In the local breeding process, the ratio between the root mean square error(RMSE) of local space forecast at each grid point and that of the initial full-field forecast is computed to rescale perturbations. Preliminary evaluations of the method based on a nature run were performed in terms of three aspects: perturbation structure, spread,and the RMSE of the forecast. The experimental results confirm that the local adaptability of perturbation schemes improves after rescaling by the LBGM method. For perturbation physical variables and some near-surface meteorological elements, the LBGM method could increase the spread and reduce the RMSE of forecast,improving the performance of the ensemble forecast system.In addition, different from those existing methods of global orthogonalization approach, this new initial-condition perturbation method takes into full consideration the local characteristics of the convective-scale weather system, thus making convectionallowing ensemble forecast more accurate.

基于Local-BGM法的冷涡暴雨集合预报试验及评估检验

基于传统增长模繁殖法(Breeding Growing Mode,BGM)和局地增长模繁殖法(Local Breeding Growing Mode,Local-BGM)生成初始扰动成员,对一次冷涡暴雨过程进行集合预报试验,从多方面比较两种方案的预报效果,并且在邻域概率法(Neighborhood Probability,NP)中引入时间邻域,评估概率预报结果。结果表明,引入局地化思想的Local-BGM方案能够生成比传统BGM方案更合理的初始扰动,具有很明显的局地特征。对于扰动变量的预报,Local-BGM方案在均方根误差和离散度等方面均表现更好,同时能够提高各量级降水的预报技巧。邻域集合概率法能够综合各个集合成员预报的降水信息得到优于集合平均的概率预报,分数技巧评分更高。并且在考虑时间不确定性后,无论是控制预报、集合平均还是邻域集合概率法,分数技巧评分均有很大改善,并且降水阈值越大改善效果越明显,能够为极端强降水天气提供较为客观的概率预报信息。

Ecological Scale Breeding Technique of Local Chickens

Developing ecological scale breeding of local chickens with natural conditions, such as forest lands, grass lands, orchards and mulberry fields, not only can improve the quality of poultry products and the production benefits of chicken breeding, but also can develop and use local chicken germplasm effectively and promote their breed protection and industrialization. From integration and application of breed selection, breeding management, nutrient regulation, grass planting and grazing, a new ecological scale breeding technique of local chickens is proposed.

Implementation of Breed-Specific Traits for a Local Sheep Breed

In recent decades, a considerable number of local breeds have been replaced by high-yielding breeds for reasons of profitability. Many local breeds are now threatened by extinction and the loss of their native genetic diversity. The need to conserve breeds and their genetic diversity has a major importance due to the necessity for genetic change within and between populations. Novel approaches have to be explored and extended to maintain this genetic diversity. The aim of this study was the identification and implementation of breed-specific traits for a small, local sheep breed in northern Germany. The data comprised pedigree information, estimated breeding values (EBVs) of several conventional traits, and phenotypic information from a field experiment for two novel traits: 1) average daily gain under extensive circumstances (ADGE) and 2) ultrasonic measurements of muscle-fat ratio (UMFR). The experimental design included a dataset of 47 progeny from 14 pure-bred rams of German White-Headed Mutton (GWM). The methodical approach was divided into four parts: 1) the analysis of the breeding programme, 2) the identification of breed-specific traits, 3) the estimation and correlation of novel breeding values, and 4) the consequences of implementing these novel traits. Genetic parameters and correlations were conducted by applying linear mixed models. The estimates for the heritability (repeatability) were between 0.70 and 0.83 (0.42 and 0.46). The genetic correlation was positive (0.61) and in accordance with the phenotypic correlation (0.62). Average daily gain under intensive circumstances (ADGI) was moderately positive correlated with muscularity (0.60), as opposed to ADGE, which was moderately negative correlated with muscularity (-0.68). The EBV of ADGE was also moderately positive correlated with UMFR (0.64). Genetic response for ADGE enhanced to values of 481.09 g/day, 639.97 g/day, >700 g/day and >850 g/day for different selection intensity scenarios. Corresponding rates of inbreeding were 1.4%, 2.7%, 5.1%, and 7.9% after 10 years of selection. Genetic response for UMFR increased to 0.92, 1.34, 2.41, and >2.75, whereas remaining rates of inbreeding increased to 1.1%, 2.2%, 5.1%, and 7.9%. ADGI and ADGE were tendentially negatively correlated (-0.11), which strengthen the assumption of a biased ADGI. ADGE has a positive influence on meat-quality aspects (UMFR). Optimal use of reference sires with predefined selection intensity achieves genetic response for ADGE and UMFR with simultaneously acceptable rates of inbreeding.

2019—2021年皖南地区地方品种鸡源沙门菌的血清型鉴定、毒力基因和耐药性检测

为了分析皖南地区地方品种鸡(淮南麻黄鸡、淮北麻鸡、霍邱鸡和五华鸡)来源沙门菌的分布、毒力基因和耐药性情况,本试验于2019—2021年采集该地区地方品种鸡养殖场疑似沙门菌感染病死鸡的肝脏组织、肛拭子和死胚等病料组织456份,采用细菌分离培养、形态学观察、生化试验和特异性invA基因的PCR检测进行沙门菌鉴定,采用Kauffmann-White法、PCR法和K-B纸片法分别检测分离菌株的血清型、毒力基因、耐药基因和耐药性。结果显示,共分离得到127株沙门菌,分属于13种血清型,其中以鸡白痢沙门菌、禽伤寒沙门菌和肠炎沙门菌为流行的优势血清型,分别占分离菌株的26.0%、20.5%和17.3%;127株沙门菌中携带的4种毒力基因(spvA、spvB、spvC和spvR)检出率介于7.1%~74.8%,携带的4种毒力岛基因(SPI-1 SPI-2、SPI-3和SPI-5)检出率介于38.6%~81.1%;127株沙门菌对阿莫西林、氨苄西林和磺胺二甲氧嘧啶等8种药物的耐药率介于56.7%~99.2%,以耐10(12.6%)、9(15.0%)和8(20.5%)种药物为主,耐药基因sul 1、sul 2、sul 3、tet(A)、tet(M)和tet(R)检出率介于32.3%~89.8%;经分析,地方品种鸡流行优势血清型与毒力基因和耐药基因均有一定的相关性。结果表明,从安徽省皖南地区4种地方品种鸡中分离的沙门菌具有多种血清型、携带多种毒力基因、耐药性严重,且携带多种耐药基因。

Reproductive Performance and Mortality Rate in Local and Dorper &#215 Local Crossbred Sheep Following Controlled Breeding in Ethiopia

The reproductive and lamb mortality data (n = 187) of the Local and crosses of Dorper × Local ewes following natural controlled breeding in Ethiopia were analysed. Data were collected during 2009-2011 at Sirinka breeding, evaluation and distribution site, eastern Amhara region of Ethiopia. Breed, lamb sex, birth season, birth year, birth type and ewes’ parity were considered as fixed effects. Data analyses were performed using general linear model procedures. Breed was a significant source of variation: the local sheep attained faster the age at first lambing than the crossbred ewe lambs (469 ± 8.45 vs. 555 ± 6.25 days, p < 0.0001), whereas the crossbred ewes weighed more than the local sheep ewes at the age of first lambing (32.7 ± 0.63 vs. 22.8 ± 0.43 kg, p < 0.0001). Birth year had also important influence on the age and weight at first lambing of ewes. Ewes showed better performance during the later study years, differences attributed due to the improved management advantages in later years. The crossbred and local ewes were comparable in their litter size, despite the fact that the lambing interval of crossbred ewes was longer than the local ewes (306 ± 4.62 vs. 287 ± 2.38 days). Additionally, there was no significant difference in mortality rate between the two breeds. This study confirms that the local ewes had higher annual reproductive rate than that of the crossbred sheep ewes (1.49 ± 0.02 vs. 1.37 ± 0.01 lambs) under the same environmental conditions. The present results suggested that better management and breeding program probably will increase the productivity of the local sheep.

我国地方肉牛品种差异化高质量发展模式探究

近年来,肉牛产业比较效益较低,受猪牛肉市场价格非常态联动以及地方品种普遍的生产效益较低等因素影响,肉牛产业发展的支撑效应逐渐弱化。该文解析了新常态下我国肉牛产业的新特征,并对地方品种支撑肉牛产业差异化发展新模式进行了探究,提出了我国地方肉牛差异化高质量发展模式的关键举措。

Growth Performance of Crocodile Fed with Chicken Intestine and Trash Fish at Smallholder Farm in Siem Reap Province,Cambodia

The experiment was conducted at the smallholder crocodile farm at Pouk district,Siem reap province,and lasted 12 months,commenced from January 1st to December 31st,2023.The CRBD(Completely Randomized Block Design),was used in 3 treatments,such as T1(fed chicken intestine only),T2(fed chicken intestine+trash fish)and T3(fed trash fish only),with 4 replications in each treatment.The block was set by gender of crocodile,male and female.The 36 of local breed crocodiles 4 months old were allocated into each replication randomly.The result found that the length of crocodile gradually increased in the first semester,then it greatly increased from or for second semester for all treatments.In addition,the final body length of crocodile was significant different among treatments(p<0.001),the treatment of T2(fed chicken intestine+trash fish)had the longest one.Body length was also affected by gender,and male crocodile had longer body length(p<0.001).However,there were no significant differences for the interaction between types of feed with gender(p>0.05)(Table 1).The body weight of crocodile had gradually increased in the first semester,then it greatly increased from or for second semester for all treatments,while the final body weight of crocodile was also significant different among treatments(p<0.001)and the gender of crocodile(p<0.001).The average ADG(Daily Weight Gain)was significant different among treatments(p<0.001).Treatment of T2(fed chicken intestine+trash fish)had highest ADG,11.05 g,followed by T3(fed trash fish only),while the T1 had the lowest one.The gender of crocodile affected the ADG of crocodile,and male crocodile had higher ADG than female crocodile(p<0.001).However,there were no significant differences for the interaction between type of feed with gender(p>0.05).Feed intake was calculated based on amount of feed offer and measured in fresh basis.The amount of intake feed in all treatments was the same.FCR(Feed Conversion Ratio)was significant different among treatments(p<0.001)and also gender of crocodile(p<0.001).However,there were no significant differences for the interaction between types of feed with gender(p>0.05).In conclusion,the uses of trash fish and chicken intestine are an alternative feed source for crocodile to result in higher growth performance of crocodile.

Operating in Tandem Chinese experts in Sao Tome and Principe cooperate with local farmers to raise medical standards in the breeding industry

Santomean pig farmer Simao Vicente was hopeful when he came to ask Zou Rui for help. His pig was suffering from hernia, and Zou, a 42-year-old Chinese agricultural expert working in Sao Tomé and Príncipe, was the only person on the island who could provide emergency surgery.

8个地方鸡品种的体尺、屠宰性能及肉品质的比较及综合评价

【目的】通过比较分析贵州省8个地方鸡品种的体尺、屠宰性能及肉品质性状差异,为贵州地方鸡种的保护开发和利用提供基础数据。【方法】采用常规方法对乌蒙乌骨鸡、威宁鸡、普定高脚鸡、兴义矮脚鸡、黔东南小香鸡、赤水乌骨鸡、长顺绿壳蛋鸡和瑶山鸡的体尺指标、屠宰性能和肉品质性状指标进行测定,利用主成分分析法构建肉用性状综合评价模型。【结果】贵州8个地方鸡品种体尺性状、屠宰性能及肉品质指标存在明显差异,但屠宰率均大于86%,全净膛率均大于67%,8个品种均表现出了较佳的产肉性能;成功构建了肉用鸡综合评价模型,评分结果为:威宁鸡>乌蒙乌骨鸡>普定高脚鸡>赤水乌骨鸡>瑶山鸡>兴义矮脚鸡>黔东南小香鸡>长顺绿壳蛋鸡。【结论】8个地方鸡品种均表现出了良好的产肉性,是优质的肉鸡种质资源;综合评价结果显示,威宁鸡和乌蒙乌骨鸡肉用性能比较出色。

中国地方猪种保护利用价值及策略研究

近年来,中国大量进口国外猪种,种猪业出现“育不如引”的说法,形成“引种—退化—再引种—再退化”的恶性循环,对地方猪种的保护与利用产生了一定影响。为破解这一难题,需要有效挖掘丰富的地方猪种资源,以地方猪种的多重价值满足市场多元化需求。本研究在对中国地方猪种保护现状调研分析的基础上,总结出中国优良地方猪种不仅具有耐粗饲、抗逆性强、肉质鲜美、繁殖能力强等丰富的遗传价值,而且具有珍贵的民俗文化价值、景观休闲价值以及经济价值。开发中国地方猪种的多样价值,有助于助力其快速扩大市场容量,提升品种影响力。最后,针对中国地方猪种的目前的保护与利用情况,提出育种创新、加强场区库保护建设、打造区域特色品牌、加大宣传推广等全方位增强中国地方猪种市场竞争力、促进生猪种业高质量发展的策略。

贵州地方品种鸡ALV流行病学调查

为了解2019—2021年贵州地方品种鸡AL病毒(Avian leukosis virus,ALV)流行情况。采用DF-1细胞对贵州9个地方品种鸡331份血浆进行ALV的分离;利用ALV p27抗原ELISA检测法对贵州地方品种鸡708份血样、180份蛋清、61份泄殖腔棉拭子进行检测。结果表明:贵州地方品种鸡331份血浆样品分离出6株ALV,总阳性率1.81%(6/331);2019—2021年采集贵州省不同品种鸡血样708份进行ALV p27抗原ELISA检测,共检测出289份阳性,总阳性率40.81%(289/708);180份蛋清中检测出39份阳性,总阳性率21.7%(39/180)。61份泄殖腔棉拭子中检测出16份阳性,总阳性率26.20%(16/61);说明贵州地方不同品种鸡存在不同程度的ALV感染,本研究为丰富贵州地区品种鸡感染ALV情况资料和贵州地方品种鸡AL的防控奠定基础。

锥栗农家品种人工授粉杂交果实性状的变异分析

【目的】筛选锥栗优良授粉组合与杂交组合。【方法】以5个锥栗主栽优良农家品种为试验材料进行杂交授粉,对所得果实性状进行变异分析。【结果】16个杂交组合果实性状间变异幅度最大的为栗苞质量、坚果质量,变异幅度最小为果型指数,不同组合间性状差异显著,具有较好的选择潜力;总苞质量、坚果质量、坚果长、坚果宽、出籽率等性状间具有不同程度的正相关性,可进行联合选择;总苞质量、坚果质量、栗苞长、栗苞宽、栗苞高、出籽率等性状存在不同程度的花粉直感效应;以亲本ZL1为母本、亲本ZL12为父本的各授粉组合果实性状表现优良,并选择出5个优良授粉组合;ZL1的GCA效应较高,而杂交组合ZL1×ZL9、ZL6×ZL12、ZL3×ZL6的SCA效应最高。【结论】研究结果可为锥栗杂交育种和丰产栽培提供参考。

一例龙岩地方品种鸡禽白血病诊断及病原学分析

为掌握龙岩地方品种鸡禽白血病病毒的感染情况与流行毒株的分子特征,采用剖检、病理组织学检查以及RT-PCR等方法对疑似感染禽白血病的鸡只进行诊断,并扩增病毒的gp85基因序列进行分析。结果表明,病鸡出现肝脏和心脏肿大,且器官表面伴有针尖状出血点,腹腔积液明显,内脏器官中有大量淋巴细胞的灶性浸润;该毒株gp85基因序列与J亚群的参考毒株存在较高的同源性,与原型毒株HPRS-103的同源性为87.8%,与J亚群的HN0001参考毒株处于同一小分支。该发现对于监测龙岩地方品种鸡鸡场禽白血病病毒的流行趋势、制定有效的防控措施以及掌握病毒的遗传演变规律具有重要的参考价值。

河南奶山羊品种资源及其开发利用

河南奶山羊是河南省特有的优良地方奶山羊品种。文章描述了河南奶山羊的品种来源、产区分布、存栏数量、体型特征、生产性能,分析了影响其发展的制约因素,提出河南奶山羊保护和产业发展的对策,为河南奶山羊品种资源的保护和利用提供参考。

地方猪品种改良及营养调控研究进展

我国是生猪养殖和肉产品消费大国,猪肉在我国肉类食品消费中占据主导地位。近年来,随着人们对优质畜产品需求的不断增加,保障优质猪肉供给成为畜牧业发展的重中之重。我国地方猪种相较于外来猪种具有更好的抗逆性能和更高的肉品质,因此保护并发展丰富多样的地方猪品种、加强对优质地方猪品种资源的合理利用显得尤为重要。然而目前在保护地方猪种的过程中“重引进、轻保护”的现象普遍存在,导致地方猪种的遗传丰富度降低、地方猪种优良性状的挖掘评估与选育利用不足,在生猪产业中利用地方品种资源生产的商品猪肉占比偏低等。因此本文主要综述我国地方猪品种改良的主要措施及主要的营养调控手段,为充分开发利用地方猪种资源,推动我国生猪产业健康发展提供参考。

Whole-genome analysis reveals distinct adaptation signatures to diverse environments in Chinese domestic pigs

Background Long-term natural and artificial selection has resulted in many genetic footprints within the genomes of pig breeds across distinct agroecological zones.Nevertheless,the mechanisms by which these signatures contribute to phenotypic diversity and facilitate environmental adaptation remain unclear.Results Here,we leveraged whole-genome sequencing data from 82 individuals from 6 domestic pig breeds originating in tropical,high-altitude,and frigid regions.Population genetic analysis suggested that habitat isolation significantly shaped the genetic diversity and contributed to population stratification in local Chinese pig breeds.Analysis of selection signals revealed regions under selection for adaptation in tropical(55.5 Mb),high-altitude(43.6 Mb),and frigid(17.72 Mb)regions.The potential functions of the selective sweep regions were linked to certain complex traits that might play critical roles in different geographic environments,including fat coverage in frigid environments and blood indicators in tropical and high-altitude environments.Candidate genes under selection were significantly enriched in biological pathways involved in environmental adaptation.These pathways included blood circulation,protein degradation,and inflammation for adaptation to tropical environments;heart and lung development,hypoxia response,and DNA damage repair for high-altitude adaptation;and thermogenesis,cold-induced vasodilation(CIVD),and the cell cycle for adaptation to frigid environments.By examining the chromatin state of the selection signatures,we identified the lung and ileum as two candidate functional tissues for environmental adaptation.Finally,we identified a mutation(chr1:G246,175,129A)in the cis-regulatory region of ABCA1 as a plausible promising variant for adaptation to tropical environments.Conclusions In this study,we conducted a genome-wide exploration of the genetic mechanisms underlying the adaptability of local Chinese pig breeds to tropical,high-altitude,and frigid environments.Our findings shed light on the prominent role of cis-regulatory elements in environmental adaptation in pigs and may serve as a valuable biological model of human plateau-related disorders and cardiovascular diseases.