Eukaryotic genomes are hierarchically packaged into cell nucleus,affecting gene regulation.The genome is organized into multiscale structural units,including chromosome territories,compartments,topologically associati...Eukaryotic genomes are hierarchically packaged into cell nucleus,affecting gene regulation.The genome is organized into multiscale structural units,including chromosome territories,compartments,topologically associating domains(TADs),and DNA loops.The identification of these hierarchical structures has benefited from the development of experimental approaches,such as 3C-based methods(Hi-C,ChIA-PET,etc.),imaging tools(2D-FISH,3D-FISH,Cryo-FISH,etc.)and ligation-free methods(GAM,SPRITE,etc.).In recent two decades,numerous studies have shown that the 3D organization of genome plays essential roles in multiple cellular processes via various mechanisms,such as regulating enhancer activity and promoter-enhancer interactions.However,there are relatively few studies about the 3D genome in livestock species.Therefore,studies for exploring the function of 3D genomes in livestock are urgently needed to provide a more comprehensive understanding of potential relationships between the genome and production traits.In this review,we summarize the recent advances of 3D genomics and its biological functions in human and mouse studies,drawing inspiration to explore the 3D genomics of livestock species.We then mainly focus on the biological functions of 3D genome organization in muscle development and its implications in animal breeding.展开更多
With the rapid development of molecular biology and related disciplines, animal breeding has moved from conventional breeding to molecular breeding. Marker-assisted selection and genomic selection have become mainstre...With the rapid development of molecular biology and related disciplines, animal breeding has moved from conventional breeding to molecular breeding. Marker-assisted selection and genomic selection have become mainstream practices in molecular breeding of livestock. However, these techniques only use information from genomic variation but not multi-omics information, thus do not fully explain the molecular basis of phenotypic variations in complex traits. In addition, the accuracy of breeding value estimation based on these techniques is occasionally controversial in different populations or varieties. Given the rapid development of high-throughput sequencing techniques and functional genome and dramatic reductions in the overall cost of sequencing, it is possible to clarify the interactions between genes and formation of phenotypes using massive sets of omic-level data from studies of the transcriptome, proteome, epigenome, and metabolome. During livestock breeding, multi-omics information regarding breeding populations and individuals should be taken into account. The interactive regulatory networks governing gene regulation and phenotype formation in diverse livestock population, varieties and species should be analyzed. In addition, a multi-omics regulatory breeding model should be constructed. Precision, population-personalized breeding is expected to become a crucial practice in future livestock breeding. Precision breeding of individuals can be achieved by combining population genomic information at multi-omics levels together with genomic selection and genome editing techniques.展开更多
Meat and milk production needs to increase ～ 70–80% relative to its current levels for satisfying the human needs in 2050.However,it is impossible to achieve such genetic gain by conventional animal breeding systems...Meat and milk production needs to increase ～ 70–80% relative to its current levels for satisfying the human needs in 2050.However,it is impossible to achieve such genetic gain by conventional animal breeding systems.Based on recent advances with regard to in vitro induction of germ cell from pluripotent stem cells,herein we propose a novel embryo-stem cell breeding system.Distinct from the conventional breeding system in farm animals that involves selecting and mating individuals,the novel breeding system completes breeding cycles from parental to offspring embryos directly by selecting and mating embryos in a dish.In comparison to the conventional dairy breeding scheme,this system can rapidly achieve 30–40 times more genetic gain by significantly shortening generation interval and enhancing selection intensity.However,several major obstacles must be overcome before we can fully use this system in livestock breeding,which include derivation and mantaince of pluripotent stem cells in domestic animals,as well as in vitro induction of primordial germ cells,and subsequent haploid gametes.Thus,we also discuss the potential efforts needed in solving the obstacles for application this novel system,and elaborate on their groundbreaking potential in livestock breeding.This novel system would provide a revolutionary animal breeding system by offering an unprecedented opportunity for meeting the fast-growing meat and milk demand of humans.展开更多
[Objectives]The aim of this paper was to reveal the changes of large livestock industry and their influence on animal husbandry economy in Guyuan City of Ningxia.[Methods]The linear trend method was employed to quanti...[Objectives]The aim of this paper was to reveal the changes of large livestock industry and their influence on animal husbandry economy in Guyuan City of Ningxia.[Methods]The linear trend method was employed to quantify the change trends of the indicators for large livestock industry,and the ridge regression model was conducted to analyze their impacts on the gross output value of animal husbandry(GOVAH).[Results]The numbers of sold and slaughtered cattle and sheep in Guyuan presented a significant upward trend,while the number for hog had a significant downward trend,during 2000-2019.The GOVAH in Guyuan and its 5 counties had increased by 2-3 times in recent 20 years,which was mainly driven by large-scale livestock breeding.The cattle and sheep breeding sectors had positive effects on GOVAH,while the hog breeding sector had negative effect.[Conclusions]This study provides a reference for the structural adjustment and large-scale development of animal husbandry.展开更多
Rice(Oryza sativa L.)stands as the most significantly influential food crop in the developing world,with its total production and yield stability affected by environmental stress.Drought stress impacts about 45%of the...Rice(Oryza sativa L.)stands as the most significantly influential food crop in the developing world,with its total production and yield stability affected by environmental stress.Drought stress impacts about 45%of the world’s rice area,affecting plants at molecular,biochemical,physiological,and phenotypic levels.The conventional breeding method,predominantly employing single pedigree selection,has been widely utilized in breeding numerous drought-tolerant rice varieties since the Green Revolution.With rapid progress in plant molecular biology,hundreds of drought-tolerant QTLs/genes have been identified and tested in rice crops under both indoor and field conditions.Several genes have been introgressed into elite germplasm to develop commercially accepted drought-tolerant varieties,resulting in the development of several drought-tolerant rice varieties through marker-assisted selection and genetically engineered approaches.This review provides up-to-date information on proof-of-concept genes and breeding methods in the molecular breeding era,offering guidance for rice breeders to develop drought-tolerant rice varieties.展开更多
Wheat germplasm is a fundamental resource for basic research,applied studies,and wheat breeding,which can be enriched normally by several paths,such as collecting natural lines,accumulating breeding lines,and introduc...Wheat germplasm is a fundamental resource for basic research,applied studies,and wheat breeding,which can be enriched normally by several paths,such as collecting natural lines,accumulating breeding lines,and introducing mutagenesis materials.Ethyl methane sulfonate(EMS)is an alkylating agent that can effectively introduce genetic variations in a wide variety of plant species.In this study,we created a million-scale EMS population(MEP)that started with the Chinese wheat cultivars‘Luyan 128’,‘Jimai 38’,‘Jimai 44’,and‘Shannong 30’.In the M1 generation,the MEP had numerous phenotypical variations,such as>3,000 chlorophyll-deficient mutants,2,519 compact spikes,and 1,692 male sterile spikes.There were also rare mutations,including 30 independent tillers each with double heads.Some M1 variations of chlorophyll-deficiency and compact spikes were inheritable,appearing in the M2 or M3 generations.To advance the entire MEP to higher generations,we adopted a single-seed descendent(SSD)approach.All other seed composites of M2 were used to screen other agronomically important traits,such as the tolerance to herbicide quizalofop-P-methyl.The MEP is available for collaborative projects,and provides a valuable toolbox for wheat genetics and breeding for sustainable agriculture.展开更多
Semidwarf breeding has boosted crop production and is a well-known outcome from the first Green Revolution. The Green Revolution gene Semidwarf 1(SD1), which modulates gibberellic acid(GA) biosynthesis, plays a princi...Semidwarf breeding has boosted crop production and is a well-known outcome from the first Green Revolution. The Green Revolution gene Semidwarf 1(SD1), which modulates gibberellic acid(GA) biosynthesis, plays a principal role in determining rice plant height. Mutations in SD1 reduce rice plant height and promote lodging resistance and fertilizer tolerance to increase grain production. The plant height mediated by SD1 also favors grain yield under certain conditions. However, it is not yet known whether the function of SD1 in upland rice promotes adaptation and grain production. In this study, the plant height and grain yield of irrigated and upland rice were comparatively analyzed under paddy and dryland conditions. In response to dryland environments, rice requires a reduction in plant height to cope with water deficits. Upland rice accessions had greater plant heights than their irrigated counterparts under both paddy and dryland conditions, and appropriately reducing plant height could improve adaptability to dryland environments and maintain high grain yield formation. Moreover, upland rice cultivars with thicker stem diameters had stronger lodging resistance, which addresses the lodging problem. Knockout of SD1 in the upland rice cultivar IRAT104 reduced the plant height and grain yield, demonstrating that the adjustment of plant height mediated by SD1 could increase grain production in dryland fields. In addition, an SD1 genetic diversity analysis verified that haplotype variation causes phenotypic variation in plant height. During the breeding history of rice, SD1 allelic mutations were selected from landraces to improve the grain yield of irrigated rice cultivars, and this selection was accompanied by a reduction in plant height. Thus, five known mutant alleles were analyzed to verify that functional SD1 is required for upland rice production. All these results suggest that SD1 might have undergone artificial positive selection in upland rice, which provides further insights concerning greater plant height in upland rice breeding.展开更多
In this work,we report long-term trends in the abundance and breeding performance of Adélie penguins(Pygoscelis adeliae)nesting in three Antarctic colonies(i.e.,at Martin Point,South Orkneys Islands;Stranger Poin...In this work,we report long-term trends in the abundance and breeding performance of Adélie penguins(Pygoscelis adeliae)nesting in three Antarctic colonies(i.e.,at Martin Point,South Orkneys Islands;Stranger Point/Cabo Funes,South Shetland Islands;and Esperanza/Hope Bay in the Antarctic Peninsula)from 1995/96 to 2022/23.Using yearly count data of breeding groups selected,we observed a decline in the number of breeding pairs and chicks in crèche at all colonies studied.However,the magnitude of change was higher at Stranger Point than that in the remaining colonies.Moreover,the index of breeding success,which was calculated as the ratio of chicks in crèche to breeding pairs,exhibited no apparent trend throughout the study period.However,it displayed greater variability at Martin Point compared to the other two colonies under investigation.Although the number of chicks in crèche of Adélie penguins showed a declining pattern,the average breeding performance was similar to that reported in gentoo penguin colonies,specifically,those undergoing a population increase(even in sympatric colonies facing similar local conditions).Consequently,it is plausible to assume a reduction of the over-winter survival as a likely cause of the declining trend observed,at least in the Stranger Point and Esperanza colonies.However,we cannot rule out local effects during the breeding season affecting the Adélie population of Martin Point.展开更多
The aim of the study was to assess feeding practices and the use of lysine and methionine in pig rationing on intensified and semi-intensive pig breeding in the Koudougou and Bobo-Dioulasso areas. To this end, a cross...The aim of the study was to assess feeding practices and the use of lysine and methionine in pig rationing on intensified and semi-intensive pig breeding in the Koudougou and Bobo-Dioulasso areas. To this end, a cross-sectional survey was carried out on 87 breeding in these towns. A Discriminant Factorial Analysis (DFA) confirming a k-means classification of the data collected was used to retain 71 breeding divided into three breeding classes: Class A (32.4% of breeding), Class B (14.08%) and Class C (53.52%). The results show that the majority of pig breeders were men between the ages of 36 and 59. Average herd sizes were 35 ± 28;79 ± 42 and 89 ± 21 pigs for Classes A, B and C respectively. The main breeds of pig found on the breeding were crossbred, Large white, local, Landrace and Duroc. Class A (26.1%), B (30%) and C (15.8%) breeders were familiar with both lysine and methionine. Class A breeders distributed feed staggered (65.2%) and in rations (34.8%). Lysine (13%) and methionine (8.7%) were purchased at 5250 FCFA/kg. Those in class B distributed feed staggered (50%) and in the form of rations (50%), in which they incorporated lysine (30%) and methionine (30%) purchased at a cost of 2500 FCFA/kg and 3000 FCFA/kg respectively. Rationing and staggered feeding were practiced by 23.7% and 76.3% of Class C breeders respectively. Only lysine purchased at 3400 FCFA/kg was incorporated into rations by 10.5% of breeders. The high cost of lysine and methionine was incriminated by Class A (100%), B (33.3%) and C (50%) breeders. In conclusion, intensive pig breeding, the practice of rationing and the incorporation of the amino acids lysine and methionine are of ascending importance from classes C, A to B. The high cost of feedstuffs, particularly lysine and methionine, compromises their use in rations, which could have a negative impact on expected breeding performance. The screening and use of feeds rich in and/or enriched with these amino acids, through the development or adaptation of technologies, could improve the efficiency of rations and the productivity of intensive pig breeding in Burkina Faso.展开更多
Based on the arable land situation in Gejiu City,upland dry planting of indica hybrid rice is being expanded in Karst mountain areas with a rainfall of over 1400 mm and an altitude of 1100-1600 m to develop grain prod...Based on the arable land situation in Gejiu City,upland dry planting of indica hybrid rice is being expanded in Karst mountain areas with a rainfall of over 1400 mm and an altitude of 1100-1600 m to develop grain production.This paper gives a specific description of hybrid rice upland dry seedling technology,upland transplanting technology,fertilization technology,field management,weed prevention and control technology,and disease and pest control.展开更多
In order to verify the accuracy of ion chromatography for cyanide detection,optimization conditions were studied,and comparison was made for the detection results of cyanide between titration and isonicotinic acid pyr...In order to verify the accuracy of ion chromatography for cyanide detection,optimization conditions were studied,and comparison was made for the detection results of cyanide between titration and isonicotinic acid pyrazolone spectrophotometry. The results showed that ion chromatography has good linearity and reproducibility,with the recovery rate of 95%-105% and the limit of detection of 0. 001 mg/L. This method is simple,rapid,safe,selective,and suitable for the determination of cyanide in pollution-free livestock product breeding water.展开更多
Grapevine is one of the most economically important crops worldwide.However,the previous versions of the grapevine reference genome tipically consist of thousands of fragments with missing centromeres and telomeres,li...Grapevine is one of the most economically important crops worldwide.However,the previous versions of the grapevine reference genome tipically consist of thousands of fragments with missing centromeres and telomeres,limiting the accessibility of the repetitive sequences,the centromeric and telomeric regions,and the study of inheritance of important agronomic traits in these regions.Here,we assembled a telomere-to-telomere(T2T)gap-free reference genome for the cultivar PN40024 using PacBio HiFi long reads.The T2T reference genome(PN_T2T)is 69 Mb longer with 9018 more genes identified than the 12X.v0 version.We annotated 67%repetitive sequences,19 centromeres and 36 telomeres,and incorporated gene annotations of previous versions into the PN_T2T assembly.We detected a total of 377 gene clusters,which showed associations with complex traits,such as aroma and disease resistance.Even though PN40024 derives from nine generations of selfing,we still found nine genomic hotspots of heterozygous sites associated with biological processes,such as the oxidation–reduction process and protein phosphorylation.The fully annotated complete reference genome therefore constitutes an important resource for grapevine genetic studies and breeding programs.展开更多
In order to reveal the immune antibody levels and immune effect of livestock and poultry in the locality,we performed antibody surveillance on severe animal diseases in 17 livestock and poultry fields in six administr...In order to reveal the immune antibody levels and immune effect of livestock and poultry in the locality,we performed antibody surveillance on severe animal diseases in 17 livestock and poultry fields in six administrative districts of Wuhan City. The results showed that the vaccines had a good protective efficacy on highly pathogenic avian influenza( HPAI) and Newcastle disease( ND) in Wuhan City. The whole antibody levels kept above the ministerial standard( > 70%).However,the vaccine immunity of porcine reproductive and respiratory syndrome( PRRS),swine fever( SF) and foot and mouth disease( FMD) was still poorly protective. The data indicated that the vaccines are protecting the severe animal diseases well,but there are still some potential security holes in some administrative districts.展开更多
[Objectives] The paper was to study the effects of probiotics on breeding environment of livestock and poultry and intestinal microorgan-isms of breeding animals. [Method] Chicken houses and hog houses were selected a...[Objectives] The paper was to study the effects of probiotics on breeding environment of livestock and poultry and intestinal microorgan-isms of breeding animals. [Method] Chicken houses and hog houses were selected as the research objects. The breeding house supplemented with basal diet was used as the control group;the breeding house sprayed with probiotics product 1 was experimental group 1(exogenous treatment);the basal diet mixed with probiotics product 2 and drinking water mixed with product 3 was experimental group 2(endogenous treatment);and the com-bination of the two experimental groups was experimental group 3. [Results] Experimental groups 1 and 2 reduced the concentration of ammonia in hog houses and chicken houses, and the effect of experimental group 2 was better than that of experimental group 1. Experimental group 3 had the best effect, which significantly reduced the ammonia concentration in hog houses and chicken houses by 28.67% and 34.09%, respectively, and the average ammonia concentration outside the house within the range of 100-300 m was less than 2 mg/m^(3). Moreover, it significantly increased the number of intestinal lactobacillus and reduced the number of Escherichia coli. [Conclusions] Probiotics can effectively reduce the ammonia concentration in livestock and poultry breeding environment, and improve the intestinal microbial structure of breeding animals. The technology of spraying exogenous probiotics combined with the use of content-derived probiotics has great potential for popularization and application.展开更多
To assess the status of environmental bearing capacity of livestock and poultry manure in Nanjing City,the environmental pollution warning value and environmental bearing potential of livestock and poultry manure in v...To assess the status of environmental bearing capacity of livestock and poultry manure in Nanjing City,the environmental pollution warning value and environmental bearing potential of livestock and poultry manure in various districts of Nanjing were calculated according to livestock and poultry manure discharge coefficient and manure content. The results showed that based on planting-breeding pattern,the livestock and poultry manure load in Nanjing City was14. 08 t/hm^2 pig manure equivalent; the warning values of environmental bearing capacity of livestock and poultry breeding calculated by nitrogen and phosphorus were 0. 23 and 0. 26,respectively,which were within the scope of environmental bearing capacity,with no threat to the environment. Under the premise of reasonable planing of livestock and poultry breeding and comprehensive utilization of manure,the environmental bearing potential of livestock and poultry breeding in Nanjing City were 5. 667 3 million( nitrogen) and 11. 109 1 million( phosphorus) pigs equivalent,and there were nearly one third of bearing space more than the existing total breeding quantity.展开更多
As large-scale genomic studies have progressed,it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level.While domestic animals tend to have complex routes of ...As large-scale genomic studies have progressed,it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level.While domestic animals tend to have complex routes of origin and migration,suggesting a possible omission of some population-specific sequences in the current reference genome.Conversely,the pangenome is a collection of all DNA sequences of a species that contains sequences shared by all individuals(core genome)and is also able to display sequence information unique to each individual(variable genome).The progress of pangenome research in humans,plants and domestic animals has proved that the missing genetic components and the identification of large structural variants(SVs)can be explored through pangenomic studies.Many individual specific sequences have been shown to be related to biological adaptability,phenotype and important economic traits.The maturity of technologies and methods such as third-generation sequencing,Tel-omere-to-telomere genomes,graphic genomes,and reference-free assembly will further promote the development of pangenome.In the future,pangenome combined with long-read data and multi-omics will help to resolve large SVs and their relationship with the main economic traits of interest in domesticated animals,providing better insights into animal domestication,evolution and breeding.In this review,we mainly discuss how pangenome analysis reveals genetic variations in domestic animals(sheep,cattle,pigs,chickens)and their impacts on phenotypes and how this can contribute to the understanding of species diversity.Additionally,we also go through potential issues and the future perspectives of pangenome research in livestock and poultry.展开更多
Rape is the third largest oil crop in the world and the first one in China.The national average rapeseed yield is only 2077.5 kg/hm^(2),and the rapeseed oil yield is 894 kg/hm^(2).This paper introduced the main types,...Rape is the third largest oil crop in the world and the first one in China.The national average rapeseed yield is only 2077.5 kg/hm^(2),and the rapeseed oil yield is 894 kg/hm^(2).This paper introduced the main types,germplasm resources,breeding bases and breeding progress of Chinese rape,and studied its high-quality varieties,breeding patents and new varieties of agricultural plants.We analyzed the main problems such as serious loss of germplasm resources in Brassica campestris L.and Brassica juncea(L.)Czern.et Coss and weak"agricultural chip"in rape field,and put forward strategies such as strengthening the protection of rape germplasm resources,encouraging the development of"agricultural chip"in rape industry clusters with national advantages and characteristics,and strengthening the protection of agricultural intellectual property rights.展开更多
Rapeseed(Brassica napus)is an oil crop grown worldwide,making it a key plant species in molecular breeding research.However,the complexity of its polyploid genome increases sequencing costs and reduces sequencing accu...Rapeseed(Brassica napus)is an oil crop grown worldwide,making it a key plant species in molecular breeding research.However,the complexity of its polyploid genome increases sequencing costs and reduces sequencing accuracy.Target capture coupled with high-throughput sequencing is an efficient approach for detecting genetic variation at genomic regions or loci of interest.In this study,588 resequenced accessions of rapeseed were used to develop a target capture sequencing SNP genotyping platform named BnaPan50T.The platform comprised 54,765,with 54,058 resequenced markers from the pan-genome,and 855 variant trait-associated markers for 12 agronomic traits.The capture quality of BnaPan50T was demonstrated well in 12 typical accessions.Compared with a conventional genotyping array,BnaPan50T has a high SNP density and a high proportion of SNPs in unique physical positions and in annotated functional genes,promising wide application.Target capture sequencing and wholegenome resequencing in 90 doubled-haploid lines yielded 60%specificity,78%uniformity within tenfold coverage range,and 93%genotyping accuracy for the platform.BnaPan50T was used to construct a genetic map for quantitative trait loci(QTL)mapping,identify 21 unique QTL,and predict several candidate genes for yield-related traits in multiple environments.A set of 132 core SNP loci was selected from BnaPan50T to construct DNA fingerprints and germplasm identification resources.This study provides genomics resources to support target capture sequencing,genetic analysis and genomic breeding of rapeseed.展开更多
A cross-sectional study of 150 purposively selected multiple livestock species farmers was conducted in Central Uganda aimed at distinguishing between mixed and integrated livestock systems. Performance and operationa...A cross-sectional study of 150 purposively selected multiple livestock species farmers was conducted in Central Uganda aimed at distinguishing between mixed and integrated livestock systems. Performance and operational-based challenges misconstrued to cause incorrect comparison between the two systems were considered. Ten multiple-livestock species system with five ruminant species-based and five monogastric species-based combinations were categorised. Poultry, pig, fish, goats and sheep kept in both the 3 and 4-species combinations were considered. Over 80% of the families are male dominated, smallholder and occupying > 1.0 Ha of land. Exotic and crossbred breeds were adopted away from less productive and noncommercial local species. Mixed monogastric-fish systems with monogastric species dominated (P 1000) stock per farm. Stalls dominate pig management systems with 15% of the farmers upgraded to commercial level with (>50) stock per farm. Ineffective livestock policies contribute to inefficient performance of 55% of livestock farmers. In conclusion, mixed livestock systems should be upgraded to integrated livestock systems with input resource synergy for improved production and sustainability.展开更多
A large amount of genome-wide association study(GWAS)panels together with quantitative-trait locus(QTL)information associated with breeding-targeted traits have been described in wheat(Triticum aestivum L.).However,th...A large amount of genome-wide association study(GWAS)panels together with quantitative-trait locus(QTL)information associated with breeding-targeted traits have been described in wheat(Triticum aestivum L.).However,the application of mapping results from a GWAS panel to conventional wheat breeding remains a challenge.In this study,we first report a general genetic map which was constructed from 44 published linkage maps.It permits the estimation of genetic distances between any two genetic loci with physical map positions,thereby unifying the linkage relationships between QTL,genes,and genomic markers from multiple genetic populations.Second,we describe QTL mapping in a wheat GWAS panel of 688 accessions,identifying 77 QTL associated with 12 yield and grain-quality traits.Because these QTL have known physical map positions,they could be mapped onto the general map.Finally,we present a design approach to wheat breeding by using known QTL information and computer simulation.Potential crosses between parents in the GWAS panel may be evaluated by the relative frequency of the target genotype,trait correlations in simulated progeny populations,and genetic gain of selected progenies.It is possible to simultaneously improve yield and grain quality by suitable parental selection,progeny population size,and progeny selection scheme.Applying the design approach will allow identifying the most promising crosses and selection schemes in advance of the field experiment,increasing predictability and efficiency in wheat breeding.展开更多
基金supported by the National Natural Science Foundation of China(31972558)the Agricultural Improved Seed Project of Shandong Province,China(2020LZGC014)。
文摘Eukaryotic genomes are hierarchically packaged into cell nucleus,affecting gene regulation.The genome is organized into multiscale structural units,including chromosome territories,compartments,topologically associating domains(TADs),and DNA loops.The identification of these hierarchical structures has benefited from the development of experimental approaches,such as 3C-based methods(Hi-C,ChIA-PET,etc.),imaging tools(2D-FISH,3D-FISH,Cryo-FISH,etc.)and ligation-free methods(GAM,SPRITE,etc.).In recent two decades,numerous studies have shown that the 3D organization of genome plays essential roles in multiple cellular processes via various mechanisms,such as regulating enhancer activity and promoter-enhancer interactions.However,there are relatively few studies about the 3D genome in livestock species.Therefore,studies for exploring the function of 3D genomes in livestock are urgently needed to provide a more comprehensive understanding of potential relationships between the genome and production traits.In this review,we summarize the recent advances of 3D genomics and its biological functions in human and mouse studies,drawing inspiration to explore the 3D genomics of livestock species.We then mainly focus on the biological functions of 3D genome organization in muscle development and its implications in animal breeding.
基金supported by National High Technology Plan of China (2013 AA102502)the National Natural Science Foundation of China (313300453)the National Key Basic Research Program of China (2015CB943101)
文摘With the rapid development of molecular biology and related disciplines, animal breeding has moved from conventional breeding to molecular breeding. Marker-assisted selection and genomic selection have become mainstream practices in molecular breeding of livestock. However, these techniques only use information from genomic variation but not multi-omics information, thus do not fully explain the molecular basis of phenotypic variations in complex traits. In addition, the accuracy of breeding value estimation based on these techniques is occasionally controversial in different populations or varieties. Given the rapid development of high-throughput sequencing techniques and functional genome and dramatic reductions in the overall cost of sequencing, it is possible to clarify the interactions between genes and formation of phenotypes using massive sets of omic-level data from studies of the transcriptome, proteome, epigenome, and metabolome. During livestock breeding, multi-omics information regarding breeding populations and individuals should be taken into account. The interactive regulatory networks governing gene regulation and phenotype formation in diverse livestock population, varieties and species should be analyzed. In addition, a multi-omics regulatory breeding model should be constructed. Precision, population-personalized breeding is expected to become a crucial practice in future livestock breeding. Precision breeding of individuals can be achieved by combining population genomic information at multi-omics levels together with genomic selection and genome editing techniques.
基金supported by Strategy Research on Disruptive Technology in Agriculture(China Academy of Engineering,2017-ZD-10-07)supported by grants from the National Key R&D Program(2017YFD0501901+1 种基金2017YFD0501905)the Earmarked Fund for the Innovative Teams of Beijing Swine Industrialization Research Program.National Waterfowl-industry Technology Research System(CARS-42)
文摘Meat and milk production needs to increase ～ 70–80% relative to its current levels for satisfying the human needs in 2050.However,it is impossible to achieve such genetic gain by conventional animal breeding systems.Based on recent advances with regard to in vitro induction of germ cell from pluripotent stem cells,herein we propose a novel embryo-stem cell breeding system.Distinct from the conventional breeding system in farm animals that involves selecting and mating individuals,the novel breeding system completes breeding cycles from parental to offspring embryos directly by selecting and mating embryos in a dish.In comparison to the conventional dairy breeding scheme,this system can rapidly achieve 30–40 times more genetic gain by significantly shortening generation interval and enhancing selection intensity.However,several major obstacles must be overcome before we can fully use this system in livestock breeding,which include derivation and mantaince of pluripotent stem cells in domestic animals,as well as in vitro induction of primordial germ cells,and subsequent haploid gametes.Thus,we also discuss the potential efforts needed in solving the obstacles for application this novel system,and elaborate on their groundbreaking potential in livestock breeding.This novel system would provide a revolutionary animal breeding system by offering an unprecedented opportunity for meeting the fast-growing meat and milk demand of humans.
基金Ningxia Key Research and Development Program(Special Talents)(2020BEB04028)(2019BEB04040).
文摘[Objectives]The aim of this paper was to reveal the changes of large livestock industry and their influence on animal husbandry economy in Guyuan City of Ningxia.[Methods]The linear trend method was employed to quantify the change trends of the indicators for large livestock industry,and the ridge regression model was conducted to analyze their impacts on the gross output value of animal husbandry(GOVAH).[Results]The numbers of sold and slaughtered cattle and sheep in Guyuan presented a significant upward trend,while the number for hog had a significant downward trend,during 2000-2019.The GOVAH in Guyuan and its 5 counties had increased by 2-3 times in recent 20 years,which was mainly driven by large-scale livestock breeding.The cattle and sheep breeding sectors had positive effects on GOVAH,while the hog breeding sector had negative effect.[Conclusions]This study provides a reference for the structural adjustment and large-scale development of animal husbandry.
基金the National Natural Science Foundation of China(Grant No.31900361).
文摘Rice(Oryza sativa L.)stands as the most significantly influential food crop in the developing world,with its total production and yield stability affected by environmental stress.Drought stress impacts about 45%of the world’s rice area,affecting plants at molecular,biochemical,physiological,and phenotypic levels.The conventional breeding method,predominantly employing single pedigree selection,has been widely utilized in breeding numerous drought-tolerant rice varieties since the Green Revolution.With rapid progress in plant molecular biology,hundreds of drought-tolerant QTLs/genes have been identified and tested in rice crops under both indoor and field conditions.Several genes have been introgressed into elite germplasm to develop commercially accepted drought-tolerant varieties,resulting in the development of several drought-tolerant rice varieties through marker-assisted selection and genetically engineered approaches.This review provides up-to-date information on proof-of-concept genes and breeding methods in the molecular breeding era,offering guidance for rice breeders to develop drought-tolerant rice varieties.
基金This work was supported by the National Key Research and Development Program of China(2022YFF1002300)the Quancheng‘5150’Talent Program,China(07962021047)the Agriculture Applied Technology Initiative of Jinan Government,China(CX202113).
文摘Wheat germplasm is a fundamental resource for basic research,applied studies,and wheat breeding,which can be enriched normally by several paths,such as collecting natural lines,accumulating breeding lines,and introducing mutagenesis materials.Ethyl methane sulfonate(EMS)is an alkylating agent that can effectively introduce genetic variations in a wide variety of plant species.In this study,we created a million-scale EMS population(MEP)that started with the Chinese wheat cultivars‘Luyan 128’,‘Jimai 38’,‘Jimai 44’,and‘Shannong 30’.In the M1 generation,the MEP had numerous phenotypical variations,such as>3,000 chlorophyll-deficient mutants,2,519 compact spikes,and 1,692 male sterile spikes.There were also rare mutations,including 30 independent tillers each with double heads.Some M1 variations of chlorophyll-deficiency and compact spikes were inheritable,appearing in the M2 or M3 generations.To advance the entire MEP to higher generations,we adopted a single-seed descendent(SSD)approach.All other seed composites of M2 were used to screen other agronomically important traits,such as the tolerance to herbicide quizalofop-P-methyl.The MEP is available for collaborative projects,and provides a valuable toolbox for wheat genetics and breeding for sustainable agriculture.
基金supported by grants from the National Natural Science Foundation of China(32272079 and 32060474)the Yunnan Provincial Science and Technology Department,China(202101AS070001 and 202201BF070001-011)。
文摘Semidwarf breeding has boosted crop production and is a well-known outcome from the first Green Revolution. The Green Revolution gene Semidwarf 1(SD1), which modulates gibberellic acid(GA) biosynthesis, plays a principal role in determining rice plant height. Mutations in SD1 reduce rice plant height and promote lodging resistance and fertilizer tolerance to increase grain production. The plant height mediated by SD1 also favors grain yield under certain conditions. However, it is not yet known whether the function of SD1 in upland rice promotes adaptation and grain production. In this study, the plant height and grain yield of irrigated and upland rice were comparatively analyzed under paddy and dryland conditions. In response to dryland environments, rice requires a reduction in plant height to cope with water deficits. Upland rice accessions had greater plant heights than their irrigated counterparts under both paddy and dryland conditions, and appropriately reducing plant height could improve adaptability to dryland environments and maintain high grain yield formation. Moreover, upland rice cultivars with thicker stem diameters had stronger lodging resistance, which addresses the lodging problem. Knockout of SD1 in the upland rice cultivar IRAT104 reduced the plant height and grain yield, demonstrating that the adjustment of plant height mediated by SD1 could increase grain production in dryland fields. In addition, an SD1 genetic diversity analysis verified that haplotype variation causes phenotypic variation in plant height. During the breeding history of rice, SD1 allelic mutations were selected from landraces to improve the grain yield of irrigated rice cultivars, and this selection was accompanied by a reduction in plant height. Thus, five known mutant alleles were analyzed to verify that functional SD1 is required for upland rice production. All these results suggest that SD1 might have undergone artificial positive selection in upland rice, which provides further insights concerning greater plant height in upland rice breeding.
基金Nacional de Promoción Científica y Tecnológica(Grant:PICTO 2010-0111)the Instituto Antártico Argentino-Dirección Nacional del Antártico(PINST-05)provided financial and logistical support.
文摘In this work,we report long-term trends in the abundance and breeding performance of Adélie penguins(Pygoscelis adeliae)nesting in three Antarctic colonies(i.e.,at Martin Point,South Orkneys Islands;Stranger Point/Cabo Funes,South Shetland Islands;and Esperanza/Hope Bay in the Antarctic Peninsula)from 1995/96 to 2022/23.Using yearly count data of breeding groups selected,we observed a decline in the number of breeding pairs and chicks in crèche at all colonies studied.However,the magnitude of change was higher at Stranger Point than that in the remaining colonies.Moreover,the index of breeding success,which was calculated as the ratio of chicks in crèche to breeding pairs,exhibited no apparent trend throughout the study period.However,it displayed greater variability at Martin Point compared to the other two colonies under investigation.Although the number of chicks in crèche of Adélie penguins showed a declining pattern,the average breeding performance was similar to that reported in gentoo penguin colonies,specifically,those undergoing a population increase(even in sympatric colonies facing similar local conditions).Consequently,it is plausible to assume a reduction of the over-winter survival as a likely cause of the declining trend observed,at least in the Stranger Point and Esperanza colonies.However,we cannot rule out local effects during the breeding season affecting the Adélie population of Martin Point.
文摘The aim of the study was to assess feeding practices and the use of lysine and methionine in pig rationing on intensified and semi-intensive pig breeding in the Koudougou and Bobo-Dioulasso areas. To this end, a cross-sectional survey was carried out on 87 breeding in these towns. A Discriminant Factorial Analysis (DFA) confirming a k-means classification of the data collected was used to retain 71 breeding divided into three breeding classes: Class A (32.4% of breeding), Class B (14.08%) and Class C (53.52%). The results show that the majority of pig breeders were men between the ages of 36 and 59. Average herd sizes were 35 ± 28;79 ± 42 and 89 ± 21 pigs for Classes A, B and C respectively. The main breeds of pig found on the breeding were crossbred, Large white, local, Landrace and Duroc. Class A (26.1%), B (30%) and C (15.8%) breeders were familiar with both lysine and methionine. Class A breeders distributed feed staggered (65.2%) and in rations (34.8%). Lysine (13%) and methionine (8.7%) were purchased at 5250 FCFA/kg. Those in class B distributed feed staggered (50%) and in the form of rations (50%), in which they incorporated lysine (30%) and methionine (30%) purchased at a cost of 2500 FCFA/kg and 3000 FCFA/kg respectively. Rationing and staggered feeding were practiced by 23.7% and 76.3% of Class C breeders respectively. Only lysine purchased at 3400 FCFA/kg was incorporated into rations by 10.5% of breeders. The high cost of lysine and methionine was incriminated by Class A (100%), B (33.3%) and C (50%) breeders. In conclusion, intensive pig breeding, the practice of rationing and the incorporation of the amino acids lysine and methionine are of ascending importance from classes C, A to B. The high cost of feedstuffs, particularly lysine and methionine, compromises their use in rations, which could have a negative impact on expected breeding performance. The screening and use of feeds rich in and/or enriched with these amino acids, through the development or adaptation of technologies, could improve the efficiency of rations and the productivity of intensive pig breeding in Burkina Faso.
文摘Based on the arable land situation in Gejiu City,upland dry planting of indica hybrid rice is being expanded in Karst mountain areas with a rainfall of over 1400 mm and an altitude of 1100-1600 m to develop grain production.This paper gives a specific description of hybrid rice upland dry seedling technology,upland transplanting technology,fertilization technology,field management,weed prevention and control technology,and disease and pest control.
文摘In order to verify the accuracy of ion chromatography for cyanide detection,optimization conditions were studied,and comparison was made for the detection results of cyanide between titration and isonicotinic acid pyrazolone spectrophotometry. The results showed that ion chromatography has good linearity and reproducibility,with the recovery rate of 95%-105% and the limit of detection of 0. 001 mg/L. This method is simple,rapid,safe,selective,and suitable for the determination of cyanide in pollution-free livestock product breeding water.
基金This work was supported by the National Natural Science Fund for Excellent Young Scientists Fund Program(Overseas)to Y.Z.,the National Key Research and Development Program of China(grant 2019YFA0906200)the Agricultural Science and Technology Innovation Program(CAAS-ZDRW202101)+1 种基金the Shenzhen Science and Technology Program(grant KQTD2016113010482651)the BMBF-funded de.
文摘Grapevine is one of the most economically important crops worldwide.However,the previous versions of the grapevine reference genome tipically consist of thousands of fragments with missing centromeres and telomeres,limiting the accessibility of the repetitive sequences,the centromeric and telomeric regions,and the study of inheritance of important agronomic traits in these regions.Here,we assembled a telomere-to-telomere(T2T)gap-free reference genome for the cultivar PN40024 using PacBio HiFi long reads.The T2T reference genome(PN_T2T)is 69 Mb longer with 9018 more genes identified than the 12X.v0 version.We annotated 67%repetitive sequences,19 centromeres and 36 telomeres,and incorporated gene annotations of previous versions into the PN_T2T assembly.We detected a total of 377 gene clusters,which showed associations with complex traits,such as aroma and disease resistance.Even though PN40024 derives from nine generations of selfing,we still found nine genomic hotspots of heterozygous sites associated with biological processes,such as the oxidation–reduction process and protein phosphorylation.The fully annotated complete reference genome therefore constitutes an important resource for grapevine genetic studies and breeding programs.
基金Supported by High Tech Industry Development Plan of Wuhan City(201220812240-6)
文摘In order to reveal the immune antibody levels and immune effect of livestock and poultry in the locality,we performed antibody surveillance on severe animal diseases in 17 livestock and poultry fields in six administrative districts of Wuhan City. The results showed that the vaccines had a good protective efficacy on highly pathogenic avian influenza( HPAI) and Newcastle disease( ND) in Wuhan City. The whole antibody levels kept above the ministerial standard( > 70%).However,the vaccine immunity of porcine reproductive and respiratory syndrome( PRRS),swine fever( SF) and foot and mouth disease( FMD) was still poorly protective. The data indicated that the vaccines are protecting the severe animal diseases well,but there are still some potential security holes in some administrative districts.
基金Supported by Instructive Project of Fujian Provincial Science and Technology Plan(2019Y6005)。
文摘[Objectives] The paper was to study the effects of probiotics on breeding environment of livestock and poultry and intestinal microorgan-isms of breeding animals. [Method] Chicken houses and hog houses were selected as the research objects. The breeding house supplemented with basal diet was used as the control group;the breeding house sprayed with probiotics product 1 was experimental group 1(exogenous treatment);the basal diet mixed with probiotics product 2 and drinking water mixed with product 3 was experimental group 2(endogenous treatment);and the com-bination of the two experimental groups was experimental group 3. [Results] Experimental groups 1 and 2 reduced the concentration of ammonia in hog houses and chicken houses, and the effect of experimental group 2 was better than that of experimental group 1. Experimental group 3 had the best effect, which significantly reduced the ammonia concentration in hog houses and chicken houses by 28.67% and 34.09%, respectively, and the average ammonia concentration outside the house within the range of 100-300 m was less than 2 mg/m^(3). Moreover, it significantly increased the number of intestinal lactobacillus and reduced the number of Escherichia coli. [Conclusions] Probiotics can effectively reduce the ammonia concentration in livestock and poultry breeding environment, and improve the intestinal microbial structure of breeding animals. The technology of spraying exogenous probiotics combined with the use of content-derived probiotics has great potential for popularization and application.
文摘To assess the status of environmental bearing capacity of livestock and poultry manure in Nanjing City,the environmental pollution warning value and environmental bearing potential of livestock and poultry manure in various districts of Nanjing were calculated according to livestock and poultry manure discharge coefficient and manure content. The results showed that based on planting-breeding pattern,the livestock and poultry manure load in Nanjing City was14. 08 t/hm^2 pig manure equivalent; the warning values of environmental bearing capacity of livestock and poultry breeding calculated by nitrogen and phosphorus were 0. 23 and 0. 26,respectively,which were within the scope of environmental bearing capacity,with no threat to the environment. Under the premise of reasonable planing of livestock and poultry breeding and comprehensive utilization of manure,the environmental bearing potential of livestock and poultry breeding in Nanjing City were 5. 667 3 million( nitrogen) and 11. 109 1 million( phosphorus) pigs equivalent,and there were nearly one third of bearing space more than the existing total breeding quantity.
基金supported by the National Natural Science Foundation of China (grant numbers 31961143021)the earmarked fund for Modern Agro-industry Technology Research System (grant numbers CARS-39-01)+1 种基金the Science and Technology Innovation Project of the Chinese Academy of Agricultural Sciences (grant numbers ASTIP-IAS01) to YM and LJsupported by the Elite Youth Program in Chinese Academy of Agricultural Sciences
文摘As large-scale genomic studies have progressed,it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level.While domestic animals tend to have complex routes of origin and migration,suggesting a possible omission of some population-specific sequences in the current reference genome.Conversely,the pangenome is a collection of all DNA sequences of a species that contains sequences shared by all individuals(core genome)and is also able to display sequence information unique to each individual(variable genome).The progress of pangenome research in humans,plants and domestic animals has proved that the missing genetic components and the identification of large structural variants(SVs)can be explored through pangenomic studies.Many individual specific sequences have been shown to be related to biological adaptability,phenotype and important economic traits.The maturity of technologies and methods such as third-generation sequencing,Tel-omere-to-telomere genomes,graphic genomes,and reference-free assembly will further promote the development of pangenome.In the future,pangenome combined with long-read data and multi-omics will help to resolve large SVs and their relationship with the main economic traits of interest in domesticated animals,providing better insights into animal domestication,evolution and breeding.In this review,we mainly discuss how pangenome analysis reveals genetic variations in domestic animals(sheep,cattle,pigs,chickens)and their impacts on phenotypes and how this can contribute to the understanding of species diversity.Additionally,we also go through potential issues and the future perspectives of pangenome research in livestock and poultry.
基金Supported by Youth Program of National Social Science Foundation of China(22CMZ015)。
文摘Rape is the third largest oil crop in the world and the first one in China.The national average rapeseed yield is only 2077.5 kg/hm^(2),and the rapeseed oil yield is 894 kg/hm^(2).This paper introduced the main types,germplasm resources,breeding bases and breeding progress of Chinese rape,and studied its high-quality varieties,breeding patents and new varieties of agricultural plants.We analyzed the main problems such as serious loss of germplasm resources in Brassica campestris L.and Brassica juncea(L.)Czern.et Coss and weak"agricultural chip"in rape field,and put forward strategies such as strengthening the protection of rape germplasm resources,encouraging the development of"agricultural chip"in rape industry clusters with national advantages and characteristics,and strengthening the protection of agricultural intellectual property rights.
基金supported by the National Natural Science Foundation of China(31871653 to K.L.,31830067 to J.L.)the Talent Project of Chongqing Natural Science Foundation(cstc2021ycjhbgzxm0033 to K.L.)Germplasm Creation Special Program of Southwest University.
文摘Rapeseed(Brassica napus)is an oil crop grown worldwide,making it a key plant species in molecular breeding research.However,the complexity of its polyploid genome increases sequencing costs and reduces sequencing accuracy.Target capture coupled with high-throughput sequencing is an efficient approach for detecting genetic variation at genomic regions or loci of interest.In this study,588 resequenced accessions of rapeseed were used to develop a target capture sequencing SNP genotyping platform named BnaPan50T.The platform comprised 54,765,with 54,058 resequenced markers from the pan-genome,and 855 variant trait-associated markers for 12 agronomic traits.The capture quality of BnaPan50T was demonstrated well in 12 typical accessions.Compared with a conventional genotyping array,BnaPan50T has a high SNP density and a high proportion of SNPs in unique physical positions and in annotated functional genes,promising wide application.Target capture sequencing and wholegenome resequencing in 90 doubled-haploid lines yielded 60%specificity,78%uniformity within tenfold coverage range,and 93%genotyping accuracy for the platform.BnaPan50T was used to construct a genetic map for quantitative trait loci(QTL)mapping,identify 21 unique QTL,and predict several candidate genes for yield-related traits in multiple environments.A set of 132 core SNP loci was selected from BnaPan50T to construct DNA fingerprints and germplasm identification resources.This study provides genomics resources to support target capture sequencing,genetic analysis and genomic breeding of rapeseed.
文摘A cross-sectional study of 150 purposively selected multiple livestock species farmers was conducted in Central Uganda aimed at distinguishing between mixed and integrated livestock systems. Performance and operational-based challenges misconstrued to cause incorrect comparison between the two systems were considered. Ten multiple-livestock species system with five ruminant species-based and five monogastric species-based combinations were categorised. Poultry, pig, fish, goats and sheep kept in both the 3 and 4-species combinations were considered. Over 80% of the families are male dominated, smallholder and occupying > 1.0 Ha of land. Exotic and crossbred breeds were adopted away from less productive and noncommercial local species. Mixed monogastric-fish systems with monogastric species dominated (P 1000) stock per farm. Stalls dominate pig management systems with 15% of the farmers upgraded to commercial level with (>50) stock per farm. Ineffective livestock policies contribute to inefficient performance of 55% of livestock farmers. In conclusion, mixed livestock systems should be upgraded to integrated livestock systems with input resource synergy for improved production and sustainability.
基金the Hainan Yazhou Bay Seed Laboratory(B21Y10209 and B22C10212)China Postdoctoral Science Foundation(2022M713433)+1 种基金National Natural Science Foundation of China(31861143003)Innovation Program of Chinese Academy of Agricultural Sciences.
文摘A large amount of genome-wide association study(GWAS)panels together with quantitative-trait locus(QTL)information associated with breeding-targeted traits have been described in wheat(Triticum aestivum L.).However,the application of mapping results from a GWAS panel to conventional wheat breeding remains a challenge.In this study,we first report a general genetic map which was constructed from 44 published linkage maps.It permits the estimation of genetic distances between any two genetic loci with physical map positions,thereby unifying the linkage relationships between QTL,genes,and genomic markers from multiple genetic populations.Second,we describe QTL mapping in a wheat GWAS panel of 688 accessions,identifying 77 QTL associated with 12 yield and grain-quality traits.Because these QTL have known physical map positions,they could be mapped onto the general map.Finally,we present a design approach to wheat breeding by using known QTL information and computer simulation.Potential crosses between parents in the GWAS panel may be evaluated by the relative frequency of the target genotype,trait correlations in simulated progeny populations,and genetic gain of selected progenies.It is possible to simultaneously improve yield and grain quality by suitable parental selection,progeny population size,and progeny selection scheme.Applying the design approach will allow identifying the most promising crosses and selection schemes in advance of the field experiment,increasing predictability and efficiency in wheat breeding.
