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Composition,function,and timing:exploring the early‑life gut microbiota in piglets for probiotic interventions

Journal of animal science and Biotechnology 2024年第2期15卷 659-678页

作者： Jianping Quan Cineng Xu Donglin Ruan Yong Ye Yibin Qiu Jie Wu Shenping Zhou Menghao Luan Xiang Zhao Yue Chen Danyang Lin Ying Sun Jifei Yang Enqin Zheng Gengyuan Cai Zhenfang Wu Jie Yang college of animal science and national engineering research center for breeding swine industry South China Agricultural UniversityGuangzhouGuangdongPeople’s Republic of China guangdong provincial key laboratory of agro‑animal genomics and molecular breeding South China Agricultural UniversityGuangzhouGuangdongChina Yunfu Subcenter of guangdong laboratory for Lingnan Modern Agriculture YunfuGuangdongChina national engineering research center for breeding swine industry Wens Foodstuff Group Co.Ltd.YunfuGuangdongPeople’s Republic of China

Background The establishment of a robust gut microbiota in piglets during their early developmental stage holds the potential for long-term advantageous ***,the optimal timeframe for introducing probiotics to achieve this outcome remains *** In the context of this investigation,we conducted a longitudinal assessment of the fecal microbiota of 63 piglets at three distinct pre-weaning time ***,we gathered vaginal and fecal samples from 23 *** 16S rRNA gene and metagenomic sequencing methodologies,we conducted a comprehensive analysis of the fluctuation patterns in microbial composition,functional capacity,interaction networks,and colonization resistance within the gut microbiota of *** the piglets progressed in age,discernible modifications in intestinal microbial diversity,composition,and function were observed.A source-tracking analysis unveiled the pivotal role of fecal and vaginal microbiota derived from sows in populating the gut microbiota of neonatal *** D21,the microbial interaction network displayed a more concise and efficient configuration,accompanied by enhanced colonization resistance relative to the other two time ***,we identified three strains of Ruminococcus *** D10 as potential candidates for improving piglets’weight gain during the weaning *** The findings of this study propose that D10 represents the most opportune juncture for the introduction of external probiotic interventions during the early stages of piglet *** investigation augments our comprehension of the microbiota dynamics in early-life of piglets and offers valuable insights for guiding forthcoming probiotic interventions.

关键词： Colonization resistance Intestinal microbiota Piglet Weaning Weight gain

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Transcriptome analysis of adipose tissue and muscle of Laiwu and Duroc pigs

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animal Nutrition 2024年第2期17卷 134-143页

作者： Jie Wu Fangyuan Yu Zhaoyang Di Liwen Bian Jie Yang Lina Wang Qingyan Jiang Yulong Yin Lin Zhang national engineering research center for breeding swine industry State Key Laboratory of Swine and Poultry Breeding IndustryGuangdong Laboratory of Lingnan Modern AgricultureGuangdong Provincial Key Laboratory of Animal Nutrition ControlCollege of Animal ScienceSouth China Agricultural University key laboratory of agro-Ecological Processes in Subtropical Region Laboratory of Animal Nutritional Physiology and Metabolic ProcessInstitute of Subtropical AgricultureChinese Academy of Sciences

Fat content is an important trait in pig production. Adipose tissue and muscle are important sites for fat deposition and affect production efficiency and quality. To regulate the fat content in these tissues, we need to understand the mechanisms behind fat deposition. Laiwu pigs, a Chinese indigenous breed, have significantly higher fat content in both adipose tissue and muscle than commercial breeds such as *** this study, we analyzed the transcriptomes in adipose tissue and muscle of 21-d-old Laiwu and Duroc piglets. Results showed that there were 828 and 671 differentially expressed genes(DEG) in subcutaneous adipose tissue(SAT) and visceral adipose tissue(VAT), respectively. Functional enrichment analysis showed that these DEG were enriched in metabolic pathways, especially carbohydrate and lipid metabolism. Additionally, in the longissimus muscle(LM) and psoas muscle(PM), 312 and 335 DEG were identified, demonstrating enrichment in the cell cycle and metabolic pathways. The protein-protein interaction(PPI) networks of these DEG were analyzed and potential hub genes were identified, such as FBP1 and SCD in adipose tissues and RRM2 and GADL1 in muscles. Meanwhile, results showed that there were common DEG between adipose tissue and muscle, such as LDHB, THRSP, and DGAT2. These findings showed that there are significant differences in the transcriptomes of the adipose tissue and muscle between Laiwu and Duroc piglets(P < 0.05), especially in metabolic patterns. This insight serves to advance our comprehensive understanding of metabolic regulation in these tissues and provide targets for fat content regulation.

关键词： Laiwu Duroc Adipose Muscle Transcriptome Carbohydrate and lipid metabolism

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Dynamic intrauterine crosstalk promotes porcine embryo implantation during early pregnancy

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science China(Life sciences) 2024年第8期67卷 1676-1696页

作者： Xupeng Zang Shengchen Gu Wenjing Wang Junsong Shi Jianyu Gan Qun Hu Chen Zhou Yue Ding Yanjuan He Lei Jiang Ting Gu Zheng Xu Sixiu Huang Huaqiang Yang Fanming Meng Zicong Li Gengyuan Cai Linjun Hong Zhenfang Wu State key laboratory of swine and Poultry breeding industry National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou 510642China guangdong provincial key laboratory of agro-animal genomics and molecular breeding South China Agricultural UniversityGuangzhou 510642China Yunfu Subcenter of guangdong laboratory for Lingnan Modern Agriculture Yunfu 527300China guangdong key laboratory of animal breeding and Nutrition Institute of Animal ScienceGuangdong Academy of Agricultural SciencesGuangzhou 510640China key laboratory of South China Modern Biological Seed industry Ministry of Agriculture and Rural AffairsGuangzhou 510520China

Dynamic crosstalk between the embryo and mother is crucial during ***,we comprehensively profile the single-cell transcriptome of pig peri-implantation embryos and corresponding maternal endometrium,identifying 4 different lineages in embryos and 13 cell types in the ***-specific gene expression characterizes 4 distinct trophectoderm subpopulations,showing development from undifferentiated trophectoderm to polar and mural *** expression of genes in different types of endometrial cells illustrates their molecular response to embryos during ***,we developed a novel tool,ExtraCellTalk,generating an overall dynamic map of maternal-foetal crosstalk using uterine luminal proteins as *** cross-species comparisons,we identified a conserved RBP4/STRA6 pathway in which embryonic-derived RBP4 could target the STRA6 receptor on stromal cells to regulate the interaction with other endometrial *** results provide insight into the maternal-foetal crosstalk during embryo implantation and represent a valuable resource for further studies to improve embryo implantation.

关键词： endometrial remodeling ExtraCellTalk implantation maternal-foetal crosstalk trophoblast

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Dietary supplementation of benzoic acid and essential oils combination enhances intestinal resilience against LPS stimulation in weaned piglets

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Journal of animal science and Biotechnology 2024年第2期15卷 878-897页

作者： Chang Cui Yulong Wei Yibo Wang Wen Ma Xiaoyu Zheng Jun Wang Ziwei Ma Caichi Wu Licui Chu Shihai Zhang Wutai Guan Fang Chen guangdong provincial key laboratory of animal Nutrition Control College of Animal ScienceSouth China Agricultural UniversityGuangzhou 510642China college of animal science and national engineering research center for breeding swine industry South China Agricultural UniversityGuangzhou 510642China guangdong laboratory for Lingnan Modern Agriculture South China Agricultural UniversityGuangzhou 510642China

Background The benefits of combining benzoic acid and essential oils(BAO)to mitigate intestinal impairment during the weaning process have been well established,while the detailed underlying mechanism has not been fully *** research has primarily focused on the reparative effects of BAO on intestinal injury,while neglecting its potential in enhancing intestinal stress *** In this study,we investigated the pre-protective effect of BAO against LPS-induced stress using a modified experimental *** were pre-supplemented with BAO for 14 d,followed by a challenge with LPS or saline to collect blood and intestinal *** Our findings demonstrated that BAO supplementation led to significant improvements in piglets’final weight,average daily gain,and feed intake/body gain ***,BAO supplementation positively influenced the composition of intestinal microbiota,increasing beneficial Actinobacteriota and Alloprevotella while reducing harmful Desulfobacterota,Prevotella and ***,BAO supplementation effectively mitigated oxidative disturbances and inflammatory responses induced by acute LPS *** was evidenced by elevated levels of T-AOC,SOD,and GSH,as well as decreased levels of MDA,TNF-α,and IL-6 in the ***,piglets subjected to LPS challenge and pre-supplemented with BAO exhibited significant improvements in intestinal morphological structure and enhanced integrity,as indicated by restored expression levels of Occludin and Claudin-1 compared to the non-supplemented *** analysis revealed that BAO supplementation enhanced the jejunal antioxidative capacity by increasing GSH-Px levels and decreasing MDA levels under the LPS challenge and stimulated the activation of the Nrf2 signaling ***,the reduction of TLR4/NF-κB/MAPK signaling pathways activation and proinflammatory factor were also observed in the jejunal of those piglets fed with ***

关键词： Anti-stress Benzoic acid Essential oils Intestine LPS Weaned piglets

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MiR-106a targets ATG7 to inhibit autophagy and angiogenesis after myocardial infarction

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animal Models and Experimental Medicine 2024年第4期7卷 408-418页

作者： Guofeng Bai Jinghao Yang Weili Liao Xiaofeng Zhou Yingting He Nian Li Liuhong Zhang Yifei Wang Xiaoli Dong Hao Zhang Jinchun Pan Liangxue Lai Xiaolong Yuan Xilong Wang guangdong provincial key laboratory of laboratory animals Guangdong Laboratory Animals Monitoring InstituteGuangzhouChina guangdong laboratory of Lingnan Modern Agriculture National Engineering Research Center for Breeding Swine IndustryState Key Laboratory of Swine and Poultry Breeding IndustryGuangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular BreedingCollege of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina Huidong County animal Quarantine and Inspection Institute HuizhouGuangdongChina Department of Cardiology Hainan General HospitalHainan Affiliated Hospital of Hainan Medical UniversityHainan Clinical Medicine Research InstitutionHaikouPeople's Republic of China key laboratory of Regenerative Biology Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouGuangdongChina

Background:Myocardial infarction(MI)is an acute condition in which the heart mus-cle dies due to the lack of blood *** research has suggested that au-tophagy and angiogenesis play vital roles in the prevention of heart failure after MI,and miR-106a is considered to be an important regulatory factor in *** the specific mechanism remains *** this study,using cultured venous endothelial cells and a rat model of MI,we aimed to identify the potential target genes of miR-106a and discover the mechanisms of inhibiting autophagy and ***:We first explored the biological functions of miR-106a on autophagy and angiogenesis on endothelial *** we identified ATG7,which was the down-stream target gene of *** expression of miR-106a and ATG7 was investi-gated in the rat model of ***:We found that miR-106a inhibits the proliferation,cell cycle,autophagy and angiogenesis,but promoted the apoptosis of vein endothelial ***,ATG7 was identified as the target of miR-106a,and ATG7 rescued the inhibition of autophagy and angiogenesis by *** expression of miR-106a in the rat model of MI was decreased but the expression of ATG7 was increased in the infarction ***:Our results indicate that miR-106a may inhibit autophagy and angiogenesis by targeting *** mechanism may be a potential therapeutic treatment for MI.

关键词： angiogenesis ATG7 autophagy miR-106a miRNAs myocardial infarction

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Identification of Shell Color-Associated Genes Using Mantle Branch-Specific RNA Sequencing of Yellow-Colored Line of Pearl Oyster Pinctada fucata martensii

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Journal of Ocean University of China 2024年第4期23卷 1076-1086页

作者： PENG Haiming LIAO Yongshan YANG Chuangye MKUYE Robert DENG Yuewen YUE Chenyang Fisheries college Guangdong Ocean UniversityZhanjiang 524088China Pearl research Institute Guangdong Ocean UniversityZhanjiang 524088China guangdong science and Innovation center for Pearl Culture Zhanjiang 524088China Pearl breeding and Processing engineering Technology research center of guangdong Province Zhanjiang 524088China guangdong provincial key laboratory of Aquatic animal Disease Control and Healthy Culture Zhanjiang 524088China

The yellow-colored line of pearl oyster Pinctada fucata martensii displays a yellow prismatic layer and a white nacreous layer that can be used as an ideal model for research on shell color ***-Raman spectroscopy and transcriptome analyses were performed to explore the potential molecular mechanism underlying the phenotype *** micro-Raman spectroscopy results indicate that the prismatic layer exhibits distinct characteristic peaks of carotenoids,while these peaks are not prominent in the nacreous *** the transcriptome comparison of the central zone of mantle and mantle edge tissue,which function in nacreous and prismatic layer formation,respectively,935 significantly differentially expressed genes(DEGs)were identified,with 385 genes upregulated and 227 genes downregulated(|log_(2)(Fold change)|>1 and false discovery rate<0.05)in the mantle edge *** these genes,some were associated with melanoma/melanogenesis,such as tyrosinase,zinc metalloprotease,glutathione S-transferase,and ATP-binding cassette sub-family;some were associated with the carotenoid-related pathway,including scavenger receptors,cytochrome P450 and lipoprotein *** associated with porphyrin metabolism,including porphobilinogen deaminase,and copper/zinc superoxide dismutase,and genes associated with shell matrix protein,including amorphous calcium carbonate binding protein,shematrin,PIF,and collagen,also exhibited significantly different *** is speculated that the different colours between prismatic layer and nacreous layer in the yellow-colored line of *** might be resulted from melanin,carotenoids and porphyrin metabolism,while genes related to shell structure and biomineralization might also affect *** results provide new insights to understand the mechanism of shell color formation in mollusca.

关键词： Pinctada fucata martensii shell coloration transcriptome

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A 9.5-kb deletion in the 1st intron of OsMADS51 enhances temperature sensitivity in rice

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The Crop Journal 2024年第4期12卷 1031-1040页

作者： Lei Zhao Haifei Hu Junyu Chen Chongrong Wang Yibo Chen Hong Li Daoqiang Huang Zhidong Wang Degui Zhou Rong Gong Yangyang Pan Junliang Zhao Liangyong Ma Shaochuan Zhou Rice research Institute Guangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina State key laboratory of Rice Biology and Chinese national center for Rice Improvement China National Rice Research InstituteHangzhou 310006ZhejiangChina guangdong laboratory for Lingnan Modern Agriculture Guangzhou 510640GuangdongChina key laboratory of Genetics and breeding of High Quality Rice in Southern China(Co-construction by Ministry and Province) Ministry of Agriculture and Rural AffairsGuangzhou 510640GuangdongChina guangdong Rice engineering laboratory Guangzhou 510640GuangdongChina guangdong key laboratory of New Technology in Rice breeding Guangzhou 510640GuangdongChina

Temperature is an important environmental factor affecting heading date of *** its importance,genes responsible for temperature-sensitive heading in rice have remained *** previous study identified a quantitative trait locus qHd1 which advances heading date under high temperatures.A 9.5-kb insertion was found in the first intron of OsMADS51 in indica variety Zhenshan 97(ZS97).However,the function of this natural variant in controlling temperature sensitivity has not been *** this study,we used CRISPR/Cas9 to knock out the 9.5-kb insertion in *** conducted under cotrolled conditions in phytotrons confirmed that deletion increased temperature sensitivity and advanced heading by downregulating the expression level of ***-hybrid assays in yeast,ChIP-quantitative polymerase chain reaction,electrophoretic mobility shift,and luciferase-based transient transactivation assays collectively confirmed that OsMADS51 affects heading date by regulation of heading date gene *** further determined that the long non-coding RNA HEATINR is generated from the first intron of OsMADS51,offering an explanation for how the 9.5-kb insertion affects temperature *** also found that OsMADS51 was strongly selected in early/late-season rice varieties in South China,possibly accounting for their strong temperature *** insights not only advance our understanding of the molecular mechanisms underlying the temperature-responsive regulation of heading date in rice but also provide a valuable genetic target for molecular breeding.

关键词： OsMADS51 Insertion Long non-coding RNA Oryza sativa

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Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep

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genomics, Proteomics & Bioinformatics 2024年第2期22卷 43-56页

作者： Chao Li Bingchun Chen Suo Langda Peng Pu Xiaojia Zhu Shiwei Zhou Peter Kalds Ke Zhang Meenu Bhati Alexander Leonard Shuhong Huang Ran Li Awang Cuoji Xiran Wang Haolin Zhu Yujiang Wu Renqin Cuomu Ba Gui Ming Li Yutao Wang Yan Li Wenwen Fang Ting Jia Tianchun Pu Xiangyu Pan Yudong Cai Chong He Liming Wang Yu Jiang Jian-Lin Han Yulin Chen Ping Zhou Hubert Pausch Xiaolong Wang International Joint Agriculture research center for animal Bio-breeding Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal GeneticsBreeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYangling 712100China animal genomics ETH ZürichZürich 8092Switzerland Institute of animal science Tibet Academy of Agricultural and Animal Husbandry SciencesLhasa 850009China School of Biological and Pharmaceutical engineering Lanzhou Jiaotong UniversityLanzhou 730070China college of Life sciences Shaanxi Normal UniversityXi’an 710119China Zoology and Evolutionary Biology Department of BiologyUniversity of Konstanz78457 KonstanzGermany college of Life and Geographic sciences Kashi UniversityKashi 844000China Beijing key laboratory of Captive Wildlife Technologies Beijing ZooBeijing 100044China Department of Medical research Guangdong Provincial People’s HospitalGuangdong Academy of Medical SciencesGuangzhou 510080China key laboratory of Agricultural Internet of Things Ministry of Agriculture and Rural Affairs/Shaanxi Key Laboratory of Agricultural Information Perception and Intelligent ServiceCollege of Information EngineeringNorthwest A&F UniversityYangling 712100China Institute of animal Husbandry and Veterinary Medicine Xinjiang Academy of Agricultural and Reclamation SciencesShihezi 832000China State key laboratory of Sheep Genetic Improvement and Healthy Production Xinjiang Academy of Agricultural and Reclamation SciencesShihezi 832000China CAAS-ILRI Joint laboratory on Livestock and Forage Genetic Resources Institute of Animal ScienceChinese Academy of Agricultural SciencesBeijing 100193China Livestock Genetics Program International Livestock Research InstituteNairobi 00100Kenya

Sheep were domesticated in the Fertile Crescent and then spread globally,where they have been encountering various environmental *** Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau over the past 3000 *** explore genomic variants associated with high-altitude adaptation in Tibetan sheep,we analyzed Illumina short-reads of 994 whole genomes representing∼60 sheep breeds/populations at varied altitudes,PacBio High fidelity(HiFi)reads of 13 breeds,and 96 transcriptomes from 12 sheep *** testing between the inhabited altitudes and 34,298,967 variants was conducted to investigate the genetic architecture of altitude *** accurate HiFi reads were used to complement the current ovine reference assembly at the most significantly associatedβ-globin locus and to validate the presence of two haplotypes A and B among 13 sheep *** haplotype A carried two homologous gene clusters:(1)HBE1,HBE2,HBB-like,and HBBC,and(2)HBE1-like,HBE2-like,HBB-like,and HBB;while the haplotype B lacked the first *** high-altitude sheep showed highly frequent or nearly fixed haplotype A,while the low-altitude sheep dominated by haplotype *** further demonstrated that sheep with haplotype A had an increased hemoglobin–O2 affinity compared with those carrying haplotype *** highly associated genomic region contained the EGLN1 gene which showed varied expression between high-altitude and low-altitude *** results provide evidence that the rapid adaptive evolution of advantageous alleles play an important role in facilitating the environmental adaptation of Tibetan sheep.

关键词： Environmental adaptation High altitude Hypoxia Selection signature Sheep

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Chromosome-level genome assembly of the glass catfish(Kryptopterus vitreolus)reveals molecular clues to its transparent phenotype

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Zoological research 2024年第5期45卷 1027-1036页

作者： Chao Bian Rui-Han Li Zhi-Qiang Ruan Wei-Ting Chen Yu Huang Li-Yue Liu Hong-Ling Zhou Cheong-Meng Chong Xi-Dong Mu Qiong Shi laboratory of Aquatic genomics College of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdong 518057China key laboratory of Prevention and Control for Aquatic Invasive Alien Species Ministry of Agriculture and Rural AffairsGuangdong Modern.Recreational Fisheries Engineering Technology CenterPearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouGuangdong 510380China Shenzhen key Lab of Marine genomics Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic AnimalsBGI Academy of Marine SciencesBGI MarineShenzhenGuangdong 518081China CAS key laboratory of Mountain Ecological Restoration and Bioresource Utilization&Ecological Restoration and Biodiversity Conservation key laboratory of Sichuan Province Chengdu Institute of BiologyChinese Academy of SciencesChengduSichuan 610041China School of Life sciences Jiaying UniversityMeizhouGuangdong 514015China China Zebrafish Resource center National Aquatic Biological Resource CenterState Key Laboratory of Freshwater Ecology and BiotechnologyInstitute of HydrobiologyChinese Academy of ScienceWuhanHubei 430072China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518116China State key laboratory of Quality research in Chinese Medicine Institute of Chinese Medical SciencesUniversity of MacaoMacaoMacao 999078China center for Aquatic genomics College of Life SciencesNeijiang Normal UniversityNeijiangSichuan 641100China

Glass catfish(Kryptopterus vitreolus)are notable in the aquarium trade for their highly transparent body *** transparency is due to the loss of most reflective iridophores and light-absorbing melanophores in the main body,although certain black and silver pigments remain in the face and *** date,however,the molecular mechanisms underlying this transparent phenotype remain largely *** explore the genetic basis of this transparency,we constructed a chromosome-level haplotypic genome assembly for the glass catfish,encompassing 32 chromosomes and 23344 protein-coding genes,using PacBio and Hi-C sequencing technologies and standard assembly and annotation *** revealed a premature stop codon in the putative albinism-related tyrp1b gene,encoding tyrosinase-related protein 1,rendering it a nonfunctional ***,a synteny comparison with over 30 other fish species identified the loss of the endothelin-3(edn3b)gene in the glass catfish *** investigate the role of edn3b,we generated edn3b^(−/−)mutant zebrafish,which exhibited a remarkable reduction in black pigments in body surface stripes compared to wild-type *** findings indicate that edn3b loss contributes to the transparent phenotype of the glass *** high-quality chromosome-scale genome assembly and identification of key genes provide important molecular insights into the transparent phenotype of glass *** findings not only enhance our understanding of the molecular mechanisms underlying transparency in glass catfish,but also offer a valuable genetic resource for further research on pigmentation in various animal species.

关键词： Glass catfish Whole-genome sequencing edn3b−/−mutant Transparent phenotype

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Imputation from SNP chip to sequence: a case study in a Chinese indigenous chicken population

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Journal of animal science and Biotechnology 2018年第2期9卷 294-305页

作者： Shaopan Ye Xiaolong Yuan Xiran Lin Ning Gao Yuanyu Luo Zanmou Chen Jiaqi Li Xiquan Zhang Zhe Zhang guangdong provincial key Lab of agro-animal genomics and molecular breeding National Engineering Research Centre for Breeding Swine IndustryCollege of Animal Science South China Agricultural University

Background: Genome-wide association studies and genomic predictions are thought to be optimized by using whole-genome sequence(WGS) data. However, sequencing thousands of individuals of interest is *** from SNP panels to WGS data is an attractive and less expensive approach to obtain WGS data. The aims of this study were to investigate the accuracy of imputation and to provide insight into the design and execution of genotype ***: We genotyped 450 chickens with a 600 K SNP array, and sequenced 24 key individuals by whole genome re-sequencing. Accuracy of imputation from putative 60 K and 600 K array data to WGS data was 0.620 and 0.812 for Beagle, and 0.810 and 0.914 for FImpute, respectively. By increasing the sequencing cost from 24 X to 144 X, the imputation accuracy increased from 0.525 to 0.698 for Beagle and from 0.654 to 0.823 for FImpute. With fixed sequence depth(12 X), increasing the number of sequenced animals from 1 to 24, improved accuracy from 0.421 to0.897 for FImpute and from 0.396 to 0.777 for Beagle. Using optimally selected key individuals resulted in a higher imputation accuracy compared with using randomly selected individuals as a reference population for resequencing. With fixed reference population size(24), imputation accuracy increased from 0.654 to 0.875 for FImpute and from 0.512 to 0.762 for Beagle as the sequencing depth increased from 1 X to 12 X. With a given total cost of genotyping, accuracy increased with the size of the reference population for FImpute, but the pattern was not valid for Beagle, which showed the highest accuracy at six fold coverage for the scenarios used in this ***: In conclusion, we comprehensively investigated the impacts of several key factors on genotype imputation. Generally, increasing sequencing cost gave a higher imputation accuracy. But with a fixed sequencing cost, the optimal imputation enhance the performance of WGP and GWAS. An optimal imputation strategy

关键词： Chickens Imputation Re-sequencing SNP

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