Journal of Genetics and Genomics(JGG),launched in 1974,celebrates its 50th birthday in 2023.With continuous support from our authors,reviewers,readers,and the editorial board,JGG has made remarkable progress in the pa...Journal of Genetics and Genomics(JGG),launched in 1974,celebrates its 50th birthday in 2023.With continuous support from our authors,reviewers,readers,and the editorial board,JGG has made remarkable progress in the past year by publishing 122 papers covering major disciplines in life sciences and medical genetics with exciting discoveries.It is worthwhile to note that we have recruited 66 young talents to join JGG as junior editors,resulting in significant improvement in manuscript evaluation and journal promotion.Here,we summarize major progresses reported in JGG in 2023 fromaneditorial view.展开更多
Fungi are a diverse kingdom characterized by remarkable genomic plasticity that facilitates pathogenicity and adaptation to adverse environmental conditions.In this review,we delve into the dynamic organization of fun...Fungi are a diverse kingdom characterized by remarkable genomic plasticity that facilitates pathogenicity and adaptation to adverse environmental conditions.In this review,we delve into the dynamic organization of fungal genomes and its implications for host adaptation and antifungal resistance.We examine key features and the heterogeneity of genomes across different fungal species,including but not limited to their chromosome content,DNA composition,distribution and arrangement of their content across chromosomes,and other major traits.We further highlight how this variability in genomic traits influences their virulence and adaptation to adverse conditions.Fungal genomes exhibit large variations in size,gene content,and structural features,such as the abundance of transposable elements(TEs),compartmentalization into gene-rich and TE-rich regions,and the presence or absence of dispensable chromosomes.Genomic structural variations are equally diverse in fungi,ranging from whole-chromosome duplications that may enhance tolerance to antifungal compounds,to targeted deletion of effector encoding genes that may promote virulence.Finally,the often-overlooked fungal mitochondrial genomes can also affect virulence and resistance to fungicides.Such and other features of fungal genome organization are reviewed and discussed in the context of host-microbe interactions and antifungal resistance.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
Pathogens are imminent threats to crop production. Among the management tools available to protect crops from diseases, the use of host-plant resistance had been hindered by a lack of tools and resources to identify r...Pathogens are imminent threats to crop production. Among the management tools available to protect crops from diseases, the use of host-plant resistance had been hindered by a lack of tools and resources to identify resistance genes (R-genes). Genomic technologies have empowered acquisition of a new level and quality of information on plant-pathogen interactions. Next generation sequencing, differential transcriptome analysis, gene editing, and use of bioinformatics have greatly expanded the numbers of R-genes identified, enriched understanding of R-avirulence gene interactions, and disease diagnosis. In this review, we highlight the application of genomic technologies to identification of pathogen machinery for future improvement of host plant resistance.展开更多
Chicken body weight(BW)is a critical trait in breeding.Although genetic variants associated with BW have been investigated by genome-wide association studies(GWAS),the contributions of causal variants and their molecu...Chicken body weight(BW)is a critical trait in breeding.Although genetic variants associated with BW have been investigated by genome-wide association studies(GWAS),the contributions of causal variants and their molecular mechanisms remain largely unclear in chickens.In this study,we construct a comprehensive genetic atlas of chicken BW by integrative analysis of 30 age points and 5 quantitative trait loci(QTL)across 27 tissues.We find that chicken growth is a cumulative non-linear process,which can be divided into three distinct stages.Our GWAS analysis reveals that BW-related genetic variations show ordered patterns in these three stages.Genetic variations in chromosome 1 may regulate the overall growth process,likely by modulating the hypothalamus-specific expression of SLC25A30 and retina-specific expression of NEK3.Moreover,genetic variations in chromosome 4 and chromosome 27 may play dominant roles in regulating BW during Stage 2(8-22 weeks)and Stage 3(23-72 weeks),respectively.In summary,our study presents a comprehensive genetic atlas regulating developmental stage-specific changes in chicken BW,thus providing important resources for genomic selection in breeding programs.展开更多
Objective N6-methyladenosine(m^(6)A)is a common epigenetic modification in eukaryotes.In this study,we explore the potential impact of m^(6)A-associated single nucleotide polymorphisms(m^(6)A-SNPs)on heart failure(HF)...Objective N6-methyladenosine(m^(6)A)is a common epigenetic modification in eukaryotes.In this study,we explore the potential impact of m^(6)A-associated single nucleotide polymorphisms(m^(6)A-SNPs)on heart failure(HF).Methods Data from genome-wide association studies(GWAS)investigating HF in humans and from m^(6)A-SNPs datasets were used to identify HF-associated m^(6)A-SNPs.Their functions were explored using expression quantitative trait locus(eQTL),gene expression,and gene enrichment analyses.Mediation protein quantitative trait locus(pQTL)-Mendelian randomization(MR)was used to investigate the potential mechanism between critical protein levels and risk factors for HF.Results We screened 44 HF-associated m^(6)A-SNPs,including 10 m^(6)A-SNPs that showed eQTL signals and differential expressions in HF.The SNP rs1801270 in CDKN1A showed the strongest association with HF(P=7.75×10^(−6)).Additionally,MR verified the genetic association between the CDKN1A protein and HF,as well as the mediating effect of blood pressure(BP)in this pathway.Higher circulating level of CDKN1A was associated with a lower risk of HF(odds ratio[OR]=0.82,95%confidence interval[CI]:0.69 to 0.99).The proportions of hypertension,systolic BP,and diastolic BP were 48.10%,28.94%,and 18.02%,respectively.Associations of PDIA6(P=1.30×10^(−2))and SMAD3(P=4.80×10^(−2))with HF were also detected.Conclusion Multiple HF-related m^(6)A-SNPs were identified in this study.Genetic associations of CDKN1A and other proteins with HF and its risk factors were demonstrated,providing new ideas for further exploration of the molecular mechanisms of HF.展开更多
Oligoasthenoteratozoospermia is an important factor affecting male fertility and has been found to be associated with genetic factors.However,there are stll a proportion of oligoasthenoteratozoospermia cases that cann...Oligoasthenoteratozoospermia is an important factor affecting male fertility and has been found to be associated with genetic factors.However,there are stll a proportion of oligoasthenoteratozoospermia cases that cannot be explained by known pathogenic genetic variants.Here,we perform genetic analyses and identify bi-allelic loss-of-function variants of MFSD6L from an oligoasthenoteratozoospermia-affected family.Mfsd6l knock-out male mice also present male subfertility with reduced sperm concentration,motility,and deformed acrosomes.Further mechanistic analyses reveal that MFsD6L,as an acrosome membrane protein,plays an important role in the formation of acrosome by interacting with the inner acrosomal membrane protein SPACA1.Moreover,poor embryonic development is consistently observed after intracytoplasmic sperm injection treatment using spermatozoa from the MFSD6L-deficient man and male mice.Collectively,our findings reveal that MFSD6L is required for the anchoring of sperm acrosome and head shaping.The deficiency of MFsD6L affects male fertility and causes oligoasthenoter-atozoospermia in humans and mice.展开更多
Background:The growth of the B-cell lymphoma subtype,Hodgkin lymphoma(HL),is associated with increased autophagy.A mycobacterial antigen,Ag85,has been reported to inhibit cell autophagy under a variety of conditions.W...Background:The growth of the B-cell lymphoma subtype,Hodgkin lymphoma(HL),is associated with increased autophagy.A mycobacterial antigen,Ag85,has been reported to inhibit cell autophagy under a variety of conditions.Whether Ag85 could inhibit autophagy in HL is unknown.Methods:Lymph node samples from patients with HL and healthy controls were collected to assess proliferation and autophagy.The human HL cell line,L-428,was cultured and subjected to Ag85B treatment.Autophagy in L-428 cells was evaluated through western blotting analysis,immunohistochemistry,and transmission electron microscopy.Apoptosis in these cells was measured using flow cytometry and western blotting.The associated signaling pathways were also analyzed utilizing western blotting.The in vivo impact of Ag85B was studied using BALB/c Nude mice xenografted with L-428 cells.Results:We observed increased proliferation and autophagy in primary lymphoma tissues of patients.Administration of Ag85B inhibited the proliferation and autophagy of HL cell lines.Moreover,Ag85B promoted apoptotic pathway activation in vitro,which might be associated with mitochondrial dysfunction.Mechanistically,Ag85B inhibits autophagy by activating the phosphatidylinositol-4,5-bisphosphate 3-kinase/protein kinase B/mechanistic target of rapamycin kinase(PI3K/AKT/mTOR)and mitogen-activated protein kinase(MAPK)pathways.Ag85B also inhibited lymphoma growth in mice xenografted with HL cell lines,but no potential toxicity was observed.Conclusion:Altogether,these results suggest that Ag85B inhibits HL growth via autophagy regulation.Current treatments for HL are associated with adverse events;therefore,Ag85B-mediated autophagy inhibition might be a promising strategy in to treat HL.展开更多
Aquaculture,a fast-growing sector,plays an important role in the supply of nutrient-rich food for humans.Selective breeding is a promising approach to ensure the development and sustainability of intensive aquaculture...Aquaculture,a fast-growing sector,plays an important role in the supply of nutrient-rich food for humans.Selective breeding is a promising approach to ensure the development and sustainability of intensive aquaculture systems by achieving cumulative and permanent improvements in desirable traits.The advancement of omics technologies offers unprecedented opportunities for genetic improvement,especially in the prioritization of SNPs to be used in the genomic selection and editing of economically important traits.This review highlights novel breeding strategies in aquaculture,emphasizing how multi-omics data can be integrated into selective breeding programs.Specifically,we discuss the current achievements in integrating functional data into conventional genomic prediction models and highlight the potential of artificial intelligence to efficiently map genes and predict phenotypes or genetic merit using multi-omics data.Ultimately,we discuss genome editing methods for their potential to fix existing alleles,introduce alleles from wild populations or related species,and create de novo alleles,with the general goal of improving commercially important traits in aquaculture species.展开更多
Human endogenous retroviruses(HERVs)comprise approximately 8%of the human genome,integrated into the dynamic regulatory network of cellular potency during early embryonic development.In recent studies,resurgent the tr...Human endogenous retroviruses(HERVs)comprise approximately 8%of the human genome,integrated into the dynamic regulatory network of cellular potency during early embryonic development.In recent studies,resurgent the transcriptional activity of HERVs has been frequently observed in many types of human cancers,suggesting their potential functions in the occurrence and progression of malignancy.However,a dedicated web resource for querying the relationship between the activation of HERVs and cancer development is lacking.Here,we construct a database to explore the sequence information,expression profiles,survival prognosis,and genetic interactions of HERVs in diverse cancer types.Our database currently contains RNA sequencing data of 580 HERVs across 16,246 samples,including that of 6478 tumoral and 634 normal tissues,932 cancer cell lines,as well as 151 early embryonic and 8051 human adult tissues.The primary goal is to provide an easily accessible and user-friendly database for professionals in the fields of bioinformatics,pathology,pharmacology,and related areas,enabling them to efficiently screen the activity of HERVs of interest in normal and cancerous tissues and evaluate the clinical relevance.The ERVcancer database is available at http://kyuanlab.com/ervcancer/.展开更多
Background: The objective of the present study was to estimate(co)variance components of female fertility traits in Chinese Holsteins, considering fertility traits in different parities as different traits. Data on 88...Background: The objective of the present study was to estimate(co)variance components of female fertility traits in Chinese Holsteins, considering fertility traits in different parities as different traits. Data on 88,647 females with 215,632 records(parities) were collected during 2000 to 2014 from 32 herds in the Sanyuan Lvhe Dairy Cattle Center, Beijing, China. The analyzed female fertility traits included interval from calving to first insemination, interval from first to last insemination, days open, conception rate at first insemination, number of inseminations per conception and non-return rates within 56 days after first insemination.Results: The descriptive statistics showed that the average fertility of heifers was superior to that of cows. Moreover,the genetic correlations between the performances of a trait in heifers and in cows were all moderate to high but far from one, which suggested that the performances of a trait in heifers and cows should be considered as different but genetically correlated traits in genetic evaluations. On the other hand, genetic correlations between performances of a trait in different parities of cows were greater than 0.87, with only a few exceptions, but variances were not homogeneous across parities for some traits. The estimated heritabilities of female fertility traits were low; all were below 0.049(except for interval from calving to first insemination). Additionally, the heritabilities of the heifer interval traits were lower than those of the corresponding cow interval traits. Moreover, the heritabilities of the interval traits were higher than those of the threshold traits when measuring similar fertility functions. In general, estimated genetic correlations between traits were highly consistent with the biological categories of the female fertility traits.Conclusions: Interval from calving to first insemination, interval from first to last insemination and non-return rates within 56 days after first insemination are recommended to be included in the selection index of the Chinese Holstein population. The parameters estimated in the present study will facilitate the development of a genetic evaluation system for female fertility traits to improve the reproduction efficiency of Chinese Holsteins.展开更多
Neuroinformatics is a fascinating research field that applies computational models and analytical tools to high dimensional experimental neuroscience data for a better understanding of how the brain functions or dysfu...Neuroinformatics is a fascinating research field that applies computational models and analytical tools to high dimensional experimental neuroscience data for a better understanding of how the brain functions or dysfunctions in brain diseases. Neuroinformaticians work in the intersection of neuroscience and informatics supporting the integration of various sub-disciplines（behavioural neuroscience, genetics, cognitive psychology, etc.） working on brain research. Neuroinformaticians are the pathway of information exchange between informaticians and clinicians for a better understanding of the outcome of computational models and the clinical interpretation of the analysis. Machine learning is one of the most significant computational developments in the last decade giving tools to neuroinformaticians and finally to radiologists and clinicians for an automatic and early diagnosis-prognosis of a brain disease. Random forest（RF） algorithm has been successfully applied to high-dimensional neuroimaging data for feature reduction and also has been applied to classify the clinical label of a subject using single or multi-modal neuroimaging datasets. Our aim was to review the studies where RF was applied to correctly predict the Alzheimer＇s disease（AD）, the conversion from mild cognitive impairment（MCI） and its robustness to overfitting, outliers and handling of non-linear data. Finally, we described our RF-based model that gave us the 1 ^（st） position in an international challenge for automated prediction of MCI from MRI data.展开更多
Postpartum psychosis is a severe psychiatric condition which affects 1-2 of every 1000 mothers shortly after childbirth. Whilst there is convincing evidence that the condition is precipitated by a complex combination ...Postpartum psychosis is a severe psychiatric condition which affects 1-2 of every 1000 mothers shortly after childbirth. Whilst there is convincing evidence that the condition is precipitated by a complex combination of biological and environmental factors, as yet the pathophysiological mechanisms remain extremely poorly defined. Here, I critically review approaches that have been, or are being, employed to identify and characterise such mechanisms; I also review a recent animal model approach, and describe a novel biological risk model that it suggests. Clarification of biological risk mechanisms underlying disorder risk should permit the identification of relevant predictive biomarkers which will ensure that "at risk" subjects receive prompt clinical intervention if required.展开更多
Ten novel polymorphic microsatellite loci were developed using an enrichment and colony hybridization protocol and characterized for the cuttlefish,Sepiella maindroni.Polymorphism was explored by using 30 individuals ...Ten novel polymorphic microsatellite loci were developed using an enrichment and colony hybridization protocol and characterized for the cuttlefish,Sepiella maindroni.Polymorphism was explored by using 30 individuals from the coastal waters of Zhanjiang,Guangdong province,China,in December 2007.The number of alleles ranged from 5 to 13.The ranges of observed and expected heterozygosity were from 0.578 9 to 1.000 0 and 0.682 8 to 0.925 7,respectively,and the average polymorphic information content （P IC） was 0.778 5.These microsatellite loci will certainly facilitate the detection of the genetic variation and population structure of S.maindroni.展开更多
Intensification in rice crop production is generally understood as requiring increased use of material inputs: water, inorganic fertilizers, and agrochemicals. However, this is not the only kind of intensification ava...Intensification in rice crop production is generally understood as requiring increased use of material inputs: water, inorganic fertilizers, and agrochemicals. However, this is not the only kind of intensification available. More productive crop phenotypes, with traits such as more resistance to biotic and abiotic stresses and shorter crop cycles, are possible through modifications in the management of rice plants, soil, water, and nutrients, reducing rather than increasing material inputs. Greater factor productivity can be achieved through the application of new knowledge and more skill, and(initially) more labor, as seen from the System of Rice Intensification(SRI), whose practices are used in various combinations by as many as 10 million farmers on about 4 million hectares in over 50 countries. The highest yields achieved with these management methods have come from hybrids and improved rice varieties, confirming the importance of making genetic improvements. However,unimproved varieties are also responsive to these changes, which induce better growth and functioning of rice root systems and more abundance, diversity, and activity of beneficial soil organisms. Some of these organisms as symbiotic endophytes can affect and enhance the expression of rice plants' genetic potential as well as their phenotypic resilience to multiple stresses, including those of climate change. SRI experience and data suggest that decades of plant breeding have been selecting for the best crop genetic endowments under suboptimal growing conditions, with crowding of plants that impedes their photosynthesis and growth, flooding of rice paddies that causes roots to degenerate and forgoes benefits derived from aerobic soil organisms, and overuse of agrochemicals that adversely affect these organisms as well as soil and human health. This review paper reports evidence from research in India and Indonesia that changes in crop and water management can improve the expression of rice plants' genetic potential, thereby creating more productive and robustphenotypes from given rice genotypes. Data indicate that increased plant density does not necessarily enhance crop yield potential, as classical breeding methods suggest. Developing cultivars that can achieve their higher productivity under a wide range of plant densities—breeding for density-neutral cultivars using alternative selection strategies—will enable more effective exploitation of available crop growth resources. Density-neutral cultivars that achieve high productivity under ample environmental growth resources can also achieve optimal productivity under limited resources, where lower densities can avert crop failure due to overcrowding. This will become more important to the extent that climatic and other factors become more adverse to crop production. Focusing more on which management practices can evoke the most productive and robust phenotypes from given genotypes is important for rice breeding and improvement programs since it is phenotypes that feed our human populations.展开更多
Like the wars predating the First World War where human foot soldiers were deemed tools in the battlefield against an enemy, so too are the host immune cells of a patient battling a malignant gastric cancer. Indeed, t...Like the wars predating the First World War where human foot soldiers were deemed tools in the battlefield against an enemy, so too are the host immune cells of a patient battling a malignant gastric cancer. Indeed, the tumour microenvironment resembles a battlefield, where the patient's immune cells are the defence against invading tumour cells. However, the relationship between different immune components of the host response to cancer is more complex than an "us against them" model. Components of the immune system inadvertently work against the interests of the host and become pro-tumourigenic while other components soldier on against the common enemy – the tumour cell.展开更多
Date palm(Phoenix dactylifera),one of the most ancient crops,is grown commercially in>30 countries.Using whole plastome assemblies,phylogenetic analyses revealed that cultivated date palm accessions share the same ...Date palm(Phoenix dactylifera),one of the most ancient crops,is grown commercially in>30 countries.Using whole plastome assemblies,phylogenetic analyses revealed that cultivated date palm accessions share the same clade with Phoenix sylvestris,Phoenix pusilla and Phoenix acaulis,which are native to the Indian subcontinent,and Phoenix caespitosa that is native to the Arabian Peninsula and the deserts of Somalia.Analysis of genetic diversity and genetic relationships among date palm accessions from 13 producing countries involved 195 date palm accessions that were genotyped at 19 microsatellite loci.Extensive genetic diversity was observed,with many accessions heterozygous for most markers in this clonally propagated crop.The average number of alleles per locus(42.1),expected heterozygosity(0.8),observed heterozygosity(0.47)and fixation indices(FST=0.42)demonstrated substantial genetic diversity and population structure.Iraqi accessions were found to have the richest allelic diversity,and the most private alleles.The model-based Bayesian method indicated that these accessions could be broadly divided into two structure groups,one group with predominantly African accessions and another predominantly Asian.Some germplasm,especially from Tunisia and Iraq,deviated from this generalization.Many accessions in the STRUCTURE-derived groups were found to be genetic admixtures,with gene flow between Asian and African groups.Indian and Pakistani date palms were found to be most closely related to North African germplasm.展开更多
Switchgrass is native to the tallgrass prairie of North America. It is self-incompatible and has varied ploidy levels from diploid（2x） to dodecaploid（12x） with tetraploid and octoploid being the most common. The h...Switchgrass is native to the tallgrass prairie of North America. It is self-incompatible and has varied ploidy levels from diploid（2x） to dodecaploid（12x） with tetraploid and octoploid being the most common. The high yielding potential and the ability to grow well in marginal lands make switchgrass an ideal species as a dedicated biomass producer for lignocellulosic ethanol production. Genetic transformation is an important tool for studying gene function and for germplasm improvement in switchgrass, the genome of which has been sequenced recently. This paper intends to provide a comprehensive review on plant regeneration and genetic transformation in switchgrass. We first reviewed the effect of explants, basal medium and plant growth regulators on plant regeneration in switchgrass, which is a prerequisite for genetic transformation. We then reviewed the progresses on genetic transformation with either the biolistic or Agrobacterium-mediated method in switchgrass, and discussed various techniques employed to improve the transformation efficiency. Finally we reviewed the recent progresses on the use of genetic transformation in improving biomass quality such as the reduction of lignin, and in increasing biomass yield in switchgrass. We also provided a future perspective on the use of new genome editing technologies in switchgrass and its potential impact on regulatory processes.展开更多
The genomic structures of Oryza sativa （A genome） and O. meyeriana （G genome） were comparatively studied using bicolor genomic in situ hybridization （GISH）. GISH was clearly able to discriminate between the chro...The genomic structures of Oryza sativa （A genome） and O. meyeriana （G genome） were comparatively studied using bicolor genomic in situ hybridization （GISH）. GISH was clearly able to discriminate between the chromosomes of O. sativa and O. meyeriana in the interspecific F1 hybrids without blocking DNA, and co-hybridization was hardly detected. The average mitotic chromosome length of O. meyeriana was found to be 1.69 times that of O. sativa. A comparison of 4,6-diamidino-2-phenylindole staining showed that the chromosomes of O. meyeriana were more extensively labelled, suggesting that the G genome is amplified with more repetitive sequences than the A genome. In interphase nuclei, 9-12 chromocenters were normally detected and nearly all the chromocenters constituted the G genome-specific DNA. More and larger chromocenters formed by chromatin compaction corresponding to the G genome were detected in the hybrid compared with its parents. During pachytene of the F1 hybrid, most chromosomes of A and G did not synapse each other except for 1-2 chromosomes paired at the end of their arms. At meiotic metaphase I, three types of chromosomal associations, i.e.O, sativa-O, sativa （A-A）, O. sativa-O, meyeriana （A-G） and O. meyeriana-O, meyeriana （G-G）, were observed in the F1 hybrid. The A-G chromosome pairing configurations included bivalents and trivalents. The results provided a foundation toward studying genome organization and evolution of O. meyeriana.展开更多
Background:Survival from birth to slaughter is an important economic trait in commercial pig productions.Increasing survival can improve both economic efficiency and animal welfare.The aim of this study is to explore ...Background:Survival from birth to slaughter is an important economic trait in commercial pig productions.Increasing survival can improve both economic efficiency and animal welfare.The aim of this study is to explore the impact of genotyping strategies and statistical models on the accuracy of genomic prediction for survival in pigs during the total growing period from birth to slaughter.Results:We simulated pig populations with different direct and maternal heritabilities and used a linear mixed model,a logit model,and a probit model to predict genomic breeding values of pig survival based on data of individual survival records with binary outcomes(0,1).The results show that in the case of only alive animals having genotype data,unbiased genomic predictions can be achieved when using variances estimated from pedigreebased model.Models using genomic information achieved up to 59.2%higher accuracy of estimated breeding value compared to pedigree-based model,dependent on genotyping scenarios.The scenario of genotyping all individuals,both dead and alive individuals,obtained the highest accuracy.When an equal number of individuals(80%)were genotyped,random sample of individuals with genotypes achieved higher accuracy than only alive individuals with genotypes.The linear model,logit model and probit model achieved similar accuracy.Conclusions:Our conclusion is that genomic prediction of pig survival is feasible in the situation that only alive pigs have genotypes,but genomic information of dead individuals can increase accuracy of genomic prediction by 2.06%to 6.04%.展开更多
文摘Journal of Genetics and Genomics(JGG),launched in 1974,celebrates its 50th birthday in 2023.With continuous support from our authors,reviewers,readers,and the editorial board,JGG has made remarkable progress in the past year by publishing 122 papers covering major disciplines in life sciences and medical genetics with exciting discoveries.It is worthwhile to note that we have recruited 66 young talents to join JGG as junior editors,resulting in significant improvement in manuscript evaluation and journal promotion.Here,we summarize major progresses reported in JGG in 2023 fromaneditorial view.
基金supported by the National Science Foundation(NSF),Award Number 1557995(IS,AZZ)IS was partially supported by the U.S.Department of Agriculture's National Institute of Food and Agriculture(USDA-NIFA)Hatch project CA-D-PPA-2739-H.
文摘Fungi are a diverse kingdom characterized by remarkable genomic plasticity that facilitates pathogenicity and adaptation to adverse environmental conditions.In this review,we delve into the dynamic organization of fungal genomes and its implications for host adaptation and antifungal resistance.We examine key features and the heterogeneity of genomes across different fungal species,including but not limited to their chromosome content,DNA composition,distribution and arrangement of their content across chromosomes,and other major traits.We further highlight how this variability in genomic traits influences their virulence and adaptation to adverse conditions.Fungal genomes exhibit large variations in size,gene content,and structural features,such as the abundance of transposable elements(TEs),compartmentalization into gene-rich and TE-rich regions,and the presence or absence of dispensable chromosomes.Genomic structural variations are equally diverse in fungi,ranging from whole-chromosome duplications that may enhance tolerance to antifungal compounds,to targeted deletion of effector encoding genes that may promote virulence.Finally,the often-overlooked fungal mitochondrial genomes can also affect virulence and resistance to fungicides.Such and other features of fungal genome organization are reviewed and discussed in the context of host-microbe interactions and antifungal resistance.
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.
文摘Pathogens are imminent threats to crop production. Among the management tools available to protect crops from diseases, the use of host-plant resistance had been hindered by a lack of tools and resources to identify resistance genes (R-genes). Genomic technologies have empowered acquisition of a new level and quality of information on plant-pathogen interactions. Next generation sequencing, differential transcriptome analysis, gene editing, and use of bioinformatics have greatly expanded the numbers of R-genes identified, enriched understanding of R-avirulence gene interactions, and disease diagnosis. In this review, we highlight the application of genomic technologies to identification of pathogen machinery for future improvement of host plant resistance.
基金supported by the National Key Research and Development Program of China(2022YFF1000204 and 2021YFD1300600)STI 2030-Major Projects(2023ZD04052)+2 种基金the Open Projects of Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province(JQLAB-KF-202301)China Agriculture Research Systems(CARS-40)the 2115 Talent Development Program of China Agricultural University。
文摘Chicken body weight(BW)is a critical trait in breeding.Although genetic variants associated with BW have been investigated by genome-wide association studies(GWAS),the contributions of causal variants and their molecular mechanisms remain largely unclear in chickens.In this study,we construct a comprehensive genetic atlas of chicken BW by integrative analysis of 30 age points and 5 quantitative trait loci(QTL)across 27 tissues.We find that chicken growth is a cumulative non-linear process,which can be divided into three distinct stages.Our GWAS analysis reveals that BW-related genetic variations show ordered patterns in these three stages.Genetic variations in chromosome 1 may regulate the overall growth process,likely by modulating the hypothalamus-specific expression of SLC25A30 and retina-specific expression of NEK3.Moreover,genetic variations in chromosome 4 and chromosome 27 may play dominant roles in regulating BW during Stage 2(8-22 weeks)and Stage 3(23-72 weeks),respectively.In summary,our study presents a comprehensive genetic atlas regulating developmental stage-specific changes in chicken BW,thus providing important resources for genomic selection in breeding programs.
基金supported by the National Natural Science Foundation of China[82070473,82170480,82030102]Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences[2021-I2M-1-010].
文摘Objective N6-methyladenosine(m^(6)A)is a common epigenetic modification in eukaryotes.In this study,we explore the potential impact of m^(6)A-associated single nucleotide polymorphisms(m^(6)A-SNPs)on heart failure(HF).Methods Data from genome-wide association studies(GWAS)investigating HF in humans and from m^(6)A-SNPs datasets were used to identify HF-associated m^(6)A-SNPs.Their functions were explored using expression quantitative trait locus(eQTL),gene expression,and gene enrichment analyses.Mediation protein quantitative trait locus(pQTL)-Mendelian randomization(MR)was used to investigate the potential mechanism between critical protein levels and risk factors for HF.Results We screened 44 HF-associated m^(6)A-SNPs,including 10 m^(6)A-SNPs that showed eQTL signals and differential expressions in HF.The SNP rs1801270 in CDKN1A showed the strongest association with HF(P=7.75×10^(−6)).Additionally,MR verified the genetic association between the CDKN1A protein and HF,as well as the mediating effect of blood pressure(BP)in this pathway.Higher circulating level of CDKN1A was associated with a lower risk of HF(odds ratio[OR]=0.82,95%confidence interval[CI]:0.69 to 0.99).The proportions of hypertension,systolic BP,and diastolic BP were 48.10%,28.94%,and 18.02%,respectively.Associations of PDIA6(P=1.30×10^(−2))and SMAD3(P=4.80×10^(−2))with HF were also detected.Conclusion Multiple HF-related m^(6)A-SNPs were identified in this study.Genetic associations of CDKN1A and other proteins with HF and its risk factors were demonstrated,providing new ideas for further exploration of the molecular mechanisms of HF.
基金This study was supported by the National Key Research and Development Program of China(2021YFC2701400 and 2023YFC2705600)the National Natural Science Foundation of China(32288101,32100480,32370654,82271639,32322017,and32200485).
文摘Oligoasthenoteratozoospermia is an important factor affecting male fertility and has been found to be associated with genetic factors.However,there are stll a proportion of oligoasthenoteratozoospermia cases that cannot be explained by known pathogenic genetic variants.Here,we perform genetic analyses and identify bi-allelic loss-of-function variants of MFSD6L from an oligoasthenoteratozoospermia-affected family.Mfsd6l knock-out male mice also present male subfertility with reduced sperm concentration,motility,and deformed acrosomes.Further mechanistic analyses reveal that MFsD6L,as an acrosome membrane protein,plays an important role in the formation of acrosome by interacting with the inner acrosomal membrane protein SPACA1.Moreover,poor embryonic development is consistently observed after intracytoplasmic sperm injection treatment using spermatozoa from the MFSD6L-deficient man and male mice.Collectively,our findings reveal that MFSD6L is required for the anchoring of sperm acrosome and head shaping.The deficiency of MFsD6L affects male fertility and causes oligoasthenoter-atozoospermia in humans and mice.
基金supported by the Natural Science Foundation of Xinjiang Uygur Autonomous Region of China(grant number 2022D01C739)the National Natural Science Foundation of China(grant numbers 82160031,82071276)the Key Research and Development Program of Xinjiang Uyghur Autonomous Region of China(grant number 2024B03038-1).
文摘Background:The growth of the B-cell lymphoma subtype,Hodgkin lymphoma(HL),is associated with increased autophagy.A mycobacterial antigen,Ag85,has been reported to inhibit cell autophagy under a variety of conditions.Whether Ag85 could inhibit autophagy in HL is unknown.Methods:Lymph node samples from patients with HL and healthy controls were collected to assess proliferation and autophagy.The human HL cell line,L-428,was cultured and subjected to Ag85B treatment.Autophagy in L-428 cells was evaluated through western blotting analysis,immunohistochemistry,and transmission electron microscopy.Apoptosis in these cells was measured using flow cytometry and western blotting.The associated signaling pathways were also analyzed utilizing western blotting.The in vivo impact of Ag85B was studied using BALB/c Nude mice xenografted with L-428 cells.Results:We observed increased proliferation and autophagy in primary lymphoma tissues of patients.Administration of Ag85B inhibited the proliferation and autophagy of HL cell lines.Moreover,Ag85B promoted apoptotic pathway activation in vitro,which might be associated with mitochondrial dysfunction.Mechanistically,Ag85B inhibits autophagy by activating the phosphatidylinositol-4,5-bisphosphate 3-kinase/protein kinase B/mechanistic target of rapamycin kinase(PI3K/AKT/mTOR)and mitogen-activated protein kinase(MAPK)pathways.Ag85B also inhibited lymphoma growth in mice xenografted with HL cell lines,but no potential toxicity was observed.Conclusion:Altogether,these results suggest that Ag85B inhibits HL growth via autophagy regulation.Current treatments for HL are associated with adverse events;therefore,Ag85B-mediated autophagy inhibition might be a promising strategy in to treat HL.
基金supported by the National Key Research and Development Program of China(2023YFD2400101)the Key R&D Project of Shandong Province(2022ZLGX01)+3 种基金the Key R&D Project of Hainan Province(ZDYF2024XDNY275)the Postdoctoral Fellowship Program of CPSF(GZC20232507)the China Postdoctoral Science Foundation funded project(343739)the Shandong Postdoctoral Science Foundation(SDBX2023014)。
文摘Aquaculture,a fast-growing sector,plays an important role in the supply of nutrient-rich food for humans.Selective breeding is a promising approach to ensure the development and sustainability of intensive aquaculture systems by achieving cumulative and permanent improvements in desirable traits.The advancement of omics technologies offers unprecedented opportunities for genetic improvement,especially in the prioritization of SNPs to be used in the genomic selection and editing of economically important traits.This review highlights novel breeding strategies in aquaculture,emphasizing how multi-omics data can be integrated into selective breeding programs.Specifically,we discuss the current achievements in integrating functional data into conventional genomic prediction models and highlight the potential of artificial intelligence to efficiently map genes and predict phenotypes or genetic merit using multi-omics data.Ultimately,we discuss genome editing methods for their potential to fix existing alleles,introduce alleles from wild populations or related species,and create de novo alleles,with the general goal of improving commercially important traits in aquaculture species.
基金supported by the National Natural Science Foundation of China(32370821,32170821,and 92153301 to K.Y)National Key Research and Development Program of China(2021YFC2701200)+2 种基金Department of Science&Technology of Hunan Province(2023RC1028,and 2023SK2091 to K.Y)Middle/Young aged Teachers'Research Ability Improvement Project of Guangxi Higher Education(2024KY0111 to X.L)Joint Project on Regional High-lncidence Diseases Research of Guangxi Natural Science Foundation(2023JJB140356 to X.L).
文摘Human endogenous retroviruses(HERVs)comprise approximately 8%of the human genome,integrated into the dynamic regulatory network of cellular potency during early embryonic development.In recent studies,resurgent the transcriptional activity of HERVs has been frequently observed in many types of human cancers,suggesting their potential functions in the occurrence and progression of malignancy.However,a dedicated web resource for querying the relationship between the activation of HERVs and cancer development is lacking.Here,we construct a database to explore the sequence information,expression profiles,survival prognosis,and genetic interactions of HERVs in diverse cancer types.Our database currently contains RNA sequencing data of 580 HERVs across 16,246 samples,including that of 6478 tumoral and 634 normal tissues,932 cancer cell lines,as well as 151 early embryonic and 8051 human adult tissues.The primary goal is to provide an easily accessible and user-friendly database for professionals in the fields of bioinformatics,pathology,pharmacology,and related areas,enabling them to efficiently screen the activity of HERVs of interest in normal and cancerous tissues and evaluate the clinical relevance.The ERVcancer database is available at http://kyuanlab.com/ervcancer/.
基金supported by the earmarked fund for the Modern Agro-industry Technology Research System(CARS-37)the Genomic Selection in Plants and Animals(Gen SAP)research project financed by the Danish Council of Strategic Research(Aarhus,Denmark)+1 种基金the Program for Changjiang Scholar and Innovation Research Team in University(IRT1191)provided by the China Scholarship Council(CSC)
文摘Background: The objective of the present study was to estimate(co)variance components of female fertility traits in Chinese Holsteins, considering fertility traits in different parities as different traits. Data on 88,647 females with 215,632 records(parities) were collected during 2000 to 2014 from 32 herds in the Sanyuan Lvhe Dairy Cattle Center, Beijing, China. The analyzed female fertility traits included interval from calving to first insemination, interval from first to last insemination, days open, conception rate at first insemination, number of inseminations per conception and non-return rates within 56 days after first insemination.Results: The descriptive statistics showed that the average fertility of heifers was superior to that of cows. Moreover,the genetic correlations between the performances of a trait in heifers and in cows were all moderate to high but far from one, which suggested that the performances of a trait in heifers and cows should be considered as different but genetically correlated traits in genetic evaluations. On the other hand, genetic correlations between performances of a trait in different parities of cows were greater than 0.87, with only a few exceptions, but variances were not homogeneous across parities for some traits. The estimated heritabilities of female fertility traits were low; all were below 0.049(except for interval from calving to first insemination). Additionally, the heritabilities of the heifer interval traits were lower than those of the corresponding cow interval traits. Moreover, the heritabilities of the interval traits were higher than those of the threshold traits when measuring similar fertility functions. In general, estimated genetic correlations between traits were highly consistent with the biological categories of the female fertility traits.Conclusions: Interval from calving to first insemination, interval from first to last insemination and non-return rates within 56 days after first insemination are recommended to be included in the selection index of the Chinese Holstein population. The parameters estimated in the present study will facilitate the development of a genetic evaluation system for female fertility traits to improve the reproduction efficiency of Chinese Holsteins.
基金supported by Medical Research Council(MRC)grant MR/K004360/1 to SIDMARIE CURIE COFUND EU-UK Research Fellowship to SID
文摘Neuroinformatics is a fascinating research field that applies computational models and analytical tools to high dimensional experimental neuroscience data for a better understanding of how the brain functions or dysfunctions in brain diseases. Neuroinformaticians work in the intersection of neuroscience and informatics supporting the integration of various sub-disciplines（behavioural neuroscience, genetics, cognitive psychology, etc.） working on brain research. Neuroinformaticians are the pathway of information exchange between informaticians and clinicians for a better understanding of the outcome of computational models and the clinical interpretation of the analysis. Machine learning is one of the most significant computational developments in the last decade giving tools to neuroinformaticians and finally to radiologists and clinicians for an automatic and early diagnosis-prognosis of a brain disease. Random forest（RF） algorithm has been successfully applied to high-dimensional neuroimaging data for feature reduction and also has been applied to classify the clinical label of a subject using single or multi-modal neuroimaging datasets. Our aim was to review the studies where RF was applied to correctly predict the Alzheimer＇s disease（AD）, the conversion from mild cognitive impairment（MCI） and its robustness to overfitting, outliers and handling of non-linear data. Finally, we described our RF-based model that gave us the 1 ^（st） position in an international challenge for automated prediction of MCI from MRI data.
基金Supported by Medical Research Council Centre for Neuro-psychiatric Genetics and Genomics,No.MR/L010305/1
文摘Postpartum psychosis is a severe psychiatric condition which affects 1-2 of every 1000 mothers shortly after childbirth. Whilst there is convincing evidence that the condition is precipitated by a complex combination of biological and environmental factors, as yet the pathophysiological mechanisms remain extremely poorly defined. Here, I critically review approaches that have been, or are being, employed to identify and characterise such mechanisms; I also review a recent animal model approach, and describe a novel biological risk model that it suggests. Clarification of biological risk mechanisms underlying disorder risk should permit the identification of relevant predictive biomarkers which will ensure that "at risk" subjects receive prompt clinical intervention if required.
基金The National Key Technology R & D Program of China under contract No.2007BAD43B05the Key Science & Technology Specific Projects of Zhejiang Province under contract No.2007C12062the National Natural Science Foundation of China under contract No.31001109
文摘Ten novel polymorphic microsatellite loci were developed using an enrichment and colony hybridization protocol and characterized for the cuttlefish,Sepiella maindroni.Polymorphism was explored by using 30 individuals from the coastal waters of Zhanjiang,Guangdong province,China,in December 2007.The number of alleles ranged from 5 to 13.The ranges of observed and expected heterozygosity were from 0.578 9 to 1.000 0 and 0.682 8 to 0.925 7,respectively,and the average polymorphic information content （P IC） was 0.778 5.These microsatellite loci will certainly facilitate the detection of the genetic variation and population structure of S.maindroni.
文摘Intensification in rice crop production is generally understood as requiring increased use of material inputs: water, inorganic fertilizers, and agrochemicals. However, this is not the only kind of intensification available. More productive crop phenotypes, with traits such as more resistance to biotic and abiotic stresses and shorter crop cycles, are possible through modifications in the management of rice plants, soil, water, and nutrients, reducing rather than increasing material inputs. Greater factor productivity can be achieved through the application of new knowledge and more skill, and(initially) more labor, as seen from the System of Rice Intensification(SRI), whose practices are used in various combinations by as many as 10 million farmers on about 4 million hectares in over 50 countries. The highest yields achieved with these management methods have come from hybrids and improved rice varieties, confirming the importance of making genetic improvements. However,unimproved varieties are also responsive to these changes, which induce better growth and functioning of rice root systems and more abundance, diversity, and activity of beneficial soil organisms. Some of these organisms as symbiotic endophytes can affect and enhance the expression of rice plants' genetic potential as well as their phenotypic resilience to multiple stresses, including those of climate change. SRI experience and data suggest that decades of plant breeding have been selecting for the best crop genetic endowments under suboptimal growing conditions, with crowding of plants that impedes their photosynthesis and growth, flooding of rice paddies that causes roots to degenerate and forgoes benefits derived from aerobic soil organisms, and overuse of agrochemicals that adversely affect these organisms as well as soil and human health. This review paper reports evidence from research in India and Indonesia that changes in crop and water management can improve the expression of rice plants' genetic potential, thereby creating more productive and robustphenotypes from given rice genotypes. Data indicate that increased plant density does not necessarily enhance crop yield potential, as classical breeding methods suggest. Developing cultivars that can achieve their higher productivity under a wide range of plant densities—breeding for density-neutral cultivars using alternative selection strategies—will enable more effective exploitation of available crop growth resources. Density-neutral cultivars that achieve high productivity under ample environmental growth resources can also achieve optimal productivity under limited resources, where lower densities can avert crop failure due to overcrowding. This will become more important to the extent that climatic and other factors become more adverse to crop production. Focusing more on which management practices can evoke the most productive and robust phenotypes from given genotypes is important for rice breeding and improvement programs since it is phenotypes that feed our human populations.
文摘Like the wars predating the First World War where human foot soldiers were deemed tools in the battlefield against an enemy, so too are the host immune cells of a patient battling a malignant gastric cancer. Indeed, the tumour microenvironment resembles a battlefield, where the patient's immune cells are the defence against invading tumour cells. However, the relationship between different immune components of the host response to cancer is more complex than an "us against them" model. Components of the immune system inadvertently work against the interests of the host and become pro-tumourigenic while other components soldier on against the common enemy – the tumour cell.
基金funded by endowment funds from the University of Georgia Giles Professorship and the Georgia Research Alliance
文摘Date palm(Phoenix dactylifera),one of the most ancient crops,is grown commercially in>30 countries.Using whole plastome assemblies,phylogenetic analyses revealed that cultivated date palm accessions share the same clade with Phoenix sylvestris,Phoenix pusilla and Phoenix acaulis,which are native to the Indian subcontinent,and Phoenix caespitosa that is native to the Arabian Peninsula and the deserts of Somalia.Analysis of genetic diversity and genetic relationships among date palm accessions from 13 producing countries involved 195 date palm accessions that were genotyped at 19 microsatellite loci.Extensive genetic diversity was observed,with many accessions heterozygous for most markers in this clonally propagated crop.The average number of alleles per locus(42.1),expected heterozygosity(0.8),observed heterozygosity(0.47)and fixation indices(FST=0.42)demonstrated substantial genetic diversity and population structure.Iraqi accessions were found to have the richest allelic diversity,and the most private alleles.The model-based Bayesian method indicated that these accessions could be broadly divided into two structure groups,one group with predominantly African accessions and another predominantly Asian.Some germplasm,especially from Tunisia and Iraq,deviated from this generalization.Many accessions in the STRUCTURE-derived groups were found to be genetic admixtures,with gene flow between Asian and African groups.Indian and Pakistani date palms were found to be most closely related to North African germplasm.
基金supported by a grant from the Bill Melinda Gates FoundationNational Institute of Food and Agriculture of the United States Department of Agriculture for support (Award number 2013-33522-21091)
文摘Switchgrass is native to the tallgrass prairie of North America. It is self-incompatible and has varied ploidy levels from diploid（2x） to dodecaploid（12x） with tetraploid and octoploid being the most common. The high yielding potential and the ability to grow well in marginal lands make switchgrass an ideal species as a dedicated biomass producer for lignocellulosic ethanol production. Genetic transformation is an important tool for studying gene function and for germplasm improvement in switchgrass, the genome of which has been sequenced recently. This paper intends to provide a comprehensive review on plant regeneration and genetic transformation in switchgrass. We first reviewed the effect of explants, basal medium and plant growth regulators on plant regeneration in switchgrass, which is a prerequisite for genetic transformation. We then reviewed the progresses on genetic transformation with either the biolistic or Agrobacterium-mediated method in switchgrass, and discussed various techniques employed to improve the transformation efficiency. Finally we reviewed the recent progresses on the use of genetic transformation in improving biomass quality such as the reduction of lignin, and in increasing biomass yield in switchgrass. We also provided a future perspective on the use of new genome editing technologies in switchgrass and its potential impact on regulatory processes.
文摘The genomic structures of Oryza sativa （A genome） and O. meyeriana （G genome） were comparatively studied using bicolor genomic in situ hybridization （GISH）. GISH was clearly able to discriminate between the chromosomes of O. sativa and O. meyeriana in the interspecific F1 hybrids without blocking DNA, and co-hybridization was hardly detected. The average mitotic chromosome length of O. meyeriana was found to be 1.69 times that of O. sativa. A comparison of 4,6-diamidino-2-phenylindole staining showed that the chromosomes of O. meyeriana were more extensively labelled, suggesting that the G genome is amplified with more repetitive sequences than the A genome. In interphase nuclei, 9-12 chromocenters were normally detected and nearly all the chromocenters constituted the G genome-specific DNA. More and larger chromocenters formed by chromatin compaction corresponding to the G genome were detected in the hybrid compared with its parents. During pachytene of the F1 hybrid, most chromosomes of A and G did not synapse each other except for 1-2 chromosomes paired at the end of their arms. At meiotic metaphase I, three types of chromosomal associations, i.e.O, sativa-O, sativa （A-A）, O. sativa-O, meyeriana （A-G） and O. meyeriana-O, meyeriana （G-G）, were observed in the F1 hybrid. The A-G chromosome pairing configurations included bivalents and trivalents. The results provided a foundation toward studying genome organization and evolution of O. meyeriana.
基金funded by the"Genetic improvement of pig survival"project from Danish Pig Levy Foundation (Aarhus,Denmark)The China Scholarship Council (CSC)for providing scholarship to the first author。
文摘Background:Survival from birth to slaughter is an important economic trait in commercial pig productions.Increasing survival can improve both economic efficiency and animal welfare.The aim of this study is to explore the impact of genotyping strategies and statistical models on the accuracy of genomic prediction for survival in pigs during the total growing period from birth to slaughter.Results:We simulated pig populations with different direct and maternal heritabilities and used a linear mixed model,a logit model,and a probit model to predict genomic breeding values of pig survival based on data of individual survival records with binary outcomes(0,1).The results show that in the case of only alive animals having genotype data,unbiased genomic predictions can be achieved when using variances estimated from pedigreebased model.Models using genomic information achieved up to 59.2%higher accuracy of estimated breeding value compared to pedigree-based model,dependent on genotyping scenarios.The scenario of genotyping all individuals,both dead and alive individuals,obtained the highest accuracy.When an equal number of individuals(80%)were genotyped,random sample of individuals with genotypes achieved higher accuracy than only alive individuals with genotypes.The linear model,logit model and probit model achieved similar accuracy.Conclusions:Our conclusion is that genomic prediction of pig survival is feasible in the situation that only alive pigs have genotypes,but genomic information of dead individuals can increase accuracy of genomic prediction by 2.06%to 6.04%.
