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copy number variation of B1 controls awn length in wheat

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The Crop Journal 2023年第3期11卷 817-824页

作者： Jinlong Li Xin Xin Fangyao Sun Zhenzhen Zhu Xiangru Xu Jiatian Yang Xiaoming Xie Jiazheng Yu Xiaobo Wang Sen Li Shilin Tian Baoyun Li Chaojie Xie Jun Ma college of Agronomy and Biotechnology China Agricultural UniversityBeijing 100193China State Key Laboratory of Crop Biology College of Life SciencesShandong Agricultural UniversityTai’an 271018ShandongChina novogene bioinformatics technology co. Ltd.Beijing 100015China

Wheat awns contribute to photosynthesis and grain production.In this study,an F2population and F2:3families from a cross between the awned line 7D12 and the Chinese awnless variety Shiyou 20(SY20)were used to identify loci associated with awn length.Bulked-segregant RNA sequencing and linkage mapping identified a single dominant locus in a 0.3 cM interval on chromosome 5AL.Five genes were in the interval,including the recently cloned awn inhibitor B1.Although a single copy of the B1 gene was detected in 7D12,SY20 carried five copies of the gene.Increased copy number of B1 in SY20enhanced gene expression.Based on sequence variation among the promoter regions of five B1 gene copies in SY20,two dominant markers were developed and found to cosegregate with B1 in a population of 931 wheat accessions.All 77 awnless accessions harbored sequence variations in the B1 promoter regions similar to those of SY20 and thus carried multiple copies of the gene,whereas 15 randomly selected awned wheats carried only one copy.These results suggest that an increase in copy number of the B1 gene is associated with inhibition of awn length.

关键词： Wheat Awn Awnless,B1 gene copy number variation

Single cell transcriptomic analysis identifies novel vascular smooth muscle subsets under high hydrostatic pressure

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Science China(Life Sciences) 2021年第10期64卷 1677-1690页

作者： Zhenzhen Chen Haizeng Zhang Yingnan Bai Changting Cui Shuangyue Li Wenjie Wang Yue Deng Qiannan Gao Lu Wang Wei Qi Lijun Zhang Yan Yang Bin Geng Jun Cai Hypertension Center Department of Cardiac SurgeryFuwai HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeState Key Laboratory of Cardiovascular DiseaseNational Center for Cardiovascular DiseasesBeijing 100191China novogene bioinformatics technology co. Ltd.Beijing 100015China

Although some co-risk factors and hemodynamic alterations are involved in hypertension progression,their direct biomechanical effects are unclear.Here,we constructed a high-hydrostatic-pressure cell-culture system to imitate constant hypertension and identified novel molecular classifications of human aortic smooth muscle cells(HASMCs)by single-cell transcriptome analysis.Under 100-mmHg(analogous to healthy human blood pressure)or 200-mmHg(analogous to hypertension)hydrostatic pressure for 48 h,HASMCs showed six distinct vascular SMC(VSMC)clusters according to differential gene expression and gene ontology enrichment analysis.Especially,two novel HASMC subsets were identified,named the inflammatory subset,with CXCL2,CXCL3 and CCL2 as markers,and the endothelial-function inhibitory subset,with AKR1C2,AKR1C3,SERPINF1 as markers.The inflammatory subset promoted CXCL2&3 and CCL2 chemokine expression and secretion,triggering monocyte migration;the endothelial-function inhibitory subset secreted SERPINF1 and accelerated prostaglandin F2αgeneration to inhibit angiogenesis.The expression of the two VSMC subsets was greatly increased in arterial media from patients with hypertension and experimental animal models of hypertension.collectively,we identified high hydrostatic pressure directly driving VSMCs into two new subsets,promoting or exacerbating endothelial dysfunction,thereby contributing to the pathogenesis of cardiovascular diseases.

关键词： single cell RNA-seq hypertension VSMCs hydrostatic pressure

Genome-Wide Dissection of Quan 9311A Breeding Process and Application Advantages

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Rice science 2023年第6期30卷 552-566页

作者： LI Qianlong FENG Qi WANG Heqin KANG Yunhai ZHANG conghe DU Ming ZHANG Yunhu WANG Hui CHEN Jinjie HAN Bin FANG Yu WANG Ahong Center for Excellence in Molecular Plant Sciences Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200032China Shanghai ZKW Molecular Breeding technology co.ltd Shanghai 200234China Win-all Hi-tech Seed co.ltd/Key Laboratory for New Variety Creative of Hybrid Rice Ministry of Agriculture and Rural AffairsHefei 230088China Institute of Crop Science&Institute of bioinformatics Zhejiang UniversityHangzhou 310058China

Germplasm resource innovation is a crucial factor for cultivar development,particularly within the context of hybrid rice breeding based on the three-line system.Quan 9311A,a cytoplasmic male sterile(CMS)line,has been successfully cultivated using rice restoration materials and extensively employed as a female parent in hybrid breeding program in China.This line was developed by crossing the CMS line Zhong 9A with a two-line restorer line 93-11,with the intention of eliminating the restoring ability of 93-11 while retaining the sterility gene WA352c from Zhong 9A.Quan 9311A effectively amalgamates the most favorable agronomic traits from both parental lines.In this study,the relationship between phenotypic characteristics and the known functional genes of Quan 9311A were analyzed using the rice genome navigation technology based on whole-genome sequencing.The findings revealed that Quan 9311A harbors multiple superior alleles from both 93-11 and Zhong 9A,providing exceptional agronomic traits that are unavailable in earlier CMS lines.Despite the removal of the fertility restorer gene Rf3 from 93-11,numerous chromosomal segments from 93-11 persist in the Quan 9311A genome.Furthermore,the hybrid rice Quanyousimiao(QYSM)and the restorer line Wushansimiao(WSSM)were used as examples to illustrate the important role of Quan 9311A as the female parent in heterosis.It was found that QYSM carries a great number of superior alleles,which accounts for its high grain yield and wide adaptability.These insights not only advanced the utilization of hybrid rice pairing groups but also provided guidance for future breeding endeavors.The study introduced innovative concepts to further integrate genomics with traditional breeding techniques.Ultimately,Quan 9311A signified a significant milestone in rice breeding technology,opening up novel avenues for hybrid rice development.

关键词： breeding hybrid rice phenotype quantitative trait nucleotide locus rice genome navigation system whole-genome sequencing

High-purity magnesium pin enhances bone consolidation in distraction osteogenesis via regulating Ptch protein activating Hedgehog-alternative Wnt signaling

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Bioactive Materials 2021年第6期6卷 1563-1574页

作者： Musha Hamushan Weijie Cai Yubo Zhang Zun Ren Jiafei Du Shaoxiang Zhang Changli Zhao Pengfei Cheng Xiaonong Zhang Hao Shen Pei Han Orthopaedic Department Shanghai Jiao Tong University Affiliated Sixth People’s HospitalShanghai200233China Suzhou Origin Medical technology co.ltd Suzhou215513China School of Materials Science and Engineering Shanghai Jiao Tong UniversityShanghai200240China

Magnesium alloys are promising biomaterials for orthopedic implants because of their degradability,osteogenic effects,and biocompatibility.Magnesium has been proven to promote distraction osteogenesis.However,its mechanism of promoting distraction osteogenesis is not thoroughly studied.In this work,a high-purity magnesium pin developed and applied in rat femur distraction osteogenesis.Mechanical test,radiological and histological analysis suggested that high-purity magnesium pin can promote distraction osteogenesis and shorten the consolidation time.Further RNA sequencing investigation found that alternative Wnt signaling was activated.In further bioinformatics analysis,it was found that the Hedgehog pathway is the upstream signaling pathway of the alternative Wnt pathway.We found that Ptch protein is a potential target of magnesium and verified by molecular dynamics that magnesium ions can bind to Ptch protein.In conclusion,HP Mg implants have the potential to enhance bone consolidation in the DO application,and this process might be via regulating Ptch protein activating Hedgehog-alternative Wnt signaling.

关键词： magnesium purity consolidation

The First High-quality Reference Genome of Sika Deer Provides Insights into High-tannin Adaptation

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Genomics, Proteomics & bioinformatics 2023年第1期21卷 203-215页

作者： Xiumei Xing Cheng Ai Tianjiao Wang Yang Li Huitao Liu Pengfei Hu Guiwu Wang Huamiao Liu Hongliang Wang Ranran Zhang Junjun Zheng Xiaobo Wang Lei Wang Yuxiao Chang Qian Qian Jinghua Yu Lixin Tang Shigang Wu Xiujuan Shao Alun Li Peng Cui Wei Zhan Sheng Zhao Zhichao Wu Xiqun Shao Yimeng Dong Min Rong Yihong Tan Xuezhe Cui Shuzhuo Chang Xingchao Song Tongao Yang Limin Sun Yan Ju Pei Zhao Huanhuan Fan Ying Liu Xinhui Wang Wanyun Yang Min Yang Tao Wei Shanshan Song Jiaping Xu Zhigang Yue Qiqi Liang Chunyi Li Jue Ruan Fuhe Yang Key Laboratory of Genetics Breeding and Reproduction of Special Economic AnimalsMinistry of Agriculture and Rural AffairsInstitute of Special Animal and Plant SciencesChinese Academy of Agricultural SciencesChangchun 130112China Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China CAS Key Laboratory of Forest Ecology and Management Institute of Applied EcologyChinese Academy of SciencesShenyang 110016China Annoroad Gene technology(Beijing)co. LtdBeijing 100176China novogene bioinformatics Institute Beijing 100083China

Sika deer are known to prefer oak leaves,which are rich in tannins and toxic to most mammals;however,the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear.In identifying the mechanism responsible for the tolerance of a highly toxic diet,we have made a major advancement by explaining the genome of sika deer.We generated the first high-quality,chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments.comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food,especially the expansion of the UGT family 2 subfamily B of UGT genes.The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation.Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.

关键词： Sika deer Whole-genome sequencing Chromosome-scale assembly Oak leaf Tannin tolerance

The First Crested Duck Genome Reveals Clues to Genetic compensation and Crest Cushion Formation

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Genomics, Proteomics & bioinformatics 2023年第3期21卷 483-500页

作者： Guobin Chang Xiaoya Yuan Qixin Guo Hao Bai Xiaofang Cao Meng Liu Zhixiu Wang Bichun Li Shasha Wang Yong Jiang Zhiquan Wang Yang Zhang Qi Xu Qianqian Song Rui Pan Lingling Qiu Tiantian Gu Xinsheng Wu Yulin Bi Zhengfeng Cao Yu Zhang Yang Chen Hong Li Jianfeng Liu Wangcheng Dai Guohong Chen Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province College of Animal Science and TechnologyYangzhou UniversityYangzhou 225009China Joint International Research Laboratory of Agriculture and Agri-Product Safety Ministry of EducationInstitutes of Agricultural Science and Technology DevelopmentYangzhou UniversityYangzhou 225009China novogene bioinformatics Institute Beijing 100080China Department of Agricultural Foodand Nutritional SciencesUniversity of AlbertaEdmontonAB T6G 2R3Canada college of Animal Science and technology China Agricultural UniversityBeijing 100091China Zhenjiang Tiancheng Agricultural Science and technology co. LtdZhenjiang 210034China

The Chinese crested(CC)duck is a unique indigenous waterfowl breed,which has a crest cushion that affects its survival rate.Therefore,the CC duck is an ideal model to investigate the genetic compensation response to maintain genetic stability.In the present study,we first generated a chromosome-level genome of CC ducks.comparative genomics revealed that genes related to tissue repair,immune function,and tumors were under strong positive selection,indicating that these adaptive changes might enhance cancer resistance and immune response to maintain the genetic stability of CC ducks.We also assembled a Chinese spot-billed(Csp-b)duck genome,and detected the structural variations(SVs)in the genome assemblies of three ducks(i.e.,CC duck,Csp-b duck,and Peking duck).Functional analysis revealed that several SVs were related to the immune system of CC ducks,further strongly suggesting that genetic compensation in the anti-tumor and immune systems supports the survival of CC ducks.Moreover,we confirmed that the CC duck originated from the mallard ducks.Finally,we revealed the physiological and genetic basis of crest traits and identified a causative mutation in TAS2R40 that leads to crest formation.Overall,the findings of this study provide new insights into the role of genetic compensation in adaptive evolution.

关键词： Genetic compensation Genome assembly Chinese crested duck Crest cushion Genome adaptive evolution

Differential protein expression in patients with urosepsis

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Chinese Journal of Traumatology 2018年第6期21卷 316-322页

作者： Xu-Kai Yang Nan Wang Cheng Yang Yang-Min Wang Tuan-Jie Che Department of Urology Lanzhou General Hospital PLALanzhou 730050China Department of Infection Xi'an Central HospitalXi'an 710033China Student teams Basic Medical CollegeThe Fourth Military Medical UniversityXi'an710032 China Lanzhou Baiyuan Gene technology co.ltd Lanzhou 730000China

Purpose:Urosepsis in adults comprises approximately 25% of all sepsis cases, and is due to complicated urinary tract infections in most cases. However, its mechanism is not fully clarified. Urosepsis is a very complicated disease with no effective strategy for early diagnosis and treatment. This study aimed to identify possible target-related proteins involved in urosepsis using proteomics and establish possible networks using bioinformatics.Methods:Fifty patients admitted to the Urology Unit of Lanzhou General PLA (Lanzhou, China), from October 2012 to October 2015, were enrolled in this study. The patients were further divided into shock and matched-pair non-shock groups. 2-DE technique, mass spectrometry and database search were used to detect differentially expressed proteins in serum from the two groups.Results:Six proteins were found at higher levels in the shock group compared with non-shock individuals, including serum amyloid A-1 protein (SAA1), apolipoprotein L1 (APOL1), ceruloplasmin (CP), haptoglobin (HP), antithrombin-III (SERPINC1) and prothrombin (F2), while three proteins showed lower levels, including serotransferrin (TF), transthyretin (TTR) and alpha-2-macroglobulin (A2M).conclusion:Nine proteins were differentially expressed between uroseptic patients (non-shock groups) and severe uroseptic patients (shock groups), compared with non-shock groups, serum SAA1, APOL1,CP, HP, SERPINC1 and F2 at higher levels, while TF, TTR and A2M at lower levels in shock groups.these proteins were mainly involved in platelet activation, signaling and aggregation, acute phase protein pathway, lipid homeostasis, and iron ion transport, deserve further research as potential candidates for early diagnosis and treatment. (The conclusion seems too simple and vague, please re-write it. You may focus at what proteins have been expressed and introduce more detail about its significance.)

关键词： Protein expression Urosepsis Proteomics

Novel hydroxymethylbilane synthase gene mutation identified and confirmed in a woman with acute intermittent porphyria:A case report

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World Journal of Clinical Cases 2022年第33期10卷 12319-12327页

作者： Yu-Qing Zhou Xiao-Qing Wang Jun Jiang Shu-Ling Huang Zhuo-Jin Dai Qiao-Qiong Kong Department of Endocrinology Dongguan Hospital of Traditional Chinese MedicineDongguan 523003Guangdong ProvinceChina Department of Science and technology ServicesChina Beijing Macro and Micro Test Biotech co.ltd Beijing 100318China The First Clinical Medical college Guangdong Medical UniversityZhanjiang 523003Guangdong ProvinceChina Department of Medicine Wanjiang People's Hospital of DongguanDongguan 523003Guangdong ProvinceChina

BACKGROUND Acute intermittent porphyria(AIP)is a rare autosomal dominant porphyrin metabolic disease caused by a mutation in the hydroxymethylbilane synthase(HMBS)gene.This study aimed to explore the clinical manifestations of a patient with AIP,to identify a novel HMBS gene mutation in the proband and some of her family members,and to confirm the pathogenicity of the variant.CASE SUMMARY A 22-year-old Chinese woman developed severe abdominal pain,lumbago,sinus tachycardia,epileptic seizure,hypertension,and weakness in lower limbs in March,2018.Biochemical examinations indicated hypohepatia and hyponatremia.Her last menstrual period was 45 d prior to admission,and she was unaware of the pregnancy,which was confirmed by a pregnancy test after admission.Sunlight exposure of her urine sample for 1 h turned it from yellow to wine red.Urinary porphyrin test result was positive.Based on these clinical manifestations,AIP was diagnosed.After increasing her daily glucose intake(250–300 g/d),abdominal pain was partially relieved.Three days after hospitalization,spontaneous vaginal bleeding occurred,which was confirmed as spontaneous abortion;thereafter,her clinical symptoms completely resolved.Genetic testing revealed a novel heterozygous splicing variant of the HMBS gene in exon 10(c.648_651+1delCCAGG)in the proband and four other family members.The pathogenicity of the variant was verified through bioinformatic methods and a minigene assay.coNCLUSION We identified a novel HMBS gene mutation in a Chinese patient with AIP and confirmed its pathogenicity.

关键词： Acute intermittent porphyria Hydroxymethylbilane synthase gene Novel mutation Minigene assay bioinformatics analysis Case report

comparative population genomics dissects the genetic basis of seven domestication traits in jujube

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Horticulture Research 2020年第1期7卷 1769-1782页

作者： Mingxin Guo Zhongren Zhang Yanwei Cheng Sunan Li Peiyin Shao Qiang Yu Junjie Wang Gan Xu Xiaotian Zhang Jiajia Liu Linlin Hou Hanxiao Liu Xusheng Zhao college of Life Sciences Luoyang Normal UniversityLuoyang 471934China Jujube Research Center Luoyang Normal UniversityLuoyang 471934China novogene bioinformatics Institute Beijing 100083China

Jujube(Ziziphus jujuba Mill.)is an important perennial fruit tree with a range of interesting horticultural traits.It was domesticated from wild jujube(Ziziphus acidojujuba),but the genomic variation dynamics and genetic changes underlying its horticultural traits during domestication are poorly understood.Here,we report a comprehensive genome variation map based on the resequencing of 350 accessions,including wild,semi-wild and cultivated jujube plants,at a>15×depth.Using the combination of a genome-wide association study(GWAS)and selective sweep analysis,we identified several candidate genes potentially involved in regulating seven domestication traits in jujube.For fruit shape and kernel shape,we integrated the GWAS approach with transcriptome profiling data,expression analysis and the transgenic validation of a candidate gene to identify a causal gene,ZjFS3,which encodes an ethyleneresponsive transcription factor.Similarly,we identified a candidate gene for bearing-shoot length and the number of leaves per bearing shoot and two candidate genes for the seed-setting rate using GWAS.In the selective sweep analysis,we also discovered several putative genes for the presence of prickles on bearing shoots and the postharvest shelf life of fleshy fruits.This study outlines the genetic basis of jujube domestication and evolution and provides a rich genomic resource for mining other horticulturally important genes in jujube.

关键词： jujube traits mining