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Journal of genetics and Genomics 2024年第4期51卷 394-406页

作者： Xin Li Quan Liu Chong Fu Mengxun Li Changchun Li Xinyun Li Shuhong Zhao Zhuqing Zheng Key Lab of Agricultural Animal genetics Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of AgricultureCollege of Animal Science and TechnologyHuazhong Agricultural UniversityWuhanHubei 430070China Institute of Agricultural Biotechnology Jingchu University of TechnologyJingmenHubei 448000China The Cooperative Innovation Center for Sustainable Pig Production WuhanHubei 430070China Hubei Hongshan Laboratory WuhanHubei 430070China

Structural variants(SVs),such as deletions(DELs)and insertions(INSs),contribute substantially to pig genetic diversity and phenotypic variation.Using a library of SVs discovered from long-read primary assemblies and short-read sequenced genomes,we map pig genomic SVs with a graph-based method for re-genotyping SVs in 402 genomes.Our results demonstrate that those SVs harboring specific trait-associated genes may greatly shape pig domestication and local adaptation.Further characterization of SVs reveals that some population-stratified SVs may alter the transcription of genes by affecting regulatory elements.We identify that the genotypes of two DELs(296-bp DEL,chr7:52,172,101e52,172,397;278-bp DEL,chr18:23,840,143 e23,840,421)located in muscle-specific enhancers are associated with the expression of target genes related to meat quality(FSD2)and muscle fiber hypertrophy(LMOD2 and WASL)in pigs.Our results highlight the role of SVs in domestic porcine evolution,and the identified candidate functional genes and SVs are valuable resources for future genomic research and breeding programs in pigs.

关键词： Pigs Structural variation Selection signatures Regulatory elements

Two ABCI family transporters,OsABCI15 and OsABCI16,are involved in grain-filling in rice

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Journal of genetics and Genomics 2024年第5期51卷 492-506页

作者： Bin Ma Xiubiao Cao Xiaoyuan Li Zhong Bian Qi-Qi Zhang Zijun Fang Jiyun Liu Qun Li Qiaoquan Liu Lin Zhang Zuhua He Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop genetics and Physiology Agricultural College of Yangzhou UniversityYangzhouJiangsu 225009China Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops Jiangsu Key Laboratory of Crop Genetics and PhysiologyYangzhou UniversityYangzhouJiangsu 225009China National Key Laboratory of Plant Molecular genetics CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology&EcologyChinese Academy of SciencesShanghai 200032China Institute of Biotechnology Hangzhou Academy of Agricultural SciencesHangzhouZhejiang 310024China Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education Yangzhou UniversityYangzhouJiangsu 225009China

Seed development is critical for plant reproduction and crop yield,with panicle seed-setting rate,grain-filling,and grain weight being key seed characteristics for yield improvement.However,few genes are known to regulate grain filling.Here,we identify two adenosine triphosphate(ATP)-binding cassette(ABC)I-type transporter genes,OsABCI15 and OsABCI16,involved in rice grain-filling.Both genes are highly expressed in developing seeds,and their proteins are localized to the plasma membrane and cytosol.Interestingly,knockout of OsABCI15 and OsABCI16 results in a significant reduction in seed-setting rate,caused predominantly by the severe empty pericarp phenotype,which differs from the previously reported low seed-setting phenotype resulting from failed pollination.Further analysis indicates that OsABCI15 and OsABCI16 participate in ion homeostasis and likely export ions between filial tissues and maternal tissues during grain filling.Importantly,overexpression of OsABCI15 and OsABCI16 enhances the seed-setting rate and grain yield in transgenic plants and decreases ion accumulation in brown rice.Moreover,the OsABCI15/16 orthologues in maize exhibit a similar role in kernel development,as demonstrated by their disruption in transgenic maize.Therefore,ourﬁndings reveal the important roles of two ABC transporters in cereal grain filling,highlighting their value in crop yield improvement.

关键词： ABC transporters Rice Grain filling Ion homeostasis Grain yield

Genetic and epigenetic dependencies in colorectal cancer development

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Gastroenterology Report 2022年第1期10卷 115-131页

作者： Sehej Parmar Hariharan Easwaran Cancer genetics and epigenetics OncologySidney Kimmel Comprehensive Cancer CenterJohns Hopkins University School of MedicineBaltimoreMDUSA

Recent studies have mapped key genetic changes in colorectal cancer(CRC)that impact important pathways contributing to the multistep models for CRC initiation and development.In parallel with genetic changes,normal and cancer tissues harbor epigenetic alterations impacting regulation of critical genes that have been shown to play profound roles in the tumor initiation.Cumulatively,these molecular changes are only loosely associated with heterogenous transcriptional programs,reflecting the heterogeneity in the various CRC molecular subtypes and the paths to CRC development.Studies from mapping molecular alterations in early CRC lesions and use of experimental models suggest that the intricate dependencies of various genetic and epigenetic hits shape the early development of CRC via different pathways and its manifestation into various CRC subtypes.We highlight the dependency of epigenetic and genetic changes in driving CRC development and discuss factors affecting epigenetic alterations over time and,by extension,risk for cancer.

关键词： colorectal cancer epigenetics aging classification subtyping DNA methylation consensus molecular subtypes

The interplay between H3K36 methylation and DNA methylation in cancer

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癌症生物学与医学:英文版 2023年第8期20卷 545-552页

作者： Jiameng Dan Zeling Du Jinghong Zhang Taiping Chen State Key Laboratory of Primate Biomedical Research Institute of Primate Translational MedicineKunming University of Science and TechnologyKunming 650500China Yunnan Key Laboratory of Primate Biomedical Research Kunming 650500China Department of epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer CenterHouston 77030USA programs in genetics and epigenetics The University of Texas MD Anderson Cancer Center UT Health Graduate School of Biomedical SciencesHouston 77030USA

Cancer refers to a diverse collection of diseases characterized by several well-established hallmarks,including the abilities to sustain proliferative signaling,evade growth suppressors,activate invasion and metastasis,enable replicative immortality,induce angiogenesis,and resist cell death1.Historically,genetic alterations(deletions,point mutations,and translocations)were thought to be the basis for tumor formation via the inactivation of tumor suppressors and activation of oncogenes.

关键词： alterations invasion mortality

Systematic identification of wheat spike developmental regulators by integrated multiomics, transcriptional network, GWAS, and genetic analyses

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Molecular Plant 2024年第3期17卷 438-459页

作者： Xuelei Lin Yongxin Xu Dongzhi Wang Yiman Yang Xiaoyu Zhang Xiaomin Bie Lixuan Gui Zhongxu Chen Yiliang Ding Long Mao Xueyong Zhang Fei Lu Xiansheng Zhang Cristobal Uauyo Xiangdong Fu Jun Xiao Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Nanjing Agricultural University NanjingJiangsu 210095China Key Laboratory of Crop Biology College of Life SciencesShandong Agricultural UniversityTaianShandong 271018China Department of Life Science Tcuni Inc.ChengduSichuan 610000China John Innes Centre Norwich Research ParkNorwich NR47UHUK Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China CAS-JIC Centre of Excellence for Plant and Microbial Science(CEPAMS) Institute of Genetics and Developmental BiologyCASBeijing 100101China

The spike architecture of wheat plays a crucial role in determining grain number,making it a key trait for optimization in wheat breeding programs.In this study,we used a multi-omic approach to analyze the transcriptome and epigenome profiles of the young spike at eight developmental stages,revealing co-ordinated changes in chromatin accessibility and H3K27me3 abundance during the flowering transition.We constructed a core transcriptional regulatory network(TRN)that drives wheat spike formation and experimentally validated a multi-layer regulatorymodule involving TaSPL15,TaAGLG1,and TaFUL2.By integrating the TRN with genome-wide association studies,we identified 227 transcription factors,including 42 with known functions and 185 with unknown functions.Further investigation of 61 novel transcription factors using multiple homozygous mutant lines revealed 36 transcription factors that regulate spike architecture or flowering time,such as TaMYC2-A1,TaMYB30-A1,and TaWRKY37-A1.Of particular interest,TaMYB30-A1,downstream of and repressed by WFzP,was found to regulate fertile spikelet number.Notably,the excellent haplotype of TaMYB30-A1,which contains a C allele at the WFzP binding site,was enriched during wheat breeding improvement in China,leading to improved agronomic traits.Finally,we constructed a free and open access Wheat Spike Multi-Omic Database(http://39.***.48.156:8800/#/).Our study identifies novel and high-confidence regulators and offers an effective strategy for dissecting the genetic basis of wheat spike development,with practical value forwheat breeding.

关键词： wheat spike development epigenome TRN TaMYB30-A1 breeding selection

Establishing VIGS and CRISPR/Cas9 techniques to verify RsPDS function in radish

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Journal of Integrative Agriculture 2024年第5期23卷 1557-1567页

作者： Jiali Ying Yan Wang Liang Xu Tiaojiao Qin Kai Xia Peng Zhang Yinbo Ma Keyun Zhang Lun Wang Junhui Dong Lianxue Fan Yuelin Zhu Liwang Liu National Key Laboratory of Crop genetics&Germplasm Enhancement and Utilization/Key Laboratory of Horticultural Crop Biology and Genetic Improvement(East China)of Ministry of Agriculture and Rural Affairs/College of Horticulture Nanjing Agricultural UniversityNanjing210095China College of Horticulture and Landscape Architecture Yangzhou UniversityYangzhou 225009China College of Life Sciences Nanjing Agricultural UniversityNanjing 210095China

Virus-induced gene silencing(VIGS)and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein(CRISPR/Cas)systems are effective technologies for rapid and accurate gene function verification in modern plant biotechnology.However,the investigation of gene silencing and editing in radish remains limited.In this study,a bleaching phenotype was generated through the knockdown of RsPDS using tobacco rattle virus(TRV)-and turnip yellow mosaic virus(TYMV)-mediated gene silencing vectors.The TYMV-mediated gene silencing efficiency was higher than the TRV-based VIGS system in radish.The expression level of RsPDS was significantly inhibited using VIGS in'NAU-067'radish leaves.The rootless seedlings of‘NAU-067'were infected with Agrobacterium rhizogenes using the 2300GN-Ubi-RsPDS-Cas9 vector with two target sequences.Nine adventitious roots were blue with GUs staining,and four of these adventitious roots were edited at target sequence 1 of the RsPDS gene as indicated by Sanger sequencing.Furthermore,albino lines were generated with A.tumefaciens-mediated transformation of radish cotyledons.Five base substitutions and three base deletions occurred at target sequence 2 in Line 1,and three base insertions and three base substitutions occurred at target sequence 1 in Line 2.This study shows that VIGS and CRISPR/Cas9 techniques can be employed to precisely verify the biological functions of genes in radish,which will facilitate the genetic improvement of vital horticultural traits in radish breeding programs.

关键词： Raphanus sativus L. VIGS CRISPR/Cas9 Agrobacterium rhizogenes A.tumefaciens RsPDS

The challenge of defining rare genetic programs by single-cell RNA sequencing:Insights from phloem studies

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Molecular Plant 2024年第1期17卷 22-25页

作者： Xiaomin Liu Pawel Roszak YkäHelariutta State Key Laboratory of Tree genetics and Breeding College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing 100083China The Sainsbury Laboratory University of CambridgeCB21TN CambridgeUK Wood Development Group University of Helsinki00100 HelsinkiFinland Organismal and Evolutionary Biology Research Programme Faculty of Biological and Environmental Sciences and Viikki Plant Science CentreUniversity of Helsinki00100 HelsinkiFinland

Single-cell RNA sequencing technology provides unprecedented opportunities to capture the spatiotemporal aspects of genetic programs that drive cell differentiation.Phloem is a subtype of vascular tissue that is crucial for transporting sugars,proteins,and other organic molecules.Its critical role in the redistribution of carbon between photosynthetically active“source”organs(leaves,shoots)and“sink”tissues/organs incapable of fixing carbon(wood,storage organs,root system,etc.)has made phloem development and its transcriptional regulation a prime research focus.

关键词： organs sugar rare

Mapping of powdery mildew resistance genes transferred to common wheat from wild emmer wheat revealed three functional Pm60 haplotypes

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The Crop Journal 2024年第2期12卷 540-548页

作者： Wenxin Wei Nannan Liu Shengnan Zhang Jing Zhang Wei Pan Xiaoming Xie Zuhuan Yang Junna Sun Jun Ma Zhaorong Hu Weilong Guo Qiaoling Luo Jingzhong Xie Fei He Yinghui Li Chaojie Xie Qixin Sun Key Laboratory of Crop Heterosis and Utilization(MOE)/Key Laboratory of Crop Genetic Improvement China Agricultural UniversityBeijing 100193China Institute of Advanced Agricultural Science Peking UniversityWeifang 261200ShandongChina Institute of genetics and Developmental Biology Chinese Academy of SciencesBeijing 100101China Triticeae Research Institute Sichuan Agricultural UniversityChengdu 611130SichuanChina Institute of Evolution University of HaifaMt.CarmelHaifa 3498838Israel

Powdery mildew(PM),caused by Blumeria graminis f.***.tritici(Bgt),is one of the destructive wheat diseases worldwide.Wild emmer wheat(Triticum turgidum ssp.dicoccoides,WEW),a tetraploid progenitor of common wheat,is a valuable genetic resource for wheat disease resistance breeding programs.We developed three hexaploid pre-breeding lines with PM resistance genes derived from three WEW accessions.These resistant pre-breeding lines were crossed with susceptible common wheat accessions.Segregations in the F2populations were 3 resistant:1 susceptible,suggesting a single dominant allele in each resistant parent.Mapping of the resistance gene in each line indicated a single locus on the long arm of chromosome 7A,at the approximate location of previously cloned Pm60 from T.urartu.Sanger sequencing revealed three different Pm60 haplotypes(Hap 3,Hap 5,and Hap 6).Co-segregating diagnostic markers were developed for identification and selection of each haplotype.The resistance function of each haplotype was verified by the virus-induced gene silencing(VIGS).Common wheat lines carrying each of these Pm60 haplotypes were resistant to most Bgt isolates and differences in the response arrays suggested allelic variation in response.

关键词： Alleles Blumeria graminus Marker-assisted selection Molecular marker Triticum dicoccoides

Genetic basis of geographical differentiation,breeding selection,domestication effects,and breeding application for TaJAZ1 in wheat

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Journal of genetics and Genomics 2024年第6期51卷 665-668页

作者： Botao Ye Yangyang Liu Ziying Wang Liping Shen Changbin Yin Kuocheng Shen Jiaqiang Sun Xiaowan Xu Mengjing Sun Jianhui Wu Zhonghu He Xuchang Yu Fei Lu Yuanfeng Hao Zifeng Guo Key Laboratory of Plant Molecular Physiology Institute of BotanyChinese Academy of SciencesBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China China National Botanical Garden Beijing 100093China State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyInnovative Academy of Seed DesignChinese Academy of SciencesBeijing 100101China Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China State Key Laboratory of Crop Stress Biology for Arid Areas Northwest A&F UniversityYanglingShaanxi 712100China International Maize and Wheat Improvement Center China Office c/o CAASBejing 100081China CAS-JIC Centre of Excellence for Plant and Microbial Science Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China

Common wheat(Triticum aestivum L.,2n=6x=42,AABBDD)is one of the most widely grown crops worldwide,providing about 20%of the daily calories and protein consumed by humans(Shiferaw et al.,2013).The world population is projected to reach 9.8 billion in 2050(https://***/en/desa/world-population-projectedreach-98-billion-2050-and-112-billion-2100);thus,to meet the challenges of global food and nutritional security,wheat yields must continue to be increased through breeding programs and improved agricultural techniques(Hunter et al.,2017).

关键词： breeding crops wheat

Efficiency of Botanical and Chemical Pesticides on the Control of Field Insect Pests under Cowpea Production

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American Journal of Plant Sciences 2024年第3期15卷 203-221页

作者： John Ssengo Brian Zebosi Jeninah Karungi Department of Plant Pathology Entomology and Microbiology Iowa State University Ames IA USA Department of Agricultural Production Makerere University Kampala Uganda Department of genetics Development and Cell Biology Iowa State University Ames IA USA

The pulse cowpea [Vigna unguiculata (L.) Walp] holds a significant agricultural position in Uganda, ranking fourth among legume crops, following common beans, groundnuts, and soybeans. Known for its versatility, cowpeas are consumable at various developmental stages, from early seedling to maturity. However, the crop faces persistent pest challenges at each stage, leading to substantial yield losses. In Uganda, chemical insecticides are the primary pest control means, but their increased and excessive use raises environmental, health, and economic concerns. This has prompted a quest for alternative and sustainable solutions, prompting an exploration of botanical insecticides. This study, conducted at Makerere University Agricultural Research Institute (MUARIK), aimed to evaluate the effectiveness of three selected botanical insecticides versus four established chemical insecticides for managing cowpea insect pests under field conditions. The treatments included: Carbofuran, Cypermethrin 10% EC, Dimethoate, Pestwin, Pyrethrum ewc , Pyrethrum 5ew, Profenofos 40% Cypermethrin 4% EC mix, and Untreated, arranged in a randomized complete block design with three replications. The significant pests studied were aphids, thrips, pod-sucking bugs, and legume pod borer. Results indicated substantial impacts of the treatments on pest infestation, with Profenofos 40% Cypermethrin 4% EC being the most effective against most pests. The plant parameter, plant height, was significantly affected by treatments in 2016B, while the number of pods was impacted in 2017A. Pestwin, a botanical insecticide blend (containing Azadirachtin indica, Pongamia pinnata, and Ricinus communis extracts) demonstrated superior efficacy against cowpea aphids. Moreover, it positively influenced plant height, number of pods, and pod biomass, surpassing many chemical insecticides. Pestwin’s environmental friendliness positions it as a potential contributor to reducing environmental pollution, making it a promising candidate for inclusion in IPM programs. O

关键词： Cowpea Pest Management Botanical Solutions Profenofos Sustainability