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Large-scale population structure and genetic architecture of agronomic traits of garlic

Horticulture Research 2023年第4期10卷 187-199页

作者： Huixia Jia Qing Zhao Jiangping Song Xiaohui Zhang Wenlong Yang Zhenzhen Du Yue Zhu Haiping Wang State Key Laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China

Garlic,an asexually propagated crop,is the second important bulb crop after the onion and is used as a vegetable and medicinal plant.Abundant and diverse garlic resources have been formed over thousands of years of cultivation.However,genome variation,population structure and genetic architecture of garlic agronomic traits were still not well elucidated.Here,1100258 single nucleotide polymorphisms(SNPs)were identified using genotyping-by-sequencing in 606 garlic accessions collected from43 countries.Population structure,principal component and phylogenetic analysis showed that these accessions were divided into five subpopulations.Twenty agronomic traits,including above-ground growth traits,bulb-related and bolt-related traits in two consecutive years were implemented in a genome-wide association study.In total,542 SNPs were associated with these agronomic traits,among which 188 SNPs were repeatedly associated with more than two traits.One SNP(chr6:1896135972)was repeatedly associated with ten traits.These associated SNPs were located within or near 858 genes,56 of which were transcription factors.Interestingly,one non-synonymous SNP(Chr4:166524085)in ribosomal protein S5 was repeatedly associated with above-ground growth and bulb-related traits.Additionally,gene ontology enrichment analysis of candidate genes for genomic selection regions between complete-bolting and non-bolting accessions showed that these genes were significantly enriched in‘vegetative to reproductive phase transition of meristem’,‘shoot system development’,‘reproductive process’,etc.These results provide valuable information for the reliable and efficient selection of candidate genes to achieve garlic genetic improvement and superior varieties.

关键词： agronomic traits repeatedly

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Understanding divergent domestication traits from the whole-genome sequencing of swamp-and river-buffalo populations

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National Science Review 2020年第3期7卷 686-701页

作者： Xier Luo Yu Zhou Bing Zhang Yi Zhang Xiaobo Wang Tong Feng Zhipeng Li Kuiqing Cui Zhiqiang Wang Chan Luo Hui Li Yanfei Deng Fenghua Lu Jianlin Han Yongwang Miao Huaming Mao Xiaoyan Yi Cheng Ai Shigang Wu Alun Li Zhichao Wu Zijun Zhuo Do Da Giang Bikash Mitra Mohammad Farhad Vahidi Shahid Mansoor Sahar Ahmed Al-Bayatti Eka Meutia Sari Neena Amatya Gorkhali Sigit Prastowo Laiba Shafique Guoyou Ye Qian Qian Baoshan Chen Deshun Shi Jue Ruan Qingyou Liu Animal Biotechnology Department Agricultural Biotechnology Research Institute of Iran-North Region 11. National Institute for Biotechnology and Genetic Engineering 12. Animal Genetic Sources DepartmentDirectorate of Animal Resources Ministry of Agriculture 13. Department of Animal Science Faculty of Agriculture Syiah Kuala University 14. Animal Breeding DivisionNational Animal Science Research Institute Nepal Agriculture Research Council 15. Animal Science Department Universitas Sebelas Maret 16. International Rice Research Institute State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources Guangxi University CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics Breeding and Reproduction of Ministry of Agriculture and Rural AffairsCollege of Animal Science and Technology China Agricultural University Guangdong Laboratory for Lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of Agriculture Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources Institute of Animal ScienceChinese Academy of Agricultural Sciences International Livestock Research Institute Faculty of Animal Science and Technology Yunnan Agricultural University Bacgiang Agriculture and Forestry University Cellular Immunology Lab Department of Zoology University of North Bengal

Domesticated buffaloes have been integral to rice-paddy agro-ecosystems for millennia, yet relatively little is known about the buffalo genomics. Here, we sequenced and assembled reference genomes for both swamp and river buffaloes and we re-sequenced 230 individuals(132 swamp buffaloes and 98 river buffaloes)sampled from across Asia and Europe. Beyond the many actionable insights that our study revealed about the domestication, basic physiology and breeding of buffalo, we made the striking discovery that the divergent domestication traits between swamp and river buffaloes can be explained with recent selections of genes on social behavior, digestion metabolism, strengths and milk production.

关键词： Bubalus bubalis genome buffalo domestication re-sequencing traits

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Almond population genomics and non-additive GWAS reveal new insights into almond dissemination history and candidate genes for nut traits and blooming time

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Horticulture Research 2023年第10期10卷 262-272页

作者： Felipe Pérez de los Cobos Eva Coindre Naima Dlalah Bénédicte Quilot-Turion Ignasi Batlle Pere Arús Iban Eduardo Henri Duval Fruticultura Institut de Recerca i Tecnologia Agroalimentàries(IRTA)Mas BovéCtra.Reus-El Morell Km 3843120 ConstantíTarragonaSpain Centre de Recerca en Agrigenòmica(CRAG) CSIC-IRTA-UAB-UB.Institut de Recerca i Tecnologia Agroalimentàries(IRTA)Cerdanyola del Vallès(Bellaterra)08193 BarcelonaSpain Centre for Research in Agricultural Genomics(CRAG)CSIC-IRTA-UAB-UB Campus UABEdifici CRAGCerdanyola del Vallès(Bellaterra)08193 BarcelonaSpain INRAE GAFLF-84143MontfavetFrance

Domestication drastically changed crop genomes,fixing alleles of interest and creating different genetic populations.Genome-wide association studies(GWASs)are a powerful tool to detect these alleles of interest(and so QTLs).In this study,we explored the genetic structure as well as additive and non-additive genotype-phenotype associations in a collection of 243 almond accessions.Our genetic structure analysis strongly supported the subdivision of the accessions into five ancestral groups,all formed by accessions with a common origin.One of these groups was formed exclusively by Spanish accessions,while the rest were mainly formed by accessions from China,Italy,France,and the USA.These results agree with archaeological and historical evidence that separate modern almond dissemination into four phases:Asiatic,Mediterranean,Californian,and southern hemisphere.In total,we found 13 independent QTLs for nut weight,crack-out percentage,double kernels percentage,and blooming time.Of the 13 QTLs found,only one had an additive effect.Through candidate gene analysis,we proposed Prudul26A013473 as a candidate gene responsible for the main QTL found in crack-out percentage,Prudul26A012082 and Prudul26A017782 as candidate genes for the QTLs found in double kernels percentage,and Prudul26A000954 as a candidate gene for the QTL found in blooming time.Our study enhances our knowledge of almond dissemination history and will have a great impact on almond breeding.

关键词： additive GWAS traits

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Genome resequencing reveals the evolutionary history of garlic reproduction traits

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Horticulture Research 2023年第11期10卷 208-221页

作者： Haiping Wang Einat Shemesh-Mayer Jiangjiang Zhang Song Gao Zheng Zeng Zemao Yang Xueyu Zhang Huixia Jia Yanzhou Wang Jiangping Song Xiaohui Zhang Wenlong Yang Qiaoyun He Amir Sherman Lin Li Rina Kamenetsky Touming Liu State Key Laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina Institute of Plant Sciences Agricultural Research Organization-The Volcani InstituteRishon LeZionIsrael Institute of Bast Fiber Crops Chinese Academy of Agricultural SciencesChangshaChina College of Horticulture and Landscape Architecture Yangzhou UniversityYangzhouChina Industrial Research Institute of garlic(IBFC-Jinxiang) JinxiangChina College of Plant Science and Technology Huazhong Agricultural UniversityWuhanChina

The propagation of cultivated garlic relies on vegetative cloves,thus flowers become non-essential for reproduction in this species,driving the evolution of reproductive feature-derived traits.To obtain insights into the evolutionary alteration of reproductive traits in the clonally propagated garlic,the evolutionary histories of two main reproduction-related traits,bolting and flower differentiation,were explored by genome analyses using 134 accessions displaying wide diversity in these two traits.Resequencing identified 272.8 million variations in the garlic genome,198.0million of which represent novel variants.Population analysis identified five garlic groups that have evolved into two clades.Gene expression,single-cell transcriptome sequencing,and genome-wide trait association analyses have identified numerous candidates that correlate with reproductive transition and flower development,some of which display distinct selection signatures.Selective forces acting on the B-box zinc finger protein-encoding Asa2G00291.1,the global transcription factor group E protein-encoding Asa5G01527.1,and VERNALIZATION INSENSITIVE 3-like Asa3G03399.1 appear to be representative of the evolution of garlic bolting.Plenty of novel genomic variations and trait-related candidates represent valuable resources for biological studies of garlic.Numerous selective signatures from genes associated with the two chosen reproductive traits provide important insights into the evolutionary history of reproduction in this clonally propagated crop.

关键词： traits evolutionary signature

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Application of UAV Multisensor Data and Ensemble Approach for High-Throughput Estimation of Maize Phenotyping traits

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Plant Phenomics 2022年第1期4卷 110-126页

作者： Meiyan Shu Shuaipeng Fei Bingyu Zhang Xiaohong Yang Yan Guo Baoguo Li Yuntao Ma College of Land Science and Technology China Agricultural UniversityBeijing 100091China State Key Laboratory of Plant Physiology and Biochemistry National Maize Improvement Center of ChinaChina Agricultural UniversityBeijing 100091China

High-throughput estimation of phenotypic traits from UAV(unmanned aerial vehicle)images is helpful to improve the screening efficiency of breeding maize.Accurately estimating phenotyping traits of breeding maize at plot scale helps to promote gene mining for specific traits and provides a guarantee for accelerating the breeding of superior varieties.Constructing an efficient and accurate estimation model is the key to the application of UAV-based multiple sensors data.

关键词： breeding estimation traits

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A Post-domestication Mutation, Dt2, Triggers Systemic Modification of Divergent and Convergent Pathways Modulating Multiple Agronomic traits in Soybean

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Molecular Plant 2019年第10期12卷 1366-1382页

作者： Dajian Zhang Xutong Wang Shuo Li Chaofan Wang Michael JGosney Michael VMickelbart Jianxin Ma Department of Agronomy Purdue UniversityWest LafayetteIN 47907USA College of Agronomy Shandong Agricultural UniversityTai'anShandong 271018China School of Life Sciences Shandong UniversityQingdaoShandong 266237China Department of Botany and Plant Pathology Purdue UniversityWest LafayetteIN 47907USA Center for Plant Biology Purdue UniversityWest LafayetteIN 47907USA

The semi-determinate stem growth habit in leguminous crops,similar to the“green revolution”semi-dwarf trait in cereals,is a key plant architecture trait that affects several other traits determining grain yield.In soybean semi-determinacy is modulated by a post-domestication gain-of-function mutation in the gene,Dt2,which encodes an MADS-box transcription factor.However,its role in systemic modification of stem growth and other traits is unknown.In this study,we show that Dt2 functions not only as a direct repressor of Dt1,which prevents terminal flowering,but also as a direct activator of putative floral integrator/identity genes including GmSOC1,GmAP1,and GmFUL,which likely promote flowering.We also demonstrate that Dt2 functions as a direct repressor of the putative drought-responsive transcription factor gene GmDREB1D,and as a direct activator of GmSPCH and GmGRP7,which are potentially associated with asymmetric division of young epidermal cells and stomatal opening,respectively,and may affect the plant's water-use efficiency(WUE).Intriguingly,Dt2 was found to be a direct activator or repressor of the precursors of eight microRNAs targeting genes potentially associated with meristem maintenance,flowering time,stomatal density,WUE,and/or stress responses.This study thus reveals the molecular basis of pleiotropy associated with plant productivity,adaptability,and environmental resilience.

关键词： abiotic stress agronomic traits convergent pathways stem growth habit pleiotropy soybean

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Nondestructive 3D Image Analysis Pipeline to Extract Rice Grain traits Using X-Ray Computed Tomography

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Plant Phenomics 2020年第1期2卷 106-117页

作者： Weijuan Hu Can Zhang Yuqiang Jiang Chenglong Huang Qian Liu Lizhong Xiong Wanneng Yang Fan Chen Crop Phenomics Joint Research Center Wuhan 430070China Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101China Britton Chance Center for Biomedical Photonics Wuhan National Laboratory for Optoelectronicsand Key Laboratory of Ministry of Education for Biomedical PhotonicsDepartment of Biomedical EngineeringHuazhong University of Science and TechnologyWuhan 430074China National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene ResearchAgricultural Bioinformatics Key Laboratory of Hubei Provinceand College of EngineeringHuazhong Agricultural UniversityWuhan 430070China

The traits of rice panicles play important roles in yield assessment,variety classification,rice breeding,and cultivation management.Most traditional grain phenotyping methods require threshing and thus are time-consuming and labor-intensive;moreover,these methods cannot obtain 3D grain traits.In this work,based on X-ray computed tomography,we proposed an image analysis method to extract twenty-two 3D grain traits.After 104 samples were tested,the R^(2) values between the extracted and manual measurements of the grain number and grain length were 0.980 and 0.960,respectively.We also found a high correlation between the total grain volume and weight.In addition,the extracted 3D grain traits were used to classify the rice varieties,and the support vector machine classifier had a higher recognition accuracy than the stepwise discriminant analysis and random forest classifiers.In conclusion,we developed a 3D image analysis pipeline to extract rice grain traits using X-ray computed tomography that can provide more 3D grain information and could benefit future research on rice functional genomics and rice breeding.

关键词： breeding forest traits

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Genetic dissection of root morphological traits as related to potassium use efficiency in rapeseed under two contrasting potassium levels by hydroponics

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Science China(Life Sciences) 2019年第6期62卷 746-757页

作者： Xiaoling Dun Jiaqin Shi Huiping Liu Jie Wang Xinfa Wang Hanzhong Wang Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops Ministry of Agriculture

To reveal the genetic basis of potassium use efficiency(KUE) in rapeseed, root morphology(RM), biomass and KUE-related traits were measured in a recombinant inbred line population with 175 F7 lines that were subjected to high-potassium(HK) and low-potassium(LK) treatments by hydroponics. A total of 109 significant QTLs were identified to be associated with the examined traits. Sixty-one of these QTLs were integrated into nine stable QTLs. The higher heritability for RM and biomass traits and lower heritability for KUE-related traits, as well as nine stable QTLs for RM traits and only two for KUE-related traits,suggested that regulating RM traits would be more effective than selecting KUE traits directly to improve KUE by markerassisted selection. Furthermore, the integration of stable QTLs identified in the HK, LK, high-nitrogen(HN) and low-nitrogen(LN) conditions gave 10 QTL clusters. Seven of these clusters were classified into major QTLs that explained 7.4%–23.7% of the total phenotypic variation. Five of the major QTL clusters were detected under all of the treated conditions, and four clusters were specifically detected under the LK and LN conditions. These common and specific QTL clusters may be useful for the simultaneous improvement of multiple traits by marker-assisted selection.

关键词： Brassica napus L. root traits potassium efficiency QTL mapping QTL cluster

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Exploring Seasonal and Circadian Rhythms in Structural traits of Field Maize from LiDAR Time Series

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Plant Phenomics 2021年第1期3卷 389-403页

作者： Shichao Jin Yanjun Su Yongguang Zhang Shilin Song Qing Li Zhonghua Liu Qin Ma Yan Ge LingLi Liu Yanfeng Ding Frédéric Baret Qinghua Guo Plant Phenomics Research Centre Academy for Advanced Interdisciplinary StudiesCollaborative Innovation Centre for Modern Crop Production Co-Sponsored by Province and MinistryJiangsu Key Laboratory for Information AgricultureNanjing Agricultural UniversityNanjing 210095China Jiangsu Provincial Key Laboratory of Geographic Information Science and Technology International Institute for Earth System SciencesNanjing UniversityNanjingJiangsu 210023China State Key Laboratory of Vegetation and Environmental Change Institute of BotanyChinese Academy of SciencesBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Ecophysiology Ministry of AgricultureNanjing Agricultural UniversityNanjing210095 JiangsuChina Department of Forestry Mississippi State UniversityMississippi State 39759USA Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes(EMMAH) Institut National de la Recherche AgronomiqueUnitéMixte de Recherche 1114 Domaine Saint-PaulAvignon Cedex 84914France Department of Ecology College of Environmental Sciencesand Key Laboratory of Earth Surface Processes of the Ministry of EducationPeking UniversityBeijing 100871China

Plant growth rhythm in structural traits is important for better understanding plant response to the ever-changing environment.Terrestrial laser scanning(TLS)is a well-suited tool to study structural rhythm under field conditions.Recent studies have used TLS to describe the structural rhythm of trees,but no consistent patterns have been drawn.Meanwhile,whether TLS can capture structural rhythm in crops is unclear.Here,we aim to explore the seasonal and circadian rhythms in maize structural traits at both the plant and leaf levels from time-series TLS.The seasonal rhythm was studied using TLS data collected at four key growth periods,including jointing,bell-mouthed,heading,and maturity periods.Circadian rhythms were explored by using TLS data acquired around every 2 hours in a whole day under standard and cold stress conditions.Results showed that TLS can quantify the seasonal and circadian rhythm in structural traits at both plant and leaf levels.(1)Leaf inclination angle decreased significantly between the jointing stage and bell-mouthed stage.Leaf azimuth was stable after the jointing stage.(2)Some individual-level structural rhythms(e.g.,azimuth and projected leaf area/PLA)were consistent with leaf-level structural rhythms.(3)The circadian rhythms of some traits(e.g.,PLA)were not consistent under standard and cold stress conditions.(4)Environmental factors showed better correlations with leaf traits under cold stress than standard conditions.Temperature was the most important factor that significantly correlated with all leaf traits except leaf azimuth.This study highlights the potential of time-series TLS in studying outdoor agricultural chronobiology.

关键词： crops heading traits

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Osa-miR1873 fine-tunes rice immunity against Magnaporthe oryzae and yield traits

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Journal of Integrative Plant Biology 2020年第8期62卷 1213-1226页

作者： Shi-Xin Zhou Yong Zhu Liang-Fang Wang Ya-Ping Zheng Jin-Feng Chen Ting-Ting Li Xue-Mei Yang He Wang Xu-Pu Li Xiao-Chun Ma Ji-Qun Zhao Mei Pu Hui Feng Yan Li Jing Fan Ji-Wei Zhang Yan-Yan Huang Wen-Ming Wang State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China Sichuan Agricultural UniversityChengdu 611130China Rice Research Institute and Key Lab for Major Crop Diseases Sichuan Agricultural UniversityChengdu 611130China

MicroRNAs(miRNAs)are known to fine-tune growth,development,and stress-induced responses.Osa-miR1873 is a rice-specific miRNA targeting LOC_Os05g01790.Here,we show that Osa-miR1873 fine-tunes rice immunity against Magnaporthe oryzae and yield traits via LOC_Os05g01790.Osa-miR1873 was significantly upregulated in a susceptible accession but downregulated in a resistance accession at 24 h post-inoculation(hpi)of M.oryzae.Overexpressing Osa-miR1873 enhanced susceptibility to M.oryzae and compromised induction of defense responses.In contrast,blocking Osa-miR1873 through target mimicry compromised susceptibility to M.oryzae and enhanced induction of defense responses.Altered expression of Osa-miR1873 also resulted in some defects in yield traits,including grain numbers and seed setting rate.Moreover,overexpression of the target gene LOC_Os05g01790 increased rice blast disease resistance but severely penalized growth and yield.Taken together,we demonstrate that Osa-miR1873 fine-tunes the rice immunity-growth trade-off via LOC_Os05g01790,and blocking Osa-miR1873 could improve blast disease resistance without significant yield penalty.Thus,the Osa-miR1873-LOC_Os05g01790 regulatory module is valuable in balancing yield traits and blast resistance.

关键词： miR187 immunity traits

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