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Transcriptome profiles reveal that gibberellin-related genes regulate weeping traits in crape myrtle

Horticulture Research 2020年第1期7卷 2068-2081页

作者： Suzhen Li Tangchun Zheng Xiaokang Zhuo Zhuojiao Li Lulu Li Ping Li Like Qiu Huitang Pan Jia Wang Tangren Cheng Qixiang Zhang Beijing Advanced Innovation Center for Tree Breeding by Molecular Design Beijing Forestry UniversityBeijing 100083China Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding National Engineering Research Center for FloricultureBeijing Laboratory of Urban and Rural Ecological EnvironmentEngineering Research Center of Landscape Environment of the Ministry of EducationKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of EducationSchool of Landscape ArchitectureBeijing Forestry UniversityBeijing 100083China

Plant architecture includes vital traits that influence and benefit crops,and economically important trees.Different plant architectures provide natural beauty.Weeping ornamental plants are aesthetically appealing to people.The regulatory mechanism controlling the weeping trait is poorly understood in crape myrtle.To investigate the weeping trait mechanism,transcriptional profiling of different organs in weeping and upright crape myrtle was performed based on phenotype.Phenotypic and histological analyses demonstrated that endodermal cells were absent,and that new shoot phenotypes could be rescued by the GA3 treatment of weeping plants.The transcriptional analysis and coexpression network analysis(WGCNA)of differentially expressed genes indicated that GA synthesis and signal transduction pathways play a role in weeping traits.When the expression level of a negative element of GA signaling,LfiGRAS1,was reduced by virus-induced gene silencing(VIGS),new branches grew in infected plants in a negatively geotropic manner.An integrated analysis implied that GA had a strong influence on weeping crape myrtle by interacting with other factors.This study helps to elucidate the mechanism governing the weeping trait and can improve the efficiency of breeding in Lagerstroemia.

关键词： traits breeding crops

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High-density genetic map construction and identification of loci controlling flower-type traits in Chrysanthemum(Chrysanthemum×morifolium Ramat.)

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Horticulture Research 2020年第1期7卷 1469-1481页

作者： Xuebin Song Yuhui Xu Kang Gao Guangxun Fan Fan Zhang Chengyan Deng Silan Dai He Huang Huaigen Xin Yingying Li Beijing Advanced Innovation Center for Tree Breeding by Molecular Design Beijing Key Laboratory of Ornamental Plants Germplasm Innovation&Molecular BreedingNational Engineering Research Center for FloricultureBeijing Laboratory of Urban and Rural Ecological EnvironmentKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of the Ministry of EducationBeijing Forestry UniversitySchool of Landscape ArchitectureBeijing Forestry University35 East Qinghua RoadBeijing 100083China College of Landscape Architecture and Forestry Qingdao Agricultural UniversityQingdao 266109 ShandongChina Biomarker Technologies Co. LTDBeijing 101300China LC Science Co. LTD.Hangzhou 310018China

Flower type is an important and extremely complicated trait of chrysanthemum.The corolla tube merged degree(CTMD)and the relative number of ray florets(RNRF)are the two key factors affecting chrysanthemum flower type.However,few reports have clarified the inheritance of these two complex traits,which limits directed breeding for flower-type improvement.In this study,305 F1 hybrids were obtained from two parents with obvious differences in CTMD and RNRF performance.Using specific-locus amplified fragment sequencing(SLAF-seq)technology,we constructed a high-density genetic linkage map with an average map distance of 0.76 cM.Three major QTLs controlling CTMD and four major QTLs underlying RNRF were repeatedly detected in the 2 years.Moreover,the synteny between the genetic map and other Compositae species was investigated,and weak collinearity was observed.In QTL regions with a high degree of genomic collinearity,eight annotated genes were probed in the Helianthus annuus L.and Lactuca sativa L.var.ramosa Hort.genomes.Furthermore,20 and 11 unigenes were identified via BLAST searches between the SNP markers of the QTL regions and the C.vestitum and C.lavandulifolium transcriptomes,respectively.These results lay a foundation for molecular marker-assisted breeding and candidate gene exploration in chrysanthemum without a reference assembly.

关键词： breeding controlling traits

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Dietary β-glucan supplementation improves growth performance,carcass traits and meat quality of finishing pigs

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Animal Nutrition 2019年第4期5卷 380-385页

作者： Junqiu Luo Dafu Zeng Long Cheng Xiangbing Mao Jie Yu Bing Yu Daiwen Chen Institute of Animal Nutrition Sichuan Agricultural UniversityKey Laboratory of AnimalDisease Resistance NutritionMinistry of EducationChengdu 611130China Sichuan Synlight Biotech Ltd. Chengdu 610041China Faculty of Veterinary and Agricultural Sciences Dookie Campus 3647The University of MelbourneParkvilleVIC3052Australia

This experiment was conducted to investigate growth performance,carcass traits and meat quality of finishing pigs with dietary β-glucan supplementation.A total of 96 healthy pigs(Duroc x Landrace x Yorkshire;initial average BW=25 kg) were randomly allocated into 4 dietary treatments with 6 replicates per treatment and 4 pigs per replicate.The control group was fed a basal diet,and the experimental diets were supplemented with 50,100 and 200 mg/kg Agrobacterium sp.ZX09β-glucan,respectively.The experiment lasted 103 d.The basal diet supplemented with 100 mg/kg β-glucan significantly increased average daily gain and feed conversion ratio,probably due to the improved digestibility of dry matter,gross energy and crude protein(P <0.05).Beta-glucan supplementation from100 to 200 mg/kg of diet significantly increased carcass length(P <0.05).The basal diet supplemented with 100 mg/kg β-glucan supplementation also significantly(P <0.05) increased muscle pH,reduced drip losses and increased a~*values.The basal diet supplemented with 100 mg/kg β-glucan increased the content of intramuscular fat and changed the proportion of saturated fatty acid and unsaturated fatty acid,thereby improved the flavor of meat.In conclusion,the basal diet supplemented with 100 mg/kg Agrobacterium sp.ZX09 β-glucan improves growth performance,nutrient digestibility,carcass length,and pork quality of finishing pigs.

关键词： Growth performance β-glucan Carcass traits Meat quality Finishing pigs

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QTL analysis of ear leaf traits in maize(Zea mays L.)under different planting densities

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The Crop Journal 2017年第5期5卷 387-395页

作者： Hongwu Wang Qianjin Liang Kun Li Xiaojiao Hu Yujin Wu Hui Wang Zhifang Liu Changling Huang Institute of Crop Science Chinese Academy of Agricultural Sciences

Modem maize varieties have become more productive than ever, owing largely to increased tolerance of high plant density. However, the genetics of ear leaf traits under different densities remains poorly understood. In this study, Zhongdan 909 recombinant inbred lines(RILs) derived from a cross between Z58 and HD568 were genotyped for 3072 single-nucleotide polymorphisms(SNPs), and phenotyped for leaf length(LL), leaf width(LW), and leaf angle(LA) of the uppermost ear leaf under three planting densities(52,500,67,500, and 82,500 plants ha-1, respectively). A genetic map was then constructed using1358 high-quality SNPs. The total length of the linkage map was 1985.2 cM and the average interval between adjacent markers 1.46 cM. With increasing density, LL and LW decreased from 63.68 to 63.02 cm and from 8.56 to 8.21 cm, respectively, while LA increased from19.42° to 19.66°. All three traits had high heritabilities, of 0.75, 0.78, and 0.84, respectively.Using inclusive composite interval mapping, 23, 25, and 17 quantitative trait loci(QTL) were detected for LL, LW, and LA, respectively. Of these, 35 were simultaneously detected under two or three plant densities, while 30 were detected under only one. Sixty-five individual QTL explained 2.41% to 16.53% of phenotypic variation, while eight accounted for >10%.These findings will help us understand the genetic basis of leaf traits in maize as well as the response of maize to increased plant density.

关键词： Maize Quantitative trait loci Leaf traits Density treatment

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Efficient protocols and methods for high-throughput utilization of the Collaborative Cross mouse model for dissecting the genetic basis of complex traits

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Animal Models and Experimental Medicine 2019年第3期2卷 137-149页

作者： Hanifa J.Abu-Toamih Atamni Fuad A.Iraqi Department of Clinical Microbiology and Immunology Sackler Faculty of Medicine Tel Aviv University

The Collaborative Cross(CC)mouse model is a next‐generation mouse genetic reference population(GRP)designated for a high‐resolution quantitative trait loci(QTL)mapping of complex traits during health and disease.The CC lines were generated from reciprocal crosses of eight divergent mouse founder strains composed of five classical and three wild‐derived strains.Complex traits are defined to be controlled by variations within multiple genes and the gene/environment interactions.In this article,we introduce and present variety of protocols and results of studying the host response to infectious and chronic diseases,including type 2 diabetes and metabolic diseases,body composition,immune response,colorectal cancer,susceptibility to Aspergillus fumigatus,Klebsiella pneumoniae,Pseudomonas aeruginosa,sepsis,and mixed infections of Porphyromonas gingivalis and Fusobacterium nucleatum,which were conducted at our laboratory using the CC mouse population.These traits are observed at multiple levels of the body systems,including metabolism,body weight,immune profile,susceptibility or resistance to the development and progress of infectious or chronic diseases.Herein,we present full protocols and step‐by‐step methods,implemented in our laboratory for the phenotypic and genotypic characterization of the different CC lines,mapping the gene underlying the host response to these infections and chronic diseases.The CC mouse model is a unique and powerful GRP for dissecting the host genetic architectures underlying complex traits,including chronic and infectious diseases.

关键词： Collaborative Cross(CC)mouse model complex traits genetic reference population(GRP),infectious and chronic diseases quantitative trait loci(QTL)

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Differences in leaf functional traits between exotic and native Compositae plant species

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Journal of Central South University 2017年第10期24卷 2468-2474页

作者：王从彦刘君周嘉伟肖鸿光 School of the Environment and Safety Engineering Jiangsu University State Key Laboratory of Soil and Sustainable Agriculture (Institute of Soil Science Chinese Academy of Sciences)

This study aims to determine the differences in leaf functional traits and phenotypic plasticity of leaf functional traits between exotic and native Compositae plant species. Leaf width of exotic plants was significantly lower than that of native species. Leaf length, specific leaf area(SLA), single-leaf wet and dry weights, leaf moisture, and leaf thickness of exotic plants were also lower than those of native species but not significantly. The leaf shape index of exotic plants was higher than that of native species but not significantly. This implies that the relatively low leaf construction cost for exotic plants may play an important role in the success of their invasions. The higher leaf shape index and lower leaf width of exotic plants can enhance the efficiency of resource capture(especially sunlight capture) via adjustments to leaf shape and size, thereby increasing the survival of exotic plants. The plasticity indices of single-leaf wet weight and leaf thickness of exotic plants were significantly lower than those of native species. The lower phenotypic plasticity of single-leaf wet weight and leaf thickness of exotic plants may be the result of a cost to plasticity. That is, if the plasticity is too high, the fitness of plant species might be reduced sharply under unfavorable environments. Thus, lower plasticity of leaf functional traits may compensate for the negative impact of adverse environments and stabilize leaf construction costs for exotic plants. Moreover, reduced phenotypic plasticity might be one of the key competitive strategies by which exotic plants successfully invade new habitats. Overall, exotic plants did not always exhibit higher values of leaf functional traits or increased phenotypic plasticity of leaf functional traits compared with native species.

关键词： leaf functional traits specific leaf area (SLA) phenotypic plasticity exotic plants Compositae

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Morphological, phenological, and transcriptional analyses provide in sight into the diverse flowering traits of a mutant of the relic woody plant Liriodendron chinense

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Horticulture Research 2021年第1期8卷 2345-2360页

作者： Yu Sheng Zhaodong Hao Ye Peng Siqin Liu Lingfeng Hu Yongbao Shen Jisen Shi Jinhui Chen Key Laboratory of Forest Genetics&Biotechnology of Ministry of Education Co-Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina College of Biology and the Environment Nanjing Forestry UniversityNanjingChina Southern Tree Seed Inspection Center National Forestry Administration Nanjing Forestry UniversityNanjingChina

Flowering is crucial to plant reproduction and controlled by multiple factors.However,the mechanisms underlying the regulation of flowering in perennial plants are still largely unknown.Here,we first report a super long blooming 1(slbl)mutant of the relict tree Liriodendron chinense possessing a prolonged blooming period of more than 5 months,in contrast to the 1 month blooming period in the wild type(WT).Phenotypic characterization showed that earlier maturation of lateral shoots was caused by accelerated axillary bud fate,leading to the phenotype of continuous flowering in slbl mutants.The transcriptional activity of genes related to hormone signaling(auxin,cytokinin,and strigolactone),nutrient availability,and oxidative stress relief further indicated active outgrowth of lateral buds in slbl mutants.Interestingly,we discovered a unique FT splicing variant with intron retention specific to slbl mutants,representing a potential causal mutation in the slbl mutants.Surprisingly,most slbl inbred offspring flowered precociously with shorter juvenility(~4 months)than that(usually 8-10 years)required in WT plants,indicating heritable variation underlying continuous flowering in slbl mutants.This study reports an example of a perennial tree mutant that flowers continuously,providing a rare resource for both breeding and genetic research.

关键词： traits Morphological flowers

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A multivariate partial least squares approach to joint association analysis for multiple correlated traits

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The Crop Journal 2016年第1期4卷 21-29页

作者： Yang Xu Wenming Hu Zefeng Yang Chenwu Xu Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain CropsKey Laboratory of Plant Functional Genomics of the Ministry of Education Yangzhou University

Many complex traits are highly correlated rather than independent. By taking the correlation structure of multiple traits into account, joint association analyses can achieve both higher statistical power and more accurate estimation. To develop a statistical approach to joint association analysis that includes allele detection and genetic effect estimation, we combined multivariate partial least squares regression with variable selection strategies and selected the optimal model using the Bayesian Information Criterion(BIC). We then performed extensive simulations under varying heritabilities and sample sizes to compare the performance achieved using our method with those obtained by single-trait multilocus methods. Joint association analysis has measurable advantages over single-trait methods, as it exhibits superior gene detection power, especially for pleiotropic genes. Sample size, heritability,polymorphic information content(PIC), and magnitude of gene effects influence the statistical power, accuracy and precision of effect estimation by the joint association analysis.

关键词： Association analysis Multiple correlated traits Supersaturated model Multilocus Multivariate partial least squares

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A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant

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Horticulture Research 2020年第1期7卷 806-820页

作者： Qingzhen Wei Jinglei Wang Wuhong Wang Tianhua Hu Haijiao Hu Chonglai Bao Institute of Vegetable Research Zhejiang Academy of Agricultural SciencesHangzhou 30021China

Eggplant(Solanum melongena L.)is an economically important vegetable crop in the Solanaceae family,with extensive diversity among landraces and close relatives.Here,we report a high-quality reference genome for the eggplant inbred line HQ-1315(S.melongena-HQ)using a combination of Illumina,Nanopore and 10X genomics sequencing technologies and Hi-C technology for genome assembly.The assembled genome has a total size of~1.17 Gb and 12 chromosomes,with a contig N50 of 5.26 Mb,consisting of 36,582 protein-coding genes.Repetitive sequences comprise 70.09%(811.14 Mb)of the eggplant genome,most of which are long terminal repeat(LTR)retrotransposons(65.80%),followed by long interspersed nuclear elements(LINEs,1.54%)and DNA transposons(0.85%).The S.melongena-HQ eggplant genome carries a total of 563 accession-specific gene families containing 1009 genes.In total,73 expanded gene families(892 genes)and 34 contraction gene families(114 genes)were functionally annotated.Comparative analysis of different eggplant genomes identified three types of variations,including singlenucleotide polymorphisms(SNPs),insertions/deletions(indels)and structural variants(SVs).Asymmetric SV accumulation was found in potential regulatory regions of protein-coding genes among the different eggplant genomes.Furthermore,we performed QTL-seq for eggplant fruit length using the S.melongena-HQ reference genome and detected a QTL interval of 71.29–78.26 Mb on chromosome E03.The gene Smechr0301963,which belongs to the SUN gene family,is predicted to be a key candidate gene for eggplant fruit length regulation.Moreover,we anchored a total of 210 linkage markers associated with 71 traits to the eggplant chromosomes and finally obtained 26 QTL hotspots.The eggplant HQ-1315 genome assembly can be accessed at http://eggplant-hq.cn.In conclusion,the eggplant genome presented herein provides a global view of genomic divergence at the whole-genome level and powerful tools for the identification of candidate genes for important traits in eggplant.

关键词： traits linkage assembly

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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

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