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Journal of Integrative Agriculture 2023年第6期22卷 1695-1703页

作者： CHEN Xiao-dong CAI Wei-jian XIA Jin YUAN Hua-zhao WANG Qing-lian PANG Fu-hua ZHAO Mi-zhen Institute of Pomology Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic ImprovementNanjing 210000P.R.China

Carotenoids are an important component of the human diet, and fruit is a primary source of carotenoids. The synthesis and regulation of carotenoids in fruit are important contributors to the formation of fruit quality. In China, strawberry is one of the main seasonal fruits grown in the winter. Previous studies have shown that light has a significant effect on the metabolism of anthocyanins, sugars, and polyphenols in strawberry. However, the understanding of the role of light in regulating the metabolism of carotenoids in strawberry remains limited. This study investigated the effects of blue, red, yellow-green, and white light on carotenoid metabolism in strawberry.Blue light treatment promoted the synthesis of multiple carotenoids, including lutein, compared with the other three treatment groups. The RNA sequencing data revealed that blue light treatment promoted the expression of lycopene ε-cyclase(LCYE), and the transient overexpression of LCYE in strawberry fruit promoted lutein accumulation in strawberry. Overall, the results suggest that blue light can promote the synthesis of lutein in strawberry by inducing the expression of LCYE.

关键词： carotenoid LED light strawberry lutein

Gene regulation of anthocyanin biosynthesis in two blood-flesh peach （Prunus persica （L.） Batsch） cultivars during fruit development

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2014年第9期15卷 809-819页

作者： Yun JIAO Rui-juan MA Zhi-jun SHEN Juan YAN Ming-liang YU Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Institute of HorticultureJiangsu Academy of Agricultural Sciences

The original version of this article unfortunately contained a mistake.In the caption of Fig.1,'(a)Beijingyixianhong;(b)Heiyoutao;(c)Xuebaitao'was incorrect.The correct version should be'(a)Heiyoutao;(b)Beijingyixianh... 详细信息

关键词：红肉桃花色素苷套袋基因表达

Dynamic patterns of the translatome in a hybrid triplet show translational fractionation of the maize subgenomes

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The crop Journal 2022年第1期10卷 36-46页

作者： Wanchao Zhu Sijia Chen Tifu Zhang Jia Qian Zi Luo Han Zhao Yirong Zhang Lin Li National key laboratory of crop genetic improvement Huazhong Agricultural UniversityWuhan 430070HubeiChina jiangsu Provincial key laboratory of Agrobiology Institute of Germplasm Resources and BiotechnologyJiangsu Academy of Agricultural SciencesNanjing 210014JiangsuChina key laboratory of crop Heterosis and Utilization(MOE)and State key laboratory for Agrobiotechnology Key Laboratory of Crop Genomics and Genetic Improvement(MOA)Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China

Heterosis,the phenomenon in which hybrids outperform their parents,has been utilized in maize(Zea mays L.)for over 100 years.To provide a more complete understanding of heterosis,we collected a comprehensive transcriptome and translatome dataset on seedling leaves for B73,Mo17,and their F1 hybrid,which provided a dynamic landscape of transcriptomic and translatomic variation in maize.Although additivity accounted for a large proportion of variation at two omics-levels,an elevated nonadditive effect was observed in the translatome,especially in the translated subgenome maize1 genes,and the genes that switched from additivity in the transcriptome to nonadditivity in the translatome were significantly enriched in the subgenome maize1.Many genes with allele-specific expression and translation show dramatic regulatory switches between the transcriptome and translatome,and partial genes with allele-specific translation underlying regulatory mechanism also exhibited subgenome bias.Interestingly,we found the translated isoforms show different expression patterns compared with transcriptome and more genes changed their dominant isoforms during the genetic flow from parents to the hybrid at the translatome level.The translated genes with switched dominant isoforms significantly biased to the subgenome maize2 while genes with conserved dominant isoforms significantly enriched in subgenome maize1.Together,the dynamic changed patterns in translatome across hybrid and parental lines show translational fractionation of the maize subgenomes,which may be associated with heterosis in maize and provides a potential theoretical basis for breeding.

关键词： Heterosis Translatome Ribosome-sequencing(Ribo-seq) Subgenomes Maize

Identification and expression analysis of chlorogenic acid biosynthesis key gene PpHCT in peach

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horticultural Plant Journal 2023年第4期9卷 670-680页

作者： Ziwen Su Meng Sun Zhixiang Cai Shaolei Guo Jiyao Li Bintao Zhao Zhijun Shen Ruijuan Ma Juan Yan Mingliang Yu College of Horticulture Nanjing Agricultural UniversityNanjingJiangsu 210095China Institute of Pomology Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic ImprovementNanjingJiangsu 210014China

Shikimic acid/quinic acid hydroxy cinnamyl transferase(HCT)is one of the key enzymes in the phenylpropanoid pathway.However,the role of the HCT gene in chlorogenic acid(CGA)biosynthesis in peach fruit remains unclear.For this,we identified the accumulation pattern of CGA in four peach cultivars,cloned and characterized 11 PpHCT gene members,and further analyzed the expression patterns of these PpHCT genes during fruit development.The contents of CGAs in the four peach cultivars all exhibited a trend of increasing and then decreasing during the fruit growth and development.Moreover,the contents of CGAs in the peel and flesh were tissue-specific.Gene structure analysis indicated that the PpHCT genes were highly conserved,containing two exons and one intron.The protein structure analysis demonstrated that the PpHCT proteins contained two conserved motifs(HXXXD,DFGWG)and a transferase domain(PF02458),which belonged to the BAHD acyltransferase family.The cis-acting element analysis suggested that the promoters of PpHCT genes contained many light-related,hormone-related,stress-related,tissue-specific,and circadian-related elements,and they could participate in a variety of biological processes.Phylogenetic analysis showed that the HCT proteins of peach were closely related to the HCT proteins of plum and had a close evolutionary relationship.The qRT-PCR analysis indicated that the expression levels of PpHCT1 and PpHCT2 showed an opposite trend to the accumulation of CGA,whereas the expression levels of PpHCT4,PpHCT5,PpHCT7,PpHCT8,and PpHCT11 demonstrated the same trend as CGA accumulation.It was worth noting that only PpHCT4 and PpHCT5 were highly expressed in the two high-CGA cultivars but showed low levels of expression in the two low-CGA cultivars.Therefore,it was hypothesized that these two genes might be key genes to the synthesis of CGA in peach fruit.Those findings provide a theoretical basis for further study on the biological functions of the HCT gene and help to reveal the molecular mechanism of CGA.

关键词： Prunus persica(L.) Chlorogenic acid PpHCT Bioinformatics analysis Gene expression

OcBSA:An NGS-based bulk segregant analysis tool for outcross populations

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Molecular Plant 2024年第4期17卷 648-657页

作者： Lingkui Zhang Yanfeng Duan Zewei Zhang Lei Zhang Shumin Chen Chengcheng Cai Shaoguang Duan Kang Zhang Guangcun Li Feng Cheng State key laboratory of Vegetable Biobreeding Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsKey Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China

Constructing inbred lines for self-incompatible species and species with long generation times is challenging,making the use of F1 outcross/segregating populations the main strategy for genetic studies of such species.However,there is a lack of dedicated algorithms/tools for rapid quantitative trait locus(QTL)mapping using the F1 populations.To this end,we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 populations.OcBSA transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 population.Testing of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and accuracy.In addition,the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple,pear,peach,citrus,grape,tea,and rice.We also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this study.The OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene,which regulates potato flower color.Taken together,these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing species.For ease of use,we have developed both Windows and Linux versions of OcBSA,which are freely available at:https://***/Bioinformaticslab/OcBSA.

关键词： outcross BSA self-incompatible F1 population QTL mapping potato

Genome-wide analysis of the SCPL gene family in grape(Vitis vinifera L.)

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Journal of Integrative Agriculture 2021年第10期20卷 2666-2679页

作者： WANG Xi-cheng WU Wei-min ZHOU Bei-bei WANG Zhuang-wei QIAN Ya-ming WANG Bo YAN Li-chun Institute of Pomology Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic ImprovementNanjing 210014P.R.China

Serine carboxypeptidase-like(SCPL)proteins are a group of acyltransferase enzymes that have important roles in plant growth,development,and stress responses.Although SCPL proteins have been studied in many plants,the biological functions of SCPL genes in grape are still unknown.In this study,59 putative SCPL proteins were identified from the grape genome.A bioinformatics analysis,including chromosomal locations,exon/intron structures,phylogeny,cis-elements,and conserved motifs,was performed for the gene family.The phylogenetic analysis revealed that VvSCPL proteins could be classified into three groups,with the gene motifs in each group showing high similarity levels.The number of exons in the VvSCPL genes ranged from 1 to 19,suggesting significant variations among grape SCPL genes.The expression of the VvSCPL genes,as assessed by RNA sequencing(RNA-seq)and quantitative real-time PCR,showed that most VvSCPL genes responded to drought-and waterlogging-stress treatments,which indicated their roles in abiotic stress responses.The results provide useful information for further study of SCPL genes in grape.

关键词： serine carboxypeptidase-like(SCPL)protein grape phylogenetic relationships abiotic stress gene expression

Genome-wide analysis of the invertase genes in strawberry(Fragaria×ananassa)

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Journal of Integrative Agriculture 2021年第10期20卷 2652-2665页

作者： YUAN Hua-zhao PANG Fu-hua CAI Wei-jian CHEN Xiao-dong ZHAO Mi-zhen YU Hong-mei Institute of Pomology Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic ImprovementNanjing 210014P.R.China

Sugar is an important material basis in fruit development,and strawberry fruit flavour and sweetness largely depend on the sugar content and variety.Invertases(INVs)play an important role in the regulation of sugar accumulation because they irreversibly catalyse the hydrolysis of sucrose into the corresponding nucleoside diphosphate-glucose,glucose or fructose in fruit.In this work,we provided a comprehensive analysis of the INV gene family in octoploid strawberry(Fragaria×ananassa),including the gene structure,chromosomal locations,conserved domains,and gene evolution and expression profiles during strawberry fruit development.Our study revealed that polyploid events resulted in the abundant amplification(almost three-or four-fold)of the INV gene in the F.×ananassa genome,and these amplified INV genes showed dominant expression in strawberry fruit.More than half of the FaINVs transcripts with low expression had incomplete coding sequences by alternative splicing.Previous studies have shown that cell wall invertases(CWINV)are involved in the regulation of phloem unloading and sink strength establishment.The expression of FaCWINV1 was markedly upregulated during fruit development and strongly expressed in ripe fruit.Moreover,a significant correlation was observed between the total sugar content and the FaCWINV1 expression level.These findings suggest that FaCWINV1 may be involved in sugar accumulation in strawberry fruit.Taken together,the results of our study will be beneficial for further research into the functions of INVs in the regulation of fruit ripening.

关键词： strawberry sugar invertases fruit ripening

Evaluation of the early defoliation trait and identification of resistance genes through a comprehensive transcriptome analysis in pears

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Journal of Integrative Agriculture 2023年第1期22卷 120-138页

作者： SHAN Yan-fei LI Meng-yan WANG Run-ze LI Xiao-gang LIN Jing LI Jia-ming ZHAO Ke-jiao WU Jun College of Horticulture/State key laboratory of crop genetics and Germplasm Enhancement Nanjing Agricultural UniversityNanjing 210095P.R.China Institute of Horticulture Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic ImprovementNanjing 210095P.R.China

Early defoliation,which usually occurs during summer in pear trees,is gradually becoming a major problem that poses a serious threat to the pear industry in southern China.However,there is no system for evaluating the responses of different cultivars to early defoliation,and our knowledge of the potential molecular regulation of the genes underlying this phenomenon is still limited.In this study,we conducted field investigations of 155 pear accessions to assess their resistance or susceptibility to early defoliation.A total of 126 accessions were found to be susceptible to early defoliation,and only 29 accessions were resistant.Among them,19 resistant accessions belong to the sand pear species(Pyrus pyrifolia).To identify the resistance genes related to early defoliation,the healthy and diseased samples of two sand pear accessions,namely,the resistant early defoliation accession‘Whasan’and the susceptible early defoliation accession‘Cuiguan’,were used to perform RNA sequencing.Compared with‘Cuiguan’,a total of 444 genes were uniquely differentially expressed in‘Whasan’.Combined with GO and KEGG enrichment analyses,we found that early defoliation was closely related to the stress response.Furthermore,a weighted gene co-expression network analysis revealed a high correlation of WRKY and ethylene responsive factor(ERF)transcription factors with early defoliation resistance.This study provides useful resistant germplasm resources and new insights into potentially essential genes that respond to early defoliation in pears,which may facilitate a better understanding of the resistance mechanism and molecular breeding of resistant pear cultivars.

关键词： pear early defoliation resistance and susceptibility evaluation RNA-seq WRKY ERF

A genome-wide association study uncovers a critical role of the RsPAP2 gene in red-skinned Raphanus sativus L.

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Horticulture Research 2020年第1期7卷 793-805页

作者： Lianxue Fan YanWang Liang Xu Mingjia Tang Xiaoli Zhang Jiali Ying Cui Li Junhui Dong Liwang Liu National key laboratory of crop genetics and Germplasm Enhancement Key Laboratory of Horticultural Crop Biology and Genetic Improvement(East China)of MOARCollege of HorticultureNanjing Agricultural University210095 NanjingPR China

Radish(Raphanus sativus L.)taproot contains high concentrations of flavonoids,including anthocyanins(ATCs),in redskinned genotypes.However,little information on the genetic regulation of ATC biosynthesis in radish is available.A genome-wide association study of radish red skin color was conducted using whole-genome sequencing data derived from 179 radish genotypes.The R2R3-MYB transcription factor production of anthocyanin pigment 2(PAP2)gene was found in the region associated with a leading SNP located on chromosome 2.The amino acid sequence encoded by the RsPAP2 gene was different from those of the other published RsMYB genes responsible for the red skin color of radish.The overexpression of the RsPAP2 gene resulted in ATC accumulation in Arabidopsis and radish,which was accompanied by the upregulation of several ATC-related structural genes.RsPAP2 was found to bind the RsUFGT and RsTT8 promoters,as shown by a dual-luciferase reporter system and a yeast one-hybrid assay.The promoter activities of the RsANS,RsCHI,RsPAL,and RsUFGT genes could be strongly activated by coinfiltration with RsPAP2 and RsTT8.These findings showed the effectiveness of GWAS in identifying candidate genes in radish and demonstrated that RsPAP2 could(either directly or together with its cofactor RsTT8)regulate the transcript levels of ATC-related genes to promote ATC biosynthesis,facilitating the genetic enhancement of ATC contents and other related traits in radish.

关键词： Raphanus critical finding

ESCRT-Ⅲ component OsSNF7.2 modulates leaf rolling by trafficking and endosomal degradation of auxin biosynthetic enzyme OsYUC8 in rice

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Journal of Integrative Plant Biology 2023年第6期65卷 1408-1422页

作者： Liang Zhou Saihua Chen Maohong Cai Song Cui Yulong Ren Xinyue Zhang Tianzhen Liu Chunlei Zhou Xin Jin Limin Zhang Minxi Wu Shuyi Zhang Zhijun Cheng Xin Zhang Cailin Lei Qibing Lin Xiuping Guo Jie Wang Zhichao Zhao Ling Jiang Shanshan Zhu Jianmin Wan State key laboratory for crop genetics and Germplasm Enhancement Jiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing 210095China National key Facility for crop Gene Resources and genetic improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China jiangsu key laboratory of crop Genomics and Molecular Breeding/key laboratory of Plant Functional Genomics of the Ministry of Education/jiangsu key laboratory of crop genetics and Physiology Agricultural College of Yangzhou UniversityYangzhou 225009China

The endosomal sorting complex required for transport(ESCRT)is highly conserved in eukaryotic cells and plays an essential role in the biogenesis of multivesicular bodies and cargo degradation to the plant vacuole or lysosomes.Although ESCRT components affect a variety of plant growth and development processes,their impact on leaf development is rarely reported.Here,we found that OsSNF7.2,an ESCRT-Ⅲ component,controls leaf rolling in rice(Oryza sativa).The Ossnf7.2 mutant rolled leaf 17(rl17)has adaxially rolled leaves due to the decreased number and size of the bulliform cells.OsSNF7.2is expressed ubiquitously in all tissues,and its protein is localized in the endosomal compartments.OsSNF7.2 homologs,including OsSNF7,OsSNF7.3,and OsSNF7.4,can physically interact with OsSNF7.2,but their single mutation did not result in leaf rolling.Other ESCRT complex subunits,namely OsVPS20,OsVPS24,and OsBRO1,also interact with OsSNF7.2.Further assays revealed that OsSNF7.2 interacts with OsYUC8 and aids its vacuolar degradation.Both Osyuc8and rl17 Osyuc8 showed rolled leaves,indicating that OsYUC8 and OsSNF7.2 function in the same pathway,conferring leaf development.This study reveals a new biological function for the ESCRT-Ⅲcomponents,and provides new insights into the molecular mechanisms underlying leaf rolling.

关键词： bulliform cell leaf rolling OsSNF7.2 OsYUC8 rice(Oryza sativa) vacuolar degradation