园艺研究(英文)最新文献

IF 7.6

园艺研究(英文) Pub Date : 2024-12-05 eCollection Date: 2024-12-01 DOI: 10.1093/hr/uhae342

Zhuo Liu, Chenhao Zhang, Jinghua He, Chunjin Li, Yanhong Fu, Yongfeng Zhou, Rui Cao, Haibin Liu, Xiaoming Song

引用次数: 0

Genome-wide mapping of main histone modifications and coordination regulation of metabolic genes under salt stress in pea (Pisum sativum L).

IF 7.6

园艺研究(英文) Pub Date : 2024-09-16 eCollection Date: 2024-12-01 DOI: 10.1093/hr/uhae259

Heping Wan, Lan Cao, Ping Wang, Hanbing Hu, Rui Guo, Jingdong Chen, Huixia Zhao, Changli Zeng, Xiaoyun Liu

{"title":"Genome-wide mapping of main histone modifications and coordination regulation of metabolic genes under salt stress in pea (Pisum sativum L).","authors":"Heping Wan, Lan Cao, Ping Wang, Hanbing Hu, Rui Guo, Jingdong Chen, Huixia Zhao, Changli Zeng, Xiaoyun Liu","doi":"10.1093/hr/uhae259","DOIUrl":"10.1093/hr/uhae259","url":null,"abstract":"Pea occupy a key position in modern biogenetics, playing multifaceted roles as food, vegetable, fodder, and green manure. However, due to the complex nature of its genome and the prolonged unveiling of high-quality genetic maps, research into the molecular mechanisms underlying pea development and stress responses has been significantly delayed. Furthermore, the exploration of its epigenetic modification profiles and associated regulatory mechanisms remains uncharted. This research conducted a comprehensive investigation of four specific histone marks, namely H3K4me3, H3K27me3, H3K9ac, and H3K9me2, and the transcriptome in pea under normal conditions, and established a global map of genome-wide regulatory elements, chromatin states, and dynamics based on these major modifications. Our analysis identified epigenomic signals across ~82.6% of the genome. Each modification exhibits distinct enrichment patterns: H3K4me3 is predominantly associated with the gibberellin response pathway, H3K27me3 is primarily associated with auxin and ethylene responses, and H3K9ac is primarily associated with negative regulatory stimulus responses. We also identified a novel bivalent chromatin state (H3K9ac-H3K27me3) in pea, which is related to their development and stress response. Additionally, we unveil that these histone modifications synergistically regulate metabolic-related genes, influencing metabolite production under salt stress conditions. Our findings offer a panoramic view of the major histone modifications in pea, elucidate their interplay, and highlight their transcriptional regulatory roles during salt stress.","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"11 12","pages":"uhae259"},"PeriodicalIF":7.6,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11630261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142815135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome-wide screen and multi-omics analysis reveal OGT1 participate in the biosynthesis of safflower flavonoid glycosides.

IF 7.6

园艺研究(英文) Pub Date : 2024-09-16 eCollection Date: 2024-12-01 DOI: 10.1093/hr/uhae261

Bin Xian, Yanxun Zhou, Yueying Hu, Yanni Peng, Xiaominting Song, Ziqing Xi, Yuhang Li, Jie Yan, Chaoxiang Ren, Jin Pei, Jiang Chen

{"title":"Genome-wide screen and multi-omics analysis reveal OGT1 participate in the biosynthesis of safflower flavonoid glycosides.","authors":"Bin Xian, Yanxun Zhou, Yueying Hu, Yanni Peng, Xiaominting Song, Ziqing Xi, Yuhang Li, Jie Yan, Chaoxiang Ren, Jin Pei, Jiang Chen","doi":"10.1093/hr/uhae261","DOIUrl":"10.1093/hr/uhae261","url":null,"abstract":"Safflower, an economic crop, is renowned for its flowers, which are widely used in medicines for treating cardiovascular and cerebrovascular diseases and in dyes for food and industry. The utility of safflower depends on its flavonoid glycosides. Therefore, the biosynthesis of safflower flavonoid glycosides has been a focus of attention, but the present mechanisms remain poorly understood. This study aims to identify functional genes associated with flavonoid glycoside biosynthesis in safflower through a comprehensive approach that integrates whole-genome screen and multi-omics correlation studies. CYP and UGT are two crucial genes families involved in flavonoid glycoside biosynthesis. We have screened 264 CYP genes and 140 UGT genes in the genome of safflower and conducted analyzes including phylogenetic relationships, conserved motifs, gene structures, cis-acting elements, and chromosome mapping, which provided extensive and comprehensive data on the CYP and UGT gene families. Integration of phenotype and metabolic data from safflower different tissues helped narrow down the screening by confirming that HSYA is synthesized only in flowers. Based on the gene expression patterns and phylogenetic analysis, CtOGT1 was ultimately identified, which could catalyze the generation of glycosides using various flavonoid substrates and exhibited strong substrate affinity. Moreover, molecular docking studies elucidated CtOGT1's highly active intrinsic mechanism. In conclusion, this study effectively identified genes responsible for flavonoid glycoside biosynthesis in safflower through the integration of whole-genome screen and multi-omics analysis, established a comprehensive foundation of data, methodology, and experimental evidence for further elucidating the pathways of safflower flavonoid glycoside biosynthesis.","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"11 12","pages":"uhae261"},"PeriodicalIF":7.6,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11632156/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142815137","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrated genome-wide association and transcriptomic studies reveal genetic architecture of bulb storability of plentiful garlic germplasm resources.

IF 7.6

园艺研究(英文) Pub Date : 2024-09-16 eCollection Date: 2024-12-01 DOI: 10.1093/hr/uhae260

Yue Zhu, Huixia Jia, Jiangping Song, Tingting Zhang, Xiaohui Zhang, Wenlong Yang, Yumin Tan, Mengzhen Wang, Jiyan Zang, Haiping Wang

{"title":"Integrated genome-wide association and transcriptomic studies reveal genetic architecture of bulb storability of plentiful garlic germplasm resources.","authors":"Yue Zhu, Huixia Jia, Jiangping Song, Tingting Zhang, Xiaohui Zhang, Wenlong Yang, Yumin Tan, Mengzhen Wang, Jiyan Zang, Haiping Wang","doi":"10.1093/hr/uhae260","DOIUrl":"10.1093/hr/uhae260","url":null,"abstract":"Garlic is a widely utilized condiment and health product. However, garlic bulbs are prone to quality deterioration resulting in decrease of economic value during postharvest. In this study, the storability of 501 garlic accessions worldwide was evaluated based on the examination of decay index (DI), decay rate, sprouting rate, and bud-to-clove ratio in two consecutive years. The DI was employed as a primary index for evaluating the storability of garlic. Among these garlic, 43 accessions exhibited strong storability with DI of 0%-5%. Phenotypic and cytological observations revealed that strong storability accessions displayed delayed sprouting and decay, a slow rate of nutrient transfer to vascular bundles. Through genome-wide association study (GWAS), 234 single-nucleotide polymorphism loci (SNPs) were associated with the storability, which were located in or near 401 genes, which were annotated the functions of resistance, storage substances transport, etc. A total of 44 genes were screened using selective sweep analysis. Transcriptomic analysis was performed at four periods after storage in the 8N035 accession with strong storability and 8N258 accession with weak storability. Compared with 8N035, the upregulated genes in the 8N258 were enriched in photosynthesis and stress response, whereas the downregulated genes were enriched in response of biotic and abiotic stress and defense response. A co-expression network and GWAS identified three hub genes as key regulatory genes. Conjoint analysis of GWAS, selective sweep, and transcriptomic analysis identified 21 important candidate genes. These findings provided excellent resources with storability and vital candidate genes regulating storability for biological breeding of garlic.","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"11 12","pages":"uhae260"},"PeriodicalIF":7.6,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11630311/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142815154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A glimpse of light on the mystery of regulating temperate fruit tree blooming time.

IF 7.6

园艺研究(英文) Pub Date : 2024-08-30 eCollection Date: 2024-12-01 DOI: 10.1093/hr/uhae258

Zongrang Liu, Christopher Dardick, Marco Cirilli, Stefano Gattolin

引用次数: 0

HortDB V1.0: a genomic database of horticultural plants. HortDB V1.0：园艺植物基因组数据库。

IF 7.6

园艺研究(英文) Pub Date : 2024-08-12 eCollection Date: 2024-10-01 DOI: 10.1093/hr/uhae224

Zhidong Li, Chong Wang, Shenghao Wang, Wenquan Wang, Fei Chen

引用次数: 0

Correction to: A mutation in the brassinosteroid biosynthesis gene CpDWF5 disrupts vegetative and reproductive development and the salt stress response in squash (Cucurbita pepo). 更正：黄铜类固醇生物合成基因 CpDWF5 的突变会破坏南瓜（Cucurbita pepo）的无性和生殖发育以及盐胁迫反应。

IF 7.6

园艺研究(英文) Pub Date : 2024-08-10 eCollection Date: 2024-08-01 DOI: 10.1093/hr/uhae217

引用次数: 0

Correction to: Regulatory interaction of BcWRKY33A and BcHSFA4A promotes salt tolerance in non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis]. 更正：BcWRKY33A 和 BcHSFA4A 的调控相互作用促进了无头大白菜[Brassica campestris (syn. Brassica rapa) ssp. chinensis]的耐盐性。

IF 7.6

园艺研究(英文) Pub Date : 2024-08-10 eCollection Date: 2024-08-01 DOI: 10.1093/hr/uhae207

引用次数: 0

Genomic prediction and genome-wide association study using combined genotypic data from different genotyping systems: application to apple fruit quality traits. 利用来自不同基因分型系统的组合基因型数据进行基因组预测和全基因组关联研究：应用于苹果果实品质性状。

IF 7.6

园艺研究(英文) Pub Date : 2024-07-08 eCollection Date: 2024-07-01 DOI: 10.1093/hr/uhae131

Mai F Minamikawa, Miyuki Kunihisa, Shigeki Moriya, Tokurou Shimizu, Minoru Inamori, Hiroyoshi Iwata

{"title":"Genomic prediction and genome-wide association study using combined genotypic data from different genotyping systems: application to apple fruit quality traits.","authors":"Mai F Minamikawa, Miyuki Kunihisa, Shigeki Moriya, Tokurou Shimizu, Minoru Inamori, Hiroyoshi Iwata","doi":"10.1093/hr/uhae131","DOIUrl":"10.1093/hr/uhae131","url":null,"abstract":"With advances in next-generation sequencing technologies, various marker genotyping systems have been developed for genomics-based approaches such as genomic selection (GS) and genome-wide association study (GWAS). As new genotyping platforms are developed, data from different genotyping platforms must be combined. However, the potential use of combined data for GS and GWAS has not yet been clarified. In this study, the accuracy of genomic prediction (GP) and the detection power of GWAS increased for most fruit quality traits of apples when using combined data from different genotyping systems, Illumina Infinium single-nucleotide polymorphism array and genotyping by random amplicon sequencing-direct (GRAS-Di) systems. In addition, the GP model, which considered the inbreeding effect, further improved the accuracy of the seven fruit traits. Runs of homozygosity (ROH) islands overlapped with the significantly associated regions detected by the GWAS for several fruit traits. Breeders may have exploited these regions to select promising apples by breeders, increasing homozygosity. These results suggest that combining genotypic data from different genotyping platforms benefits the GS and GWAS of fruit quality traits in apples. Information on inbreeding could be beneficial for improving the accuracy of GS for fruit traits of apples; however, further analysis is required to elucidate the relationship between the fruit traits and inbreeding depression (e.g. decreased vigor).","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"11 7","pages":"uhae131"},"PeriodicalIF":7.6,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11228094/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141560393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Relevance and regulation of alternative splicing in plant secondary metabolism: current understanding and future directions. 植物次生代谢中替代剪接的相关性和调控：当前认识和未来方向。

IF 7.6

园艺研究(英文) Pub Date : 2024-07-02 eCollection Date: 2024-08-01 DOI: 10.1093/hr/uhae173

Zihan Xu, Ying Xiao, Jinlin Guo, Zongyou Lv, Wansheng Chen

{"title":"Relevance and regulation of alternative splicing in plant secondary metabolism: current understanding and future directions.","authors":"Zihan Xu, Ying Xiao, Jinlin Guo, Zongyou Lv, Wansheng Chen","doi":"10.1093/hr/uhae173","DOIUrl":"10.1093/hr/uhae173","url":null,"abstract":"The secondary metabolism of plants is an essential life process enabling organisms to navigate various stages of plant development and cope with ever-changing environmental stresses. Secondary metabolites, abundantly found in nature, possess significant medicinal value. Among the regulatory mechanisms governing these metabolic processes, alternative splicing stands out as a widely observed post-transcriptional mechanism present in multicellular organisms. It facilitates the generation of multiple mRNA transcripts from a single gene by selecting different splicing sites. Selective splicing events in plants are widely induced by various signals, including external environmental stress and hormone signals. These events ultimately regulate the secondary metabolic processes and the accumulation of essential secondary metabolites in plants by influencing the synthesis of primary metabolites, hormone metabolism, biomass accumulation, and capillary density. Simultaneously, alternative splicing plays a crucial role in enhancing protein diversity and the abundance of the transcriptome. This paper provides a summary of the factors inducing alternative splicing events in plants and systematically describes the progress in regulating alternative splicing with respect to different secondary metabolites, including terpenoid, phenolic compounds, and nitrogen-containing compounds. Such elucidation offers critical foundational insights for understanding the role of alternative splicing in regulating plant metabolism and presents novel avenues and perspectives for bioengineering.","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"11 8","pages":"uhae173"},"PeriodicalIF":7.6,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11317897/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141972341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0