Horticulture Research最新文献_第10页

Transcription Factors LvBBX24 and LvbZIP44 Coordinated Anthocyanin Accumulation in Response to Light in Lily Petals 转录因子 LvBBX24 和 LvbZIP44 协调百合花瓣中花青素的积累以应对光照

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2024-07-30 DOI: 10.1093/hr/uhae211

Zhenhua Gao, Yibo Sun, Ziman Zhu, Na Ni, Shaokun Sun, Mengyao Nie, Weifeng Du, Muhammad Irfan, Lijing Chen, Li Zhang

{"title":"Transcription Factors LvBBX24 and LvbZIP44 Coordinated Anthocyanin Accumulation in Response to Light in Lily Petals","authors":"Zhenhua Gao, Yibo Sun, Ziman Zhu, Na Ni, Shaokun Sun, Mengyao Nie, Weifeng Du, Muhammad Irfan, Lijing Chen, Li Zhang","doi":"10.1093/hr/uhae211","DOIUrl":"https://doi.org/10.1093/hr/uhae211","url":null,"abstract":"Lily (Lilium spp.), a horticultural crop serving both ornamental and edible functions, derives its coloration primarily from anthocyanins. However, limited studies have been conducted on the accumulation of anthocyanins within lilies. In this study, we cloned a light-induced transcription factor named as LvBBX24 in lilies. Through genetic and biochemical analysis, we determined that LvBBX24 could upregulate the transcription of LvMYB5 and facilitate anthocyanin synthesis. Moreover, we identified that darkness promoted the degradation of LvBBX24 protein. Through screening a yeast library, we identified LvbZIP44 acts as its interacting partner. Genetic testing confirmed that LvbZIP44 also plays a role in promoting lily anthocyanin synthesis. This indicates a potential synergistic regulatory effect between LvBBX24 and LvbZIP44. Our study indicates that LvBBX24 and LvbZIP44 cooperate to regulate anthocyanin accumulation in lily petals. These findings provide compelling evidence supporting the idea that LvBBX24 and LvbZIP44 may form a looped helix surrounding the LvMYB5 promoter region to regulate anthocyanin biosynthesis.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Improvement and application of vacuum-infiltration system in tomato 番茄真空过滤系统的改进和应用

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2024-07-27 DOI: 10.1093/hr/uhae197

Xinghao Yao, Ayat Taheri, Hang Liu, Yaojie Zhang, Ling Li, Jin Shao, Ke Wu, Qing Miao, Weizhi He, Xinyi Hu, Kexuan Tang

{"title":"Improvement and application of vacuum-infiltration system in tomato","authors":"Xinghao Yao, Ayat Taheri, Hang Liu, Yaojie Zhang, Ling Li, Jin Shao, Ke Wu, Qing Miao, Weizhi He, Xinyi Hu, Kexuan Tang","doi":"10.1093/hr/uhae197","DOIUrl":"https://doi.org/10.1093/hr/uhae197","url":null,"abstract":"Agrobacterium-mediated transient expression system has been developed and applied to various plants as alternatives to stable transformation. However, its application in tomatoes is still limited due to low expression efficiency. In this study, we described an improved vacuum-infiltration system that can be used in both tomato fruits and leaves. Notably, this study is the first report of vacuum infiltration in attached tomato fruits. The feasibility of the improved vacuum-infiltration system in Micro-Tom tomato was confirmed by various assays, including multiple fluorescent protein expression analysis, β-glucuronidase activity analysis, and RUBY reporter visualization. Subsequently, the improved vacuum-infiltration system was successfully applied to tomato biotechnology research. Herein, a trichome-specific promoter in tomato was identified that can drive the directional synthesis of specific plant natural products (PNPs). Additionally, based on the assessment results of the improved vacuum-infiltration system, we obtained a flavonoid-rich tomato variety through the stable transformation of AmRosea and AmDelila. In a significant practical application, we successfully synthesized the high-value scutellarin in tomato, which provides an alternative route for the production of PNPs from plants. In addition, the improved vacuum-infiltration system has been demonstrated to be suitable for commercial tomato varieties (‘Emerald’ and ‘Provence’) as well. The improved vacuum-infiltration system not only speeds up fundamental and applied research in tomato but also offers an additional powerful tool for advancing tomato synthetic biology research.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141769095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Is ATP a Signaling Regulator for Postharvest Chilling Tolerance in Fruits? ATP 是水果采后耐寒性的信号调节器吗？

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2024-07-25 DOI: 10.1093/hr/uhae204

Hansika Sati, Harinder Singh Oberoi, Sunil Pareek

引用次数: 0

A Genome Assembly of decaploid Houttuynia cordata Provides Insights into the evolution of Houttuynia and the biosynthesis of alkaloids 十倍体蕺菜基因组组装为蕺菜的进化和生物碱的生物合成提供了启示

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2024-07-24 DOI: 10.1093/hr/uhae203

Peng Huang, Zhu Li, Huan Wang, Jinqiang Huang, Guifeng Tan, Yue Fu, Xiubin Liu, Shang Zheng, Peng Xu, Mengshan Sun, Jianguo Zeng

{"title":"A Genome Assembly of decaploid Houttuynia cordata Provides Insights into the evolution of Houttuynia and the biosynthesis of alkaloids","authors":"Peng Huang, Zhu Li, Huan Wang, Jinqiang Huang, Guifeng Tan, Yue Fu, Xiubin Liu, Shang Zheng, Peng Xu, Mengshan Sun, Jianguo Zeng","doi":"10.1093/hr/uhae203","DOIUrl":"https://doi.org/10.1093/hr/uhae203","url":null,"abstract":"Houttuynia cordata Thunb., commonly known as yuxingcao in China, is known for its characteristic fishy smell and is widely recognized as an important herb and vegetable in many parts of Asia. However, the lack of genomic information on H. cordata limits the understanding of its population structure, genetic diversity and biosynthesis of medicinal compounds. Here, we used single-molecule sequencing, Illumina paired-end sequencing and chromosome conformation capture technology to construct the first chromosome-scale decaploid H. cordata reference genome. The genome assembly was 2.63 Gb in size, with 1,348 contigs and a contig N50 of 21.94 Mb further clustered and ordered into 88 pseudochromosomes based on Hi-C analysis. The results of genome evolution analysis showed that H. citrina underwent a whole-genome duplication (WGD) event approximately 17 million years ago, and an additional WGD event occurred 3.3 million years ago, which may be the main factor leading to the high abundance of multiple copies of orthologous genes. Here, transcriptome sequencing across five different tissues revealed significant expansion and distinct expression patterns of key gene families, such as L-amino acid/L-tryptophan decarboxylase and strictosidine synthase, which are essential for the biosynthesis of isoquinoline and indole alkaloids, along with the identification of genes such as TTM3, which is critical for root development. This study constructed the first decaploid medicinal plant genome and revealed the genome evolution and polyploidization events of H. cordata.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141755491","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrating QTL Mapping and Transcriptomics to Decipher the Genetic Architecture of Sterol Metabolism in Brassica napus L 整合 QTL 图谱和转录组学，破译甘蓝型油菜中甾醇代谢的遗传结构

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2024-07-24 DOI: 10.1093/hr/uhae196

Yiyi Xiong, Guangyuan Lu, Huaixin Li, Jianjie He, Shipeng Fan, Shuxiang Yan, Liangxiao Zhang, Haibo Jia, Maoteng Li

{"title":"Integrating QTL Mapping and Transcriptomics to Decipher the Genetic Architecture of Sterol Metabolism in Brassica napus L","authors":"Yiyi Xiong, Guangyuan Lu, Huaixin Li, Jianjie He, Shipeng Fan, Shuxiang Yan, Liangxiao Zhang, Haibo Jia, Maoteng Li","doi":"10.1093/hr/uhae196","DOIUrl":"https://doi.org/10.1093/hr/uhae196","url":null,"abstract":"Sterols are secondary metabolites commonly found in rapeseed that play crucial physiological roles in plants and also benefit human health. Consequently, unraveling the genetic basis of sterol synthesis in rapeseed is highly important. In this study, 21 individual sterols, as well as total sterol content (TS) were detected in a double haploid (DH) population of Brassica napus, and a total of 24 QTL and 157 mQTL were identified that were associated with TS and different individual sterols. Time-series transcriptomic analysis showed that the differentially expressed genes (DEGs) involved in sterol and lipid biosynthesis pathways were enriched. Additionally, a regulatory network between sterol-related DEGs and transcription factors (TFs) was established using coexpression analysis. Some candidate genes were identified with the integration of transcriptomic analysis and QTL mapping, and the key candidate gene BnSQS1.C03 was selected for further functional analysis. BnSQS1.C03 demonstrated squalene synthase activity in vitro and increased the TS by 3.8% when overexpressed in Arabidopsis. The present results provide new insights into sterol regulatory pathways and a valuable genetic basis for breeding rapeseed varieties with high sterol content in the future.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141755488","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Full-Length Transcriptome Sequencing of Pepper Fruit During Development and Construction of a Transcript Variation Database 辣椒果实发育过程中的全长转录组测序及转录变异数据库的构建

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2024-07-24 DOI: 10.1093/hr/uhae198

Zhoubin Liu, Bozhi Yang, Tianyuan Zhang, Hao Sun, Lianzhen Mao, Sha Yang, Xiongze Dai, Huan Suo, Zhuqing Zhang, Wenchao Chen, Hu Chen, Wangjie Xu, Komivi Dossa, Xuexiao Zou, Lijun Ou

{"title":"Full-Length Transcriptome Sequencing of Pepper Fruit During Development and Construction of a Transcript Variation Database","authors":"Zhoubin Liu, Bozhi Yang, Tianyuan Zhang, Hao Sun, Lianzhen Mao, Sha Yang, Xiongze Dai, Huan Suo, Zhuqing Zhang, Wenchao Chen, Hu Chen, Wangjie Xu, Komivi Dossa, Xuexiao Zou, Lijun Ou","doi":"10.1093/hr/uhae198","DOIUrl":"https://doi.org/10.1093/hr/uhae198","url":null,"abstract":"Chili pepper is an important spice and a model plant for fruit development studies. Large-scale omics information on chili pepper plant development continues to be gathered for understanding development as well as capsaicin biosynthesis. In this study, a full-spectrum transcriptome data of eight chili pepper tissues at five growth stages using the Oxford Nanopore long-read sequencing approach was generated. Of the 450 015 transcripts, 35 336 were recorded as reference transcripts (genes), while 327 268 were novel including coding, lnc, and other non-coding RNAs. These novel transcripts belonged to unknown/intergenic (347703), those retained introns (26336), and had multi-exons with at least one junction match (20333). In terms of alternative splicing, retained intron had the highest proportion (14795). The number of tissue-specific expressed transcripts ranged from 22 925 (stem) to 40 289 (flower). The expression changes during fruit and placenta development are discussed in detail. Integration of gene expression and capsaicin content quantification throughout the placental development clarifies that capsaicin biosynthesis in pepper is mainly derived from valine, leucin, and isoleucine degradation as well as citrate cycle and/or pyrimidine metabolism pathways. Most importantly, a user-friendly Pepper Full-Length Transcriptome Variation Database (PFTVD 1.0) (http://pepper-database.cn/) has been developed. PFTVD 1.0 provides transcriptomics and genomics information and allows users to analyze the data using various tools implemented. This work highlights the potential of long-read sequencing to discover novel genes and transcripts and their diversity in plant developmental biology.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141755489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Local and systemic transcriptome and spliceome reprogramming induced by the root-knot nematode Meloidogyne incognita in tomato 番茄根结线虫诱导的局部和系统转录组和剪接组重构

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2024-07-24 DOI: 10.1093/hr/uhae206

Selin Ozdemir, Sarbottam Piya, Valeria S Lopes-Caitar, Nicole Coffey, J Hollis Rice, Tarek Hewezi

{"title":"Local and systemic transcriptome and spliceome reprogramming induced by the root-knot nematode Meloidogyne incognita in tomato","authors":"Selin Ozdemir, Sarbottam Piya, Valeria S Lopes-Caitar, Nicole Coffey, J Hollis Rice, Tarek Hewezi","doi":"10.1093/hr/uhae206","DOIUrl":"https://doi.org/10.1093/hr/uhae206","url":null,"abstract":"Root-knot nematodes (Meloidogyne spp.) are widely spread root parasites that infect thousands of vascular plant species. These highly polyphagous nematodes engage in sophisticated interactions with host plants that results in the formation of knot-like structures known as galls whose ontogeny remains largely unknown. Here, we determined transcriptome changes and alternative splicing variants induced by Megalaima incognita in galls and neighboring root cells at two distinct infective stages. M. incognita induced substantial transcriptome changes in tomato roots both locally in galls and systemically in neighboring cells. A considerable parallel regulation of gene expression in galls and neighboring cells were detected, indicative of effective intercellular communications exemplified by suppression of basal defense responses particularly during the early stage of infection. The transcriptome analysis also revealed that M. incognita exerts a tight control over the cell cycle process as a whole that results in an increase of ploidy levels in the feeding sites and accelerated mitotic activity of the gall cells. Alternative splicing analysis indicated that M. incognita significantly modulates pre-mRNA splicing as a total of 9064 differentially spliced events from 2898 genes were identified where intron retention and exon skipping events were largely suppressed. Furthermore, a number of differentially spliced events were functionally validated using transgenic hairy root system and found to impact gall formation and nematode egg mass production. Together, our data provide unprecedented insights into the transcriptome and spliceome reprogramming induced by M. incognita in tomato with respect to gall ontogeny and nematode parasitism.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141755487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Abscisic acid regulates Cl − efflux via the ABI5-ZAT10-SLAH3 module in chloride-stressed Malus hupehensis 脱落酸通过 ABI5-ZAT10-SLAH3 模块调节氯化物胁迫下黄桷树的 Cl - 外流

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2024-07-24 DOI: 10.1093/hr/uhae200

Jianfei Song, Junhong Yan, Baozhen Sun, Bing Chen, Xiaoyue Zhu, Hongcai Wei, Zhilong Bao, Fangfang Ma, Weiwei Zhang, Hongqiang Yang

{"title":"Abscisic acid regulates Cl − efflux via the ABI5-ZAT10-SLAH3 module in chloride-stressed Malus hupehensis","authors":"Jianfei Song, Junhong Yan, Baozhen Sun, Bing Chen, Xiaoyue Zhu, Hongcai Wei, Zhilong Bao, Fangfang Ma, Weiwei Zhang, Hongqiang Yang","doi":"10.1093/hr/uhae200","DOIUrl":"https://doi.org/10.1093/hr/uhae200","url":null,"abstract":"The overload of Cl− typically causes cell damage and death in plants, especially in Cl—sensitive crops. Abscisic acid (ABA) is a stress-induced phytohormone that can alleviate chloride stress by reducing Cl− accumulation; however, the mechanism is not clear. Here, we found that the application of ABA elevated Cl− efflux from roots and reduced membrane damage and cell death in chloride-stressed Malus hupehensis. MhSLAH3, a homolog of the slow anion channel from M. hupehensis, encoded a channel controlling Cl− efflux and was induced by both chloride and ABA. MhSLAH3 overexpression accelerated Cl− efflux, which enhanced the tolerance of M. hupehensis to chloride stress, and retarded chloride-induced cell death. However, the suppression of MhSLAH3 partially offset the acceleration effect of ABA on Cl− efflux. MhZAT10L was then identified as a C2H2-type transcription factor upstream of MhSLAH3, repressing MhSLAH3 transcription under chloride stress. The suppression of MhZAT10L accelerated Cl− efflux by releasing suppressed MhSLAH3, but MhZAT10L overexpression counteracted the effects of ABA on Cl− efflux. MhABI5 promoted Cl− efflux mediated by MhSLAH3 due to induction by ABA and transcriptional repression of MhZAT10L, but this function of MhABI5 was reversed by MhZAT10L overexpression. The suppression of MhABI5 diminished the positive effects of ABA on Cl− efflux and retarding cell death. Thus, ABA repressed MhZAT10L transcription by activating MhABI5, further releasing MhSLAH3 to accelerate Cl− efflux. These findings provide a new evidence of ABA regulation of Cl− efflux.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141755490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mutation of YFT3, an isomerase in the isoprenoid biosynthetic pathway, impairs its catalytic activity and carotenoid accumulation in tomato fruit 异戊二烯生物合成途径中的异构酶 YFT3 发生突变，会影响其催化活性和番茄果实中类胡萝卜素的积累

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2024-07-24 DOI: 10.1093/hr/uhae202

Wenzhen Li, Lulu Chen, Weihua Zhao, Yuhang Li, Ying Chen, Tengjian Wen, Zhengjun Liu, Chao Huang, Lida Zhang, Lingxia Zhao

{"title":"Mutation of YFT3, an isomerase in the isoprenoid biosynthetic pathway, impairs its catalytic activity and carotenoid accumulation in tomato fruit","authors":"Wenzhen Li, Lulu Chen, Weihua Zhao, Yuhang Li, Ying Chen, Tengjian Wen, Zhengjun Liu, Chao Huang, Lida Zhang, Lingxia Zhao","doi":"10.1093/hr/uhae202","DOIUrl":"https://doi.org/10.1093/hr/uhae202","url":null,"abstract":"Tomato fruit colors are directly associated with their appearance quality and nutritional value. However, the tomato fruit color formation is an intricate biological process that remain elusive. In this work, we characterized a tomato yellow fruited tomato 3 (yft3, e9292, Solanum lycopersicum) mutant with yellow fruits. By the map-based cloning approach, we identified a transversion mutation (A2117C) in YFT3 gene encoding a putative isopentenyl diphosphate isomerase (SlIDI1) enzyme which may functions in the isoprenoid biosynthetic pathway by catalyzing conversion between isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). The mutated YFT3 (A2117C) (designated to YFT3 allele) and the YFT3 genes did not show expression difference at protein level, and their encoded YFT3 allele (S126R) and YFT3 proteins were both localized in plastids. However, the transcript levels of eight genes (DXR, DXS, HDR, PSY1, CRTISO, CYCB, CYP97A, and NCED) associated with carotenoid synthesis were up-regulated in fruits of both yft3 and YFT3 knockout (YFT3-KO) lines at 35dpa and 47dpa compared to the red-fruit tomato cultivar (M82). The in vitro and in vivo biochemical analyses indicated YFT3(S126R) possessed much lower enzymatic activities than the YFT3 protein, indicating that S126R mutation can impair YFT3 activity. The molecular docking analysis showed that YFT3 allele has higher ability to recruit IPP, but abolishes attachment of the Mg2+ cofactor with IPP, suggesting that Ser126 is a critical residue for YTF3 biochemical and physiological functions. As a result, the yft3 mutant tomato line has low carotenoid accumulation and abnormal chromoplast development, which results in the yellow ripe fruits. This study provides new insights into molecular mechanisms of tomato fruit color formation and development.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141755493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chromosome-scale reference genome of an ancient landrace: unveiling the genetic basis of seed weight in the food legume crop pigeonpea (Cajanus cajan) 古老陆地品种的染色体级参考基因组：揭示食用豆科作物鸽子豆（Cajanus cajan）种子重量的遗传基础

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2024-07-24 DOI: 10.1093/hr/uhae201

Chun Liu, Xipeng Ding, Yuanhang Wu, Jianyu Zhang, Rui Huang, Xinyong Li, Guodao Liu, Pandao Liu

{"title":"Chromosome-scale reference genome of an ancient landrace: unveiling the genetic basis of seed weight in the food legume crop pigeonpea (Cajanus cajan)","authors":"Chun Liu, Xipeng Ding, Yuanhang Wu, Jianyu Zhang, Rui Huang, Xinyong Li, Guodao Liu, Pandao Liu","doi":"10.1093/hr/uhae201","DOIUrl":"https://doi.org/10.1093/hr/uhae201","url":null,"abstract":"Pigeonpea (Cajanus cajan) is a nutrient-rich and versatile food legume crop of tropical and subtropical regions. In this study, we describe the de novo assembly of a high-quality genome for the ancient pigeonpea landrace 'D30', achieved through a combination of Pacific Biosciences high-fidelity (PacBio HiFi) and high-throughput chromatin conformation capture (Hi-C) sequencing technologies. The assembled 'D30' genome has a size of 813.54 Mb, with a contig N50 of 10.74 Mb, a scaffold N50 of 73.07 Mb, and a GC content of 35.67%. Genomic evaluation revealed that the 'D30' genome contains 99.2% of Benchmarking Universal Single-Copy Orthologs (BUSCO) and achieves a 29.06 LTR Assembly Index (LAI). Genome annotation indicated that 'D30' encompasses 431.37 Mb of repeat elements (53.02% of the genome) and 37,977 protein-coding genes. Identification of single nucleotide polymorphisms (SNPs), insertions/deletions (indels), and structural variations (SVs) between 'D30' and the published genome of pigeonpea cultivar 'Asha' suggests that genes affected by these variations may play important roles in biotic and abiotic stress responses. Further investigation of genomic regions under selection highlights genes enriched in starch and sucrose metabolism, with 42.11% of these genes highly expressed in seeds. Finally, we conducted genome-wide association studies (GWAS) to facilitate the identification of 28 marker–trait associations for six agronomic traits of pigeonpea. Notably, we discovered a calmodulin-like protein (CcCML) that harbors a dominant haplotype associated with the 100-seed weight of pigeonpea. Our study provides a foundational resource for developing genomics-assisted breeding programs in pigeonpea.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141755495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0