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Kim G, Cho H, Kim S. Identification of a candidate gene for the I locus determining the dominant white bulb color in onion (Allium cepa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:118. [PMID: 38709404 DOI: 10.1007/s00122-024-04626-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/14/2024] [Indexed: 05/07/2024]
Abstract
KEY MESSAGE Through a map-based cloning approach, a gene coding for an R2R3-MYB transcription factor was identified as a causal gene for the I locus controlling the dominant white bulb color in onion. White bulb colors in onion (Allium cepa L.) are determined by either the C or I loci. The causal gene for the C locus was previously isolated, but the gene responsible for the I locus has not been identified yet. To identify candidate genes for the I locus, an approximately 7-Mb genomic DNA region harboring the I locus was obtained from onion and bunching onion (A. fistulosum) whole genome sequences using two tightly linked molecular markers. Within this interval, the AcMYB1 gene, known as a positive regulator of anthocyanin production, was identified. No polymorphic sequences were found between white and red AcMYB1 alleles in the 4,860-bp full-length genomic DNA sequences. However, a 4,838-bp LTR-retrotransposon was identified in the white allele, in the 79-bp upstream coding region from the stop codon. The insertion of this LTR-retrotransposon created a premature stop codon, resulting in the replacement of 26 amino acids with seven different residues. A molecular marker was developed based on the insertion of this LTR-retrotransposon to genotype the I locus. A perfect linkage between bulb color phenotypes and marker genotypes was observed among 5,303 individuals of segregating populations. The transcription of AcMYB1 appeared to be normal in both red and white onions, but the transcription of CHS-A, which encodes chalcone synthase and is involved in the first step of the anthocyanin biosynthesis pathway, was inactivated in the white onions. Taken together, an aberrant AcMYB1 protein produced from the mutant allele might be responsible for the dominant white bulb color in onions.
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Affiliation(s)
- Geonjoong Kim
- Department of Horticulture, Biotechnology Research Institute, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Heejung Cho
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Sunggil Kim
- Department of Horticulture, Biotechnology Research Institute, Chonnam National University, Gwangju, 61186, Republic of Korea.
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Yang P, Yuan Y, Yan C, Jia Y, You Q, Da L, Lou A, Lv B, Zhang Z, Liu Y. AlliumDB: a central portal for comparative and functional genomics in Allium. HORTICULTURE RESEARCH 2024; 11:uhad285. [PMID: 38371639 PMCID: PMC10871970 DOI: 10.1093/hr/uhad285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/17/2023] [Indexed: 02/20/2024]
Abstract
The genus Allium belongs to the botanical family Amaryllidaceae and includes economically important crops such as onion, garlic, bunching onion, and leek, used as vegetables, spices, and traditional medicines. The large sizes of Allium genomes hamper the genetic dissection of agronomically important traits and molecular breeding. With the growing accumulation of genomic, resequencing, transcriptome, and phenotypic data, the demand for an integrative Allium database is increasing. Here we present a user-friendly database, AlliumDB (https://allium.qau.edu.cn), as a functional genomics hub integrating public and in-house data. The database contains all currently available nuclear and organelle genomes for Allium species, with genes comprehensively annotated based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, orthology, gene families, protein families (Pfam), and non-coding RNA families (Rfam). Transcriptome and variation profiles are integrated into dynamic visualization tools. We took phenotypic photographs and generated trait records for hundreds of Allium germplasms collected worldwide, which are included in the database. We incorporated JBrowse for the visualization of gene structures, RNA sequencing data, and variation data. Analysis tools such as the basic local alignment search tool (BLAST), sequence fetch, enrichment, and motif analyses are available to explore potential gene functions. This database incorporates comprehensive Allium genotypic and phenotypic datasets. As the community assembles new genomes and generates resequencing data for Allium germplasms, the database will be improved and continuously updated with these multi-omics data and comparative genomic studies. We expect the AlliumDB database to become a key resource for the study of Allium crops.
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Affiliation(s)
- Pengtao Yang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Yu Yuan
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Chao Yan
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Yue Jia
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Qi You
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Lingling Da
- College of Life Science, Northwest Normal University, Lanzhou 730070, China
| | - Ao Lou
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Bingsheng Lv
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Zhonghua Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Yue Liu
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
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Nørrevang AF, Shabala S, Palmgren M. A two-sequence motif-based method for the inventory of gene families in fragmented and poorly annotated genome sequences. BMC Genomics 2024; 25:26. [PMID: 38172704 PMCID: PMC10763278 DOI: 10.1186/s12864-023-09859-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
Databases of genome sequences are growing exponentially, but, in some cases, assembly is incomplete and genes are poorly annotated. For evolutionary studies, it is important to identify all members of a given gene family in a genome. We developed a method for identifying most, if not all, members of a gene family from raw genomes in which assembly is of low quality, using the P-type ATPase superfamily as an example. The method is based on the translation of an entire genome in all six reading frames and the co-occurrence of two family-specific sequence motifs that are in close proximity to each other. To test the method's usability, we first used it to identify P-type ATPase members in the high-quality annotated genome of barley (Hordeum vulgare). Subsequently, after successfully identifying plasma membrane H+-ATPase family members (P3A ATPases) in various plant genomes of varying quality, we tested the hypothesis that the number of P3A ATPases correlates with the ability of the plant to tolerate saline conditions. In 19 genomes of glycophytes and halophytes, the total number of P3A ATPase genes was found to vary from 7 to 22, but no significant difference was found between the two groups. The method successfully identified P-type ATPase family members in raw genomes that are poorly assembled.
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Affiliation(s)
- Anton Frisgaard Nørrevang
- NovoCrops Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, DK-1871, Denmark
| | - Sergey Shabala
- School of Biological Sciences, University of Western Australia, Crawley, WA6009, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, 528000, China
| | - Michael Palmgren
- NovoCrops Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, DK-1871, Denmark.
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Bishnoi R, Solanki R, Singla D, Mittal A, Chhuneja P, Meena OP, Dhatt AS. Comparative mitochondrial genome analysis reveals a candidate ORF for cytoplasmic male sterility in tropical onion. 3 Biotech 2024; 14:6. [PMID: 38074291 PMCID: PMC10700285 DOI: 10.1007/s13205-023-03850-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 11/08/2023] [Indexed: 01/19/2024] Open
Abstract
Cytoplasmic male sterility (CMS) has been widely exploited for hybrid seed production in onions (Allium cepa L.). In contrast to long-day onion cultivars, short-day onion has not yet been investigated for mitochondrial genome structure and DNA rearrangements associated with CMS activity. Here, we report the 3,16,321 bp complete circular mitochondrial genome of tropical onion CMS line (97A). Due to the substantial number of repetitive regions, the assembled mitochondrial genome of maintainer line (97B) remained linear with 15 scaffolds. Additionally, 13 and 20 chloroplast-derived fragments with a size ranging from 143 to 13,984 bp and 153-17,725 bp were identified in the 97A and 97B genomes, respectively. Genome annotation revealed 24 core protein-coding genes along with 24 and 28 tRNA genes in the mitochondrial genomes of 97A and 97B, respectively. Furthermore, comparative genome analysis of the 97A and 97B mitochondrial genomes showed that gene content was almost similar except for the chimeric ORF725 gene which is the extended form of the COX1 gene. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03850-2.
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Affiliation(s)
- Ritika Bishnoi
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004 India
| | - Ravindra Solanki
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004 India
| | - Deepak Singla
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004 India
| | - Amandeep Mittal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004 India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004 India
| | - Om Prakash Meena
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, 141004 India
| | - Ajmer Singh Dhatt
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, 141004 India
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Tourdot E, Grob S. Three-dimensional chromatin architecture in plants - General features and novelties. Eur J Cell Biol 2023; 102:151344. [PMID: 37562220 DOI: 10.1016/j.ejcb.2023.151344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 07/21/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Research on the three-dimensional (3D) structure of the genome and its distribution within the nuclear space has made a big leap in the last two decades. Work in the animal field has led to significant advances in our general understanding on eukaryotic genome organization. This did not only bring along insights into how the 3D genome interacts with the epigenetic landscape and the transcriptional machinery but also how 3D genome architecture is relevant for fundamental developmental processes, such as cell differentiation. In parallel, the 3D organization of plant genomes have been extensively studied, which resulted in both congruent and novel findings, contributing to a more complete view on how eukaryotic genomes are organized in multiple dimensions. Plant genomes are remarkably diverse in size, composition, and ploidy. Furthermore, as intrinsically sessile organisms without the possibility to relocate to more favorable environments, plants have evolved an elaborate epigenetic repertoire to rapidly respond to environmental challenges. The diversity in genome organization and the complex epigenetic programs make plants ideal study subjects to acquire a better understanding on universal features and inherent constraints of genome organization. Furthermore, considering a wide range of species allows us to study the evolutionary crosstalk between the various levels of genome architecture. In this article, we aim at summarizing important findings on 3D genome architecture obtained in various plant species. These findings cover many aspects of 3D genome organization on a wide range of levels, from gene loops to topologically associated domains and to global 3D chromosome configurations. We present an overview on plant 3D genome organizational features that resemble those in animals and highlight facets that have only been observed in plants to date.
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Affiliation(s)
- Edouard Tourdot
- Department of Plant and Microbial Biology, University of Zurich, Switzerland.
| | - Stefan Grob
- Department of Plant and Microbial Biology, University of Zurich, Switzerland.
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Suprasanna P, Klimek-Chodacka M, Jain SM. Editorial: CRISPR tools, technology development, and application. FRONTIERS IN PLANT SCIENCE 2023; 14:1329780. [PMID: 38023829 PMCID: PMC10679726 DOI: 10.3389/fpls.2023.1329780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023]
Affiliation(s)
- Penna Suprasanna
- Amity Centre for Nuclear Biotechnology, Amity Institute of Biotechnology, Amity University of Maharashtra, Mumbai, India
| | | | - Shri Mohan Jain
- Department of Plant Production, University of Helsinki, Helsinki, Finland
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Hao F, Liu X, Zhou B, Tian Z, Zhou L, Zong H, Qi J, He J, Zhang Y, Zeng P, Li Q, Wang K, Xia K, Guo X, Li L, Shao W, Zhang B, Li S, Yang H, Hui L, Chen W, Peng L, Liu F, Rong ZQ, Peng Y, Zhu W, McCallum JA, Li Z, Xu X, Yang H, Macknight RC, Wang W, Cai J. Chromosome-level genomes of three key Allium crops and their trait evolution. Nat Genet 2023; 55:1976-1986. [PMID: 37932434 DOI: 10.1038/s41588-023-01546-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 09/20/2023] [Indexed: 11/08/2023]
Abstract
Allium crop breeding remains severely hindered due to the lack of high-quality reference genomes. Here we report high-quality chromosome-level genome assemblies for three key Allium crops (Welsh onion, garlic and onion), which are 11.17 Gb, 15.52 Gb and 15.78 Gb in size with the highest recorded contig N50 of 507.27 Mb, 109.82 Mb and 81.66 Mb, respectively. Beyond revealing the genome evolutionary process of Allium species, our pathogen infection experiments and comparative metabolomic and genomic analyses showed that genes encoding enzymes involved in the metabolic pathway of Allium-specific flavor compounds may have evolved from an ancient uncharacterized plant defense system widely existing in many plant lineages but extensively boosted in alliums. Using in situ hybridization and spatial RNA sequencing, we obtained an overview of cell-type categorization and gene expression changes associated with spongy mesophyll cell expansion during onion bulb formation, thus indicating the functional roles of bulb formation genes.
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Affiliation(s)
- Fei Hao
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
- Center of Special Environmental Biomechanics & Biomedical Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Xue Liu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Botong Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Zunzhe Tian
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Lina Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Hang Zong
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Jiyan Qi
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Juan He
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yongting Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Peng Zeng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Qiong Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Kai Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Keke Xia
- State Key Laboratory of Agricultural Genomics, BGI, Shenzhen, China
| | - Xing Guo
- State Key Laboratory of Agricultural Genomics, BGI, Shenzhen, China
- BGI Research, Wuhan, China
| | - Li Li
- State Key Laboratory of Agricultural Genomics, BGI, Shenzhen, China
| | - Wenwen Shao
- State Key Laboratory of Agricultural Genomics, BGI, Shenzhen, China
| | | | - Shengkang Li
- State Key Laboratory of Agricultural Genomics, BGI, Shenzhen, China
| | - Haifeng Yang
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | - Linchong Hui
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | - Wei Chen
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | - Lixin Peng
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, China
| | - Feipeng Liu
- Frontiers Science Center for Flexible Electronics (FSCFE), Shaanxi Institute of Flexible Electronics (SIFE) & Shaanxi Institute of Biomedical Materials and Engineering (SIBME), Northwestern Polytechnical University, Xi'an, China
| | - Zi-Qiang Rong
- Frontiers Science Center for Flexible Electronics (FSCFE), Shaanxi Institute of Flexible Electronics (SIFE) & Shaanxi Institute of Biomedical Materials and Engineering (SIBME), Northwestern Polytechnical University, Xi'an, China
| | - Yingmei Peng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Wenbo Zhu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - John A McCallum
- The New Zealand Institute for Plant and Food Research, Christchurch, New Zealand
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, BGI, Shenzhen, China.
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China.
| | - Hui Yang
- Center of Special Environmental Biomechanics & Biomedical Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China.
| | | | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
| | - Jing Cai
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
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Mainkar P, Manape TK, Satheesh V, Anandhan S. CRISPR/Cas9-mediated editing of PHYTOENE DESATURASE gene in onion ( Allium cepa L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1226911. [PMID: 37701798 PMCID: PMC10494252 DOI: 10.3389/fpls.2023.1226911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/28/2023] [Indexed: 09/14/2023]
Abstract
Introduction Clustered regularly interspaced short palindromic repeats (CRISPR)/ CRISPR-associated protein 9 (Cas9) is a precise genome editing tool used to introduce genetic modifications in a wide range of crop species. Thus far, there is no report of CRISPR/Cas9-mediated genome editing in onions (Allium cepa L.). Methods In the present study, we targeted two exons of the gene coding for Phytoene desaturase (AcPDS) in onion cv. Bhima Super. The sgRNA-carrying constructs were co-cultivated with 8-week-old embryogenic calli using an Agrobacterium-mediated transformation protocol and incubated on the media without hygromycin B selection. Results and discussion Out of the total 617 co-cultivated calli, 21 (3.4%) regenerated shoots exhibited three distinct phenotypes: albino, chimeric, and pale green; in comparison to the wild-type non-transformed regenerated shoots. Total chlorophyll content was drastically reduced in albino shoots and significantly decreased in chimeric shoots. Out of the six Cas9 gene PCR-confirmed regenerated shoots, two exhibited the albino phenotype due to insertions/deletions (InDels) and substitution-based mutations in and around the AcPDS target sites. Deep amplicon sequencing revealed a significantly variable InDel frequency between two sgRNAs, ranging from 1.2% to 63.4%, along with a 53.4% substitution frequency. The mutation of the AcPDS gene generated a visually detectable albino phenotype, thus confirming the successful editing of the AcPDS gene. This is the first time a CRISPR/Cas9-mediated genome editing protocol has been successfully established in onion, with the AcPDS gene serving as an example. This study will provide the necessary momentum for researchers to further basic and applied research on onions.
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Affiliation(s)
- Pawan Mainkar
- ICAR-Directorate of Onion and Garlic Research, Pune, Maharashtra, India
| | | | - Viswanathan Satheesh
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA, United States
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Sahoo J, Mahanty B, Mishra R, Joshi RK. Development of SNP markers linked to purple blotch resistance for marker-assisted selection in onion ( Allium cepa L.) breeding. 3 Biotech 2023; 13:137. [PMID: 37124987 PMCID: PMC10130247 DOI: 10.1007/s13205-023-03562-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 04/15/2023] [Indexed: 05/02/2023] Open
Abstract
Purple blotch (PB), caused by Alternaria porri (Ellis) Cifferi, is one of the most destructive diseases of onion worldwide. Rapid development and deployment of resistant onion varieties is the most effective approach to control this disease. A single dominant gene, ApR1 was previously linked to PB resistance in onion cultivar 'Arka Kalyan'. In this study, an advanced RIL population derived from a cross between the resistant (Arka Kalyan) and susceptible (Agrifound Rose) cultivar of onion was used to fine map the resistant locus with SNP markers. Twenty plants from the RIL population, ten each with disease resistance and susceptibility trait, were subjected to restriction site-associated DNA sequencing (RAD-Seq) and generated 7388 single nucleotide polymorphisms (SNPs). Correlation analysis between marker genotypes and PB disease phenotype on the 20 plants identified 27 SNPs as candidate markers linked to ApR1 gene for PB resistance. Six candidate SNPs were converted to Kompetitive Allele-Specific PCR (KASP) markers designated as ApRsnip5, ApRsnip8, ApRsnip14, ApRsnip21, ApRsnip23 and ApRsnip25. Marker-trait association based on disease phenotyping and KASP genotyping data on 153 RILs confirmed that all six KASP markers were tightly associated with ApR1 gene within the genetic distance of 1.3 CentiMorgan (cM). ApRsnip14 co-segregated with the ApR1 locus. Further, the six KASP markers were tested on 27 onion lines with different genetic backgrounds. ApRsnip14, ApRsnip21, ApRsnip5 and ApRsnip23 not only showed the correct resistance allele in 3 resistance genotypes, but also clustered together in the remaining 24 susceptible lines. Alternatively, ApRsnip8 and ApRsnip25 exhibited false positives in two onion lines which do not have the R-gene. Overall, our results suggest that ApRsnip14 and ApRsnip23 with their close linkage to ApR1 locus and greater applicability on breeding germplasm are recommended in marker-assisted selection for PB resistance in onion breeding program. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03562-7.
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Affiliation(s)
- Jayashree Sahoo
- Department of Biotechnology, Rama Devi Women’s University, Vidya Vihar, Bhubaneswar, Odisha 751022 India
| | - Bijayalaxmi Mahanty
- Department of Biotechnology, Rama Devi Women’s University, Vidya Vihar, Bhubaneswar, Odisha 751022 India
| | - Rukmini Mishra
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha India
| | - Raj Kumar Joshi
- Department of Biotechnology, Rama Devi Women’s University, Vidya Vihar, Bhubaneswar, Odisha 751022 India
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Kudryavtseva N, Ermolaev A, Pivovarov A, Simanovsky S, Odintsov S, Khrustaleva L. The Control of the Crossover Localization in Allium. Int J Mol Sci 2023; 24:ijms24087066. [PMID: 37108228 PMCID: PMC10138942 DOI: 10.3390/ijms24087066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 04/05/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Meiotic crossovers/chiasmata are not randomly distributed and strictly controlled. The mechanisms behind crossover (CO) patterning remain largely unknown. In Allium cepa, as in the vast majority of plants and animals, COs predominantly occur in the distal 2/3 of the chromosome arm, while in Allium fistulosum they are strictly localized in the proximal region. We investigated the factors that may contribute to the pattern of COs in A. cepa, A. fistulosum and their F1 diploid (2n = 2x = 8C + 8F) and F1 triploid (2n = 3x = 16F + 8C) hybrids. The genome structure of F1 hybrids was confirmed using genomic in situ hybridization (GISH). The analysis of bivalents in the pollen mother cells (PMCs) of the F1 triploid hybrid showed a significant shift in the localization of COs to the distal and interstitial regions. In F1 diploid hybrid, the COs localization was predominantly the same as that of the A. cepa parent. We found no differences in the assembly and disassembly of ASY1 and ZYP1 in PMCs between A. cepa and A. fistulosum, while F1 diploid hybrid showed a delay in chromosome pairing and a partial absence of synapsis in paired chromosomes. Immunolabeling of MLH1 (class I COs) and MUS81 (class II COs) proteins showed a significant difference in the class I/II CO ratio between A. fistulosum (50%:50%) and A. cepa (73%:27%). The MLH1:MUS81 ratio at the homeologous synapsis of F1 diploid hybrid (70%:30%) was the most similar to that of the A. cepa parent. F1 triploid hybrid at the A. fistulosum homologous synapsis showed a significant increase in MLH1:MUS81 ratio (60%:40%) compared to the A. fistulosum parent. The results suggest possible genetic control of CO localization. Other factors affecting the distribution of COs are discussed.
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Affiliation(s)
- Natalia Kudryavtseva
- All-Russian Research Institute of Agricultural Biotechnology, 42 Timiryazevskaya Str., Moscow 127550, Russia
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 49 Timiryazevskaya Str., Moscow 127550, Russia
| | - Aleksey Ermolaev
- All-Russian Research Institute of Agricultural Biotechnology, 42 Timiryazevskaya Str., Moscow 127550, Russia
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 49 Timiryazevskaya Str., Moscow 127550, Russia
| | - Anton Pivovarov
- All-Russian Research Institute of Agricultural Biotechnology, 42 Timiryazevskaya Str., Moscow 127550, Russia
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 49 Timiryazevskaya Str., Moscow 127550, Russia
| | - Sergey Simanovsky
- All-Russian Research Institute of Agricultural Biotechnology, 42 Timiryazevskaya Str., Moscow 127550, Russia
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 33 Leninsky Prosp., Moscow 119071, Russia
| | - Sergey Odintsov
- All-Russian Research Institute of Agricultural Biotechnology, 42 Timiryazevskaya Str., Moscow 127550, Russia
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 49 Timiryazevskaya Str., Moscow 127550, Russia
| | - Ludmila Khrustaleva
- All-Russian Research Institute of Agricultural Biotechnology, 42 Timiryazevskaya Str., Moscow 127550, Russia
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 49 Timiryazevskaya Str., Moscow 127550, Russia
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Parreño R, Rodríguez-Alcocer E, Martínez-Guardiola C, Carrasco L, Castillo P, Arbona V, Jover-Gil S, Candela H. Turning Garlic into a Modern Crop: State of the Art and Perspectives. PLANTS (BASEL, SWITZERLAND) 2023; 12:1212. [PMID: 36986902 PMCID: PMC10057115 DOI: 10.3390/plants12061212] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/26/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Garlic is cultivated worldwide for the value of its bulbs, but its cultivation is challenged by the infertility of commercial cultivars and the accumulation of pathogens over time, which occurs as a consequence of vegetative (clonal) propagation. In this review, we summarize the state of the art of garlic genetics and genomics, highlighting recent developments that will lead to its development as a modern crop, including the restoration of sexual reproduction in some garlic strains. The set of tools available to the breeder currently includes a chromosome-scale assembly of the garlic genome and multiple transcriptome assemblies that are furthering our understanding of the molecular processes underlying important traits like the infertility, the induction of flowering and bulbing, the organoleptic properties and resistance to various pathogens.
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Affiliation(s)
- Ricardo Parreño
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Eva Rodríguez-Alcocer
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | | | - Lucía Carrasco
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Purificación Castillo
- Departamento I+D, Coopaman S.C.L., Carretera Peñas De San Pedro, km 1.6, 02006 Albacete, Spain
| | - Vicent Arbona
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, 12071 Castelló de la Plana, Spain
| | - Sara Jover-Gil
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
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12
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Vegetable biology and breeding in the genomics era. SCIENCE CHINA. LIFE SCIENCES 2023; 66:226-250. [PMID: 36508122 DOI: 10.1007/s11427-022-2248-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022]
Abstract
Vegetable crops provide a rich source of essential nutrients for humanity and represent critical economic values to global rural societies. However, genetic studies of vegetable crops have lagged behind major food crops, such as rice, wheat and maize, thereby limiting the application of molecular breeding. In the past decades, genome sequencing technologies have been increasingly applied in genetic studies and breeding of vegetables. In this review, we recapitulate recent progress on reference genome construction, population genomics and the exploitation of multi-omics datasets in vegetable crops. These advances have enabled an in-depth understanding of their domestication and evolution, and facilitated the genetic dissection of numerous agronomic traits, which jointly expedites the exploitation of state-of-the-art biotechnologies in vegetable breeding. We further provide perspectives of further directions for vegetable genomics and indicate how the ever-increasing omics data could accelerate genetic, biological studies and breeding in vegetable crops.
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13
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Li Y, Huo Y, Yang Y, Wang Z, Sun Y, Liu B, Wu X. Construction of a high-resolution genetic map and identification of single nucleotide polymorphism markers relevant to flower stalk height in onion. FRONTIERS IN PLANT SCIENCE 2023; 14:1100691. [PMID: 36818885 PMCID: PMC9928573 DOI: 10.3389/fpls.2023.1100691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Onion (Allium cepa L., 2n=16) is an economically and nutritionally important vegetable crop worldwide. Construction of a high-resolution genetic map and map-based gene mining in onion have lagged behind other vegetable crops such as tomato and pepper. METHODS In this study, we constructed a high-resolution genetic map of onion using 321 F2 individuals from a cross between two double haploid lines DH-1×DH-17 and employing specific length amplified fragment (SLAF)-seq technology. The genetic map containing 10,584 polymorphic SLAFs with 21,250 single nucleotide polymorphism (SNP) markers and 8 linkage groups was developed for onion, which spanned 928.32 cM, with an average distance of 0.09 cM between adjacent markers. RESULTS Using this map, we carried out QTL mapping of Ms locus related to the male-fertile trait and reproduced previous mapping results, which proved that this map was of good quality. Then, four QTLs (located on LG2, LG5, and LG8) were detected for flower stalk height, explaining 26.60% of the phenotypic variance. Among them, we proposed that 20 SLAF markers (in three QTLs) of flower stalk height trait were effective favorable allelic variant markers associated with heterosis. DISCUSSION Overall, the genetic map was structured using SLAF-seq based on DH lines, and it is the highest-quality and highest-resolution linkage map of onion to date. It lays a foundation for the fine mapping and candidate gene identification of flower stalk height, and provides new insights into the developmental genetic mechanisms in onion breeding.
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Affiliation(s)
| | | | | | | | | | | | - Xiong Wu
- *Correspondence: Bingjiang Liu, ; Xiong Wu,
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14
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Targeted Metabolome Profiling of Indonesian Shallots and Japanese Long-Day/Short-Day Bulb Onions. Metabolites 2022; 12:metabo12121260. [PMID: 36557300 PMCID: PMC9783499 DOI: 10.3390/metabo12121260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/16/2022] Open
Abstract
In this study, targeted metabolome analysis was applied to identify the discriminative metabolites between Indonesian shallot landraces, Japanese long-day onion (LDO) varieties, and Japanese short-day onion (SDO) varieties. In total, 172 metabolite signal intensities were subjected to multivariate PLS-DA, VIP, and random forest modeling to gain further insight into genotype-specific metabolites. PLS-DA divides the examined genotypes into three different clusters, implying that shallot landraces exhibited a distinct metabolite profile compared with Japanese LDO and SDO varieties. The PLS-DA, VIP, and random forest results indicated that the shallot and LDO are richer in metabolite constituents in comparison with the SDO. Specifically, amino acids and organosulfur compounds were the key characteristic metabolites in shallot and LDO genotypes. The analysis of S-alk(en)yl-L-cysteine sulfoxide (ACSO) compounds showed higher accumulation in the shallot landraces relative to LDO and SDO varieties, which explains the stronger pungency and odor in shallots. In addition, the LDO showed higher ACSO content compared with the SDO, implying that long-day cultivation might enhance sulfur assimilation in the Japanese onion. The LDO 'Super Kitamomiji' and the shallots 'Probolinggo' and 'Thailand' showed higher ACSO content than other varieties, making it useful for Allium breeding to improve the flavor and stress tolerance of onions.
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15
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Liao N, Hu Z, Miao J, Hu X, Lyu X, Fang H, Zhou YM, Mahmoud A, Deng G, Meng YQ, Zhang K, Ma YY, Xia Y, Zhao M, Yang H, Zhao Y, Kang L, Wang Y, Yang JH, Zhou YH, Zhang MF, Yu JQ. Chromosome-level genome assembly of bunching onion illuminates genome evolution and flavor formation in Allium crops. Nat Commun 2022; 13:6690. [PMID: 36335132 PMCID: PMC9637129 DOI: 10.1038/s41467-022-34491-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
The Allium genus is cultivated globally as vegetables, condiments, or medicinal plants and is characterized by large genomes and strong pungency. However, the genome evolution and genomic basis underlying their unique flavor formation remain poorly understood. Herein, we report an 11.27-Gb chromosome-scale genome assembly for bunching onion (A. fistulosum). The uneven bursts of long-terminal repeats contribute to diversity in genome constituents, and dispersed duplication events largely account for gene expansion in Allium genomes. The extensive duplication and differentiation of alliinase and lachrymatory factor synthase manifest as important evolutionary events during flavor formation in Allium crops. Furthermore, differential selective preference for flavor-related genes likely lead to the variations in isoalliin content in bunching onions. Moreover, we reveal that China is the origin and domestication center for bunching onions. Our findings provide insights into Allium genome evolution, flavor formation and domestication history and enable future genome-assisted breeding of important traits in these crops.
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Affiliation(s)
- Nanqiao Liao
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Zhongyuan Hu
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Jinshan Miao
- grid.460150.60000 0004 1759 7077Horticultural Institute of Science and Technology, Weifang University of Science and Technology, 262700 Weifang, Shandong P. R. China
| | - Xiaodi Hu
- grid.410753.4Novogene Bioinformatics Institute, 100083 Beijing, P. R. China
| | - Xiaolong Lyu
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, 310058 Hangzhou, Zhejiang P. R. China ,grid.13402.340000 0004 1759 700XHainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, 572025 Sanya, Hainan P. R. China
| | - Haitian Fang
- grid.260987.20000 0001 2181 583XNingxia Key Laboratory for Food Microbial-applications Technology and Safety Control, School of Food & Wine, Ningxia University, 750021 Yinchuan, Ningxia P. R. China
| | - Yi-Mei Zhou
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Ahmed Mahmoud
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Guancong Deng
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Yi-Qing Meng
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Kejia Zhang
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Yu-Yuan Ma
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Yuelin Xia
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Meng Zhao
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Haiyang Yang
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Yong Zhao
- grid.410753.4Novogene Bioinformatics Institute, 100083 Beijing, P. R. China
| | - Ling Kang
- grid.410753.4Novogene Bioinformatics Institute, 100083 Beijing, P. R. China
| | - Yiming Wang
- grid.410753.4Novogene Bioinformatics Institute, 100083 Beijing, P. R. China
| | - Jing-Hua Yang
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, 310058 Hangzhou, Zhejiang P. R. China ,grid.13402.340000 0004 1759 700XHainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, 572025 Sanya, Hainan P. R. China
| | - Yan-Hong Zhou
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, 310058 Hangzhou, Zhejiang P. R. China
| | - Ming-Fang Zhang
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, 310058 Hangzhou, Zhejiang P. R. China ,grid.13402.340000 0004 1759 700XHainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, 572025 Sanya, Hainan P. R. China
| | - Jing-Quan Yu
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, 310058 Hangzhou, Zhejiang P. R. China
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Savadi S, Muralidhara BM, Godwin J, Adiga JD, Mohana GS, Eradasappa E, Shamsudheen M, Karun A. De novo assembly and characterization of the draft genome of the cashew (Anacardium occidentale L.). Sci Rep 2022; 12:18187. [PMID: 36307541 PMCID: PMC9616956 DOI: 10.1038/s41598-022-22600-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 10/17/2022] [Indexed: 12/31/2022] Open
Abstract
Cashew is the second most important tree nut crop in the global market. Cashew is a diploid and heterozygous species closely related to the mango and pistachio. Its improvement by conventional breeding is slow due to the long juvenile phase. Despite the economic importance, very little genomics/transcriptomics information is available for cashew. In this study, the Oxford nanopore reads and Illumina reads were used for de novo assembly of the cashew genome. The hybrid assembly yielded a 356.6 Mb genome corresponding to 85% of the estimated genome size (419 Mb). The BUSCO analysis showed 91.8% of genome completeness. Transcriptome mapping showed 92.75% transcripts aligned with the assembled genome. Gene predictions resulted in the identification of 31,263 genes coding for a total of 35,000 gene isoforms. About 46% (165 Mb) of the cashew genome comprised of repetitive sequences. Phylogenetic analyses of the cashew with nine species showed that it was closely related to Mangifera indica. Analysis of cashew genome revealed 3104 putative R-genes. The first draft assembly of the genome, transcriptome and R gene information generated in this study would be the foundation for understanding the molecular basis of economic traits and genomics-assisted breeding in cashew.
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Affiliation(s)
- Siddanna Savadi
- grid.505948.50000 0004 1764 470XICAR- Directorate of Cashew Research (DCR), Puttur, D.K., Karnataka 574 202 India
| | - B. M. Muralidhara
- grid.505948.50000 0004 1764 470XICAR- Directorate of Cashew Research (DCR), Puttur, D.K., Karnataka 574 202 India
| | - Jeffrey Godwin
- Bionivid Technology Private Limited, 209, 4th Cross Rd, B Channasandra, Kasturi Nagar, Bengaluru, Karnataka 560 043 India
| | - J. D. Adiga
- grid.505948.50000 0004 1764 470XICAR- Directorate of Cashew Research (DCR), Puttur, D.K., Karnataka 574 202 India
| | - G. S. Mohana
- grid.505948.50000 0004 1764 470XICAR- Directorate of Cashew Research (DCR), Puttur, D.K., Karnataka 574 202 India
| | - E. Eradasappa
- grid.505948.50000 0004 1764 470XICAR- Directorate of Cashew Research (DCR), Puttur, D.K., Karnataka 574 202 India
| | - M. Shamsudheen
- grid.505948.50000 0004 1764 470XICAR- Directorate of Cashew Research (DCR), Puttur, D.K., Karnataka 574 202 India
| | - Anitha Karun
- grid.505948.50000 0004 1764 470XICAR- Directorate of Cashew Research (DCR), Puttur, D.K., Karnataka 574 202 India
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Yu T, Ma X, Liu Z, Feng X, Wang Z, Ren J, Cao R, Zhang Y, Nie F, Song X. TVIR: a comprehensive vegetable information resource database for comparative and functional genomic studies. HORTICULTURE RESEARCH 2022; 9:uhac213. [PMID: 36483087 PMCID: PMC9719039 DOI: 10.1093/hr/uhac213] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/14/2022] [Indexed: 06/17/2023]
Abstract
Vegetables are an indispensable part of the daily diet of humans. Therefore, it is vital to systematically study the genomic data of vegetables and build a platform for data sharing and analysis. In this study, a comprehensive platform for vegetables with a user-friendly Web interface-The Vegetable Information Resource (TVIR, http://tvir.bio2db.com)-was built based on the genomes of 59 vegetables. TVIR database contains numerous important functional genes, including 5215 auxin genes, 2437 anthocyanin genes, 15 002 flowering genes, 79 830 resistance genes, and 2639 glucosinolate genes of 59 vegetables. In addition, 2597 N6-methyladenosine (m6A) genes were identified, including 513 writers, 1058 erasers, and 1026 readers. A total of 2 101 501 specific clustered regularly interspaced short palindromic repeat (CRISPR) guide sequences and 17 377 miRNAs were detected and deposited in TVIR database. Information on gene synteny, duplication, and orthologs is also provided for 59 vegetable species. TVIR database contains 2 346 850 gene annotations by the Swiss-Prot, TrEMBL, Gene Ontology (GO), Pfam, and Non-redundant (Nr) databases. Synteny, Primer Design, Blast, and JBrowse tools are provided to facilitate users in conducting comparative genomic analyses. This is the first large-scale collection of vegetable genomic data and bioinformatic analysis. All genome and gene sequences, annotations, and bioinformatic results can be easily downloaded from TVIR. Furthermore, transcriptome data of 98 vegetables have been collected and collated, and can be searched by species, tissues, or different growth stages. TVIR is expected to become a key hub for vegetable research globally. The database will be updated with newly assembled vegetable genomes and comparative genomic studies in the future.
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Affiliation(s)
| | | | | | | | - Zhiyuan Wang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Jun Ren
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rui Cao
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Yingchao Zhang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Fulei Nie
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
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Delvento C, Pavan S, Miazzi MM, Marcotrigiano AR, Ricciardi F, Ricciardi L, Lotti C. Genotyping-by-Sequencing Defines Genetic Structure within the “Acquaviva” Red Onion Landrace. PLANTS 2022; 11:plants11182388. [PMID: 36145789 PMCID: PMC9502971 DOI: 10.3390/plants11182388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/05/2022] [Accepted: 09/11/2022] [Indexed: 11/26/2022]
Abstract
Genetic structure and distinctive features of landraces, such as adaptability to local agro-ecosystems and specific qualitative profiles, can be substantially altered by the massive introduction of allochthonous germplasm. The landrace known as “Cipolla rossa di Acquaviva” (Acquaviva red onion, further referred to as ARO) is traditionally cultivated and propagated in a small area of the Apulia region (southern Italy). However, the recent rise of its market value and cultivation area is possibly causing genetic contamination with foreign propagating material. In this work, genotyping-by-sequencing (GBS) was used to characterize genetic variation of seven onion populations commercialized as ARO, as well as one population of the landrace “Montoro” (M), which is phenotypically similar, but originates from another cultivation area and displays different qualitative features. A panel of 5011 SNP markers was used to perform parametric and non-parametric genetic structure analyses, which supported the hypothesis of genetic contamination of germplasm commercialized as ARO with a gene pool including the M landrace. Four ARO populations formed a core genetic group, homogeneous and clearly distinct from the other ARO and M populations. Conversely, the remaining three ARO populations did not display significant differences with the M population. A set of private alleles for the ARO core genetic group was identified, indicating the possibility to trace the ARO landrace by means of a SNP-based molecular barcode. Overall, the results of this study provide a framework for further breeding activities and the traceability of the ARO landrace.
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Affiliation(s)
- Chiara Delvento
- Department of Soil, Plant and Food Sciences, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Stefano Pavan
- Department of Soil, Plant and Food Sciences, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
- Correspondence: (S.P.); (C.L.)
| | - Monica Marilena Miazzi
- Department of Soil, Plant and Food Sciences, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Angelo Raffaele Marcotrigiano
- Department of Soil, Plant and Food Sciences, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Francesca Ricciardi
- Department of Agriculture, Food, Natural Resources and Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
| | - Luigi Ricciardi
- Department of Soil, Plant and Food Sciences, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Concetta Lotti
- Department of Agriculture, Food, Natural Resources and Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
- Correspondence: (S.P.); (C.L.)
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Ermolaev A, Kudryavtseva N, Pivovarov A, Kirov I, Karlov G, Khrustaleva L. Integrating Genetic and Chromosome Maps of Allium cepa: From Markers Visualization to Genome Assembly Verification. Int J Mol Sci 2022; 23:10486. [PMID: 36142398 PMCID: PMC9504663 DOI: 10.3390/ijms231810486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
The ability to directly look into genome sequences has opened great opportunities in plant breeding. Yet, the assembly of full-length chromosomes remains one of the most difficult problems in modern genomics. Genetic maps are commonly used in de novo genome assembly and are constructed on the basis of a statistical analysis of the number of recombinations. This may affect the accuracy of the ordering and orientation of scaffolds within the chromosome, especially in the region of recombination suppression. Moreover, it is impossible to assign contigs lacking DNA markers. Here, we report the use of Tyr-FISH to determine the position of the short DNA sequence of markers and non-mapped unique copy sequence on the physical chromosomes of a large-genome onion (Allium cepa L.). In order to minimize potential background masking of the target signal, we improved our earlier developed pipeline for probe design. A total of 23 markers were located on physical chromosomes 2 and 6. The order of markers was corrected by the integration of genetic, pseudochromosome maps and cytogenetic maps. Additionally, the position of the mlh1 gene, which was not on the genetic map, was defined on physical chromosome 2. Tyr-FISH mapping showed that the order of 23.1% (chromosome 2) and 27.3% (chromosome 6) of the tested genes differed between physical chromosomes and pseudochromosomes. The results can be used for the improvement of pseudochromosome 2 and 6 assembly. The present study aims to demonstrate the value of the in situ visualization of DNA sequences in chromosome-scaffold genome assembly.
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Affiliation(s)
- Aleksey Ermolaev
- Laboratory of Applied Genomics and Crop Breeding, All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskay 42 Str., 127550 Moscow, Russia
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskay 49 Str., 127550 Moscow, Russia
| | - Natalia Kudryavtseva
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskay 49 Str., 127550 Moscow, Russia
- Plant Cell Engineering Laboratory, All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskay 42 Str., 127550 Moscow, Russia
| | - Anton Pivovarov
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskay 49 Str., 127550 Moscow, Russia
- Plant Cell Engineering Laboratory, All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskay 42 Str., 127550 Moscow, Russia
| | - Ilya Kirov
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskay 42 Str., 127550 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Gennady Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskay 42 Str., 127550 Moscow, Russia
| | - Ludmila Khrustaleva
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskay 49 Str., 127550 Moscow, Russia
- Plant Cell Engineering Laboratory, All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskay 42 Str., 127550 Moscow, Russia
- Department of Botany, Breeding and Seed Production of Garden Plants, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskay 49 Str., 127550 Moscow, Russia
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20
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Sekine D, Oku S, Nunome T, Hirakawa H, Tsujimura M, Terachi T, Toyoda A, Shigyo M, Sato S, Tsukazaki H. Development of a genome-wide marker design workflow for onions and its application in target amplicon sequencing-based genotyping. DNA Res 2022; 29:6675293. [PMID: 36007888 PMCID: PMC9410872 DOI: 10.1093/dnares/dsac020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Indexed: 11/24/2022] Open
Abstract
Onions are one of the most widely cultivated vegetables worldwide; however, the development and utilization of molecular markers have been limited because of the large genome of this plant. We present a genome-wide marker design workflow for onions and its application in a high-throughput genotyping method based on target amplicon sequencing. The efficiency of the method was evaluated by genotyping of F2 populations. In the marker design workflow, unigene and genomic sequence data sets were constructed, and polymorphisms between parental lines were detected through transcriptome sequence analysis. The positions of polymorphisms detected in the unigenes were mapped onto the genome sequence, and primer sets were designed. In total, 480 markers covering the whole genome were selected. By genotyping an F2 population, 329 polymorphic sites were obtained from the estimated positions or the flanking sequences. However, missing or sparse marker regions were observed in the resulting genetic linkage map. We modified the markers to cover these regions by genotyping the other F2 populations. The grouping and order of markers on the linkages were similar across the genetic maps. Our marker design workflow and target amplicon sequencing are useful for genome-wide genotyping of onions owing to their reliability, cost effectiveness, and flexibility.
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Affiliation(s)
- Daisuke Sekine
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO) , Tsu, Mie 514-2392, Japan
| | - Satoshi Oku
- Tohoku Agricultural Research Center, NARO , Morioka, Iwate 020-0198, Japan
| | - Tsukasa Nunome
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO) , Tsu, Mie 514-2392, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute , Kisarazu, Chiba 292-0818, Japan
| | - Mai Tsujimura
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University , Otsu, Shiga 520-2194, Japan
- Plant Organelle Genome Research Center, Kyoto Sangyo University , Kyoto 603-8555, Japan
| | - Toru Terachi
- Plant Organelle Genome Research Center, Kyoto Sangyo University , Kyoto 603-8555, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics , Mishima, Shizuoka 411-8540, Japan
| | - Masayoshi Shigyo
- Laboratory of Vegetable Crop Science, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University , Yamaguchi City, Yamaguchi 753-8515, Japan
| | - Shusei Sato
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University , Sendai, Miyagi 980-8577, Japan
| | - Hikaru Tsukazaki
- Tohoku Agricultural Research Center, NARO , Morioka, Iwate 020-0198, Japan
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21
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Oku S, Ueno K, Sawazaki Y, Maeda T, Jitsuyama Y, Suzuki T, Onodera S, Fujino K, Shimura H. Functional characterization and vacuolar localization of fructan exohydrolase derived from onion (Allium cepa). JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4908-4922. [PMID: 35552692 DOI: 10.1093/jxb/erac197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Fructans such as inulin and levan accumulate in certain taxonomic groups of plants and are a reserve carbohydrate alternative to starch. Onion (Allium cepa L.) is a typical plant species that accumulates fructans, and it synthesizes inulin-type and inulin neoseries-type fructans in the bulb. Although genes for fructan biosynthesis in onion have been identified so far, no genes for fructan degradation had been found. In this study, phylogenetic analysis predicted that we isolated a putative vacuolar invertase gene (AcpVI1), but our functional analyses demonstrated that it encoded a fructan 1-exohydrolase (1-FEH) instead. Assessments of recombinant proteins and purified native protein showed that the protein had 1-FEH activity, hydrolyzing the β-(2,1)-fructosyl linkage in inulin-type fructans. Interestingly, AcpVI1 had an amino acid sequence close to those of vacuolar invertases and fructosyltransferases, unlike all other FEHs previously found in plants. We showed that AcpVI1 was localized in the vacuole, as are onion fructosyltransferases Ac1-SST and Ac6G-FFT. These results indicate that fructan-synthesizing and -degrading enzymes are both localized in the vacuole. In contrast to previously reported FEHs, our data suggest that onion 1-FEH evolved from a vacuolar invertase and not from a cell wall invertase. This demonstrates that classic phylogenetic analysis on its own is insufficient to discriminate between invertases and FEHs, highlighting the importance of functional markers in the nearby active site residues.
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Affiliation(s)
- Satoshi Oku
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Keiji Ueno
- Graduate School of Dairy Science, Rakuno Gakuen University, Ebetsu, 069-8501, Japan
| | - Yukiko Sawazaki
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Tomoo Maeda
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, 036-8561, Japan
| | - Yutaka Jitsuyama
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Takashi Suzuki
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Shuichi Onodera
- Graduate School of Dairy Science, Rakuno Gakuen University, Ebetsu, 069-8501, Japan
| | - Kaien Fujino
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Hanako Shimura
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
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22
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Steentjes MBF, Herrera Valderrama AL, Fouillen L, Bahammou D, Leisen T, Albert I, Nürnberger T, Hahn M, Mongrand S, Scholten OE, van Kan JAL. Cytotoxic activity of Nep1-like proteins on monocots. THE NEW PHYTOLOGIST 2022; 235:690-700. [PMID: 35383933 PMCID: PMC9320973 DOI: 10.1111/nph.18146] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Necrosis- and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) are found throughout several plant-associated microbial taxa and are typically considered to possess cytolytic activity exclusively on dicot plant species. However, cytolytic NLPs are also produced by pathogens of monocot plants such as the onion (Allium cepa) pathogen Botrytis squamosa. We determined the cytotoxic activity of B. squamosa BsNep1, as well as other previously characterized NLPs, on various monocot plant species and assessed the plant plasma membrane components required for NLP sensitivity. Leaf infiltration of NLPs showed that onion cultivars are differentially sensitive to NLPs, and analysis of their sphingolipid content revealed that the GIPC series A : series B ratio did not correlate to NLP sensitivity. A tri-hybrid population derived from a cross between onion and two wild relatives showed variation in NLP sensitivity within the population. We identified a quantitative trait locus (QTL) for NLP insensitivity that colocalized with a previously identified QTL for B. squamosa resistance and the segregating trait of NLP insensitivity correlated with the sphingolipid content. Our results demonstrate the cytotoxic activity of NLPs on several monocot plant species and legitimize their presence in monocot-specific plant pathogens.
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Affiliation(s)
| | | | - Laetitia Fouillen
- Laboratoire de Biogènese MembranaireUMR 5200CNRSUniversity of BordeauxF‐33140Villenave d’OrnonFrance
| | - Delphine Bahammou
- Laboratoire de Biogènese MembranaireUMR 5200CNRSUniversity of BordeauxF‐33140Villenave d’OrnonFrance
| | - Thomas Leisen
- Department of Biology, Plant PathologyUniversity of KaiserslauternKaiserslautern67663Germany
| | - Isabell Albert
- Molecular Plant PhysiologyFAU Erlangen‐NürnbergErlangen91058Germany
| | | | - Matthias Hahn
- Department of Biology, Plant PathologyUniversity of KaiserslauternKaiserslautern67663Germany
| | - Sébastien Mongrand
- Laboratoire de Biogènese MembranaireUMR 5200CNRSUniversity of BordeauxF‐33140Villenave d’OrnonFrance
| | - Olga E. Scholten
- Plant BreedingWageningen University & ResearchWageningen6708 PBthe Netherlands
| | - Jan A. L. van Kan
- Laboratory of PhytopathologyWageningen UniversityWageningen6708 PBthe Netherlands
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23
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Biosynthesis and Metabolism of Garlic Odor Compounds in Cultivated Chinese Chives (Allium tuberosum) and Wild Chinese Chives (Allium hookeri). Int J Mol Sci 2022; 23:ijms23137013. [PMID: 35806016 PMCID: PMC9266804 DOI: 10.3390/ijms23137013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/12/2022] [Accepted: 06/20/2022] [Indexed: 11/23/2022] Open
Abstract
Chinese chives is a popular herb vegetable and medicine in Asian countries. Southwest China is one of the centers of origin, and the mountainous areas in this region are rich in wild germplasm. In this study, we collected four samples of germplasm from different altitudes: a land race of cultivated Chinese chives (Allium tuberosum), wide-leaf chives and extra-wide-leaf chives (Allium hookeri), and ovoid-leaf chives (Allium funckiaefolium). Leaf metabolites were detected and compared between A. tuberosum and A. hookeri. A total of 158 differentially accumulated metabolites (DAM) were identified by Gas Chromatography—Mass Spectrometry (GC-MS) and Liquid Chromatography—Mass Spectrometry (LC-MS), among which there was a wide range of garlic odor compounds, free amino acids, and sugars. A. hookeri contains a higher content of fructose, garlic odor compounds, and amino acids than A. tuberosum, which is supported by the higher expression level of biosynthetic genes revealed by transcriptome analysis. A. hookeri accumulates the same garlic odor compound precursors that A. tuberosum does (mainly methiin and alliin). We isolated full-length gene sequences of phytochelatin synthase (PCS), γ-glutamyltranspeptidases (GGT), flavin-containing monooxygenase (FMO), and alliinase (ALN). These sequences showed closer relations in phylogenetic analysis between A. hookeri and A. tuberosum (with sequence identities ranging from 86% to 90%) than with Allium cepa or Allium sativum (which had a lower sequence identity ranging from 76% to 88%). Among these assayed genes, ALN, the critical gene controlling the conversion of odorless precursors into odor compounds, was undetected in leaves, bulbs, and roots of A. tuberosum, which could account for its weaker garlic smell. Moreover, we identified a distinct FMO1 gene in extra-wide-leaf A. hookeri that is due to a CDS-deletion and frameshift mutation. These results above reveal the molecular and metabolomic basis of impressive strong odor in wild Chinese chives.
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24
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WRKY Gene Family Drives Dormancy Release in Onion Bulbs. Cells 2022; 11:cells11071100. [PMID: 35406664 PMCID: PMC8997782 DOI: 10.3390/cells11071100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 11/16/2022] Open
Abstract
Onion (Allium cepa L.) is an important bulb crop grown worldwide. Dormancy in bulbous plants is an important physiological state mainly regulated by a complex gene network that determines a stop of vegetative growth during unfavorable seasons. Limited knowledge on the molecular mechanisms that regulate dormancy in onion were available until now. Here, a comparison between uninfected and onion yellow dwarf virus (OYDV)-infected onion bulbs highlighted an altered dormancy in the virus-infected plants, causing several symptoms, such as leaf striping, growth reduction, early bulb sprouting and rooting, as well as a lower abscisic acid (ABA) level at the start of dormancy. Furthermore, by comparing three dormancy stages, almost five thousand four hundred (5390) differentially expressed genes (DEGs) were found in uninfected bulbs, while the number of DEGs was significantly reduced (1322) in OYDV-infected bulbs. Genes involved in cell wall modification, proteolysis, and hormone signaling, such as ABA, gibberellins (GAs), indole-3-acetic acid (IAA), and brassinosteroids (BRs), that have already been reported as key dormancy-related pathways, were the most enriched ones in the healthy plants. Interestingly, several transcription factors (TFs) were up-regulated in the uninfected bulbs, among them three genes belonging to the WRKY family, for the first time characterized in onion, were identified during dormancy release. The involvement of specific WRKY genes in breaking dormancy in onion was confirmed by GO enrichment and network analysis, highlighting a correlation between AcWRKY32 and genes driving plant development, cell wall modification, and division via gibberellin and auxin homeostasis, two key processes in dormancy release. Overall, we present, for the first time, a detailed molecular analysis of the dormancy process, a description of the WRKY-TF family in onion, providing a better understanding of the role played by AcWRKY32 in the bulb dormancy release. The TF co-expressed genes may represent targets for controlling the early sprouting in onion, laying the foundations for novel breeding programs to improve shelf life and reduce postharvest.
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25
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Lee HM, Park JS, Kim SJ, Kim SG, Park YD. Using Transcriptome Analysis to Explore Gray Mold Resistance-Related Genes in Onion (Allium cepa L.). Genes (Basel) 2022; 13:genes13030542. [PMID: 35328095 PMCID: PMC8955018 DOI: 10.3390/genes13030542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 11/29/2022] Open
Abstract
Gray mold disease caused by Botrytis in onions (Allium cepa L.) during growth and storage negatively affects their yield and quality. Exploring the genes related to gray mold resistance in onion and their application to the breeding of resistant onion lines will support effective and ecological control methods of the disease. Here, the genetic relationship of 54 onion lines based on random amplified polymorphic DNA (RAPD) and in vitro-cultured onion lines infected with gray mold were used for screening resistance and susceptibility traits. Two genetically related onion lines were selected, one with a resistant and one with a susceptible phenotype. In vitro gray mold infection was repeated with these two lines, and leaf samples were collected for gene expression studies in time series. Transcript sequences obtained by RNA sequencing were subjected to DEG analysis, variant analysis, and KEGG mapping. Among the KEGG pathways, ‘α-linoleic acid metabolism’ was selected because the comparison of the time series expression pattern of Jasmonate resistant 1 (JAR1), Coronatine-insensitive protein 1 (COI 1), and transcription factor MYC2 (MYC2) genes between the resistant and susceptible lines revealed its significant relationship with gray-mold-resistant phenotypes. Expression pattern and SNP of the selected genes were verified by quantitative real-time PCR and high-resolution melting (HRM) analysis, respectively. The results of this study will be useful for the development of molecular marker and finally breeding of gray-mold-resistant onions.
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26
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Temsch EM, Koutecký P, Urfus T, Šmarda P, Doležel J. Reference standards for flow cytometric estimation of absolute nuclear DNA content in plants. Cytometry A 2021; 101:710-724. [PMID: 34405937 PMCID: PMC9545105 DOI: 10.1002/cyto.a.24495] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/31/2021] [Accepted: 08/02/2021] [Indexed: 11/11/2022]
Abstract
The estimation of nuclear DNA content has been by far the most popular application of flow cytometry in plants. Because flow cytometry measures relative fluorescence intensities of nuclei stained by a DNA fluorochrome, ploidy determination, and estimation of the nuclear DNA content in absolute units both require comparison to a reference standard of known DNA content. This implies that the quality of the results obtained depends on the standard selection and use. Internal standardization, when the nuclei of an unknown sample and the reference standard are isolated, stained, and measured simultaneously, is mandatory for precise measurements. As DNA peaks representing G1/G0 nuclei of the sample and standard appear on the same histogram of fluorescence intensity, the quotient of their position on the fluorescence intensity axis provides the quotient of DNA amounts. For the estimation of DNA amounts in absolute units, a number of well‐established standards are now available to cover the range of known plant genome sizes. Since there are different standards in use, the standard and the genome size assigned to it has always to be reported. When none of the established standards fits, the introduction of a new standard species is needed. For this purpose, the regression line approach or simultaneous analysis of the candidate standard with several established standards should be prioritized. Moreover, the newly selected standard organism has to fulfill a number of requirements: it should be easy to identify and maintain, taxonomically unambiguous, globally available, with known genome size stability, lacking problematic metabolites, suitable for isolation of sufficient amounts of nuclei, and enabling measurements with low coefficients of variation of DNA peaks, hence suitable for the preparation of high quality samples.
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Affiliation(s)
- Eva M Temsch
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Petr Koutecký
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Tomáš Urfus
- Department of Botany, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
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