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Feng S, Li N, Chen H, Liu Z, Li C, Zhou R, Zhang Y, Cao R, Ma X, Song X. Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plants. MOLECULAR HORTICULTURE 2024; 4:13. [PMID: 38589963 PMCID: PMC11003162 DOI: 10.1186/s43897-024-00090-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 03/03/2024] [Indexed: 04/10/2024]
Abstract
The auxin response factor (ARF) and auxin/indole-3-acetic acid (Aux/IAA) family of genes are central components of the auxin signaling pathway and play essential roles in plant growth and development. Their large-scale analysis and evolutionary trajectory of origin are currently not known. Here, we identified the corresponding ARF and Aux/IAA family members and performed a large-scale analysis by scanning 406 plant genomes. The results showed that the ARF and Aux/IAA gene families originated from charophytes. The ARF family sequences were more conserved than the Aux/IAA family sequences. Dispersed duplications were the common expansion mode of ARF and Aux/IAA families in bryophytes, ferns, and gymnosperms; however, whole-genome duplication was the common expansion mode of the ARF and Aux/IAA families in basal angiosperms, magnoliids, monocots, and dicots. Expression and regulatory network analyses revealed that the Arabidopsis thaliana ARF and Aux/IAA families responded to multiple hormone, biotic, and abiotic stresses. The APETALA2 and serum response factor-transcription factor gene families were commonly enriched in the upstream and downstream genes of the ARF and Aux/IAA gene families. Our study provides a comprehensive overview of the evolutionary trajectories, structural functions, expansion mechanisms, expression patterns, and regulatory networks of these two gene families.
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Affiliation(s)
- Shuyan Feng
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Nan Li
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Huilong Chen
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zhuo Liu
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Chunjin Li
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Rong Zhou
- Department of Food Science, Aarhus University, Aarhus, 8200, Denmark
| | - Yingchao Zhang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Rui Cao
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China.
| | - Xiao Ma
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China.
- College of Horticultural Science & Technology, Hebei Normal University of Science & Technology, Qinhuangdao, Hebei, 066600, China.
| | - Xiaoming Song
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China.
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2
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Zhao X, Yu J, Chanda B, Zhao J, Wu S, Zheng Y, Sun H, Levi A, Ling KS, Fei Z. Genomic and pangenomic analyses provide insights into the population history and genomic diversification of bottle gourd. THE NEW PHYTOLOGIST 2024. [PMID: 38503725 DOI: 10.1111/nph.19673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 02/27/2024] [Indexed: 03/21/2024]
Abstract
Bottle gourd (Lagenaria siceraria (Mol.) Strandl.) is an economically important vegetable crop and one of the earliest domesticated crops. However, the population history and genomic diversification of bottle gourd have not been extensively studied. We generated a comprehensive bottle gourd genome variation map from genome sequences of 197 world-wide representative accessions, which enables a genome-wide association study for identifying genomic loci associated with resistance to zucchini yellow mosaic virus, and constructed a bottle gourd pangenome that harbors 1534 protein-coding genes absent in the reference genome. Demographic analyses uncover that domesticated bottle gourd originated in Southern Africa c. 12 000 yr ago, and subsequently radiated to the New World via the Atlantic drift and to Eurasia through the efforts of early farmers in the initial Holocene. The identified highly differentiated genomic regions among different bottle gourd populations harbor many genes contributing to their local adaptations such as those related to disease resistance and stress tolerance. Presence/absence variation analysis of genes in the pangenome reveals numerous genes including those involved in abiotic/biotic stress responses that have been under selection during the world-wide expansion of bottle gourds. The bottle gourd variation map and pangenome provide valuable resources for future functional studies and genomics-assisted breeding.
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Affiliation(s)
- Xuebo Zhao
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Jingyin Yu
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Bidisha Chanda
- USDA-ARS, US Vegetable Laboratory, Charleston, SC, 29414, USA
| | - Jiantao Zhao
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Shan Wu
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Yi Zheng
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Honghe Sun
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Amnon Levi
- USDA-ARS, US Vegetable Laboratory, Charleston, SC, 29414, USA
| | - Kai-Shu Ling
- USDA-ARS, US Vegetable Laboratory, Charleston, SC, 29414, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
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3
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Nestor BJ, Bayer PE, Fernandez CGT, Edwards D, Finnegan PM. Approaches to increase the validity of gene family identification using manual homology search tools. Genetica 2023; 151:325-338. [PMID: 37817002 PMCID: PMC10692271 DOI: 10.1007/s10709-023-00196-8] [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: 06/07/2023] [Accepted: 10/01/2023] [Indexed: 10/12/2023]
Abstract
Identifying homologs is an important process in the analysis of genetic patterns underlying traits and evolutionary relationships among species. Analysis of gene families is often used to form and support hypotheses on genetic patterns such as gene presence, absence, or functional divergence which underlie traits examined in functional studies. These analyses often require precise identification of all members in a targeted gene family. Manual pipelines where homology search and orthology assignment tools are used separately are the most common approach for identifying small gene families where accurate identification of all members is important. The ability to curate sequences between steps in manual pipelines allows for simple and precise identification of all possible gene family members. However, the validity of such manual pipeline analyses is often decreased by inappropriate approaches to homology searches including too relaxed or stringent statistical thresholds, inappropriate query sequences, homology classification based on sequence similarity alone, and low-quality proteome or genome sequences. In this article, we propose several approaches to mitigate these issues and allow for precise identification of gene family members and support for hypotheses linking genetic patterns to functional traits.
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Affiliation(s)
- Benjamin J Nestor
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia.
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia.
| | - Philipp E Bayer
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - Cassandria G Tay Fernandez
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - Patrick M Finnegan
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
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4
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Wang J, Wu X, Wang Y, Wu X, Wang B, Lu Z, Li G. Genome-wide characterization and expression analysis of the MLO gene family sheds light on powdery mildew resistance in Lagenaria siceraria. Heliyon 2023; 9:e14624. [PMID: 37025859 PMCID: PMC10070393 DOI: 10.1016/j.heliyon.2023.e14624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
MLO (mildew locus O) genes play a vital role in plant disease defense system, especially powdery mildew (PM). Lagenaria siceraria is a distinct Cucurbitaceae crop, and PM is one of the most serious diseases threatening crop production and quality. Although MLOs have been exploited in many Cucurbitaceae species, genome-wide mining of MLO gene family in bottle gourd has not been surveyed yet. Here we identified 16 MLO genes in our recently assembled L. siceraria genome. A total of 343 unique MLO protein sequences from 20 species were characterized and compared to deduce a generally high level of purifying selection and the occurrence of regions related to candidate susceptibility factors in the evolutional divergence. LsMLOs were clustered in six clades containing seven conserved transmembrane domains and 10 clade-specific motifs along with deletion and variation. Three genes (LsMLO3, LsMLO6, and LsMLO13) in clade V showed high sequence identity with orthologues involved in PM susceptibility. The expression pattern of LsMLOs was tissue-specific but not cultivar-specific. Furthermore, it was indicated by qRT-PCR and RNA-seq that LsMLO3 and LsMLO13 were highly upregulated in response to PM stress. Subsequent sequence analysis revealed the structural deletion of LsMLO13 and a single nonsynonymous substitution of LsMLO3 in the PM-resistant genotype. Taken all together, it is speculated that LsMLO13 is likely a major PM susceptibility factor. The results of this study provide new insights into MLO family genes in bottle gourd and find a potential candidate S gene for PM tolerance breeding.
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Wang J, Wang Y, Wu X, Wang B, Lu Z, Zhong L, Li G, Wu X. Insight into the bZIP gene family in Lagenaria siceraria: Genome and transcriptome analysis to understand gene diversification in Cucurbitaceae and the roles of LsbZIP gene expression and function under cold stress. FRONTIERS IN PLANT SCIENCE 2023; 13:1128007. [PMID: 36874919 PMCID: PMC9981963 DOI: 10.3389/fpls.2022.1128007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
The basic leucine zipper (bZIP) as a well-known transcription factor family, figures prominently in diverse biological and developmental processes and response to abiotic/biotic stresses. However, no knowledge of the bZIP family is available for the important edible Cucurbitaceae crop bottle gourd. Herein, we identified 65 putative LsbZIP genes and characterized their gene structure, phylogenetic and orthologous relationships, gene expression profiles in different tissues and cultivars, and responsive genes under cold stress. The phylogenetic tree of 16 released Cucurbitaceae plant genomes revealed the evolutionary convergence and divergence of bZIP family. Based on the specific domains, LsbZIP family were classified into 12 clades (A-K, S) with similar motifs and exon-intron distribution. 65 LsbZIP genes have undergone 19 segmental and two tandem duplication events with purifying selection. The expression profiling of LsbZIP genes showed tissue-specific but no cultivar-specific pattern. The cold stress-responsive candidate LsbZIP genes were analyzed and validated by RNA-Seq and RT-PCR, providing new insights of transcriptional regulation of bZIP family genes in bottle gourd and their potential functions in cold-tolerant variety breeding.
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Affiliation(s)
- Jian Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ying Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyi Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Baogen Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhongfu Lu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Liping Zhong
- College of Horticulture Science, Zhejiang Agriculture and Forestry (A&F) University, Hangzhou, China
| | - Guojing Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaohua Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Huo Y, Zhang G, Yu W, Liu Z, Shen M, Zhao R, Hu S, Zheng X, Wang P, Yang Y. Forward genetic studies reveal LsAPRR2 as a key gene in regulating the green color of pericarp in bottle gourd ( Lagenaria siceraria). FRONTIERS IN PLANT SCIENCE 2023; 14:1130669. [PMID: 36875578 PMCID: PMC9975725 DOI: 10.3389/fpls.2023.1130669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
The fruit peel color is an important factor that affects its quality. However, genes involved in regulating pericarp color in bottle gourd (Lagenaria siceraria) have not been explored to date. Genetic analysis of color traits in bottle gourd peel through a genetic population of six generations demonstrated that the green color of peels is inherited as a single gene dominant trait. Combined phenotype-genotype analysis of recombinant plants using BSA-seq mapped the candidate gene to a 22.645 Kb interval at the head end of chromosome 1. We observed that the final interval contained only one gene, LsAPRR2 (HG_GLEAN_10010973). Sequence and spatiotemporal expression analyses of LsAPRR2 unraveled two nonsynonymous mutations (A→G) and (G→C) in the parental CDS sequences. Further, LsAPRR2 expression was higher in all green-skinned bottle gourds (H16) at various stages of fruit development than in white-skinned bottle gourds (H06). Cloning and sequence comparison of the two parental LsAPRR2 promoter regions indicated 11 bases insertion and 8 SNPs mutations in the region -991~-1033, upstream of the start codon in white bottle gourd. Proof of GUS reporting system, Genetic variation in this fragment significantly reduced the expression of LsAPRR2 in the pericarp of white bottle gourd. In addition, we developed a tightly linked (accuracy 93.88%) InDel marker for the promoter variant segment. Overall, the current study provides a theoretical basis for comprehensive elucidation of the regulatory mechanisms underlying the determination of bottle gourd pericarp color. This would further help in the directed molecular design breeding of bottle gourd pericarp.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Peng Wang
- *Correspondence: Yanjuan Yang, ; Peng Wang,
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7
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Fu A, Zheng Y, Guo J, Grierson D, Zhao X, Wen C, Liu Y, Li J, Zhang X, Yu Y, Ma H, Wang Q, Zuo J. Telomere-to-telomere genome assembly of bitter melon ( Momordica charantia L. var. abbreviata Ser.) reveals fruit development, composition and ripening genetic characteristics. HORTICULTURE RESEARCH 2023; 10:uhac228. [PMID: 36643758 PMCID: PMC9832870 DOI: 10.1093/hr/uhac228] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/26/2022] [Indexed: 05/19/2023]
Abstract
Momordica charantia L. var. abbreviata Ser. (Mca), known as bitter gourd or bitter melon, is a Momordica variety with medicinal value and belongs to the Cucurbitaceae family. In view of the lack of genomic information on bitter gourd and other Momordica species and to promote Mca genomic research, we assembled a 295.6-Mb telomere-to-telomere (T2T) high-quality Mca genome with six gap-free chromosomes after Hi-C correction. This genome is anchored to 11 chromosomes, which is consistent with the karyotype information, and comprises 98 contigs (N50 of 25.4 Mb) and 95 scaffolds (N50 of 25.4 Mb). The Mca genome harbors 19 895 protein-coding genes, of which 45.59% constitute predicted repeat sequences. Synteny analysis revealed variations involved in fruit quality during the divergence of bitter gourd. In addition, assay for transposase-accessible chromatin by high-throughput sequencing and metabolic analysis showed that momordicosides and other substances are characteristic of Mca fruit pulp. A combined transcriptomic and metabolomic analysis revealed the mechanisms of pigment accumulation and cucurbitacin biosynthesis in Mca fruit peels, providing fundamental molecular information for further research on Mca fruit ripening. This report provides a new genetic resource for Momordica genomic studies and contributes additional insights into Cucurbitaceae phylogeny.
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Affiliation(s)
| | | | - Jing Guo
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Donald Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Xiaoyan Zhao
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agricultural and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, Beijing 100097, China
| | - Changlong Wen
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agricultural and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, Beijing 100097, China
| | - Ye Liu
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Advanced Innovation Center for Food Nutrition and Human Health, School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, 100048, China
| | - Jian Li
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Advanced Innovation Center for Food Nutrition and Human Health, School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, 100048, China
| | - Xuewen Zhang
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Ying Yu
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Hong Ma
- Corresponding authors: Jinhua Zuo, +861051503058; Qing Wang, ; Hong Ma,
| | - Qing Wang
- Corresponding authors: Jinhua Zuo, +861051503058; Qing Wang, ; Hong Ma,
| | - Jinhua Zuo
- Corresponding authors: Jinhua Zuo, +861051503058; Qing Wang, ; Hong Ma,
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8
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Feng Z, Wu X, Wang J, Wu X, Wang B, Lu Z, Ye Z, Li G, Wang Y. Identification of Bottle Gourd ( Lagenaria siceraria) OVATE Family Genes and Functional Characterization of LsOVATE1. Biomolecules 2022; 13:biom13010085. [PMID: 36671470 PMCID: PMC9855390 DOI: 10.3390/biom13010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/26/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
The OVATE gene family is a class of conserved transcription factors that play significant roles in plant growth, development, and abiotic stress, and also affect fruit shape in vegetable crops. Bottle gourd (Lagenaria siceraria), commonly known as calabash or gourd, is an annual climber belonging to the Cucurbitaceae family. Studies on bottle gourd OVATE genes are limited. In this study, we performed genome-wide identification of the OVATE gene family in bottle gourd, and identified a total of 20 OVATE family genes. The identified genes were unevenly distributed across 11 bottle gourd chromosomes. We also analyzed the gene homology, amino acid sequence conservation, and three-dimensional protein structure (via prediction) of the 20 OVATE family genes. We used RNA-seq data to perform expression analysis, which found 20 OVATE family genes to be differentially expressed based on spatial and temporal characteristics, suggesting that they have varying functions in the growth and development of bottle gourd. In situ hybridization and subcellular localization analysis showed that the expression characteristics of the LsOVATE1 gene, located on chromosome 7 homologous to OVATE, is a candidate gene for affecting the fruit shape of bottle gourd. In addition, RT-qPCR data from bottle gourd roots, stems, leaves, and flowers showed different spatial expression of the LsOVATE1 gene. The ectopic expression of LsOVATE1 in tomato generated a phenotype with a distinct fruit shape and development. Transgenic-positive plants that overexpressed LsOVATE1 had cone-shaped fruit, calyx hypertrophy, petal degeneration, and petal retention after flowering. Our results indicate that LsOVATE1 could serve important roles in bottle gourd development and fruit shape determination, and provide a basis for future research into the function of LsOVATE1.
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Affiliation(s)
- Zishan Feng
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Xiaohua Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310012, China
| | - Jian Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310012, China
| | - Xinyi Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310012, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310012, China
| | - Baogen Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310012, China
| | - Zhongfu Lu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310012, China
| | - Zihong Ye
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Guojing Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310012, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310012, China
| | - Ying Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310012, China
- Correspondence: ; Tel.: +86-0571-8640-3050
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9
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Yu J, Wu S, Sun H, Wang X, Tang X, Guo S, Zhang Z, Huang S, Xu Y, Weng Y, Mazourek M, McGregor C, Renner SS, Branham S, Kousik C, Wechter W, Levi A, Grumet R, Zheng Y, Fei Z. CuGenDBv2: an updated database for cucurbit genomics. Nucleic Acids Res 2022; 51:D1457-D1464. [PMID: 36271794 PMCID: PMC9825510 DOI: 10.1093/nar/gkac921] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 01/30/2023] Open
Abstract
The Cucurbitaceae (cucurbit) family consists of about 1,000 species in 95 genera, including many economically important and popular fruit and vegetable crops. During the past several years, reference genomes have been generated for >20 cucurbit species, and variome and transcriptome profiling data have been rapidly accumulated for cucurbits. To efficiently mine, analyze and disseminate these large-scale datasets, we have developed an updated version of Cucurbit Genomics Database. The updated database, CuGenDBv2 (http://cucurbitgenomics.org/v2), currently hosts 34 reference genomes from 27 cucurbit species/subspecies belonging to 10 different genera. Protein-coding genes from these genomes have been comprehensively annotated by comparing their protein sequences to various public protein and domain databases. A novel 'Genotype' module has been implemented to facilitate mining and analysis of the functionally annotated variome data including SNPs and small indels from large-scale genome sequencing projects. An updated 'Expression' module has been developed to provide a comprehensive gene expression atlas for cucurbits. Furthermore, synteny blocks between any two and within each of the 34 genomes, representing a total of 595 pair-wise genome comparisons, have been identified and can be explored and visualized in the database.
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Affiliation(s)
- Jingyin Yu
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Shan Wu
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Honghe Sun
- Boyce Thompson Institute, Ithaca, NY 14853, USA,Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Xin Wang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuemei Tang
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Shaogui Guo
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Zhonghua Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Yong Xu
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Yiqun Weng
- U.S. Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706, USA,Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
| | - Michael Mazourek
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Cecilia McGregor
- Department of Horticulture, University of Georgia, Athens, GA 30602, USA
| | - Susanne S Renner
- Faculty of Biology, Systematic Botany and Mycology, University of Munich (LMU), 80638 Munich, Germany,Department of Biology, Washington University, Saint Louis, MO 63130, USA
| | - Sandra Branham
- Coastal Research and Educational Center, Clemson University, Charleston, SC 29414, USA
| | - Chandrasekar Kousik
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - W Patrick Wechter
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Amnon Levi
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Yi Zheng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China,Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Zhangjun Fei
- To whom correspondence should be addressed. Tel: +1 607 2543234; Fax: +1 607 2541242;
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10
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Wang Y, Li Y, Wu X, Wu X, Feng Z, Wang J, Wang B, Lu Z, Li G. Elucidation of the Flavor Aspects and Flavor-Associated Genomic Regions in Bottle Gourd ( Lagenaria siceraria) by Metabolomic Analysis and QTL-seq. Foods 2022; 11:foods11162450. [PMID: 36010450 PMCID: PMC9407550 DOI: 10.3390/foods11162450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/04/2022] [Accepted: 08/11/2022] [Indexed: 12/04/2022] Open
Abstract
Bottle gourd (Lagenaria siceraria) is a commercially important cucurbitaceous vegetable with health-promoting properties whose collections and cultivars differ considerably in their flavor aspects. However, the metabolomic profile related to flavor has not yet been elucidated. In the present study, a comprehensive metabolite analysis revealed the metabolite profile of the strong-flavor collection “J120” and weak-flavor collection “G32”. The major differentially expressed metabolites included carboxylic acids, their derivatives, and organooxygen compounds, which are involved in amino acid biosynthesis and metabolism. QTL-seq was used to identify candidate genomic regions controlling flavor in a MAGIC population comprising 377 elite lines. Three significant genomic regions were identified, and candidate genes likely associated with flavor were screened. Our study provides useful information for understanding the metabolic causes of flavor variation among bottle gourd collections and cultivars. Furthermore, the identified candidate genomic regions may facilitate rational breeding programs to improve bottle gourd quality.
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Affiliation(s)
- Ying Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yanwei Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaohua Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xinyi Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Zishan Feng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Baogen Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Zhongfu Lu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Guojing Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Correspondence: ; Tel.: +86-0571-86403050
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11
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Mahapatra S, Sureja AK, Behera TK, Verma M. Assessment of genetic diversity of ninety-one bottle gourd [Lagenaria siceraria (Mol.) Standl.] genotypes from fourteen different agro-climatic zones of India using agro-morphological traits and SSR markers. Mol Biol Rep 2022; 49:6367-6383. [PMID: 35435602 DOI: 10.1007/s11033-022-07446-6] [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: 12/14/2021] [Accepted: 04/01/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND The evaluation of the magnitude of genetic diversity present in the germplasm collection is prerequisite for bottle gourd improvement programme. The characterization of the diversity pattern of Indian bottle gourd accessions will facilitate the optimal use of genetic resources for breeding improved cultivars. METHODS In the present study, the magnitude of genetic diversity was evaluated in ninety-one genotypes of bottle gourd collected across fourteen different agro-climatic zones of India. RESULTS Significant variations were observed for all the studied ten quantitative and nine qualitative traits. The ninety-one genotypes were grouped into nine clusters based on cluster analysis of morphological characteristics. Eigen value from principal component analysis depicted first seven quantitative traits accounted for more than 97.5 cumulative percent of the total variations. The first two components accounted for 50 cumulative percent of the total variation, which signifies a high degree of correlation between the analyzed traits. Molecular diversity with the 40 SSR markers screened revealed 11 polymorphic markers in the genotypes studied. Population structure analysis divulged five populations, conforming to the Principal Coordinate Analysis. Molecular analysis revealed genetically diverse genotypes along with the morphologically divergent genotypes from the quantitative traits and highest inter-cluster distance would be the most appropriate parents for exploiting heterosis. CONCLUSIONS The results of this study will facilitate the optimal use of genetic resources for breeding improved cultivars of bottle gourd and the adoption of the identified superior genotypes directly by the breeders.
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Affiliation(s)
- Sourav Mahapatra
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
| | - Amish Kumar Sureja
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India.
| | | | - Manjusha Verma
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012, India
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12
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Wu X, Fang P, Zhang P, Sun T, Wang X, Branca F, Xu P. Editorial: Improvement for Quality and Safety Traits in Horticultural Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:927779. [PMID: 35712592 PMCID: PMC9194942 DOI: 10.3389/fpls.2022.927779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Xinyang Wu
- College of Life Sciences, China Jiliang University, Hangzhou, China
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, Hangzhou, China
| | - Pingping Fang
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Peipei Zhang
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Ting Sun
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Xinchao Wang
- National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Hangzhou, China
| | - Ferdinando Branca
- Departments of Agriculture, Food, and Environment, University of Catania, Catania, Italy
| | - Pei Xu
- College of Life Sciences, China Jiliang University, Hangzhou, China
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, Hangzhou, China
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13
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Ma L, Wang Q, Zheng Y, Guo J, Yuan S, Fu A, Bai C, Zhao X, Zheng S, Wen C, Guo S, Gao L, Grierson D, Zuo J, Xu Y. Cucurbitaceae genome evolution, gene function and molecular breeding. HORTICULTURE RESEARCH 2022; 9:uhab057. [PMID: 35043161 PMCID: PMC8969062 DOI: 10.1093/hr/uhab057] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/28/2021] [Indexed: 05/07/2023]
Abstract
The Cucurbitaceae is one of the most genetically diverse plant families in the world. Many of them are important vegetables or medicinal plants and are widely distributed worldwide. The rapid development of sequencing technologies and bioinformatic algorithms has enabled the generation of genome sequences of numerous important Cucurbitaceae species. This has greatly facilitated research on gene identification, genome evolution, genetic variation and molecular breeding of cucurbit crops. So far, genome sequences of 18 different cucurbit species belonging to tribes Benincaseae, Cucurbiteae, Sicyoeae, Momordiceae and Siraitieae have been deciphered. This review summarizes the genome sequence information, evolutionary relationship, and functional genes associated with important agronomic traits (e.g., fruit quality). The progress of molecular breeding in cucurbit crops and prospects for future applications of Cucurbitaceae genome information are also discussed.
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Affiliation(s)
- Lili Ma
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yanyan Zheng
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jing Guo
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Shuzhi Yuan
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Anzhen Fu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Chunmei Bai
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xiaoyan Zhao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Shufang Zheng
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Changlong Wen
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Shaogui Guo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Lipu Gao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Donald Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yong Xu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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14
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Wang Y, Wu X, Li Y, Feng Z, Mu Z, Wang J, Wu X, Wang B, Lu Z, Li G. Identification and Validation of a Core Single-Nucleotide Polymorphism Marker Set for Genetic Diversity Assessment, Fingerprinting Identification, and Core Collection Development in Bottle Gourd. FRONTIERS IN PLANT SCIENCE 2021; 12:747940. [PMID: 34868131 PMCID: PMC8636714 DOI: 10.3389/fpls.2021.747940] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Germplasm collections are indispensable resources for the mining of important genes and variety improvement. To preserve and utilize germplasm collections in bottle gourd, we identified and validated a highly informative core single-nucleotide polymorphism (SNP) marker set from 1,100 SNPs. This marker set consisted of 22 uniformly distributed core SNPs with abundant polymorphisms, which were established to have strong representativeness and discriminatory power based on analyses of 206 bottle gourd germplasm collections and a multiparent advanced generation inter-cross (MAGIC) population. The core SNP markers were used to assess genetic diversity and population structure, and to fingerprint important accessions, which could provide an optimized procedure for seed authentication. Furthermore, using the core SNP marker set, we developed an accessible core population of 150 accessions that represents 100% of the genetic variation in bottle gourds. This core population will make an important contribution to the preservation and utilization of bottle gourd germplasm collections, cultivar identification, and marker-assisted breeding.
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Affiliation(s)
- Ying Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaohua Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yanwei Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zishan Feng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zihan Mu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiang Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyi Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Baogen Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhongfu Lu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guojing Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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