93 results on '"Feishi Luan"'
Search Results
2. Comparative chloroplast genome analysis of seven extant Citrullus species insight into genetic variation, phylogenetic relationships, and selective pressure
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Cong Zhou, Putao Wang, Qun Zeng, Rongbin Zeng, Wei Hu, Lei Sun, Shi Liu, Feishi Luan, and Qianglong Zhu
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Multidisciplinary - Abstract
Citrullus ecirrhosus, Citrullus rehmii, and Citrullus naudinianus are three important related wild species of watermelon in the genus Citrullus, and their morphological differences are clear, however, their chloroplast genome differences remain unknown. This study is the first to assemble, analyze, and publish the complete chloroplast genomes of C. ecirrhosus, C. rehmii, and C. naudinianus. A comparative analysis was then conducted among the complete chloroplast genomes of seven extant Citrullus species, and the results demonstrated that the average genome sizes of Citrullus is 157,005 bp, a total of 130–133 annotated genes were identified, including 8 rRNA, 37 tRNA and 85–88 protein-encoding genes. Their gene content, order, and genome structure were similar. However, noncoding regions were more divergent than coding regions, and rps16-trnQ was a hypervariable fragment. Thirty-four polymorphic SSRs, 1,271 SNPs and 234 INDELs were identified. Phylogenetic trees revealed a clear phylogenetic relationship of Citrullus species, and the developed molecular markers (SNPs and rps16-trnQ) could be used for taxonomy in Citrullus. Three genes (atpB, clpP1, and rpoC2) were identified to undergo selection and would promote the environmental adaptation of Citrullus.
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- 2023
3. Correction to: A recessive gene Cmpmr2F confers powdery mildew resistance in melon (Cucumis melo L.)
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Taifeng Zhang, Haonan Cui, Feishi Luan, Hongyu Liu, Zhuo Ding, Sikandar Amanullah, Manlin Zhang, Tingting Ma, and Peng Gao
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Genetics ,General Medicine ,Agronomy and Crop Science ,Biotechnology - Published
- 2023
4. Integrated analysis of biparental and natural populations reveals CRIB domain-containing protein underlying seed coat crack trait in watermelon
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Qi Mi, Hongqian Pang, Feishi Luan, Peng Gao, and Shi Liu
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Genetics ,General Medicine ,Agronomy and Crop Science ,Biotechnology - Published
- 2023
5. BSA‐seq and quantitative trait locus mapping reveals a major effective QTL for carpel number in watermelon ( <scp> Citrullus lanatus </scp> )
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Boyan Qiu, Taifeng Zhang, Shuqing Zhang, Qianrui Qu, Zicheng Zhu, Shusen Liu, Zhengfeng Song, Lianqin Xia, Zhongzhou Yang, Qian Zhang, Feishi Luan, Peng Gao, and Shi Liu
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Genetics ,Plant Science ,Agronomy and Crop Science - Published
- 2022
6. Biparental genetic mapping reveals that CmCLAVATA3 (CmCLV3) is responsible for the variation in carpel number in melon (Cucumis melo L.)
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Lihuan Wang, Yaping Wang, Feishi Luan, Xian Zhang, Jingchao Zhao, Zhongzhou Yang, and Shi Liu
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Cucumis melo ,Genetics ,Chromosome Mapping ,Sequence Analysis, DNA ,General Medicine ,Cucumis sativus ,Genes, Plant ,Agronomy and Crop Science ,Biotechnology - Abstract
Genetic analysis revealed that CmCLV3 is a candidate gene for the variation in melon carpel number. Carpel number (CN) is an important trait in melon. Three-CN melon fruit is oval, while 5-CN melon fruit has a round or flat shape. Herein, a genetic analysis of a population in which the CN locus was segregated indicated that 3-CN is controlled by a major dominant effective gene. Bulked segregant analysis and initial linkage mapping placed the CN locus in a 6.67 Mb region on chromosome 12, and it was narrowed to 882.19 kb with molecular markers and recombinant plants. Fine mapping with a large F
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- 2022
7. Screening of rootstocks with resistance to chilling and continuous cropping but without compromising fruit quality for protected watermelon production
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Kai Xu, Zhixiang Lan, Qing Liu, Yuxing Xue, Jingyi Yan, Zhuangzhuang Su, Mengjie Cheng, Feishi Luan, Xian Zhang, and Hao Li
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- 2022
8. Primary mapping of quantitative trait loci regulating multivariate horticultural phenotypes of watermelon (Citrullus lanatus L.)
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Sikandar Amanullah, Shenglong Li, Benjamin Agyei Osae, Tiantian Yang, Farhat Abbas, Meiling Gao, Xuezheng Wang, Hongyu Liu, Peng Gao, and Feishi Luan
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Plant Science - Abstract
Watermelon fruits exhibit a remarkable diversity of important horticultural phenotypes. In this study, we initiated a primary quantitative trait loci (QTL) mapping to identify the candidate regions controlling the ovary, fruit, and seed phenotypes. Whole genome sequencing (WGS) was carried out for two differentiated watermelon lines, and 350 Mb (96%) and 354 Mb (97%) of re-sequenced reads covered the reference de novo genome assembly, individually. A total of 45.53% non-synonymous single nucleotide polymorphism (nsSNPs) and 54.47% synonymous SNPs (sSNPs) were spotted, which produced 210 sets of novel SNP-based cleaved amplified polymorphism sequence (CAPS) markers by depicting 46.25% co-dominant polymorphism among parent lines and offspring. A biparental F2:3 mapping population comprised of 100 families was used for trait phenotyping and CAPS genotyping, respectively. The constructed genetic map spanned a total of 2,398.40 centimorgans (cM) in length and averaged 11.42 cM, with 95.99% genome collinearity. A total of 33 QTLs were identified at different genetic positions across the eight chromosomes of watermelon (Chr-01, Chr-02, Chr-04, Chr-05, Chr-06, Chr-07, Chr-10, and Chr-11); among them, eight QTLs of the ovary, sixteen QTLs of the fruit, and nine QTLs of the seed related phenotypes were classified with 5.32–25.99% phenotypic variance explained (PVE). However, twenty-four QTLs were identified as major-effect and nine QTLs were mapped as minor-effect QTLs across the flanking regions of CAPS markers. Some QTLs were exhibited as tightly localized across the nearby genetic regions and explained the pleiotropic effects of multigenic nature. The flanking QTL markers also depicted significant allele specific contributions and accountable genes were predicted for respective traits. Gene Ontology (GO) functional enrichment was categorized in molecular function (MF), cellular components (CC), and biological process (BP); however, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were classified into three main classes of metabolism, genetic information processing, and brite hierarchies. The principal component analysis (PCA) of multivariate phenotypes widely demonstrated the major variability, consistent with the identified QTL regions. In short, we assumed that our identified QTL regions provide valuable genetic insights regarding the watermelon phenotypes and fine genetic mapping could be used to confirm them.
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- 2023
9. A recessive gene Cmpmr2F confers powdery mildew resistance in melon (Cucumis melo L.)
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Taifeng Zhang, Haonan Cui, Feishi Luan, Hongyu Liu, Zhuo Ding, Sikandar Amanullah, Manlin Zhang, Tingting Ma, and Peng Gao
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Genetics ,General Medicine ,Agronomy and Crop Science ,Biotechnology - Published
- 2023
10. QTL analysis of flowering‐related traits by specific length amplified fragment sequencing in melon
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Dandan Li, Limei Tian, Dongyang Dai, Ling Wang, Yunyan Sheng, Di Wang, Feishi Luan, and Guichao Wang
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Genetics ,Qtl analysis ,Melon ,Fragment (computer graphics) ,Biology ,Quantitative trait locus ,Agronomy and Crop Science - Published
- 2021
11. Novel Bisexual Flower Control Gene Regulates Sex Differentiation in Melon (
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Zhongyuan, Wang, Siyu, Zhang, Yongchao, Yang, Zheng, Li, Hao, Li, Rong, Yu, Feishi, Luan, Xian, Zhang, and Chunhua, Wei
- Abstract
The sex-control system involves several mechanisms in melon. The present study identified a novel bisexual flower control gene from the hermaphroditic melon germplasm, different from the previously recognized one. Genetic analysis showed that a single recessive gene in the newly identified locus
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- 2022
12. Molecular mapping of candidate gene regulating fruit stripe trait in watermelon
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Xiaoxue Liang, Meiling Gao, Sikandar Amanullah, Yu Guo, Hongguo Xu, Xiaosong Liu, Xiujie Liu, Jixiu Liu, Yue Gao, Chengzhi Yuan, Xuezheng Wang, and Feishi Luan
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Genetics ,Plant Science ,Horticulture ,Agronomy and Crop Science - Published
- 2022
13. Nucleotide variation in the phytoene synthase (ClPsy1) gene contributes to golden flesh in watermelon (Citrullus lanatus L.)
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Qian Zhang, Zuyun Dai, Shi Liu, Xuezheng Wang, Zhongzhou Yang, Zhongqi Gao, and Feishi Luan
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Genetic Markers ,Candidate gene ,Citrullus lanatus ,Genetic Linkage ,Sequence analysis ,Inheritance Patterns ,Genes, Recessive ,Locus (genetics) ,Genes, Plant ,Genetic analysis ,Citrullus ,Gene Expression Regulation, Plant ,Genetics ,MYB ,RNA-Seq ,Promoter Regions, Genetic ,Gene ,Genetic Association Studies ,Phytoene synthase ,biology ,Nucleotides ,Pigmentation ,Genetic Variation ,General Medicine ,biology.organism_classification ,Geranylgeranyl-Diphosphate Geranylgeranyltransferase ,biology.protein ,Agronomy and Crop Science ,Biotechnology - Abstract
Vitamin A deficiency is a worldwide public nutrition problem, and β-carotene is the precursor for vitamin A synthesis. Watermelon with golden flesh (gf, due to accumulated abundance of β-carotene) is an important germplasm resource. In this study, a genetic analysis of gf segregating populations indicated that gf was controlled by a single recessive gene. BSA-seq and an initial linkage analysis placed the gf locus in a 290-Kb region on watermelon chromosome 1. Further fine mapping in a large population with over 1,000 F2 plants narrowed this region to 39.08 Kb harboring two genes, Cla97C01G008760 and Cla97C01G008770, which encode phytoene synthase (ClPsy1) and GATA zinc finger domain-containing protein, respectively. Gene sequence alignment and expression analysis between parental lines revealed Cla97C01G008760 as the best possible candidate gene for gf trait. Nonsynonymous SNP mutations in the first exon of ClPsy1 between parental lines cosegregated with the gf trait only among individuals in the genetic population but were not related to flesh color in natural watermelon panels. Promoter sequence analysis of 26 watermelon accessions revealed two SNPs in the cis-acting element sequences corresponding to MYB and MYC2 transcription factors. RNA-seq data and qRT-PCR verification showed that two MYBs and one MYC2 exhibited expression trends similar as ClPsy1 in the parental lines, which may thus play roles in the regulation of ClPsy1 expression. Our research findings indicate that the gf trait is determined not only by ClPsy1 but also by ClLCYB, ClCRTISO and ClNCED7, which play important roles in β-carotene accumulation in watermelon flesh.
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- 2021
14. QTL-seq identifies major quantitative trait loci of stigma color in melon
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Hongyu Liu, Feishi Luan, Shi Liu, Aohan Qiao, Peng Gao, and Xufeng Fang
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0106 biological sciences ,0301 basic medicine ,BSA ,Pollination ,QTL ,Melon ,Population ,Plant Science ,Quantitative trait locus ,01 natural sciences ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,Genetic analysis ,SB1-1110 ,03 medical and health sciences ,CAPS ,education ,Gene ,Ecology, Evolution, Behavior and Systematics ,Genetics ,education.field_of_study ,Ecology ,biology ,Renewable Energy, Sustainability and the Environment ,Bulked segregant analysis ,Plant culture ,Stigma color ,biology.organism_classification ,Cucumis melo L ,chlorophyll content ,030104 developmental biology ,Cucumis ,010606 plant biology & botany - Abstract
Stigma color plays an important role in pollination. In nature, melon (Cucumis melo L.) stigmas are either yellow or green; however, a review of the literature found no report on how stigma color affects pollination and fruit development in melon. Here, we used an F2 melon population derived from a cross between ‘MR-1’ (P1, with green stigmas) and ‘M1–32’ (P2, with yellow stigmas), and performed genetic analysis and mapping. The results of bulked segregant analysis allowed the identification of genetic loci controlling stigma color on chromosomes 6 and 8. An F2 population consisting of 150 individuals was used for initial mapping. A genetic map of 304.17 cM was constructed using 37 cleaved amplified polymorphism sequence (CAPS) markers. We identified one major quantitative trait locus (QTL) and one minor QTL for stigma color. The major QTL GS8.1 was further mapped to a 4.13 cM interval between CAPS markers 8C-10 and 8C-16, which explained 27.04% of the phenotypic variation. In addition, GS6.1 was mapped between E-49 and 6A-7, explaining 18.6% of the phenotypic variation. This study provides a theoretical basis for the fine mapping and cloning of melon genes controlling stigma color.
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- 2021
15. Fine Mapping of Cla015407 Controlling Plant Height in Watermelon
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Sikandar Amanullah, Zhuo Ding, Jiajun Liu, Peng Gao, Haonan Cui, Feishi Luan, and Taifeng Zhang
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Genetics ,Horticulture ,Biology - Abstract
The plant compact and dwarf growth habit is an important agronomic trait when breeding watermelon (Citrullus lanatus) cultivars because of their reduced vine length, high-density planting, and better land utilization; however, the genetic basis of the dwarf growth habit is not well-known. In this study, the plant population of six generations, P1, P2, F1, F2, BC1P1, and BC1P2, were studied. A genetic segregation analysis demonstrated that dwarfism is mainly controlled by a single recessive Cldw gene. Furthermore, whole-genome sequencing of two distinct watermelon cultivars, W1-1 (P1) and 812 (P2), was performed and preliminarily mapped through a bulked segregant analysis of F2 individuals that revealed the Cldw gene locus on chromosome 9. Two candidate genes, Cla015407 and Cla015408, were discovered at the delimited region of 43.2 kb by fine mapping, and gene annotation exposed that the Cla015407 gene encodes gibberellic acid 3β-hydroxylase protein. In addition, a comparative analysis of gene sequence and cultivars sequences across the reference genome of watermelon revealed the splice site mutation in the intron region of the Cldw gene in dwarf-type cultivar 812. The quantitative real-time polymerase chain reaction exhibited a significantly higher expression of the Cla015407 gene in cultivar W1-1 compared with 812. There was no significant difference in the vine length of both cultivars after gibberellic acid treatment. In brief, our fine mapping demonstrated that Cla015407 is a candidate gene controlling dwarfism of watermelon plants.
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- 2021
16. Genetic analysis and mapping of a short-internode gene (cladw) in watermelon (Citrullus lanatus L.)
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Jiajun Liu, Peng Gao, Xuezheng Wang, Hongyu Liu, Shuangwu Ma, Jiming Wang, and Feishi Luan
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Genetics ,Plant Science ,Horticulture ,Agronomy and Crop Science - Published
- 2022
17. Transcriptomic Analysis of Fusarium oxysporum Stress-Induced Pathosystem and Screening of Fom-2 Interaction Factors in Contrasted Melon Plants
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Tiantian Yang, Jiajun Liu, Xiaomei Li, Sikandar Amanullah, Xueyan Lu, Mingchong Zhang, Yanhang Zhang, Feishi Luan, Hongyu Liu, and Xuezheng Wang
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Plant Science - Abstract
Fusarium wilt is one of the most destructive and less controllable diseases in melon, which is usually caused byfusarium oxysporum. In this study, transcriptome sequencing and Yeast Two-Hybrid (Y2H) methods were used for quantification of differentially expressed genes (DEGs) involved infusarium oxysporum(f. sp.melonisrace 1) stress-induced mechanisms in contrasted melon varieties (M4-45 “susceptible” and MR-1 “resistant”). The interaction factors ofFom-2resistance genes were also explored in response to the plant-pathogen infection mechanism. Transcriptomic analysis exhibited total 1,904 new genes; however, candidate DEGs analysis revealed a total of 144 specific genes (50 upregulated and 94 downregulated) for M4-45 variety and 104 specific genes (71 upregulated and 33 downregulated) for MR-1 variety, respectively. The analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway depicted some candidate DEGs, including Phenylalanine metabolism, phenylpropane biosynthesis, plants-pathogen interaction, and signal transduction of plant hormones, which were mainly involved in disease resistance metabolic pathways. The weighted gene co-expression network analysis (WGCNA) analysis revealed a strong correlation module and exhibited the disease resistance-related genes encoding course proteins, transcription factors, protein kinase, benzene propane biosynthesis path, plants-pathogen interaction pathway, and glutathione S-transferase. Meanwhile, the resistance-related specific genes expression was relatively abundant in MR-1 compared to the M4-45, and cell wall-associated receptor kinases (MELO3C008452andMELO3C008453), heat shock protein (Cucumis_melo_newGene_172), defensin-like protein (Cucumis_melo_newGene_5490), and disease resistance response protein (MELO3C016325), activator response protein (MELO3C021623), leucine-rich repeat receptor protein kinase (MELO3C024412), lactyl glutathione ligase (Cucumis_melo_newGene_36), and unknown protein (MELO3C007588) were persisted by exhibiting the upregulated expressions. At the transcription level, the interaction factors between the candidate genes in response to thefusarium oxysporuminduced stress, and Y2H screening signified the main contribution of MYB transcription factors (MELO3C009678andMELO3C014597), BZIP (MELO3C011839andMELO3C019349), unknown proteins, and key enzymes in the ubiquitination process (4XM334FK014). The candidate genes were further verified in exogenously treated melon plants withf. oxysporum(Fom-2, Race 1), Abscisic acid (ABA), Methyl Jasmonite (MeJA), and Salicylic acid (SA), using the fluorescence quantitative polymerase chain reaction (qRT-PCR) analysis. The overall expression results indicated that the SA signal pathway is involved in effective regulation of theFom-2gene activity.
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- 2022
18. H
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Mengjie, Cheng, Yanliang, Guo, Qing, Liu, Sanwa, Nan, Yuxing, Xue, Chunhua, Wei, Yong, Zhang, Feishi, Luan, Xian, Zhang, and Hao, Li
- Abstract
Seed germination is a critical stage and the first step in the plant's life cycle. H
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- 2022
19. Transcriptomic Analysis of
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Tiantian, Yang, Jiajun, Liu, Xiaomei, Li, Sikandar, Amanullah, Xueyan, Lu, Mingchong, Zhang, Yanhang, Zhang, Feishi, Luan, Hongyu, Liu, and Xuezheng, Wang
- Abstract
Fusarium wilt is one of the most destructive and less controllable diseases in melon, which is usually caused by
- Published
- 2022
20. Identification and Characterization Roles of Phytoene Synthase (
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Xufeng, Fang, Peng, Gao, Feishi, Luan, and Shi, Liu
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Citrullus ,Plant Breeding ,Carotenoids ,Phylogeny - Abstract
Phytoene synthase (
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- 2022
21. Comparative Transcriptome Analysis Identified Key Pathways and Genes Regulating Differentiated Stigma Color in Melon (
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Yuanzuo, Lv, Sikandar, Amanullah, Shi, Liu, Chen, Zhang, Hongyu, Liu, Zicheng, Zhu, Xian, Zhang, Peng, Gao, and Feishi, Luan
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Chlorophyll ,Cucurbitaceae ,Cucumis melo ,Gene Expression Regulation, Plant ,Gene Expression Profiling ,Transcriptome - Abstract
Stigma color is an important morphological trait in many flowering plants. Visual observations in different field experiments have shown that a green stigma in melons is more attractive to natural pollinators than a yellow one. In the current study, we evaluated the characterization of two contrasted melon lines (MR-1 with a green stigma and M4-7 with a yellow stigma). Endogenous quantification showed that the chlorophyll and carotenoid content in the MR-1 stigmas was higher compared to the M4-7 stigmas. The primary differences in the chloroplast ultrastructure at different developmental stages depicted that the stigmas of both melon lines were mainly enriched with granum, plastoglobulus, and starch grains. Further, comparative transcriptomic analysis was performed to identify the candidate pathways and genes regulating melon stigma color during key developmental stages (S1-S3). The obtained results indicated similar biological processes involved in the three stages, but major differences were observed in light reactions and chloroplast pathways. The weighted gene co-expression network analysis (WGCNA) of differentially expressed genes (DEGs) uncovered a "black" network module (655 out of 5302 genes), mainly corresponding to light reactions, light harvesting, the chlorophyll metabolic process, and the chlorophyll biosynthetic process, and exhibited a significant contribution to stigma color. Overall, the expression of five key genes of the chlorophyll synthesis pathway
- Published
- 2022
22. Development of Whole Genome SNP-CAPS Markers and Preliminary QTL Mapping of Fruit Pedicel Traits in Watermelon
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Sikandar Amanullah, Benjamin Agyei Osae, Tiantian Yang, Shenglong Li, Farhat Abbas, Shi Liu, Shusen Liu, Zhengfeng Song, Xuezheng Wang, Peng Gao, and Feishi Luan
- Subjects
Plant Science - Abstract
Fruit pedicel (FP) is an important determinant of premium fruit quality that directly affects commercial market value. However, in-depth molecular and genetic basis of pedicel-related traits has not been identified in watermelon. Herein, a quantitative trait locus (QTL) mapping strategy was used to identify the potential genetic regions controlling FP traits based on newly derived whole-genome single nucleotide polymorphism based cleaved amplified polymorphism sequence (SNP-CAPS) markers. Next-generation sequencing based whole-genome re-sequencing of two watermelon parent lines revealed 98.30 and 98.40% of average coverage, 4,989,869 SNP variants, and 182,949 CAPS loci pairs across the reference genome, respectively. A total of 221 sets of codominant markers exhibited 46.42% polymorphism rate and were effectively genotyped within 100-F2:3 derived mapping population. The developed linkage map covered a total of 2,630.49 cM genetic length with averaged 11.90 cM, and depicted a valid marker-trait association. In total, 6 QTLs (qFPL4.1, qFPW4.1, qFPD2.1, qFPD2.2, qFPD8.1, qFPD10.1) were mapped with five major effects and one minor effect between the whole genome adjacent markers positioned over distinct chromosomes (02, 04, 08, 10), based on the ICIM-ADD mapping approach. These significant QTLs were similarly mapped in delimited flanking regions of 675.10, 751.38, 859.24, 948.39, and 947.51 kb, which collectively explained 8.64–13.60% PVE, respectively. A highly significant and positive correlation was found among the observed variables. To our knowledge, we first time reported the mapped QTLs/genes affecting FP traits of watermelon, and our illustrated outcomes will deliver the potential insights for fine genetic mapping as well as functional gene analysis through MAS-based breeding approaches.
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- 2022
23. Quantitative trait loci and candidate genes responsible for pale green flesh colour in watermelon ( Citrullus lanatus )
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Feishi Luan, Zhongzhou Yang, Shuang Pei, Shi Liu, Xuezheng Wang, Qian Zhang, Zheng Liu, and Zuyun Dai
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Genetics ,Candidate gene ,Citrullus lanatus ,Flesh ,Plant Science ,Biology ,Quantitative trait locus ,biology.organism_classification ,chemistry.chemical_compound ,chemistry ,Gene mapping ,Molecular marker ,Agronomy and Crop Science - Published
- 2021
24. Isolation and Activity Analysis of Phytoene Synthase (ClPsy1) Gene Promoter of Canary-Yellow and Golden Flesh-Color Watermelon
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Yue Cao, Xufeng Fang, Shi Liu, and Feishi Luan
- Subjects
cis-element ,MYB transcription factor ,phytoene synthase ,promoter ,watermelon ,Agronomy and Crop Science - Abstract
Watermelon (Citrullus lanatus) is an economically important cucurbit crop. Its pulp is rich in antioxidant carotenoids, which confer a variety of flesh colors. ClPsy1 (Phytoene Synthase) is the rate-limiting enzyme for carotenoid synthesis; however, the promoter activity of ClPsy1 is still unknown. In the present study, promoter sequences were isolated from four watermelon accessions: Cream of Saskatchewan pale yellow (COS), canary yellow flesh (PI 635597), golden flesh (PI 192938), and red flesh (LSW-177), all of which express ClPsy1 at extremely high levels. Sequence alignment and cis-element analysis disclosed six SNPs between the four lines all in COS, two of which (at the 598th and 1257th positions) caused MYC and MYB cis-element binding sequence variations, respectively. To confirm ClPsy1 gene promoter activity, full-length and deletion fragments of the promoter were constructed and connected to a β-D-glucosidase (GUS) vector and transferred into tomato fruits. GUS staining was performed to analyze the key segment of the promoter. The activity of the PI 192938 ClPsy1 full-length promoter exceeded that of COS. The deletion fragment from −1521 bp to −1043 bp exhibited strong promoter activity, and contained a MYB transcription factor-binding site mutation. We combined RNA-seq with qRT-PCR to analyze the gene expression pattern between the MYB transcription factor Cla97C10G196920 and ClPsy1 gene and found that Cla97C10G196920 (ClMYB21) showed the same expression trend with ClPsy1, which positively regulates carotenoid synthesis and metabolism.
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- 2023
25. Identification of chromosome region and candidate genes for canary-yellow flesh (Cyf) locus in watermelon (Citrullus lanatus)
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Shi Liu, Mengqiu Liu, Yue Cao, Yan Xu, Hongyu Liu, Qianglong Zhu, Xian Zhang, and Feishi Luan
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Genetics ,Plant Science ,General Medicine ,Agronomy and Crop Science - Published
- 2023
26. Genetic analysis and mapping of a short internode gene (cladw) in watermelon (Citrullus lanatus L.)
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Jiajun Liu, Peng Gao, Hongyu Liu, Xuezheng Wang, Shuangwu Ma, Jiming Wang, and Feishi Luan
- Abstract
Internode length is an important plant type characteristic of watermelon (Citrullus lanatus L.). A dwarf phenotype can increase plant density and land utilization. In this study, W1-1 (standard vine) and ZXG01061 (dwarf) were used as the parental lines to create F1, F2, BC1P1 and BC1P2 progenies for dwarf trait inheritance analysis and candidate gene identification. Genetic analysis indicated that the watermelon dwarf trait was regulated by a single recessive gene (cladw) with phenotypic data collected over two years. The bulked segregant analysis (BSA-seq) revealed a 1.24 Mb genomic region harbouring the candidate dwarfing gene on chromosome 9. Through initial and fine mapping with 1,097 F2 plants, the cladw locus was finally delimited into a 203 kb region containing 10 candidate genes (including five genes annotated as GID1L2 gibberellin GA receptors). Hormone analysis showed that the GA content of the ZXG01061 internode was higher than that of W1-1. When ZXG01061 plants were treated with exogenous GA, the original plant height could not be recovered, indicating that ZXG01061 is GA insensitive. Cla010254 and Cla010256 (annotated as gibberellin receptor GID1L2) in ZXG01061 had base deletions compared with W1-1. The expression pattern of Cla010254 in W1-1 was significantly higher than that in ZXG01061. In conclusion, our results indicate that Cla010254 is a candidate gene for watermelon dwarfing.
- Published
- 2022
27. Identification of Candidate Chromosome Region Related to Melon (Cucumis melo L.) Fruit Surface Groove Trait Through Biparental Genetic Mapping and Genome-Wide Association Study
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Xin Du, Hongyu Liu, Zicheng Zhu, Shusen Liu, Zhengfeng Song, Lianqin Xia, Jingchao Zhao, Feishi Luan, and Shi Liu
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food and beverages ,Plant Science - Abstract
The melon fruit surface groove (fsg) not only affects peel structure and causes stress-induced fruit cracking but also fits consumers’ requirements in different regions. In this study, genetic inheritance analysis of three F2 populations derived from six parental lines revealed that the fsg trait is controlled by a simple recessive inherited gene. Through bulked segregant analysis sequencing (BSA-seq), the Cmfsg locus was detected in an 8.96 Mb interval on chromosome 11 and then initially mapped to a region of approximately 1.15 Mb. Further fine mapping with a large F2 population including 1,200 plants narrowed this region to 207 kb containing 11 genes. A genome-wide association study (GWAS) with 187 melon accessions also produced the same chromosome region for the Cmfsg locus. Due to the rare molecular markers and lack of mutations in the coding and promoter regions of the 11 candidate genes in the fine-mapped interval, we conducted in silico BSA to explore the natural melon panel to predict candidate genes for the Cmfsg locus. A 1.07 kb segment upstream of MELO3C019694.2 (annotated as the AGAMOUS MADS-box transcription factor) exhibited a correlation with the grooved and non-grooved accessions among the F2 individuals, and a natural panel consisted of 17 melon accessions. The expression level of MELO3C019694.2 in the pericarp was higher in grooved lines than in non-grooved lines and was specifically expressed in fruit compared with other tissues (female flower, male flower, root, and leaf). This work provides fundamental information for further research on melon fsg trait formation and molecular markers for melon breeding.
- Published
- 2022
28. CAPS marker-base genetic linkage mapping and QTL analysis for watermelon ovary, fruit and seed-related traits
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Benjamin Agyei Osae, Sikandar Amanullah, Hongyu Liu, Shi Liu, Arvind Saroj, Chen Zhang, Tai Liu, Peng Gao, and Feishi Luan
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Genetics ,Plant Science ,Horticulture ,Agronomy and Crop Science - Published
- 2022
29. Genome-wide identification, characterization and expression analysis of the TLP gene family in melon (Cucumis melo L.)
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Yarong Liu, Jun Cui, Feishi Luan, Yushi Luan, and Xiaoxu Zhou
- Subjects
0106 biological sciences ,Protein family ,Melon ,Plant disease resistance ,01 natural sciences ,Genome ,Chromosomes, Plant ,03 medical and health sciences ,Ascomycota ,Cucumis melo ,Sequence Analysis, Protein ,Gene Duplication ,Genetics ,Gene family ,Gene ,Phylogeny ,Plant Diseases ,Plant Proteins ,030304 developmental biology ,0303 health sciences ,biology ,food and beverages ,biology.organism_classification ,Multigene Family ,Tandem exon duplication ,Sequence Alignment ,Cucumis ,Genome, Plant ,010606 plant biology & botany - Abstract
Thaumatin-like proteins (TLPs), which belong to pathogenesis-related (PR) protein family 5 (PR5), are involved in plant host defense and various developmental processes. The functions of the TLP family have been extensively discussed in multiple organisms, whereas the detailed information of this family in melon has not been reported yet. In this study, we identified 28 TLP genes in the melon genome and a N-terminal signal peptide was found highly conserved within each member of this family. Phylogeny analysis indicated that TLPs from melon and other plant species were clustered into ten groups. Twelve segmental and seven tandem duplication gene pairs that underwent purifying selection were identified. TLP genes expressed differentially in different tissues/organs, and were significantly induced after Podosphaera xanthii infection. TLPs in breeding line MR-1 tend to express early after pathogen infection compared with cultivar Top Mark. Our study provides a comprehensive understanding of the melon TLP family and demonstrates their potential roles in disease resistance, therefore provides more reference for further research.
- Published
- 2020
30. Genetic Mapping and QTL Analysis of Stigma Color in Melon (
- Author
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Yuanzuo, Lv, Peng, Gao, Shi, Liu, Xufeng, Fang, Taifeng, Zhang, Tai, Liu, Sikandar, Amanullah, Xinying, Wang, and Feishi, Luan
- Abstract
Melon is an important Cucurbitaceae crop. Field observations had shown that the green stigmas of melon are more attractive to pollinators than yellow stigmas. In this study, F
- Published
- 2022
31. Molecular Mapping of Candidate Gene Regulating the Fruit Stripe Trait in Watermelon
- Author
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Xiaoxue Liang, Meiling Gao, Yu Guo, Hongguo Xu, Xiaosong Liu, Xiujie Liu, Jixiu Liu, Yue Gao, Chengzhi Yuan, Xuezheng Wang, and Feishi Luan
- Subjects
History ,Polymers and Plastics ,Business and International Management ,Industrial and Manufacturing Engineering - Published
- 2022
32. Genetic architecture of fruit size and shape variation in cucurbits: a comparative perspective
- Author
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Shi Liu, Feishi Luan, Cecilia McGregor, Yiqun Weng, Yuhui Wang, Yupeng Pan, and Meiling Gao
- Subjects
Genetics ,Gynoecium ,Candidate gene ,Melon ,food and beverages ,General Medicine ,Biology ,Quantitative trait locus ,Genome ,Genetic architecture ,Genetic variation ,Agronomy and Crop Science ,Cucurbitaceae ,Biotechnology - Abstract
The Cucurbitaceae family hosts many economically important fruit vegetables (cucurbits) such as cucumber, melon, watermelon, pumpkin/squash, and various gourds. The cucurbits are probably best known for the diverse fruit sizes and shapes, but little is known about their genetic basis and molecular regulation. Here, we reviewed the literature on fruit size (FS), shape (FSI), and fruit weight (FW) QTL identified in cucumber, melon, and watermelon, from which 150 consensus QTL for these traits were inferred. Genome-wide survey of the three cucurbit genomes identified 253 homologs of eight classes of fruit or grain size/weight-related genes cloned in Arabidopsis, tomato, and rice that encode proteins containing the characteristic CNR (cell number regulator), CSR (cell size regulator), CYP78A (cytochrome P450), SUN, OVATE, TRM (TONNEAU1 Recruiting Motif), YABBY, and WOX domains. Alignment of the consensus QTL with candidate gene homologs revealed widespread structure and function conservation of fruit size/shape gene homologs in cucurbits, which was exemplified with the fruit size/shape candidate genes CsSUN25-26-27a and CsTRM5 in cucumber, CmOFP1a in melon, and ClSUN25-26-27a in watermelon. In cucurbits, the andromonoecy (for 1-aminocyclopropane-1-carboxylate synthase) and the carpel number (for CLAVATA3) loci are known to have pleiotropic effects on fruit shape, which may complicate identification of fruit size/shape candidate genes in these regions. The present work illustrates the power of comparative analysis in understanding the genetic architecture of fruit size/shape variation, which may facilitate QTL mapping and cloning for fruit size-related traits in cucurbits. The limitations and perspectives of this approach are also discussed.
- Published
- 2019
33. Mapping of genetic loci controlling fruit linked morphological traits of melon using developed CAPS markers
- Author
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Sikandar Amanullah, Benjamin Agyei Osae, Tiantian Yang, Farhat Abbas, Shi Liu, Hongyu Liu, Xuezheng Wang, Peng Gao, and Feishi Luan
- Subjects
Cucurbitaceae ,Plant Breeding ,Phenotype ,Genetic Linkage ,Fruit ,Quantitative Trait Loci ,Genetics ,General Medicine ,Molecular Biology ,Polymorphism, Single Nucleotide - Abstract
Fruit morphology traits are important commercial traits that directly affect the market value. However, studying the genetic basis of these traits in un-explored botanical groups is a fundamental objective for crop genetic improvement through marker-assisted breeding.In this study, a quantitative trait loci (QTLs) mapping strategy was used for dissecting the genomic regions of fruit linked morphological traits by single nucleotide polymorphism (SNP) based cleaved amplified polymorphism sequence (CAPS) molecular markers. Next-generation sequencing was done for the genomic sequencing of two contrasted melon lines (climacteric and non-climacteric), which revealed 97% and 96% of average coverage over the reference melon genome database, respectively. A total of 57.51% non-synonymous SNPs and 42.49% synonymous SNPs were found, which produced 149 sets of codominant markers with a 24% polymorphism rate. Total 138-FIn short, our illustrated genetic loci are expected to provide the reference insights for fine QTL mapping and candidate gene(s) mining through molecular genetic breeding approaches aimed at developing the new varieties.
- Published
- 2021
34. Identification of Candidate Chromosome Region Related to Melon (
- Author
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Xin, Du, Hongyu, Liu, Zicheng, Zhu, Shusen, Liu, Zhengfeng, Song, Lianqin, Xia, Jingchao, Zhao, Feishi, Luan, and Shi, Liu
- Abstract
The melon fruit surface groove (fsg) not only affects peel structure and causes stress-induced fruit cracking but also fits consumers' requirements in different regions. In this study, genetic inheritance analysis of three F
- Published
- 2021
35. The HD-ZIP Gene Family in Watermelon: Genome-Wide Identification and Expression Analysis under Abiotic Stresses
- Author
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Xing Yan, Zhen Yue, Xiaona Pan, Fengfei Si, Jiayue Li, Xiaoyao Chen, Xin Li, Feishi Luan, Jianqiang Yang, Xian Zhang, and Chunhua Wei
- Subjects
Homeodomain Proteins ,HD-ZIP transcription factors ,phylogenetic evolution ,expression pattern ,abiotic stresses ,Stress, Physiological ,Genetics ,Genome, Plant ,Phylogeny ,Genetics (clinical) ,Transcription Factors - Abstract
Homeodomain-leucine zipper (HD-ZIP) transcription factors are one of the plant-specific gene families involved in plant growth and response to adverse environmental conditions. However, little information is available on the HD-ZIP gene family in watermelon. In this study, forty ClHDZs were systemically identified in the watermelon genome, which were subsequently divided into four distinctive subfamilies (I–IV) based on the phylogenetic topology. HD-ZIP members in the same subfamily generally shared similar gene structures and conserved motifs. Syntenic analyses revealed that segmental duplications mainly contributed to the expansion of the watermelon HD-ZIP family, especially in subfamilies I and IV. HD-ZIP III was considered the most conserved subfamily during the evolutionary history. Moreover, expression profiling together with stress-related cis-elements in the promoter region unfolded the divergent transcriptional accumulation patterns under abiotic stresses. The majority (13/23) of ClHDZs in subfamilies I and II were downregulated under the drought condition, e.g., ClHDZ4, ClHDZ13, ClHDZ18, ClHDZ19, ClHDZ20, and ClHDZ35. On the contrary, most HD-ZIP genes were induced by cold and salt stimuli with few exceptions, such as ClHDZ3 and ClHDZ23 under cold stress and ClHDZ14 and ClHDZ15 under the salt condition. Notably, the gene ClHDZ14 was predominantly downregulated by three stresses whereas ClHDZ1 was upregulated, suggesting their possible core roles in response to these abiotic stimuli. Collectively, our findings provide promising candidates for the further genetic improvement of abiotic stress tolerance in watermelon.
- Published
- 2022
36. CmPMRl and CmPMrs Were Responsible for Resistance to Powdery Mildew Caused by Podosphaera Xanthii Race 1 in Melon
- Author
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Gao Peng, Chao Fan, Yingdong Bi, Xuezheng Wang, Haonan Cui, Lili Tang, Zhuo Ding, and Feishi Luan
- Subjects
Horticulture ,Race (biology) ,biology ,Melon ,biology.organism_classification ,Podosphaera xanthii ,Powdery mildew - Abstract
Cucumis melo L. is an economically important crop, the production of which is threatened by the prevalence of melon powdery mildew (PM) infections. We herein utilized the MR-1 (P1; resistant to PM) and M4-7 (P2; susceptible to PM) accessions to assess the heritability of PM (race 1) resistance in these melon plants. PM resistance in MR-1 leaves was linked to a dominant gene (CmPMRl), whereas stem resistance was under the control of a recessive gene (CmPMrs), with the dominant gene having an epistatic effect on the recessive gene. The CmPMRl gene was mapped to a 50 Kb interval on chromosome 12, while CmPMrs was mapped to an 89 Kb interval on chromosome 10. The CmPMRl candidate gene MELO3C002441 and the CmPMrs candidate gene MELO3C012438 were identified through sequence alignment, functional annotation, and expression pattern analyses of all genes within these respective intervals. MELO3C002441 and MELO3C012438 were both localized to the cellular membrane and were contained conserved NPR gene-like and MLO domains, respectively, which were linked to PM resistance. In summary, we identified patterns of PM resistance in the disease-resistant MR-1 melon cultivar, and conducted finally-mapping to identify two putative genes linked to resistance. Our results offer new genetic resources and markers guide the future molecular marker-assisted breeding of PM-resistant melon.
- Published
- 2021
37. Identification of QTLs linked with watermelon fruit and seed traits using GBS-based high-resolution genetic mapping
- Author
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Xiaoxue Liang, Meiling Gao, Sikandar Amanullah, Yu Guo, Xiujie Liu, Hongguo Xu, Jixiu Liu, Yue Gao, Chengzhi Yuan, and Feishi Luan
- Subjects
Horticulture - Published
- 2022
38. Bulked-segregant Analysis Identified a Putative Region Related to Short Internode Length in Melon
- Author
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Taifeng Zhang, Jiajun Liu, Feishi Luan, Shi Liu, Peng Gao, and Zhuo Ding
- Subjects
Horticulture ,Melon ,Bulked segregant analysis ,Biology - Abstract
Short internode length (SIL) is one of the most commercially and important traits in melon varieties (Cucumis melo L.). SIL can result in a compact vining type that promotes concentrated fruit in high-density crops, leading to greater use of light resources for photosynthesis and greater yield per unit area. In our study, two parental melon lines ‘M1-32’ (P1, standard vine) and ‘X090’ (P2, short internodes), and their F1, F2, BC1P1, and BC1P2 progenies were evaluated after being grown in plastic greenhouse conditions in 2017 and 2018. Main stem length (MSL) and internode length (IL) of six melon generations indicated that a single recessive gene (MD7) controlled dwarfism in the ‘X090’ melon line. Whole-genome analysis revealed a genomic region harboring the candidate dwarfism gene on chromosome 7. Six polymorphic cleaved amplified polymorphic sequence (CAPS) markers from chromosome 7 were used to construct a genetic linkage that spanned 30.28 cM. The melon dwarfing locus MD7 responsible for SIL was positioned between markers M7-4 and M7-5, with 3.16 cM of flanking distance. The CAPS markers M7-4 and M7-5 developed have the potential to accelerate the development of dwarf melon varieties, especially in situations when dwarf genotypes are an important breeding goal using marker-assisted selection.
- Published
- 2019
39. Transcriptome analysis of differentially expressed genes during anther development stages on male sterility and fertility in Cucumis melo L. line
- Author
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Yanhong Wang, Yunyan Sheng, Feishi Luan, Dongyang Dai, Anping Xiong, Dandan Li, Peng Ji, Yazhong Jin, and Liwei Yuan
- Subjects
0301 basic medicine ,Plant Infertility ,Sterility ,Stamen ,Flowers ,Biology ,Transcriptome ,03 medical and health sciences ,0302 clinical medicine ,Microspore ,Cucumis melo ,Gene Expression Regulation, Plant ,Genetics ,Gene Regulatory Networks ,Gene ,Plant Proteins ,Regulation of gene expression ,Zinc finger ,Chimera ,Sequence Analysis, RNA ,Gene Expression Profiling ,Gene Expression Regulation, Developmental ,General Medicine ,biology.organism_classification ,Microscopy, Electron ,030104 developmental biology ,030220 oncology & carcinogenesis ,Cucumis - Abstract
The genic male sterility (MS) plays a major role in melon hybrids production, it could reduce the cost of pollination and increase the yield and quality. However, the molecular mechanism underlying genetic male sterility is yet poorly understood. The morphological differences of flower buds of melon were observed showed that the flower buds were tetrad when they were 1 mm stage and monocyte microspore when they were 2 mm stage. Electron microscopy showed that there was significant difference between MS lines and MF (male fertility) lines. In order to detect the global expression of the genes during the melon anther development and association with MS, 12 DEGs (differentially expressed genes) libraries were constructed from the anther of MS and MF in the bud stage with 1 and 2 mm diameter, respectively. A total of 765 DEGs expressed in anther during different developmental stage (MS 1 mm vs. MS 2 mm), 148 and 309 DEGs were found to be related to MS as compared to MF (MS 1 mm vs. MF 1 mm, and MS 2 mm vs. MF 2 mm) at a false discovery rate FDR
- Published
- 2019
40. Identification and Characterization Roles of Phytoene Synthase (PSY) Genes in Watermelon Development
- Author
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Xufeng Fang, Peng Gao, Feishi Luan, and Shi Liu
- Subjects
Genetics ,flesh color ,phytoene synthase ,gene expression ,functional analysis ,carotenoid biosynthesis pathway ,Genetics (clinical) - Abstract
Phytoene synthase (PSY) plays an essential role in carotenoid biosynthesis. In this study, three ClPSY genes were identified through the watermelon genome, and their full-length cDNA sequences were cloned. The deduced proteins of the three ClPSY genes were ranged from 355 to 421 amino acid residues. Phylogenetic analysis suggested that the ClPSYs are highly conserved with bottle gourd compared to other cucurbit crops PSY proteins. Variation in ClPSY1 expression in watermelon with different flesh colors was observed; ClPSY1 was most highly expressed in fruit flesh and associated with the flesh color formation. ClPSY1 expression was much lower in the white-fleshed variety than the colored fruits. Gene expression analysis of ClPSY genes in root, stem, leaf, flower, ovary and flesh of watermelon plants showed that the levels of ClPSY2 transcripts found in leaves was higher than other tissues; ClPSY3 was dominantly expressed in roots. Functional complementation assays of the three ClPSY genes suggested that all of them could encode functional enzymes to synthesize the phytoene from Geranylgeranyl Pyrophosphate (GGPP). Some of the homologous genes clustered together in the phylogenetic tree and located in the synteny chromosome region seemed to have similar expression profiles among different cucurbit crops. The findings provide a foundation for watermelon flesh color breeding with regard to carotenoid synthesis and also provide an insight for the further research of watermelon flesh color formation.
- Published
- 2022
41. The complete chloroplast genome sequence of the
- Author
-
Haonan, Cui, Zicheng, Zhu, Zhaokai, Lu, Zhuo, Ding, Chen, Zhang, and Feishi, Luan
- Subjects
Sechium edule ,phylogenetic analysis ,chloroplast genome ,Mitogenome Announcement ,Research Article - Abstract
Sechium edule (Jacq.) Swartz is an important vegetable with both food and medicinal values. The complete chloroplast genome sequence of S. edule has been reported in this study. The total genome size is 154,558 bp in length and contains a pair of inverted repeats (IRs) of 19,128 bp, which were separated by large single-copy (LSC) and small single-copy (SSC) of 98,806 and 17,496 bp, respectively. A total of 122 genes were predicted including 78 protein-coding genes, 8 rRNA genes, and 36 tRNA genes. Further, the phylogenetic analysis confirmed that S. edule belongs to the family Cucurbitaceae. The complete chloroplast genome of S. edule would play a significant role in the development of molecular markers for plant phylogenetic and population genetic studies.
- Published
- 2021
42. The complete chloroplast genome sequence of the
- Author
-
Chen, Zhang, Qianglong, Zhu, Shi, Liu, Peng, Gao, Zicheng, Zhu, Xuezheng, Wang, and Feishi, Luan
- Subjects
chloroplast genome ,zucchini ,Mitogenome Announcement ,Cucurbita pepo L ,summer squash ,Research Article - Abstract
Cucurbita pepo is an important economic plant cultivated widely in the world. The complete chloroplast genome sequence of C. pepo is reported here. The genome is 157,343 bp in length and exhibits a typical quadripartite structure of the large (LSC, 87,970 bp) and small (SSC, 18,167 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 25,603 bp). A total of 131 genes were predicted including 85 protein-coding genes, eight rRNA genes and 38 tRNA genes. Further, phylogenetic analysis showed that C. pepo were closely related to other species in the family Cucurbitaceae. The complete chloroplast genome of C. pepo would be taken as a useful molecular tool for species discrimination, taxonomy, and phylogenetic relationships in the family Cucurbitaceae.
- Published
- 2021
43. CmPMRl and CmPMrs are responsible for resistance to powdery mildew caused by Podosphaera xanthii race 1 in Melon
- Author
-
Haonan Cui, Chao Fan, Zhuo Ding, Xuezheng Wang, Lili Tang, Yingdong Bi, Feishi Luan, and Peng Gao
- Subjects
Cucurbitaceae ,Plant Breeding ,Ascomycota ,Cucumis melo ,Genetics ,General Medicine ,Agronomy and Crop Science ,Biotechnology ,Disease Resistance ,Plant Diseases - Abstract
Two genes for resistance to Podosphaera xanthii race 1 in melon were identified on chromosomes 10 and 12 of the Cucumis melo cultivar MR-1. Cucumis melo L. is an economically important crop, the production of which is threatened by the prevalence of melon powdery mildew (PM) infections. We herein utilized the MR-1 (P
- Published
- 2020
44. QTL mapping for significant seed traits of watermelon (Citrullus lanatus Schrad)
- Author
-
Peng Gao, Feishi Luan, Chao Fan, Benjamin Agyei Osae, Shi Liu, and Sikandar Amanullah
- Subjects
Horticulture ,Citrullus lanatus ,biology ,Plant Science ,Quantitative trait locus ,biology.organism_classification - Published
- 2020
45. QTL Mapping of Fruit and Seed-related Traits in Watermelon Using Genotyping-by-Sequencing-based High-density Linkage Mapping
- Author
-
Meiling Gao, Xiujie Liu, Yu Guo, Gao Yue, Chengzhi Yuan, Jixiu Liu, Xu Hongguo, Feishi Luan, and Xiaoxue Liang
- Subjects
Genotyping by sequencing ,Genetic linkage ,High density ,Computational biology ,Biology ,Quantitative trait locus - Abstract
BackgroundWatermelon is an important vegetable crop with dual use of both fruit and seeds. Understanding the genetic basis of fruit quality and seed size-related traits is important for efficient marker-assisted breeding in watermelon. Linkage mapping in watermelon segregating populations using genotyping-by-sequencing (GBS) provides insights into genetic control of fruit- and seed-related traits and genome collinearity in commercial watermelon cultivars. ResultsIn the present study, we conducted QTL mapping of 12 horticulturally important traits on external and internal fruit quality and seed size/weight using segregating populations derived a cross between two commercial varieties. A high-density genetic map was developed with GBS which contained more than 6,000 SNP loci in 1,004 bins with a total map length of 1261.1 cM and average marker interval of 1.26 cM or 329 kb. Phenotypic data of fruit rind color (RC), rind stripe pattern (RSP), flesh color (FFC), fruit diameter (FD), fruit length (FL), fruit shape index (FSI), fruit weight (FW), Brix content central (BCC), Brix content edge (BCE), seed length (SL), width (SW), and weight (20SWT) were collected from two locations in two years. QTL analysis identified 47 QTL for the 12 traits, of which 24 had moderate- or major-effects, and 34 were novel QTL not identified in previous studies. The QTL for RSP were identified overlapped with previous reports, and mapped the QTL to a small interval on chromosome 6. From the detected novel QTL, we identify FD (qfd2.1), FL (qfl2.1) co-located with FSI (qfsi2.1) QTL on chromosome 2, and the minor QTL qfw3.2 co-located with previously reported fruit shape QTL (qfd3.1, qfl3.1, qfsi3.1), and SW (qsw10.1) co-located with 20SWT QTL (q20swt10.1) on chromosome 10, and 5 minor QTL (qbcc2.1, qbcc5.1, qbce2.1, qbce2.2, qbce5.1) were found to be likely new locus for Brix content.ConclusionWe conducted GBS consisting of 120 F2 individuals and developed a high-density linkage map with more than 6,000 SNP loci in 1004 bins in watermelon. We identified 47 QTL for 12 fruit and seed related traits including 34 novel QTL. Our work expands the molecular breeding toolbox for watermelon to improve the yield and fruit quality.
- Published
- 2020
46. Identification of major-effect QTL CmFpl3.1 controlling fruit pedicel length in melon (Cucumis melo L.)
- Author
-
Feishi Luan, Xuezheng Wang, Haonan Cui, Peng Gao, Shi Liu, Zhuo Ding, and Zicheng Zhu
- Subjects
Germplasm ,Genetics ,Candidate gene ,biology ,Melon ,food and beverages ,Locus (genetics) ,Horticulture ,Quantitative trait locus ,biology.organism_classification ,humanities ,Pedicel ,Cucumis ,Gene - Abstract
Fruit pedicel length (FPL) is among the most important traits associated with melon (Cucumis melo L.), impacting their appearance and management. Melon pedicels are also utilized in the preparation of certain traditional Chinese medicine formulations. Herein, we analyzed a melon parental lines with long and short pedicles (M125 and X055, respectively), and found that the primary differences between these lines included changes in both cell number and cytokinin content in the fruit pedicel. This study is the first to report that the CmFpl3.1 is associated with the regulation of melon pedicel length, and we were able to narrow this locus to an 89 Kb region containing 10 genes on chromosome 3 via bulk segregant analysis (BSA) and quantitative trait loci (QTL) analysis. Microscopy, qPCR, functional annotation, and gene sequence alignment studies further led us to identify MELO3C010972, which encodes cytokinin oxidase, as a candidate gene of CmFpl3.1 likely to regulate melon FPL. Furthermore, the concomitant cleave amplified polymorphic sequence (CAPS) marker genotyping data sets from 95 germplasm accessions strongly supported a role for MELO3C010972 as a regulator of FPL variability. In conclusion, our results offer new insights regarding the mechanistic basis for FPL determination, offering a foundation for future breeding programs or efforts to understand the mechanisms governing melon FPL development.
- Published
- 2022
47. Editorial: Translational Research for Cucurbit Molecular Breeding: Traits, Markers, and Genes
- Author
-
Feishi Luan, Yiqun Weng, Jordi Garcia-Mas, and Amnon Levi
- Subjects
Genetics ,Molecular breeding ,QTL mapping ,translational genomics ,Editorial ,cucurbits ,Translational research ,Translational genomics ,Plant Science ,molecular breeding ,Biology ,Gene ,marker-assisted selection - Published
- 2020
48. Optimized combination methods for exploring and verifying disease-resistant transcription factors in melon
- Author
-
Xiaoxu Zhou, Feishi Luan, Yushi Luan, Zhicheng Wang, Jun Meng, and Jun Cui
- Subjects
0303 health sciences ,Genomics ,Computational biology ,Plant disease resistance ,Biology ,WRKY protein domain ,Transcriptome ,03 medical and health sciences ,Cucurbitaceae ,0302 clinical medicine ,Gene Expression Regulation, Plant ,030220 oncology & carcinogenesis ,Transcriptional regulation ,Molecular Biology ,Gene ,Transcription factor ,030304 developmental biology ,Information Systems ,Regulator gene ,Disease Resistance ,Plant Proteins ,Transcription Factors - Abstract
A large amount of omics data and number of bioinformatics tools has been produced. However, the methods for further exploring omics data are simple, in particular, to mine key regulatory genes, which are a priority concern in biological systems, and most of the specific functions are still unknown. First, raw data of two genotypes of melon (susceptible and resistant) were obtained by transcriptome analysis. Second, 391 transcription factors (TFs) were identified from the plant transcription factor database and cucurbit genomics database. Then, functional enrichment analysis indicated that these genes were mainly annotated in the process of transcription regulation. Third, 243 and 230 module-specific TFs were screened by weighted gene coexpression network analysis and short time series expression miner, respectively. Several TF genes, such as WRKYs and bHLHs, were regarded as key regulatory genes according to the values of significantly different modules. The coexpression network showed that these TF genes were significant correlated with resistance (R) genes, such as DRP2, RGA3, DRP1 and NB-ARC. Fourth, cis-acting element analysis illustrated that these R genes may bind to WRKY and bHLH. Finally, the expression of WRKY genes was verified by quantitative reverse transcription PCR (RT-qPCR). Phylogenetic analysis was carried out to further confirm that these TFs may play a critical role in Curcurbitaceae disease resistance. This study provides a new optimized combination strategy to explore the functions of TFs in a wide spectrum of biological processes. This strategy may also effectively predict potential relationships in the interactions of essential genes.
- Published
- 2020
49. Linkage Mapping and Comparative Transcriptome Analysis of Firmness in Watermelon (Citrullus lanatus)
- Author
-
Lei Sun, Yushu Zhang, Haonan Cui, Lupeng Zhang, Tongyun Sha, Chaonan Wang, Chao Fan, Feishi Luan, and Xuezheng Wang
- Subjects
0106 biological sciences ,0301 basic medicine ,Citrullus lanatus ,QTL ,Plant Science ,lcsh:Plant culture ,Quantitative trait locus ,firmness ,01 natural sciences ,Transcriptome ,Cell wall ,03 medical and health sciences ,chemistry.chemical_compound ,lcsh:SB1-1110 ,Hemicellulose ,mapping ,Abscisic acid ,biology ,Flesh ,watermelon ,food and beverages ,Ripening ,biology.organism_classification ,Horticulture ,030104 developmental biology ,chemistry ,transcriptome ,010606 plant biology & botany - Abstract
Watermelon fruit texture and quality are determined by flesh firmness. As a quality trait, flesh firmness is controlled by multigenes. Defining the key regulatory factors of watermelon flesh firmness is of great significance for watermelon genetic breeding. In this study, the hard-flesh egusi seed watermelon PI186490 was used as the male parent, the soft-flesh cultivated watermelon W1-1 was used as the female parent, and 175 F2 generations were obtained from selfing F1. Primary mapping of the major genes controlling center flesh firmness was achieved by bulked-segregant analysis (BSA)-Seq analysis and molecular marker technology. Finally, major genes were delimited in the physical interval between 6,210,787 and 7,742,559 bp on chromosome 2 and between 207,553 and 403,137 bp on chromosome 8. The content of each cell wall component and hormone was measured, and comparative transcriptome analysis was performed during fruit development in watermelon. The protopectin, cellulose, hemicellulose, indole-3-acetic acid (IAA) and abscisic acid (ABA) contents were measured, and paraffin sections were made during the three fruit developmental stages. The results revealed that protopectin, celluloses, and hemicelluloses exhibited similar trends for flesh firmness, while the IAA and ABA concentrations continued to decrease with fruit ripening. Paraffin sections showed that PI186490 cells were more numerous, were more tightly packed, had clearer cell wall edges and had thicker cell walls than W1-1 cells at every developmental stage. Comparative transcriptome analysis was conducted on RNA samples of flesh during fruit development and ripening in W1-1 and PI186490. The results from the localization interval transcriptome analysis showed that Cla016033 (DUF579 family member), which may influence the cell wall component contents to adjust the flesh firmness in watermelon fruit, was different in W1-1 and PI186490 and that Cla012507 (MADS-box transcription factor) may be involved in the regulation of fruit ripening and affect the hardness of watermelon fruit.
- Published
- 2020
50. Quantitative Trait Loci for Seed Size Variation in Cucurbits – A Review
- Author
-
Yu Guo, Meiling Gao, Xiaoxue Liang, Ming Xu, Xiaosong Liu, Yanling Zhang, Xiujie Liu, Jixiu Liu, Yue Gao, Shuping Qu, and Feishi Luan
- Subjects
0106 biological sciences ,0301 basic medicine ,comparative analysis ,QTL ,Melon ,Review ,Plant Science ,lcsh:Plant culture ,Biology ,Quantitative trait locus ,01 natural sciences ,Genome ,03 medical and health sciences ,cucurbits ,melon ,lcsh:SB1-1110 ,seed size ,Synteny ,Whole genome sequencing ,Genetics ,watermelon ,food and beverages ,pumpkin/squash ,030104 developmental biology ,Trait ,cucumber ,Cucurbitaceae ,010606 plant biology & botany ,Squash - Abstract
Cucurbits (Cucurbitaceae family) include many economically important fruit vegetable crops such as watermelon, pumpkin/squash, cucumber, and melon. Seed size (SS) is an important trait in cucurbits breeding, which is controlled by quantitative trait loci (QTL). Recent advances have deciphered several signaling pathways underlying seed size variation in model plants such as Arabidopsis and rice, but little is known on the genetic basis of SS variation in cucurbits. Here we conducted literature review on seed size QTL identified in watermelon, pumpkin/squash, cucumber and melon, and inferred 14, 9 and 13 consensus SS QTL based on their physical positions in respective draft genomes. Among them, four from watermelon (ClSS2.2, ClSS6.1, ClSS6.2, and ClSS8.2), two from cucumber (CsSS4.1 and CsSS5.1), and one from melon (CmSS11.1) were major-effect, stable QTL for seed size and weight. Whole genome sequence alignment revealed that these major-effect QTL were located in syntenic regions across different genomes suggesting possible structural and functional conservation of some important genes for seed size control in cucurbit crops. Annotation of genes in the four watermelon consensus SS QTL regions identified genes that are known to play important roles in seed size control including members of the zinc finger protein and the E3 ubiquitin-protein ligase families. The present work highlights the utility of comparative analysis in understanding the genetic basis of seed size variation, which may help future mapping and cloning of seed size QTL in cucurbits.
- Published
- 2020
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