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Wen G, Xie Z, Yang Y, Yang Y, Guo Q, Liang G, Dang J. NpPP2-B10, an F-Box-Nictaba Gene, Promotes Plant Growth and Resistance to Black Shank Disease Incited by Phytophthora nicotianae in Nicotiana tabacum. Int J Mol Sci 2023; 24:ijms24087353. [PMID: 37108517 PMCID: PMC10138871 DOI: 10.3390/ijms24087353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/09/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Black shank, a devastating disease affecting tobacco production worldwide, is caused by Phytophthora nicotianae. However, few genes related to Phytophthora resistance have been reported in tobacco. Here, we identified NpPP2-B10, a gene strongly induced by P. nicotianae race 0, with a conserved F-box motif and Nictaba (tobacco lectin) domain, in the highly resistant tobacco species Nicotiana plumbaginifolia. NpPP2-B10 is a typical F-box-Nictaba gene. When it was transferred into the black shank-susceptible tobacco cultivar 'Honghua Dajinyuan', it was found to promote resistance to black shank disease. NpPP2-B10 was induced by salicylic acid, and some resistance-related genes (NtPR1, NtPR2, NtCHN50, and NtPAL) and resistance-related enzymes (catalase and peroxidase) were significantly upregulated in the overexpression lines after infection with P. nicotianae. Furthermore, we showed that NpPP2-B10 actively regulated the tobacco seed germination rate, growth rate, and plant height. The erythrocyte coagulation test of purified NpPP2-B10 protein showed that NpPP2-B10 had plant lectin activity, and the lectin content in the overexpression lines was significantly higher than that in the WT, which could lead to accelerated growth and improved resistance of tobacco. SKP1 is an adaptor protein of the E3 ubiquitin ligase SKP1, Cullin, F-box (SCF) complex. We demonstrated that NpPP2-B10 could interact with the NpSKP1-1A gene in vivo and in vitro through yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC), indicating that NpPP2-B10 likely participates in the plant immune response by mediating the ubiquitin protease pathway. In conclusion, our study provides some important insights concerning NpPP2-B10-mediated regulation of tobacco growth and resistance.
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Affiliation(s)
- Guo Wen
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhongyi Xie
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
- College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yao Yang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
| | - Yuxue Yang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
| | - Qigao Guo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
| | - Guolu Liang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
| | - Jiangbo Dang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
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Wang H, Dang J, Guo Q, Liang G. qPCR Genotyping of Polyploid Species. Methods Mol Biol 2023; 2638:115-122. [PMID: 36781638 DOI: 10.1007/978-1-0716-3024-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
A simple and cost-effective method for genotyping polyploid plants using quantitative PCR (qPCR) is described in this chapter. There is no additional operation, only simultaneous amplification of alleles and reference sequences with constant copy number in the genome. The qPCR genotyping can detect the genotypes of important traits in polyploid plants without whole genome sequencing data.
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Affiliation(s)
- Haiyan Wang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China
| | - Jiangbo Dang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China
| | - Qigao Guo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China
| | - Guolu Liang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China.
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Photosynthetic Efficiency and Glyco-Metabolism Changes in Artificial Triploid Loquats Contribute to Heterosis Manifestation. Int J Mol Sci 2022; 23:ijms231911337. [PMID: 36232635 PMCID: PMC9570370 DOI: 10.3390/ijms231911337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Previous studies indicated that extensive genetic variations could be generated due to polyploidy, which is considered to be closely associated with the manifestation of polyploid heterosis. Our previous studies confirmed that triploid loquats demonstrated significant heterosis, other than the ploidy effect, but the underlying mechanisms are largely unknown. This study aimed to overcome the narrow genetic distance of loquats, increase the genetic variation level of triploid loquats, and systematically illuminate the heterosis mechanisms of triploid loquats derived from two cross combinations. Here, inter-simple sequence repeats (ISSRs) and simple sequence repeats (SSRs) were adopted for evaluating the genetic diversity, and transcriptome sequencing (RNA-Seq) was performed to investigate gene expression as well as pathway changes in the triploids. We found that extensive genetic variations were produced during the formation of triploid loquats. The polymorphism ratios of ISSRs and SSRs were 43.75% and 19.32%, respectively, and almost all their markers had a PIC value higher than 0.5, suggesting that both ISSRs and SSRs could work well in loquat assisted breeding. Furthermore, our results revealed that by broadening the genetic distance between the parents, genetic variations in triploids could be promoted. Additionally, RNA-Seq results suggested that numerous genes differentially expressed between the triploids and parents were screened out. Moreover, KEGG analyses revealed that “photosynthetic efficiency” and “glyco-metabolism” were significantly changed in triploid loquats compared with the parents, which was consistent with the results of physiological indicator analyses, leaf micro-structure observations, and qRT-PCR validation. Collectively, our results suggested that extensive genetic variations occurred in the triploids and that the changes in the “photosynthetic efficiency” as well as “glyco-metabolism” of triploids might have further resulted in heterosis manifestation in the triploid loquats.
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Wei X, Kong D, Zhu S, Li S, Zhou S, Wu W. Rapid Identification of Soybean Varieties by Terahertz Frequency-Domain Spectroscopy and Grey Wolf Optimizer-Support Vector Machine. FRONTIERS IN PLANT SCIENCE 2022; 13:823865. [PMID: 35360340 PMCID: PMC8963758 DOI: 10.3389/fpls.2022.823865] [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: 12/15/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Different soybean varieties vary greatly in their nutritional value and composition. Screening for superior varieties is also essential for the development of the soybean seed industry. The objective of the paper was to analyze the feasibility of terahertz (THz) frequency-domain spectroscopy and chemometrics for soybean variety identification. Meanwhile, a grey wolf optimizer-support vector machine (GWO-SVM) soybean variety identification model was proposed. Firstly, the THz frequency-domain spectra of experimental samples (6 varieties, 270 in total) were collected. Principal component analysis (PCA) was used to analyze the THz spectra. After that, 203 samples from the calibration set were used to establish a soybean variety identification model. Finally, 67 samples from the test set were used for prediction validation. The experimental results demonstrated that THz frequency-domain spectroscopy combined with GWO-SVM could quickly and accurately identify soybean varieties. Compared with discriminant partial least squares (DPLS) and particles swarm optimization support vector machine, GWO-SVM combined with the second derivative could establish a better soybean variety identification model. The overall correct identification rate of its prediction set was 97.01%.
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Affiliation(s)
- Xiao Wei
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
- College of Engineering and Technology, Southwest University, Chongqing, China
| | - Dandan Kong
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Shiping Zhu
- College of Engineering and Technology, Southwest University, Chongqing, China
| | - Song Li
- College of Engineering and Technology, Southwest University, Chongqing, China
| | - Shengling Zhou
- College of Engineering and Technology, Southwest University, Chongqing, China
| | - Weiji Wu
- China Tianjin Grain and Oil Wholesale Trade Market, Tianjin, China
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Genome-Wide Identification, Characterization and Expression Profiling of Aluminum-Activated Malate Transporters in Eriobotrya japonica Lindl. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7110441] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Aluminum-activated malate transporters (ALMTs) have multiple potential roles in plant metabolism such as regulation of organic acids in fruits, movement of guard cells and inducing tolerance against aluminum stress. However, the systematic characterization of ALMT genes in loquat is yet to be performed. In the current study, 24 putative ALMT genes were identified in the genome of Eriobotrya japonica Lindl. To further investigate the role of those ALMT genes, comprehensive bioinformatics and expression analysis were performed. In bioinformatics analysis, the physiochemical properties, conserved domains, gene structure, conserved motif, phylogenetic and syntenic analysis of EjALMT genes were conducted. The result revealed that the ALMT superfamily domain was conserved in all EjALMT proteins. EjALMT proteins were predicted to be localized in the plasma membrane. Genomic structural and motif analysis showed that the exon and motif number of each EjALMT gene ranged dramatically, from 5 to 7, and 6 to 10, respectively. Syntenic analysis indicated that the segmental or whole-genome duplication played a vital role in extension of the EjALMT gene family. The Ka and Ks values of duplicated genes depicted that EjALMT genes have undergone a strong purifying selection. Furthermore, the expression analysis of EjALMT genes was performed in the root, mature leaf, stem, full-bloom flower and ripened fruit of loquat. Some genes were expressed differentially in examined loquat tissues, signifying their differential role in plant growth and development. This study provides the first genome-wide identification, characterization, and relative expression of the ALMT gene family in loquat and provides the foundation for further functional analysis.
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Wang H, Dang J, Wu D, Xie Z, Yan S, Luo J, Guo Q, Liang G. Genotyping of polyploid plants using quantitative PCR: application in the breeding of white-fleshed triploid loquats (Eriobotrya japonica). PLANT METHODS 2021; 17:93. [PMID: 34479588 PMCID: PMC8418031 DOI: 10.1186/s13007-021-00792-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/24/2021] [Indexed: 06/09/2023]
Abstract
BACKGROUND Ploidy manipulation is effective in seedless loquat breeding, in which flesh color is a key agronomic and economic trait. Few techniques are currently available for detecting the genotypes of polyploids in plants, but this ability is essential for most genetic research and molecular breeding. RESULTS We developed a system for genotyping by quantitative PCR (qPCR) that allowed flesh color genotyping in multiple tetraploid and triploid loquat varieties (lines). The analysis of 13 different ratios of DNA mixtures between two homozygous diploids (AA and aa) showed that the proportion of allele A has a high correlation (R2 = 0.9992) with parameter b [b = a1/(a1 + a2)], which is derived from the two normalized allele signals (a1 and a2) provided by qPCR. Cluster analysis and variance analysis from simulating triploid and tetraploid hybrids provided completely correct allelic configurations. Four genotypes (AAA, AAa, Aaa, aaa) were found in triploid loquats, and four (AAAA, AAAa, AAaa, Aaaa; absence of aaaa homozygotes) were found in tetraploid loquats. DNA markers analysis showed that the segregation of flesh color in all F1 hybrids conformed to Mendel's law. When tetraploid B431 was the female parent, more white-fleshed triploids occurred among the progeny. CONCLUSIONS qPCR can detect the flesh color genotypes of loquat polyploids and provides an alternative method for analyzing polyploid genotype and breeding, dose effects and allele-specific expression.
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Affiliation(s)
- Haiyan Wang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Jiangbo Dang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Di Wu
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Zhongyi Xie
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Shuang Yan
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Jingnan Luo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Qigao Guo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China
| | - Guolu Liang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, 400715, China.
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Beibei, Chongqing, 400715, China.
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