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Zhu T, Feng Y, Dong X, Yang X, Liu B, Yuan P, Song X, Chen S, Sui S. Optimizing DUS testing for Chimonanthus praecox using feature selection based on a genetic algorithm. FRONTIERS IN PLANT SCIENCE 2024; 14:1328603. [PMID: 38312354 PMCID: PMC10835806 DOI: 10.3389/fpls.2023.1328603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/27/2023] [Indexed: 02/06/2024]
Abstract
Chimonanthus praecox is a famous traditional flower in China with high ornamental value. It has numerous varieties, yet its classification is highly disorganized. The distinctness, uniformity, and stability (DUS) test enables the classification and nomenclature of various species; thus, it can be used to classify the Chimonanthus varieties. In this study, flower traits were quantified using an automatic system based on pattern recognition instead of traditional manual measurement to improve the efficiency of DUS testing. A total of 42 features were quantified, including 28 features in the DUS guidelines and 14 new features proposed in this study. Eight algorithms were used to classify wintersweet, and the random forest (RF) algorithm performed the best when all features were used. The classification accuracy of the outer perianth was the highest when the features of the different parts were used for classification. A genetic algorithm was used as the feature selection algorithm to select a set of 22 reduced core features and improve the accuracy and efficiency of the classification. Using the core feature set, the classification accuracy of the RF model improved to 99.13%. Finally, K-means was used to construct a pedigree cluster tree of 23 varieties of wintersweet; evidently, wintersweet was clustered into a single class, which can be the basis for further study of genetic relationships among varieties. This study provides a novel method for DUS detection, variety identification, and pedigree analysis.
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Affiliation(s)
- Ting Zhu
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Yaoyao Feng
- College of Computer and Information Science, Southwest University, Chongqing, China
| | - Xiaoxuan Dong
- College of Computer and Information Science, Southwest University, Chongqing, China
| | - Ximeng Yang
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Bin Liu
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Puying Yuan
- Garden and Flower Research Center, Horticultural Research Institute of Sichuan Academy of Agricultural Science, Chengdu, China
| | - Xingrong Song
- Garden and Flower Research Center, Horticultural Research Institute of Sichuan Academy of Agricultural Science, Chengdu, China
| | - Shanxiong Chen
- College of Computer and Information Science, Southwest University, Chongqing, China
| | - Shunzhao Sui
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
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Li H, Ikram M, Xia Y, Li R, Yuan Q, Zhao W, Siddique KHM, Guo P. Genome-wide identification and development of InDel markers in tobacco ( Nicotiana tabacum L.) using RAD-seq. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1077-1089. [PMID: 35722506 PMCID: PMC9203652 DOI: 10.1007/s12298-022-01187-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 05/03/2023]
Abstract
Insertions and deletions (InDels) can be used as molecular markers in genetic studies and marker-assisted selection breeding. However, genetic improvement in tobacco has been hindered by limited genetic diversity information and relatedness within available germplasm. A Chinese tobacco variety, Yueyan-98, was resequenced using restriction-site associated DNA (RAD-seq) approach to develop InDel markers. In total, 32,884 InDel loci were detected between Yueyan-98 and the K326 reference sequence [18,598 (56.55%) deletions and 14,288 (43.45%) insertions], ranging from 1 to 62 bp in length. Of the 6,733 InDels (> 4 bp) that were suitable for polyacrylamide gel electrophoresis, 150 were randomly selected. These 150 InDels were unevenly distributed on 23 chromosomes, and the highest numbers of InDels were observed on chromosomes Nt05, Nt13, and Nt23. The average density of adjacent InDels was 19.36 Mb. Thirty-seven InDels were located in genic regions. Polymerase chain reaction (PCR)-based markers were developed to validate polymorphism; 113 (79.80%) of the 150 InDel markers showed polymorphism and were further used for genetic diversity analysis of 50 tobacco accessions (13 from China, 1 from Mexico, and 36 from the USA). The average expected heterozygosity (He) and polymorphism information content (PIC) values were 0.28 ± 0.16 and 0.38 ± 0.10, respectively. The average Shannon diversity index (I) was 0.34 ± 0.18, with genetic diversity ranging from 0.13-0.57. The 50 accessions were classified into two groups with a genetic similarity coefficient of 0.68. Principal coordinate analysis (PCoA) and population structure analysis showed similar results and divided the population into two groups unrelated to their geographical origins. AMOVA showed 4% variance among the population and the remaining 96% within the population, suggesting low genetic differentiation between two subpopulations. Furthermore, 10 InDels (19 alleles) were significantly identified for tobacco plant height using GLM+Q model at P < 0.005. Among these, three markers (Nt-I-26, Nt-I-41, and Nt-I-44) were detected in at least two environments, with phenotypic variance explained (PVE) ranging from 14.03 to 32.68%. The polymorphic InDel markers developed can be used for hybrid identification, genetic diversity, genetic linkage map construction, gene mapping, and MAS breeding programs of tobacco. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01187-3.
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Affiliation(s)
- Haiyang Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, International Crop Research Center for Stress Resistance, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Muhammad Ikram
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, International Crop Research Center for Stress Resistance, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Yanshi Xia
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, International Crop Research Center for Stress Resistance, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Ronghua Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, International Crop Research Center for Stress Resistance, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Qinghua Yuan
- Guangdong Provincial Engineering & Technology Research Center for Tobacco Breeding and Comprehensive Utilization, Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, 510640 China
| | - Weicai Zhao
- Nanxiong Research Institutes of Guangdong Tobacco Co. Ltd, Nanxiong, 512400 China
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, Perth, WA 6001 Australia
| | - Peiguo Guo
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, International Crop Research Center for Stress Resistance, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
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Wang Y, Lv H, Xiang X, Yang A, Feng Q, Dai P, Li Y, Jiang X, Liu G, Zhang X. Construction of a SNP Fingerprinting Database and Population Genetic Analysis of Cigar Tobacco Germplasm Resources in China. FRONTIERS IN PLANT SCIENCE 2021; 12:618133. [PMID: 33719288 PMCID: PMC7943628 DOI: 10.3389/fpls.2021.618133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/22/2021] [Indexed: 05/12/2023]
Abstract
Cigar tobacco is an important economic crop that is widely grown around the world. In recent years, varietal identification has become a frequent problem in germplasm preservation collections, which causes considerable inconvenience and uncertainty in the cataloging and preservation of cigar germplasm resources, in the selection of parental lines for breeding, and in the promotion and use of high quality varieties. Therefore, the use of DNA fingerprints to achieve rapid and accurate identification of varieties can play an important role in germplasm identification and property rights disputes. In this study, we used genotyping-by-sequencing (GBS) on 113 cigar tobacco accessions to develop SNP markers. After filtering, 580,942 high-quality SNPs were obtained. We used the 580,942 SNPs to perform principal component analysis (PCA), population structure analysis, and neighbor joining (NJ) cluster analysis on the 113 cigar tobacco accessions. The results showed that the accessions were not completely classified based on their geographical origins, and the genetic backgrounds of these cigar resources are complex and diverse. We further selected from these high-quality SNPs to obtained 163 SNP sites, 133 of which were successfully converted into KASP markers. Finally, 47 core KASP markers and 24 candidate core markers were developed. Using the core markers, we performed variety identification and fingerprinting in 216 cigar germplasm accessions. The results of SNP fingerprinting, 2D barcoding, and genetic analysis of cigar tobacco germplasm in this study provide a scientific basis for screening and identifying high-quality cigar tobacco germplasm, mining important genes, and broadening the basis of cigar tobacco genetics and subsequent breeding work at the molecular level.
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Affiliation(s)
- Yanyan Wang
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Hongkun Lv
- Haikou Cigar Research Institute, Hainan Provincial Tobacco Company of China National Tobacco Corporation, Haikou, China
| | - Xiaohua Xiang
- Haikou Cigar Research Institute, Hainan Provincial Tobacco Company of China National Tobacco Corporation, Haikou, China
| | - Aiguo Yang
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Quanfu Feng
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Peigang Dai
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yuan Li
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Xun Jiang
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Guoxiang Liu
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- *Correspondence: Guoxiang Liu
| | - Xingwei Zhang
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- Xingwei Zhang
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citSATdb: Genome-Wide Simple Sequence Repeat (SSR) Marker Database of Citrus Species for Germplasm Characterization and Crop Improvement. Genes (Basel) 2020; 11:genes11121486. [PMID: 33321957 PMCID: PMC7764524 DOI: 10.3390/genes11121486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 11/17/2022] Open
Abstract
Microsatellites or simple sequence repeats (SSRs) are popular co-dominant markers that play an important role in crop improvement. To enhance genomic resources in general horticulture, we identified SSRs in the genomes of eight citrus species and characterized their frequency and distribution in different genomic regions. Citrus is the world's most widely cultivated fruit crop. We have implemented a microsatellite database, citSATdb, having the highest number (~1,296,500) of putative SSR markers from the genus Citrus, represented by eight species. The database is based on a three-tier approach using MySQL, PHP, and Apache. The markers can be searched using multiple search parameters including chromosome/scaffold number(s), motif types, repeat nucleotides (1-6), SSR length, patterns of repeat motifs and chromosome/scaffold location. The cross-species transferability of selected markers can be checked using e-PCR. Further, the markers can be visualized using the Jbrowse feature. These markers can be used for distinctness, uniformity, and stability (DUS) tests of variety identification, marker-assisted selection (MAS), gene discovery, QTL mapping, and germplasm characterization. citSATdb represents a comprehensive source of markers for developing/implementing new approaches for molecular breeding, required to enhance Citrus productivity. The potential polymorphic SSR markers identified by cross-species transferability could be used for genetic diversity and population distinction in other species.
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