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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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Scariolo F, Palumbo F, Vannozzi A, Sacilotto GB, Gazzola M, Barcaccia G. Genotyping Analysis by RAD-Seq Reads Is Useful to Assess the Genetic Identity and Relationships of Breeding Lines in Lavender Species Aimed at Managing Plant Variety Protection. Genes (Basel) 2021; 12:genes12111656. [PMID: 34828262 PMCID: PMC8621978 DOI: 10.3390/genes12111656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/16/2021] [Accepted: 10/18/2021] [Indexed: 12/18/2022] Open
Abstract
Lavender species are widely distributed in their wild forms around the Mediterranean Basin and they are also cultivated worldwide as improved and registered clonal varieties. The economic interest of the species belonging to the Lavandula genus is determined by their use as ornamental plants and important source of essential oils that are destinated to the production of cosmetics, pharmaceuticals and foodstuffs. Because of the increasing number of cases of illegal commercialization of selected varieties, the protection of plant breeders’ rights has become of main relevance for the recognition of breeding companies’ royalties. With this aim, genomic tools based on molecular markers have been demonstrated to be very reliable and transferable among laboratories, and also much more informative than morphological descriptors. With the rising of the next-generation sequencing (NGS) technologies, several genotyping-by-sequencing approaches are now available. This study deals with a deep characterization of 15 varietal clones, belonging to two distinct Lavandula species, by means of restriction-site associated DNA sequencing (RAD-Seq). We demonstrated that this technology screens single nucleotide variants that enable to assess the genetic identity of individual accessions, to reconstruct genetic relationships among related breeding lines, to group them into genetically distinguishable main subclusters, and to assign their molecular lineages to distinct ancestors. Moreover, a number of polymorphic sites were identified within genes putatively involved in biosynthetic pathways related to both tissue pigmentation and terpene production, useful for breeding and/or protecting newly registered varieties. Overall, the results highlighted the presence of pure ancestries and interspecific hybrids for the analyzed Lavandula species, and demonstrated that RAD-Seq analysis is very informative and highly reliable for characterizing Lavandula clones and managing plant variety protection.
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Affiliation(s)
- Francesco Scariolo
- Department of Agronomy Food Natural Resources Animals Environment, Campus of Agripolis, University of Padova, 35020 Legnaro, Italy; (F.S.); (F.P.); (A.V.)
| | - Fabio Palumbo
- Department of Agronomy Food Natural Resources Animals Environment, Campus of Agripolis, University of Padova, 35020 Legnaro, Italy; (F.S.); (F.P.); (A.V.)
| | - Alessandro Vannozzi
- Department of Agronomy Food Natural Resources Animals Environment, Campus of Agripolis, University of Padova, 35020 Legnaro, Italy; (F.S.); (F.P.); (A.V.)
| | - Gio Batta Sacilotto
- Gruppo Padana Ortofloricoltura S.S., Via Olimpia 41, 31038 Treviso, Italy; (G.B.S.); (M.G.)
| | - Marco Gazzola
- Gruppo Padana Ortofloricoltura S.S., Via Olimpia 41, 31038 Treviso, Italy; (G.B.S.); (M.G.)
| | - Gianni Barcaccia
- Department of Agronomy Food Natural Resources Animals Environment, Campus of Agripolis, University of Padova, 35020 Legnaro, Italy; (F.S.); (F.P.); (A.V.)
- Correspondence:
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Image-Based On-Panicle Rice [Oryza sativa L.] Grain Counting with a Prior Edge Wavelet Correction Model. AGRONOMY-BASEL 2018. [DOI: 10.3390/agronomy8060091] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Iquebal MA, Jaiswal S, Mahato AK, Jayaswal PK, Angadi UB, Kumar N, Sharma N, Singh AK, Srivastav M, Prakash J, Singh SK, Khan K, Mishra RK, Rajan S, Bajpai A, Sandhya BS, Nischita P, Ravishankar KV, Dinesh MR, Rai A, Kumar D, Sharma TR, Singh NK. MiSNPDb: a web-based genomic resources of tropical ecology fruit mango (Mangifera indica L.) for phylogeography and varietal differentiation. Sci Rep 2017; 7:14968. [PMID: 29097776 PMCID: PMC5668432 DOI: 10.1038/s41598-017-14998-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/20/2017] [Indexed: 01/20/2023] Open
Abstract
Mango is one of the most important fruits of tropical ecological region of the world, well known for its nutritive value, aroma and taste. Its world production is >45MT worth >200 billion US dollars. Genomic resources are required for improvement in productivity and management of mango germplasm. There is no web-based genomic resources available for mango. Hence rapid and cost-effective high throughput putative marker discovery is required to develop such resources. RAD-based marker discovery can cater this urgent need till whole genome sequence of mango becomes available. Using a panel of 84 mango varieties, a total of 28.6 Gb data was generated by ddRAD-Seq approach on Illumina HiSeq 2000 platform. A total of 1.25 million SNPs were discovered. Phylogenetic tree using 749 common SNPs across these varieties revealed three major lineages which was compared with geographical locations. A web genomic resources MiSNPDb, available at http://webtom.cabgrid.res.in/mangosnps/ is based on 3-tier architecture, developed using PHP, MySQL and Javascript. This web genomic resources can be of immense use in the development of high density linkage map, QTL discovery, varietal differentiation, traceability, genome finishing and SNP chip development for future GWAS in genomic selection program. We report here world’s first web-based genomic resources for genetic improvement and germplasm management of mango.
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Affiliation(s)
- M A Iquebal
- Centre for Agricultural Bioinformatics, ICAR-IASRI, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-IASRI, New Delhi, India
| | - Ajay Kumar Mahato
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Pawan K Jayaswal
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - U B Angadi
- Centre for Agricultural Bioinformatics, ICAR-IASRI, New Delhi, India
| | - Neeraj Kumar
- Centre for Agricultural Bioinformatics, ICAR-IASRI, New Delhi, India
| | - Nimisha Sharma
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anand K Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Jai Prakash
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - S K Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Kasim Khan
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, India
| | - Rupesh K Mishra
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, India
| | - Shailendra Rajan
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, India
| | - Anju Bajpai
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, India
| | - B S Sandhya
- ICAR-Indian Institute of Horticultural Research, Bengaluru, India
| | | | - K V Ravishankar
- ICAR-Indian Institute of Horticultural Research, Bengaluru, India
| | - M R Dinesh
- ICAR-Indian Institute of Horticultural Research, Bengaluru, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-IASRI, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-IASRI, New Delhi, India.
| | - Tilak R Sharma
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Nagendra K Singh
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
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Gichuhi E, Himi E, Takahashi H, Zhu S, Doi K, Tsugane K, Maekawa M. Identification of QTLs for yield-related traits in RILs derived from the cross between pLIA-1 carrying Oryza longistaminata chromosome segments and Norin 18 in rice. BREEDING SCIENCE 2016; 66:720-733. [PMID: 28163588 PMCID: PMC5282759 DOI: 10.1270/jsbbs.16083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/01/2016] [Indexed: 05/04/2023]
Abstract
To improve rice yield, a wide genetic pool is necessary. It is therefore important to explore wild rice relatives. Oryza longistaminata is a distantly related wild rice relative that carries the AA genome. Its potential for improving agronomic traits is not well studied. Introgression line (pLIA-1) that carries Oryza longistaminata's chromosome segments, showed high performance in yield-related traits under non-fertilized conditions. Therefore, to illustrate Oryza longistaminata's potential for improving yield-related traits, RILs from the F1 of a cross between pLIA-1 and Norin 18 were developed and QTL analysis was done using the RAD-Seq method. In total, 36 QTLs for yield-related traits were identified on chromosomes 1, 2, 3, 5, 6, 7, 8, 10, and 11. Clusters of QTLs for strongly correlated traits were also identified on chromosomes 1, 3, 6, and 8. Phenotypic data from recombinant plants for chromosomes 1 and 8 QTL clusters revealed that the pLIA-1 genotype on chromosome 1 region was more important for panicle-related traits and a combination of pLIA-1 genotypes on chromosomes 1 and 8 showed a favorable phenotype under non-fertilized conditions. These results suggest that Oryza longistaminata's chromosome segments carry important alleles that can be used to improve yield-related traits of rice.
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Affiliation(s)
- Emily Gichuhi
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan; Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Eiko Himi
- Institute of Plant Science and Resources, Okayama University , Kurashiki, Okayama 710-0046 , Japan
| | - Hidekazu Takahashi
- Graduate School of Bioresource Sciences, Akita Prefectural University , Akita 010-0195 , Japan
| | - Sinhao Zhu
- Graduate School of Bioagricultural Sciences, Nagoya University , Nagoya, Aichi 464-8601 , Japan
| | - Kazuyuki Doi
- Graduate School of Bioagricultural Sciences, Nagoya University , Nagoya, Aichi 464-8601 , Japan
| | - Kazuo Tsugane
- National Institute for Basic Biology , Okazaki, Aichi 444-8585 , Japan
| | - Masahiko Maekawa
- Institute of Plant Science and Resources, Okayama University , Kurashiki, Okayama 710-0046 , Japan
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