Comparative genome-wide characterization leading to simple sequence repeat marker development for  Nicotiana

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Abstract

Background

Simple sequence repeats (SSRs) are tandem repeats of DNA that have been used to develop robust genetic markers. These molecular markers are powerful tools for basic and applied studies such as molecular breeding. In the model plants in Nicotiana genus e.g. N. benthamiana, a comprehensive assessment of SSR content has become possible now because several Nicotiana genomes have been sequenced. We conducted a genome-wide SSR characterization and marker development across seven Nicotiana genomes.

Results

Here, we initially characterized 2,483,032 SSRs (repeat units of 1–10 bp) from seven genomic sequences of Nicotiana and developed SSR markers using the GMATA® software package. Of investigated repeat units, mono-, di- and tri-nucleotide SSRs account for 98% of all SSRs in Nicotiana. More complex SSR motifs, although rare, are highly variable between Nicotiana genomes. A total of 1,224,048 non-redundant Nicotiana (NIX) markers were developed, of which 99.98% are novel. An efficient and uniform genotyping protocol for NIX markers was developed and validated. We created a web-based database of NIX marker information including amplicon sizes of alleles in each genome for downloading and online analysis.

Conclusions

The present work constitutes the first deep characterization of SSRs in seven genomes of Nicotiana, and the development of NIX markers for these SSRs. Our online marker database and an efficient genotyping protocol facilitate the application of these markers. The NIX markers greatly expand Nicotiana marker resources, thus providing a useful tool for future research and breeding. We demonstrate a novel protocol for SSR marker development and utilization at the whole genome scale that can be applied to any lineage of organisms.

The Tobacco Markers & Primers Database (TMPD) is available at http://biodb.sdau.edu.cn/tmpd/index.html

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4878-4) contains supplementary material, which is available to authorized users.

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Most cited references 36

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Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes.

Michele Morgante, Michael Hanafey, Wayne Powell (2002)

Microsatellites are a ubiquitous class of simple repetitive DNA sequence. An excess of such repetitive tracts has been described in all eukaryotes analyzed and is thought to result from the mutational effects of replication slippage. Large-scale genomic and EST sequencing provides the opportunity to evaluate the abundance and relative distribution of microsatellites between transcribed and nontranscribed regions and the relationship of these features to haploid genome size. Although this has been studied in microbial and animal genomes, information in plants is limited. We assessed microsatellite frequency in plant species with a 50-fold range in genome size that is mostly attributable to the recent amplification of repetitive DNA. Among species, the overall frequency of microsatellites was inversely related to genome size and to the proportion of repetitive DNA but remained constant in the transcribed portion of the genome. This indicates that most microsatellites reside in regions pre-dating the recent genome expansion in many plants. The microsatellite frequency was higher in transcribed regions, especially in the untranslated portions, than in genomic DNA. Contrary to previous reports suggesting a preferential mechanism for the origin of microsatellites from repetitive DNA in both animals and plants, our findings show a significant association with the low-copy fraction of plant genomes.

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A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research.

Aureliano Bombarely, Hernan Rosli, Julia Vrebalov … (2012)

Nicotiana benthamiana is a widely used model plant species for the study of fundamental questions in molecular plant-microbe interactions and other areas of plant biology. This popularity derives from its well-characterized susceptibility to diverse pathogens and, especially, its amenability to virus-induced gene silencing and transient protein expression methods. Here, we report the generation of a 63-fold coverage draft genome sequence of N. benthamiana and its availability on the Sol Genomics Network for both BLAST searches and for downloading to local servers. The estimated genome size of N. benthamiana is 3 Gb (gigabases). The current assembly consists of approximately 141,000 scaffolds, spanning 2.6 Gb with 50% of the genome sequence contained within scaffolds >89 kilobases. Of the approximately 16,000 N. benthamiana unigenes available in GenBank, >90% are represented in the assembly. The usefulness of the sequence was demonstrated by the retrieval of N. benthamiana orthologs for 24 immunity-associated genes from other species including Ago2, Ago7, Bak1, Bik1, Crt1, Fls2, Pto, Prf, Rar1, and mitogen-activated protein kinases. The sequence will also be useful for comparative genomics in the Solanaceae family as shown here by the discovery of microsynteny between N. benthamiana and tomato in the region encompassing the Pto and Prf genes.

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Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops

Reyazul Rouf Mir, Mainassara Zaman-Allah, Nese Sreenivasulu … (2012)

Drought is one of the most serious production constraint for world agriculture and is projected to worsen with anticipated climate change. Inter-disciplinary scientists have been trying to understand and dissect the mechanisms of plant tolerance to drought stress using a variety of approaches; however, success has been limited. Modern genomics and genetic approaches coupled with advances in precise phenotyping and breeding methodologies are expected to more effectively unravel the genes and metabolic pathways that confer drought tolerance in crops. This article discusses the most recent advances in plant physiology for precision phenotyping of drought response, a vital step before implementing the genetic and molecular-physiological strategies to unravel the complex multilayered drought tolerance mechanism and further exploration using molecular breeding approaches for crop improvement. Emphasis has been given to molecular dissection of drought tolerance by QTL or gene discovery through linkage and association mapping, QTL cloning, candidate gene identification, transcriptomics and functional genomics. Molecular breeding approaches such as marker-assisted backcrossing, marker-assisted recurrent selection and genome-wide selection have been suggested to be integrated in crop improvement strategies to develop drought-tolerant cultivars that will enhance food security in the context of a changing and more variable climate.

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Author and article information

Contributors

Xuewen Wang:

ORCID: http://orcid.org/0000-0003-2820-9255

wangxuewen@mail.kib.ac.cn , xwwang@uga.edu

Shuai Yang: longtoutengs@163.com

Yongdui Chen: yongduichen@126.com

Shumeng Zhang: shumeng.zhang25@uga.edu

Qingshi Zhao: qingshi.zhao@outlook.com

Meng Li: limeng@mail.kib.ac.cn

Yulong Gao: gyl3000@163.com

Long Yang: 0538-8241324 , lyang@sdau.edu.cn

Jeffrey L. Bennetzen: 01-706-542-3698 , maize@uga.edu

Journal

Journal ID (nlm-ta): BMC Genomics

Journal ID (iso-abbrev): BMC Genomics

Title: BMC Genomics

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2164

Publication date (Electronic): 27 June 2018

Publication date PMC-release: 27 June 2018

Publication date Collection: 2018

Volume: 19

Electronic Location Identifier: 500

Affiliations

[1 ]ISNI 0000000119573309, GRID grid.9227.e, Germplasm Bank of Wild Species, Kunming Institute of Botany, , Chinese Academy of Sciences, ; 132 Lanhei Road, Kunming, 650201 People’s Republic of China

[2 ]ISNI 0000 0004 1936 738X, GRID grid.213876.9, Department of Genetics, , University of Georgia, ; Athens, GA 30602 USA

[3 ]ISNI 0000 0000 9482 4676, GRID grid.440622.6, Agricultural Big-Data Research Center, College of Plant Protection, , Shandong Agricultural University, ; Tai’an, 271018 China

[4 ]ISNI 0000 0004 1799 1111, GRID grid.410732.3, Biotechnology and Germplasm Resources Institute, , Yunnan Academy of Agricultural Sciences, ; Kunming, 650223 People’s Republic of China

[5 ]ISNI 0000 0004 1799 1111, GRID grid.410732.3, Tobacco Breeding Center, , Yunnan Academy of Tobacco Agricultural Sciences, ; Kunming, 650021 Yunnan China

Author information

Xuewen Wang http://orcid.org/0000-0003-2820-9255

Article

Publisher ID: 4878

DOI: 10.1186/s12864-018-4878-4

PMC ID: 6020451

PubMed ID: 29945549

SO-VID: 6b6c9b84-83b0-4cb3-9109-c11e4d117cb3

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 5 July 2017

Date accepted : 18 June 2018

Funding

Funded by: the Kunming Institute of Botany, Chinese Academy of Sciences

Custom metadata

ScienceOpen disciplines: Genetics

Keywords: genotyping technology,marker database,marker polymorphism,ssr,tobacco

Data availability:

ScienceOpen disciplines: Genetics

Keywords: genotyping technology, marker database, marker polymorphism, ssr, tobacco

Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana

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Genome Integrity

Most cited references 36

Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes.

A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research.

Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops

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