2
|
Pawełkowicz M, Zieliński K, Zielińska D, Pląder W, Yagi K, Wojcieszek M, Siedlecka E, Bartoszewski G, Skarzyńska A, Przybecki Z. Next generation sequencing and omics in cucumber (Cucumis sativus L.) breeding directed research. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:77-88. [PMID: 26566826 DOI: 10.1016/j.plantsci.2015.07.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 06/29/2015] [Accepted: 07/28/2015] [Indexed: 05/10/2023]
Abstract
In the post-genomic era the availability of genomic tools and resources is leading us to novel generation methods in plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. In this study we have mainly concentrated on the Cucumis sativus and (but much less) Cucurbitaceae family several important vegetable crops. There are many reports on research conducted in Cucurbitaceae plant breeding programs on the ripening process, phloem transport, disease resistance, cold tolerance and fruit quality traits. This paper presents the role played by new omic technologies in the creation of knowledge on the mechanisms of the formation of the breeding features. The analysis of NGS (NGS-next generation sequencing) data allows the discovery of new genes and regulatory sequences, their positions, and makes available large collections of molecular markers. Genome-wide expression studies provide breeders with an understanding of the molecular basis of complex traits. Firstly a high density map should be created for the reference genome, then each re-sequencing data could be mapped and new markers brought out into breeding populations. The paper also presents methods that could be used in the future for the creation of variability and genomic modification of the species in question. It has been shown also the state and usefulness in breeding the chloroplastomic and mitochondriomic study.
Collapse
Affiliation(s)
- Magdalena Pawełkowicz
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Konrad Zieliński
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Dorota Zielińska
- Department of Food Gastronomy and Food Hygiene, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Wojciech Pląder
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Kouhei Yagi
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Michał Wojcieszek
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Ewa Siedlecka
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Grzegorz Bartoszewski
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Agnieszka Skarzyńska
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Zbigniew Przybecki
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
| |
Collapse
|
3
|
Wóycicki R, Witkowicz J, Gawroński P, Dąbrowska J, Lomsadze A, Pawełkowicz M, Siedlecka E, Yagi K, Pląder W, Seroczyńska A, Śmiech M, Gutman W, Niemirowicz-Szczytt K, Bartoszewski G, Tagashira N, Hoshi Y, Borodovsky M, Karpiński S, Malepszy S, Przybecki Z. The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants. PLoS One 2011; 6:e22728. [PMID: 21829493 PMCID: PMC3145757 DOI: 10.1371/journal.pone.0022728] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 07/05/2011] [Indexed: 01/01/2023] Open
Abstract
Cucumber (Cucumis sativus L.), a widely cultivated crop, has originated from Eastern Himalayas and secondary domestication regions includes highly divergent climate conditions e.g. temperate and subtropical. We wanted to uncover adaptive genome differences between the cucumber cultivars and what sort of evolutionary molecular mechanisms regulate genetic adaptation of plants to different ecosystems and organism biodiversity. Here we present the draft genome sequence of the Cucumis sativus genome of the North-European Borszczagowski cultivar (line B10) and comparative genomics studies with the known genomes of: C. sativus (Chinese cultivar – Chinese Long (line 9930)), Arabidopsis thaliana, Populus trichocarpa and Oryza sativa. Cucumber genomes show extensive chromosomal rearrangements, distinct differences in quantity of the particular genes (e.g. involved in photosynthesis, respiration, sugar metabolism, chlorophyll degradation, regulation of gene expression, photooxidative stress tolerance, higher non-optimal temperatures tolerance and ammonium ion assimilation) as well as in distributions of abscisic acid-, dehydration- and ethylene-responsive cis-regulatory elements (CREs) in promoters of orthologous group of genes, which lead to the specific adaptation features. Abscisic acid treatment of non-acclimated Arabidopsis and C. sativus seedlings induced moderate freezing tolerance in Arabidopsis but not in C. sativus. This experiment together with analysis of abscisic acid-specific CRE distributions give a clue why C. sativus is much more susceptible to moderate freezing stresses than A. thaliana. Comparative analysis of all the five genomes showed that, each species and/or cultivars has a specific profile of CRE content in promoters of orthologous genes. Our results constitute the substantial and original resource for the basic and applied research on environmental adaptations of plants, which could facilitate creation of new crops with improved growth and yield in divergent conditions.
Collapse
MESH Headings
- Adaptation, Physiological
- Chromosome Mapping
- Chromosomes, Artificial, Bacterial
- Chromosomes, Plant/genetics
- Cucumis sativus/genetics
- DNA, Plant/genetics
- Evolution, Molecular
- Gene Expression Regulation, Plant
- Genes, Plant
- Genome, Plant
- Polymerase Chain Reaction
- Promoter Regions, Genetic/genetics
- Regulatory Sequences, Nucleic Acid
- Sequence Analysis, DNA
Collapse
Affiliation(s)
- Rafał Wóycicki
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
- * E-mail: (ZP); (SK); (RW)
| | - Justyna Witkowicz
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Joanna Dąbrowska
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Alexandre Lomsadze
- Center for Bioinformatics and Computational Genomics, Joint Wallace H. Coulter Georgia Tech and Emory Department of Biomedical Engineering, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Magdalena Pawełkowicz
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Ewa Siedlecka
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Kohei Yagi
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Wojciech Pląder
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Anna Seroczyńska
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Mieczysław Śmiech
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Wojciech Gutman
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Katarzyna Niemirowicz-Szczytt
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Grzegorz Bartoszewski
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Norikazu Tagashira
- Department of Living Design and Information Science, Faculty of Human Development, Hiroshima Jogakuin University, Higashi-ku, Japan
| | - Yoshikazu Hoshi
- Department of Plant Science, Tokai University, Minamiaso-mura, Kumamoto, Japan
| | - Mark Borodovsky
- Center for Bioinformatics and Computational Genomics, Joint Wallace H. Coulter Georgia Tech and Emory Department of Biomedical Engineering, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Stanisław Karpiński
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
- * E-mail: (ZP); (SK); (RW)
| | - Stefan Malepszy
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Zbigniew Przybecki
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
- * E-mail: (ZP); (SK); (RW)
| |
Collapse
|
4
|
Adventures in the enormous: a 1.8 million clone BAC library for the 21.7 Gb genome of loblolly pine. PLoS One 2011; 6:e16214. [PMID: 21283709 PMCID: PMC3025025 DOI: 10.1371/journal.pone.0016214] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 12/10/2010] [Indexed: 11/19/2022] Open
Abstract
Loblolly pine (LP; Pinus taeda L.) is the most economically important tree in the U.S. and a cornerstone species in southeastern forests. However, genomics research on LP and other conifers has lagged behind studies on flowering plants due, in part, to the large size of conifer genomes. As a means to accelerate conifer genome research, we constructed a BAC library for the LP genotype 7-56. The LP BAC library consists of 1,824,768 individually-archived clones making it the largest single BAC library constructed to date, has a mean insert size of 96 kb, and affords 7.6X coverage of the 21.7 Gb LP genome. To demonstrate the efficacy of the library in gene isolation, we screened macroarrays with overgos designed from a pine EST anchored on LP chromosome 10. A positive BAC was sequenced and found to contain the expected full-length target gene, several gene-like regions, and both known and novel repeats. Macroarray analysis using the retrotransposon IFG-7 (the most abundant repeat in the sequenced BAC) as a probe indicates that IFG-7 is found in roughly 210,557 copies and constitutes about 5.8% or 1.26 Gb of LP nuclear DNA; this DNA quantity is eight times the Arabidopsis genome. In addition to its use in genome characterization and gene isolation as demonstrated herein, the BAC library should hasten whole genome sequencing of LP via next-generation sequencing strategies/technologies and facilitate improvement of trees through molecular breeding and genetic engineering. The library and associated products are distributed by the Clemson University Genomics Institute (www.genome.clemson.edu).
Collapse
|
5
|
Gonthier L, Bellec A, Blassiau C, Prat E, Helmstetter N, Rambaud C, Huss B, Hendriks T, Bergès H, Quillet MC. Construction and characterization of two BAC libraries representing a deep-coverage of the genome of chicory (Cichorium intybus L., Asteraceae). BMC Res Notes 2010; 3:225. [PMID: 20701751 PMCID: PMC2933585 DOI: 10.1186/1756-0500-3-225] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Accepted: 08/11/2010] [Indexed: 11/19/2022] Open
Abstract
Background The Asteraceae represents an important plant family with respect to the numbers of species present in the wild and used by man. Nonetheless, genomic resources for Asteraceae species are relatively underdeveloped, hampering within species genetic studies as well as comparative genomics studies at the family level. So far, six BAC libraries have been described for the main crops of the family, i.e. lettuce and sunflower. Here we present the characterization of BAC libraries of chicory (Cichorium intybus L.) constructed from two genotypes differing in traits related to sexual and vegetative reproduction. Resolving the molecular mechanisms underlying traits controlling the reproductive system of chicory is a key determinant for hybrid development, and more generally will provide new insights into these traits, which are poorly investigated so far at the molecular level in Asteraceae. Findings Two bacterial artificial chromosome (BAC) libraries, CinS2S2 and CinS1S4, were constructed from HindIII-digested high molecular weight DNA of the contrasting genotypes C15 and C30.01, respectively. C15 was hermaphrodite, non-embryogenic, and S2S2 for the S-locus implicated in self-incompatibility, whereas C30.01 was male sterile, embryogenic, and S1S4. The CinS2S2 and CinS1S4 libraries contain 89,088 and 81,408 clones. Mean insert sizes of the CinS2S2 and CinS1S4 clones are 90 and 120 kb, respectively, and provide together a coverage of 12.3 haploid genome equivalents. Contamination with mitochondrial and chloroplast DNA sequences was evaluated with four mitochondrial and four chloroplast specific probes, and was estimated to be 0.024% and 1.00% for the CinS2S2 library, and 0.028% and 2.35% for the CinS1S4 library. Using two single copy genes putatively implicated in somatic embryogenesis, screening of both libraries resulted in detection of 12 and 13 positive clones for each gene, in accordance with expected numbers. Conclusions This indicated that both BAC libraries are valuable tools for molecular studies in chicory, one goal being the positional cloning of the S-locus in this Asteraceae species.
Collapse
Affiliation(s)
- Lucy Gonthier
- Univ Lille Nord de France, F-59000 Lille, France, Stress Abiotiques et Différenciation des Végétaux Cultivés (SADV), UMR INRA-USTL 1281, Bât, SN2, F-59655 Villeneuve d'Ascq, France.
| | | | | | | | | | | | | | | | | | | |
Collapse
|