Published Date

January 2016, Vol.242:77–88, doi:10.1016/j.plantsci.2015.07.025

From genomics to breeding

Title Next generation sequencing and omics in cucumber (Cucumis sativus L.) breeding directed research

• Author 

• Magdalena Pawełkowicz ^a
• Konrad Zieliński ^a
• Dorota Zielińska ^b
• Wojciech Pląder ^a
• Kouhei Yagi ^a
• Michał Wojcieszek ^a
• Ewa Siedlecka ^a
• Grzegorz Bartoszewski ^a
• Agnieszka Skarzyńska ^a
• Zbigniew Przybecki ^a,,

• aDepartment of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
• bDepartment of Food Gastronomy and Food Hygiene, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland

Received 10 April 2015. Revised 29 June 2015. Accepted 28 July 2015. Available online 31 July 2015.

Highlights

• •
  NGS in cucumber genome display by the integration of mapping technology.
• •
  Organellar cucumber omics study.
• •
  NGS in cucumber genome regulation study.
• •
  Checking gene functionality for the new traits in breeding.

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.

Key words

• NGS
• BAC-FISH
• TILLinG
• Plastomics
• Mitochondriomics
• Cucumis sativus L.
• Reverse genetics

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• ⁎ 
  Corresponding author. Fax: +48 22 59 32151.

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http://www.sciencedirect.com/science/article/pii/S0168945215300315