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Agronomy
Special Issues
Application of Sequencing Technologies to Crop Breeding
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Application of Sequencing Technologies to Crop Breeding

A special issue of Agronomy (ISSN 2073-4395).

Deadline for manuscript submissions: closed (31 May 2017)

Special Issue Editor

Prof. Dr. Chengdao Li

E-Mail Website
Guest Editor
Western Barley Genetics Alliance, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
Interests: plant genetics and breeding; plant molecular genetics; cereal genomics

Special Issue Information

Dear Colleagues,

In recent years, next-generation sequencing (NGS), genome sequencing, and whole genome re-sequencing have been widely applied in plant research. These technologies are now being increasingly applied to crop genetic improvement. Some key research areas include: (1) Application of NGS as DNA fingerprinting for rapid marker-trait association discovery; (2) Application of NGS for rapid genetic mapping and QTL analysis; (3) Development of cost-effective markers for molecular marker-assisted selection; (4) Development of functional markers through genome sequencing and resequencing; (5) Rapid developing diagnostic markers from dense genetic maps through whole genome re-sequencing; and (6) Developing diagnostic markers by marker mining on genome sequencing scaffolds. Genome sequencing and whole genome re-sequencing generate millions of markers in many crop species. Recent advances in parallel genotyping platforms permit genomic selection (GS) in crop breeding. GS simultaneously estimates all loci or all markers in a genome to calculate the genomic estimated breeding value, which increases the accuracy of the prediction of breeding and genotypic values. Genome sequencing and resequencing technologies are particularly valuable for economic important complex traits such as yield, quality, and environmental adaption, which lead to more rapid and lower cost in crop breeding. This Special Issue will cover recent advances in application of NGS for crop improvement.

Prof. Chengdao Li
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agronomy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • next generation sequencing
  • functional molecular markers
  • genomic selection
  • crop breeding

Published Papers (2 papers)

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Research

1029 KiB  
Article
Characterisation of Faba Bean (Vicia faba L.) Transcriptome Using RNA-Seq: Sequencing, De Novo Assembly, Annotation, and Expression Analysis
by Shivraj Braich, Shimna Sudheesh, John W. Forster and Sukhjiwan Kaur
Agronomy 2017, 7(3), 53; https://doi.org/10.3390/agronomy7030053 - 08 Aug 2017
Cited by 12 | Viewed by 7798
Abstract
RNA sequencing (RNA-Seq) is a deep sequencing method used for transcriptome profiling. RNA-Seq assemblies have successfully been used for a broad variety of applications, such as gene characterisation, functional genomic studies, and gene expression analysis, particularly useful in the absence of a well-studied [...] Read more.
RNA sequencing (RNA-Seq) is a deep sequencing method used for transcriptome profiling. RNA-Seq assemblies have successfully been used for a broad variety of applications, such as gene characterisation, functional genomic studies, and gene expression analysis, particularly useful in the absence of a well-studied genome reference sequence. This study reports on the development of reference unigene sets from faba bean using RNA-Seq. Two Australian faba bean cultivars (Doza and Farah) that differ in terms of disease resistance, breeding habit, and adaptation characteristics, and have been extensively used in breeding programs, were utilised in this study. The de novo assembly resulted in a total of 58,962 and 53,275 transcripts with approximately 67 Mbp (1588 bp N50) and 61 Mbp (1629 bp N50) for Doza and Farah, respectively. The generated transcripts have been compared to the protein and nucleotide databases of NCBI, as well as to the gene complements of several related legume species such as Medicago truncatula, soybean, and chickpea. Both assemblies were compared to previously-published faba bean transcriptome reference sets for the degree of completeness and utility. Annotation of unigenes has been performed, and patterns of tissue-specific expression identified. The gene complement derived from this comprehensive transcriptome analysis shows that faba bean, despite its complex 13 Gbp genome, compares well to other legumes in expressed gene content. This study in faba bean represents the most comprehensive reference transcriptomes from two different Australian cultivars available to date and it provides a valuable resource for future genomics-assisted breeding activities in this species. Full article
(This article belongs to the Special Issue Application of Sequencing Technologies to Crop Breeding)
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1936 KiB  
Article
Generation and Characterisation of a Reference Transcriptome for Phalaris (Phalaris aquatica L.)
by Rebecca C. Baillie, Michelle C. Drayton, Luke W. Pembleton, Sukhjiwan Kaur, Richard A. Culvenor, Kevin F. Smith, German C. Spangenberg, John W. Forster and Noel O. I. Cogan
Agronomy 2017, 7(1), 14; https://doi.org/10.3390/agronomy7010014 - 15 Feb 2017
Cited by 8 | Viewed by 6553
Abstract
Phalaris aquatica is a cool-season perennial grass species that is extensively cultivated in Australia, with additional usage in other areas of the world. Phalaris displays a number of desirable agronomic characteristics, although unfavourable traits include excessive seed shattering, sensitivity to aluminium toxicity, and [...] Read more.
Phalaris aquatica is a cool-season perennial grass species that is extensively cultivated in Australia, with additional usage in other areas of the world. Phalaris displays a number of desirable agronomic characteristics, although unfavourable traits include excessive seed shattering, sensitivity to aluminium toxicity, and several toxicosis syndromes. Varietal development has to date been based on traditional selection methods, but would benefit from the application of genomics-based approaches, which require the development of large-scale sequence resources. Due to a large nuclear DNA content, methods that target the expressed component of the genome and reduce the complexity of analysis are most amenable to current sequencing technologies. A reference unigene set has been developed by transcriptome sequencing of multiple tissues from a single plant belonging to the variety Landmaster. Comparisons have been made to gene complements from related species, as well as reference protein databases, and patterns of gene expression in different tissues have been evaluated. A number of candidate genes relevant to removal of undesirable attributes have been identified. The reference unigene set will provide the basis for detailed studies of differential gene expression and identification of candidate genes for potential transgenic deployment, as well as a critical resource for genotypic analysis to support future genomics-assisted breeding activities for phalaris improvement. Full article
(This article belongs to the Special Issue Application of Sequencing Technologies to Crop Breeding)
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