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Agronomy
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Recent Developments for Integrating Multi-Omics Data into Prediction Models for...
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Recent Developments for Integrating Multi-Omics Data into Prediction Models for Plant Breeding Applications

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: closed (20 June 2021) | Viewed by 3541

Special Issue Editor

Dr. Reka Howard

E-Mail Website
Guest Editor
Department of Statistics, University of Nebraska–Lincoln, Lincoln, NE 68583-0963, USA
Interests: statistics; genomic prediction; model development for genotype by environmental interaction for genomic prediction; digital agriculture
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear colleagues,

Recent developments of technologies that produce molecular and multi-omics data enabled us to collect information on living organisms that were not available before. With this set of information (e.g. high-throughput phenotyping and genotyping, weather information, soil characterization, biotic and abiotic factors, management, etc.), we have the potential to better understand the agronomically important traits and use them for prediction purposes. The ultimate goal of plant breeding is to increase the genetic gain, and the integration of these technologies can enable us to achieve this by improving the precision of selection. However, the integration of these multi-omics data is not trivial and can cause a bottleneck in leveraging the availability of these sources of information for selection purposes.

In this special issue, we invite original research studies, review articles and other types of articles related to the integration of multi-omics data to improve existing methods for accelerating the breeding cycles and enhance selection procedures.

Dr. Reka Howard
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.

Published Papers (1 paper)

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Research

19 pages, 7548 KiB  
Article
De Novo Transcriptome Sequencing in Kiwifruit (Actinidia chinensis var. deliciosa (A Chev) Liang et Ferguson) and Development of Tissue-Specific Transcriptomic Resources
by Juan Alfonso Salazar, Cristian Vergara-Pulgar, Claudia Jorquera, Patricio Zapata, David Ruiz, Pedro Martínez-Gómez, Rodrigo Infante and Claudio Meneses
Agronomy 2021, 11(5), 919; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy11050919 - 07 May 2021
Cited by 6 | Viewed by 2703
Abstract
Kiwifruit (Actinidia chinensis var. deliciosa (A Chev) Liang et Ferguson) is a sub-tropical vine species from the Actinidiaceae family native to China. This species has an allohexaploid genome (from diploid and autotetraploid parents), contained in 174 chromosomes producing a climacteric and fleshy [...] Read more.
Kiwifruit (Actinidia chinensis var. deliciosa (A Chev) Liang et Ferguson) is a sub-tropical vine species from the Actinidiaceae family native to China. This species has an allohexaploid genome (from diploid and autotetraploid parents), contained in 174 chromosomes producing a climacteric and fleshy fruit called kiwifruit. Currently, only a small body of transcriptomic and proteomic data are available for A. chinensis var. deliciosa. In this low molecular knowledge context, the main goal of this study is to construct a tissue-specific de novo transcriptome assembly, generating differential expression analysis among these specific tissues, to obtain new useful transcriptomic information for a better knowledge of vegetative, floral and fruit growth in this species. In this study, we have analyzed different whole transcriptomes from shoot, leaf, flower bud, flower and fruit at four development stages (7, 50, 120 and 160 days after flowering; DAF) in kiwifruit obtained through RNA-seq sequencing. The first version of the developed A. chinensis var. deliciosa de novo transcriptome contained 142,025 contigs (x¯ = 1044 bp, N50 = 1133 bp). Annotation was performed with BLASTX against the TAIR10 protein database, and we found an annotation proportion of 35.6% (50,508), leaving 64.4% (91,517) of the contigs without annotation. These results represent a reference transcriptome for allohexaploid kiwifruit generating a database of A. chinensis var. deliciosa genes related to leaf, flower and fruit development. These results provided highly valuable information identifying over 20,000 exclusive genes including all tissue comparisons, which were associated with the proteins involved in different biological processes and molecular functions. Full article
(This article belongs to the Special Issue Recent Developments for Integrating Multi-Omics Data into Prediction Models for Plant Breeding Applications)
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