Special Issue "Plant Genomics and Epigenomics for Trait Improvement"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: 30 November 2017

Special Issue Editors

Guest Editor
Prof. Dr. Klaus Humbeck

Director of the Institute of Biology/Plant Physiology, Martin-Luther-Universität Halle-Wittenberg, Weinbergweg 10, D-06120 Halle (Saale), Germany
E-Mail
Phone: +49 345-5526410
Interests: Plant physiology; plant epigenetics; leaf senescence; plant responses to abiotic stresses
Guest Editor
Dr. Vladimir Brukhin

(ORCID: 0000-0003-1836-0437), Leading scientist, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
E-Mail
Interests: plant genomics; plant developmental biology and botany
Guest Editor
Dr. Hieu X. Cao

(ORCID: 0000-0003-1230-4127), Post-doctoral scientist, Institute of Biology/Plant Physiology, Martin-Luther-Universität Halle-Wittenberg, Weinbergweg 10, D-06120 Halle (Saale), Germany
E-Mail
Phone: +49 345-5526251
Interests: Plant genome size and karyotype evolution; plant epigenomics; cytogenetics; plant genomics
Guest Editor
Dr. Sowjanya K. Sree

Assistant Professor, Department of Environmental Science, School of Earth Science Systems, Central University of Kerala, RSTC, Padanakkad- 671314, Kerala, India
E-Mail
Phone: +91 9999672921
Interests: Crop pest management; plant systematics; stress physiology and flowering
Guest Editor
Dr. Giang T.H. Vu

(ORCID: 0000-0001-8394-9067), Post-doctoral scientist, Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben Corrensstraße 3, D-06466 Gatersleben, Germany
E-Mail
Phone: +49 394825291
Interests: Plant genome evolution; plant epigenomics, plant genome editing; DNA repair
Guest Editor
Dr. Wenqin Wang

(ORCID: 0000-0001-6427-6338), Associate Professor, College of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
E-Mail
Phone: +86 2134206942
Interests: Plant genomics; transcriptomics and GWAS; agriculture genomics

Special Issue Information

Dear Colleagues,

Our understanding of plant traits and biological mechanisms have been enormously improved over the past decade, mainly thanks to advancements in so-called ‘next generation’ sequencing technologies. Recent plant breeding programs have taken into account available genomic/transcriptomic information, e.g., for (1) dissecting the genetic architecture of agronomic traits through quantitative genetic approaches and mapping studies; (2) unlocking the hidden favorable genetic diversity from genetic resources; or (3) discovering, validating and characterizing candidate genes behind agronomic traits or biological mechanisms by genome-wide analysis. In addition, evidence has been accumulating that heritable variation of a trait is not solely determined by DNA sequence polymorphism but involves epigenetic processes that impact chromatin structure and gene expression. Especially, with the rapid development of CRISPR-Cas technology for genome and epigenetic editing, it is believed that the promise of novel and improved crops with greater yield and tolerance to the stresses of climate change and extreme weather is around the corner.

The purpose of this Special Issue is to publish original, high-quality research papers as well as review articles addressing recent advances on plant genomics and epigenomics as emerging approaches for plant breeding. Potential topics include, but are not limited to:

  • Genotyping and marker assisted breeding

  • Gene families and their function

  • Discovery, validation and characterization of gene functions behind agronomic traits

  • Genetic diversity from plant genetic resources

  • Genome-wide association studies and their utilization

  • Comparative genomics and transcriptomics

  • Epigenetic processes in model and non-model plants

  • Genome and epigenetic editing

Prof. Dr. Klaus Humbeck
Dr. Hieu X. Cao
Dr. Sowjanya K. Sree
Dr. Wenqin Wang
Dr. Vladimir Brukhin
Dr. Giang T.H. Vu
Guest Editors

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 papers will be 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. Genes 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 1200 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 (2 papers)

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Research

Open AccessArticle Transcription Factors Responding to Pb Stress in Maize
Genes 2017, 8(9), 231; doi:10.3390/genes8090231
Received: 3 August 2017 / Revised: 7 September 2017 / Accepted: 15 September 2017 / Published: 18 September 2017
PDF Full-text (5693 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Pb can damage the physiological function of human organs by entering the human body via food-chain enrichment. Revealing the mechanisms of maize tolerance to Pb is critical for preventing this. In this study, a Pb-tolerant maize inbred line, 178, was used to analyse
[...] Read more.
Pb can damage the physiological function of human organs by entering the human body via food-chain enrichment. Revealing the mechanisms of maize tolerance to Pb is critical for preventing this. In this study, a Pb-tolerant maize inbred line, 178, was used to analyse transcription factors (TFs) expressed under Pb stress based on RNA sequencing data. A total of 464 genes expressed in control check (CK) or Pb treatment samples were annotated as TFs. Among them, 262 differentially expressed transcription factors (DETs) were identified that responded to Pb treatment. Furthermore, the DETs were classified into 4 classes according to their expression patterns, and 17, 12 and 2 DETs were significantly annotated to plant hormone signal transduction, basal transcription factors and base excision repair, respectively. Seventeen DETs were found to participate in the plant hormone signal transduction pathway, where basic leucine zippers (bZIPs) were the most significantly enriched TFs, with 12 members involved. We further obtained 5 Arabidopsis transfer DNA (T-DNA) mutants for 6 of the maize bZIPs, among which the mutants atbzip20 and atbzip47, representing ZmbZIP54 and ZmbZIP107, showed obviously inhibited growth of roots and above-ground parts, compared with wild type. Five highly Pb-tolerant and 5 highly Pb-sensitive in maize lines were subjected to DNA polymorphism and expression level analysis of ZmbZIP54 and ZmbZIP107. The results suggested that differences in bZIPs expression partially accounted for the differences in Pb-tolerance among the maize lines. Our results contribute to the understanding of the molecular regulation mechanisms of TFs in maize under Pb stress. Full article
(This article belongs to the Special Issue Plant Genomics and Epigenomics for Trait Improvement)
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Open AccessArticle Mapping of QTLs for Seed Phorbol Esters, a Toxic Chemical in Jatropha curcas (L.)
Genes 2017, 8(8), 205; doi:10.3390/genes8080205
Received: 5 July 2017 / Revised: 12 August 2017 / Accepted: 17 August 2017 / Published: 18 August 2017
PDF Full-text (2305 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Jatropha (Jatropha curcas L.) is an oil-bearing plant that has potential to be cultivated as a biodiesel crop. The seed cake after oil extraction has 40–50% protein that can be used in animal feeds. A major limitation in utilizing the cake is
[...] Read more.
Jatropha (Jatropha curcas L.) is an oil-bearing plant that has potential to be cultivated as a biodiesel crop. The seed cake after oil extraction has 40–50% protein that can be used in animal feeds. A major limitation in utilizing the cake is the presence of phorbol esters (PE), a heat-tolerant toxic chemical. To identify the quantitative trait loci (QTLs) for PE, we constructed a genetic linkage map from an F2 population of 95 individuals from a cross “Chai Nat” × “M10” using 143 simple sequence repeat (SSR) markers. M10 is low in seed PE while Chai Nat is high. Seeds from each F2 individual were quantified for PE content by high performance liquid chromatography. A single marker analysis revealed five markers from linkage group 3 (LG3) and nine markers from LG8 associated with seed PE. Inclusive composite interval mapping identified two QTLs, each on LG3 (qPE3.1) and LG8 (qPE8.1) responsible for the PE. qPE3.1 and qPE8.1 accounted for 14.10%, and 15.49% of total variation in seed PE, respectively. Alelle(s) from M10 at qPE3.1 increased seed PE, while at qPE8.1 decreased seed PE. qPE3.1 is a new loci for PE, while qPE8.1 is the same locus with that reported recently for PE. Full article
(This article belongs to the Special Issue Plant Genomics and Epigenomics for Trait Improvement)
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Figure 1

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