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

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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 (5 papers)

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Research

Open AccessArticle High Quality Unigenes and Microsatellite Markers from Tissue Specific Transcriptome and Development of a Database in Clusterbean (Cyamopsis tetragonoloba, L. Taub)
Genes 2017, 8(11), 313; doi:10.3390/genes8110313
Received: 23 August 2017 / Revised: 23 October 2017 / Accepted: 6 November 2017 / Published: 9 November 2017
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Abstract
Clusterbean (Cyamopsis tetragonoloba L. Taub), is an important industrial, vegetable and forage crop. This crop owes its commercial importance to the presence of guar gum (galactomannans) in its endosperm which is used as a lubricant in a range of industries. Despite its
[...] Read more.
Clusterbean (Cyamopsis tetragonoloba L. Taub), is an important industrial, vegetable and forage crop. This crop owes its commercial importance to the presence of guar gum (galactomannans) in its endosperm which is used as a lubricant in a range of industries. Despite its relevance to agriculture and industry, genomic resources available in this crop are limited. Therefore, the present study was undertaken to generate RNA-Seq based transcriptome from leaf, shoot, and flower tissues. A total of 145 million high quality Illumina reads were assembled using Trinity into 127,706 transcripts and 48,007 non-redundant high quality (HQ) unigenes. We annotated 79% unigenes against Plant Genes from the National Center for Biotechnology Information (NCBI), Swiss-Prot, Pfam, gene ontology (GO) and KEGG databases. Among the annotated unigenes, 30,020 were assigned with 116,964 GO terms, 9984 with EC and 6111 with 137 KEGG pathways. At different fragments per kilobase of transcript per millions fragments sequenced (FPKM) levels, genes were found expressed higher in flower tissue followed by shoot and leaf. Additionally, we identified 8687 potential simple sequence repeats (SSRs) with an average frequency of one SSR per 8.75 kb. A total of 28 amplified SSRs in 21 clusterbean genotypes resulted in polymorphism in 13 markers with average polymorphic information content (PIC) of 0.21. We also constructed a database named ‘ClustergeneDB’ for easy retrieval of unigenes and the microsatellite markers. The tissue specific genes identified and the molecular marker resources developed in this study is expected to aid in genetic improvement of clusterbean for its end use. Full article
(This article belongs to the Special Issue Plant Genomics and Epigenomics for Trait Improvement)
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Open AccessArticle Targeted Next-Generation Sequencing Identification of Mutations in Disease Resistance Gene Analogs (RGAs) in Wild and Cultivated Beets
Genes 2017, 8(10), 264; doi:10.3390/genes8100264
Received: 3 September 2017 / Revised: 2 October 2017 / Accepted: 4 October 2017 / Published: 11 October 2017
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Abstract
Resistance gene analogs (RGAs) were searched bioinformatically in the sugar beet (Beta vulgaris L.) genome as potential candidates for improving resistance against different diseases. In the present study, Ion Torrent sequencing technology was used to identify mutations in 21 RGAs. The DNA
[...] Read more.
Resistance gene analogs (RGAs) were searched bioinformatically in the sugar beet (Beta vulgaris L.) genome as potential candidates for improving resistance against different diseases. In the present study, Ion Torrent sequencing technology was used to identify mutations in 21 RGAs. The DNA samples of ninety-six individuals from six sea beets (Beta vulgaris L. subsp. maritima) and six sugar beet pollinators (eight individuals each) were used for the discovery of single-nucleotide polymorphisms (SNPs). Target amplicons of about 200 bp in length were designed with the Ion AmpliSeq Designer system in order to cover the DNA sequences of the RGAs. The number of SNPs ranged from 0 in four individuals to 278 in the pollinator R740 (which is resistant to rhizomania infection). Among different groups of beets, cytoplasmic male sterile lines had the highest number of SNPs (132) whereas the lowest number of SNPs belonged to O-types (95). The principal coordinates analysis (PCoA) showed that the polymorphisms inside the gene Bv8_184910_pkon (including the CCCTCC sequence) can effectively differentiate wild from cultivated beets, pointing at a possible mutation associated to rhizomania resistance that originated directly from cultivated beets. This is unlike other resistance sources that are introgressed from wild beets. This gene belongs to the receptor-like kinase (RLK) class of RGAs, and is associated to a hypothetical protein. In conclusion, this first report of using Ion Torrent sequencing technology in beet germplasm suggests that the identified sequence CCCTCC can be used in marker-assisted programs to differentiate wild from domestic beets and to identify other unknown disease resistance genes in beet. Full article
(This article belongs to the Special Issue Plant Genomics and Epigenomics for Trait Improvement)
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Open AccessArticle Comparative Genomics of Non-TNL Disease Resistance Genes from Six Plant Species
Genes 2017, 8(10), 249; doi:10.3390/genes8100249
Received: 12 July 2017 / Revised: 14 September 2017 / Accepted: 20 September 2017 / Published: 30 September 2017
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Abstract
Disease resistance genes (R genes), as part of the plant defense system, have coevolved with corresponding pathogen molecules. The main objectives of this project were to identify non-Toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (nTNL) genes and elucidate their evolutionary divergence across six
[...] Read more.
Disease resistance genes (R genes), as part of the plant defense system, have coevolved with corresponding pathogen molecules. The main objectives of this project were to identify non-Toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (nTNL) genes and elucidate their evolutionary divergence across six plant genomes. Using reference sequences from Arabidopsis, we investigated nTNL orthologs in the genomes of common bean, Medicago, soybean, poplar, and rice. We used Hidden Markov Models for sequence identification, performed model-based phylogenetic analyses, visualized chromosomal positioning, inferred gene clustering, and assessed gene expression profiles. We analyzed 908 nTNL R genes in the genomes of the six plant species, and classified them into 12 subgroups based on the presence of coiled-coil (CC), nucleotide binding site (NBS), leucine rich repeat (LRR), resistance to Powdery mildew 8 (RPW8), and BED type zinc finger domains. Traditionally classified CC-NBS-LRR (CNL) genes were nested into four clades (CNL A-D) often with abundant, well-supported homogeneous subclades of Type-II R genes. CNL-D members were absent in rice, indicating a unique R gene retention pattern in the rice genome. Genomes from Arabidopsis, common bean, poplar and soybean had one chromosome without any CNL R genes. Medicago and Arabidopsis had the highest and lowest number of gene clusters, respectively. Gene expression analyses suggested unique patterns of expression for each of the CNL clades. Differential gene expression patterns of the nTNL genes were often found to correlate with number of introns and GC content, suggesting structural and functional divergence. Full article
(This article belongs to the Special Issue Plant Genomics and Epigenomics for Trait Improvement)
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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
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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
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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
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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
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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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