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Plant Genomics and Epigenomics for Trait Improvement

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

Deadline for manuscript submissions: closed (30 November 2017) | Viewed by 79616

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Special Issue Editors

Prof. Dr. Klaus Humbeck

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

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Department of Plant Embryology & Reproductive Biology, Komarov Botanical Institute RAS, 2 Professor Popov Street, 197376 Saint-Petersburg, Russia
Interests: development; sexual and asexual reproduction; genomics
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Dr. Cao Xuan Hieu

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Martin-Luther-Universität Halle-Wittenberg, Institute of Biology/Plant Physiology, Weinbergweg, D-06120, Halle (Saale), Germany
Interests: plant genomics; epigenetics; plant physiology; plant development; genome evolution; plant cytogenetics; stress tolerance; next-generation sequencing; ChIP-seq; proteomics; protein–protein interaction; genome editing
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Dr. Sowjanya Sree Kandregula

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Department of Environmental Science, Central University of Kerala, Periye 671320, India
Interests: duckweed research and applications
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Dr. Vu Thi Ha Giang

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Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany
Interests: plant genetics; plant genomics; epigenetics; genome evolution; DNA repair; chromosome biology; crop breeding; next-generation sequencing; genome editing
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Dr. Wenqin Wang

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College of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
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

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Published Papers (11 papers)

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11 pages, 1387 KiB

Open AccessCommunication

AtPAP2, a Unique Member of the PAP Family, Functions in the Plasma Membrane

by Qingqing Sun, Jinyu Li, Wenzhen Cheng, Huihong Guo, Xiaomin Liu and Hongbo Gao

Genes 2018, 9(5), 257; https://doi.org/10.3390/genes9050257 - 17 May 2018

Cited by 8 | Viewed by 4474

Abstract

Purple acid phosphatases (PAPs) play various physiological roles in plants. AtPAP2 was previously shown to localize to both chloroplasts and mitochondria and to modulate carbon metabolism in Arabidopsis. Over-expression of AtPAP2 resulted in faster growth and increased biomass in several plant species, indicating its great potential for crop improvement of phosphate use and yield. Here, we studied the localization of AtPAP2 by transient expression in tobacco leaves. The results showed AtPAP2 was localized to the plasma membrane through the secretory pathway, which is different from previous studies. We also found that AtPAP2 had a close relationship with fungal PAP2-like proteins based on phylogenetic analysis. In addition, the C-terminal transmembrane domain conserved in land plants is unique among other AtPAPs except AtPAP9, which is a close homolog of AtPAP2. Taken together, our results provide information for further study of AtPAP2 in understanding its special function in crop improvement. Full article

(This article belongs to the Special Issue Plant Genomics and Epigenomics for Trait Improvement)

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15 pages, 4515 KiB

Open AccessArticle

Genome-Wide Characterization of Heat-Shock Protein 70s from Chenopodium quinoa and Expression Analyses of Cqhsp70s in Response to Drought Stress

by Jianxia Liu, Runmei Wang, Wenying Liu, Hongli Zhang, Yaodong Guo and Riyu Wen

Genes 2018, 9(2), 35; https://doi.org/10.3390/genes9020035 - 23 Jan 2018

Cited by 44 | Viewed by 5912

Abstract

Heat-shock proteins (HSPs) are ubiquitous proteins with important roles in response to biotic and abiotic stress. The 70-kDa heat-shock genes (Hsp70s) encode a group of conserved chaperone proteins that play central roles in cellular networks of molecular chaperones and folding catalysts across all the studied organisms including bacteria, plants and animals. Several Hsp70s involved in drought tolerance have been well characterized in various plants, whereas no research on Chenopodium quinoa HSPs has been completed. Here, we analyzed the genome of C. quinoa and identified sixteen Hsp70 members in quinoa genome. Phylogenetic analysis revealed the independent origination of those Hsp70 members, with eight paralogous pairs comprising the Hsp70 family in quinoa. While the gene structure and motif analysis showed high conservation of those paralogous pairs, the synteny analysis of those paralogous pairs provided evidence for expansion coming from the polyploidy event. With several subcellular localization signals detected in CqHSP70 protein paralogous pairs, some of the paralogous proteins lost the localization information, indicating the diversity of both subcellular localizations and potential functionalities of those HSP70s. Further gene expression analyses revealed by quantitative polymerase chain reaction (qPCR) analysis illustrated the significant variations of Cqhsp70s in response to drought stress. In conclusion, the sixteen Cqhsp70s undergo lineage-specific expansions and might play important and varied roles in response to drought stress. Full article

(This article belongs to the Special Issue Plant Genomics and Epigenomics for Trait Improvement)

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13 pages, 2155 KiB

Open AccessArticle

Analysis of the Genetic Diversity and Population Structure of Austrian and Belgian Wheat Germplasm within a Regional Context Based on DArT Markers

by Mohamed A. El-Esawi, Jacques Witczak, Abd El-Fatah Abomohra, Hayssam M. Ali, Mohamed S. Elshikh and Margaret Ahmad

Genes 2018, 9(1), 47; https://doi.org/10.3390/genes9010047 - 22 Jan 2018

Cited by 25 | Viewed by 6545

Abstract

Analysis of crop genetic diversity and structure provides valuable information needed to broaden the narrow genetic base as well as to enhance the breeding and conservation strategies of crops. In this study, 95 Austrian and Belgian wheat cultivars maintained at the Centre for Genetic Resources (CGN) in the Netherlands were characterised using 1052 diversity array technology (DArT) markers to evaluate their genetic diversity, relationships and population structure. The rarefacted allelic richness recorded in the Austrian and Belgian breeding pools (A₂₅ = 1.396 and 1.341, respectively) indicated that the Austrian germplasm contained a higher genetic diversity than the Belgian pool. The expected heterozygosity (H_E) values of the Austrian and Belgian pools were 0.411 and 0.375, respectively. Moreover, the values of the polymorphic information content (PIC) of the Austrian and Belgian pools were 0.337 and 0.298, respectively. Neighbour-joining tree divided each of the Austrian and Belgian germplasm pools into two genetically distinct groups. The structure analyses of the Austrian and Belgian pools were in a complete concordance with their neighbour-joining trees. Furthermore, the 95 cultivars were compared to 618 wheat genotypes from nine European countries based on a total of 141 common DArT markers in order to place the Austrian and Belgian wheat germplasm in a wider European context. The rarefacted allelic richness (A₁₀) varied from 1.224 (Denmark) to 1.397 (Austria). Cluster and principal coordinates (PCoA) analyses divided the wheat genotypes of the nine European countries into two main clusters. The first cluster comprised the Northern and Western European wheat genotypes, whereas the second included the Central European cultivars. The structure analysis of the 618 European wheat genotypes was in a complete concordance with the results of cluster and PCoA analyses. Interestingly, a highly significant difference was recorded between regions (26.53%). In conclusion, this is the first study to reveal the high diversity levels and structure of the uncharacterised Austrian and Belgian wheat germplasm maintained at the CGN as well as place them in a wider European context. The results should help plant breeders to utilise the most promising wheat genotypes of this study in future breeding programmes for enhancing wheat cultivars. Full article

(This article belongs to the Special Issue Plant Genomics and Epigenomics for Trait Improvement)

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Open AccessArticle

High Quality Unigenes and Microsatellite Markers from Tissue Specific Transcriptome and Development of a Database in Clusterbean (Cyamopsis tetragonoloba, L. Taub)

by Hukam C. Rawal, Shrawan Kumar, Amitha Mithra S.V., Amolkumar U. Solanke, Deepti Nigam, Swati Saxena, Anshika Tyagi, Sureshkumar V., Neelam R. Yadav, Pritam Kalia, Narendra Pratap Singh, Nagendra Kumar Singh, Tilak Raj Sharma and Kishor Gaikwad

Genes 2017, 8(11), 313; https://doi.org/10.3390/genes8110313 - 9 Nov 2017

Cited by 33 | Viewed by 6862

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 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

by Piergiorgio Stevanato, Chiara Broccanello, Luca Pajola, Filippo Biscarini, Chris Richards, Lee Panella, Mahdi Hassani, Elide Formentin, Claudia Chiodi, Giuseppe Concheri and Bahram Heidari

Genes 2017, 8(10), 264; https://doi.org/10.3390/genes8100264 - 11 Oct 2017

Cited by 9 | Viewed by 5685

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 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

by Madhav P. Nepal, Ethan J. Andersen, Surendra Neupane and Benjamin V. Benson

Genes 2017, 8(10), 249; https://doi.org/10.3390/genes8100249 - 30 Sep 2017

Cited by 20 | Viewed by 8229

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 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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5693 KiB

Open AccessArticle

Transcription Factors Responding to Pb Stress in Maize

by Yanling Zhang, Fei Ge, Fengxia Hou, Wenting Sun, Qi Zheng, Xiaoxiang Zhang, Langlang Ma, Jun Fu, Xiujing He, Huanwei Peng, Guangtang Pan and Yaou Shen

Genes 2017, 8(9), 231; https://doi.org/10.3390/genes8090231 - 18 Sep 2017

Cited by 22 | Viewed by 4378

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 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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2305 KiB

Open AccessArticle

Mapping of QTLs for Seed Phorbol Esters, a Toxic Chemical in Jatropha curcas (L.)

by Kitiya Amkul, Kularb Laosatit, Prakit Somta, Sangrea Shim, Suk-Ha Lee, Patcharin Tanya and Peerasak Srinives

Genes 2017, 8(8), 205; https://doi.org/10.3390/genes8080205 - 18 Aug 2017

Cited by 11 | Viewed by 4676

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 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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Review

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16 pages, 529 KiB

Open AccessReview

Single-Cell Genomic Analysis in Plants

by Yuxuan Yuan, HueyTyng Lee, Haifei Hu, Armin Scheben and David Edwards

Genes 2018, 9(1), 50; https://doi.org/10.3390/genes9010050 - 22 Jan 2018

Cited by 30 | Viewed by 9031

Abstract

Individual cells in an organism are variable, which strongly impacts cellular processes. Advances in sequencing technologies have enabled single-cell genomic analysis to become widespread, addressing shortcomings of analyses conducted on populations of bulk cells. While the field of single-cell plant genomics is in its infancy, there is great potential to gain insights into cell lineage and functional cell types to help understand complex cellular interactions in plants. In this review, we discuss current approaches for single-cell plant genomic analysis, with a focus on single-cell isolation, DNA amplification, next-generation sequencing, and bioinformatics analysis. We outline the technical challenges of analysing material from a single plant cell, and then examine applications of single-cell genomics and the integration of this approach with genome editing. Finally, we indicate future directions we expect in the rapidly developing field of plant single-cell genomic analysis. Full article

(This article belongs to the Special Issue Plant Genomics and Epigenomics for Trait Improvement)

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15 pages, 1092 KiB

Open AccessReview

Isoform Sequencing and State-of-Art Applications for Unravelling Complexity of Plant Transcriptomes

by Dong An, Hieu X. Cao, Changsheng Li, Klaus Humbeck and Wenqin Wang

Genes 2018, 9(1), 43; https://doi.org/10.3390/genes9010043 - 18 Jan 2018

Cited by 46 | Viewed by 10475

Abstract

Single-molecule real-time (SMRT) sequencing developed by PacBio, also called third-generation sequencing (TGS), offers longer reads than the second-generation sequencing (SGS). Given its ability to obtain full-length transcripts without assembly, isoform sequencing (Iso-Seq) of transcriptomes by PacBio is advantageous for genome annotation, identification of novel genes and isoforms, as well as the discovery of long non-coding RNA (lncRNA). In addition, Iso-Seq gives access to the direct detection of alternative splicing, alternative polyadenylation (APA), gene fusion, and DNA modifications. Such applications of Iso-Seq facilitate the understanding of gene structure, post-transcriptional regulatory networks, and subsequently proteomic diversity. In this review, we summarize its applications in plant transcriptome study, specifically pointing out challenges associated with each step in the experimental design and highlight the development of bioinformatic pipelines. We aim to provide the community with an integrative overview and a comprehensive guidance to Iso-Seq, and thus to promote its applications in plant research. Full article

(This article belongs to the Special Issue Plant Genomics and Epigenomics for Trait Improvement)

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719 KiB

Open AccessReview

Genome Sequencing and Assembly by Long Reads in Plants

by Changsheng Li, Feng Lin, Dong An, Wenqin Wang and Ruidong Huang

Genes 2018, 9(1), 6; https://doi.org/10.3390/genes9010006 - 28 Dec 2017

Cited by 72 | Viewed by 11514

Abstract

Plant genomes generated by Sanger and Next Generation Sequencing (NGS) have provided insight into species diversity and evolution. However, Sanger sequencing is limited in its applications due to high cost, labor intensity, and low throughput, while NGS reads are too short to resolve abundant repeats and polyploidy, leading to incomplete or ambiguous assemblies. The advent and improvement of long-read sequencing by Third Generation Sequencing (TGS) methods such as PacBio and Nanopore have shown promise in producing high-quality assemblies for complex genomes. Here, we review the development of sequencing, introducing the application as well as considerations of experimental design in TGS of plant genomes. We also introduce recent revolutionary scaffolding technologies including BioNano, Hi-C, and 10× Genomics. We expect that the informative guidance for genome sequencing and assembly by long reads will benefit the initiation of scientists’ projects. Full article

(This article belongs to the Special Issue Plant Genomics and Epigenomics for Trait Improvement)

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