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Special Issue "Functional Genomics for Plant Breeding"

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: 30 November 2020.

Special Issue Editors

Dr. Fatemeh Maghuly
Website
Guest Editor
Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, VIBT, Muthgasse 18, 1190, Vienna, Austria
Interests: plant functional genomics; plant breeding; plant physiology; population genetics; omic strategies and molecular biology
Dr. Joanna Jankowicz-Cieślak
Website
Guest Editor
Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division on Nuclear Techniques in Food and Agriculture, Department of Nuclear Applications, International Atomic Energy Agency, A-1400 Vienna, Austria
Interests: plant biotechnology; mutations; forward and reverse genetics; functional genomics; biotic and abiotic stresses; molecular breeding
Dr. Bradley John Till
Website
Guest Editor
Genomics Unit. CGNA, Temuco, Chile
Interests: reverse-genetics; TILLING; induced mutations; population genomics; comparative genomics; understudied crops; domestication; climate adaptation; bioinformatics
Dr. Beata Myśków
Website
Guest Editor
Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology in Szczecin (ZUT)), Szczecin, Poland
Interests: genetic mapping; crop breeding; quantitative traits loci (QTL); drought stress; earliness; pre-harvest sprouting
Dr. Ilona Czyczyło-Mysza
Website
Guest Editor
Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Poland
Interests: plant physiology; phenotyping; quantitative traits loci (QTL); drought stress; plant molecular biology; tissue cultures; double haploids

Special Issue Information

Dear Colleagues,

Next-generation genome sequencing technology in plants has accelerated the generation of multiomic data at the DNA, RNA, protein, and metabolite levels, leading to a new era of "big data". This can provide us an integrative view, and opens up new possibilities to draw attention to the importance of recording and analyzing large-scale omics data obtained in different systems and their relationship to phenotypes, and also for understanding how the exploration of these relationships can be used for management intervention and agricultural innovation in breeding programs.

Large-scale sequence-based markers and precise phenotypic data provide a crucial basis for the application of GWAS and QTL-mapping analysis. Besides, genomic research has facilitated and accelerated the breeding process and offers applications for genetic improvement such as GS, MAS, and gene pyramiding.

On the other hand, it is not just the sequence of plant DNA that matters: how do some genes get activated, and why are others silenced? How can genomics facilitate the study of complex traits in plant breeding? These are questions of widespread interest, and genome editing has shown to be a crucial tool for functional genomic research that could be utilized as a precision-breeding approach for any programs seeking to improve traits of interest.

This Special Issue, “Functional Genomics for Plant Breeding”, will cover a selection of research topics and review articles regarding the recent development of genomics, epigenomics, and epitranscriptomics, that can enhance breeding strategies to shorten the time and efficiency of development of new crop cultivars.

Dr. Fatemeh Maghuly
Dr. Bradley John Till
Dr. Beata Myśków
Dr. Ilona Czyczyło-Mysza
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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 (7 papers)

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Research

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Open AccessArticle
Al-Tolerant Barley Mutant hvatr.g Shows the ATR-Regulated DNA Damage Response to Maleic Acid Hydrazide
Int. J. Mol. Sci. 2020, 21(22), 8500; https://doi.org/10.3390/ijms21228500 - 12 Nov 2020
Abstract
ATR, a DNA damage signaling kinase, is required for cell cycle checkpoint regulation and detecting DNA damage caused by genotoxic factors including Al3+ ions. We analyzed the function of the HvATR gene in response to chemical clastogen-maleic acid hydrazide (MH). For this [...] Read more.
ATR, a DNA damage signaling kinase, is required for cell cycle checkpoint regulation and detecting DNA damage caused by genotoxic factors including Al3+ ions. We analyzed the function of the HvATR gene in response to chemical clastogen-maleic acid hydrazide (MH). For this purpose, the Al-tolerant barley TILLING mutant hvatr.g was used. We described the effects of MH on the nuclear genome of hvatr.g mutant and its WT parent cv. “Sebastian”, showing that the genotoxic effect measured by TUNEL test and frequency of cells with micronuclei was much stronger in hvatr.g than in WT. MH caused a significant decrease in the mitotic activity of root cells in both genotypes, however this effect was significantly stronger in “Sebastian”. The impact of MH on the roots cell cycle, analyzed using flow cytometry, showed no differences between the mutant and WT. Full article
(This article belongs to the Special Issue Functional Genomics for Plant Breeding)
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Open AccessArticle
Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L.
Int. J. Mol. Sci. 2020, 21(21), 8148; https://doi.org/10.3390/ijms21218148 - 31 Oct 2020
Abstract
The wide natural variation present in rice is an important source of genes to facilitate stress tolerance breeding. However, identification of candidate genes from RNA-Seq studies is hampered by the lack of high-quality genome assemblies for the most stress tolerant cultivars. A more [...] Read more.
The wide natural variation present in rice is an important source of genes to facilitate stress tolerance breeding. However, identification of candidate genes from RNA-Seq studies is hampered by the lack of high-quality genome assemblies for the most stress tolerant cultivars. A more targeted solution is the reconstruction of transcriptomes to provide templates to map RNA-seq reads. Here, we sequenced transcriptomes of ten rice cultivars of three subspecies on the PacBio Sequel platform. RNA was isolated from different organs of plants grown under control and abiotic stress conditions in different environments. Reconstructed de novo reference transcriptomes resulted in 37,500 to 54,600 plant-specific high-quality isoforms per cultivar. Isoforms were collapsed to reduce sequence redundancy and evaluated, e.g., for protein completeness (BUSCO). About 40% of all identified transcripts were novel isoforms compared to the Nipponbare reference transcriptome. For the drought/heat tolerant aus cultivar N22, 56 differentially expressed genes in developing seeds were identified at combined heat and drought in the field. The newly generated rice transcriptomes are useful to identify candidate genes for stress tolerance breeding not present in the reference transcriptomes/genomes. In addition, our approach provides a cost-effective alternative to genome sequencing for identification of candidate genes in highly stress tolerant genotypes. Full article
(This article belongs to the Special Issue Functional Genomics for Plant Breeding)
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Open AccessArticle
How Machine Learning Methods Helped Find Putative Rye Wax Genes Among GBS Data
Int. J. Mol. Sci. 2020, 21(20), 7501; https://doi.org/10.3390/ijms21207501 - 12 Oct 2020
Abstract
The standard approach to genetic mapping was supplemented by machine learning (ML) to establish the location of the rye gene associated with epicuticular wax formation (glaucous phenotype). Over 180 plants of the biparental F2 population were genotyped with the DArTseq (sequencing-based diversity [...] Read more.
The standard approach to genetic mapping was supplemented by machine learning (ML) to establish the location of the rye gene associated with epicuticular wax formation (glaucous phenotype). Over 180 plants of the biparental F2 population were genotyped with the DArTseq (sequencing-based diversity array technology). A maximum likelihood (MLH) algorithm (JoinMap 5.0) and three ML algorithms: logistic regression (LR), random forest and extreme gradient boosted trees (XGBoost), were used to select markers closely linked to the gene encoding wax layer. The allele conditioning the nonglaucous appearance of plants, derived from the cultivar Karlikovaja Zelenostebelnaja, was mapped at the chromosome 2R, which is the first report on this localization. The DNA sequence of DArT-Silico 3585843, closely linked to wax segregation detected by using ML methods, was indicated as one of the candidates controlling the studied trait. The putative gene encodes the ABCG11 transporter. Full article
(This article belongs to the Special Issue Functional Genomics for Plant Breeding)
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Open AccessArticle
Silencing of HvGSK1.1—A GSK3/SHAGGY-Like Kinase–Enhances Barley (Hordeum vulgare L.) Growth in Normal and in Salt Stress Conditions
Int. J. Mol. Sci. 2020, 21(18), 6616; https://doi.org/10.3390/ijms21186616 - 10 Sep 2020
Abstract
Glycogen synthase kinase 3 (GSK3) is a highly conserved kinase present in all eukaryotes and functions as a key regulator of a wide range of physiological and developmental processes. The kinase, known in land plants as GSK3/SHAGGY-like kinase (GSK), is a key player [...] Read more.
Glycogen synthase kinase 3 (GSK3) is a highly conserved kinase present in all eukaryotes and functions as a key regulator of a wide range of physiological and developmental processes. The kinase, known in land plants as GSK3/SHAGGY-like kinase (GSK), is a key player in the brassinosteroid (BR) signaling pathway. The GSK genes, through the BRs, affect diverse developmental processes and modulate responses to environmental factors. In this work, we describe functional analysis of HvGSK1.1, which is one of the GSK3/SHAGGY-like orthologs in barley. The RNAi-mediated silencing of the target HvGSK1.1 gene was associated with modified expression of its paralogs HvGSK1.2, HvGSK2.1, HvGSK3.1, and HvGSK4.1 in plants grown in normal and in salt stress conditions. Low nucleotide similarity between the silencing fragment and barley GSK genes and the presence of BR-dependent transcription factors’ binding sites in promoter regions of barley and rice GSK genes imply an innate mechanism responsible for co-regulation of the genes. The results of the leaf inclination assay indicated that silencing of HvGSK1.1 and the changes of GSK paralogs enhanced the BR-dependent signaling in the plants. The strongest phenotype of transgenic lines with downregulated HvGSK1.1 and GSK paralogs had greater biomass of the seedlings grown in normal conditions and salt stress as well as elevated kernel weight of plants grown in normal conditions. Both traits showed a strong negative correlation with the transcript level of the target gene and the paralogs. The characteristics of barley lines with silenced expression of HvGSK1.1 are compatible with the expected phenotypes of plants with enhanced BR signaling. The results show that manipulation of the GSK-encoding genes provides data to explore their biological functions and confirm it as a feasible strategy to generate plants with improved agricultural traits. Full article
(This article belongs to the Special Issue Functional Genomics for Plant Breeding)
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Open AccessArticle
Combination of Linkage Mapping, GWAS, and GP to Dissect the Genetic Basis of Common Rust Resistance in Tropical Maize Germplasm
Int. J. Mol. Sci. 2020, 21(18), 6518; https://doi.org/10.3390/ijms21186518 - 06 Sep 2020
Abstract
Common rust (CR) caused by Puccina sorghi is one of the destructive fungal foliar diseases of maize and has been reported to cause moderate to high yield losses. Providing CR resistant germplasm has the potential to increase yields. To dissect the genetic architecture [...] Read more.
Common rust (CR) caused by Puccina sorghi is one of the destructive fungal foliar diseases of maize and has been reported to cause moderate to high yield losses. Providing CR resistant germplasm has the potential to increase yields. To dissect the genetic architecture of CR resistance in maize, association mapping, in conjunction with linkage mapping, joint linkage association mapping (JLAM), and genomic prediction (GP) was conducted on an association-mapping panel and five F3 biparental populations using genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs). Analysis of variance for the biparental populations and the association panel showed significant genotypic and genotype x environment (GXE) interaction variances except for GXE of Pop4. Heritability (h2) estimates were moderate with 0.37–0.45 for the individual F3 populations, 0.45 across five populations and 0.65 for the association panel. Genome-wide association study (GWAS) analyses revealed 14 significant marker-trait associations which individually explained 6–10% of the total phenotypic variances. Individual population-based linkage analysis revealed 26 QTLs associated with CR resistance and together explained 14–40% of the total phenotypic variances. Linkage mapping revealed seven QTLs in pop1, nine QTL in pop2, four QTL in pop3, five QTL in pop4, and one QTL in pop5, distributed on all chromosomes except chromosome 10. JLAM for the 921 F3 families from five populations detected 18 QTLs distributed in all chromosomes except on chromosome 8. These QTLs individually explained 0.3 to 3.1% and together explained 45% of the total phenotypic variance. Among the 18 QTL detected through JLAM, six QTLs, qCR1-78, qCR1-227, qCR3-172, qCR3-186, qCR4-171, and qCR7-137 were also detected in linkage mapping. GP within population revealed low to moderate correlations with a range from 0.19 to 0.51. Prediction correlation was high with r = 0.78 for combined analysis of the five F3 populations. Prediction of biparental populations by using association panel as training set reveals positive correlations ranging from 0.05 to 0.22, which encourages to develop an independent but related population as a training set which can be used to predict diverse but related populations. The findings of this study provide valuable information on understanding the genetic basis of CR resistance and the obtained information can be used for developing functional molecular markers for marker-assisted selection and for implementing GP to improve CR resistance in tropical maize. Full article
(This article belongs to the Special Issue Functional Genomics for Plant Breeding)
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Open AccessArticle
Mining for Candidate Genes Controlling Secondary Growth of the Carrot Storage Root
Int. J. Mol. Sci. 2020, 21(12), 4263; https://doi.org/10.3390/ijms21124263 - 15 Jun 2020
Abstract
Background: Diverse groups of carrot cultivars have been developed to meet consumer demands and industry needs. Varietal groups of the cultivated carrot are defined based on the shape of roots. However, little is known about the genetic basis of root shape determination. Methods: [...] Read more.
Background: Diverse groups of carrot cultivars have been developed to meet consumer demands and industry needs. Varietal groups of the cultivated carrot are defined based on the shape of roots. However, little is known about the genetic basis of root shape determination. Methods: Here, we used 307 carrot plants from 103 open-pollinated cultivars for a genome wide association study to identify genomic regions associated with the storage root morphology. Results: A 180 kb-long region on carrot chromosome 1 explained 10% of the total observed phenotypic variance in the shoulder diameter. Within that region, DcDCAF1 and DcBTAF1 genes were proposed as candidates controlling secondary growth of the carrot storage root. Their expression profiles differed between the cultivated and the wild carrots, likely indicating that their elevated expression was required for the development of edible roots. They also showed higher expression at the secondary root growth stage in cultivars producing thick roots, as compared to those developing thin roots. Conclusions: We provided evidence for a likely involvement of DcDCAF1 and/or DcBTAF1 in the development of the carrot storage root and developed a genotyping assay facilitating the identification of variants in the region on carrot chromosome 1 associated with secondary growth of the carrot root. Full article
(This article belongs to the Special Issue Functional Genomics for Plant Breeding)
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Review

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Open AccessReview
Functional Markers for Precision Plant Breeding
Int. J. Mol. Sci. 2020, 21(13), 4792; https://doi.org/10.3390/ijms21134792 - 06 Jul 2020
Abstract
Advances in molecular biology including genomics, high-throughput sequencing, and genome editing enable increasingly faster and more precise cultivar development. Identifying genes and functional markers (FMs) that are highly associated with plant phenotypic variation is a grand challenge. Functional genomics approaches such as transcriptomics, [...] Read more.
Advances in molecular biology including genomics, high-throughput sequencing, and genome editing enable increasingly faster and more precise cultivar development. Identifying genes and functional markers (FMs) that are highly associated with plant phenotypic variation is a grand challenge. Functional genomics approaches such as transcriptomics, targeting induced local lesions in genomes (TILLING), homologous recombinant (HR), association mapping, and allele mining are all strategies to identify FMs for breeding goals, such as agronomic traits and biotic and abiotic stress resistance. The advantage of FMs over other markers used in plant breeding is the close genomic association of an FM with a phenotype. Thereby, FMs may facilitate the direct selection of genes associated with phenotypic traits, which serves to increase selection efficiencies to develop varieties. Herein, we review the latest methods in FM development and how FMs are being used in precision breeding for agronomic and quality traits as well as in breeding for biotic and abiotic stress resistance using marker assisted selection (MAS) methods. In summary, this article describes the use of FMs in breeding for development of elite crop cultivars to enhance global food security goals. Full article
(This article belongs to the Special Issue Functional Genomics for Plant Breeding)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Functional Markers for Precision Plant Breeding

Authors: Romesh K. Salgotra and C. Neal Stewart, Jr

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