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Agronomy
Special Issues
Bioinformatics Applied to Genetic Improvement of Crop Species
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Bioinformatics Applied to Genetic Improvement of Crop Species

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

Deadline for manuscript submissions: closed (15 March 2020) | Viewed by 13820

Special Issue Editor

Dr. Nunzio D'Agostino

E-Mail Website
Guest Editor
Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
Interests: bioinformatics; computational biology; genomics; transcriptomics; population genomics; molecular breeding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

It is well known to you all that the huge amount of “omics” data points available is demanding and challenging in its analysis, management, and accessibility. Bioinformatics plays a key role in data mining and knowledge discovery and has the potential, together with the most recent and breakthrough technologies, to accelerate crop improvement in a scenario of increasing climate changes.

Major advances in sequencing technologies and bioinformatics have allowed a huge leap forward in the ability to explore the “sequence space” in order to identify useful/superior alleles and haplotypes to be used in breeding programs as well as in the discovery of significant associations between genetic markers and important agronomic traits.

In this Special Issue, we would like to consider submissions of high-quality original research or review (Mini Review) articles on topics that remark on the crucial role of bioinformatics in the analysis and interpretation of data and in the application of the acquired knowledge to develop novel cultivars and expedite the rate of genetic gains. Submissions should be in line with the journal's scope.

Dr. Nunzio D'Agostino
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.

Keywords

  • bioinformatics
  • “omics” data
  • data mining
  • next generation sequencing
  • RNA-sequencing
  • gene expression profiling
  • genetic diversity
  • single nucleotide polymorphisms
  • genome-wide association studies
  • genomic selections

Published Papers (4 papers)

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Research

15 pages, 2681 KiB  
Article
Bioinformatic Extraction of Functional Genetic Diversity from Heterogeneous Germplasm Collections for Crop Improvement
by Patrick A. Reeves, Hannah M. Tetreault and Christopher M. Richards
Agronomy 2020, 10(4), 593; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy10040593 - 22 Apr 2020
Cited by 6 | Viewed by 2661
Abstract
Efficient utilization of genetic variation in plant germplasm collections is impeded by large collection size, uneven characterization of traits, and unpredictable apportionment of allelic diversity among heterogeneous accessions. Distributing compact subsets of the complete collection that contain maximum allelic diversity at functional loci [...] Read more.
Efficient utilization of genetic variation in plant germplasm collections is impeded by large collection size, uneven characterization of traits, and unpredictable apportionment of allelic diversity among heterogeneous accessions. Distributing compact subsets of the complete collection that contain maximum allelic diversity at functional loci of interest could streamline conventional and precision breeding. Using heterogeneous population samples from Arabidopsis, Populus and sorghum, we show that genomewide single nucleotide polymorphism (SNP) data permits the capture of 3–78 fold more haplotypic diversity in subsets than geographic or environmental data, which are commonly used surrogate predictors of genetic diversity. Using a large genomewide SNP data set from landrace sorghum, we demonstrate three bioinformatic approaches to extract functional genetic diversity. First, in a “candidate gene” approach, we assembled subsets that maximized haplotypic diversity at 135 putative lignin biosynthetic loci, relevant to biomass breeding programs. Secondly, we applied a keyword search against the Gene Ontology to identify 1040 regulatory loci and assembled subsets capturing genomewide regulatory gene diversity, a general source of phenotypic variation. Third, we developed a machine-learning approach to rank semantic similarity between Gene Ontology term definitions and the textual content of scientific publications on crop adaptation to climate, a complex breeding objective. We identified 505 sorghum loci whose defined function is semantically-related to climate adaptation concepts. The assembled subsets could be used to address climatic pressures on sorghum production. To face impending agricultural challenges and foster rapid extraction and use of novel genetic diversity resident in heterogeneous germplasm collections, whole genome resequencing efforts should be prioritized. Full article
(This article belongs to the Special Issue Bioinformatics Applied to Genetic Improvement of Crop Species)
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18 pages, 2882 KiB  
Article
Marginal Grapevine Germplasm from Apulia (Southern Italy) Represents an Unexplored Source of Genetic Diversity
by Monica Marilena Miazzi, Nunzio D’Agostino, Valentina di Rienzo, Pasquale Venerito, Vito Nicola Savino, Vincenzo Fucilli, Paola Ruffa, Vincenzo Roseti, Costantino Pirolo, Pierfederico La Notte, Cinzia Montemurro and Francesca Taranto
Agronomy 2020, 10(4), 563; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy10040563 - 14 Apr 2020
Cited by 11 | Viewed by 3021
Abstract
The investigation on the genetic diversity of grapevine germplasm is crucial for a more efficient use of grapevine genetic resources in light of changing environmental conditions. Here, we used simple sequence repeats (SSRs) coupled with single nucleotide polymorphism (SNP) markers to disclose grapevine [...] Read more.
The investigation on the genetic diversity of grapevine germplasm is crucial for a more efficient use of grapevine genetic resources in light of changing environmental conditions. Here, we used simple sequence repeats (SSRs) coupled with single nucleotide polymorphism (SNP) markers to disclose grapevine genetic diversity of a collection of Apulian minor/neglected genotypes. Their relationships with national or international cultivars were also examined. Genetic diversity was investigated using 10 SSR markers and 1,178 SNPs generated by genotyping by sequencing (GBS). Based on the SSR data, the 128 genotypes were classified into six main genetic clusters. Twenty-four putative cases of synonymy and 2 of misnamings were detected. Ten “unknown” autochthonous genotypes did not show high similarity to Apulian, national, or international varieties. We took advantage of available GBS-derived SNP data points for only forty genotypes to better investigate the genetic distance among them, identify private SNP alleles, and divergent loci putatively under selection. Based on SNP alleles, two interesting gene pools of minor/neglected Apulian samples were identified. Genetic divergence was investigated by FST and allowed the detection of loci capable of differentiating the gene pools. Overall, this work emphasizes the need for recovering the untapped genetic variability that characterizes minor/neglected grapevine Apulian genotypes and the requirement to preserve and use more efficiently grapevine genetic resources in breeding programs. Full article
(This article belongs to the Special Issue Bioinformatics Applied to Genetic Improvement of Crop Species)
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14 pages, 2146 KiB  
Article
Propagation Fidelity and Kinship of Tomato Varieties ‘UC 82’ and ‘M82’ Revealed by Analysis of Sequence Variation
by Vladimir Cambiaso, Gustavo Rubén Rodríguez and David Merrill Francis
Agronomy 2020, 10(4), 538; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy10040538 - 09 Apr 2020
Cited by 3 | Viewed by 3045
Abstract
Plant varieties are named and released based on distinct, unique and stable characteristics but may be maintained separately by genebanks or stock centers under separate accession identification numbers. Genetic heterogeneity of the original variety, genetic drift, failure to exclude cross pollination, and propagation [...] Read more.
Plant varieties are named and released based on distinct, unique and stable characteristics but may be maintained separately by genebanks or stock centers under separate accession identification numbers. Genetic heterogeneity of the original variety, genetic drift, failure to exclude cross pollination, and propagation error may erode the integrity of genetic resources. The availability of resequencing and genotyping data for duplicate samples enables an analysis to clarify the relationship between specific varieties or independently curated accessions of the same variety while also assessing the fidelity of germplasm maintenance. We accessed both Single Nucleotide Polymorphism (SNP) array genotypes and resequencing data for two important tomato varieties ‘UC 82’and ‘M82’ that have been maintained as separate accessions in collections as important resources for the research and breeding communities. Our analysis of these data suggests that polymorphism rates from resequencing of cultivated tomato are overestimated in the literature due to heterozygous calls caused by either sequence error or coalignment of repetitive sequences. We defined a set of 32,352 robust SNPs from a file containing data for all samples and we compared the distribution of data with SNPs called from a genotyping array. For both analyses, intravariety variation was found in haplotype blocks, with the same haplotypes identified using SNPs detected from array and sequence data. The distribution pattern of variation across the entire genome sequence was similar for both ‘UC 82’and ‘M82’. Overall, the differences between distinct accessions of a variety were nearly as great as the differences between ‘UC 82’and ‘M82’. The similarities between ‘UC82’ and ‘M82’ range from 99.33% to 99.74% and are highly consistent with a common pedigree and shared selection from partially inbred progeny. The data also suggest that these tomato genetic resources have been propagated with high fidelity. Full article
(This article belongs to the Special Issue Bioinformatics Applied to Genetic Improvement of Crop Species)
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25 pages, 5686 KiB  
Article
Genome-Wide Identification, Structure Characterization, and Expression Profiling of Dof Transcription Factor Gene Family in Wheat (Triticum aestivum L.)
by Zhengwu Fang, Wenqiang Jiang, Yiqin He, Dongfang Ma, Yike Liu, Shuping Wang, Yingxin Zhang and Junliang Yin
Agronomy 2020, 10(2), 294; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy10020294 - 19 Feb 2020
Cited by 35 | Viewed by 4315
Abstract
DNA binding with one finger (Dof) proteins are plant-specific transcription factors with crucial roles in plant growth and stress response. Even so, little is known about them in wheat. In this study, 108 wheat Dof (TaDof) genes across 21 chromosomes were detected. Although [...] Read more.
DNA binding with one finger (Dof) proteins are plant-specific transcription factors with crucial roles in plant growth and stress response. Even so, little is known about them in wheat. In this study, 108 wheat Dof (TaDof) genes across 21 chromosomes were detected. Although variable in sequence length, molecular weight, and isoelectric point, all TaDof proteins contained conserved zinc-finger structures and were phylogenetically divided into 7 sub-groups. Exon/intron and motif analyses suggested that TaDof structures and conserved motifs were similar within sub-groups but diverse among sub-groups. Many segmental duplications were identified and Ka/Ks and inter-species synthetic analyses indicated that polyploidization was main reason for increased number of TaDofs. Prediction and experimental confirmation revealed that TaDofs functioned as transcription factors in the nucleus. Expression pattern profiling showed that TaDofs specifically affected growth and development, and biotic and abiotic stress responses. Wheat miRNAs and cis-regulator were predicted as essential players in molding TaDofs expression patterns. qRT-PCR analysis revealed that TaDofs were induced by salt and drought stresses. Customized annotation revealed that TaDofs were widely involved in phytohormone response, defense, growth and development, and metabolism. Our study provided a comprehensive understanding to wheat TaDofs. Full article
(This article belongs to the Special Issue Bioinformatics Applied to Genetic Improvement of Crop Species)
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