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Plants
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Genomics for Plant Breeding 2020–2021
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Genomics for Plant Breeding 2020–2021

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (15 April 2021) | Viewed by 13073

Special Issue Editors

Prof. Dr. Gianni Barcaccia

E-Mail Website1 Website2
Guest Editor
Laboratory of Genomics for Breeding, Department of Agronomy, Food, Natural resources, Animals and Environment—DAFNAE, University of Padova, Campus of Agripolis—Legnaro, 35020 Padova, Italy
Interests: plant genetics; plant reproductive systems and population genetics; genomics applied to plant breeding
Special Issues, Collections and Topics in MDPI journals
Dr. Alessandro Vannozzi

E-Mail Website
Guest Editor
Department of Agronomy Food Natural Resources Animals Environment, Campus of Agripolis, University of Padova, 35020 Legnaro, Italy
Interests: genetics and genomics; regulation of secondary metabolism; plant reproduction; abiotic stress response; plasticity; food traceability
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the past several decades, methods for plant breeding have been largely and successfully exploited in developing improved varieties using conventional schemes and morphological descriptors. Currently, the availability of molecular tools and genomics resources is leading to a new revolution in plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, not only for Mendelian traits but also for polygenic traits. Next-generation sequencing (NGS) technologies allow the quick and cheap sequencing of genomes and transcriptomes, making available a huge array of genetic information and predictive markers. The analysis of NGS data by means of bioinformatics allows the discovery of new genes and regulatory sequences, and makes available large collections of molecular markers useful for marker-assisted selection (MAS) for specific genes. Genome-wide expression studies provide breeders with an understanding of the molecular basis of complex traits. Genomic approaches such as GWAS and GBS make it possible to screen individual mutants and germplasm collections for allelic variants in target genes. The re-sequencing of genomes is very useful for the genome-wide discovery of markers amenable for high-throughput genotyping platforms like SSRs and SNPs, or the construction of high-density genetic linkage maps, which are then exploitable for marker-assisted breeding (MAB) approaches. All these tools and resources facilitate the study of genetic diversity, which is important for germplasm management, enhancement, and use. They also allow the identification of markers linked to Mendelian genes and QTLs by means of conventional genetic mapping or association mapping. On the whole, these marker panels and molecular tools pave the way for breeding-by-design and genomic-selection strategies. In conclusion, advances in applied genomics are providing breeders with new tools and methodologies that will allow a great leap forward in plant breeding, including the genetic dissection of complex traits and a better genetic exploitation of heterotic effects in F1 hybrids. The 2020 edition of this Special Issue is aimed at grouping additional studies and contributions that make use of conventional schemes and genomic tools for plant breeding. Overall analyses and findings will continue to facilitate the development of modern breeding programs, superior variety standards, and quality assurance tools, which are essential for a faster transition to economic, social, and environmental sustainability of plant productions in the frame of Agriculture 4.0.

Prof. Dr. Gianni Barcaccia
Dr. Alessandro Vannozzi
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 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. Plants is an international peer-reviewed open access semimonthly 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 2700 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 (4 papers)

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Research

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11 pages, 15079 KiB  
Article
Preliminary Identification of Key Genes Controlling Peach Pollen Fertility Using Genome-Wide Association Study
by Zhenyu Huang, Fei Shen, Yuling Chen, Ke Cao and Lirong Wang
Plants 2021, 10(2), 242; https://doi.org/10.3390/plants10020242 - 27 Jan 2021
Cited by 1 | Viewed by 2058
Abstract
Previous genetic mapping helped detect a ~7.52 Mb putative genomic region for the pollen fertility trait on peach Chromosome 06 (Chr.06), which was too long for candidate gene characterization. In this study, using the whole-genome re-sequencing data of 201 peach accessions, we performed [...] Read more.
Previous genetic mapping helped detect a ~7.52 Mb putative genomic region for the pollen fertility trait on peach Chromosome 06 (Chr.06), which was too long for candidate gene characterization. In this study, using the whole-genome re-sequencing data of 201 peach accessions, we performed a genome-wide association study to identify key genes related to peach pollen fertility trait. The significant association peak was detected at Chr.06: 2,116,368 bp, which was in accordance with the previous genetic mapping results, but displayed largely improved precision, allowing for the identification of nine candidate genes. Among these candidates, gene PpABCG26, encoding an ATP-binding cassette G (ABCG) transporter and harboring the most significantly associated SNP (Single Nucleotide Polymorphism) marker in its coding region, was hypothesized to control peach pollen fertility/sterility based on the results of gene function comparison, gene relative expression, and nucleotide sequence analysis. The obtained results will help us to understand the genetic basis of peach pollen fertility trait, and to discover applicable markers for pre-selection in peach. Full article
(This article belongs to the Special Issue Genomics for Plant Breeding 2020–2021)
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12 pages, 1723 KiB  
Article
Identification and Analysis of NBS-LRR Genes in Actinidia chinensis Genome
by Tao Wang, Zhan-Hui Jia, Ji-Yu Zhang, Min Liu, Zhong-Ren Guo and Gang Wang
Plants 2020, 9(10), 1350; https://doi.org/10.3390/plants9101350 - 13 Oct 2020
Cited by 21 | Viewed by 3399
Abstract
Nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes represent the most important disease resistance genes in plants. The genome sequence of kiwifruit (Actinidia chinensis) provides resources for the characterization of NBS-LRR genes and identification of new R-genes in kiwifruit. In the present [...] Read more.
Nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes represent the most important disease resistance genes in plants. The genome sequence of kiwifruit (Actinidia chinensis) provides resources for the characterization of NBS-LRR genes and identification of new R-genes in kiwifruit. In the present study, we identified 100 NBS-LRR genes in the kiwifruit genome and they were grouped into six distinct classes based on their domain architecture. Of the 100 genes, 79 are truncated non-regular NBS-LRR genes. Except for 37 NBS-LRR genes with no location information, the remaining 63 genes are distributed unevenly across 18 kiwifruit chromosomes and 38.01% of them are present in clusters. Seventeen families of cis-acting elements were identified in the promoters of the NBS-LRR genes, including AP2, NAC, ERF and MYB. Pseudomonas syringae pv. actinidiae (pathogen of the kiwifruit bacterial canker) infection induced differential expressions of 16 detected NBS-LRR genes and three of them are involved in plant immunity responses. Our study provides insight of the NBS-LRR genes in kiwifruit and a resource for the identification of new R-genes in the fruit. Full article
(This article belongs to the Special Issue Genomics for Plant Breeding 2020–2021)
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Review

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23 pages, 3028 KiB  
Review
A Review of Unreduced Gametes and Neopolyploids in Alfalfa: How to Fill the Gap between Well-Established Meiotic Mutants and Next-Generation Genomic Resources
by Fabio Palumbo, Elisa Pasquali, Emidio Albertini and Gianni Barcaccia
Plants 2021, 10(5), 999; https://doi.org/10.3390/plants10050999 - 17 May 2021
Cited by 5 | Viewed by 3252
Abstract
The gene flow mediated by unreduced gametes between diploid and tetraploid plants of the Medicagosativa-coerulea-falcata complex is pivotal for alfalfa breeding. Sexually tetraploidized hybrids could represent the best way to exploit progressive heterosis simultaneously derived from gene diversity, heterozygosity, and polyploidy. Moreover, [...] Read more.
The gene flow mediated by unreduced gametes between diploid and tetraploid plants of the Medicagosativa-coerulea-falcata complex is pivotal for alfalfa breeding. Sexually tetraploidized hybrids could represent the best way to exploit progressive heterosis simultaneously derived from gene diversity, heterozygosity, and polyploidy. Moreover, unreduced gametes combined with parthenogenesis (i.e., apomixis) would enable the cloning of plants through seeds, providing a unique opportunity for the selection of superior genotypes with permanently fixed heterosis. This reproductive strategy has never been detected in the genus Medicago, but features of apomixis, such as restitutional apomeiosis and haploid parthenogenesis, have been reported. By means of an original case study, we demonstrated that sexually tetraploidized plants maintain apomeiosis, but this trait is developmentally independent from parthenogenesis. Alfalfa meiotic mutants producing unreduced egg cells revealed a null or very low capacity for parthenogenesis. The overall achievements reached so far are reviewed and discussed along with the efforts and strategies made for exploiting reproductive mutants that express apomictic elements in alfalfa breeding programs. Although several studies have investigated the cytological mechanisms responsible for 2n gamete formation and the inheritance of this trait, only a very small number of molecular markers and candidate genes putatively linked to unreduced gamete formation have been identified. Furthermore, this scenario has remained almost unchanged over the last two decades. Here, we propose a reverse genetics approach, by exploiting the genomic and transcriptomic resources available in alfalfa. Through a comparison with 9 proteins belonging to Arabidopsis thaliana known for their involvement in 2n gamete production, we identified 47 orthologous genes and evaluated their expression in several tissues, paving the way for novel candidate gene characterization studies. An overall view on strategies suitable to fill the gap between well-established meiotic mutants and next-generation genomic resources is presented and discussed. Full article
(This article belongs to the Special Issue Genomics for Plant Breeding 2020–2021)
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14 pages, 942 KiB  
Review
An Overview of Key Factors Affecting Genomic Selection for Wheat Quality Traits
by Ivana Plavšin, Jerko Gunjača, Zlatko Šatović, Hrvoje Šarčević, Marko Ivić, Krešimir Dvojković and Dario Novoselović
Plants 2021, 10(4), 745; https://doi.org/10.3390/plants10040745 - 11 Apr 2021
Cited by 7 | Viewed by 3170
Abstract
Selection for wheat (Triticum aestivum L.) grain quality is often costly and time-consuming since it requires extensive phenotyping in the last phases of development of new lines and cultivars. The development of high-throughput genotyping in the last decade enabled reliable and rapid [...] Read more.
Selection for wheat (Triticum aestivum L.) grain quality is often costly and time-consuming since it requires extensive phenotyping in the last phases of development of new lines and cultivars. The development of high-throughput genotyping in the last decade enabled reliable and rapid predictions of breeding values based only on marker information. Genomic selection (GS) is a method that enables the prediction of breeding values of individuals by simultaneously incorporating all available marker information into a model. The success of GS depends on the obtained prediction accuracy, which is influenced by various molecular, genetic, and phenotypic factors, as well as the factors of the selected statistical model. The objectives of this article are to review research on GS for wheat quality done so far and to highlight the key factors affecting prediction accuracy, in order to suggest the most applicable approach in GS for wheat quality traits. Full article
(This article belongs to the Special Issue Genomics for Plant Breeding 2020–2021)
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