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Plants
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Genomics-Enabled Chromosome Engineering in Plant Breeding and Genome Studies
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Genomics-Enabled Chromosome Engineering in Plant Breeding and Genome Studies

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 (31 August 2023) | Viewed by 5087

Special Issue Editors

Dr. Xiwen Cai

E-Mail Website
Guest Editor
USDA-ARS, University of Nebraska-Lincoln, Lincoln, NE, USA
Interests: plant genome/chromosome characterization ; plant haploidization and polyploidization; plant breeding technologies and resources
Dr. Jeffrey Boehm

E-Mail Website
Guest Editor
USDA-ARS, University of Nebraska-Lincoln, Lincoln, NE, USA
Interests: wheat breeding; germplasm development

Special Issue Information

Dear Colleagues,

Climate change and variability have increasingly led to new biotic and abiotic stresses for plants, which constantly threatens plant production worldwide. Developing superior varieties resilient to climate change/variability has been considered an economically efficient and environmentally friendly strategy to sustain plant productivity under these stresses. Genetic variation/diversity is a vital determinant of success in plant breeding. Extensive breeding efforts have drained the primary gene pool, which may potentially reduce the genetic diversity of the domesticated plants/crops and increase their vulnerability to the emerging stresses. Thus, there is a constant need to introduce novel genetic variation into the primary gene pools of plant breeding programs.

Significant work has been performed to bridge the gene flow from the secondary and tertiary gene pools (relatives and wild species) into the primary gene pools of domesticated plants/crops via meiotic homoeologous recombination-based chromosome engineering, especially in the current genomics era. The genomic technologies and resources currently available have dramatically improved the efficacy and throughput of chromosome engineering in alien introgression and genome studies in plants. This will enrich and diversify the genomes of plants to meet the need of genetic variation in plant breeding.

We are editing a Special Issue on “Genomics-Enabled Chromosome Engineering in Plant Breeding and Genome Studies” to highlight the major accomplishments and progress in this research field, including meiotic homoeologous recombination-based alien introgression and genome mapping/analysis, genome modification and evolution, haploidization and polyploidization, and genetic control/manipulation of breeding-related mitotic and meiotic processes. We welcome your contributions to this Special Issue.      

Dr. Xiwen Cai
Dr. Jeffrey Boehm
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 (2 papers)

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Research

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14 pages, 1647 KiB  
Article
Agronomic Evaluation and Molecular Cytogenetic Characterization of Triticum aestivum × Thinopyrum spp. Derivative Breeding Lines Presenting Perennial Growth Habits
by Robin Morgan, Tatiana Danilova, Matthew Newell, Xiwen Cai and Stephen Jones
Plants 2023, 12(18), 3217; https://doi.org/10.3390/plants12183217 - 9 Sep 2023
Cited by 2 | Viewed by 1221
Abstract
The transition from annual to perennial growth habits can contribute to increased sustainability and diversification of staple cropping systems like those based on annual wheat. Amphiploids between Triticum aestivum and Thinopyrum spp. can present a wheat-like morphology and post sexual cycle regrowth. The [...] Read more.
The transition from annual to perennial growth habits can contribute to increased sustainability and diversification of staple cropping systems like those based on annual wheat. Amphiploids between Triticum aestivum and Thinopyrum spp. can present a wheat-like morphology and post sexual cycle regrowth. The complex and unpredictable nature of the chromosomal rearrangements typical of inter-generic hybrids can hamper progress in the development of this new crop. By using fluorescence in situ hybridization, we described the genomic constitution of three perennial wheat breeding lines that regrew and completed a second year of production in field conditions in Washington state (USA). Two breeding lines presented stable, 56-chromosome partial amphiploids; however, their chromosome composition differed significantly. The third breeding line presented an unstable karyotype with a chromosome number ranging from 53 to 58 across eight individuals. The agronomic performance of the perennial breeding lines was evaluated for two growing seasons from 2020 to 2022. The grain yields of the perennial lines were lower than the grain production of the annual wheat control line in the first season. The perennial lines displayed vigorous regrowth after the initial harvest; however, worsening environmental conditions in the second season of growth hampered subsequent growth and grain yield. This information facilitates the breeding work necessary to improve key traits by grouping agronomically valuable individuals according to their genomic constitution. Full article
(This article belongs to the Special Issue Genomics-Enabled Chromosome Engineering in Plant Breeding and Genome Studies)
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Review

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16 pages, 1448 KiB  
Review
Accelerated Breeding for Helianthus annuus (Sunflower) through Doubled Haploidy: An Insight on Past and Future Prospects in the Era of Genome Editing
by Londiwe M. Mabuza, Nokuthula P. Mchunu, Bridget G. Crampton and Dirk Z. H. Swanevelder
Plants 2023, 12(3), 485; https://doi.org/10.3390/plants12030485 - 20 Jan 2023
Cited by 2 | Viewed by 3444
Abstract
The aim of any breeding process is to fully express the targeted, superior/desirable parent characteristic in the progeny. Hybrids are often used in this dynamic, and complex process for which homozygous parents—which may require up to eight generations of back crossing and selection—are [...] Read more.
The aim of any breeding process is to fully express the targeted, superior/desirable parent characteristic in the progeny. Hybrids are often used in this dynamic, and complex process for which homozygous parents—which may require up to eight generations of back crossing and selection—are required. Doubled haploid (DH) technologies can facilitate the production of true breeding lines faster and in a more efficient manner than the traditional back crossing and selection strategies. Sunflower is the third most important oilseed crop in the world and has no available double haploid induction procedure/technique that can be efficiently used in breeding programs. A reproducible and efficient doubled haploid induction method would be a valuable tool in accelerating the breeding of new elite sunflower varieties. Although several attempts have been made, the establishment of a sunflower doubled haploid induction protocol has remained a challenge owing recalcitrance to in vitro culture regeneration. Approaches for haploid development in other crops are often cultivar specific, difficult to reproduce, and rely on available tissue culture protocols—which on their own are also cultivar and/or species specific. As an out-crossing crop, the lack of a double haploid system limits sunflower breeding and associated improvement processes, thereby delaying new hybrid and trait developments. Significant molecular advances targeting genes, such as the centromeric histone 3 (CenH3) and Matrilineal (MTL) gene with CRISPR/Cas9, and the successful use of viral vectors for the delivery of CRISPR/Cas9 components into plant cells eliminating the in vitro culture bottleneck, have the potential to improve double haploid technology in sunflower. In this review, the different strategies, their challenges, and opportunities for achieving doubled haploids in sunflower are explored. Full article
(This article belongs to the Special Issue Genomics-Enabled Chromosome Engineering in Plant Breeding and Genome Studies)
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