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Agronomy
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Chromosome Manipulation for Plant Breeding Purposes
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Chromosome Manipulation for Plant Breeding Purposes

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

Deadline for manuscript submissions: closed (20 July 2020) | Viewed by 43335

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editor

Dr. Pilar Prieto

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Guest Editor
Dpto. de Mejora Genética Vegetal, Instituto de Agricultura Sostenible, Agencia Estatal Consejo Superior de Investigaciones Científicas, Avenida Menéndez Pidal s/n. Campus Alameda del Obispo, 14004 Córdoba, Spain
Interests: plant breeding; meiosis; chromosome pairing; chromosome dynamics
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Special Issue Information

Dear Colleagues,

The ability to exploit the potential of wild relatives carrying beneficial traits is a major goal in breeding programs. However, it relies on the possibility of the chromosomes from the crop and the wild species in interspecific crosses to recognize, associate and undergo crossover formation during meiosis, the cellular process responsible for producing gametes with half the genetic content of the parent cells. Unfortunately, in most of the cases, a barrier exists preventing successful hybridization between the wild and the crop chromosomes. Understanding the mechanisms controlling chromosome associations during meiosis are of great interest in plant breeding. Thus, examining how chromosomes recognize, associate in pairs, synapse and recombine, which are prerequisites for the balanced segregation of half-bivalents during meiosis, will allow chromosome manipulation to introduce genetic variability from related species into a crop. In addition to interspecific hybrids, other materials, such as natural and synthetic polyploids and introgression lines derived from allopolyploids, among others, are powerful tools in the study of meiosis. For example, an extra pair of alien chromosomes in the full genome complement of a crop species has been frequently used as a first step to access genetic variation from the secondary gene pool in breeding programs. However, such introgression lines are also pivotal in the study of interspecific genetic interactions, in the chromosomal location of genetic markers and in the study of chromosome structure and behavior in somatic and meiotic cells.

This Special Issue invites original research, technology reports, methods, opinion, perspectives, reviews and mini reviews dissecting how chromosomes associate in pairs, recombine and segregate in the gametes during meiosis, with the aim of manipulating such processes and promoting non-homologous recombination in the framework of plant breeding. In addition, the development of new aneuploid lines and interspecific hybrids; new methods to identify, isolate and manipulate single chromosomes; improved genomic in situ hybridization techniques to identify new chromosome organizations and specific meiotic events; chromosome engineering protocols to detect critical recombinants, etc. will be considered within the general scope of this Special Issue.

We strongly believe that this compilation of high quality scientific papers shedding light on the key processes involved in chromosome associations during meiosis will enable a better understanding of chromosome manipulation for plant breeding purposes.

Dr. Pilar Prieto
Guest Editor

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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

  • meiosis
  • chromosome engineering
  • chromosome pairing
  • non-homologous recombination
  • cytogenetics
  • alien chromosome
  • polyploidy
  • aneuploidy

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Published Papers (10 papers)

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Editorial

Jump to: Research, Review

4 pages, 190 KiB  
Editorial
Chromosome Manipulation for Plant Breeding Purposes
by Pilar Prieto
Agronomy 2020, 10(11), 1695; https://doi.org/10.3390/agronomy10111695 - 2 Nov 2020
Cited by 5 | Viewed by 4407
Abstract
The transfer of genetic variability from related species into crops has been a main objective for decades in breeding programs. Breeders have used interspecific genetic crosses and alien introgression lines to achieve this goal, but the success is always dependent on the interspecific [...] Read more.
The transfer of genetic variability from related species into crops has been a main objective for decades in breeding programs. Breeders have used interspecific genetic crosses and alien introgression lines to achieve this goal, but the success is always dependent on the interspecific chromosome associations between the alien chromosomes and those from the crop during early meiosis. In this Special Issue, the strength of chromosome manipulation in a breeding framework is revealed through research and review papers that combine molecular markers, cytogenetics tools and other traditional breeding techniques. The papers and reviews included in this Special Issue “Chromosome manipulation for plant breeding purposes” describe the development and/or characterization of new plant material carrying desirable traits and the study of chromosome associations and recombination during meiosis. New tools to facilitate the transfer of desired traits from a donor species into a crop can be developed by expanding the knowledge of chromosome associations during meiosis. Full article
(This article belongs to the Special Issue Chromosome Manipulation for Plant Breeding Purposes)

Research

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9 pages, 1319 KiB  
Article
Analysis of Wheat Bread-Making Gene (wbm) Evolution and Occurrence in Triticale Collection Reveal Origin via Interspecific Introgression into Chromosome 7AL
by Ilya Kirov, Andrey Pirsikov, Natalia Milyukova, Maxim Dudnikov, Maxim Kolenkov, Ivan Gruzdev, Stanislav Siksin, Ludmila Khrustaleva, Gennady Karlov and Alexander Soloviev
Agronomy 2019, 9(12), 854; https://doi.org/10.3390/agronomy9120854 - 5 Dec 2019
Cited by 9 | Viewed by 3757
Abstract
Bread-making quality is a crucial trait for wheat and triticale breeding. Several genes significantly influence these characteristics, including glutenin genes and the wheat bread-making (wbm) gene. World wheat collection screening showed that only a few percent of cultivars carry the valuable [...] Read more.
Bread-making quality is a crucial trait for wheat and triticale breeding. Several genes significantly influence these characteristics, including glutenin genes and the wheat bread-making (wbm) gene. World wheat collection screening showed that only a few percent of cultivars carry the valuable wbm variant, providing a useful source for wheat breeding. In contrast, no such analysis has been performed for triticale (wheat (AABB genome) × rye (RR) amphidiploid) collections. Despite the importance of the wbm gene, information about its origin and genomic organization is lacking. Here, using modern genomic resources available for wheat and its relatives, as well as PCR screening, we aimed to examine the evolution of the wbm gene and its appearance in the triticale genotype collection. Bioinformatics analysis revealed that the wheat Chinese Spring genome does not have the wbm gene but instead possesses the orthologous gene, called wbm-like located on chromosome 7A. The analysis of upstream and downstream regions revealed the insertion of LINE1 (Long Interspersed Nuclear Elements) retrotransposons and Mutator DNA transposon in close vicinity to wbm-like. Comparative analysis of the wbm-like region in wheat genotypes and closely related species showed low similarity between the wbm locus and other sequences, suggesting that wbm originated via introgression from unknown species. PCR markers were developed to distinguish wbm and wbm-like sequences, and triticale collection was screened resulting in the detection of three genotypes carrying wbm-specific introgression, providing a useful source for triticale breeding programs. Full article
(This article belongs to the Special Issue Chromosome Manipulation for Plant Breeding Purposes)
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12 pages, 4064 KiB  
Communication
Recovery of 2R.2Sk Triticale-Aegilops kotschyi Robertsonian Chromosome Translocations
by Waldemar Ulaszewski, Jolanta Belter, Halina Wiśniewska, Joanna Szymczak, Roksana Skowrońska, Dylan Phillips and Michał T. Kwiatek
Agronomy 2019, 9(10), 646; https://doi.org/10.3390/agronomy9100646 - 17 Oct 2019
Cited by 4 | Viewed by 5154
Abstract
Robertsonian translocations (RobTs) in the progeny of triticale (×Triticosecale Wittmack) plants with monosomic substitution of Aegilops kotschyi chromosome 2Sk (2R) were investigated by fluorescence in-situ hybridization. Chromosome 2Sk of Ae. kotschyi is reported to possess many valuable loci, such as [...] Read more.
Robertsonian translocations (RobTs) in the progeny of triticale (×Triticosecale Wittmack) plants with monosomic substitution of Aegilops kotschyi chromosome 2Sk (2R) were investigated by fluorescence in-situ hybridization. Chromosome 2Sk of Ae. kotschyi is reported to possess many valuable loci, such as Lr54 + Yr37 leaf and stripe (yellow) rust resistance genes. We used a standard procedure to produce RobTs, which consisted of self-pollination of monosomic triticale plants, carrying 2R and 2Sk chromosomes in monosomic condition. This approach did not result in RobTs. Simultaneously, we succeeded in producing 11 plants carrying 2R.2Sk compensatory RobTs using an alternative approach that utilized ditelosomic lines of triticale carrying 2RS (short arm) and 2RL (long arm) telosomic chromosomes. Identification of molecular markers linked to Lr54 + Yr37 genes in the translocation plants confirmed that these resources can be exploited in current triticale breeding programmes. Full article
(This article belongs to the Special Issue Chromosome Manipulation for Plant Breeding Purposes)
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11 pages, 3495 KiB  
Article
The Confirmation of a Ploidy Periclinal Chimera of the Meiwa Kumquat (Fortunella crassifolia Swingle) Induced by Colchicine Treatment to Nucellar Embryos and Its Morphological Characteristics
by Tsunaki Nukaya, Miki Sudo, Masaki Yahata, Tomohiro Ohta, Akiyoshi Tominaga, Hiroo Mukai, Kiichi Yasuda and Hisato Kunitake
Agronomy 2019, 9(9), 562; https://doi.org/10.3390/agronomy9090562 - 18 Sep 2019
Cited by 5 | Viewed by 4197
Abstract
A ploidy chimera of the Meiwa kumquat (Fortunella crassifolia Swingle), which had been induced by treating the nucellar embryos with colchicine, and had diploid (2n = 2x = 18) and tetraploid (2n = 4x = 36) cells, was examined for its ploidy [...] Read more.
A ploidy chimera of the Meiwa kumquat (Fortunella crassifolia Swingle), which had been induced by treating the nucellar embryos with colchicine, and had diploid (2n = 2x = 18) and tetraploid (2n = 4x = 36) cells, was examined for its ploidy level, morphological characteristics, and sizes of its cells in its leaves, flowers, and fruits to reveal the ploidy level of each histogenic layer. Furthermore, the chimera was crossed with the diploid kumquat to evaluate the ploidy level of its reproductive organs. The morphological characteristics and the sizes of the cells in the leaves, flowers, and fruits of the chimera were similar to those of the tetraploid Meiwa kumquat and the ploidy periclinal chimera known as “Yubeni,” with diploids in the histogenic layer I (L1) and tetraploids in the histogenic layer II (L2) and III (L3). However, the epidermis derived from the L1 of the chimera showed the same result as the diploid Meiwa kumquat in all organs and cells. The sexual organs derived from the L2 of the chimera were significantly larger than those of the diploid. Moreover, the ploidy level of the seedlings obtained from the chimera was mostly tetraploid. In the midrib derived from the L3, the chimera displayed the fluorescence intensity of a tetraploid by flow cytometric analysis and had the same size of the cells as the tetraploid and the Yubeni. According to these results, the chimera is thought to be a ploidy periclinal chimera with diploid cells in the outermost layer (L1) and tetraploid cells in the inner layers (L2 and L3) of the shoot apical meristem. The chimera had desirable fruit traits for a kumquat such as a thick pericarp, a high sugar content, and a small number of developed seeds. Furthermore, triploid progenies were obtained from reciprocal crosses between the chimera and diploid kumquat. Full article
(This article belongs to the Special Issue Chromosome Manipulation for Plant Breeding Purposes)
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14 pages, 5438 KiB  
Article
Physical Location of New Stripe Rust Resistance Gene(s) and PCR-Based Markers on Rye (Secale cereale L.) Chromosome 5 Using 5R Dissection Lines
by Wei Xi, Zongxiang Tang, Jie Luo and Shulan Fu
Agronomy 2019, 9(9), 498; https://doi.org/10.3390/agronomy9090498 - 30 Aug 2019
Cited by 12 | Viewed by 3202
Abstract
The rye (Secale cereale L.) 5R chromosome contains some elite genes that can be used to improve wheat cultivars. In this study, a set of 5RKu dissection lines was obtained, and 111 new PCR-based and 5RKu-specific markers were developed [...] Read more.
The rye (Secale cereale L.) 5R chromosome contains some elite genes that can be used to improve wheat cultivars. In this study, a set of 5RKu dissection lines was obtained, and 111 new PCR-based and 5RKu-specific markers were developed using the specific length amplified fragment sequencing (SLAF-seq) method. The 111 markers were combined with the 52 5RKu-specific markers previously reported, and 65 S. cereale Lo7 scaffolds were physically mapped to six regions of the 5RKu chromosome using the 5RKu dissection lines. Additionally, the 5RLKu arm carried stripe rust resistance gene(s) and it was located to the region L2, the same region where 22 5RKu-specific markers and 11 S. cereale Lo7 scaffolds were mapped. The stripe rust resistance gene(s) located in the 5RLKu arm might be new one(s) because its source and location are different from the previously reported ones, and it enriches the resistance source of stripe rust for wheat breeding programs. The markers and the S. cereale Lo7 scaffolds that were mapped to the six regions of the 5RKu chromosome can facilitate the utilization of elite genes on the 5R chromosome in the improvement of wheat cultivars. Full article
(This article belongs to the Special Issue Chromosome Manipulation for Plant Breeding Purposes)
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12 pages, 4944 KiB  
Article
Development of wheat—Hordeum chilense Chromosome 2Hch Introgression Lines Potentially Useful for Improving Grain Quality Traits
by Carmen Palomino and Adoracion Cabrera
Agronomy 2019, 9(9), 493; https://doi.org/10.3390/agronomy9090493 - 28 Aug 2019
Cited by 6 | Viewed by 3247
Abstract
The chromosome 2Hch of Hordeum chilense. has the potential to improve seed carotenoid content in wheat as it carries a set of endosperm carotenoid-related genes. We have obtained structural changes in chromosome 2Hch in a common wheat (Triticum aestivum [...] Read more.
The chromosome 2Hch of Hordeum chilense. has the potential to improve seed carotenoid content in wheat as it carries a set of endosperm carotenoid-related genes. We have obtained structural changes in chromosome 2Hch in a common wheat (Triticum aestivum L. “Chinese Spring”) background by crossing a wheat double disomic substitution 2Hch(2D) and 7Hch(7D) line with a disomic addition line carrying chromosome 2Cc from Aegilops cylindrica Host.. Seven introgressions of chromosome 2Hch into wheat were characterized by fluorescence in situ hybridization (FISH) and DNA markers. Chromosome-specific simple sequence repeats (SSRs) were used for identifying wheat chromosomes. In addition, we tested 82 conserved orthologous set (COS) markers for homoeologous group 2, of which 65 amplified targets in H. chilense and 26 showed polymorphism between H. chilense and wheat. A total of 24 markers were assigned to chromosome 2Hch with eight allocated to 2HchS and 16 to 2HchL. Among the seven introgressions there was a disomic substitution line 2Hch(2D), a ditelosomic addition line for the 2HchL arm, an isochromosome for the 2HchL arm, a homozygous centromeric 2HchS·2DL translocation, a double monosomic 2HchS·2DL plus 7HchS·D translocation, a homozygous centromeric 7HchS·2HchL translocation and, finally, a 2HchL·7HchL translocation. Wheat—H. chilense macrosyntenic comparisons using COS markers revealed that H. chilense chromosome 2Hch exhibits synteny to wheat homoeologous group 2 chromosomes, and the COS markers assigned to this chromosome will facilitate alien gene introgression into wheat. The genetic stocks developed here include new wheat—H. chilense recombinations which are useful for studying the effect of chromosome 2Hch on grain quality traits. Full article
(This article belongs to the Special Issue Chromosome Manipulation for Plant Breeding Purposes)
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12 pages, 1880 KiB  
Article
Wx Gene in Hordeum chilense: Chromosomal Location and Characterisation of the Allelic Variation in the Two Main Ecotypes of the Species
by Juan B. Alvarez, Laura Castellano, Rocío Recio and Adoración Cabrera
Agronomy 2019, 9(5), 261; https://doi.org/10.3390/agronomy9050261 - 22 May 2019
Cited by 5 | Viewed by 3399
Abstract
Starch, as the main grain component, has great importance in wheat quality, with the ratio between the two formed polymers, amylose and amylopectin, determining the starch properties. Granule-bound starch synthase I (GBSSI), or waxy protein, encoded by the Wx gene is the sole [...] Read more.
Starch, as the main grain component, has great importance in wheat quality, with the ratio between the two formed polymers, amylose and amylopectin, determining the starch properties. Granule-bound starch synthase I (GBSSI), or waxy protein, encoded by the Wx gene is the sole enzyme responsible for amylose synthesis. The current study evaluated the variability in Wx genes in two representative lines of Hordeum chilense Roem. et Schult., a wild barley species that was used in the development of tritordeum (×Tritordeum Ascherson et Graebner). Two novel alleles, Wx-Hch1a and Wx-Hch1b, were detected in this material. Molecular characterizations of these alleles revealed that the gene is more similar to the Wx gene of barley than that of wheat, which was confirmed by phylogenetic studies. However, the enzymatic function should be similar in all species, and, consequently, the variation present in H. chilense could be utilized in wheat breeding by using tritordeum as a bridge species. Full article
(This article belongs to the Special Issue Chromosome Manipulation for Plant Breeding Purposes)
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16 pages, 6766 KiB  
Article
Genome-Wide Distribution of Novel Ta-3A1 Mini-Satellite Repeats and Its Use for Chromosome Identification in Wheat and Related Species
by Tao Lang, Guangrong Li, Zhihui Yu, Jiwei Ma, Qiheng Chen, Ennian Yang and Zujun Yang
Agronomy 2019, 9(2), 60; https://doi.org/10.3390/agronomy9020060 - 29 Jan 2019
Cited by 11 | Viewed by 4115
Abstract
A large proportion of the genomes of grasses is comprised of tandem repeats (TRs), which include satellite DNA. A mini-satellite DNA sequence with a length of 44 bp, named Ta-3A1, was found to be highly accumulated in wheat genome, as revealed by a [...] Read more.
A large proportion of the genomes of grasses is comprised of tandem repeats (TRs), which include satellite DNA. A mini-satellite DNA sequence with a length of 44 bp, named Ta-3A1, was found to be highly accumulated in wheat genome, as revealed by a comprehensive sequence analysis. The physical distribution of Ta-3A1 in chromosomes 3A, 5A, 5B, 5D, and 7A of wheat was confirmed by nondenaturing fluorescence in situ hybridization (ND-FISH) after labeling the oligonucleotide probe. The analysis of monomer variants indicated that rapid sequence amplification of Ta-3A1 occurred first on chromosomes of linkage group 5, then groups 3 and 7. Comparative ND-FISH analysis suggested that rapid changes occurred in copy number and chromosomal locations of Ta-3A1 among the different species in the tribe Triticeae, which may have been associated with chromosomal rearrangements during speciation and polyploidization. The labeling and subsequent use of Ta-3A1 by ND-FISH may assist in the precise identification and documentation of novel wheat germplasm engineered by chromosome manipulation. Full article
(This article belongs to the Special Issue Chromosome Manipulation for Plant Breeding Purposes)
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Review

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11 pages, 1019 KiB  
Review
Chromosome Engineering in Tropical Cash Crops
by Pablo Bolaños-Villegas
Agronomy 2020, 10(1), 122; https://doi.org/10.3390/agronomy10010122 - 15 Jan 2020
Cited by 3 | Viewed by 5748
Abstract
Tropical and subtropical crops such as coffee, cacao, and papaya are valuable commodities, and their consumption is a seemingly indispensable part of the daily lives of billions of people worldwide. Conventional breeding of these crops is long, and yields are threatened by global [...] Read more.
Tropical and subtropical crops such as coffee, cacao, and papaya are valuable commodities, and their consumption is a seemingly indispensable part of the daily lives of billions of people worldwide. Conventional breeding of these crops is long, and yields are threatened by global warming. Traditional chromosome engineering and new synthetic biology methods could be used to engineer new chromosomes, facilitate the transmission of wild traits to improve resistance to stress and disease in these crops, and hopefully boost yields. This review gives an overview of these approaches. The adoption of these approaches may contribute to the resilience of agricultural communities, lead to economic growth and secure the availability of key resources for generations to come. Full article
(This article belongs to the Special Issue Chromosome Manipulation for Plant Breeding Purposes)
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Graphical abstract

23 pages, 331 KiB  
Review
The Effect of Chromosome Structure upon Meiotic Homologous and Homoeologous Recombinations in Triticeae
by Tomás Naranjo
Agronomy 2019, 9(9), 552; https://doi.org/10.3390/agronomy9090552 - 14 Sep 2019
Cited by 13 | Viewed by 3743
Abstract
The tribe Triticeae contains about 500 diploid and polyploid taxa, among which are important crops, such as wheat, barley and rye. The phylogenetic relationships, genome compo-sition and chromosomal architecture, were already reported in the pioneer genetic studies on these species, given their implications [...] Read more.
The tribe Triticeae contains about 500 diploid and polyploid taxa, among which are important crops, such as wheat, barley and rye. The phylogenetic relationships, genome compo-sition and chromosomal architecture, were already reported in the pioneer genetic studies on these species, given their implications in breeding-related programs. Hexaploid wheat, driven by its high capacity to develop cytogenetic stocks, has always been at the forefront of these studies. Cytogenetic stocks have been widely used in the identification of homoeologous relationships between the chromosomes of wheat and related species, which has provided valuable information on genome evolution with implications in the transfer of useful agronomical traits into crops. Meiotic recombination is non-randomly distributed in the Triticeae species, and crossovers are formed in the distal half of the chromosomes. Also of interest for crops improvement is the possibility of being able to modulate the intraspecific and interspecific recombination landscape to increase its frequency in crossover-poor regions. Structural changes may help in this task. In fact, chromosome truncation increases the recombination frequency in the adjacent intercalary region. However, structural changes also have a negative effect upon recombination. Gross chromosome rearrangements produced in the evolution usually suppress meiotic recombination between non-syntenic homoeologs. Thus, the chromosome structural organization of related genomes is of great interest in designing strategies of the introgression of useful genes into crops. Full article
(This article belongs to the Special Issue Chromosome Manipulation for Plant Breeding Purposes)
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