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Genetics and Breeding of Polyploid Plants

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (20 November 2024) | Viewed by 11802

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Special Issue Editors

Dr. Eric Javier Martínez

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Guest Editor

IBONE, Instituto de Botánica del Nordeste, CONICET, National University of the Northeast, W3400 BCH, Corrientes, Argentina
Interests: apomixis; plant genetic systems; plant evolutionary genetics; plant genetic resources; plant genomic analysis; plant molecular genetics; plant reproduction; forage grass improvement; polyploidy
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Dr. Ana Isabel Honfi

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Guest Editor

IBS, Instituto de Biología Subtropical, CONICET, National University of Misiones, N3304 Posadas, Misiones, Argentina
Interests: polyploidy; genetic systems; plant fertility; plant meiotic behavior; plant hybridization; plant evolutionary genetics; plant genetic resource characterization; plant genetics; apomixis; plant reproduction

Special Issue Information

Dear Colleagues,

Polyploidy has long been recognized as an important evolutionary force for speciation, adaptation, and diversification in plants. Polyploidization events to be associated with genetic and epigenetic changes, include structural chromosome rearrangements, aneuploidy, point mutations, loss of duplicated genes and gene conversion, modifications in the chromatin compaction levels, RNA interference and dosage compensation. These changes often involve alterations in the reproduction modes and fertility, increase the organs size, phenotypic variability, colonization of new habitats, heterosis, mutational robustness, among others. The revelation that a large number of plant species have a polyploid genome, including several important crops, has attracted the attention of plant breeders for the application of artificial polyploidy as a tool for crop improvement.

In recent years, important advances have been made on the origin and evolution, establishment and diversification, genetic and epigenetic changes, and on the genetic improvement of cultivated polyploid species. The use of new tools for genomic analysis and bioinformatics has generated novel information on polyploidy in plants.

This Special Issue invites contributions focused on cytogenetics, genetic resources, genetic systems (ploidy level, reproductive mode, pollination syndrome and fertility), patterns of inheritance, genetic diversity, phylogeny, evolution, genomic analysis, epigenetics, and genetic breeding of polyploid plants.

Dr. Eric Javier Martínez
Dr. Ana Isabel Honfi
Guest Editors

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Keywords

cytogenetics
epigenetics
evolutionary genetics
forage grass improvement
genetic diversity
genetic resources
genetic systems
genomics analysis
molecular genetic
phylogenetic analysis
plant breeding
plant reproduction

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Published Papers (7 papers)

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Research

19 pages, 2854 KiB

Open AccessArticle

New Observations of the Effects of the Cytoplasm of Aegilops kotschyi Boiss. in Bread Wheat Triticum aestivum L.

by Chaolan Fan, Joanna Melonek and Adam J. Lukaszewski

Genes 2024, 15(7), 855; https://doi.org/10.3390/genes15070855 - 28 Jun 2024

Viewed by 1203

Abstract

The cytoplasm of Aegilops kotschyi is known for the induction of male sterility and haploidy in wheat. Both systems originally appeared rather simple, but manipulation of the standard chromosome constitution of the nuclear genome revealed additional interactions. This study shows that while there is little or no allelic variation at the main fertility restorer locus Rf^multi on chromosome arm 1BS, additional genes may also be involved in the nuclear–mitochondrial genome interactions, affecting not only male fertility but also the growth rate, from pollen competition for fertilization and early endosperm divisions all the way to seed size and plant maturity. Some of these effects appear to be of a sporophytic nature; others are gametophytic. Induction of parthenogenesis by a rye inducer in conjunction with the Ae. kotschyi cytoplasm is well known. However, here we show that the cytoplasmic-nuclear interactions affect all aspects of double fertilization: producing maternal haploids from unfertilized eggs, diploids from fertilized eggs or synergids, embryo-less kernels, and fertilized eggs without fertilization of the double nucleus in the embryo sack. It is unclear how frequent the inducers of parthenogenesis are, as variation, if any, is obscured by suppressors present in the wheat genome. Genetic dissection of a single wheat accession revealed five distinct loci affecting the rate of maternal haploid production: four acting as suppressors and one as an enhancer. Only when the suppressing haplotypes are confirmed may it be possible to the identify genetic variation of haploidy inducers, map their position(s), and determine their nature and the mode of action. Full article

(This article belongs to the Special Issue Genetics and Breeding of Polyploid Plants)

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18 pages, 3597 KiB

Open AccessArticle

Assessing myBaits Target Capture Sequencing Methodology Using Short-Read Sequencing for Variant Detection in Oat Genomics and Breeding

by Khalid Mahmood, Pernille Sarup, Lukas Oertelt, Ahmed Jahoor and Jihad Orabi

Genes 2024, 15(6), 700; https://doi.org/10.3390/genes15060700 - 27 May 2024

Viewed by 1469

Abstract

The integration of target capture systems with next-generation sequencing has emerged as an efficient tool for exploring specific genetic regions with a high resolution and facilitating the rapid discovery of novel alleles. Despite these advancements, the application of targeted sequencing methodologies, such as the myBaits technology, in polyploid oat species remains relatively unexplored. In this study, we utilized the myBaits target capture method offered by Daicel Arbor Biosciences to detect variants and assess their reliability for variant detection in oat genomics and breeding. Ten oat genotypes were carefully chosen for targeted sequencing, focusing on specific regions on chromosome 2A to detect variants. The selected region harbors 98 genes. Precisely designed baits targeting the genes within these regions were employed for the target capture sequencing. We employed various mappers and variant callers to identify variants. After the identification of variants, we focused on the variants identified via all variants callers to assess the applicability of the myBaits sequencing methodology in oat breeding. In our efforts to validate the identified variants, we focused on two SNPs, one deletion and one insertion identified via all variant callers in the genotypes KF-318 and NOS 819111-70 but absent in the remaining eight genotypes. The Sanger sequencing of targeted SNPs failed to reproduce target capture data obtained through the myBaits technology. Similarly, the validation of deletion and insertion variants via high-resolution melting (HRM) curve analysis also failed to reproduce target capture data, again suggesting limitations in the reliability of the myBaits target capture sequencing using short-read sequencing for variant detection in the oat genome. This study shed light on the importance of exercising caution when employing the myBaits target capture strategy for variant detection in oats. This study provides valuable insights for breeders seeking to advance oat breeding efforts and marker development using myBaits target capture sequencing, emphasizing the significance of methodological sequencing considerations in oat genomics research. Full article

(This article belongs to the Special Issue Genetics and Breeding of Polyploid Plants)

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12 pages, 1437 KiB

Open AccessArticle

Autotetraploid Induction of Three A-Genome Wild Peanut Species, Arachis cardenasii, A. correntina, and A. diogoi

by Robert W. Suppa, Ryan J. Andres, Jeffrey C. Dunne, Ramsey F. Arram, Thomas B. Morgan and Hsuan Chen

Genes 2024, 15(3), 303; https://doi.org/10.3390/genes15030303 - 27 Feb 2024

Viewed by 1503

Abstract

A-genome Arachis species (AA; 2n = 2x = 20) are commonly used as secondary germplasm sources in cultivated peanut breeding, Arachis hypogaea L. (AABB; 2n = 4x = 40), for the introgression of various biotic and abiotic stress resistance genes. Genome doubling is critical to overcoming the hybridization barrier of infertility that arises from ploidy-level differences between wild germplasm and cultivated peanuts. To develop improved genome doubling methods, four trials of various concentrations of the mitotic inhibitor treatments colchicine, oryzalin, and trifluralin were tested on the seedlings and seeds of three A-genome species, A. cardenasii, A. correntina, and A. diogoi. A total of 494 seeds/seedlings were treated in the present four trials, with trials 1 to 3 including different concentrations of the three chemical treatments on seedlings, and trial 4 focusing on the treatment period of 5 mM colchicine solution treatment of seeds. A small number of tetraploids were produced from the colchicine and oryzalin gel treatments of seedlings, but all these tetraploid seedlings reverted to diploid or mixoploid states within six months of treatment. In contrast, the 6-h colchicine solution treatment of seeds showed the highest tetraploid conversion rate (6–13% of total treated seeds or 25–40% of surviving seedlings), and the tetraploid plants were repeatedly tested as stable tetraploids. In addition, visibly and statistically larger leaves and flowers were produced by the tetraploid versions of these three species compared to their diploid versions. As a result, stable tetraploid plants of each A-genome species were produced, and a 5 mM colchicine seed treatment is recommended for A-genome and related wild Arachis species genome doubling. Full article

(This article belongs to the Special Issue Genetics and Breeding of Polyploid Plants)

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21 pages, 2328 KiB

Open AccessArticle

Genome-Wide Mapping of Quantitative Trait Loci for Yield-Attributing Traits of Peanut

by Pushpesh Joshi, Pooja Soni, Vinay Sharma, Surendra S. Manohar, Sampath Kumar, Shailendra Sharma, Janila Pasupuleti, Vincent Vadez, Rajeev K. Varshney, Manish K. Pandey and Naveen Puppala

Genes 2024, 15(2), 140; https://doi.org/10.3390/genes15020140 - 23 Jan 2024

Cited by 1 | Viewed by 1725

Abstract

Peanuts (Arachis hypogaea L.) are important high-protein and oil-containing legume crops adapted to arid to semi-arid regions. The yield and quality of peanuts are complex quantitative traits that show high environmental influence. In this study, a recombinant inbred line population (RIL) (Valencia-C × JUG-03) was developed and phenotyped for nine traits under two environments. A genetic map was constructed using 1323 SNP markers spanning a map distance of 2003.13 cM. Quantitative trait loci (QTL) analysis using this genetic map and phenotyping data identified seventeen QTLs for nine traits. Intriguingly, a total of four QTLs, two each for 100-seed weight (HSW) and shelling percentage (SP), showed major and consistent effects, explaining 10.98% to 14.65% phenotypic variation. The major QTLs for HSW and SP harbored genes associated with seed and pod development such as the seed maturation protein-encoding gene, serine-threonine phosphatase gene, TIR-NBS-LRR gene, protein kinase superfamily gene, bHLH transcription factor-encoding gene, isopentyl transferase gene, ethylene-responsive transcription factor-encoding gene and cytochrome P450 superfamily gene. Additionally, the identification of 76 major epistatic QTLs, with PVE ranging from 11.63% to 72.61%, highlighted their significant role in determining the yield- and quality-related traits. The significant G × E interaction revealed the existence of the major role of the environment in determining the phenotype of yield-attributing traits. Notably, the seed maturation protein-coding gene in the vicinity of major QTLs for HSW can be further investigated to develop a diagnostic marker for HSW in peanut breeding. This study provides understanding of the genetic factor governing peanut traits and valuable insights for future breeding efforts aimed at improving yield and quality. Full article

(This article belongs to the Special Issue Genetics and Breeding of Polyploid Plants)

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17 pages, 1576 KiB

Open AccessArticle

Manifestation of Triploid Heterosis in the Root System after Crossing Diploid and Autotetraploid Energy Willow Plants

by Dénes Dudits, András Cseri, Katalin Török, Radomira Vankova, Petre I. Dobrev, László Sass, Gábor Steinbach, Ildikó Kelemen-Valkony, Zoltán Zombori, Györgyi Ferenc and Ferhan Ayaydin

Genes 2023, 14(10), 1929; https://doi.org/10.3390/genes14101929 - 12 Oct 2023

Cited by 1 | Viewed by 1500

Abstract

Successful use of woody species in reducing climatic and environmental risks of energy shortage and spreading pollution requires deeper understanding of the physiological functions controlling biomass productivity and phytoremediation efficiency. Targets in the breeding of energy willow include the size and the functionality of the root system. For the combination of polyploidy and heterosis, we have generated triploid hybrids (THs) of energy willow by crossing autotetraploid willow plants with leading cultivars (Tordis and Inger). These novel Salix genotypes (TH3/12, TH17/17, TH21/2) have provided a unique experimental material for characterization of Mid-Parent Heterosis (MPH) in various root traits. Using a root phenotyping platform, we detected heterosis (TH3/12: MPH 43.99%; TH21/2: MPH 26.93%) in the size of the root system in soil. Triploid heterosis was also recorded in the fresh root weights, but it was less pronounced (MPH%: 9.63–19.31). In agreement with root growth characteristics in soil, the TH3/12 hybrids showed considerable heterosis (MPH: 70.08%) under in vitro conditions. Confocal microscopy-based imaging and quantitative analysis of root parenchyma cells at the division–elongation transition zone showed increased average cell diameter as a sign of cellular heterosis in plants from TH17/17 and TH21/2 triploid lines. Analysis of the hormonal background revealed that the auxin level was seven times higher than the total cytokinin contents in root tips of parental Tordis plants. In triploid hybrids, the auxin–cytokinin ratios were considerably reduced in TH3/12 and TH17/17 roots. In particular, the contents of cytokinin precursor, such as isopentenyl adenosine monophosphate, were elevated in all three triploid hybrids. Heterosis was also recorded in the amounts of active gibberellin precursor, GA₁₉, in roots of TH3/12 plants. The presented experimental findings highlight the physiological basics of triploid heterosis in energy willow roots. Full article

(This article belongs to the Special Issue Genetics and Breeding of Polyploid Plants)

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16 pages, 1485 KiB

Open AccessArticle

Genetic Mapping of Genotype-by-Ploidy Effects in Arabidopsis thaliana

by Cris L. Wijnen, Frank F. M. Becker, Andries A. Okkersen, C. Bastiaan de Snoo, Martin P. Boer, Fred A. van Eeuwijk, Erik Wijnker and Joost J. B. Keurentjes

Genes 2023, 14(6), 1161; https://doi.org/10.3390/genes14061161 - 26 May 2023

Cited by 1 | Viewed by 1586

Abstract

Plants can express different phenotypic responses following polyploidization, but ploidy-dependent phenotypic variation has so far not been assigned to specific genetic factors. To map such effects, segregating populations at different ploidy levels are required. The availability of an efficient haploid inducer line in Arabidopsis thaliana allows for the rapid development of large populations of segregating haploid offspring. Because Arabidopsis haploids can be self-fertilised to give rise to homozygous doubled haploids, the same genotypes can be phenotyped at both the haploid and diploid ploidy level. Here, we compared the phenotypes of recombinant haploid and diploid offspring derived from a cross between two late flowering accessions to map genotype × ploidy (G × P) interactions. Ploidy-specific quantitative trait loci (QTLs) were detected at both ploidy levels. This implies that mapping power will increase when phenotypic measurements of monoploids are included in QTL analyses. A multi-trait analysis further revealed pleiotropic effects for a number of the ploidy-specific QTLs as well as opposite effects at different ploidy levels for general QTLs. Taken together, we provide evidence of genetic variation between different Arabidopsis accessions being causal for dissimilarities in phenotypic responses to altered ploidy levels, revealing a G × P effect. Additionally, by investigating a population derived from late flowering accessions, we revealed a major vernalisation-specific QTL for variation in flowering time, countering the historical bias of research in early flowering accessions. Full article

(This article belongs to the Special Issue Genetics and Breeding of Polyploid Plants)

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22 pages, 4303 KiB

Open AccessArticle

Alternative Evolutionary Pathways in Paspalum Involving Allotetraploidy, Sexuality, and Varied Mating Systems

by Mara Schedler, Anna Verena Reutemann, Diego Hernán Hojsgaard, Alex Leonel Zilli, Elsa Andrea Brugnoli, Florencia Galdeano, Carlos Alberto Acuña, Ana Isabel Honfi and Eric Javier Martínez

Genes 2023, 14(6), 1137; https://doi.org/10.3390/genes14061137 - 24 May 2023

Cited by 1 | Viewed by 1709

Abstract

The genetic systems of Paspalum species have not been extensively studied. We analyzed the ploidy, reproductive mode, mating system, and fertility of four Paspalum species—Paspalum durifolium, Paspalum ionanthum, Paspalum regnellii, and Paspalum urvillei. An analysis of 378 individuals from 20 populations of northeastern Argentina was conducted. All populations of the four Paspalum species were pure tetraploid and had a sexual and stable reproductive mode. However, some populations of P. durifolium and P. ionanthum showed low levels of apospory. Populations of P. durifolium and P. ionanthum had low seed sets under self-pollination but were fertile under open pollination, showing that self-incompatibility likely caused self-sterility. In contrast, populations of P. regnellii or P. urvillei showed no evidence of apospory, and seed sets in both self- and open pollination conditions were high, suggesting that they are self-compatible due to the absence of pollen–pistil molecular incompatibility mechanisms. The evolutionary origin of the four Paspalum species could explain these differences. This study supplies valuable insights into the genetic systems of Paspalum species, which could have implications for their conservation and management. Full article

(This article belongs to the Special Issue Genetics and Breeding of Polyploid Plants)

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