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Albrecht E Melchinger - One of the best experts on this subject based on the ideXlab platform.
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selection theory for marker assisted Backcrossing
Genetics, 2005Co-Authors: Matthias Frisch, Albrecht E MelchingerAbstract:Marker-assisted Backcrossing is routinely applied in breeding programs for gene introgression. While selection theory is the most important tool for the design of breeding programs for improvement of quantitative characters, no general selection theory is available for marker-assisted Backcrossing. In this treatise, we develop a theory for marker-assisted selection for the proportion of the genome originating from the recurrent parent in a backcross program, carried out after preselection for the target gene(s). Our objectives were to (i) predict response to selection and (ii) give criteria for selecting the most promising backcross individuals for further Backcrossing or selfing. Prediction of response to selection is based on the marker linkage map and the marker genotype of the parent(s) of the backcross population. In comparison to standard normal distribution selection theory, the main advantage of our approach is that it considers the reduction of the variance in the donor genome proportion due to selection. The developed selection criteria take into account the marker genotype of the candidates and consider whether these will be used for selfing or Backcrossing. Prediction of response to selection is illustrated for model genomes of maize and sugar beet. Selection of promising individuals is illustrated with experimental data from sugar beet. The presented approach can assist geneticists and breeders in the efficient design of gene introgression programs.
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marker assisted Backcrossing for simultaneous introgression of two genes
Crop Science, 2001Co-Authors: Matthias Frisch, Albrecht E MelchingerAbstract:Marker-assisted selection is used to accelerate recovery of the recurrent parent genome (RPG) in backcross programs. Our objectives were to compare various selection strategies and breeding plans for the simultaneous introgression of two genes with respect to the RPG recovered and the number of marker data points (MDP) required. Computer simulations were performed with a published genetic map in maize (Zea mays L.) consisting of 80 markers and assuming selection for dominant target genes on the basis of phenotypic evaluation. For unlinked as well as for linked target genes, a shortening of the backcross program from six to three generations resulted from applying marker-assisted background selection. In breeding programs with three backcross generations, the least MDP were required when (i) applying selection strategies consisting of three or four selection steps on the basis of presence of the target genes and selection indices calculated from the marker genotype, (ii) increasing the population size from early to advanced generations, and (iii) merging the target genes in an early generation. These principles can be used for optimizing the design of marker-assisted backcross programs for the simultaneous introgression of two genes.
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marker assisted Backcrossing for introgression of a recessive gene
Crop Science, 2001Co-Authors: Matthias Frisch, Albrecht E MelchingerAbstract:Molecular markers are used to trace the presence of target genes (foreground selection) and accelerate recovery of the recurrent parent genome (background selection) in backcross programs. In this study, we present an approach for introgression of a recessive target gene from a donor into the genetic background of a recipient line by foreground selection combined with background selection for reducing the donor chromosome segment around the target gene. The goal of the proposed breeding plan is to generate with a given probability, q 2 , up to the second backcross generation (BC 2 ) at least k ≥ 1 individuals, which carry the target gene and are homozygous for the recurrent parent alleles at flanking markers, by means of a minimum number of individuals. We provide formulas for calculation of (i) the population size required in generation BC 1 and (ii) the probability of success q 2 of the breeding program in generation BC 2 . The latter depends on the number and genotype of the BC 1 individuals selected for further Backcrossing and the size of their BC 2 families. The optimum allocation of individuals to generations BC 1 and BC 2 was determined by computer simulations for various map distances between the target gene and the flanking markers. Our approach is demonstrated by a numerical example and can assist breeders in the optimum design of breeding programs for marker-assisted introgression of a recessive gene.
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the length of the intact donor chromosome segment around a target gene in marker assisted Backcrossing
Genetics, 2001Co-Authors: Matthias Frisch, Albrecht E MelchingerAbstract:Recurrent Backcrossing is an established procedure to transfer target genes from a donor into the genetic background of a recipient genotype. By assessing the parental origin of alleles at markers flanking the target locus one can select individuals with a short intact donor chromosome segment around the target gene and thus reduce the linkage drag. We investigated the probability distribution of the length of the intact donor chromosome segment around the target gene in recurrent Backcrossing with selection for heterozygosity at the target locus and homozygosity for the recurrent parent allele at flanking markers for a diploid species. Assuming no interference in crossover formation, we derived the cumulative density function, probability density function, expected value, and variance of the length of the intact chromosome segment for the following cases: (1) backcross generations prior to detection of a recombinant individual between the target gene and the flanking marker; (2) the backcross generation in which for the first time a recombinant individual is detected, which is selected for further Backcrossing; and (3) subsequent backcross generations after selection of a recombinant. Examples are given of how these results can be applied to investigate the efficiency of marker-assisted Backcrossing for reducing the length of the intact donor chromosome segment around the target gene under various situations relevant in breeding and genetic research.
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plabsim software for simulation of marker assisted Backcrossing
Journal of Heredity, 2000Co-Authors: Matthias Frisch, Martin O Bohn, Albrecht E MelchingerAbstract:In plant breeding and population genetics, computer simulations are a useful tool to investigate problems for which no analytical solutions are available. We present PLABSIM, a computer program to simulate marker-assisted selection in arbitrarily designed backcross programs. The simulated data can be evaluated with PLABSIM for gene frequencies, genotype frequencies, frequency of homozygous loci, length of chromosome segments originating from one ancestor, and the number of marker data points required for a breeding program. In addition to data analysis with PLABSIM, the simulated data can be exported for analysis with statistical software. For investigations of the potential applications of marker-assisted selection, computer simulations are a useful tool. They have been used to investigate problems concerning the use of flanking markers in selection for one or more target genes (Hospital and Charcosset 1997; Visscher et al. 1996) or to accelerate the recovery of the recurrent parent genome in markerassisted backcross programs (Frisch et al. 1999; Hospital et al. 1992; Openshaw et al. 1994). Following Hospital and Charcosset (1997), we refer to the first approach as foreground selection and to the second as background selection. Until now, no software allowed one to simulate marker-assisted selection under realistic genetic models. The program GREGOR (Tinker and Mather 1993) implements the basic principles, but the interactive use and the fact that it simulates only some predefined genetic linkage maps restricts its feasibility for simulation of breeding programs. In this article we present PLABSIM, a tool for simulation of marker-assisted selection programs. The software can be used to investigate the effect of varying population size, marker density, marker positions, and selection strategies on the genetic composition of the breeding product and on the required number of marker data points. PLABSIM is characterized by the following features: (1) Simulations can be made for any diploid genome with an arbitrary number of loci at arbitrary positions on an arbitrary number of chromosomes. (2) The implemented reproduction schemes include all common breeding methods. (3) An arbitrary number of selection steps can be combined to a selection strategy. Selection can be carried out for genotypes at defined loci, or for selection indices calculated from allele frequencies at several loci. (4) The simulated data can be analyzed for a broad range of genetic parameters with PLABSIM. In addition, the data can be exported for analysis with statistical software.
Apichart Vanavichit - One of the best experts on this subject based on the ideXlab platform.
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pseudo Backcrossing design for rapidly pyramiding multiple traits into a preferential rice variety
Rice, 2015Co-Authors: Siriphat Ruengphayak, Ekawat Chaichumpoo, Supaporn Phromphan, Wintai Kamolsukyunyong, Wissarut Sukhaket, Ekapol Phuvanartnarubal, Siripar Korinsak, Apichart VanavichitAbstract:Pyramiding multiple genes into a desirable genetic background can take years to accomplish. In this paper, a pseudo-Backcrossing scheme was designed to shorten the Backcrossing cycle needed. PinK3, an aromatic and potentially high-yielding rice variety—although one that is intolerant to flash flooding (Sub) and susceptible to bacterial leaf blight (BB), leaf-neck blast (BL) and the brown planthopper (BPH)—was used as a genetic basis for significant improvements through gene pyramiding. Four resistance donors with five target genes (Sub1A-C, xa5, Xa21, TPS and SSIIa) and three QTLs (qBph3, qBL1 and qBL11) were backcrossed individually using markers into the pseudo-recurrent parent ‘PinK3’ via one cycle of Backcrossing followed by two cycles of pseudo-Backcrossing and three selfings with rigorous foreground marker-assisted selection. In total, 29 pseudo-backcross inbred lines (BILs) were developed. Genome composition was surveyed using 61 simple sequence repeats (SSRs), 35 of which were located on six carrier chromosomes, with the remainder located on six non-carrier chromosomes. The recurrent genome content (%RGC) and donor genome content (%DGC), which were based on the physical positions of BC1F2, ranged from 69.99 to 88.98% and 11.02 to 30.01%, respectively. For the pseudo-BC3F3BILs, the %RGC and %DGC ranged from 74.50 to 81.30% and 18.70 to 25.50%, respectively. These results indicated that without direct background selection, no further increases in %RGC were obtained during pseudo-Backcrossing, whereas rigorous foreground marker-assisted selection tended to reduce linkage drag during pseudo-Backcrossing. The evaluation of new traits in selected pseudo-BC3F3BILs indicated significant improvements in resistance to BB, BL, BPH and Sub compared with PinK3, as well as significant improvements in grain yield (21-68%) over the donors, although yield was 7-26% lower than in ‘PinK3’. All pyramided lines were aromatic and exhibited improved starch profiles, rendering them suitable for industrial food applications. Results show that our new pyramiding platform, which is based on marker-assisted pseudo-Backcrossing, can fix five target genes and three QTLs into a high-yielding pseudo-recurrent background within seven breeding cycles in four years. This multiple pseudo-Backcrossing platform decreases the time required to generate new rice varieties exhibiting complex, durable resistance to biotic and abiotic stresses in backgrounds with desirable qualities.
Matthias Frisch - One of the best experts on this subject based on the ideXlab platform.
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selection strategies for marker assisted Backcrossing with high throughput marker systems
Theoretical and Applied Genetics, 2011Co-Authors: Eva Herzog, Matthias FrischAbstract:Application of marker-assisted Backcrossing for gene introgression is still limited by the high costs of marker analysis. High-throughput (HT) assays promise to reduce these costs, but new selection strategies are required for their efficient implementation in breeding programs. The objectives of our study were to investigate the properties of HT marker systems compared to single-marker (SM) assays, and to develop optimal selection strategies for marker-assisted Backcrossing with HT assays. We employed computer simulations with a genetic model consisting of 10 chromosomes of 160 cM length to investigate the introgression of a dominant target gene. We found that a major advantage of HT marker systems is that they can provide linkage maps with equally spaced markers, whereas the possibility to provide linkage maps with high marker densities smaller than 10 cM is only of secondary use in marker-assisted Backcrossing. A three-stage selection strategy that combines selection for recombinants at markers flanking the target gene with SM assays and genome-wide background selection with HT markers in the first backcross generation was more efficient than genome-wide background selection with HT markers alone. Selection strategies that combine SM and HT assays were more efficient than genome-wide background selection with HT assays alone. This result was obtained for a broad range of cost ratios of HT and SM assays. A further considerable reduction of the costs could be achieved if the population size in the first backcross generation was twice the population size in generations BC2 and BC3 of a three-generation Backcrossing program. We conclude that selection strategies combining SM and HT assays have the potential to greatly increase the efficiency and flexibility of marker-assisted Backcrossing.
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selection theory for marker assisted Backcrossing
Genetics, 2005Co-Authors: Matthias Frisch, Albrecht E MelchingerAbstract:Marker-assisted Backcrossing is routinely applied in breeding programs for gene introgression. While selection theory is the most important tool for the design of breeding programs for improvement of quantitative characters, no general selection theory is available for marker-assisted Backcrossing. In this treatise, we develop a theory for marker-assisted selection for the proportion of the genome originating from the recurrent parent in a backcross program, carried out after preselection for the target gene(s). Our objectives were to (i) predict response to selection and (ii) give criteria for selecting the most promising backcross individuals for further Backcrossing or selfing. Prediction of response to selection is based on the marker linkage map and the marker genotype of the parent(s) of the backcross population. In comparison to standard normal distribution selection theory, the main advantage of our approach is that it considers the reduction of the variance in the donor genome proportion due to selection. The developed selection criteria take into account the marker genotype of the candidates and consider whether these will be used for selfing or Backcrossing. Prediction of response to selection is illustrated for model genomes of maize and sugar beet. Selection of promising individuals is illustrated with experimental data from sugar beet. The presented approach can assist geneticists and breeders in the efficient design of gene introgression programs.
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marker assisted Backcrossing for simultaneous introgression of two genes
Crop Science, 2001Co-Authors: Matthias Frisch, Albrecht E MelchingerAbstract:Marker-assisted selection is used to accelerate recovery of the recurrent parent genome (RPG) in backcross programs. Our objectives were to compare various selection strategies and breeding plans for the simultaneous introgression of two genes with respect to the RPG recovered and the number of marker data points (MDP) required. Computer simulations were performed with a published genetic map in maize (Zea mays L.) consisting of 80 markers and assuming selection for dominant target genes on the basis of phenotypic evaluation. For unlinked as well as for linked target genes, a shortening of the backcross program from six to three generations resulted from applying marker-assisted background selection. In breeding programs with three backcross generations, the least MDP were required when (i) applying selection strategies consisting of three or four selection steps on the basis of presence of the target genes and selection indices calculated from the marker genotype, (ii) increasing the population size from early to advanced generations, and (iii) merging the target genes in an early generation. These principles can be used for optimizing the design of marker-assisted backcross programs for the simultaneous introgression of two genes.
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marker assisted Backcrossing for introgression of a recessive gene
Crop Science, 2001Co-Authors: Matthias Frisch, Albrecht E MelchingerAbstract:Molecular markers are used to trace the presence of target genes (foreground selection) and accelerate recovery of the recurrent parent genome (background selection) in backcross programs. In this study, we present an approach for introgression of a recessive target gene from a donor into the genetic background of a recipient line by foreground selection combined with background selection for reducing the donor chromosome segment around the target gene. The goal of the proposed breeding plan is to generate with a given probability, q 2 , up to the second backcross generation (BC 2 ) at least k ≥ 1 individuals, which carry the target gene and are homozygous for the recurrent parent alleles at flanking markers, by means of a minimum number of individuals. We provide formulas for calculation of (i) the population size required in generation BC 1 and (ii) the probability of success q 2 of the breeding program in generation BC 2 . The latter depends on the number and genotype of the BC 1 individuals selected for further Backcrossing and the size of their BC 2 families. The optimum allocation of individuals to generations BC 1 and BC 2 was determined by computer simulations for various map distances between the target gene and the flanking markers. Our approach is demonstrated by a numerical example and can assist breeders in the optimum design of breeding programs for marker-assisted introgression of a recessive gene.
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the length of the intact donor chromosome segment around a target gene in marker assisted Backcrossing
Genetics, 2001Co-Authors: Matthias Frisch, Albrecht E MelchingerAbstract:Recurrent Backcrossing is an established procedure to transfer target genes from a donor into the genetic background of a recipient genotype. By assessing the parental origin of alleles at markers flanking the target locus one can select individuals with a short intact donor chromosome segment around the target gene and thus reduce the linkage drag. We investigated the probability distribution of the length of the intact donor chromosome segment around the target gene in recurrent Backcrossing with selection for heterozygosity at the target locus and homozygosity for the recurrent parent allele at flanking markers for a diploid species. Assuming no interference in crossover formation, we derived the cumulative density function, probability density function, expected value, and variance of the length of the intact chromosome segment for the following cases: (1) backcross generations prior to detection of a recombinant individual between the target gene and the flanking marker; (2) the backcross generation in which for the first time a recombinant individual is detected, which is selected for further Backcrossing; and (3) subsequent backcross generations after selection of a recombinant. Examples are given of how these results can be applied to investigate the efficiency of marker-assisted Backcrossing for reducing the length of the intact donor chromosome segment around the target gene under various situations relevant in breeding and genetic research.
Gavin J Horsburgh - One of the best experts on this subject based on the ideXlab platform.
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Hybridization but No Evidence for Backcrossing and Introgression in a Sympatric Population of Great Reed
2016Co-Authors: Clamorous Reed Warblers, Bengt Hansson, Maja Tarka, Deborah A Dawson, Gavin J HorsburghAbstract:Hybridization is observed frequently in birds, but often it is not knownwhether the hybrids are fertile and if Backcrossing occurs. The breeding ranges of the great reed warbler (Acrocephalus arundinaceus) and the clamorous reed warbler (A. stentoreus) overlap in southern Kazakhstan and a previous study has documented hybridization in a sympatric population. In the present study, we first present a large set of novel microsatellite loci isolated and characterised in great reed warblers. Secondly, we evaluate whether hybridization in the sympatric breeding population has been followed by Backcrossing and introgression. We isolated 181 unique microsatellite loci in great reed warblers. Of 41 loci evaluated, 40 amplified and 30 were polymorphic. Bayesian clustering analyses based on genotype data from 23 autosomal loci recognised two well-defined genetic clusters corresponding to the two species. Individuals clustered to a very high extent to either of these clusters (admixture proportions $0.984) with the exception of four previously suggested arundinaceus–stentoreus hybrid birds that showed mixed ancestry (admixture proportions 0.495–0.619). Analyses of simulated hybrids and backcrossed individuals showed that the sampled birds do not correspond to first–fourth-generation backcrosses, and that fifth or higher generation backcrosses to a high extent resemble ‘pure ’ birds at this set of markers. We conclude that these novel microsatellite loci provide a useful molecular resource for Acrocephalus warblers. The time to reach reproductive isolation is believed to be very long in birds, approximately 5 Myrs, and with an estimated divergence time of 2 Myrs between these warblers, some Backcrossing and introgression coul
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hybridization but no evidence for Backcrossing and introgression in a sympatric population of great reed warblers and clamorous reed warblers
PLOS ONE, 2012Co-Authors: Bengt Hansson, Maja Tarka, Deborah A Dawson, Gavin J HorsburghAbstract:Hybridization is observed frequently in birds, but often it is not known whether the hybrids are fertile and if Backcrossing occurs. The breeding ranges of the great reed warbler (Acrocephalus arundinaceus) and the clamorous reed warbler (A. stentoreus) overlap in southern Kazakhstan and a previous study has documented hybridization in a sympatric population. In the present study, we first present a large set of novel microsatellite loci isolated and characterised in great reed warblers. Secondly, we evaluate whether hybridization in the sympatric breeding population has been followed by Backcrossing and introgression. We isolated 181 unique microsatellite loci in great reed warblers. Of 41 loci evaluated, 40 amplified and 30 were polymorphic. Bayesian clustering analyses based on genotype data from 23 autosomal loci recognised two well-defined genetic clusters corresponding to the two species. Individuals clustered to a very high extent to either of these clusters (admixture proportions ≥0.984) with the exception of four previously suggested arundinaceus–stentoreus hybrid birds that showed mixed ancestry (admixture proportions 0.495–0.619). Analyses of simulated hybrids and backcrossed individuals showed that the sampled birds do not correspond to first–fourth-generation backcrosses, and that fifth or higher generation backcrosses to a high extent resemble ‘pure’ birds at this set of markers. We conclude that these novel microsatellite loci provide a useful molecular resource for Acrocephalus warblers. The time to reach reproductive isolation is believed to be very long in birds, approximately 5 Myrs, and with an estimated divergence time of 2 Myrs between these warblers, some Backcrossing and introgression could have been expected. However, there was no evidence for Backcrossing and introgression suggesting that hybrids are either infertile or their progeny inviable. Very low levels of introgression cannot be excluded, which still may be an important factor as a source of new genetic variation.
Shree P Singh - One of the best experts on this subject based on the ideXlab platform.
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introgressing white mold resistance from phaseolus species of the secondary gene pool into common bean
Crop Science, 2009Co-Authors: Shree P Singh, Henry Teran, Howard F Schwartz, Kristen Otto, Margarita LemaAbstract:White mold (WM) caused by Sclerotinia scle- rotiorum (Lib.) de Bary is a severe disease of common bean (Phaseolus vulgaris L.) in North America. Common bean has only partial resis- tance. However, some accessions of P. coc- cineus L. and other species of the secondary gene pool (SGP) are highly resistant. The objectives of this study were to (i) introgress WM resistance from the SGP and (ii) compare resistance of interspecifi c breeding lines (IBL) VCW 54 and VCW 55, developed by congruity Backcrossing between 'ICA Pijao' and P. coc- cineus accession G 35172, and VRW 32, derived from recurrent Backcrossing of ICA Pijao with P. costaricensis accession S 33720 with known sources of resistance. The three IBL, ICA Pijao, and susceptible ('Othello') and resistant (92BG- 7, A 195, G 122, I9365-25, 'ICA Bunsi', and VA 19) genotypes were screened in the greenhouse in Colorado and Idaho in 2007 and 2008 and in the fi eld in Idaho in 2007. White mold resistance was successfully introgressed from two of the three Phaseolus species (P. coccineus and P. costaricensis) of the SGP. VCW 54 had the high- est WM resistance, and VCW 55 and VRW 32 had similar resistance as previously reported. These sources of WM resistance should be introgressed into common bean cultivars.
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comparison of recurrent and congruity Backcrossing for interracial hybridization in common bean
Euphytica, 1995Co-Authors: Carlos A Urrea, Shree P SinghAbstract:Two common bean (Phaseolus vulgaris L.) cultivars were used for recurrent Backcrossing (i.e., repeated Backcrossing to one of the parents) to both parents independently and for congruity Backcrossing (i.e., Backcrossing alternately to both parents). One cultivar, ‘ICA Pijao’ of race Mesoamerica, was late maturing, with erect type II growth habit and small seeds. The other was ‘Pinto UI 114’ of race Durango, an early maturing cultivar with prostrate type III growth habit and medium seeds. One to three recurrent backcrosses (RBC) to both parents, and two rounds of congruity backcrosses (CBC), were made. Thirty-two random lines from each method along with two parents were compared in a reps-in-set design at two locations (Popayan and Quilichao) in Colombia in 1992–1993.
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interspecific hybridization between common and tepary beans increased hybrid embryo growth fertility and efficiency of hybridization through recurrent and congruity Backcrossing
Theoretical and Applied Genetics, 1994Co-Authors: A Mejiajimenez, Claritza Munoz, Hansjorg Jacobsen, William M Roca, Shree P SinghAbstract:Cultivated common bean (Phaseolus vulgaris L.) and tepary bean (Phaseolus acutifolius A. Gray) genotypes possessing desirable agronomic traits were hybridized. The F1 hybrids were backcrossed twice with the common bean (i.e., recurrent Backcrossing). Also, alternate backcrosses with common and tepary beans (i.e., congruity Backcrossing) were carried out. Embryo culture was necessary for all initial interspecific crosses, and its requirement was proportionally lower when the common bean was used as the recurrent parent and as the last parent of congruity backcrosses. Modification of the embryo culture technique was necessary to produce congruity hybrids. Effects of both tepary and common bean genotypes on the success rate of hybridization were observed. Tepary accession G 40001 and common bean cultivar ICA Pijao facilitated interspecies hybridization. Growth of hybrid embryos before rescue, recovery of mature hybrid plants, and the vigor and fertility of F1 hybrids all increased with increased recurrent and congruity backcrosses and intermatings between male-sterile F1 and selected fertile F2 plants of the third and fifth congruity backcrosses. Introgression of tepary genes was verified by means of seed protein electrophoretic analysis and morphological markers. The results suggest that congruity Backcrossing can help to gradually reduce or overcome P. vulgaris x P. acutifolius hybridization barriers such as genotype incompatibility, early embryo abortion, hybrid sterility, and lower frequencies of hybridization.
