Detecting and mapping repulsion-phase linkage in polyploids with polysomic inheritance

2001 ◽  
Vol 103 (1) ◽  
pp. 136-143 ◽  
Author(s):  
L. Qu ◽  
J. F. Hancock
Keyword(s):  
Repulsion Phase ◽  
Polysomic Inheritance

Molecular mapping of a thermosensitive genetic male sterility gene in rice using bulked segregant analysis

Genome ◽  
1997 ◽  
Vol 40 (2) ◽  
pp. 188-194 ◽  
Author(s):  
P. K. Subudhi ◽  
R. P. Borkakati ◽  
S. S. Virmani ◽  
N. Huang
Keyword(s):  
Male Sterility ◽  
Molecular Mapping ◽  
Bulked Segregant Analysis ◽  
Pcr Primers ◽  
Rflp Markers ◽  
Arbitrary Primers ◽  
Repulsion Phase ◽  
Genetic Male Sterility ◽  
True Breeding ◽  
Efficient Alternative

The thermosensitive genetic male sterility (TGMS) system is considered to be a more efficient alternative to the cytoplasmic male sterility (CMS) system for hybrid rice. An F2 population from a cross between a TGMS mutant line (IR32364TGMS) and IR68 was used to map the TGMS gene tms3(t). Fertile and sterile bulks were constructed following the classification of F2 plants into true breeding sterile, fertile, and segregating fertile plants based on F3 family studies. From the survey of 389 arbitrary primers in bulked segregant analysis, four RAPD markers were identified in which three, OPF182600, OPB19750, and OPAA7550, were linked to tms3(t) in repulsion phase and one, OPAC3640, was linked to tms3(t) in coupling phase. The tms3(t) gene was flanked by OPF182600 and OPAC3640 on one side and by OPAA7550 and OPB19750 on the other side. All four markers were low-copy sequences and two of them (OPF182600 and OPAC3640) detected polymorphism when the markers were used to probe the genomic blots. Subsequently, OPAC3640 was mapped to the short arm of chromosome 6 using a mapping population available at IRRI. However, no RFLP markers from this region showed linkage to tms3(t) owing to the lack of polymorphism between the parents. All RAPD fragments were cloned and partially sequenced from both ends. Thus, PCR primers can be designed to develop PCR markers for marker-assisted breeding to facilitate the transfer of tms3(t) from one genetic background to another.Key words: bulked segregant analysis, gene tagging, marker-assisted selection, RAPD, TGMS.

Development of SCAR markers linked to zt-2, one of the genes controlling absence of tannins in faba bean

2008 ◽  
Vol 59 (1) ◽  
pp. 62 ◽  
Author(s):  
Natalia Gutierrez ◽  
C. M. Avila ◽  
M. T. Moreno ◽  
A. M. Torres
Keyword(s):  
Faba Bean ◽  
Bulked Segregant Analysis ◽  
Consensus Sequence ◽  
Flower Colour ◽  
Cost Effective ◽  
Tannin Content ◽  
Repulsion Phase ◽  
Protein Levels ◽  
F2 Population ◽  
Faba Beans

Faba beans (Vicia faba L.) have a great potential as a protein-rich fodder crop, but anti-nutritional factors such as condensed tannins reduce the biological value of their protein. Tannins can be removed from seeds by any of the two complementary genes, zt-1 and zt-2, which also determine white-flowered plants. The less common gene, zt-2, is also associated with increased protein levels and energy values and reduced fibre content of the seeds. To identify a cost-effective marker linked to zt-2, we analysed a segregating F2 population derived from the cross between the coloured flower and high tannin content genotype Vf6 and a zt-2 line. By using Bulked Segregant Analysis (BSA), five RAPD markers linked in coupling and repulsion phase to zt-2 were identified and their conversion into Sequence Characterised Amplified Regions (SCARs) was attempted. Amplification of the SCARS was more consistent, although the initial polymorphism was lost. Restriction digestion of SCAR SCAD16589 with AluI (SCAD16-A), Bsp120I (SCAD16-B) and HinfI (SCAD16-H) revealed clear differences due to the amplification of different loci. The consensus sequence of these CAPs (Cleavage Amplification Polymorphisms) markers allowed discrimination of three bands from which two new forward SCAR primers were developed based on specific sequences from zero tannin and high tannin content genotypes. To improve the efficiency of the marker screening, a multiplex PCR was developed that allowed the simultaneous amplification of the SCAR with the same advantages as a codominant marker. Marker validation was carried out with a new F2 population segregating for flower colour and tannin content, underscoring the potential of these markers in breeding selection to introgress the zt-2 gene for the development of new tannin free faba bean cultivars.

scholarly journals Analysis of Molecular Markers Genetically Linked to the Leptosphaeria maculans Avirulence Gene AvrLm1 in Field Populations Indicates a Highly Conserved Event Leading to Virulence on Rlm1 Genotypes

2002 ◽  
Vol 15 (7) ◽  
pp. 672-682 ◽  
Author(s):  
Agnès Attard ◽  
Lilian Gout ◽  
Mathieu Gourgues ◽  
Marie-Line Kühn ◽  
Jacques Schmit ◽  
...  
Keyword(s):  
Genetic Map ◽  
Large Scale ◽  
Polymerase Chain Reaction Amplification ◽  
Leptosphaeria Maculans ◽  
Avirulence Gene ◽  
Bac Contig ◽  
Genome Region ◽  
Repulsion Phase ◽  
Field Isolates

Map-based cloning of the avirulence gene AvrLm1 of Leptosphaeria maculans was initiated utilizing a genetic map of the fungus and a BAC library constructed from an AvrLm1 isolate. Seven polymorphic DNA markers closely linked to AvrLm1 were identified. Of these, two were shown to border the locus on its 5′ end and were present, with size polymorphism, in both the virulent and the avirulent isolates. In contrast, three markers, J19-1.1, J53-1.3 (in coupling phase with avirulence), and Vir1 (in repulsion phase with avirulence), cosegregated with AvrLm1 in 312 progeny from five in vitro crosses. J19-1.1 and J53-1.3 were never amplified in the virulent parents or progeny, whereas Vir1 was never amplified in the avirulent parents or progeny. J19-1.1 and J53-1.3 were shown to be separated by 40 kb within a 184-kb BAC contig. In addition, the 1.6-cM genetic distance between J53-1.3 and the nearest recombinant marker corresponded to a 121-kb physical distance. When analyzing a European Union-wide collection of 192 isolates, J53-1.3, J19-1.1, and Vir1 were found to be closely associated with the AvrLm1 locus. The results of polymerase chain reaction amplification with primers for the three markers were in accordance with the interaction phenotype for 92.2% (J53-1.3), 90.6% (J19-1.1), and 88.0% (Vir1) of the isolates. In addition, genome organization of the AvrLm1 region was highly conserved in field isolates, because 89.1% of the avirulent isolates and 79.0% of the virulent isolates showed the same association of markers as that of the parents of in vitro crosses. The large-scale analysis of field isolates with markers originating from the genetic map therefore confirms (i) the physical proximity between the markers and the target locus and (ii) that AvrLm1 is located in (or close to) a recombination-deficient genome region. As a consequence, map-based markers provided us with high-quality markers for an overview of the occurrence of race “AvrLm1” at the field scale. These data were used to propose hypotheses on evolution towards virulence in field isolates.

scholarly journals MEIOTIC BEHAVIOR OF COMPOUND AUTOSOMES IN FEMALES OF DROSOPHILA MELANOGASTER: INTERCHROMOSOMAL EFFECTS AND THE SOURCE OF SPONTANEOUS NONSEGREGATION

Genetics ◽  
1980 ◽  
Vol 96 (2) ◽  
pp. 455-470
Author(s):  
Hideh Harger ◽  
David G Holm
Keyword(s):  
Drosophila Melanogaster ◽  
X Chromosome ◽  
Inverse Correlation ◽  
Proximal Region ◽  
Crossing Over ◽  
X Chromosomes ◽  
Repulsion Phase ◽  
Base Level ◽  
Exchange Processes ◽  
Spontaneous Frequency

ABSTRACT In females of Drosophila melanogaster, compound autosomes enter the repulsion phase of meiosis uncommitted to a particular segregation pattern because their centromeres are not restricted to a bivalent pairing complex as a consequence of crossing over. Their distribution at anaphase, therefore, is determined by some meiotic property other than exchange pairing, a property that for many years has been associated with the concept of nonhomologous pairing. In the absence of heterologous rearrangements or a free Y chromosome, C(3L) and C(3R) are usually recovered in separate gametes, that is as products of meiotic segregation. Nevertheless, there is a regular, albeit infrequent, recovery of reciprocal meiotic products (the nonsegregational products) that are disomic and nullosomic for compound thirds. The frequency of these exceptions, which is normally between 0.5 and 5.0%, differs for the various strains examined, but remains constant for any given strain. Since previous studies have not uncovered a cause for this base level of nonsegregation, it has been referred to as the spontaneous frequency. In this study, crosses between males and females whose X chromosomes, as well as compound autosomes, are differentially marked reveal a highly significant positive correlation between the frequency of compound-autosome nonsegregation and the frequency of X-chromosome nondisjunction. However, an inverse correlation is found when the frequency of nondisjunction is related to the frequency of crossing over in the proximal region of the X chromosome. These findings have been examined with reference to the distributive pairing and the chromocentral models and interpreted as demonstrating (1) that nonsegregational meiotic events arise primarily as a result of nonhomologous interactions, (2) that forces responsible for the segregation of nonhomologous chromosomes are properties of the chromocentral region, and (3) that these forces come into expression after the exchange processes are complete.

Efficient multipoint mapping: making use of dominant repulsion-phase markers

2003 ◽  
Vol 107 (6) ◽  
pp. 1102-1112 ◽  
Author(s):  
D. I. Mester ◽  
Y. I. Ronin ◽  
Y. Hu ◽  
J. Peng ◽  
E. Nevo ◽  
...  
Keyword(s):  
Repulsion Phase ◽  
Multipoint Mapping

scholarly journals Multiple Resistance to Meloidogyne spp. and to Bipartite and Monopartite Begomovirus spp. in Wild Solanum (Lycopersicon) Accessions

Plant Disease ◽  
2010 ◽  
Vol 94 (2) ◽  
pp. 179-185 ◽  
Author(s):  
R. C. Pereira-Carvalho ◽  
L. S. Boiteux ◽  
M. E. N. Fonseca ◽  
J. A. Díaz-Pendón ◽  
E. Moriones ◽  
...  
Keyword(s):  
Large Scale ◽  
Virus Disease ◽  
Systemic Infection ◽  
Severity Index ◽  
Bipartite Begomovirus ◽  
Monopartite Begomovirus ◽  
Repulsion Phase ◽  
Rugose Mosaic ◽  
Infested Field ◽  
Meloidogyne Spp

The Ty-1 locus confers tolerance to monopartite and bipartite Begomovirus spp. (genus Begomovirus, family Geminiviridae) and this phenotype is improved in homozygous tomato lines. However, the gene Mi (Meloidogyne spp. resistance) is in repulsion phase linkage with Ty-1, which hampers the large-scale development of multiresistant inbred lines. Seventy-one Solanum (section Lycopersicon) accessions were whitefly inoculated with the bipartite Begomovirus sp. Tomato rugose mosaic virus (ToRMV) and simultaneously infested with a mixture of Meloidogyne incognita and M. javanica under greenhouse conditions in Brazil. Accessions were then transplanted into a nematode-infested field with natural ToRMV infection. A severity index was used to evaluate ToRMV reaction. Nematode evaluation was done by counting the number of galls per root system. Seventeen accessions with Meloidogyne spp. and ToRMV resistance were selected and evaluated in Spain against three monopartite Begomovirus spp. associated with the tomato yellow leaf curl virus disease, using infectious clones. Systemic infection was monitored by DNA hybridization. Five S. peruvianum accessions (PI-306811, PI-365951, LA-1609, LA-2553, and CNPH-1194) displayed nematode and broad-spectrum resistance to all Begomovirus spp. tested in both continents. From the breeding standpoint, accessions combining resistance to Meloidogyne spp. and to bipartite and monopartite Begomovirus spp. would be useful for the development of elite lines expressing all traits in homozygous condition.

Identification of coupling and repulsion phase RAPD markers for powdery mildew resistance gene er-1 in pea

Genome ◽  
1998 ◽  
Vol 41 (3) ◽  
pp. 440-444 ◽  
Author(s):  
K R Tiwari ◽  
G A Penner ◽  
T D Warkentin
Keyword(s):  
Powdery Mildew ◽  
Resistance Gene ◽  
Rapd Markers ◽  
Powdery Mildew Resistance ◽  
Bulked Segregant Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Powdery Mildew Resistance Gene ◽  
Erysiphe Pisi ◽  
Mildew Resistance ◽  
Repulsion Phase

Powdery mildew is a serious disease of pea caused by the obligate parasite Erysiphe pisi Syd. Random amplified polymorphic DNA (RAPD) analysis has emerged as a cost-effective and efficient marker system. The objective of this study was to identify RAPD markers for powdery mildew resistance gene er-1. The resistant cultivar Highlight (carrying er-1) and the susceptible cultivar Radley were crossed, and F3 plants were screened with Operon (OP) and University of British Columbia (UBC) primers, using bulked segregant analysis. A total of 416 primers were screened, of which amplicons of three Operon primers, OPO-18, OPE-16, and OPL-6, were found to be linked to er-1. OPO-181200 was linked in coupling (trans to er-1) and no recombinants were found. OPE-161600 (4 ± 2 cM) and OPL-61900 (2 ± 2 cM) were linked in repulsion (cis to er-1). The fragments OPO-181200 and OPE-161600 were sequenced and specific primers designed. The specific primer pair Sc-OPO-181200 will be useful in identifying homozygous resistant individuals in F2 and subsequent segregating generations. Sc-OPE-161600 will have greatest utility in selecting heterozygous BC\dn6 nF1 individuals in backcross breeding programs.Key words: bulked segregant analysis,Erysiphe pisi, pea, RAPD.

scholarly journals Improved Selection with Newly Identified RAPD Markers Linked to Resistance Gene to Four Pathotypes of Colletotrichum lindemuthianum in Common Bean

1999 ◽  
Vol 89 (4) ◽  
pp. 281-285 ◽  
Author(s):  
Ana Lilia Alzate-Marin ◽  
Henrique Menarim ◽  
Geraldo Assis de Carvalho ◽  
Trazilbo José de Paula ◽  
Everaldo Gonçalves de Barros ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Resistance Genes ◽  
Rapd Markers ◽  
Single Gene ◽  
Colletotrichum Lindemuthianum ◽  
Susceptible Cultivar ◽  
Coupling Phase ◽  
Repulsion Phase ◽  
Complex Locus ◽  
Two Populations

Three F2 populations derived from crosses between the resistant cultivar AB 136 and the susceptible cultivar Michelite (MiA), and one F2 population derived from a cross between AB 136 and Mexico 222 (MeA), were used to identify markers linked to anthracnose resistance genes present in cultivar AB 136. Primer OPZ04 produced a DNA band (OPZ04560) linked in coupling phase to the resistance gene for pathotype 89 (8.5 ± 0.025 cM) in one population derived from the cross MiA. In the same population, primer OPZ09 produced one band (OPZ09950) linked in repulsion phase (20.4 ± 0.014 cM) to the same resistance gene. The simultaneous use of markers in coupling and in repulsion phases allowed the identification of the three genotypic classes. In the other two populations from cross MiA, OPZ04560 was linked in coupling phase to resistance genes for pathotypes 73 (2.9 ± 0.012 cM) and 81 (2.8 ± 0.017 cM). In population MeA, OPZ04560 was linked in coupling phase (7.5 ± 0.033 cM) to resistance to pathotype 64. These data suggest that a single gene or complex locus of linked resistance genes present in cultivar AB 136 confers resistance to all four pathotypes of C. lindemuthianum.

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