scholarly journals Genetic Mapping of the HLA1 Locus Causing Hybrid Lethality in Nicotiana Interspecific Hybrids

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2062
Author(s):  
Takahiro Tezuka ◽  
Naoto Kitamura ◽  
Sae Imagawa ◽  
Akira Hasegawa ◽  
Kumpei Shiragaki ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Dna Markers ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Interspecific Cross ◽  
Disease Resistance Gene ◽  
Hybrid Lethality ◽  
F1 Hybrid ◽  
F2 Population ◽  
Simple Sequence

Hybrid lethality, a postzygotic mechanism of reproductive isolation, is a phenomenon that causes the death of F1 hybrid seedlings. Hybrid lethality is generally caused by the epistatic interaction of two or more loci. In the genus Nicotiana, N. debneyi has the dominant allele Hla1-1 at the HLA1 locus that causes hybrid lethality in F1 hybrid seedlings by interaction with N. tabacum allele(s). Here, we mapped the HLA1 locus using the F2 population segregating for the Hla1-1 allele derived from the interspecific cross between N. debneyi and N. fragrans. To map HLA1, several DNA markers including random amplified polymorphic DNA, amplified fragment length polymorphism, and simple sequence repeat markers, were used. Additionally, DNA markers were developed based on disease resistance gene homologs identified from the genome sequence of N. benthamiana. Linkage analysis revealed that HLA1 was located between two cleaved amplified polymorphic sequence markers Nb14-CAPS and NbRGH1-CAPS at a distance of 10.8 and 10.9 cM, respectively. The distance between these markers was equivalent to a 682 kb interval in the genome sequence of N. benthamiana.

scholarly journals Comparative Analysis of Genetic Similarity between Perennial Ryegrass Genotypes Investigated With AFLPs, ISSRs, RAPDs and SSRs

2011 ◽  
Vol 42 (No. 3) ◽  
pp. 87-94 ◽  
Author(s):  
U.K. Posselt ◽  
P. Barre ◽  
G. Brazauskas ◽  
L.B. Turner
Keyword(s):  
Perennial Ryegrass ◽  
Simple Sequence Repeat ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Correlation Coefficients ◽  
Inter Simple Sequence Repeat ◽  
Grass Species ◽  
Sequence Repeat ◽  
Simple Sequence

Perennial ryegrass (Lolium perenne L.) is the most important grass species used in temperate grassland agriculture. Our objective was to obtain an overview of the genetic relationships between 20 individual genotypes of perennial ryegrass of diverse origins, using amplified fragment length polymorphism (AFLP), inter-simple sequence repeat (ISSR), random amplified polymorphic DNA (RAPD) and two sets of simple sequence repeat (SSR) markers. All 20 individuals were uniquely fingerprinted by all four marker systems and comparisons were made on the basis of 85 markers each. Mean genetic similarities were estimated at 0.31, 0.43, 0.23 and 0.15 for AFLPs, ISSRs, RAPDs and SSRs, respectively. Cophenetic values resulted in good (AFLP and SSR-B = 0.88) to moderately good fits (ISSR = 0.76, RAPD = 0.70, and SSR-A = 0.79). Comparing the four marker systems to each other, AFLP and SSR-A were correlated best (r = 0.57). All other comparisons revealed rather low correlation coefficients in the Mantel Z test. With twice as many markers cophenetic values increased to a very good fit for AFLPs (0.90) and SSRs (0.92).      

scholarly journals Identification of Simple-sequence Repeats in Malus (Apple)

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 855D-855 ◽  
Author(s):  
Amy K. Szewc-McFadden ◽  
Sharon Bliek ◽  
Christopher G. Alpha ◽  
Warren F. Lamboy ◽  
James R. McFerson
Keyword(s):  
Simple Sequence Repeats ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Germplasm Characterization ◽  
The Core ◽  
Marker Data ◽  
Core Subset ◽  
Germplasm Collections ◽  
Ssr Loci ◽  
Simple Sequence

Simple-sequence repeats (SSRs) are efficient and informative DNA markers with great potential for germplasm characterization. When used to characterize large arrays of accessions, such as the core subset of the USDA/ARS Malus collection, SSRs may be more effective than other approaches, such as restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD). For example, SSRs can be PCR-amplified and fluorescence-based detected; they also appear to be abundantly disbursed throughout plant genomes and yield abundant polymorphisms in most taxa studied. We are conducting an extensive screening of a size-fractionated library of Malus ×domestica cv. Golden Delicious to identify and characterize selected SSR loci. We are applying genetic information revealed by SSR loci in combination with passport and horticultural data to better comprehend genetic identity and relatedness in Malus germplasm collections and help develop the Malus core subset. Ultimately, application of molecular marker data will permit improved conservation and use of genetic resources.

Correction of the misclassification of species in the Portuguese collection of Cucurbita pepo L. using DNA markers

2014 ◽  
Vol 12 (S1) ◽  
pp. S160-S163 ◽  
Author(s):  
Ricardo Rodrigues ◽  
Iris Veiga ◽  
António Marreiros ◽  
Filomena Rocha ◽  
José Leitão
Keyword(s):  
Dna Markers ◽  
Cucurbita Pepo ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Germplasm Collection ◽  
Phenotypic Analysis ◽  
Germplasm Collections ◽  
Molecular Patterns ◽  
Rapd And Issr ◽  
Single Sequence

In this study, the genetic variability among 130 accessions of the Portuguese germplasm collection of Cucurbita pepo L. maintained at the Banco Português de Germoplasma Vegetal was assessed using AFLP (amplified fragment length polymorphism) and RAPD (random amplified polymorphic DNA) techniques for the identification of a genetically diverse core group of accessions for field phenotypic analysis. The surprisingly completely different molecular patterns exhibited by multiple accessions was later confirmed in the distribution of the putative C. pepo plants into two clusters drastically separated at a very low level of genetic similarity (DICE coefficient = 0.37). Additional analyses with RAPD and ISSR (inter single sequence repeat) markers and the introduction of standard genotypes of C. maxima L. and C. moschata L. into the analyses allowed the identification of multiple accessions of the last species wrongly included in the C. pepo collection. This study is a good example of the usefulness of DNA markers in the establishment and management of plant germplasm collections.

A gene controlling sex in grapevines placed on a molecular marker-based genetic map

Genome ◽  
2000 ◽  
Vol 43 (2) ◽  
pp. 333-340 ◽  
Author(s):  
M A Dalbó ◽  
G N Ye ◽  
N F Weeden ◽  
H Steinkellner ◽  
K M Sefc ◽  
...  
Keyword(s):  
Molecular Marker ◽  
Dna Markers ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Basic Number ◽  
Genetic Maps ◽  
Hybrid Population ◽  
Linkage Groups ◽  
Starting Point ◽  
Map Distance

Genetic maps of Vitis (2n = 38) have been constructed from an interspecific hybrid population of 58 seedlings of the cross 'Horizon' ('Seyval' × 'Schuyler') × Illinois 547-1 (V. cinerea B9 × V. rupestris B38). The maps were initially constructed based on 277 RAPD (random amplified polymorphic DNA) markers using a double-pseudotestcross strategy. Subsequently, 25 microsatellites, 4 CAPS (cleaved amplified polymorphic sequence), and 12 AFLP (amplified fragment length polymorphism) markers were added to the maps. Another 120 markers, mostly those segregating 3:1, were also assigned but not positioned on the linkage groups in the two maps. The 'Horizon' map consisted of 153 markers covering 1199 cM, with an average map distance of 7.6 cM between markers. The Illinois 547-1 map had 179 markers covering 1470 cM, with an average map distance of 8.1 cM. There were 20 linkage groups in each map, one more than the basic number of chromosomes in grapes. Ten linkage groups in each map were identified as homologous using 16 microsatellite and 2 CAPS markers polymorphic in both parents. A single locus controlling sex in grapes mapped close to a microsatellite marker. These maps provide enough coverage of the genome for QTL (quantitative trait loci) analysis and as a starting point for positional gene cloning in grapes. Key words: Vitis, RAPD, microsatellite, SSR, CAPS.

scholarly journals Separation of the genera in the subtribe Cassiinae (Leguminosae: Caesalpinioidae) using molecular markers

2011 ◽  
Vol 25 (1) ◽  
pp. 223-233 ◽  
Author(s):  
Laxmikanta Acharya ◽  
Arup Kumar Mukherjee ◽  
Pratap Chandra Panda
Keyword(s):  
Molecular Markers ◽  
Simple Sequence Repeat ◽  
Fragment Length Polymorphism ◽  
Molecular Level ◽  
Random Amplified Polymorphic Dna ◽  
Inter Simple Sequence Repeat ◽  
Aflp Data ◽  
High Bootstrap ◽  
Simple Sequence ◽  
Issr Primers

Random amplified polymorphic DNA (RAPD), Inter simple sequence repeat (ISSR) and Amplified fragment length polymorphism (AFLP) markers were used to verify the segregation of the genus Cassia L. senso lato into three distinct genera namely Chamaecrista Moench., Senna P. Mill. and Cassia L. sensostricto Eighteen representatives of the three taxa were characterized using the molecular markers. 25 RAPD, six ISSR primers and six AFLP primer combinations resulted in the amplification of 612, 115 and 622 bands (loci) respectively. Most of the loci are found to be polymorphic, showing high degrees of genetic diversity among the different taxa studied. The dendrogram constructed on the basis of the RAPD, ISSR and AFLP data using SHAN clustering, divided Cassia L. senso lato. into three different clusters as Chamaecrista Moench. Senna P. Mill. and Cassia L. senso stricto High bootstrap value revealed that all the clusters were stable and robust. It was observed from the present investigation that these genera have their identity at molecular level, which supports the elevation of the genus Cassia L. senso lato to the level of subtribe Cassiinae and segregation into three distinct genera instead of intrageneric categories.

DNA markers for downy mildew resistance genes in sorghum

Genome ◽  
1995 ◽  
Vol 38 (4) ◽  
pp. 823-826 ◽  
Author(s):  
P. S. Bhavanishankara Gowda ◽  
Richard A. Frederiksen ◽  
Clint W. Magill ◽  
Guo-Wei Xu
Keyword(s):  
Downy Mildew ◽  
Resistance Gene ◽  
Dna Markers ◽  
Fragment Length Polymorphism ◽  
Mapping Population ◽  
Random Amplified Polymorphic Dna ◽  
Downy Mildew Resistance ◽  
Mildew Resistance ◽  
Sorghum Line ◽  
Rflp Rapd

The random amplified polymorphic DNA technique was used to find markers for a downy mildew resistance gene in sorghum. Of the 674 random primers screened for polymorphism, 2 amplified fragments were linked to a downy mildew resistance gene in sorghum line SC414. Utilization of an existing restriction fragment length polymorphism mapping population (IS3620C × BTx623) also revealed two markers that are linked to a different resistance gene in another sorghum line, BTx623.Key words: sorghum, downy mildew, RFLP, RAPD.

Development of a second generation linkage map for almond using RAPD and SSR markers

Genome ◽  
2000 ◽  
Vol 43 (4) ◽  
pp. 649-655 ◽  
Author(s):  
T Joobeur ◽  
N Periam ◽  
M C de Vicente ◽  
G J King ◽  
P Arús
Keyword(s):  
Simple Sequence Repeats ◽  
Dna Markers ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Maps ◽  
Linkage Groups ◽  
Prunus Amygdalus ◽  
Total Size ◽  
Length Polymorphisms ◽  
Simple Sequence

Fifty-four RAPD (random amplified polymorphic DNA) markers and 6 SSRs (simple sequence repeats) were included in a molecular marker map with 120 RFLPs (restriction fragment length polymorphisms) and 7 isozyme genes previously constructed using the offspring of a cross between the almond (Prunus amygdalus) cultivars 'Ferragnès' and 'Tuono'. Only highly reproducible RAPDs segregating 1:1 were used. To identify these markers, a total of 325 primers were screened, from which 41 produced RAPDs useful for mapping. Polymorphism was detected in six of the eight Prunus SSRs (simple sequence repeats) studied, thus enabling these to be mapped. All markers were placed on the 8 linkage groups previously identified. The number of new markers included in the map of 'Ferragnès' was 33 for a total of 126, and 30 in the map of 'Tuono' for a total of 99. The sizes of the maps of 'Ferragnès' (415 cM) and 'Tuono' (416 cM) were similar, representing a 5% increase over the maps constructed solely with isozymes and RFLPs. The estimated total size of the almond map was of 457 cM. Some markers were placed in zones with low density of markers and others in the extreme of linkage groups. The use of RAPD markers to complete genetic maps constructed with transferable markers is discussed.Key words: almond, Prunus amygdalus, RAPD, SSR, mapping.

Regional and racial specificities in sorghum germplasm assessed with DNA markers

Genome ◽  
1996 ◽  
Vol 39 (3) ◽  
pp. 579-587 ◽  
Author(s):  
Antonio C. de Oliveira ◽  
Todd Richter ◽  
Jeffrey L. Bennetzen
Keyword(s):  
Fragment Length Polymorphism ◽  
Geographical Origin ◽  
Random Amplified Polymorphic Dna ◽  
Region Of Origin ◽  
Distinctive Group ◽  
Dna Restriction ◽  
Germplasm Diversity ◽  
Novel Alleles ◽  
Simple Sequence ◽  
Sorghum Germplasm

Three different molecular marker technologies were used to determine the relatedness of 84 different lines of sorghum. Both racial characterization and geographical origin were found to be correlated with relatedness. In some cases, the region of origin was the more significant factor, where samples of different races from the same locality were more closely related than were samples of the same race from different localities. Wild sorghums were shown to have few novel alleles, suggesting that they would be poor sources of germplasm diversity. The results also indicated that Chinese sorghums are a narrow and distinctive group that is most closely related to race bicolor. Key words : Sorghum bicolor, germplasm diversity, random amplified polymorphic DNA, restriction fragment length polymorphism, simple sequence repeats.

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