Segmental allotetraploidy and allelic interactions in buffelgrass (Pennisetum ciliare (L.) Link syn. Cenchrus ciliaris L.) as revealed by genome mapping

Genome ◽  
2003 ◽  
Vol 46 (2) ◽  
pp. 304-313 ◽  
Author(s):  
R W Jessup ◽  
B L Burson ◽  
G Burow ◽  
Y -W Wang ◽  
C Chang ◽  
...  
Keyword(s):  
Restriction Fragment ◽  
Fragment Length ◽  
Genome Mapping ◽  
Linkage Groups ◽  
Cenchrus Ciliaris ◽  
Preferential Pairing ◽  
Pennisetum Ciliare ◽  
Length Polymorphisms ◽  
A Genome ◽  
Restriction Fragment Length

Linkage analyses increasingly complement cytological and traditional plant breeding techniques by providing valuable information regarding genome organization and transmission genetics of complex polyploid species. This study reports a genome map of buffelgrass (Pennisetum ciliare (L.) Link syn. Cenchrus ciliaris L.). Maternal and paternal maps were constructed with restriction fragment length polymorphisms (RFLPs) segregating in 87 F1 progeny from an intraspecific cross between two heterozygous genotypes. A survey of 862 heterologous cDNAs and gDNAs from across the Poaceae, as well as 443 buffelgrass cDNAs, yielded 100 and 360 polymorphic probes, respectively. The maternal map included 322 RFLPs, 47 linkage groups, and 3464 cM, whereas the paternal map contained 245 RFLPs, 42 linkage groups, and 2757 cM. Approximately 70 to 80% of the buffelgrass genome was covered, and the average marker spacing was 10.8 and 11.3 cM on the respective maps. Preferential pairing was indicated between many linkage groups, which supports cytological reports that buffelgrass is a segmental allotetraploid. More preferential pairing (disomy) was found in the maternal than paternal parent across linkage groups (55 vs. 38%) and loci (48 vs. 15%). Comparison of interval lengths in 15 allelic bridges indicated significantly less meiotic recombination in paternal gametes. Allelic interactions were detected in four regions of the maternal map and were absent in the paternal map.Key words: linkage map, segmental allopolyploidy, restriction fragment length polymorphism, Poaceae, chromosome pairing.

scholarly journals A genetic linkage map for the domesticated silkworm, Bombyx mori, based on restriction fragment length polymorphisms

1995 ◽  
Vol 66 (2) ◽  
pp. 109-126 ◽  
Author(s):  
Jinrui Shi ◽  
David G. Heckel ◽  
Marian R. Goldsmith
Keyword(s):  
Linkage Map ◽  
Bombyx Mori ◽  
Restriction Fragment ◽  
Fragment Length ◽  
Restriction Fragment Length Polymorphisms ◽  
Genetic Maps ◽  
Crossing Over ◽  
Linkage Groups ◽  
Length Polymorphisms ◽  
Restriction Fragment Length

SummaryWe present data for the initial construction of a molecular linkage map for the domesticated silkworm, Bombyx mori, based on 52 progeny from an F2 cross from a pair mating of inbred strains p50 and C108, using restriction fragment length polymorphisms (RFLPs). The map contains 15 characterized single copy sequences, 36 anonymous sequences derived from a follicular cDNA library, and 10 loci corresponding to a low copy number retrotransposon, mag. The 15 linkage groups and 8 ungrouped loci account for 23 of the 28 chromosomes and span a total recombination length of 413 cM; 10 linkage groups were correlated with established classic genetic maps. Scoring data from Southern blots were analysed using two Pascal programs written specifically to analyse linkage data in Lepidoptera, where females are the heterogametic sex and have achiasmatic meiosis (no crossing-over). These first examine evidence for linkage by calculating the maximum lod score under the hypothesis that the two loci are linked over the likelihood under the hypothesis that the two loci assort independently, and then determine multilocus linkage maps for groups of putatively syntenic loci by calculating the maximum likelihood estimate of the recombination fractions and the log likelihood using the EM algorithm for a specified order of loci along the chromosome. In addition, the possibility of spurious linkage was exhaustively tested by searching for genotypes forbidden by the absence of crossing-over in one sex.

scholarly journals LINKAGE OF RESTRICTION FRAGMENT LENGTH POLYMORPHISMS AND ISOZYMES IN A BACKCROSS OF CITRUS AND PONCIRUS

HortScience ◽  
1990 ◽  
Vol 25 (9) ◽  
pp. 1154d-1154 ◽  
Author(s):  
Richard Durham ◽  
Gloria Moore ◽  
Charles Guy
Keyword(s):  
Linkage Analysis ◽  
Restriction Fragment ◽  
Fragment Length ◽  
Segregation Ratio ◽  
Interspecific Backcross ◽  
Poncirus Trifoliata ◽  
Genetic Linkage Analysis ◽  
Linkage Groups ◽  
Length Polymorphisms ◽  
Restriction Fragment Length

Genetic linkage analysis was performed on an interspecific backcross of citrus [Citrus grandis (L.) Osbeck cv. Thong Dee X (Thong Dee X Poncirus trifoliata (L.) Raf. cv. Pomeroy)], using restriction fragment length polymorphism (RFLP) and isozyme analysis. Sixty-five progeny were analyzed for a total of 57 segregating markers including 9 isozymes and 48 RFLPs. Significant (p = 0.05) deviation from an expected 1:1 segregation ratio was observed for 21 (37%) of the 57 loci, but this did not exclude their use in the mapping study. Linkage analysis revealed that 50 loci mapped to 12 linkage groups while 7 loci segregated independently from all other markers. The total map distance included in the 12 linkage groups was 472 cM with the mean distance between markers being 12.8 cM. This does not represent a saturation of the genome with markers; however, this work demonstrates the potential for mapping traits of economic importance in citrus.

Mapping flagellar genes in Chlamydomonas using restriction fragment length polymorphisms.

Genetics ◽  
1988 ◽  
Vol 120 (1) ◽  
pp. 109-122
Author(s):  
L P Ranum ◽  
M D Thompson ◽  
J A Schloss ◽  
P A Lefebvre ◽  
C D Silflow
Keyword(s):  
Molecular Markers ◽  
Linkage Group ◽  
Restriction Fragment ◽  
Cdna Clone ◽  
Fragment Length ◽  
Linkage Groups ◽  
Length Polymorphisms ◽  
Gene Maps ◽  
Flagellar Genes ◽  
Restriction Fragment Length

Abstract To correlate cloned nuclear DNA sequences with previously characterized mutations in Chlamydomonas and, to gain insight into the organization of its nuclear genome, we have begun to map molecular markers using restriction fragment length polymorphisms (RFLPs). A Chlamydomonas reinhardtii strain (CC-29) containing phenotypic markers on nine of the 19 linkage groups was crossed to the interfertile species Chlamydomonas smithii. DNA from each member of 22 randomly selected tetrads was analyzed for the segregation of RFLPs associated with cloned genes detected by hybridization with radioactive DNA probes. The current set of markers allows the detection of linkage to new molecular markers over approximately 54% of the existing genetic map. This study focused on mapping cloned flagellar genes and genes whose transcripts accumulate after deflagellation. Twelve different molecular clones have been assigned to seven linkage groups. The alpha-1 tubulin gene maps to linkage group III and is linked to the genomic sequence homologous to pcf6-100, a cDNA clone whose corresponding transcript accumulates after deflagellation. The alpha-2 tubulin gene maps to linkage group IV. The two beta-tubulin genes are linked, with the beta-1 gene being approximately 12 cM more distal from the centromere than the beta-2 gene. A clone corresponding to a 73-kD dynein protein maps to the opposite arm of the same linkage group. The gene corresponding to the cDNA clone pcf6-187, whose mRNA accumulates after deflagellation, maps very close to the tightly linked pf-26 and pf-1 mutations on linkage group V.

A Consensus Linkage Map for Sugi (Cryptomeria japonica) From Two Pedigrees, Based on Microsatellites and Expressed Sequence Tags

Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1551-1568 ◽  
Author(s):  
Naoki Tani ◽  
Tomokazu Takahashi ◽  
Hiroyoshi Iwata ◽  
Yuzuru Mukai ◽  
Tokuko Ujino-Ihara ◽  
...  
Keyword(s):  
Linkage Group ◽  
Restriction Fragment ◽  
Fragment Length ◽  
Dna Markers ◽  
Cryptomeria Japonica ◽  
Linkage Groups ◽  
Consensus Map ◽  
Length Polymorphisms ◽  
Cleaved Amplified Polymorphic Sequences ◽  
Restriction Fragment Length

Abstract A consensus map for sugi (Cryptomeria japonica) was constructed by integrating linkage data from two unrelated third-generation pedigrees, one derived from a full-sib cross and the other by self-pollination of F1 individuals. The progeny segregation data of the first pedigree were derived from cleaved amplified polymorphic sequences, microsatellites, restriction fragment length polymorphisms, and single nucleotide polymorphisms. The data of the second pedigree were derived from cleaved amplified polymorphic sequences, isozyme markers, morphological traits, random amplified polymorphic DNA markers, and restriction fragment length polymorphisms. Linkage analyses were done for the first pedigree with JoinMap 3.0, using its parameter set for progeny derived by cross-pollination, and for the second pedigree with the parameter set for progeny derived from selfing of F1 individuals. The 11 chromosomes of C. japonica are represented in the consensus map. A total of 438 markers were assigned to 11 large linkage groups, 1 small linkage group, and 1 nonintegrated linkage group from the second pedigree; their total length was 1372.2 cM. On average, the consensus map showed 1 marker every 3.0 cM. PCR-based codominant DNA markers such as cleaved amplified polymorphic sequences and microsatellite markers were distributed in all linkage groups and occupied about half of mapped loci. These markers are very useful for integration of different linkage maps, QTL mapping, and comparative mapping for evolutional study, especially for species with a large genome size such as conifers.

An RFLP species-specific DNA sequence for the A genome of rice

Genome ◽  
1993 ◽  
Vol 36 (3) ◽  
pp. 445-448 ◽  
Author(s):  
John F. Dallas ◽  
C. Lynne McIntyre ◽  
J. Perry Gustafson
Keyword(s):  
Oryza Sativa ◽  
Dna Sequence ◽  
Restriction Fragment ◽  
Fragment Length ◽  
Restriction Fragment Length Polymorphisms ◽  
Length Polymorphisms ◽  
A Genome ◽  
Species Specific ◽  
Hybridization Stringency ◽  
Restriction Fragment Length

A DNA sequence, pOs6.20, was cloned from the nuclear genome of cultivated rice (Oryza sativa L.) by hybridization with a human minisatellite sequence. At high hybridization stringency, a subfragment of the rice sequence, pOs6.20.3, detected low-copy restriction fragment length polymorphisms (RFLPs), which behaved as Mendelian genetic markers. This subfragment detected multicopy RFLPs between an indica and a javanica cultivar at medium hybridization stringency. The sequences detected by pOs6.20.3 at high hybridization stringency did not occur in rice species possessing the B, C, D, E, and F genomes. These results suggest that the RFLPs detected by this sequence can be placed on a genetic map of rice and that this sequence can be used as a species-specific probe for the A genome of rice.Key words: restriction fragment length polymorphisms, Oryza sativa.

An RFLP-based linkage map of oats based on a cross between two diploid taxa (Avena atlantica × A. hirtula)

Genome ◽  
1992 ◽  
Vol 35 (5) ◽  
pp. 765-771 ◽  
Author(s):  
L. S. O'Donoughue ◽  
Z. Wang ◽  
M. Röder ◽  
B. Kneen ◽  
M. Leggett ◽  
...  
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Rflp Markers ◽  
Linkage Groups ◽  
Marker Selection ◽  
A Genome ◽  
Restriction Fragment Length

A restriction fragment length polymorphism (RFLP) map for the A genome of Avena has been developed using F3 families from the cross A. atlantica × A. hirtula. The main source of markers were an oat cDNA and a barley cDNA library. A total of 194 RFLP markers was used, 192 of which were mapped or assigned to linkage groups. Seven main linkage groups, presumably corresponding to the seven chromosomes of the haploid genome, were identified. The linkage groups varied in size from 30 to 118 cM for a total map length of 614 cM. This map provides a tool for the interpretation of genome organization in Avena and for marker selection in the development of a map of hexaploid oats.Key words: restriction fragment length polymorphism, Avena, mapping.

A molecular linkage map of cultivated oat

Genome ◽  
1995 ◽  
Vol 38 (2) ◽  
pp. 368-380 ◽  
Author(s):  
L. S. O'Donoughue ◽  
M. E. Sorrells ◽  
S. D. Tanksley ◽  
E. Autrique ◽  
A. Van Deynze ◽  
...  
Keyword(s):  
Linkage Map ◽  
Restriction Fragment ◽  
Fragment Length ◽  
Recombinant Inbred Lines ◽  
Cdna Clones ◽  
Linkage Groups ◽  
Total Size ◽  
Molecular Linkage Map ◽  
A Genome ◽  
Restriction Fragment Length

A molecular linkage map of cultivated oat composed of 561 loci has been developed using 71 recombinant inbred lines from a cross between Avena byzantina cv. Kanota and A. sativa cv. Ogle. The loci are mainly restriction fragment length polymorphisms detected by oat cDNA clones from leaf, endosperm, and root tissue, as well as by barley leaf cDNA clones. The loci form 38 linkage groups ranging in size from 0.0 to 122.1 cM (mean, 39 cM) and consist of 2–51 loci each (mean, 14). Twenty-nine loci remain unlinked. The current map size is 1482 cM and the total size, on the basis of the number of unlinked loci, is estimated to be 2932.0 cM. This indicates that this map covers at least 50% of the cultivated oat genome. Comparisons with an A-genome diploid oat map and between linkage groups exhibiting homoeology to each other indicate that several major chromosomal rearrangements exist in cultivated oat. This map provides a tool for marker-assisted selection, quantitative trait loci analyses, and studies of genome organization in oat.Key words: Avena, restriction fragment length polymorphism, linkage map, polyploidy, genome evolution.

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