Mapping of the Dioscorea tokoro genome: AFLP markers linked to sex

Genome ◽  
1999 ◽  
Vol 42 (4) ◽  
pp. 752-762 ◽  
Author(s):  
Ryohei Terauchi ◽  
Günter Kahl
Keyword(s):  
Key Words ◽  
Fragment Length ◽  
Aflp Markers ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Morphological Marker ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Heterogametic Sex ◽  
Wild Yam

Two framework linkage maps were constructed for the genome of the dioecious wild yam species Dioscorea tokoro. The pseudo-testcross strategy was employed, using 271 amplified fragment length polymorphisms (AFLPs), five sequence-tagged microsatellite sites, one isozyme, and one morphological marker. For the two parents DT7 and DT5 used in the cross, 13 and 12 linkage groups, respectively, were identified. The total map lengths were 669 and 613 cM, respectively, for DT7 and DT5, which cover more than 75% of the D. tokoro genome. Ten AFLP markers heterozygous only in the male parent showed tight linkages with the sex of its progeny, which suggests that male is the heterogametic sex (XY) and the female is the homogametic sex (XX).Key words: Dioscorea tokoro, yam, linkage map, AFLP, sex determination.

scholarly journals Genetic Relationships among Schizolobium parahybum (Vell.) Blake (Leguminosae) Ecotypes from Ecuador and other Countries

2007 ◽  
Vol 56 (1-6) ◽  
pp. 214-221 ◽  
Author(s):  
H. F. Canchignia-Martínez ◽  
S. Hernández-Delgado ◽  
M. González-Paz ◽  
E. Motte ◽  
N. Mayek-Pérez
Keyword(s):  
Costa Rica ◽  
Fragment Length ◽  
Geographical Origin ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Aflp Markers ◽  
Diversity Patterns ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Genetic Status

Abstract Fifteen ecotypes of Schizolobium parahybum (Vell.) Blake collected in Ecuador (9), Brazil (3), Bolivia (1) Costa Rica (1), and Peru (1) were analyzed using Random Amplified Polymorphic DNA (RAPDs), Amplified Fragment Length Polymorphisms (AFLPs) and microsatellites (SSRs) in order to determine their genetic relationships and diversity patterns among ecotypes and to identify the origin of cultivated germplasm in Ecuador. Although AFLP markers were the most informative technique based on amplified products, SSRs clearly differentiated the ecotypes of Ecuador based on their geographical origin or genetic status into two groups: commercial ecotypes growing at western Ecuador very similar to the ecotype from Costa Rica, and native germplasm from eastern Ecuador and ecotypes from Brazil, Peru and Bolivia.

scholarly journals Expanded Genetic Map of Gibberella moniliformis (Fusarium verticillioides)

2002 ◽  
Vol 68 (4) ◽  
pp. 1972-1979 ◽  
Author(s):  
James E. Jurgenson ◽  
Kurt A. Zeller ◽  
John F. Leslie
Keyword(s):  
Genetic Map ◽  
Fragment Length ◽  
Fusarium Verticillioides ◽  
Pathogenic Fungi ◽  
Aflp Markers ◽  
Crop Species ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Further Development ◽  
Gibberella Moniliformis

ABSTRACT Gibberella moniliformis (Fusarium verticillioides) is primarily a pathogen of maize, but it can also cause disease in other crop species. This pathogenicity, as well as the contamination of food- and feedstuffs with the fumonisin mycotoxins, results in economically significant losses to both farmers and food processors. The dissection of important biological characters in this fungus has been hampered by the lack of a uniformly dense genetic map. The existing restriction fragment length polymorphism-based map contains significant gaps, making it difficult to routinely locate biologically important genes, such as those involved in pathogenicity or mycotoxin production, with precision. We utilized amplified fragment length polymorphisms (AFLPs) to saturate the existing genetic map and added 486 AFLP markers to the ∼150 markers on the existing map. The resulting map has an average marker interval of 3.9 map units and averages ∼21 kb/map unit. The additional markers expanded the map from 1,452 to 2,188 map units distributed across 12 chromosomes. The maximum distance between adjacent markers is 29 map units. We identified AFLP markers less than 1 map unit from the mating type (MAT) locus and 2.5 map units from the spore killer (SK) locus; eight AFLP markers map within 8.5 units of the FUM1 (fumonisin biosynthetic) locus. The increased saturation of this map will facilitate further development of G. moniliformis as a model system for the genetic and population genetic studies of related, but less genetically tractable, plant pathogenic fungi.

Linkage map of birch, Betula pendula Roth, based on microsatellites and amplified fragment length polymorphisms

Genome ◽  
2005 ◽  
Vol 48 (4) ◽  
pp. 619-625 ◽  
Author(s):  
M Pekkinen ◽  
S Varvio ◽  
K K.M Kulju ◽  
H Kärkkäinen ◽  
S Smolander ◽  
...  
Keyword(s):  
Linkage Map ◽  
Fragment Length ◽  
Betula Pendula ◽  
Linkage Data ◽  
Linkage Groups ◽  
Betula Pendula Roth ◽  
Mapping Strategy ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Map Distance

The first genetic linkage map for silver birch, Betula pendula Roth, was constructed by using a pseudo-testcross mapping strategy and integration of linkage data from 3 unrelated 2-generation pedigrees. The map is based on the genetic inheritance and segregation of 82 amplified fragment length polyhmorphisms and 19 microsatellite markers, and was constructed by simultaneously comparing the performance of CRI-MAP and OUTMAP packages. The analysis revealed 16 linkage groups, and the total map coverage is 1561 cM (Kosambi units). Average map distance between adjacent markers is 15.5 cM. Linkage groups range between 6 and 18 loci and from 81.2 to 326.5 cM; the remaining 9 linkage groups consist of 2 or 3 loci ranging from 6.3 to 42.4 cM. The uncertainty of the map is illustrated with sensitivity analysis. This initial map can serve as a basis for developing a more detailed genetic map.Key words: Betula pendula, linkage map, microsatellite, AFLP, CRI-MAP, OUTMAP.

A linkage map of hexaploid oat based on grass anchor DNA clones and its relationship to other oat maps

Genome ◽  
2001 ◽  
Vol 44 (2) ◽  
pp. 249-265 ◽  
Author(s):  
V A Portyanko ◽  
D L Hoffman ◽  
M Lee ◽  
J B Holland
Keyword(s):  
Linkage Map ◽  
Fragment Length ◽  
Rflp Markers ◽  
Linkage Groups ◽  
Sequence Tagged Sites ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Incomplete Coverage ◽  
Marker Loci ◽  
Isozyme Loci

A cultivated oat linkage map was developed using a recombinant inbred population of 136 F6:7 lines from the cross 'Ogle' × 'TAM O-301'. A total of 441 marker loci, including 355 restriction fragment length polymorphism (RFLP) markers, 40 amplified fragment length polymorphisms (AFLPs), 22 random amplified polymorphic DNAs (RAPDs), 7 sequence-tagged sites (STSs), 1 simple sequence repeat (SSR), 12 isozyme loci, and 4 discrete morphological traits, was mapped. Fifteen loci remained unlinked, and 426 loci produced 34 linkage groups (with 2–43 loci each) spanning 2049 cM of the oat genome (from 4.2 to 174.0 cM per group). Comparisons with other Avena maps revealed 35 genome regions syntenic between hexaploid maps and 16–34 regions conserved between diploid and hexaploid maps. Those portions of hexaploid oat maps that could be compared were completely conserved. Considerable conservation of diploid genome regions on the hexaploid map also was observed (89–95%); however, at the whole-chromosome level, colinearity was much lower. Comparisons among linkage groups, both within and among Avena mapping populations, revealed several putative homoeologous linkage group sets as well as some linkage groups composed of segments from different homoeologous groups. The relationships between many Avena linkage groups remain uncertain, however, due to incomplete coverage by comparative markers and to complications introduced by genomic duplications and rearrangements.Key words: Avena, linkage map, comparative mapping, homoeology.

AFLP assessment of the genetic relationships among 12 Thymus taxa occurring in Portugal

2015 ◽  
Vol 15 (1) ◽  
pp. 89-92
Author(s):  
David V. da Silva ◽  
João M. Duarte ◽  
Maria G. Miguel ◽  
José M. Leitão
Keyword(s):  
Essential Oil ◽  
Iberian Peninsula ◽  
Fragment Length ◽  
Mediterranean Region ◽  
Morphological Traits ◽  
Oil Content ◽  
Genetic Relationships ◽  
Aflp Markers ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms

Thymus is a widely distributed genus in the Mediterranean region with several species endemic to the Iberian Peninsula. The genetic relationships among the 12 major Thymus taxa, T. albicans, T. caespititius, T. camphoratus, T. capitellatus, T. carnosus, T.lotocephalus, T. mastichina L. ssp. mastichina, T. pulegioides, T. villosus ssp. lusitanicus, T. villosus ssp. villosus, T. zygis ssp. sylvestris and T. zygis ssp. zygis, which occur in Portugal were assessed by AFLP (Amplified Fragment Length Polymorphisms) markers. A general agreement was found between the genetic relationships estimated by the AFLP markers and the accepted Thymus taxonomy based on morphological traits and essential oil content. The AFLP markers also supported suggestions for refinement of the taxonomy of this genus.

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.

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