scholarly journals Evidence for Colinearity among Genetic Linkage Maps in Cucumber

HortScience ◽  
2007 ◽  
Vol 42 (1) ◽  
pp. 20-27 ◽  
Author(s):  
Jack E. Staub ◽  
Zhanyong Sun ◽  
Sang-Min Chung ◽  
Richard L. Lower
Keyword(s):  
Quantitative Trait Loci ◽  
Fragment Length ◽  
Quantitative Trait ◽  
Yield Component ◽  
Genetic Maps ◽  
Linkage Groups ◽  
Length Polymorphisms ◽  
Trait Loci ◽  
Processing Line ◽  
Simple Sequence

Cucumber (Cucumis sativus L. var. sativus; 2n = 2x = 14), has a narrow genetic base (3% to 8% polymorphism). Nevertheless, several genetic maps exist for this species. It is important to know the degree of colinearity among these maps. Thus, the positions of random amplified polymorphic DNAs, sequenced characterized amplified regions, simple sequence repeat, restriction fragment length polymorphisms, and fluorescent amplified fragment length polymorphism markers were compared in four maps. A previously unreported map was constructed in a narrow cross (processing line 2A × Gy8; C. s. var. sativus; ≈7% polymorphism) and compared with the three published maps [two narrow-based (processing type; C. s. var. sativus; 8% to 12% polymorphism) and a broad-based (C. s. var. sativus × C. s. var. hardwickii (R.) Alef. ≈12%)]. Common makers were identified in seven linkage groups, providing evidence for microsynteny. These common markers were used as anchor markers for map position comparisons of yield component quantitative trait loci. The relative order of anchor markers in each of six linkage groups (linkage groups 1, 2, and 4–7) that had two or more anchor markers within each group was colinear, and instances of microsynteny were detected. Commonalities in the position of some yield component quantitative trait loci exist in linkage groups 1 and 4 of the maps examined, and the general synteny among these maps indicates that identification and mapping of additional anchor markers would lead to successful map merging to increase cucumber map saturation for use in cucumber breeding.

Construction of a molecular linkage map of pepper and a comparison of synteny with tomato

Genome ◽  
1993 ◽  
Vol 36 (3) ◽  
pp. 404-417 ◽  
Author(s):  
James P. Prince ◽  
Edmond Pochard ◽  
Steven D. Tanksley
Keyword(s):  
Quantitative Trait Loci ◽  
Genome Evolution ◽  
Restriction Fragment ◽  
Fragment Length ◽  
Quantitative Trait ◽  
Chromosome Breakage ◽  
Length Polymorphisms ◽  
Trait Loci ◽  
Pepper Genome ◽  
Restriction Fragment Length

A molecular map of pepper (Capsicum sp.) totalling 720 cM has been constructed in an interspecific F2 cross with restriction fragment length polymorphisms and isozymes. Nineteen linkage groups were formed from 192 molecular markers. Twenty-six markers showed no linkage to any others. Twenty-eight markers showed significant deviation from expected Mendelian ratios and clustered in the genome. Two quantitative trait loci controlling the number of flowers per node were mapped to linkage group 10. The order of markers in at least 228 cM (31.7%) of the pepper genome is conserved with respect to the tomato genome, with a minimum of 15 chromosome breakage events postulated to have occurred since their divergence from a common ancestor. Comparisons of meiotic recombination in 14 conserved intervals indicates that tomato has a higher rate of recombination than does pepper in the crosses studied. Evidence suggests that centric fusions and resulting chromosome breakage events are mechanisms for genome evolution in the Solanaceae.Key words: restriction fragment length polymorphism, genome evolution, quantitative trait loci, multiple flowers, Capsicum, Lycopersicon esculentum.

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 A method for computing identity by descent probabilities and quantitative trait loci mapping with dominant (AFLP) markers

2002 ◽  
Vol 79 (3) ◽  
pp. 247-258 ◽  
Author(s):  
MIGUEL PÉREZ-ENCISO ◽  
ODILE ROUSSOT
Keyword(s):  
Quantitative Trait Loci ◽  
Qtl Mapping ◽  
Quantitative Trait ◽  
Cost Effective ◽  
Significant Loss ◽  
Outbred Population ◽  
Identity By Descent ◽  
Fluorescent Band ◽  
Length Polymorphisms ◽  
Trait Loci

Amplified fragment length polymorphisms (AFLPs) are a widely used marker system: the technique is very cost-effective, easy and rapid, and reproducibly generates hundreds of markers. Unfortunately, AFLP alleles are typically scored as the presence or absence of a band and, thus, heterozygous and dominant homozygous genotypes cannot be distinguished. This results in a significant loss of information, especially as regards mapping of quantitative trait loci (QTLs). We present a Monte Carlo Markov Chain method that allows us to compute the identity by descent probabilities (IBD) in a general pedigree whose individuals have been typed for dominant markers. The method allows us to include the information provided by the fluorescent band intensities of the markers, the rationale being that homozygous individuals have on average higher band intensities than heterozygous individuals, as well as information from linked markers in each individual and its relatives. Once IBD probabilities are obtained, they can be combined into the QTL mapping strategy of choice. We illustrate the method with two simulated populations: an outbred population consisting of full sib families, and an F2 cross between inbred lines. Two marker spacings were considered, 5 or 20 cM, in the outbred population. There was almost no difference, for the practical purpose of QTL estimation, between AFLPs and biallelic codominant markers when the band density is taken into account, especially at the 5 cM spacing. The performance of AFLPs every 5 cM was also comparable to that of highly polymorphic markers (microsatellites) spaced every 20 cM. In economic terms, QTL mapping with a dense map of AFLPs is clearly better than microsatellite QTL mapping and little is lost in terms of accuracy of position. Nevertheless, at low marker densities, AFLPs or other biallelic markers result in very inaccurate estimates of QTL position.

scholarly journals Quantitative Trait Loci Associated with Foliar Trigonelline Accumulation inGlycine MaxL

2002 ◽  
Vol 2 (3) ◽  
pp. 151-157 ◽  
Author(s):  
Youngkoo Cho ◽  
Victor N. Njiti ◽  
Xinbo Chen ◽  
Kanokporn Triwatayakorn ◽  
My Abdelmajid Kassem ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Recombinant Inbred Lines ◽  
Development Stage ◽  
Linkage Groups ◽  
Frequency Distributions ◽  
Trait Loci ◽  
Pod Development ◽  
Pod Development Stage ◽  
Departure From Normality

The objective of this study was to utilize aGlycine maxRIL population to (1) evaluate foliar trigonelline (TRG) content in field-grown soybean, (2) determine the heritability of TRG accumulation, and (3) identify DNA markers linked to quantitative trait loci (QTLs) conditioning variation in TRG accumulation. Frequency distributions of 70 recombinant inbred lines showed statistically no significant departure from normality(P>.05)for TRG accumulation measured at pod development stage (R4). Six different molecular linkage groups (LGs) (B2, C2, D2, G, J, and K) were identified to be linked to QTLs for foliar TRG accumulation. Two unique microsatellite markers (SSR) on two different linkage groups identified QTL significantly associated with foliar TRG accumulation: a region on LG J (Satt285)(P=.0019, R2=15.9%)and a second region on LG C2 (Satt079)(P=.0029, R2=13.4%).

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