A population ‘consensus’, partial linkage map of Picea abies Karst. based on RAPD markers |
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Authors: | G Bucci T L Kubisiak W L Nance P Menozzi |
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Institution: | (1) Dipartimento di Scienze Ambientali, Università di Parma, v.le delle Scienze, I-43100 Parma, Italy, IT;(2) USDA Forest Service, USDA-Southern Institute of Forest Genetics, Harrison Experimental Forest, 23332 Hwy 67, Saucier, MS 39574, USA, US |
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Abstract: | We built a “consensus” partial linkage map based on RAPD markers using 48 sibships of eight megagametophytes each from a
natural population of Norway spruce. A RAPD linkage map for a single individual from the same population had previously been
constructed. Using 30 random decamers that had yielded 83 RAPD markers in the single-tree map, eight megagametophytes for
each of the 48 sibships were screened. The linkage relationship among markers was estimated considering each family of eight
megagametophytes as a progeny of a phase-unknown backcross mating between a heterozygous mother and a fictitious ‘recessive’
father. Markers were assigned to windows using LOD=2.0 and θ=0.4 as thresholds, and ordered using a criterion of interval
support ≥2.0. For eight “windows” of recombination selected on the single-tree map, we investigated the consistency of marker
order in the two maps. We adopted restrictive criteria for rejecting co-linearity between the two locus orders. For each window
we imposed the most likely locus order obtained from one data set to the other (and vice versa), obtaining two symmetrical
log-likelihood differences. We considered the hypothesis of co-linearity rejected when both symmetrical differences were significant
(ΔLOD>3.0). By bootstrapping a subset of markers for each window (highly informative, ‘framework’ loci chosen on the previous
single-tree map using a matrix correlation method) the sampling variability of the single-tree and population maps was estimated.
As expected the population map was affected by a larger variability than the single-tree map. Heterogeneity in pairwise recombination
fractions among groups of sibship revealed a (possible) alternative genomic arrangement detected within a single recombination
window.
Received : 4 January 1997 / Accepted : 24 January 1997 |
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Keywords: | Norway spruce Genomic co-linearity Integrated map Log-likelihood Genomic arrangements |
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