A RAPD, AFLP and SSR linkage map, and QTL analysis in European beech (Fagus sylvatica L.)

Scalfi, Marta; Troggio, Michela; Piovani, P.; Leonardi, Stefano; Magnaschi, G.; Vendramin, G. G.; Menozzi, Paolo

doi:10.1007/s00122-003-1583-7

Cited by 15 publications

(21 citation statements)

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“…The female parent (S30) used in the V1 variety development and the present female parent S36 variety were evolved from the same EMS-treated open-pollinated seeds of the Berhampore Local genotype; hence, more similarities have been found between female (S36) and male (V1) parents. In this study, the higher percentage of intercross markers (61.32%) was similar to those found for other intraspecific crosses of forest trees (Barreneche et al 1998;Scalfi et al 2004). All intercross markers segregating 3:1 were excluded from map construction because these markers provide little information for linkage analysis (Maliepaard et al 1997).…”

Section: Discussionsupporting

confidence: 87%

A first genetic linkage map of mulberry (Morus spp.) using RAPD, ISSR, and SSR markers and pseudotestcross mapping strategy

Venkateswarlu

Urs

Nath

et al. 2006

Tree Genetics & Genomes

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To lay the foundation for molecular breeding efforts, the first genetic linkage map of mulberry (2n=2x=28) was constructed with 50 F1 full-sib progeny using randomly amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), and simple sequence repeat (SSR) markers and two-way pseudotestcross mapping strategy. We selected 100 RAPD, 42 ISSR, and 9 SSR primers that amplified 517 markers, of which 188 (36.36%) showed a test-cross configuration, corresponding to the heterozygous condition in one parent and null in the other. Two separate female and male maps were constructed using 94 each of female-and male-specific testcross markers, containing 12 female linkage groups and 14 male linkage groups. At a minimum logarithm of the odds (LOD) score threshold of 6.0 and at a maximum map distance of 20 cM, the female map covered a 1,196.6-cM distance, with an average distance of 15.75 cM and maximum map distance of 37.9 cM between two loci; the male-specific map covered a 1,351.7-cM distance, with an average distance of 18.78 cM and a maximum map distance between two loci is of 34.7 cM. The markers distributed randomly in all linkage groups without any clustering. All 12 linkage groups in the female-specific map consisted of 4-10 loci ranging in length from 0 to 140.4 cM, and in the malespecific map, the 13 largest linkage groups (except linkage group 12, which contained three loci) consisted of 4-12 loci, ranging in length from 53.9 to 145.9 cM and accounting for 97.22% of the total map distance. When mapping, progeny pass through their juvenile phase and assume their adult characters, mapping morphological markers and identification of quantitative trait loci for adaptive traits will be the primary target. In that sense, our map provides reference information for future molecular breeding work on Morus and its relatives.

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Section: Discussionsupporting

confidence: 87%

A first genetic linkage map of mulberry (Morus spp.) using RAPD, ISSR, and SSR markers and pseudotestcross mapping strategy

Venkateswarlu

Urs

Nath

et al. 2006

Tree Genetics & Genomes

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“…Both maps resulted in 12 linkage groups which correspond to the haploid chromosome complement in pine. Several other AFLP maps have been generated for conifers (Travis et al 1998;Yin et al 2003) and hardwoods (Cervera et al 2001;Scalfi et al 2004;Wu et al 2000;Zhang et al 2004). Generally, these conifer linkage maps result in greater than 12 linkage groups, more than the number of chromosomes.…”

Section: Discussionmentioning

confidence: 99%

“…Grouping was initially carried out from LOD 2 to 10 with a step of one LOD, but in the end, the linkage map was grouped at LOD thresholds of 3 and subsequently filled in with those at 2; the lower end for trees (Cervera et al 2001;Chagne et al 2002;Jermstad et al 1998;Scalfi et al 2004;Travis et al 1998;Wu et al 2000), but deemed appropriate for this data set which employed a multiple family approach to linkage construction. All groups with ≥3 markers were retained for mapping.…”

Section: Linkage Analysismentioning

confidence: 99%

“…An important component of this process is the development of a linkage and quantitative trait loci (QTL) map for the study of a species, which requires the development of molecular markers. One such technique, amplified fragment length polymorphisms (AFLP), has proven to be one of the most reliable molecular marker techniques for saturating linkage maps (Cabrita et al 2001;Cervera et al 2000;Jones et al 1997;Vos et al 1995) and has been used for genetic mapping of several tree species (Cervera et al 2001;Chagne et al 2002;Remington et al 1999;Scalfi et al 2004;Travis et al 1998;Wu et al 2000;Yin et al 2003;Zhang et al 2004). Currently, there is no AFLP linkage map for Douglas-fir, although several linkage maps have been developed utilizing random amplification of polymorphic DNAs (RAPDs) and restriction fragment length polymorphisms (RFLPs; Jermstad et al 1998;Krutovskii et al 1998).…”

Section: Introductionmentioning

confidence: 98%

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An AFLP linkage map for Douglas-fir based upon multiple full-sib families

Ukrainetz

Ritland

Mansfield

2007

Tree Genetics & Genomes

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An amplified fragment length polymorphism (AFLP) linkage map for coastal Douglas-fir (Pseudotsuga menziesii) was constructed from eight full-sib families each consisting of 40 progeny. These families were part of the British Columbia Ministry of Forests second-generation progeny test program and represent typical family sizes used in progeny trials. For map construction, ten primer pairs using EcoRI+3 and MseI+4 were employed to identify and assay AFLP loci that segregated in backcross configurations. A new technique was used to obtain a single recombination rate for each pair of marker loci: for each locus pair, a recombination rate and log-odd value were estimated across all segregating families using a joint maximum likelihood function that considered the full dataset of segregating genotypes. The resulting matrix of recombination rates between all pairs of loci was used to construct an integrated linkage map using JoinMap. The final map consisted of 19 linkage groups spanning 938.6 cM at an average distance of 9.3 cM between markers. The simultaneous integration of data from multiple families may provide an effective way to construct a linkage map, using the genetic resources inherent in most tree improvement programs, where progeny tests of small size are conducted. The statistical property of number of families used is briefly discussed. For our data, at least three to four families greatly increased the chance of obtaining an informative locus in at least one family. Families as small as ten are adequate for closely linked loci (<10 cM), while the size used in our study (40) is adequate for loci within 30 cM.

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“…This approach allows also more finetuned studies of the genetic control of transpiration traits. These parameters can be directly used in search for association between genes and phenotypes such as QTL mapping (Scalfi et al 2004).…”

Section: Discussionmentioning

confidence: 99%

A simple general method to evaluate intra-specific transpiration parameters within and among seedling families

et al. 2006

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A method to evaluate the genetic control of plant response to increasing soil water deficit is proposed. A description of single tree transpiration behavior was obtained considering parameters independent from air and soil conditions. We removed environmental effects by using two approaches: the normalization of drought data to control (watered) plants and the fitting of a process model. We analyzed the transpiration of 475 4-year-old European beech seedlings, belonging to eight full-sib families. Approximately, one-third of the seedlings were kept in well-watered conditions while the others were exposed to drought for 14 days. Daily plant transpiration was estimated as the difference between two subsequent gravimetric measurements. A mechanistic model was fitted to transpiration data separately for each tree. In the model, the relationship of transpiration with vapor pressure deficit and soil water deficit of each tree is modulated by three parameters: maximum leaf conductance (gM1), maximum transpiration in well-watered soil conditions E(M0)1 and a parameter describing stomatal sensitivity to soil water deficit (c). The model successfully fitted most single tree data and a distribution of estimates for the three parameters (gM1, E(M0)1 and c) was obtained. Predicted transpiration values were in good agreement with observed data (R (2) = 0.86). The model approach produced parameters significantly correlated with those of the "normalization to control" approach. Estimated parameters vary considerably among trees, suggesting the presence of individual differences in stomatal behavior and response to drought. In spite of a large among tree (within family) variation, the among families component for gM1, E(M0)1 and c explained 9.5, 3.3 and 0.1% of total parameters variation suggesting a significant genetic control of transpiration processes.

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A RAPD, AFLP and SSR linkage map, and QTL analysis in European beech (Fagus sylvatica L.)

Cited by 15 publications

References 0 publications

A first genetic linkage map of mulberry (Morus spp.) using RAPD, ISSR, and SSR markers and pseudotestcross mapping strategy

A first genetic linkage map of mulberry (Morus spp.) using RAPD, ISSR, and SSR markers and pseudotestcross mapping strategy

An AFLP linkage map for Douglas-fir based upon multiple full-sib families

A simple general method to evaluate intra-specific transpiration parameters within and among seedling families

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