The European Project Hidras: Innovative Multidisciplinary Approaches to Breeding High Quality Disease Resistant Apples

Gianfranceschi, L.; Soglio, V.

doi:10.17660/actahortic.2004.663.55

Cited by 46 publications

(23 citation statements)

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“…Considering the extent of linkage drag that is still present in Prima (King et al 1999), Prima's 214 allele of Md-Exp7 should also be derived from M. floribunda. Further validation on the role of Md-Exp7 may be obtained by data generated in the HiDRAS project (Gianfranceschi and Soglio 2004), where more than 600 Vf-possessing seedlings, deriving from 13 crosses, have been phenotyped for firmness and softening. The approximately 130 (=number of individuals×interval size (22 cm)/100) seedlings that show recombination within the current 2-LOD QTL interval should allow a considerable narrowing down of this interval.…”

Section: Association Of Md-exp7 With Softeningmentioning

confidence: 99%

Map position and functional allelic diversity of Md-Exp7, a new putative expansin gene associated with fruit softening in apple (Malus × domestica Borkh.) and pear (Pyrus communis)

Costa

Weg²,

Stella

et al. 2008

Tree Genetics & Genomes

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Fruit ripening can be considered as a complex set of biochemical and physiological changes occurring at the end of the developmental stage. Ripe fruit texture notably affects overall quality and consumer appreciation. Excessive softening limits shelf-life and storability, thereby increasing disease susceptibility and economic loss. Fruit softening is a process due to the depolymerisation of different polysaccharide classes, an event controlled by a synergic and coordinated action of several enzymes among which expansins play a fundamental role. To date, six expansin genes are known to be expressed during apple fruit ontogeny, from full bloom up to fruit ripening. We identified a novel expansin apple homolog (Md-Exp7) sharing high sequence similarity with specific-ripening expansin genes of other crops. A functional marker (MdExp7 SSR ) based on an SSR motif located within the untranslated region of the gene was developed and mapped on Linkage Group 1 of the apple and pear genomes in a region where one major apple QTL for fruit firmness had been previously identified. The allelic composition of 31 apple varieties for the SSR marker was associated with differences in fruit softening.

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Section: Association Of Md-exp7 With Softeningmentioning

confidence: 99%

Map position and functional allelic diversity of Md-Exp7, a new putative expansin gene associated with fruit softening in apple (Malus × domestica Borkh.) and pear (Pyrus communis)

Costa

Weg²,

Stella

et al. 2008

Tree Genetics & Genomes

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“…The pairwise relatedness estimation was performed on a set of 33 parents of multiple mapping populations that were the resource for a large QTL mapping study for apples in the EU project HiDRAS (Gianfranceschi and Soglio 2004) (http://www.hidras.unimi.it/). As this project was still ongoing and both marker and pedigree data may be added or modified, we took the dataset available on 25 June 2007 (Table 1).…”

Section: Hidras Datamentioning

confidence: 99%

Comparison of marker-based pairwise relatedness estimators on a pedigreed plant population

et al. 2008

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Several estimators have been proposed that use molecular marker data to infer the degree of relatedness for pairs of individuals. The objective of this study was to evaluate the performance of seven estimators when applied to marker data of a set of 33 key individuals from a large complex apple pedigree. The evaluation considered different scenarios of allele frequencies and different numbers of marker loci. The method of moments estimators were Similarity, Queller-Goodknight, Lynch-Ritland and Wang. The maximum likelihood estimators were Thompson, Anderson-Weir and Jacquard. The pedigree-based coancestry coefficients were taken as the point of reference in calculating correlations and root mean square error (RMSE). The marker data comprised 86 multi-allelic SSR markers on 17 linkage groups, covering 11 Morgans. Additionally, we simulated 10 datasets conditional on the real pedigree to support the results on the real dataset. None of the estimators outperformed the others. Knowledge of allele frequencies appeared to be the most influential, i.e., the highest correlations and lowest RMSE were found when frequencies from the founder population were available. When equal allele frequencies were used, all estimators resulted in very similar, but on average lower, correlations. The use of allele frequencies estimated from the set of 33 individuals gave, on average, the poorest results. The maximum likelihood estimators and the Lynch-Ritland estimator were the most sensitive to allele frequencies. The results from the simulation study fully supported the trends in results of the real dataset. This study indicated that high correlations (up to 0.90) and small RMSE (below 0.03), may be obtained when population allelic frequencies are available. In this scenario, the performances of the various estimators were similar, but seemed to favor the maximum likelihood estimators. In the absence of reliable allele frequencies the method of moments estimators were shown to be more robust. The number of marker loci influenced the average performance of the estimators; however, the ranking was not affected. Correlations up to 0.80 were obtained when two markers per chromosome and appropriate allele frequencies were available. Adding more markers to the current dataset may lead to marginal improvements.

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“…For apple, completion of a genome covering set of SSR-markers is under way (e.g. Liebhard et al, 2002;Gianfranceschi and Soglio, 2004).…”

Section: Requirementsmentioning

confidence: 99%

Pedigree Genotyping: A New Pedigree-Based Approach of QTL Identification and Allele Mining

Weg¹,

Voorrips²,

Finkers³

et al. 2004

Acta Hortic.

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To date, molecular markers are available for many economically important traits. Unfortunately, lack of knowledge of the allelic variation of the related genes hampers their full exploitation in commercial breeding programs. These markers have usually been identified in one single cross. Consequently, only one or two favourable alleles of the related QTL are identified and exploitable for markerassisted breeding (MAB), whereas a breeding program may include several alleles. Selection for just these alleles means that many favourable genotypes are ignored, which decreases efficiency and leads to genetic erosion. A new approach, called Pedigree Genotyping, allows the identification and exploitation of most alleles present in an ongoing breeding program. This is achieved by including breeding material itself in QTL detection, thus covering multiple generations and linking many crosses through their common ancestors in the pedigree. The principle of Identity by Descent (IBD) is utilised to express the identity of an allele of a modern selection in terms of alleles of founding cultivars. These founder alleles are used as factors in statistical analyses. Co-dominant markers like SSR (microsatellite) markers are essential in this approach since they are able to connect cultivars, breeding selections and progenies at the molecular marker level by monitoring specific chromosomal segments along family trees. Additional advantages of the use of breeding genetic material are (1) a major reduction in experimental costs since plant material is already available and phenotyped by default (2) continuity over generations within breeding programs with regard to marker research (3) the testing of QTL-alleles against a wide range of genetic backgrounds, making results generally applicable, (4) intra-as well as inter-QTL interactions can be explored. Fruit firmness in apple will be used as an example to illustrate the principles of this powerful approach to detect QTLs and estimate their allelic variation. INTRODUCTIONTo date, molecular markers have been identified for many loci governing important horticultural traits. These markers have usually been identified in one single cross. As a consequence, only one or two favourable alleles of a locus are identified, whereas a breeding program usually includes many favourable alleles. If a breeder focuses his selection on these alleles, he would unnecessarily discard many favourable genotypes. This reduces the efficiency of the breeding program. Moreover, the genetic diversity of his material is unnecessarily narrowed. A new approach called 'Pedigree Genotyping' makes it possible to find markers for all favourable alleles present in a breeding program. The costs of this approach are low compared to traditional marker research, because it utilises data from the ongoing breeding program.

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The European Project Hidras: Innovative Multidisciplinary Approaches to Breeding High Quality Disease Resistant Apples

Cited by 46 publications

References 0 publications

Map position and functional allelic diversity of Md-Exp7, a new putative expansin gene associated with fruit softening in apple (Malus × domestica Borkh.) and pear (Pyrus communis)

Map position and functional allelic diversity of Md-Exp7, a new putative expansin gene associated with fruit softening in apple (Malus × domestica Borkh.) and pear (Pyrus communis)

Comparison of marker-based pairwise relatedness estimators on a pedigreed plant population

Pedigree Genotyping: A New Pedigree-Based Approach of QTL Identification and Allele Mining

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