Optimization of AFLP fingerprinting of organisms with a large-sized genome: a study on Alstroemeria spp.

Han, Tae-Ho; Eck, Herman J. van; Jeu, M.J. de; Jacobsen, E.

doi:10.1007/s001220051093

Cited by 44 publications

(44 citation statements)

References 22 publications

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“…To avoid this problem and ensure full genome coverage, we used Eco -Mse PECs. By using two selective nucleotides in the pre-amplification step (EcoRI + 2, MseI + 2), and three to four nucleotides in the selective amplification step (EcoRI + 3 / +4 MseI + 4), we could circumvent the complexity of the pine genome to produce clear AFLP patterns [15,25].…”

Section: Aflp Markersmentioning

confidence: 99%

A high density genetic map of maritime pine based on AFLPs

et al. 2002

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-We constructed a high-density linkage map of maritime pine (Pinus pinaster Ait.) based on AFLP (Amplified Fragment Length Polymorphism) markers using a three-generation outbred pedigree. In a first step, male and female maps were established independently with test-cross markers segregating 1:1 (presence:absence of the amplified fragment in the full-sib progeny). In a second step, both maps were merged using intercross markers segregating 3:1 in the progeny. A combination of MAPMAKER and JOINMAP softwares was used for the mapping process. A consensus map was obtained and is available at URL http://www.pierroton.inra.fr/genetics/pinus/Map3/index.html. It covers 1441 cM and comprises a total of 620 AFLP markers on 12 linkage groups. The physical size of the maritime pine genome (51.5 pg/2C) was measured by flow cytometry, providing a physical/genetic size ratio of 13.78 Mb/cM. This map will be used to dissect the genetic architecture of economically (growth, wood quality) and ecologically (water-use efficiency) important traits into mendelian inherited components (QTLs: Quantitative Trait Loci). It will also provide a framework to localize more informative markers (ESTs: Expressed Sequence Tags) to be used as candidate genes in QTL detection experiments. The location of orthologous markers (ESTs and SSRs: Simple Sequence Repeats) will also allow the study of the genome structure of closely related conifer species using a comparative genome mapping approach.Pinus pinaster / genetic linkage map / AFLP / double pseudo-testcross / physical size Résumé -Établissement d'une carte génétique à haute densité du pin maritime à partir de marqueurs AFLP. Nous avons construit une carte génétique du pin maritime (Pinus pinaster Ait.) en génotypant une famille de plein-frères appartenant à la troisième génération du programme d'amélioration, avec des marqueurs AFLP. Dans un premier temps, les cartes des parents mâle et femelle ont été établies indépendam-ment avec des marqueurs de type « test-cross » ségréguant dans les proportions 1:1 (présence:absence du fragment amplifié dans la famille de plein-frères). Dans un second temps ces deux cartes ont été fusionnées à l'aide de marqueurs de type « intercross », ségréguant dans les proportions 3:1. La construction des cartes a été réalisée à l'aide des logiciels de cartographie génétique JOINMAP et MAPMAKER. Une carte géné-tique consensus des deux parents comprenant 12 groupes de liaison a finalement été obtenue et est accessible à l'URL suivante : http://www.pierroton.inra.fr/genetics/pinus/Map3/index.html. Elle couvre 1441 cM et comprend 620 marqueurs. Par ailleurs, la taille physique du génome du pin maritime a été estimée par cytométrie de flux à 51.5 pg/2C, donnant un rapport taille physique/taille génétique de 13.78 Mb/cM. Cette carte sera maintenant utilisée pour étudier l'architecture génétique de caractères d'intérêt économique (croissance, qualité du bois) et écologique (efficience d'utilisation de l'eau). Il s'agira de localiser les zones du génome (QTL, Quantita...

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Section: Aflp Markersmentioning

confidence: 99%

A high density genetic map of maritime pine based on AFLPs

et al. 2002

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“…Amplified fragment length polymorphism (AFLP; Vos et al, 1995) is reported to be suitable for construction of high-density genetic maps (Becker et al, 1995;Wang et al, 1997). AFLP is also applicable to large-genome plants by increasing the number of selective nucleotides that are added to core primers (Han et al, 1999). van Heusden et al (2000) constructed an AFLP-based genetic map using F 2 progeny from the interspecific cross A. roylei × A. cepa.…”

Section: Introductionmentioning

confidence: 99%

Genetic mapping of AFLP markers in Japanese bunching onion (Allium fistulosum)

et al. 2005

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The first genetic linkage map of Japanese bunching onion (Allium fistulosum) based primarily on AFLP markers was constructed using reciprocally backcrossed progenies. They were 120 plants each of (P 1 )BC 1 and (P 2 )BC 1 populations derived from a cross between single plants of two inbred lines: D1s-15s-22 (P 1 ) and J1s-14s-20 (P 2 ). Based on the (P 2 )BC 1 population, a linkage map of P 1 was constructed. It comprises 164 markers -149 amplified fragment length polymorphisms (AFLPs), 2 cleaved amplified polymorphic sequences (CAPSs), and 12 simple sequence repeats (SSRs) from Japanese bunching onion, and 1 SSR from bulb onion (A. cepa) -on 15 linkage groups covering 947 centiMorgans (cM). The linkage map of P 2 was constructed with the (P 1 )BC 1 population and composed of 120 loci -105 AFLPs, 1 CAPS, and 13 SSRs developed from Japanese bunching onion and 1 SSR from bulb onion -on 14 linkage groups covering 775 cM. Both maps were not saturated but were considered to cover the majority of the genome. Nine linkage groups in P 2 map were connected with their counterparts in P 1 map using co-dominant anchor markers, 13 SSRs and 1 CAPS.

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“…This demonstrates the value of fingerprinting techniques with molecular markers as a new strategy for breeders to claim their rights on these "derived varieties". Anastassopolous and Keil, 1996;Han et al, 1999Loh et al, 1999Zhang et al, 2000a Obara-Okeyo and Kako, 1998…”

Section: Sports and Their Ancestral Varieties Have Been Investigatedmentioning

confidence: 96%

Molecular Markers as a Tool for Analyses of Genetic Relatedness and Selection in Ornamentals

Debener

2002

Breeding for Ornamentals: Classical and Molecular Approaches

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Optimization of AFLP fingerprinting of organisms with a large-sized genome: a study on Alstroemeria spp.

Cited by 44 publications

References 22 publications

A high density genetic map of maritime pine based on AFLPs

A high density genetic map of maritime pine based on AFLPs

Genetic mapping of AFLP markers in Japanese bunching onion (Allium fistulosum)

Molecular Markers as a Tool for Analyses of Genetic Relatedness and Selection in Ornamentals

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