Codominant PCR-based markers for Pinus taeda developed from mapped cDNA clones

Harry, David E.; Temesgen, Berhanu; Neale, David B.

doi:10.1007/s001220050903

Cited by 41 publications

(14 citation statements)

References 25 publications

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“…EST primers were obtained from the information provided on http://www.pierroton.inra.fr/genetics/pinus/ primers.htm. EST analysis was performed according to [12].…”

Section: Molecular Methodsmentioning

confidence: 99%

Towards construction of an ultra high density linkage map for Pinus pinaster

Ritter

Aragonés

Markussen³

et al. 2002

Ann. For. Sci.

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-Two parental linkage maps have been constructed from the P. pinaster reference population (0024 × C803) based on AFLP, SSR and EST markers. Although segregating polymorphism was low due to a high degree of homozygosity in the parents, 12 linkage groups with 26 to 46 markers each were obtained for each parent. The availibility of 70 anchor points based on fragments common to both parents and based on codominant SSR and EST markers allowed to determine homologous chromosomes for both maps and to construct one integrated map. Total genome length of the integrated map is around 2000 cM including 1182 markers. Since some of the EST and SSR markers are also mapped in different pine species, association of linkage groups of our reference population with those of other published maps was possible.

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“…EST primers were obtained from the information provided on http://www.pierroton.inra.fr/genetics/pinus/ primers.htm. EST analysis was performed according to [12].…”

Section: Molecular Methodsmentioning

confidence: 99%

Towards construction of an ultra high density linkage map for Pinus pinaster

Ritter

Aragonés

Markussen³

et al. 2002

Ann. For. Sci.

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“…Although AFLP markers have been shown to be poorly transferable between pine species, orthologous markers such as RFLPs, ESTPs [61] or SSRs can be used as anchor-points between the different maps already available for conifer species. ESTs which have been mapped in Pinus taeda [26,61] and ESTs from P. pinaster cDNA libraries are currently being located in the AFLP map of maritime pine as part of the Conifer Comparative Genome Project (CCGP; http://dendrome.ucdavis.edu/Synteny/index.html). The aim of CCGP is to compare conifer genetic maps with the P. taeda reference map by providing orthologous markers.…”

Section: Perspectivesmentioning

confidence: 99%

“…Alternatively, other research groups started to use codominant markers such as RFLPs [10,19,54], PCR-RFLP [26], ESTs (Expressed Sequence Tags) [12,47,61] and more recently SSRs (Simple Sequence Repeats) [19,22,43], allowing gene action to be precisely defined (estimation of additive and dominant effects of QTLs, [55]) and providing anchor points in comparative mapping experiments [39].…”

Section: Introductionmentioning

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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“…짧은 single copy DNA 염기서열 영역을 프라이머로 이 용하는 STS (Sequence Tag Site) 방법을 이용하기 때문에 특이 성과 재현성이 높은 장점을 가지고 있으며 (Olson et al, 1989) (Allona et al, 1998;Cairney et al, 2006;Lorenz et al, 2006;Liang et al, 2007;Ralph et al, 2008), Picea mariana (Perry and Bousquet, 1998)를 비롯하여 다수의 침엽 수를 대상으로 EST 표지 개발이 이루어졌다 (Harry et al, 1998;Temesgen et al, 2001;Komulainen et al, 2003;Chagné et al, 2003;Brown et al, 2004;Chagné et al, 2004;González-Martínez et al, 2006b;Eckert et al, 2009). 최근에는 EST표지를 이용 한 침엽수류 집단 수준에서의 적응유전변이 구명도 활발히 이루 어지고 있다 (Schubert et al, 2001;Jaramillo-Correa et al, 2001;Achere et al, 2005;Tsumura et al, 2007;Eckert et al, 2009) …”

Section: Fig 1 Location Of 13unclassified

Genetic Variation of Pinus densiflora Populations in South Korea Based on ESTP Markers

Ahn¹,

Hong²,

Lee³

et al. 2015

Korean Journal of Plant Resources

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-Genetic diversity and genetic differentiation of thirteen Pinus densiflora populations in South Korea were estimated using nine ESTP (Expressed Sequence Tag Polymorphism) markers. The numbers of allele and the effective allele were 2.2 and 1.8, respectively. The percentage of polymorphic loci (P) was 98.8%. The observed and the expected heterozygosity were 0.391 and 0.402, respectively, and the eleven populations except for Ahngang and Gangneung population were under Hardy-Weinberg equilibrium state. The level of genetic differentiation (Wright's FST = 0.057) was higher than those of isozyme or nSSR markers. We could not find out any relationship between the genetic distance and geographic distribution among populations from cluster analysis. Also, the genetic differentiation between populations was not correlated with the geographic distance (r = 0.017 and P = 0.344 from Mantel test). From the result of FST-outlier analysis to identify a locus under selection, six loci were detected at confidence interval of 99% by the frequentist's method. However, only three loci (sams2+AluⅠ, sams2+RsaⅠ, PtNCS_p14A9+HaeⅢ) were presumed as outliers by Bayesian method. The sams2+AluⅠ and sams2+RsaⅠlocus were originated from the sams2 gene and seemed to be the loci under balancing selection.

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Codominant PCR-based markers for Pinus taeda developed from mapped cDNA clones

Cited by 41 publications

References 25 publications

Towards construction of an ultra high density linkage map for Pinus pinaster

Towards construction of an ultra high density linkage map for Pinus pinaster

A high density genetic map of maritime pine based on AFLPs

Genetic Variation of Pinus densiflora Populations in South Korea Based on ESTP Markers

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