Generation de marqueurs de séquences exprimées et développement de marqueurs microsatellites pour Castanopsis sieboldii var. sieboldii (Fagaceae)

Ueno, S.; Aoki, Kyoko; Tsumura, Yoshihiko

doi:10.1051/forest/2009037

Cited by 22 publications

(28 citation statements)

References 52 publications

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“…The frequencies of SSR types and motifs that we found in C. mollissima ESTs are in general agreement with those reported for other species in the Fagaceae Ueno et al 2009;Inoue et al 2009;Cheng and Huang 2009;Durand et al 2010). Based on our SSR search criteria, 18.1 % of the 48,335 C. mollissima CCall_Unige-ne_V2 ESTs contained at least one SSR.…”

Section: Marker Identification and Characterizationsupporting

confidence: 90%

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A transcriptome-based genetic map of Chinese chestnut (Castanea mollissima) and identification of regions of segmental homology with peach (Prunus persica)

Kubisiak

Nelson

Staton

et al. 2012

Tree Genetics & Genomes

126

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The Chinese chestnut (Castanea mollissima) carries resistance to Cryphonectria parasitica, the fungal pathogen inciting chestnut blight. The pathogen, introduced from Asia, devastated the American chestnut (Castanea dentata) throughout its native range early in the twentieth century. A highly informative genetic map of Chinese chestnut was constructed to extend genomic studies in the Fagaceae and to aid the introgression of Chinese chestnut blight resistance genes into American chestnut. Two mapping populations were established with three Chinese chestnut parents, 'Mahogany', 'Nanking', and 'Vanuxem', totaling 337 progeny. The transcriptome-based genetic map was created with 329 simple sequence repeat and 1,064 single nucleotide polymorphism markers all derived from expressed sequence tag sequences. Genetic maps for each parent were developed and combined to establish 12 consensus linkage groups spanning 742 cM, providing the the most comprehensive genetic map for a Fagaceae species to date. Over 75 % of the mapped markers from the Chinese chestnut consensus genetic map were placed on the physical map using overgo hybridization, providing a fully integrated genetic and physical map resource for Castanea spp. About half (57 %) of the Chinese chestnut genetic map could be assigned to regions of segmental homology with 58 % of the peach (Prunus persica) genome assembly. A three quantitative trait loci (QTL) model for blight resistance was verified using the new genetic markers and an existing interspecies (C. mollissima × C. dentata) F 2 mapping population. Two of the blight resistance QTLs in chestnut shared synteny with two QTLs for powdery mildew resistance in peach, indicating the potential conservation of disease resistance genes at these loci.

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Section: Marker Identification and Characterizationsupporting

confidence: 90%

“…Based on our SSR search criteria, 18.1 % of the 48,335 C. mollissima CCall_Unige-ne_V2 ESTs contained at least one SSR. A search for SSRs in Castanopsis sieboldii ESTs (Ueno et al 2009) found 13 % to contain at least one SSR. Similarly, 18.6 % of Quercus ESTs (Durand et al 2010) contained at least one SSR.…”

Section: Marker Identification and Characterizationmentioning

confidence: 99%

A transcriptome-based genetic map of Chinese chestnut (Castanea mollissima) and identification of regions of segmental homology with peach (Prunus persica)

Kubisiak

Nelson

Staton

et al. 2012

Tree Genetics & Genomes

126

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“…A total of 168 EST-SSR primer pairs, including 124 polymorphic EST-SSRs in Castanea mollissima (www.fagaceae.org), 16 in Castanopsis sieboldii (Ueno et al, 2009) and 28 in Quercus mongolica , were screened in a pilot experiment using 20 individuals of C. fargesii. Finally, 32 primer pairs (Table 2) with clear, polymorphic banding patterns were picked to genotype all individuals.…”

Section: Samples Dna Extraction and Est-ssr Genotypingmentioning

confidence: 99%

“…Three loci (CC20303, CcC02075 and CcC02464) was identified as possibly being under balancing selection. The first two loci were linked to uncharacterized protein, while CcC02464 assigned to a 5 0 -nucleotidase SurE-like survival protein in Arabidopsis (Ueno et al, 2009).…”

Section: Figurementioning

confidence: 99%

Footprints of divergent selection in natural populations of Castanopsis fargesii (Fagaceae)

Sun

Huang

et al. 2014

Heredity

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Given predicted rapid climate change, an understanding of how environmental factors affect genetic diversity in natural populations is important. Future selection pressures are inherently unpredictable, so forest management policies should maintain both overall diversity and identify genetic markers associated with the environmental factors expected to change most rapidly, like temperature and rainfall. In this study, we genotyped 648 individuals in 28 populations of Castanopsis fargesii (Fagaceae) using 32 expressed sequence tag (EST)-derived microsatellite markers. After removing six loci that departed from Hardy-Weinberg equilibrium, we measured genetic variation, population structure and identified candidate loci putatively under selection by temperature and precipitation. We found that C. fargesii populations possessed high genetic diversity and moderate differentiation among them, indicating predominant outcrossing and few restrictions to gene flow. These patterns reduce the possible impact of stochastic effects or the influence of genetic isolation. Clear footprints of divergent selection at four loci were discovered. Frequencies of five alleles at these loci were strongly correlated with environmental factors, particularly extremes in precipitation. These alleles varied from being near fixation at one end of the gradient to being completely absent at the other. Our study species is an important forest tree in the subtropical regions of China and could have a major role in future management and reforestation plans. Our results demonstrate that the gene flow is widespread and abundant in natural populations, maintaining high diversity, while diversifying selection is acting on specific genomic regions.

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“…crispula (Ueno et al 2008), Castanopsis sieboldii (Ueno et al 2009a), and Fagus crenata (Ueno et al 2009b) to develop genic microsatellite (SSR) markers. Because SSRs are frequent within ESTs, they are a good source of genetic markers with functional annotation, though SSR frequency varies depending on the program and criteria used for SSR detection (12.8 % for Q. mongolica var.…”

Section: Large Scale Transcriptomic Investigationsmentioning

confidence: 99%

Genomics of Fagaceae

Kremer

Abbott

Carlson

et al. 2012

Tree Genetics & Genomes

Self Cite

116

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An overview of recent achievements and development of genomic resources in the Fagaceae is provided, with major emphasis on the genera Castanea and Quercus. The Fagaceae is a large plant family comprising more than 900 species belonging to 8-10 genera. Using a wide range of molecular markers, population genetics and gene diversity surveys were the focus of many studies during the past 20 years. This work set the stage for investigations in genomics beginning in the early 1990s and facilitated the application of genetic and quantitative trait loci mapping approaches. Transferability of markers across species and comparative mapping have indicated tight macrosynteny between Quercus and Castanea. Omic technologies were more recently developed and the corresponding resources are accessible via electronic and physical repositories (expressed sequence tag sequences, single-nucleotide polymorphisms, candidate genes, cDNA clones, bacterial artificial chromosome (BAC) libraries) that have been installed in North America and Europe. BAC libraries and physical maps were also constructed in Castanea and Quercus and provide the necessary resources for full nuclear genome sequencing projects that are currently under way in Castanea mollissima (Chinese chestnut) and Quercus robur (pedunculate oak). Communicated by T. DrudgeA contribution to the Special Issue "The genomes of the giants: a walk through the forest of tree genomes" A. Kremer :

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Generation de marqueurs de séquences exprimées et développement de marqueurs microsatellites pour Castanopsis sieboldii var. sieboldii (Fagaceae)

Cited by 22 publications

References 52 publications

A transcriptome-based genetic map of Chinese chestnut (Castanea mollissima) and identification of regions of segmental homology with peach (Prunus persica)

A transcriptome-based genetic map of Chinese chestnut (Castanea mollissima) and identification of regions of segmental homology with peach (Prunus persica)

Footprints of divergent selection in natural populations of Castanopsis fargesii (Fagaceae)

Genomics of Fagaceae

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