SNP discovery in apple cultivars using next generation sequencing

Alencar, Sergio de; Silva‐Junior, Orzenil B.; Togawa, Roberto Coiti; Costa, Marcos Mota do Carmo; Revers, L. F.; Παππάς, Γεώργιος

doi:10.1186/1753-6561-5-s7-p42

Cited by 4 publications

(2 citation statements)

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“…The data set of sequences generated was deposited under the access number PRJNA479978. With this sequence data, a large number of SNPs shared by the plant lines were detected ( Alencar et al, 2011 ). These SNPs were further inspected for the development of genotyping assays targeting high-density mapping of apple LG9 based on the integration of the apple genetic map ( Muranty et al, 2014 ) with contigs in the apple genome sequence.…”

Section: Methodsmentioning

confidence: 99%

Spring Is Coming: Genetic Analyses of the Bud Break Date Locus Reveal Candidate Genes From the Cold Perception Pathway to Dormancy Release in Apple (Malus × domestica Borkh.)

et al. 2019

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Chilling requirement (CR) for bud dormancy completion determines the time of bud break in apple (Malus × domestica Borkh.). The molecular control of bud dormancy is highly heritable, suggesting a strong genetic control of the trait. An available Infinium II SNP platform for genotyping containing 8,788 single nucleotide polymorphic markers was employed, and linkage maps were constructed in a F1 cross from the low CR M13/91 and the moderate CR cv. Fred Hough. These maps were used to identify quantitative trait loci (QTL) for bud break date as a trait related to dormancy release. A major QTL for bud break was detected at the beginning of linkage group 9 (LG9). This QTL remained stable during seven seasons in two different growing sites. To increase mapping efficiency in detecting contributing genes underlying this QTL, 182 additional SNP markers located at the locus for bud break were used. Combining linkage mapping and structural characterization of the region, the high proportion of the phenotypic variance in the trait explained by the QTL is related to the coincident positioning of Arabidopsis orthologs for ICE1, FLC, and PRE1 protein-coding genes. The proximity of these genes from the most explanatory markers of this QTL for bud break suggests potential genetic additive effects, reinforcing the hypothesis of inter-dependent mechanisms controlling dormancy induction and release in apple trees.

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Section: Methodsmentioning

confidence: 99%

Spring Is Coming: Genetic Analyses of the Bud Break Date Locus Reveal Candidate Genes From the Cold Perception Pathway to Dormancy Release in Apple (Malus × domestica Borkh.)

et al. 2019

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“…DNA resequencing was carried out for parental individuals from the population segregating for dormancy traits established by our group, and as a result, more than 80,000 SNPs were discovered (Alencar et al 2011). After validation, these new markers will be fundamental for the fine characterization of the apple dormancyrelated traits QTLs.…”

Section: Linkage Mapping Of Dormancy-related Traitsmentioning

confidence: 99%