Apple Structural Genomics

Korban, Schuyler S.; Tartarini, Stefano

doi:10.1007/978-0-387-77491-6_5

Cited by 17 publications

(8 citation statements)

References 136 publications

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“…The domesticated apple, Malus × domestica Borkh., is self-incompatible, highly heterozygous, and displays a juvenile period of 6–10 years or more ( Korban and Tartarini, 2009 ). The apple is a diploid (2 n =34) with a relatively small genome size of ∼750 Mb per haploid.…”

Section: Introductionmentioning

confidence: 99%

Integration of physical and genetic maps in apple confirms whole-genome and segmental duplications in the apple genome

Han

Zheng

Vimolmangkang

et al. 2011

Journal of Experimental Botany

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A total of 355 simple sequence repeat (SSR) markers were developed, based on expressed sequence tag (EST) and bacterial artificial chromosome (BAC)-end sequence databases, and successfully used to construct an SSR-based genetic linkage map of the apple. The consensus linkage map spanned 1143 cM, with an average density of 2.5 cM per marker. Newly developed SSR markers along with 279 SSR markers previously published by the HiDRAS project were further used to integrate physical and genetic maps of the apple using a PCR-based BAC library screening approach. A total of 470 contigs were unambiguously anchored onto all 17 linkage groups of the apple genome, and 158 contigs contained two or more molecular markers. The genetically mapped contigs spanned ∼421 Mb in cumulative physical length, representing 60.0% of the genome. The sizes of anchored contigs ranged from 97 kb to 4.0 Mb, with an average of 995 kb. The average physical length of anchored contigs on each linkage group was ∼24.8 Mb, ranging from 17.0 Mb to 37.73 Mb. Using BAC DNA as templates, PCR screening of the BAC library amplified fragments of highly homologous sequences from homoeologous chromosomes. Upon integrating physical and genetic maps of the apple, the presence of not only homoeologous chromosome pairs, but also of multiple locus markers mapped to adjacent sites on the same chromosome was detected. These findings demonstrated the presence of both genome-wide and segmental duplications in the apple genome and provided further insights into the complex polyploid ancestral origin of the apple.

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Section: Introductionmentioning

confidence: 99%

Integration of physical and genetic maps in apple confirms whole-genome and segmental duplications in the apple genome

Han

Zheng

Vimolmangkang

et al. 2011

Journal of Experimental Botany

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“…Domestication of species provides not only insights into cultures and lifestyles of human civilizations, but also serves as a well‐designed natural experiment to gain new knowledge about evolution, and allows us to pursue studies on the influence of selection on modifying functions of genes controlling desirable traits (Purugganan and Fuller, 2009; Olsen and Wendel, 2013). To date, several studies have focused on the genetics and genomics of the evolution of animals (e.g., dogs (Pollinger et al, 2010), horses (Outram et al, 2009), and cattle (Götherström et al, 2005), and plants, such as maize ( Zea mays L.; Wang et al, 1999; Clark et al, 2004; Hufford et al, 2012) and rice ( Oryza sativa L.; Konishi et al, 2006; Fuller et al, 2009; Huang et al, 2012). Evaluation and analysis of genome‐wide genetic diversity and linkage disequilibrium (LD) in crops and their wild progenitors can be used in “selective sweep” mapping and in other population genetic studies to identify genomic regions targeted for selection during domestication (Tian et al, 2009).…”

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Fruit Quality Traits Have Played Critical Roles in Domestication of the Apple

et al. 2014

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With its long history of cultivation, the domesticated apple, Malus × domestica Borkh., is an excellent model for studying domestication in long-lived perennial plants. As apples have been transported from their center of origin in the Tian Shan region in central Asia and moved along the famous Silk Road trading path, they have undergone selection for distinct phenotypic traits. In this study, a high-throughput single nucleotide polymorphism (SNP) genotyping assay is used to investigate relationships of Malus species, draw inferences on the domestication history, identify traits critical for domestication, and assess potential genetic loci under selection. A total of 160 Malus accessions, including wild species, old and new apple cultivars, and advanced selections, were genotyped. Of 1536 SNPs from GoldenGate oligonucleotide pool assays (OPAs), 901 SNPs fulfilled filtering criteria. A principal component analysis (PCA) revealed that most M. × domestica accessions grouped together. A total of 67 loci, including 13 genomic SNPs and 54 genic SNPs, have been identified as potential targets for selection during evolution of the apple genome from its wild progenitor M. sieversii. Genes introgressed from local wild species into M. × domestica are associated with adaptation to local environments, while genes for fruit quality traits are derived from M. sieversii.

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“…The first controlled crosses of apple trees for breeding purposes date from 1806, and apple breeders usually select genotypes carrying desired traits from the F1 progenies (Kellerhals 2009). Many of the target traits to be introgressed to apple cultivars are related to disease resistance, tree architecture, flowering and fruit quality (Korban and Tartarini 2009). Pear breeding also typically involves generation of genetic variation by crossing, aiming to improve fruit quality, disease resistance, storage ability, among other traits (Yamamoto and Chevreau 2009).…”

Section: Linkage Mapping Of Dormancy-related Traitsmentioning

confidence: 99%