Genomics-Based Opportunities in Apricot

Folta, Kevin M.; Gardiner, Susan E.

doi:10.1007/978-0-387-77491-6_15

Cited by 16 publications

(20 citation statements)

References 86 publications

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“…With regards to tomato, apple shows three chromosomes characterized by the presence of PPO elements, but chromosome 2 contains only one element, and chromosomes 5 and 10 are homoeologous, due to the recent genome duplication occurring in this species [23]. Moreover, other authors have already presented the duplication of these two chromosomes in apple in previous publications [32-35]. Recently, a comprehensive survey performed on 25 sequenced genomes revealed that other species shared a similar number of PPO genes [36], such as Sorghum bicolour (8), Glycine max (11) and Populus trichocarpa (11).…”

Section: Resultsmentioning

confidence: 99%

A Multidisciplinary Approach Providing New Insight into Fruit Flesh Browning Physiology in Apple (Malus x domestica Borkh.)

et al. 2013

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In terms of the quality of minimally processed fruit, flesh browning is fundamentally important in the development of an aesthetically unpleasant appearance, with consequent off-flavours. The development of browning depends on the enzymatic action of the polyphenol oxidase (PPO). In the ‘Golden Delicious’ apple genome ten PPO genes were initially identified and located on three main chromosomes (2, 5 and 10). Of these genes, one element in particular, here called Md-PPO, located on chromosome 10, was further investigated and genetically mapped in two apple progenies (‘Fuji x Pink Lady’ and ‘Golden Delicious x Braeburn’). Both linkage maps, made up of 481 and 608 markers respectively, were then employed to find QTL regions associated with fruit flesh browning, allowing the detection of 25 QTLs related to several browning parameters. These were distributed over six linkage groups with LOD values spanning from 3.08 to 4.99 and showed a rate of phenotypic variance from 26.1 to 38.6%. Anchoring of these intervals to the apple genome led to the identification of several genes involved in polyphenol synthesis and cell wall metabolism. Finally, the expression profile of two specific candidate genes, up and downstream of the polyphenolic pathway, namely phenylalanine ammonia lyase (PAL) and polyphenol oxidase (PPO), provided insight into flesh browning physiology. Md-PPO was further analyzed and two haplotypes were characterised and associated with fruit flesh browning in apple.

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Section: Resultsmentioning

confidence: 99%

A Multidisciplinary Approach Providing New Insight into Fruit Flesh Browning Physiology in Apple (Malus x domestica Borkh.)

et al. 2013

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“…1) have been more scarce (Dirlewanger et al 2004(Dirlewanger et al , 2009aShulaev et al 2008;Peace and Norelli 2009). These molecular studies have been performed mainly in peach Pozzi and Vecchietti 2009), considered the model species; followed by almond (Martínez-Gómez et al 2007;Arús et al 2009), a very close species to peach; apricot (Folta and Gardiner 2009); cherry (Dirlewanger et al 2009b); and plum (Esmenjaud and Dirlewanger 2007). As a result of many of these genome studies and using high-information content fingerprinting (HICF), the first physical map of Prunus has been generated in peach .…”

Section: Introductionmentioning

confidence: 97%

New approaches to Prunus transcriptome analysis

et al. 2011

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The recent sequencing of the complete genome of the peach offers new opportunities for further transcriptomic studies in Prunus species in the called post-genomics era. First works on transcriptome analysis in Prunus species started in the early 2000s with the development of ESTs (expressed sequence tags) and the analysis of several candidate genes. Later, new strategies of massive analysis (high throughput) of transcriptomes have been applied, producing larger amounts of data in terms of expression of a large number of genes in a single experiment. One of these systems is massive transcriptome analysis using cDNA biochips (microarrays) to analyze thousands of genes by hybridization of mRNA labelled with fluorescence. However, the recent emergence of a massive sequencing methodology ("deep-sequencing") of the transcriptome (RNA-Seq), based on lowering the costs of DNA (in this cases complementary, cDNA) sequencing, could be more suitable than the application of microarrays. Recent papers have described the tremendous power of this technology, both in terms of profiling coverage and quantitative accuracy in transcriptomic studies. Now this technology is being applied to plant species, including Prunus. In this work, we analyze the potential in using this RNA-Seq technology in the study of Prunus transcriptomes and the development of genomic tools. In addition, the strengths and limitations of RNA-Seq relative to microarray profiling have been discussed.

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“…Koch, subgenus Prunophora Focke, and genus Prunus (Rosaceae) 2 . According to different taxonomic systems, apricots are divided into three to twelve species 3,4 . However, six species are recognized by most scholars 3,5,6 : Prunus armeniaca L., Prunus sibirica L., Prunus mandshurica (Maxim.)…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity, population structure, and relationships of apricot (Prunus) based on restriction site-associated DNA sequencing

Liu

Wang

et al. 2020

Hortic Res

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Single-nucleotide polymorphisms (SNPs) are the most abundant form of genomic polymorphisms and are widely used in population genetics research. Here, high-throughput sequencing was used to examine the genome-level diversity, population structure, and relationships of apricot, which are important for germplasm conservation and molecular breeding. Restriction site-associated DNA sequencing (RAD-seq) was adopted to sequence 168 Prunus spp. accessions distributed in five ecological groups, including 74 accessions of cultivated Prunus armeniaca L. and 94 accessions of wild apricots (P. armeniaca L. and Prunus sibirica L.), which generated 417,961 high-quality SNPs. We used cluster, genetic structure, and principal component analyses to examine the genetic diversities and genetic relationships of the 168 accessions. The Dzhungar-Ili ecological group accessions showed the highest genetic diversity in terms of private allele number, observed heterozygosity, and nucleotide diversity. We speculate that the Central Asian ecological group accessions were domesticated from the Dzhungar-Ili ecological group accessions. The population structure and gene flow of the North China and European ecological group accessions suggested a genetic background of P. sibirica. We argue that the two groups should be considered hybrid swarms connected to P. sibirica by continuous and extensive gene flow. P. armeniaca originated in Northwest China (Ili Valley), subsequently spread throughout Central Asia, and eventually spread to Europe. In addition, selective sweep signatures in P. armeniaca during domestication from wild to cultivated apricots, combined with differentially expressed genes, underlie distinct fruit traits, including sugars, aromas, organic acids, and carotenoids. This study provides substantive and valuable genomic resources that will significantly advance apricot improvement and effective utilization.

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Genomics-Based Opportunities in Apricot

Cited by 16 publications

References 86 publications

A Multidisciplinary Approach Providing New Insight into Fruit Flesh Browning Physiology in Apple (Malus x domestica Borkh.)

A Multidisciplinary Approach Providing New Insight into Fruit Flesh Browning Physiology in Apple (Malus x domestica Borkh.)

New approaches to Prunus transcriptome analysis

Genetic diversity, population structure, and relationships of apricot (Prunus) based on restriction site-associated DNA sequencing

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