Reconstruction of multi-generation pedigrees involving numerous old apple cultivars thanks to whole-genome SNP data

A number of European apple cultivars are old, some of them dating back to the Renaissance, Middle Ages or even earlier. Many other cultivars have been developed during subsequent times. In order to decipher the relationships that link some of these old cultivars, whole-genome SNP data (~ 250K) for over 1400 genotypes were analyzed to infer first-degree relationships and reconstruct pedigrees. We used simple exclusion tests based on a count of Mendelian error to identify up to a thousand potential parent-offspring duos, including 295 complete parent-offspring trios and a hundred duos that could be oriented. grand-parents for some missing parents could also be inferred. Combining all this information allowed us to reconstruct pedigrees (up to 6 generations) highlighting the central role of major founders such as ‘Reinette Franche’, ‘Margil’, and ‘Alexander’. Haplotypes were deduced from genotypic data and pedigrees, and used to measure haplotype sharing between supposedly unrelated cultivars, allowing investigating further links between them.To our knowledge, such a large analysis to reconstruct multigeneration pedigrees involving (very) old cultivars selected over such time has never before been performed in perennial fruit species

MONITORING FRUIT LANDRACES IN THE CZECH REPUBLIC, TRACING THEIR ORIGIN AND POTENTIAL FOR THEIR CONSERVATION

Landraces of cultivated plants originated from the beginning of agriculture through selection from wild ecotypes and cultivated by farmers in their domestic region were investigated with the goal to conserve fragments of still existing fruit landraces, including restoration of variable countryside with scattered and roadside trees, wind-breaking and snow-catching functions including fruit consumption. Individual trees were identified, attributed to cultivars, localized by GPS and mapped in the Geobase Map of the Czech Republic. The inventory listed 388 fruits out of total number of 2866 accessions. It is a basis for searching lost and extinct materials. The database was analyzed for cultivars, regionality and their longevity by the length of registration. The best indigenous materials were proposed for in situ conservation mainly in the territory of National Parks and Protected Landscape Areas

Genetic diversity of phytoplasmas infecting apple trees in the Czech Republic.

Apple trees are affected by the apple proliferation (AP) disease in several European countries. Samples from apple trees showing proliferation disease symptoms were collected during 2010 all over the Czech Republic. Phytoplasma strains were detected through polymerase chain reaction and restriction fragment length polymorphism analyses of 16S rDNA-spacer region-23rDNA, ribosomal protein gene sequences rpl22 and rps3 and non ribosomal DNA fragment (nitroreductase-like gene). All 74 apple trees examined were positive for phytoplasma presence, predominantly \u2018Candidatus Phytoplasma mali\u2019. \u2018Ca. P. asteris\u2019 alone and in mixed infection with \u2018Ca. P. mali\u2019 was also found. In the 16S plus spacer region of \u2018Ca. P. mali\u2019 two profiles were determined (P-I mainly, P-II rarely). Correspondingly, two genetic lineages were found in PCR amplified fragments covering 16S rDNA-spacer region-23rDNA (pattern \u20181a\u2019 rarely, \u20182a\u2019 mainly). \u2018Ca. P. mali\u2019 strains belonging to ribosomal protein rpX-A subgroup were identified in the majority of apple samples while phytoplasmas belonging to rpX-B subgroup were erratically found. Apple proliferation subtypes AP-15 and AT-2 revealed nearly equal occurrence. AT-1 subtype and a mixture of two or all three AP subtypes was not frequent. The PCR/RFLP results were confirmed by nucleotide sequence analyses of the 16S-23S ribosomal operon, ribosomal proteins L22, S3 and nitroreductase-like protein gene of five selected apple proliferation strains. This is the first study of molecular diversity among \u2018Ca. P. mali\u2019 strains in the Czech Republic

Sugar composition of apple cultivars and its relationship to sensory evaluation

The increasing consumption of sugars is one of the factors contributing to the obesity epidemic. Our research was carried out on the sugar composition of apples. The purpose of the study was to determine the quantitative and qualitative composition of sugars of different apple varieties from the East Bohemia region. In this study dry matter content and sensory characteristics were also evaluated. Apples contain fructose, glucose and sucrose. Fructose is known to be a highly lipogenic sugar that has profound metabolic effects in the liver, and has been associated with many of the components of the metabolic syndrome (insulin resistance, elevated waist circumference, dyslipidemia, and hypertension). Fructose, glucose and sucrose in different apple cultivars were extracted with ethanol, derivatized, and determined by gas chromatography. 17 cultivars of apple were analysed. The average fructose content was 6.52 ± 1 g/100 g of apple (8.1 – ‘Golden Delicious’, 4.8 – ‘Selena’), glucose content 1.46 ± 0.55 g/100 g of apple (3 – ‘Red Delicious’, 0.9 – ‘Ontario’), and sucrose content 4.75 ± 1.35 g/100 g of apple (7.2 – ‘Opal’, 2.1 – ‘Melrose’). The cultivars suitable for nutrition of patients with metabolic syndrome are ‘Selena’ and ‘Ontario’.Zwiększenie spożycia cukrów jest jednym z czynników mających wpływ na epidemię otyłości. Prezentowane wyniki badań dotyczą składu cukrów w jabłkach. Celem badań był wybór odmian jabłek odpowiednich pod względem zdrowego odżywiania, tj. ilościowego i jakościowego składu cukrów. Jabłka zawierają fruktozę, glukozę i sacharozę. Dla przykładu fruktoza jest cukrem wysoce lipogennym, który ma istotny wpływ na metabolizm w wątrobie i wiąże się z wieloma czynnikami zespołu metabolicznego (oporność na insulinę, otyłość brzuszna, dyslipidemia i nadciśnienie). Fruktoza, glukoza i sacharoza z jabłek różnych odmian zostały wyekstrahowane etanolem, derywatyzowane i oznaczane metodą chromatografii gazowej. Analizie poddano 17 odmian jabłek. Zawartość fruktozy kształtowała się na poziomie 6,52 ± 1 g/100 g jabłek (8,1 – ‘Golden Delicious’, 4,8 – ‘Selena’). Zawartość glukozy wynosiła 1,46 ± 0,55 g/100 g jabłek (3,0 – ‘Red Delicious’, 0,9 – ‘Ontario’), a sacharozy – 4,75 ± 1,35 g/100 g jabłek (7,2 – ‘Opal’, 2,1 – ‘Melrose’). Odmiany jabłek ‘Selena’ i ‘Ontario’ okazały się jako najbardziej odpowiednie do stosowania w żywieniu pacjentów z zespołem metabolicznym

Genome wide association study of two phenology traits (flowering time and maturity date) in apple

The aim of Genome Wide Association Studies (GWAS) is to identify markers in tight linkage disequilibrium with loci controlling quantitative trait variation. These markers can then be used in marker-assisted selection (MAS) in fruit crops such as apple. The GWAS approach involves both phenotyping of a large population of mostly unrelated individuals for the traits of interest, and genotyping at high marker density. In the EU-FP7 project FruitBreedomics, almost 1,200 European diploid dessert apple accessions (old and/or local cultivars) from six germplasm collections were genotyped with the Affymetrix Axiom_Apple480K array (487,000 SNPs). Phenotypic data on a large number of traits have been gathered during the project. Here we focus on flowering period and harvesting date. Knowledge of the genetic control of these traits is necessary to develop cultivars that can face the challenges imposed by global climate change and to target cultivar development as a function of a prolonged vegetation period in the production regions. Different models were tested, including control for effects of population structure and relatedness between cultivars. The full model, controlling for both structure and relatedness, was shown to be the most appropriate to avoid spurious marker-trait associations. When analyzing data over all collections, one significant marker-trait association was obtained for each trait, on chromosomes 9 and 3, for flowering period and harvesting date, respectively. Thereby, genomic locations previously identified in bi-parental populations could now be confirmed for a genetically diverse germplasm

Deciphering the genetic determinism of flowering/harvest period and several fruit sensory quality traits in apple by a Genome-Wide Association approach

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