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Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm
Background Apple (Malus x domestica Borkh.) is one of the most important fruit tree crops of temperate areas, with great economic and cultural value. Apple cultivars can be maintained for centuries in plant collections through grafting, and some are thought to date as far back as Roman times. Molecular markers provide a means to reconstruct pedigrees and thus shed light on the recent history of migration and trade of biological materials. The objective of the present study was to identify relationships within a set of over 1400 mostly old apple cultivars using whole-genome SNP data (~253K SNPs) in order to reconstruct pedigrees. Results Using simple exclusion tests, based on counting the number of Mendelian errors, more than one thousand parent-offspring relations and 295 complete parent-offspring families were identified. Additionally, a grandparent couple was identified for the missing parental side of 26 parent-offspring pairings. Among the 407 parent-offspring relations without a second identified parent, 327 could be oriented because one of the individuals was an offspring in a complete family or by using historical data on parentage or date of recording. Parents of emblematic cultivars such as 'Ribston Pippin', 'White Transparent' and 'Braeburn' were identified. The overall pedigree combining all the identified relationships encompassed seven generations and revealed a major impact of two Renaissance cultivars of French and English origin, namely 'Reinette Franche' and 'Margil', and one North-Eastern Europe cultivar from the 1700s, 'Alexander'. On the contrary, several older cultivars, from the Middle Ages or the Roman times, had no, or only single, identifiable offspring in the set of studied accessions. Frequent crosses between cultivars originating from different European regions were identified, especially from the 19th century onwards. Conclusions The availability of over 1400 apple genotypes, previously filtered for genetic uniqueness and providing a broad representation of European germplasm, has been instrumental for the success of this large pedigree reconstruction. It enlightens the history of empirical selection and recent breeding of apple cultivars in Europe and provides insights to speed-up future breeding and selection
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
<em>Cherry virus A</em> infecting cherries and plums in the Czech Republic – Short communication
The presence of Cherry virus A (CVA) in the germplasm collections of sweet cherries and plums was studied. CVA was detected using the specific RT-PCR assay in six of eight sweet cherry and one of four plum cultivars. Specifity of amplicons and distant position of cherry and non-cherry isolates was verified by sequencing and phylogenetic analysis. Results indicate that the cherry landraces and cultivars could be infected by CVA more than it has been assumed
Role of PPARγ in COX-2 Activation in Mycobacterial Pulmonary Inflammation
The presence of Cherry virus A (CVA) in the germplasm collections of sweet cherries and plums was studied. CVA was detected using the specific RT-PCR assay in six of eight sweet cherry and one of four plum cultivars. Specifity of amplicons and distant position of cherry and non-cherry isolates was verified by sequencing and phylogenetic analysis. Results indicate that the cherry landraces and cultivars could be infected by CVA more than it has been assumed
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