Identification of a major QTL for Xanthomonas arboricola pv. pruni resistance in apricot

Xanthomonas arboricola pv. pruni causes bacterial spot of stone fruit resulting in severe yield losses in apricot production systems. Present on all continents, the pathogen is regulated in Europe as a quarantine organism. Host resistance is an important component of integrated pest management; however, little work has been done describing resistance against X. arboricola pv. pruni. In this study, an apricot population derived from the cross “Harostar” × “Rouge de Mauves” was used to construct two parental genetic maps and to perform a quantitative trait locus analysis of resistance to X. arboricola pv. pruni. A population of 101 F1 individuals was inoculated twice for two consecutive years in a quarantine greenhouse with a mixture of bacterial strains, and disease incidence and resistance index data were collected. A major QTL for disease incidence and resistance index accounting respectively for 53 % (LOD score of 15.43) and 46 % (LOD score of 12.26) of the phenotypic variation was identified at the same position on linkage group 5 of “Rouge de Mauves.” Microsatellite marker UDAp-452 co-segregated with the resistance, and two flanking microsatellites, namely BPPCT037 and BPPCT038A, were identified. When dividing the population according to the alleles of UDAp-452, the subgroup with unfavorable allele had a disease incidence of 32.6 % whereas the group with favorable allele had a disease incidence of 21 %, leading to a reduction of 35.6 % in disease incidence. This study is a first step towards the marker-assisted breeding of new apricot varieties with an increased tolerance to X. arboricola pv. pruni

Genetic Variability Study in a Wide Germplasm of Domesticated Peach Through High Throughput

Peach (Prunus persica (L.) Batsch) is one of the most economically important fruit crops in temperate areas. Classical fruit tree breeding is generally slow and inefficient. Molecular markers could improve its efficiency but, although nowadays many Mendelian traits are mapped in peach and SSR markers have been found to be linked to some of the key major genes, its use in breeding programs is still limited. Main reasons for that are insufficient linkage between the markers and the genes and the lack of markers suitable for medium-high degree of multiplexing. To address this limitation, about 1,300 peach cultivars were genotyped with the 9K peach SNP chip (Verde et al. 2012) in the frame of FruitBreedomics project. This germplasm was chosen to be representative of the genetic diversity present in five germplasm collection in Europe and in China. Out of the 8144SNPs present in the chip, about 4300 were positively genotyped and used for the further analysis. The average number of heterozygous loci in the genotyped accessions was 1186 (spanning from 13 to 2775). The preliminary results of the population structure reveal three main subpopulations and the presence of high number of admixed individuals. LD seems to decay at distance longer than ca. 1 Mb. These results will be instrumental for implementing LD-based mapping of QTLs and genes in peach

Population genetic analysis of brazilian peach breeding germplasm.

ABSTRACT Peach has great economic and social importance in Brazil. Diverse sources of germplasm were used to introduce desirable traits in the Brazilian peach breeding pool, composed mainly by local selections and accessions selected from populations developed by the national breeding programs, adapted to subtropical climate, with low chill requirement, as well as accessions introduced from several countries. In this research, we used SSR markers, selected by their high level of polymorphism, to access genetic diversity and population structure of a set composed by 204 peach selected genotypes, based on contrasting phenotypes for valuable traits in peach breeding. A total of 80 alleles were obtained, giving an average of eight alleles per locus. In general, the average value of observed heterozygosity (0.46) was lower than the expected heterozygosity (0.63). STRUCTURE analysis assigned 162 accessions splitted into two subpopulations based mainly on their flesh type: melting (96) and non-melting (66) flesh cultivars. The remaining accessions (42) could not be assigned under the 80% membership coefficient criteria. Genetic variability was greater in melting subpopulation compared to non-melting. Additionally, 55% of the alleles present in the breeding varieties were also present in the founder varieties, indicating that founding clones are well represented in current peach cultivars and advanced selections developed. Overall, this study gives a first insight of the peach genetic variability available and evidence for population differentiation (structure) in this peach panel to be exploited and provides the basis for genome-wide association studies

Construction of an almond linkage map in an Australian population Nonpareil × Lauranne

Background: Despite a high genetic similarity to peach, almonds (Prunus dulcis) have a fleshless fruit and edible kernel, produced as a crop for human consumption. While the release of peach genome v1.0 provides an excellent opportunity for almond genetic and genomic studies, well-assessed segregating populations and the respective saturated genetic linkage maps lay the foundation for such studies to be completed in almond. Results: Using an almond intraspecific cross between ‘Nonpareil’ and ‘Lauranne’ (N × L), we constructed a moderately saturated map with SSRs, SNPs, ISSRs and RAPDs. The N × L map covered 591.4 cM of the genome with 157 loci. The average marker distance of the map was 4.0 cM. The map displayed high synteny and colinearity with the Prunus T × E reference map in all eight linkage groups (G1-G8). The positions of 14 mapped gene-anchored SNPs corresponded approximately with the positions of homologous sequences in the peach genome v1.0. Analysis of Mendelian segregation ratios showed that 17.9% of markers had significantly skewed genotype ratios at the level of P < 0.05. Due to the large number of skewed markers in the linkage group 7, the potential existence of deleterious gene(s) was assessed in the group. Integrated maps produced by two different mapping methods using JoinMap® 3 were compared, and their high degree of similarity was evident despite the positional inconsistency of a few markers. Conclusions: We presented a moderately saturated Australian almond map, which is highly syntenic and collinear with the Prunus reference map and peach genome V1.0. Therefore, the well-assessed almond population reported here can be used to investigate the traits of interest under Australian growing conditions, and provides more information on the almond genome for the international community.Iraj Tavassolian, Gholmereza Rabiei, Davina Gregory, Mourad Mnejja, Michelle G Wirthensohn, Peter W Hunt, John P Gibson, Christopher M Ford, Margaret Sedgley, and Shu-Biao W

Aktuelle Herausforderungen in der Therapie des Typ-1-Diabetes beim Kind

Das 1921 entdeckte Insulin wurde 1922 erstmals als Therapie für Typ-1-Diabetes eingeführt. Hundert Jahre später wird es immer noch als einzige medikamentöse Behandlung eingesetzt. Die jüngsten Fortschritte haben zu einer erheblichen Optimierung der Stoffwechselkontrolle beigetragen. Einleitung Typ-1-Diabetes (T1D) ist eine der häufigsten chronischen Erkrankungen bei Kindern, mit einer jährlichen Inzidenzzunahme von 3% [1]. Die Ätiologie des T1D ist unbekannt, aber eine Dysregulation der Autoimmunität, dokumentiert durch die Zirkulation von Autoantikörpern, sowie eine genetische Prädisposition sind ursächlich beteiligt. Das Risiko, an T1D zu erkranken, beträgt bei Kindern 0,4%; gibt es bereits an T1D-erkrankte Familienangehörige, steigt das Risiko um das Zehnfache. Neueste Daten weisen auf einen deutlichen Anstieg der weltweiten Inzidenz während der Corona-Pandemie hin [2–5]. Ziel dieses Beitrags ist es, die neuesten Entwicklungen und aktuellen Herausforderungen bei der Behandlung des T1D bei Kindern darzustellen

Grafting versus seed propagated apricot populations: two main gene pools in Tunisia evidenced by SSR markers and model-based Bayesian clustering

Apricot was introduced into the Mediterranean Basin from China and Asian mountains through the Middle-East and the Central Europe. Traditionally present in Tunisia, we were interested in accessing the origin of apricot species in the country, and in particular in the number and the location of its introductions. A set of 82 representative apricot accessions including 49 grafted cultivars and 33 seed propagated ‘Bargougs’ were genotyped using 24 microsatellite loci revealing a total of 135 alleles. The model-based Bayesian clustering analysis using both Structure and InStruct programs as well as the multivariate method revealed five distinct genetic clusters. The genetic differentiation among clusters showed that cluster 1, with only four cultivars, was the most differentiated from the four remaining genetic clusters, which constituted the largest part of the studied germplasm. According to their geographic origin, the five identified groups (north, centre, south, Gafsa oasis and other oases groups) enclosed a similar variation within group, with a low level of differentiation. Overall results highlighted the distinction of two apricot gene pools in Tunisia related to the different mode of propagation of the cultivars: grafted and seed propagated apricot, which enclosed a narrow genetic basis. Our findings support the assumption that grafting and seed propagated apricots shared the same origin

Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family

Abstract Background Comparative genome mapping studies in Rosaceae have been conducted until now by aligning genetic maps within the same genus, or closely related genera and using a limited number of common markers. The growing body of genomics resources and sequence data for both Prunus and Fragaria permits detailed comparisons between these genera and the recently released Malus × domestica genome sequence. Results We generated a comparative analysis using 806 molecular markers that are anchored genetically to the Prunus and/or Fragaria reference maps, and physically to the Malus genome sequence. Markers in common for Malus and Prunus, and Malus and Fragaria, respectively were 784 and 148. The correspondence between marker positions was high and conserved syntenic blocks were identified among the three genera in the Rosaceae. We reconstructed a proposed ancestral genome for the Rosaceae. Conclusions A genome containing nine chromosomes is the most likely candidate for the ancestral Rosaceae progenitor. The number of chromosomal translocations observed between the three genera investigated was low. However, the number of inversions identified among Malus and Prunus was much higher than any reported genome comparisons in plants, suggesting that small inversions have played an important role in the evolution of these two genera or of the Rosaceae.Apple genome research at FEM is supported by the research office of the Provincia autonoma di Trento. DJS and ELG acknowledge a grant from the East Malling Trust. Fragaria genomics at EMR is funded by the BBSRC. JMB is supported by a grant by Plant & Food Research's Excellence Programme. Apple genomics at Plant & Food Research is partially supported by the New Zealand Foundation for Research Science and Technology project C06X0812 "Exploiting Opportunities from Horticultural Genomics". Research conducted at IRTA was partly funded by the CONSOLIDER-INGENIO 2010 Program (CSD2007-00036) and project INIA-RTA2007-00063-00-00, both from the Spanish Ministry of Science and Innovation. RosCOS development at OSU/MSU was funded by the National Research Initiative Competitive Grant 2005-35300-15454 of USDA's National Institute of Food and Agriculture.Peer Reviewe

Linkage map saturation, construction, and comparison in four populations of Prunus

One of the objectives of the ISAFRUIT Project was to perform genetic analyses in four populations of Prunus, two of peach (P. persica) and two of apricot (P. armeniaca), in order to identify major genes and quantitative trait loci (QTLs) for characters related to fruit quality. This required the construction of saturated marker maps in each of these populations. Marker maps were available for an intra-specific peach × peach F2, a BC2 peach × P. davidiana (using peach as the recurrent parent), and an apricot × apricot F1. We have further saturated these maps mainly with SSR (simple sequence repeat) markers. A new map, constructed uniquely from SSRs was prepared for a fourth apricot × apricot F1 population. Using anchor markers, we compared these four maps with the reference Prunus map, constructed using an almond × peach F2 population. As previously observed, conservation of synteny and co-linearity were the general rule, providing additional evidence of the high level of similarity between all Prunus genomes. Comparisons of genetic distances between the maps suggested that those involving similar genomes had higher levels of recombination than those with more distant genomes, particularly the inter-specific crosses.The ISAFRUIT Project is funded by the European Commission under Thematic Priority 5 – Food Quality and Safety of the 6th Framework Programme of RTD (Contract No. FP6-FOOD-CT-2006-016279).Peer reviewe

High resolution synteny maps allowing direct comparisons between the coffee and tomato genomes

Tomato (Solanum lycopersicum) and coffee (Coffea canephora) belong to the sister families Solanaceae and Rubiaceae, respectively. We report herein the mapping of a common set of 257 Conserved Ortholog Set II genes in the genomes of both species. The mapped markers are well distributed across both genomes allowing the first syntenic comparison between species from these two families. The majority (75%) of the synteny blocks are short (<4 cM); however, some extend up to 50 cM. In an effort to further characterize the synteny between these two genomes, we took advantage of the available sequence for the tomato genome to show that tomato chromosome 7 is syntenic to half of the two coffee linkage groups E and F with the putative break point in tomato localized to the boundary of the heterochromatin and euchromatin on the long arm. In addition to the new insight on genome conservation and evolution between the plant families Solanaceae and Rubiaceae, the comparative maps presented herein provide a translational tool by which coffee researchers may take benefit of DNA sequence and genetic information from tomato and vice versa. It is thus expected that these comparative genome information will help to facilitate and expedite genetic and genomic research in coffee