Tunneling in Fractional Quantum Hall line junctions

We study the tunneling current between two counterpropagating edge modes described by chiral Luttinger liquids when the tunneling takes place along an extended region. We compute this current perturbatively by using a tunnel Hamiltonian. Our results apply to the case of a pair of different two-dimensional electron gases in the fractional quantum Hall regime separated by a barrier, e. g. electron tunneling. We also discuss the case of strong interactions between the edges, leading to nonuniversal exponents even in the case of integer quantum Hall edges. In addition to the expected nonlinearities due to the Luttinger properties of the edges, there are additional interference patterns due to the finite length of the barrier.Comment: 7 pages, RevTex, 12 figs, submitted to Phys Rev

Attention sports fans! The far-reaching contributions of bud sport mutants to horticulture and plant biology

A bud sport is a lateral shoot, inflorescence or single flower/fruit with a visibly different phenotype from the rest of the plant. The new phenotype is often caused by a stable somatic mutation in a single cell that is passed on to its clonal descendants and eventually populates part or all of a meristem. In many cases, a bud sport can be vegetatively propagated, thereby preserving the novel phenotype without sexual reproduction. Bud sports provide new characteristics while retaining the desirable qualities of the parent plant, which is why many bud sports have been developed into popular cultivars. We present an overview of the history of bud sports, the causes and methods of detecting somaclonal variation, and the types of mutant phenotypes that have arisen spontaneously. We focus on examples where the molecular or cytological changes causing the phenotype have been identified. Analysis of these sports has provided valuable insight into developmental processes, gene function and regulation, and in some cases has revealed new information about layer-specific roles of some genes. Examination of the molecular changes causing a phenotype and in some cases reversion back to the original state has contributed to our understanding of the mechanisms that drive genomic evolution.info:eu-repo/semantics/publishedVersio

Definition of a Core Collection and Construction of a Reference Set for Genome-Wide Association Studies from a Large Prunus persica Germplasm Collection

Genome-wide association studies take advantage of the natural variation present in germplasm repositories for identifying genes underlying agronomic traits, through plant molecular and phenotypic characterization. For tree crops, in vivo maintenance and phenotyping are particularly onerous and the reduction of redundancy and duplicates could help lowering management costs. In the frame of the European project FruitBreedomics, a collection of 1580 Prunus accessions from different institutions in Europe and China has been genotyped with the IPSC 9K SNP Array and phenotyped for different agronomic traits and a GWAS analysis with 4271 SNPs on 7 monogenic traits has been carried out (Micheletti et al. 2015). In the present work, the same set of 4271 SNP markers was used to identify a peach core collection by applying the maximization strategy implemented in the software PowerCore v 1.0 (Kim et al. 2007). Out of a total of 1540 a core of 72 (C72) accessions was identified, representing 4.7% sampling size. C72 contains the accessions with higher diversity representing the total allelic coverage with an efficiency index of 0.83 with respect to random sampling. In the view of setting up a genomic tool for GWAS analyses a reference subset of 150 accessions was also developed taking into account allelic and phenotypic traits representativeness through the maximization strategy, population stratification and controlled redundancy required to have enough statistical power. Preliminary PCA analysis shows population structure to explain less than 30% of variability due to the local varieties. Validation of the reference set will also be presented

Development and Evaluation of a 9K SNP Addition to the Peach Ipsc 9K SNP Array v1

The IPSC 9K peach SNP array released by the international community has been a valuable tool in research and application. Even though majority of SNPs (84%) were polymorphic in the evaluation panels there were many genomic regions with low coverage, including those important for breeding. The existing peach array has been updated with 9K additional SNPs covering previously identified gaps and including recently identified SNPs important for breeding. SNPs (1,808,996) identified by sequencing 49 genomes of additional peach accessions were used as the main source of additional SNPs. Focal point strategy was used to select 8,971 SNPs within 40kb window from the 2,821 focal points distributed across the genome. Additional 129 SNPs were chosen to saturate either regions important for breeding or close the gaps larger than 100kb. The array was validated with 1,770 peach and 26 Prunus accessions (almond, plum, apricot, wild relatives). The add-on contained 7,862 SNPs evenly spread across 8 peach pseudo-molecules with only one SNP positioned on scaffold 13 covering 224.99Mbp of peach genome. The 9K add-on improved the 9K peach array by increasing the total number of usable SNPs by 7,206. The number of SNPs per chromosome increased on average by 50% with only on average 0.18% increase in total physical coverage. Number of gaps larger than 0.3 Mbp was reduced to 2 one on each chromosome 3 and 8. Overall genotyping efficiency in all material was >90% except in almond, 82%. Number of informative markers, assessed by ASSIsT software, were highest in peach 64% and lowest in almond 10%, with 61% of markers being informative in wild Prunus (12) and 35% in apricot (4) and 2 - 33% in Japanese and European plum, respectively. Among 36.2% discarded markers 33% were monomorphic and 30% shifted homozygous in material used. Those markers could be informative in different background raising total number of informative markers. Ann addition of new SNPs to array improved the density and usefulness of the array in Prunus species. The practical applications of new 16K Illumina SNP peach array will be discussed. Specified Source(s) of Funding: USDA-NIFA-SCRI-Ros- BREED (2014-51181-22378

Fine mapping of the peach pollen sterility gene (Ps/ps) and detection of markers for marker-assisted selection

In peach, pollen sterility, expressed as absence of pollen in the anthers, segregates as an undesired trait in breeding programs. Pollen fertility screening in progenies is not a common practice mainly because it does not affect fruit set since cross-pollination is frequent. It is also a time-consuming activity that coincides with the busy pollination season. Segregation for this trait could be avoided by using molecular markers to identify appropriate parents or male sterile plants for early culling in progenies expected to segregate, thus increasing breeding efficiency. In peach, pollen sterility is determined by a recessive allele in homozygosis of the major gene, Ps/ps, located on chromosome 6. In this work, using a conventional mapping approach combined with bulked segregant analysis using resequencing data, we fine mapped Ps to a region of almost 160 kb and developed molecular markers for marker-assisted breeding. These markers were validated in plant materials from three peach breeding programs, including progenies, advanced selections, and cultivars, allowing us to determine that the frequency of the ps allele is high (0.23) and also to infer the genotypes of a large collection of cultivars and advanced breeding lines.info:eu-repo/semantics/acceptedVersio

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

Fine mapping of the peach pollen sterility gene (Ps/ps) and detection of markers for marker-assisted selection

Altres ajuts: CERCA Programme/Generalitat de CatalunyaIn peach, pollen sterility, expressed as absence of pollen in the anthers, segregates as an undesired trait in breeding programs. Pollen fertility screening in progenies is not a common practice mainly because it does not affect fruit set since cross-pollination is frequent. It is also a time-consuming activity that coincides with the busy pollination season. Segregation for this trait could be avoided by using molecular markers to identify appropriate parents or male sterile plants for early culling in progenies expected to segregate, thus increasing breeding efficiency. In peach, pollen sterility is determined by a recessive allele in homozygosis of the major gene, Ps/ps, located on chromosome 6. In this work, using a conventional mapping approach combined with bulked segregant analysis using resequencing data, we fine mapped Ps to a region of almost 160 kb and developed molecular markers for marker-assisted breeding. These markers were validated in plant materials from three peach breeding programs, including progenies, advanced selections and cultivars, allowing us to determine that the frequency of the ps allele is high (0.23) and also to infer the genotypes of a large collection of cultivars and advanced breeding lines

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

An integrated approach for increasing breeding efficiency in apple and peach in Europe

Despite the availability of whole genome sequences of apple and peach, there has been a considerable gap between genomics and breeding. To bridge the gap, the European Union funded the FruitBreedomics project (March 2011 to August 2015) involving 28 research institutes and private companies. Three complementary approaches were pursued: (i) tool and software development, (ii) deciphering genetic control of main horticultural traits taking into account allelic diversity and (iii) developing plant materials, tools and methodologies for breeders. Decisive breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding, development of new, dense SNP arrays in apple and peach, new phenotypic methods for some complex traits, software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis (PBA). This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies (GWAS) on several European genebank collections. FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities. Through FruitBreedomics, significant progresses were made in the field of apple and peach breeding, genetics, genomics and bioinformatics of which advantage will be made by breeders, germplasm curators and scientists. A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the public. This review covers the scientific discoveries made in this major endeavour, and perspective in the apple and peach breeding and genomics in Europe and beyond

Optimum allocation of resources for QTL detection using a nested association mapping strategy in maize

In quantitative trait locus (QTL) mapping studies, it is mandatory that the available financial resources are spent in such a way that the power for detection of QTL is maximized. The objective of this study was to optimize for three different fixed budgets the power of QTL detection 1 − β* in recombinant inbred line (RIL) populations derived from a nested design by varying (1) the genetic complexity of the trait, (2) the costs for developing, genotyping, and phenotyping RILs, (3) the total number of RILs, and (4) the number of environments and replications per environment used for phenotyping. Our computer simulations were based on empirical data of 653 single nucleotide polymorphism markers of 26 diverse maize inbred lines which were selected on the basis of 100 simple sequence repeat markers out of a worldwide sample of 260 maize inbreds to capture the maximum genetic diversity. For the standard scenario of costs, the optimum number of test environments (Eopt) ranged across the examined total budgets from 7 to 19 in the scenarios with 25 QTL. In comparison, the Eopt values observed for the scenarios with 50 and 100 QTL were slightly higher. Our finding of differences in 1 − β* estimates between experiments with optimally and sub-optimally allocated resources illustrated the potential to improve the power for QTL detection without increasing the total resources necessary for a QTL mapping experiment. Furthermore, the results of our study indicated that also in studies using the latest genomics tools to dissect quantitative traits, it is required to evaluate the individuals of the mapping population in a high number of environments with a high number of replications per environment