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A Unique Mutation in a MYB Gene Cosegregates with the Nectarine Phenotype in Peach  [PDF]
Elisa Vendramin, Giorgio Pea, Luca Dondini, Igor Pacheco, Maria Teresa Dettori, Laura Gazza, Simone Scalabrin, Francesco Strozzi, Stefano Tartarini, Daniele Bassi, Ignazio Verde, Laura Rossini
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0090574
Abstract: Nectarines play a key role in peach industry; the fuzzless skin has implications for consumer acceptance. The peach/nectarine (G/g) trait was described as monogenic and previously mapped on chromosome 5. Here, the position of the G locus was delimited within a 1.1 cM interval (635 kb) based on linkage analysis of an F2 progeny from the cross ‘Contender’ (C, peach) x ‘Ambra’ (A, nectarine). Careful inspection of the genes annotated in the corresponding genomic sequence (Peach v1.0), coupled with variant discovery, led to the identification of MYB gene PpeMYB25 as a candidate for trichome formation on fruit skin. Analysis of genomic re-sequencing data from five peach/nectarine accessions pointed to the insertion of a LTR retroelement in exon 3 of the PpeMYB25 gene as the cause of the recessive glabrous phenotype. A functional marker (indelG) developed on the LTR insertion cosegregated with the trait in the CxA F2 progeny and was validated on a broad panel of genotypes, including all known putative donors of the nectarine trait. This marker was shown to efficiently discriminate between peach and nectarine plants, indicating that a unique mutational event gave rise to the nectarine trait and providing a useful diagnostic tool for early seedling selection in peach breeding programs.
Basal temperature and thermal sum in phenological phases of nectarine and peach cultivars
Souza, Adilson Pacheco de;Leonel, Sarita;Silva, Andréa Carvalho da;
Pesquisa Agropecuária Brasileira , 2011, DOI: 10.1590/S0100-204X2011001200002
Abstract: the objective of this work was to evaluate basal temperature, thermal sum at different phenological stages, phenological phase duration, yield and seasonality of one nectarine and 14 peach cultivars, between 2006 and 2009. the considered phenological phases were: pruning-sprouting; sprouting-flowering, from swollen bud to open flower; flowering-fruiting, from petal fall to medium-sized fruit; and ripening. minimum basal temperatures (tb) obtained were: pruning-sprouting, 8°c, irrespective of the cultivars; sprouting-flowering, 10°c, except for 'cascata 968', which required 8°c tb; flowering-fruiting, 12°c, except for 'oro azteca', which required 14°c tb; ripening, 14°c, except for 'sunblaze', 'diamante mejorado' and 'precocinho' with 12°c tb. for most cultivars, the maximum basal temperatures were 30, 34, 34 and 28oc for phases pruning-sprouting, sprouting-flowering, flowering-fruiting and ripening, respectively. 'turmalina', 'marli' and 'tropic beauty' showed average yields of 3,945.0, 3,969.3 and 3,954.0 kg ha-1, respectively, in 2009, while the nectarine 'sunblaze' showed around 3,900 kg ha-1 in 2008 and 2009. the cultivars differed for their total cycle and for the accumulated thermal sums which varied, respectively, from 245 days and 1,881.4 degree-days for 'oro azteca', to144 days and 1,455.7 degree-days for 'precocinho'.
Development of a fingerprinting panel using medically relevant polymorphisms
Deanna S Cross, Lynn C Ivacic, Catherine A McCarty
BMC Medical Genomics , 2009, DOI: 10.1186/1755-8794-2-17
Abstract: A panel of polymorphisms associated with at least one disease state in multiple populations was constructed using a cut-off of 0.20 or greater confirmed minor allele frequency in a European Caucasian population. The fingerprinting assay was tested using the MALDI-TOF mass spectrometry method of allele determination on a Sequenom platform with a panel of 28 Caucasian HapMap samples; the results were compared with known genotypes to ensure accuracy. The frequencies of the alleles were compared to the expected frequencies from dbSNP and any genotype that did not achieve Hardy Weinberg equilibrium was excluded from the final assay.The final assay consisted of the AMG sex marker and 36 medically relevant polymorphisms with representation on each chromosome, encompassing polymorphisms on both the Illumina 550K bead array and the Affymetrix 6.0 chip (with over a million polymorphisms) platform. The validated assay has a P(ID) of 6.132 × 10-15 and a Psib(ID) of 3.077 × 10-8. This assay allows unique identification of our biorepository of 20,000 individuals as well and ensures that as we continue to recruit individuals they can be uniquely fingerprinted. In addition, diseases such as cancer, heart disease diabetes, obesity, and respiratory disease are well represented in the fingerprinting assay.The polymorphisms in this panel are currently represented on a number of common genotyping platforms making QA/QC flexible enough to accommodate a large number of studies. In addition, this panel can serve as a resource for investigators who are interested in the effects of disease in a population, particularly for common diseases.With the advent of genome wide association studies large bio-banks will become the stepping stones to tomorrow's medicine. The genome wide association study (GWAS) has recently proved its value with replicable findings for diseases such as coronary artery disease, prostate cancer, and diabetes [1], and many more discoveries are expected in the near future.
Fitting birth-death processes to panel data with applications to bacterial DNA fingerprinting  [PDF]
Charles R. Doss,Marc A. Suchard,Ian Holmes,Midori Kato-Maeda,Vladimir N. Minin
Quantitative Biology , 2010, DOI: 10.1214/13-AOAS673
Abstract: Continuous-time linear birth-death-immigration (BDI) processes are frequently used in ecology and epidemiology to model stochastic dynamics of the population of interest. In clinical settings, multiple birth-death processes can describe disease trajectories of individual patients, allowing for estimation of the effects of individual covariates on the birth and death rates of the process. Such estimation is usually accomplished by analyzing patient data collected at unevenly spaced time points, referred to as panel data in the biostatistics literature. Fitting linear BDI processes to panel data is a nontrivial optimization problem because birth and death rates can be functions of many parameters related to the covariates of interest. We propose a novel expectation--maximization (EM) algorithm for fitting linear BDI models with covariates to panel data. We derive a closed-form expression for the joint generating function of some of the BDI process statistics and use this generating function to reduce the E-step of the EM algorithm, as well as calculation of the Fisher information, to one-dimensional integration. This analytical technique yields a computationally efficient and robust optimization algorithm that we implemented in an open-source R package. We apply our method to DNA fingerprinting of Mycobacterium tuberculosis, the causative agent of tuberculosis, to study intrapatient time evolution of IS6110 copy number, a genetic marker frequently used during estimation of epidemiological clusters of Mycobacterium tuberculosis infections. Our analysis reveals previously undocumented differences in IS6110 birth-death rates among three major lineages of Mycobacterium tuberculosis, which has important implications for epidemiologists that use IS6110 for DNA fingerprinting of Mycobacterium tuberculosis.
Microsatellite instability analysis in hereditary non-polyposis colon cancer using the Bethesda consensus panel of microsatellite markers in the absence of proband normal tissue
Sergio G Chialina, Claudia Fornes, Carolina Landi, Carlos D de La Vega Elena, Maria V Nicolorich, Ricardo J Dourisboure, Angela Solano, Edita A Solis
BMC Medical Genetics , 2006, DOI: 10.1186/1471-2350-7-5
Abstract: In this study, we report the analysis for genetic counseling of three first-degree relatives (the mother and two sisters) of a male who died of colorectal adenocarcinoma at the age of 23. The family fulfilled strict Amsterdam-I criteria (AC-I) with the presence of extracolonic tumors in the extended pedigree. We overcame the difficulty of having a proband post-mortem non-tumor tissue sample for MSI testing by studying the alleles carried by his progenitors.Tumor MSI testing is described as initial screening in both primary and metastasis tumor tissue blocks, using the reference panel of 5 microsatellite markers standardized by the National Cancer Institute (NCI) for the screening of HNPCC (BAT-25, BAT-26, D2S123, D5S346 and D17S250). Subsequent mutation analysis of the hMLH1 and hMSH2 genes was performed.Three of five microsatellite markers (BAT-25, BAT-26 and D5S346) presented different alleles in the proband's tumor as compared to those inherited from his parents. The tumor was classified as high frequency microsatellite instability (MSI-H). We identified in the HNPCC family a novel germline missense (c.1864C>A) mutation in exon 12 of hMSH2 gene, leading to a proline 622 to threonine (p.Pro622Thr) amino acid substitution.This approach allowed us to establish the tumor MSI status using the NCI recommended panel in the absence of proband's non-tumor tissue and before sequencing the obligate carrier. According to the Human Gene Mutation Database (HGMD) and the International Society for Gastrointestinal Hereditary Tumors (InSiGHT) Database this is the first report of this mutation.Hereditary non-polyposis colorectal cancer (HNPCC) is an inherited syndrome predisposing to the early development of cancers of colon, rectum, endometrium, ovarium, small bowel, stomach and urinary tract [1,2].Since there are no premonitory signs of susceptibility to HNPCC, family history has been the primary method for identifying patients at risk. Defined by the International Collaborative
Nectarine Fruit Ripening and Quality Assessed Using the Index of Absorbance Difference ( )  [PDF]
E. Bonora,D. Stefanelli,G. Costa
International Journal of Agronomy , 2013, DOI: 10.1155/2013/242461
Abstract: Consistency of fruit quality is extremely important in horticulture. Fruit growth and quality in nectarine are affected by fruit position in the canopy, related to the tree shape. The “open shaped” training systems, such as Tatura Trellis, improve fruit growth and quality. The Index of Absorbance Difference ( ) is a new marker that characterizes climacteric fruit during ripening. A study on fruit ripening was performed by using the on nectarine to monitor fruit maturity stages of two cultivars trained as Tatura Trellis in Victoria, Australia. Fruit of cv “Summer Flare 34” (“SF34”) grown in different positions on the tree showed high ripening homogeneity. Fruit harvested at a similar ripening stage showed fruit firmness and soluble solid content homogeneity. Fruits from hand-thinned variety “Summer Flare 26” (“SF26”) were larger in size, had advanced ripening, and showed greater homogeneity. For “SF26”, a weak correlation between and SSC was observed. The experiment showed that the Tatura Trellis training system is characterized by high homogeneity of nectarine fruit when coupled with a proper management of fruit density. It also confirmed that the could be used as new nondestructive maturity index for nectarine fruit quality assessment in the field. 1. Introduction A tree training system is defined as a method of manipulating the tree structure and canopy geometry to improve the interception and distribution of light, for the purpose of optimizing fruit quality and yield [1]. In 1970, a group of Australian researchers developed the Tatura Trellis [2], suitable for the complete mechanization of harvest in intensive peach orchards. Despite of the higher light available and photosynthetic rate that this tree shape allows, it was judged too expensive because of the intensive work needed to maintain the complex scaffold. Keeping the same open canopy design, simplified and cheaper tree shapes were developed during the following decades, such as the “KAC V” [3] and “Y” [1]. Several aspects of the Tatura Trellis training system on apple and cherry trees were studied [4], but only a few experiments on tree productivity were available regarding peach fruit [5]. Numerous studies on different tree architectures pointed out that fruit position in the canopy represents one of the most critical factors for peach fruit quality development and homogeneity of fruit characteristics [6–8] related to the light availability [9]. The open center training systems increase the light available in the inner canopy, giving rise to a gradient of quality traits. Fruit that develops
Implementation of a parentage control system in Portuguese beef-cattle with a panel of microsatellite markers
Carolino, Inês;Sousa, Concei??o O.;Ferreira, Sónia;Carolino, Nuno;Silva, Fátima S.;Gama, Luís T.;
Genetics and Molecular Biology , 2009, DOI: 10.1590/S1415-47572009005000026
Abstract: a study was conducted to assess the feasibility of applying a panel of 10 microsatellite markers in parentage control of beef cattle in portugal. in the first stage, dna samples were collected from 475 randomly selected animals of the charolais, limousin and preta breeds. across breeds and genetic markers, means for average number of alleles, effective number of alleles, expected heterozygosity and polymorphic information content, were 8.20, 4.43, 0.733 and 0.70, respectively. enlightenment from the various markers differed among breeds, but the set of 10 markers resulted in a combined probability above 0.9995 in the ability to exclude a random putative parent. the marker-set thus developed was later used for parentage control in a group of 140 calves from several breeds, where there was the suspicion of possible faulty parentage recording. overall, 76.4% of the calves in this group were compatible with the recorded parents, with most incompatibilities due to misidentification of the dam. efforts must be made to improve the quality of pedigree information, with particular emphasis on information recorded at the calf's birth.
DNA fingerprinting of water yam (Dioscorea alata) cultivars in Brazil based on microsatellite markers
Siqueira, Marcos VBM;Dequigiovanni, Gabriel;Corazon-Guivin, Mike A;Feltran, José C;Veasey, Elizabeth A;
Horticultura Brasileira , 2012, DOI: 10.1590/S0102-05362012000400015
Abstract: this study aimed to fingerprint 36 water yam (dioscorea alata) accessions using microsatellite markers. ten accessions were collected in local markets from several municipalities in brazil, eight were obtained from the 'instituto agron?mico de campinas' (iac) germplasm collection and eighteen were collected directly from growers from s?o paulo state. a total of nine microsatellite loci were used in the analysis. loci revealed high polymorphism verified by elevated pic values (0.57-0.77), and by high gene diversity and shannon-wiener indices (0.69 and 1.29 on average, respectively). the accessions were classified into two groups based on clustering analysis. one group contained mostly accessions from the iac collection, including a commercial cultivar acquired in a market in the city of cuiabá, mato grosso state. the second group was composed of most accessions, including those collected directly from growers and markets in s?o paulo, a few accessions from the iac collection, and an accession from puerto rico, named 'florida', which is the most cultivated in brazil. several duplicates were identified in this study, including accessions obtained from two farmers in mogi gua?u and mogi mirim, s?o paulo state. however, some of these accessions were allocated in different sub-groups, within this second group. results suggested the hypothesis of different origins for accessions currently cultivated in brazil. similar accessions obtained from different municipalities revealed the commercialization of the same accessions at different locations.
Identification of Sweet Cherry Cultivars (Prunus avium L.) and Analysis of Their Genetic Relationship Using Microsatellite DNA Fingerprinting  [cached]
M. Turet-Sayar,A. Turkec,T. Demir
Journal of Agricultural Science , 2012, DOI: 10.5539/jas.v4n8p134
Abstract: Genetic diversity of seven Turkish sweet cherry cultivars and eight commonly grown introduced cultivars were assessed using 23 microsatellite (SSR) markers. Among the markers, nine primers produced poly-morphic patterns resulting in 56 informative alleles. The mean number of alleles per locus was 5.4 while the mean similarity over the nine polymorphic loci averaged 0.463. UPGMA cluster analysis of the data separated cultivars and accessions into two main groups. The results demonstrated that Turkish sweet cherry cultivars have less genetic variation and more closely related to each other. These cultivars contained both Turkish germplasm as well as European and American germplasm in their pedigree. In the present study, same SSR primers were also used to clarify the genetic identity of registered cultivar, 0900Ziraat, which is highly grown in different nurseries all over Turkey but confusingly referred to under different name by local growers due to certain pomological and morphological differences observed among the trees. SSR analysis of seventeen individual tree samples from eight nurseries at different locations, have revealed no genetic variation among samples. The phenotypic variations among the trees were the most probably due to local adaptations to different locations and variations in rootstocks that were used in nurseries rather than the genetic variations among the 0900Ziraat cultivars.
The effects of the parents’ genotype on susceptibility to leaf curl (Taphrina deformans (Berk.) Tul) of vineyard peach hybrid seedlings
Zec Gordan,?oli? Slavica,Jankovi? Zoran,?urovi? Sne?ana
Genetika , 2007, DOI: 10.2298/gensr0701047z
Abstract: Leaf curl is one of the peach diseases with the most economically important impact, because very strong infection can cause total defoliation. Susceptibility to a leaf curl was examined from the period 1994-1998 in a collection of selected vineyard peach genotypes and newly peach and nectarine cultivars. Selected low susceptible genotypes (vineyard peach GR/65/87 and processing peach Villa Ada) were used in cross-pollination with differently susceptible genotypes. The process produced more than 250 seedlings of F1 progeny from few combinations of the parents. Susceptibility of hybrid seedlings to the leaf curl pathogen was investigated several years in the open field, without application of pesticide. More types of inheritance of examined characteristic were determinate in the progenies from different combinations of the parents. The results agree with polygenic inheritance. .
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