scholarly journals Development of Sequence-Tagged Site Marker Set for Identification of J, JS, and St Sub-genomes of Thinopyrum intermedium in Wheat Background

2021 ◽  
Vol 12 ◽  
Author(s):  
Linyi Qiao ◽  
Shujuan Liu ◽  
Jianbo Li ◽  
Shijiao Li ◽  
Zhihui Yu ◽  
...  

Thinopyrum intermedium (2n = 6x = 42, JJJSJSStSt) is one of the important resources for the wheat improvement. So far, a few Th. intermedium (Thi)-specific molecular markers have been reported, but the number is far from enough to meet the need of identifying alien fragments in wheat-Th. intermedium hybrids. In this study, 5,877,409 contigs were assembled using the Th. intermedium genotyping-by-sequencing (GBS) data. We obtained 5,452 non-redundant contigs containing mapped Thi-GBS markers with less than 20% similarity to the wheat genome and developed 2,019 sequence-tagged site (STS) molecular markers. Among the markers designed, 745 Thi-specific markers with amplification products in Th. intermedium but not in eight wheat landraces were further selected. The distribution of these markers in different homologous groups of Th. intermedium varied from 47 (7/12/28 on 6J/6St/6JS) to 183 (54/62/67 on 7J/7St/7JS). Furthermore, the effectiveness of these Thi-specific markers was verified using wheat-Th. intermedium partial amphidiploids, addition lines, substitution lines, and translocation lines. Markers developed in this study provide a convenient, rapid, reliable, and economical method for identifying Th. intermedium chromosomes in wheat. In addition, this set of Thi-specific markers can also be used to estimate genetic and physical locations of Th. intermedium chromatin in the introgression lines, thus providing valuable information for follow-up studies such as alien gene mining.

2014 ◽  
Vol 60 (2) ◽  
pp. 44-48
Author(s):  
Annamária Szántó ◽  
Zsuzsanna Pap ◽  
Z Pávai ◽  
I Benedek ◽  
Judit Beáta Köpeczi ◽  
...  

Abstract Background: The elucidation of the genetic background of the myeloproliferative neoplasms completely changed the management of these disorders: the presence of the Philadelphia chromosome and/or the BCR-ABL oncogene is pathognomonic for chronic myeloid leukemia and identification of JAK2 gene mutations are useful in polycytemia vera (PV), essential thrombocytemia (ET) and myelofibrosis (PMF). The aim of this study was to investigate the role of molecular biology tests in the management of myeloproliferative neoplasms. Materials and methods: We tested the blood samples of 117 patients between April 2008 and February 2013 at the Molecular Biology of UMF Târgu Mureș using RQ-PCR (for M-BCR-ABL oncogene) and/or allele-specific PCR (for JAK2V617F mutation). Results: Thirty-two patients presented the M-BCR-ABL oncogene, 16 of them were regularly tested as a follow-up of the administered therapy: the majority of chronic phase patients presented decreasing or stable values, while in case of accelerated phase and blast phase the M-BCR-ABL values increased or remained at the same level. Twenty patients were identified with the JAK2V617F mutation: 8 patients with PV, 4 with ET, 3 with PMF, 4 with unclassifiable chronic myeloproliferative disease and 1 patient with chronic myelomonocytic leukemia. There was no case of concomitant occurance of both molecular markers. Conclusions: Molecular biology testing plays an important role in the management of myeloproliferative neoplasms: identification of the molecular markers confirms the final diagnosis, excluding secondary causes of abnormal blood count parameters. Regular monitoring of MBCR- ABL expression level is useful in the follow-up of therapeutic efficiency.


2008 ◽  
Vol 44 (No. 1) ◽  
pp. 22-29 ◽  
Author(s):  
K. Pánková ◽  
Z. Milec ◽  
M. Leverington-Waite ◽  
S. Chebotar ◽  
J.W. Snape

Several sets of wheat inter-varietal chromosome substitution lines (SLs) have been produced over the last fifty years at the CRI (formerly RICP) in Prague-Ruzyně, based on cytogenetic manipulations using aneuploids. Lines with defined genes have been obtained which significantly influence growth habit and flowering time and these have been used particularly in the study of the genetics and physiology of flowering. The sets of lines include substitutions of homoeologous group 5 chromosomes carrying Vrn genes that control vernalisation response, homoeologous group 2 chromosomes with Ppd genes controlling photoperiodic sensitivity, and some other substitutions, particularly those with chromosome 3B of the Czech alternative variety Česká Přesívka where a novel flowering time effect was located. Although the phenotypic and cytological analysis of substitution lines has been continually carried out during backcrossing generations, only the use of molecular markers can allow an unambiguous characterization to verify that substitutions are correct and complete. This analysis has allowed incorrect substitutions or partial substitutions to be identified and discarded. This paper summarizes the results of recent molecular checks of the substitution line collections at CRI.


2011 ◽  
Vol 55 (11) ◽  
pp. 5408-5411 ◽  
Author(s):  
Nahla B. Gadalla ◽  
Ishag Adam ◽  
Salah-Eldin Elzaki ◽  
Sahar Bashir ◽  
Izdihar Mukhtar ◽  
...  

ABSTRACTMolecular markers for surveillance ofPlasmodium falciparumresistance to current antimalarials are sorely needed. A 28-day efficacy study of artemether-lumefantrine in eastern Sudan identified 5 treatment failures among 100 evaluable patients; 9 further individuals were parasite positive by PCR during follow-up. Polymorphisms inpfatpase6andpfmdr1were evaluated by DNA sequencing. One individual carried parasites with a novelpfmdr1polymorphism (F1044L).pfmdr1gene amplification in parasites prior to treatment occurred in three individuals who had recurrent infection during follow-up.


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 4476-4476
Author(s):  
Mauricette Michallet ◽  
Mohamad Sobh ◽  
Xavier Thomas ◽  
Carole Charlot ◽  
Fiorenza Barraco ◽  
...  

Abstract We performed a retrospective analysis from our transplant registry on first allogeneic hematopoietic stem cell transplantations (HSCT) for acute myeloid leukemia (AML) patients (pts) between 1996 and 2007. Our principal objective was to analyze the impact of molecular markers on the long-term overall and disease-free survival (OS and DFS) after first allogeneic HSCT. We found 364 pts, only 63 pts had retrospectively available conserved cells at diagnosis. The expression levels of WT1, Evi1, Flt3 and Hoxa9 were performed by quantitative RT-RQPCR. The mutational status of MLL duplication, FLT3 (internal tandem duplication or nucleotide substitutions) (ITD), NPM1 and CEBPα were determined by PCR, RFLP and/or sequencing analysis. All pts except 1 had a karyotype analysis at diagnosis. Among these 63 pts, there were 27 (43%) males and 36 (57%) females, with a median age of 41 years (18-64). The FAB classification was M0: 6, M1: 10, M2: 13, M4: 6, M5: 21, M6: 3, M7: 1 and 3 unclassified. Concerning the karyotype analysis, 25 (40%) pts had a normal karyotype, 37 (60%) pts presented cytogenetic abnormalities classified as favourable prognosis in 5 cases (8%), intermediate in 13 cases (21%) and poor in 19 cases (31%). Regarding the molecular markers evaluated in all pts: 4(6%) pts had Flt3over-expressed (ov-ex), 19 (30%) FLT3 ITD+, 3 (5%) MLLdup, 10 (16%) Hoxa9 ov-ex, 7 (11%) Evi1 ov-ex, 15 (24%) NPM1mut+, 25 (40%) WT1 ov-ex and 1 CEBPαmut+ (this marker was evaluated only in 12 pts). Associations between these markers and the karyotype prognosis groups are shown in Figure1. Twenty three (36%) pts had no abnormal molecular markers and 40 (54%) pts had at least one abnormal marker: 10 (16%) 1 marker, 10 (16%) 2 markers, 12 (19%) 3 markers, 4 (6%) 4 markers and 4 (6%) 5 markers. Concerning the karyotype, among the 23 negative molecular pts, 22 have been evaluated and there were 9 (41%) normal, 11 (50%) poor and 2 (9%) favourable; and among the 40 positive pts, 16 (40%) were normal, 8 (20%) poor, 13 (32.5%) intermediate and 3 (7.5%) favourable. Concerning transplantation, 50% of HSCT were done after 2004 and the median interval between diagnosis and transplantation was 6 months (2.6–68.5). Before conditioning, 41 pts were in CR (26 CR1, 14 CR2 and 1 CR3), 8 in PR and 14 in relapse. Twenty five (40%) pts received a non-myelo-ablative conditioning and 38 (60%) a myelo-ablative one. There were 34 sex-mismatched (21 M→F and 13 F→M), 21 ABO incompatibility (6 minor and 15 major), 55 were HLA matched and 8 mismatched. Twenty three (36.5%) pts received PBSC, 37 (59%) bone marrow and 4 (6.5%) cord blood cells from 47 (75%) HLA siblings and 16 (25%) unrelated donors. After transplantation, 59 (94%) pts engrafted, 42 developed AGVHD (21gr1, 13 gr2 and 8 gr4), and among 51 evaluable pts, 13 developed cGVHD (7 limited and 6 extensive). At the last follow-up, 20 pts have relapsed, 29 pts are alive (28 CR and 1PR) and 34 died [18 (53%) from TRM and 16 (47%) from relapse]. At the median follow-up of 48 months, the OS and DFS for the whole population were 40% (33–47) and 40% (34–46) respectively with a maximum follow-up of 130 months and for the different subgroups according to karyotype and molecular markers the results are shown in Table 1. The univariate analysis showed a significant impact of FLT3 ITD and over-expression of FLT3RQ on long-term DFS, (p=0.03 and p=0.02 respectively), and a trend on long-term OS (p=0.08). Concerning the karyotype and some other markers (MLL, EVI1, NPM1 and Hoxa9), we did not observe any significant difference because of small number of pts in some subgroups. The known benefic impact of NPM1mut+, was erased because the majority of this group presented an associated FLT3 ITD+. In addition, we are performing a multivariate analysis that will be presented. In conclusion, allogeneic HSCT in this high risk population of AML pts, allowed a good probability of long-term OS and DFS, despite the presence of high number of bad molecular markers and cytogenetic abnormalities. Finally, AML pts with FLT3 ITD+ seem not benefit from allogeneic HSCT as well as patients with NPM1mut+ associated with FLT3ITD+. Figure 1. Frequencies and distribution of different molecular markers and karyotype subgroups Figure 1. Frequencies and distribution of different molecular markers and karyotype subgroups Table 1. OS and DFS according to different molecular markers and karyotype subgroups


1994 ◽  
Vol 87 (7) ◽  
pp. 789-794 ◽  
Author(s):  
L. E. Talbert ◽  
N. K. Blake ◽  
P. W. Chee ◽  
T. K. Blake ◽  
G. M. Magyar

2004 ◽  
Vol 1 (3) ◽  
pp. 143-148 ◽  
Author(s):  
You Ming-Shan ◽  
Li Bao-Yun ◽  
Tian Zhi-Hui ◽  
Tang Zhao-Hui ◽  
Liu Shou-Bin ◽  
...  

AbstractWheatgrass, Thinopyrum Löve (Elytrigia Nevski), is one of the most important alien resources for wheat improvement. To determine the transferability of wheat microsatellite primers to Thinopyrum spp., 40 wheat microsatellite primer pairs were selected to perform PCR analysis on 17 accessions of Thinopyrum spp. and two common wheat (Triticum aestivum) cultivars. Among the 40 primer pairs used, 25 pairs could produce PCR products on all or most of the alien species. Moreover, all of these 25 primer pairs, except Xgwm325, showed polymorphism in the Thinopyrum accessions. In total, 108 alleles were detected by the 25 primer pairs. The number of alleles per primer pair varied from 1 to 8, with an average of 4.3 alleles per primer. Although primer Xgwm325 did not detect polymorphic alleles in Thinopyrum spp., it could be used as a specific SSR marker for them. It amplified four specific DNA fragments in Thinopyrum spp. of length approximately 1400, 440, 120 and 100 bp. To verify the validity of these molecular markers, a further PCR programme with primer Xgwm325 was conducted on a full set of seven wheat–Thinopyrum elongatum disomic addition lines and 15 disomic substitution lines. This showed that only the 100-bp fragment appeared in all materials possessing the alien chromosome, indicating that it was a molecular marker for the entire genome of Th. elongatum, although primer Xgwm325 was specific for chromosome 6D in wheat.


2009 ◽  
Vol 35 (3) ◽  
pp. 424-431
Author(s):  
Yue ZHANG ◽  
Zhi-Shan LIN ◽  
Bao-Jiu CAO ◽  
Yi-Qiang GUO ◽  
Mei-Jiao WANG ◽  
...  

2015 ◽  
Vol 2015 ◽  
pp. 1-14 ◽  
Author(s):  
Enrique Redondo-Gonzalez ◽  
Leandro Nunes de Castro ◽  
Jesús Moreno-Sierra ◽  
María Luisa Maestro de las Casas ◽  
Vicente Vera-Gonzalez ◽  
...  

Bladder cancer occurs in the epithelial lining of the urinary bladder and is amongst the most common types of cancer in humans, killing thousands of people a year. This paper is based on the hypothesis that the use of clinical and histopathological data together with information about the concentration of various molecular markers in patients is useful for the prediction of outcomes and the design of treatments ofnonmuscle invasive bladder carcinoma(NMIBC). A population of 45 patients with a new diagnosis of NMIBC was selected. Patients withbenign prostatic hyperplasia(BPH),muscle invasive bladder carcinoma(MIBC),carcinoma in situ(CIS), and NMIBC recurrent tumors were not included due to their different clinical behavior. Clinical history was obtained by means of anamnesis and physical examination, and preoperative imaging and urine cytology were carried out for all patients. Then, patients underwent conventionaltransurethral resection(TURBT) and some proteomic analyses quantified the biomarkers (p53, neu, and EGFR). A postoperative follow-up was performed to detect relapse and progression. Clusterings were performed to find groups with clinical, molecular markers, histopathological prognostic factors, and statistics about recurrence, progression, and overall survival of patients with NMIBC. Four groups were found according to tumor sizes, risk of relapse or progression, and biological behavior. Outlier patients were also detected and categorized according to their clinical characters and biological behavior.


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