Clonal Evaluation Research Articles

Analysis of inbreeding depression in five S1 Cassava families of elite varieties at the seedling nursery and clonal evaluation trial stages.

Background Cassava is an outcrossing, highly heterozygous plant that is reported to suffer from inbreeding depression. However, unraveling recessive traits and exploring additive genes would require a limited level of inbreeding for the genetic improvement of cassava. Method The impact of inbreeding depression (ID) on agronomic and biotic tolerance of cassava was evaluated using the S1 progenies of five African cassava varieties (TMS 30572, TME 419, TMS 98/0505, TMS 01/1371, and TMS 98/0002) at the seedling and clonal evaluation stages. Results At both trial stages, the effects of ID were severe on average performance of fresh root yield and fresh foliage yield; moderate on harvest index, dry matter content, vigor, and tolerance to cassava mosaic disease, cassava bacterial blight, and cassava anthracnose diseases; and less severe on plant height. Further examination of S1 families using molecular markers showed varying levels of heterozygosity at several loci across the genome. In addition, the degree of heterozygosity and ID varied by the S1 family. The TMS 01/1371 family showed the lowest degree of heterozygosity and ID on the average performance of different agronomic attributes, indicating that inbreeding may be strategically explored in this family to increase genetic gain and identify useful recessive traits. Lastly, the observed depression from inbreeding was higher in seedling evaluation than in clonal evaluation trials for fresh root yield, fresh foliage yield, harvest index, and dry matter content. Conclusion S1 individuals showing relatively low heterozygosity based on SNP data were selected as parents to advance genetic gain in cassava. Generally, reduced heterozygosity was prominent in traits with severe ID impacts on average phenotypic performance. Our results highlight the relative importance of exploring non-additive genetic effects and transgressive segregations for favorable allele combinations in cassava improvement.

Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR.

Mid-density targeted genotyping-by-sequencing (GBS) combines trait-specific markers with thousands of genomic markers at an attractive price for linkage mapping and genomic selection. A 2.5K targeted GBS assay for potato (Solanum tuberosum L.) was developed using the DArTag technology and later expanded to 4K targets. Genomic markers were selected from the potato Infinium single nucleotide polymorphism (SNP) array to maximize genome coverage and polymorphism rates. The DArTag and SNP array platforms produced equivalent dendrograms in a test set of 298 tetraploid samples, and 83% of the common markers showed good quantitative agreement, with RMSE (root mean squared error) <0.5. DArTag is suited for genomic selection candidates in the clonal evaluation trial, coupled with imputation to a higher density platform for the training population. Using the software polyBreedR, an R package for the manipulation and analysis of polyploid marker data, the RMSE for imputation by linkage analysis was 0.15 in a small half-diallel population (N=85), which was significantly lower than the RMSE of 0.42 with the random forest method. Regarding high-value traits, the DArTag markers for resistance to potato virus Y, golden cyst nematode, and potato wart appeared to track their targets successfully, as did multi-allelic markers for maturity and tuber shape. In summary, the potato DArTag assay is a transformative and publicly available technology for potato breeding and genetics.

Clonal Evaluation and Genetic Divergence Studies in Mulberry Genotypes

Aims: This study aims to evaluate the wood quality and leaf quality traits of selected mulberry clones and assess the genetic divergence among them, providing valuable insights for the development of superior genotypes with enhanced economic value for the sericulture and agroforestry sectors.&#x0D; Study design: Twenty-one genetic resources of mulberry were collected from various regions in India and evaluated through clonal test in a Row Column Design to assess growth attributes and genetic divergence.&#x0D; Place and Duration of Study: The study was conducted in India, and the systematic progeny test and clonal evaluation were carried out in Forest College and Research Institute, Mettupalayam during 2018-2022.&#x0D; Methodology: The selected clones were evaluated for growth attributes such as plant height, diameter at breast height (DBH), volume, number of branches, leaf length, leaf width, petiole length, number of leaves, and leaf area. Genetic divergence was estimated using D2 statistics, and clustering of clones was performed using the 'GENRES' statistical package.&#x0D; Results: The study identified several clones with significantly higher growth attributes, highlighting their potential for selection in breeding and cultivation programs. Variability and heritability studies indicated that volume exhibited the highest heritability, suggesting strong genetic control and potential for improvement.&#x0D; Conclusion: Clones MI-0718, MI-0807, and MI-0845 showed superior growth performance and genetic divergence, indicating their suitability for further breeding and improvement programs. The study provides insights into the genetic variability of mulberry clones and emphasizes selecting superior clones for enhancing wood volume and overall productivity.

New protocol for rapid cassava multiplication in field conditions: a perspective on speed breeding.

Despite the economic and social importance, high-yielding cassava cultivars are only released after extensive research, mainly due to the low multiplication rate. This study aimed to assess the impact of using smaller-sized seed cuttings treated with agrochemicals (8MP) compared to the conventional planting size (16 cm) on genetic parameters, agronomic performance, and the ranking of cassava clones based on yield and growth attributes. The evaluation was carried out in clonal evaluation trial (CET), preliminary yield trial (PYT), and uniform yield trials (UYT). Additionally, a new selection scheme for cassava breeding programs was proposed. A total of 169 clones were evaluated, including 154 improved clones at different stages of selection and 15 local varieties used as checks. Field trials were conducted using both sizes of propagative material (8MP and 16 cm) in each phase of the breeding program. The data were analyzed using mixed models, considering the random effects of genotype and genotype-environment interaction (G×E) to determine variances and heritabilities. Bland-Altman concordance and correlation analysis of selection indices were employed to examine the consistency in the ranking of cassava clones using different seed cutting sizes. The distribution of variance components, heritabilities, means, and range of the 8MP and 16 cm trials in different phases of the cassava breeding program exhibited remarkable similarity, thereby enabling a comparative assessment of similar genetic effects. With a selection intensity of 30%, the concordance in clone ranking was 0.41, 0.57, and 0.85 in CET, PYT, and UYT trials, respectively, when comparing the selection based on 8MP and 16 cm trials. It is worth noting that the ranking of the top 15% remained largely unchanged. Based on the findings, proposed changes in the cassava selection scheme involve increasing the number of trials starting from the CET phase, early incorporation of G×E interaction, elimination of the PYT trial, reduction of the breeding cycle from 5 to 3 years, and a decrease in the time required for variety development from 11 to 9 years. These modifications are expected to lead to cost reduction and enhance the effectiveness of cassava breeding programs.

Abstract 140: Clonal evaluation of ERG/SPINK1 status to determine disease progression using whole mount prostatectomy specimens

Abstract Most primary prostate cancers are multifocal, marked by distinct tumor foci. Multiclonality is not routinely incorporated at clinical evaluation, however, marker status as a pathological parameter holds great potential for improving prognostic accuracy. Here, we evaluated the frequency of multiclonality and whether ERG/SPINK1 status is correlated to aggressive disease in whole-mount specimens. For each of the 89 radical prostatectomy cases, one H&amp;E-stained whole-mount slide and a corresponding dual ERG/SPINK1 IHC stained slide were collected. Aperio AT2 scanner (Leica Biosystems) digitized these slides into whole-slide images (WSIs). All WSIs were reviewed by a pathologist with the aid of an automatic Gleason grading software to identify each tumor focus and determine its Gleason grade group (GG), and the expression levels (% uptake) of ERG and SPINK1, respectively. Grade groups 4 and 5 were treated as one high-grade group (GG4-5). The associations among GG, ERG, and SPINK1 expression levels were analyzed. For each WSI, 1 to 7 (median 2, mean 2.53) tumor foci were identified, and the aforementioned values were determined, resulting in 225 data records. The number of tumor foci, ERG/SPINK1 expression statistics, and their association for each GG are shown in the table. ERG was expressed the most frequently in GG1, and its frequency decreased as the grade increased. Conversely, SPINK1 expression frequency increased with the grade group. The expression of ERG and SPINK1 was inversely correlated regardless of grade group. More detailed results on the exploratory data analysis and the association with BCR will be shared at the time of presentation. ERG or SPINK1 expression do not appear to be associated with Gleason grade groups. More studies are needed to see if these markers may predict recurrence free survival or patient response to therapy. To our knowledge, this is the first study to map molecular subtypes in whole-mount samples utilizing a foci-based approach. Table Grade group Total ERG SPINK1 ERG-SPINK1 positive ratio (%) positive ratio (%) co-positive co-negative mutually exclusive GG1 74 38 51.4 24 32.4 4 16 54 GG2 81 35 43.2 40 49.4 7 13 61 GG3 33 11 33.3 22 66.7 4 4 25 GG4-5 37 10 27.0 13 35.1 1 15 21 Overall 225 94 41.8 99 44.0 16 48 161 Citation Format: Joonyoung Cho, In Hye Suh, HyeYoon Chang, Tae-Yeong Kwak, Sun Woo Kim, Nallasivam Palanisamy. Clonal evaluation of ERG/SPINK1 status to determine disease progression using whole mount prostatectomy specimens [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 140.

Genomic and transcriptomic profiling reveals key molecules in metastatic potentials and organ-tropisms of hepatocellular carcinoma

Metastasis is a landmark event for rapid postsurgical relapse and death of HCC patients. Although distinct genomic and transcriptomic profiling of HCC metastasis had been reported previously, the causal relationships of somatic mutants, mRNA levels and metastatic potentials were difficult to be established in clinic. Therefore, 11 human HCC cell lines and 7 monoclonal derivatives with definite metastatic potentials and tropisms were subjected to whole exome sequencing (WES) and whole transcriptome sequencing (WTS). TP53, MYO5A, ROS1 and ARID2 were the prominent mutants of metastatic drivers in HCC cells. During HCC clonal evaluation, TP53, MYO5A and ROS1 mutations occurred in the early stage, EXT2 and NIN in the late stage. NF1 mutant was unique in lung tropistic cell lines, RNF126 mutant in lymphatic tropistic ones. PER1, LMO2, GAS7, NR4A3 expression levels were positively associated with relapse-free survival (RFS) of HCC patients. The integrative analysis revealed 58 genes exhibited both somatic mutation and dysregulated mRNA levels in high metastatic cells. Altogether, metastatic drivers could accumulate gradually at different stages during HCC progression, some drivers might modulate HCC metastatic potentials and the others regulate metastatic tropisms.

Whole exome sequencing facilitated diagnosis of patients with multiple mucinous neoplasms of the female genital tract.

e17513 Background: The differential diagnosis is challenging in clinical practice, especially among gastric-type AD of the cervix with ovarian metastases, multiple primary mucinous neoplasm in cervix and ovary, and synchronous mucinous metaplasia and neoplasia of the female genital tract (SMMN-FGT). Previous studies have revealed that next-generation sequencing might be a feasible tool in identifying the origin of tumor. Herein, whole exome sequencing (WES) was performed to distinguish patients with metastatic disease. Methods: WES analysis was performed on 28 tumors and 7 normal tissues derived from 8 patients. Each patient had one lesion of the cervix uteri. Most of them had lesions at other anatomical sites, including corpus uteri, ovary, oviduct, vermiform appendix and omentum. Mutations signatures and clonal evaluation inferred from single-nucleotide/copy number variants were explored. Results: Previous studies of multiple types of cancer have identified more than 40 single-base substitution (SBS) signatures. SBS3/6 referring to defective DNA mismatch repair and SBS10 reported in both uterus and colorectal AD were significantly enriched in this study. Next, we found no significant distribution of SBS3/6/10 among tumors at different anatomical sites. These findings indicate that primary cervical/ovarian AD with metastases other than multiple primary cancers was the predominant histology in 8 patients. The association of genomic alterations in POLE/ POLD1/HRR pathway with the distribution of SBS signatures was explored. SBS3 had a trend of significant distribution (p = 0.01) in four patients who had germline alterations in HRR pathway. Furthermore, SBS10 was significantly enriched (p = 0.009) in 2 patients with germline POLE/POLD1 alterations. Clonal evolution analyses revealed that 2 patients were identified as having SMMN-FGT, and other 6 patients had dominant clones in different tumors, which suggested a . Notably, besides the dominant clones and subclones, some tumors also exhibited extra independent clones, which might be the mixed histology of primary and metastatic tumor. In addition, we found the difference of overall survival in patients having gastric-type AD of the cervix with ovarian metastases and cervical AD patients with different FIGO stage disease based on SEER database data. Conclusions: Our study demonstrated that WES might be a feasible tool to distinguish patients having primary cervical AD with multiple metastases from those with multiple primary cancers of the female genital tract, which suggests that WES proved valuable in facilitating the diagnostic workup. A prospective, multi-center, large cohort study is needed to investigate the performance of WES in identifying the origin of tumors in patients with multiple tumors of the FGT.

Agronomic Performance and Carotenoid Content of Kenyan Yellow-Fleshed Cassava Clones

Vitamin A deficiency is common in Kenya; it has been reported among populations that depend on cassava as their main staple. Clonal evaluation of 324 locally developed yellow-fleshed cassava clones was carried out in two sites, Thika and Kiboko located in central and eastern Kenya respectively. Data was collected on agronomic performance, yield quality and reaction to biotic constraints. The clones rated well for the evaluated traits. The overall performance was better in Kiboko than Thika. Cassava Mosaic Disease, Cassava Brown Streak Disease (CBSD) and Cassava Green Mite (CGM) severity was scored on a scale of 1-5. The mean CBSD score was 1.17 in Kiboko and 1.46 in Thika, CMD severity was 1.15 in Kiboko but the disease was not observed at Thika. The CGM damage severity was 1.63 in Kiboko and 1.97 in Thika. The weight of roots per plant was 3.49 and 2.25 kg at Kiboko and Thika respectively. The dry, matter content of the roots was 49.86% at Kiboko and 29.06 at Thika. The cyanogenic potential was assessed using the pictrate test and rated on a scale of 1-9 and Kiboko had a score of 2.79 compared to 4.14 in Thika. A total of 91 samples were analyzed for carotenoid content using the spectrophotometry method. The Kiboko site had a higher mean carotenoid content (1736.96 &amp;micro;g/100 g) compared to Thika (1105.85 &amp;micro;g/100 g). Most of the samples (71%) analyzed had recorded a higher carotenoid content in Kiboko than Thika. The beta-carotene content was higher in Thika (374.16 &amp;micro;g/100 g) than Kiboko (291.30 &amp;micro;g/100 g). Promising clones adaptable to the two sites were identified.

Outlook of Cassava Brown Streak Disease Assessment: Perspectives of the Screening Methods of Breeders and Pathologists.

Cassava production and productivity in Eastern, Central, and Southern Africa are ravaged by cassava brown streak disease (CBSD), causing yield losses of up to 100% when susceptible varieties are grown. Efforts to develop CBSD-resistant clones are underway. However, the methods for screening CBSD resistance currently vary between breeders and pathologists, with the limited empirical data to support their choices. In this study, we used the empirical CBSD foliar and root necrosis data from two breeding populations, termed cycle zero (C0) and cycle one (C1), to assess and compare the effectiveness of the CBSD screening methods of breeders vs. pathologists. On the one hand, the estimates of broad-sense heritability (H2) for the CBSD root necrosis assessment of breeder ranged from 0.15 to 0.87, while for the assessment method of pathologists, H2 varied from 0.00 to 0.71 in C0 clones. On the other hand, the marker-based heritability estimates (h2) for C0 ranged from 0.00 to 0.70 for the assessment method of breeders and from 0.00 to 0.63 for the assessment method of pathologists. For cycle one (C1) population, where both foliar and root necrosis data were analyzed for clones assessed at clonal evaluation trials (CETs) and advanced yield trials (AYTs), H2 varied from 0.10 to 0.59 for the assessment method of breeders, while the H2 values ranged from 0.09 to 0.35 for the CBSD computation method of pathologists. In general, higher correlations were recorded for foliar severity from the assessment method of breeders (r = 0.4, p ≤ 0.01 for CBSD3s and r = 0.37, p ≤ 0.01 for CBSD6s) in C1 clones evaluated at both clonal and advanced breeding stages than from the approach of pathologists. Ranking of top 10 C1 clones by their indexed best linear unbiased predictors (BLUPs) for CBSD foliar and root necrosis showed four overlapping clones between clonal and advanced selection stages for the method of breeders; meanwhile, only a clone featured in both clonal and advanced selection stages from the CBSD assessment method of pathologists. Overall, the CBSD assessment method of breeders was more effective than the assessment method of pathologists, and thus, it justifies its continued use in CBSD resistance breeding.

Study of the Chromosomal Abnormalities and Associated Complex Karyotypes in Hematological Cancer in the Population of West Bengal: A Prospective Observational Study

AbstractIntroduction Chromosomal instability is an important feature of hematological cancer. The pathogenesis is complex and it involves genetic and epigenetic factors. As a genetic factor, chromosomal instability may play a key role in leukemogenesis. Accumulation of genetic alteration is mainly responsible for numerical and structural chromosomal rearrangement or clonal evaluation. But disease progression is often driven by chromosomal translocation, hyper- or hypodiploidy with structural abnormalities, and complex karyotypes.Objective This research aimed to study the different types of chromosomal abnormalities in clinically suspected hematological cancer patients.Materials and Methods Cytogenetic analysis was performed based on phytohemaglutinin stimulated peripheral blood lymphocyte cultures and bone marrow culture, without mitogen, of the respective patients of West Bengal from March 2016 to February 2018. All clinically suspected hematological cancer patients referred for karyotyping to the institutional genetics department have been included without any biasness of sex and age. Karyotypes were described according to the International System for Cytogenetic Nomenclature (ISCN 2005).Results In the present study, 56 clinically suspected hematological cancer cases were observed and 41 cases of chromosomal rearrangement were found which clearly show chromosomal instability as the main driving force for hematological cancer transformation. Presence of variant Philadelphia chromosomes with classical translocation, mosaic complex karyotypes, variable numerical, and structural chromosomal abnormality, along with severe-to-moderate hypo- and hyperdiploidy, and presence of marker chromosomes were the main findings of this study.Conclusion The result shows that the detection of chromosomal instability was important for preliminary diagnosis, treatment, prognosis, and further management. So the present study provided additional information about chromosomal instability in hematological cancer at Kolkata and adjoining regions.

In vitro clonal propagation and evaluation of antibacterial activity of Benghal dayflower-Commelina benghalensis L.

An efficient protocol for in vitro propagation of Commelina benghalensis was developed. Nodal segments were showed the superb explants in performance for shoot proliferation than other explants. On the other hand, BAP with auxin was better combination. The maximum (90.52) number of explants response and the highest (23.25) number of shoots per plant were obtained from nodal segments on MS medium fortified with 3.0 mg/l BAP+0.1 mg/l IBA. The highest shoot length (17.25 cm) was achieved on MS medium containing 3.0mg/l BAP+0.5mg/l IBA. In vitro proliferated shoots were transferred to full and half strength of MS media where 1.5 mg/l IBA on full strength of MS media was the best to fit for the maximum number (12.69) of roots formation per micro-shoot. Well rooted plantlets were transferred to soil and successfully acclimatized with 97% survival rate. Three extracts i.e. methanol, ethanol, Petroleum ether of C. benghalensis L and four concentrations of each extracts were used against five gram (+ve) and five gram (-ve) bacterial species for the screening of antibacterial activity. Ethanol extracts was the superior in performance. The susceptibility of tested pathogenic bacterial species was increasing compare with increasing of extracts concentration with few exceptions. The highest zone of inhibition was obtained against S. aureus (17.50 mm) and P. aeruginosa (17.44 mm) at 800 mg/l dose level of extracts. It was also noticed that Gram (+ve) bacterial species are more susceptible to Benghal dayflower crude extracts than Gram (-ve) bacterial species.

Genetic analysis and QTL mapping for multiple biotic stress resistance in cassava.

In Sub-Saharan Africa cassava (Manihot esculenta Crantz) is one of the most important food crops where more than 40% of the population relies on it as their staple carbohydrate source. Biotic constraints such as viral diseases, mainly Cassava Mosaic Disease (CMD) and Cassava Brown Streak Disease (CBSD), and arthropod pests, particularly Cassava Green Mite (CGM), are major constraints to the realization of cassava’s full production potential in Africa. To address these problems, we aimed to map the quantitative trait loci (QTL) associated with resistance to CBSD foliar and root necrosis symptoms, foliar CMD and CGM symptoms in a full-sib mapping population derived from the genotypes AR40-6 and Albert. A high-density linkage map was constructed with 2,125 SNP markers using a genotyping-by-sequencing approach. For phenotyping, clonal evaluation trials were conducted with 120 F1 individuals for two consecutive field seasons using an alpha-lattice design at Chambezi and Naliendele, Tanzania. Previously identified QTL for resistance to CBSD foliar symptoms were corroborated, and a new putative QTL for CBSD root necrosis identified (qCBSDRNc14AR) from AR40-6. Two QTL were identified within the region of the previously recognized CMD2 locus from this population in which both parents are thought to possess the CMD2 locus. Interestingly, a minor but consistent QTL, qCGM18AR, for CGM resistance at 3 months after planting stage was also detected and co-localized with a previously identified SSR marker, NS346, linked with CGM resistance. Markers underlying these QTL may be used to increase efficiencies in cassava breeding programs.

Combining Ability Analysis of Dry Matter Content, Reducing Sugars and Yield of Potato (Solanum tuberosum L.) Genotypes in Uganda

Potato (Solanum tuberosum L.) in Uganda is a major food and cash crop mainly grown in the highland regions by small-scale farmers. The increasing importance of potato as a processed product requires new varieties possessing quality processing attributes with acceptable yield. The objectives of this study were to estimate the combining ability effects for dry matter content, reducing sugars, and yield related traits in potato. Nineteen F1 families generated from eight parents using a half diallel mating design were evaluated for dry matter content, reducing sugars, average weight per tuber and total tuber yield at Kachwekano research station. Additive genetic effects were predominant for dry matter content while non-additive effects for the other traits. The GCA/SCA ratios were 0.58, 0.28, 0.17 and 0.44 for dry matter content, reducing sugars, average weight per tuber and total tuber yield respectively. Broad sense heritability estimates were 50.6% for dry matter content, 77.8% for reducing sugars, 90.3% for average weight per tuber and 29.5% for total tuber yield. Parents NAROPOT 3 and 395096.2 had desirable GCA effects for both dry matter content and reducing sugars. Families of nkrk19.17 x Rutuku had desirable SCA effects for dry matter content while Rutuku x 393077.54 and nkrk19.17 x 392657.8 had desirable SCA effects for reducing sugars. Additive genetic effects for dry matter content imply that, genetic gains can be achieved through different selection methods and trait transferred to the respective progenies. The selected parents and families will be subjected to further clonal evaluation and selection.

Clonal evaluation of prostate cancer molecular heterogeneity in biopsy samples by dual immunohistochemistry and dual RNA in situ hybridization.

Prostate cancer is frequently multifocal. Although there may be morphological variation, the genetic underpinnings of each tumor are not clearly understood. To assess the inter and intra tumor molecular heterogeneity in prostate biopsy samples, we developed a combined immunohistochemistry and RNA in situ hybridization method for the simultaneous evaluation of ERG, SPINK1, ETV1, and ETV4. Screening of 601 biopsy cores from 120 consecutive patients revealed multiple alterations in a mutually exclusive manner in 37% of patients, suggesting multifocal tumors with considerable genetic differences. Furthermore, the incidence of molecular heterogeneity was higher in African Americans patients compared with Caucasian American patients. About 47% of the biopsy cores with discontinuous tumor foci showed clonal differences with distinct molecular aberrations. ERG positivity occurred in low-grade cancer, whereas ETV4 expression was observed mostly in high-grade cancer. Further studies revealed correlation between the incidence of molecular markers and clinical and pathologic findings, suggesting potential implications for diagnostic pathology practice, such as defining dominant tumor nodules and discriminating juxtaposed but molecularly different tumors of different grade patterns.

Clonal evaluation of early onset prostate cancer by expression profiling of ERG, SPINK1, ETV1, and ETV4 on whole-mount radical prostatectomy tissue.

Expression profiles of erythroblast transformation-specific (ETS)-related gene fusions and serine protease inhibitor Kazal-type 1 (SPINK1) in early onset prostate cancer have not been thoroughly explored. We retrieved 151 radical prostatectomy specimens from young men with prostate cancer (<55 years) and characterized the expression of ETS-related gene (ERG), SPINK1, ETS Variant 1 (ETV1), and ETV4 by dual immunohistochemistry and dual RNA in situ hybridization. Age, race, family history, preoperative prostate-specific antigen, biochemical recurrence, and pathological variables using whole-mount radical prostatectomy tissue were collected. A total of 313 tumor nodules from 151 men including 68 (45%) Caucasians and 61 (40%) African Americans were included in the analysis. Positive family history of prostate cancer was seen in 65 (43%) patients. Preoperative prostate-specific antigen ranged from 0.3 to 52.7 ng/mL (mean = 7.04). The follow-up period ranged from 1 to 123.7 months (mean = 30.3). Biochemical recurrence was encountered in 8 of 151 (5%). ERG overexpression was observed in 85 of 151 (56%) cases, followed by SPINK1 in 61 of 151 (40%), ETV1 in 9 of 149 (6%), and ETV4 in 4 of 141 (3%). There were 25 of 151 (17%) cases showing both ERG and SPINK1 overexpression within different regions of either the same tumor focus or different foci. Higher frequency of ERG overexpression was seen in younger patients (≤45 years old; 76% vs 49%, P = .002), Caucasian men (71% vs 41% P = .0007), organ-confined tumors (64% vs 33%, P = .0008), and tumors of Gleason Grade groups 1 and 2 (62% vs 26%, P = .009). SPINK1 overexpression was more in African American men (68% vs 26%, P = .00008), in tumors with high tumor volume (>20%) and with anterior located tumors. ETV1 and ETV4 demonstrated rare overexpression in these tumors, particularly in the higher-grade tumors. This study expands the knowledge of the clonal evolution of multifocal cancer in young patients and support differences in relation to racial background and genetics of prostate cancer.

Genomic selection for productive traits in biparental cassava breeding populations.

Cassava improvement using traditional breeding strategies is slow due to the species’ long breeding cycle. However, the use of genomic selection can lead to a shorter breeding cycle. This study aimed to estimate genetic parameters for productive traits based on pedigree (pedigree and phenotypic information) and genomic (markers and phenotypic information) analyses using biparental crosses at different stages of selection. A total of 290 clones were genotyped and phenotyped for fresh root yield (FRY), dry matter content (DMC), dry yield (DY), fresh shoot yield (FSY) and harvest index (HI). The clones were evaluated in clonal evaluation trials (CET), preliminary yield trials (PYT), advanced yield trials (AYT) and uniform yield trials (UYT), from 2013 to 2018 in ten locations. The breeding stages were analyzed as follows: one stage (CET), two stages (CET and PYT), three stages (CET, PYT and AYT) and four stages (CET, PYT, AYT and UYT). The genomic predictions were analyzed via k-fold cross-validation based on the genomic best linear unbiased prediction (GBLUP) considering a model with genetic additive effects and genotype × location interactions. Genomic and pedigree accuracies were moderate to high (0.56–0.72 and 0.62–0.78, respectively) for important starch-related traits such as DY and FRY; when considering one breeding stage (CET) with the aim of early selection, the genomic accuracies ranged from 0.60 (DMC) to 0.71 (HI). Moreover, the correlations between the genomic estimation breeding values of one-stage genomic analysis and the estimated breeding values of the four-stage (full data set) pedigree analysis were high for all traits as well as for a selection index including all traits. The results indicate great possibilities for genomic selection in cassava, especially for selection early in the breeding cycle (saving time and effort).

Induction, Bridging, or Straight Ahead: The Ongoing Dilemma of Allografting in Advanced Myelodysplastic Syndrome

Induction, Bridging, or Straight Ahead: The Ongoing Dilemma of Allografting in Advanced Myelodysplastic Syndrome

Clinical Insignficance of Monoclonal T-Cell Populations and Duodenal Intraepithelial T-Cell Phenotypes in Celiac and Nonceliac Patients.

Refractory celiac disease (RCD) is a rare condition, usually managed at specialized centers. However, gastroenterologists and pathologists in general practices are often the first to consider a diagnosis of RCD in celiac patients with persistent symptoms. The distinction between type I and type II RCD is crucial as patients with RCD II have a shortened life expectancy. The diagnosis of RCD II requires the demonstration of abnormal intraepithelial lymphocytes and/or monoclonal T-cell populations in duodenal biopsies, typically assessed in formalin-fixed paraffin-embedded tissue. We investigated the clinical significance of T-cell receptor gene rearrangements and CD3/CD8 staining in formalin-fixed paraffin-embedded biopsies from 32 patients with RCD I (4), RCD II (3), newly diagnosed celiac disease (CD) (10), established CD patients with follow-up biopsies (10), and Helicobacter pylori-associated lymphocytosis (5). Clonal T-cell populations were present in all lymphocytosis groups but not in normal controls. No difference in the frequency of clonal populations or persistence of identical clones was found between RCD I and II patients. The degree of villous blunting did not correlate with clonal status in any group. No difference in the number of CD3/CD8-positive intraepithelial lymphocytes per 100 enterocytes was found between groups. We suggest that clonal evaluation of T cells should not be employed routinely in the evaluation of CD patients with persistent symptoms until common causes of "apparent refractoriness" have been excluded. In addition, lymphocyte phenotyping and T-cell clonal analysis appear to be insufficient as stand-alone tests to reliably distinguish RCD I and II.

Clonal evaluation and recurrent flowering of ornamental pineapple hybrid for use as miniature potted plant

The objective of this study was to evaluate the cloning and recurrent flowering of the miniature pineapple hybrid ORN-MUT based on quantitative and qualitative morphological descriptors, for possible use as a potted plant. Besides its reduced size, the ORN-MUT hybrid is notable for its pink fruit, absence of thorns and recurrent flowering at the crown, formed after the plant’s complete cycle (562 days). The hybrid was assessed in the experimental field of the Embrapa Cassava and Fruits research unit in two flowering stages (first flowering and recurrent flowering) and was characterized by quantitative and qualitative morphological descriptors. A joint analysis of the data (multivariate analysis) was performed to verify the distinguishability and uniformity of the clones and parents. ORN-MUT presented uniformity in the first flowering, completing the phenological cycle at 75.70 ± 8.01 days (first repetition) and 72.35 ± 6.17 days (second repetition) after floral induction, respectively. The recurrent flowering occurred 170.60 ± 1.85 days after induction. The peduncle is straight, with average length of 19.30 ± 3.83 cm. The syncarp is small and pink, with conical-cylindrical shape. The crown has a moderately sharp tip with greenish central color and pink edges. In the recurrent flowering stage, the plants are smaller, with average size of 24.45 ± 2.52 cm. The syncarp is miniaturized, with average of 1.20 ± 1.15 layers of fruitlets and length of 1.61 ± 0.20 cm. The quantitative and qualitative morphological traits allow classifying the hybrid as a potential potted plant.

Molecular marker assisted selection for increasing inbreeding in S1 populations of cassava.

The objective of the present work was to use MAS in self-pollinated cassava populations for obtaining individuals with high inbreeding (f) aimed at rapid development of partial inbred lines. Three progenies (F0222, F1378 and F1662) were self-pollinated, generating a total of 233 S1 individuals. The progenies and the S1 individuals were evaluated in the seedlings and clonal evaluation trials (CETs). In the CET, plants were evaluated for the following traits: plant height (PH), root dry matter content (DMC), above ground yield (AGY), root (RY) and starch yield (SY). Twenty-seven microsatellites and five minisatellites were used to determine the level of inbreeding of the S1 individuals. Inbreeding (f) values varied from 0.15 to 0.89 within progenies, whereas most of the S1 individuals presented f values above 0.50. In average, 25% of the S1 individuals were selected, which resulted in a 38% inbreeding increase in the cassava progenies. In contrast, phenotypic selection showed no differences in inbreeding increase. Furthermore, there was no correlation between the level of inbreeding and agronomic traits. MAS was efficient for the identification and selection of cassava S1 individuals, with higher inbreeding values contributing to the decrease in the breeding cycles necessary to obtain new cassava inbred lines.