Quantitative Trait Loci and Candidate Genes That Control Seed Sugars Contents in the Soybean 'Forrest' by 'Williams 82' Recombinant Inbred Line Population

Soybean seed sugars are among the most abundant beneficial compounds for human and animal consumption in soybean seeds. Higher seed sugars such as sucrose are desirable as they contribute to taste and flavor in soy-based food. Therefore, the objectives of this study were to use the 'Forrest' by 'Williams 82' (F × W82) recombinant inbred line (RIL) soybean population (n = 309) to identify quantitative trait loci (QTLs) and candidate genes that control seed sugar (sucrose, stachyose, and raffinose) contents in two environments (North Carolina and Illinois) over two years (2018 and 2020). A total of 26 QTLs that control seed sugar contents were identified and mapped on 16 soybean chromosomes (chrs.). Interestingly, five QTL regions were identified in both locations, Illinois and North Carolina, in this study on chrs. 2, 5, 13, 17, and 20. Amongst 57 candidate genes identified in this study, 16 were located within 10 Megabase (MB) of the identified QTLs. Amongst them, a cluster of four genes involved in the sugars' pathway was collocated within 6 MB of two QTLs that were detected in this study on chr. 17. Further functional validation of the identified genes could be beneficial in breeding programs to produce soybean lines with high beneficial sucrose and low raffinose family oligosaccharides.

Chemoradiotherapy versus radiotherapy in patients with advanced nasopharyngeal cancer: phase III randomized Intergroup study 0099

PURPOSE

The Southwest Oncology Group (SWOG) coordinated an Intergroup study with the participation of Radiation Therapy Oncology Group (RTOG), and Eastern Cooperative Oncology Group (ECOG). This randomized phase III trial compared chemoradiotherapy versus radiotherapy alone in patients with nasopharyngeal cancers.

MATERIALS AND METHODS

Radiotherapy was administered in both arms: 1.8- to 2.0-Gy/d fractions Monday to Friday for 35 to 39 fractions for a total dose of 70 Gy. The investigational arm received chemotherapy with cisplatin 100 mg/m2 on days 1, 22, and 43 during radiotherapy; postradiotherapy, chemotherapy with cisplatin 80 mg/m2 on day 1 and fluorouracil 1,000 mg/m2/d on days 1 to 4 was administered every 4 weeks for three courses. Patients were stratified by tumor stage, nodal stage, performance status, and histology.

RESULTS

Of 193 patients registered, 147 (69 radiotherapy and 78 chemoradiotherapy) were eligible for primary analysis for survival and toxicity. The median progression-free survival (PFS) time was 15 months for eligible patients on the radiotherapy arm and was not reached for the chemo-radiotherapy group. The 3-year PFS rate was 24% versus 69%, respectively (P < .001). The median survival time was 34 months for the radiotherapy group and not reached for the chemo-radiotherapy group, and the 3-year survival rate was 47% versus 78%, respectively (P = .005). One hundred eighty-five patients were included in a secondary analysis for survival. The 3-year survival rate for patients randomized to radiotherapy was 46%, and for the chemoradiotherapy group was 76% (P < .001).

CONCLUSION

We conclude that chemoradiotherapy is superior to radiotherapy alone for patients with advanced nasopharyngeal cancers with respect to PFS and overall survival.

Genome-wide association analysis identified consistent QTL for seed yield in a soybean diversity panel tested across multiple environments

Improving seed yield is one of the main targets of soybean [Glycine max (L.) Merr.] breeding. Identification of loci that influence productivity and understanding their genetic mechanism will help marker-assisted trait introgression. The present study evaluated a diverse panel of 541 soybean genotypes consisting of three maturity groups (MGs III-V) in four environments in Kansas, U.S. Data on seed yield, seed weight, shattering resistance, days to maturity, and plant height showed significant genotype, environmental, and genotype × environment interaction variations. Seed yield and shattering had moderate broad-sense heritability (<85%), while the rest of the traits showed high broad-sense heritability (>90%). The SoySNP50K iSelect BeadChip dataset was used to identify significantly associated loci via genome-wide association studies (GWAS). A total of 19 single-nucleotide polymorphisms (SNPs) were significantly associated with seed yield. Particularly, two stable seed yield quantitative trait loci (QTL) on chromosomes 9 and 17 were consistently detected in at least three out of four environments. Candidate gene analysis surrounding seed yield QTL on chromosome 9 showed that Glyma.09G048900, an oxygen binding protein, was the closest to the QTL peak. Similarly, Glyma.17G090200 and Glyma.17G090400 were within 20-kb region of the seed yield QTL on chromosome 17. The candidate genes warrant further analysis to determine their functional mechanisms and develop markers for seed yield improvement.

Clinical applications of high dose rate endorectal brachytherapy for patients with rectal cancer

With the establishment of total mesorectal excision for the treatment of rectal cancer, local recurrence rates have significantly decreased. The addition of preoperative external beam irradiation further reduces this risk to less than 6%. As the local treatment becomes successful and more widely used, the associated treatment-related toxicity is becoming clinically important. If 4 to 6% of the patients are to benefit from neo-adjuvant therapy before total mesorectal excision, the acute and the long-term toxicity burden must be reasonable. With the introduction of better-quality imaging for tumour visualization and treatment planning, a new-targeted radiation treatment was introduced with high dose rate endorectal brachytherapy. The treatment concept was tested in phase I and II studies first in the preoperative setting, then as a boost after external beam radiation therapy as a dose escalation study to achieve higher tumour local control in a radical treatment setting with no surgery. High dose rate endorectal brachytherapy is safe and effective in achieving high tumour regression rate and was well tolerated. It is presently explored in a phase III dose escalation study in the non-operative management of patients with operable rectal cancer.

Exploring Machine Learning Algorithms to Unveil Genomic Regions Associated With Resistance to Southern Root-Knot Nematode in Soybeans

Southern root-knot nematode [SRKN, Meloidogyne incognita (Kofold & White) Chitwood] is a plant-parasitic nematode challenging to control due to its short life cycle, a wide range of hosts, and limited management options, of which genetic resistance is the main option to efficiently control the damage caused by SRKN. To date, a major quantitative trait locus (QTL) mapped on chromosome (Chr.) 10 plays an essential role in resistance to SRKN in soybean varieties. The confidence of discovered trait-loci associations by traditional methods is often limited by the assumptions of individual single nucleotide polymorphisms (SNPs) always acting independently as well as the phenotype following a Gaussian distribution. Therefore, the objective of this study was to conduct machine learning (ML)-based genome-wide association studies (GWAS) utilizing Random Forest (RF) and Support Vector Machine (SVM) algorithms to unveil novel regions of the soybean genome associated with resistance to SRKN. A total of 717 breeding lines derived from 330 unique bi-parental populations were genotyped with the Illumina Infinium BARCSoySNP6K BeadChip and phenotyped for SRKN resistance in a greenhouse. A GWAS pipeline involving a supervised feature dimension reduction based on Variable Importance in Projection (VIP) and SNP detection based on classification accuracy was proposed. Minor effect SNPs were detected by the proposed ML-GWAS methodology but not identified using Bayesian-information and linkage-disequilibrium Iteratively Nested Keyway (BLINK), Fixed and Random Model Circulating Probability Unification (FarmCPU), and Enriched Compressed Mixed Linear Model (ECMLM) models. Besides the genomic region on Chr. 10 that can explain most of SRKN resistance variance, additional minor effects SNPs were also identified on Chrs. 10 and 11. The findings in this study demonstrated that overfitting in GWAS may lead to lower prediction accuracy, and the detection of significant SNPs based on classification accuracy limited false-positive associations. The expansion of the basis of the genetic resistance to SRKN can potentially reduce the selection pressure over the major QTL on Chr. 10 and achieve higher levels of resistance.

A141 IS SURGERY STILL THE ONLY TREATMENT OPTION FOR CURABLE RECTAL CANCER?

Background

Rectal cancer is curable by standard surgery with Total Mesorectal Excision (TME). However, there are well known associated long-term bowel and sexual dysfunctions. Non-operative management (NOM) is an emerging treatment for patients with operable rectal cancer. There is evidence supporting dose response for tumor control in rectal adenocarcinoma.

Aims

In the era of modern technologies, Image-guided adaptive endorectal brachytherapy is a means to deliver local radiotherapy boost treatments. We explored its role in a randomized phase II/III trial (NCT03051464) for patients aiming to achieve cure without surgery. Total Mesorectal Excision (TME) free survival at 2 years was the primary endpoint. We now present the interim analysis upon accrual of the first 40 patients.

Methods

In randomized trial, patients with operable cT2-3ab N0 M0 rectal cancer received 45 Gy in 25 fractions of pelvic external beam radiotherapy (EBRT) with concurrent 5-FU/ Capecitabine. They were randomized to receive either an EBRT boost of 9 Gy in 5 fractions (Arm A), or three weekly adaptive brachytherapy boosts for a total of 30 Gy in 3 fractions (Arm B).

Results

Forty patients were included (20 per arm). The median age was 66 years; baseline characteristics were well balanced in terms of age, tumor location, T stage and tumor size (Table 1). The acute treatment related toxicities are similar as shown in table 2 but in arm B, there were two deaths: one patient died during his chemotherapy and external beam treatment from congestive heart failure and one patient from a heart attack after treatment prior to salvage TME surgery. The proportion of complete clinical response was 50% (n=10/20) in Arm A and 90% in Arm B (n=18/20). With a median follow-up of 2.2 years, local regrowth at 2 years occurred in 4/10 patients (40%) in Arm A and 4/18 patients (22%) in Arm B. TME-free survival rate at 2 years was 45.9% in Arm A and 85.1% in Arm B (p=0.0036) (Figure 1).

Conclusions

The interim analysis of this trial suggests that these two strategies of radiation dose escalation are feasible and lead to high chances of organ preservation in patients with operable rectal cancer. The Independent Monitoring Comittee (IDMC) approved the continuation of patient recruitment in the phase III study as planned.

Funding Agencies

Elekta

A121 QUANTIFYING INTER-OBSERVER VARIABILITY IN THE SEGMENTATION OF RECTAL TUMORS IN ENDOSCOPY IMAGES AND ITS EFFECTS ON DEEP LEARNING

Background

Tumor delineation in endoscopy images is a crucial part of clinical diagnoses and treatment planning for rectal cancer patients. However, it is challenging to detect and adequately determine the size of tumors in these images, especially for inexperienced clinicians. This motivates the need for a standardized, automated segmentation method. While deep learning has proven to be a powerful tool for medical image segmentation, it requires a large quantity of high-quality annotated training data. Since the annotation of endoscopy images is prone to high inter-observer variability, creating a robust unbiased deep learning model for this task is challenging.

Aims

To quantify the inter-observer variability in the manual segmentation of tumors in endoscopy images of rectal cancer patients and investigate an automated approach using deep learning.

Methods

Three gastrointestinal physicians and radiation oncologists (G1, G2, and G3) segmented 2833 endoscopy images into tumor and non-tumor regions. The whole image classifications and the pixelwise classifications into tumor and non-tumor were compared to quantify the inter-observer variability. Each manual annotator is from a different institution.

Three different deep learning architectures (FCN32, U-Net, and SegNet) were trained on the binary contours created by G2. This naive approach investigates the effectiveness of neglecting any information about the uncertainty associated with the task of tumor delineation.

Finally, segmentations from G2 and the deep learning models’ predictions were compared against ground truth labels from G1 and G3, and accuracy, sensitivity, specificity, precision, and F1 scores were computed for images where both segmentations contained tumors.

Results

The deep-learning segmentation took less than 1 second, while manual segmentation took approximately 10 seconds per image. There was significant inter-observer variability for the whole-image classifications made by the manual annotators (Figure 1A). The segmentation scores achieved by the deep learning models (SegNet F1:0.80±0.08) were comparable to the inter-observer variability for the pixel-wise image classification (Figure 1B).

Conclusions

The large inter-observer variability observed in this study indicates a need for an automated segmentation tool for tumors in endoscopy images of rectal cancer patients. While deep learning models trained on a single observer’s labels can segment tumors with an accuracy similar to the inter-observer variability, these models do not accurately reflect the intrinsic uncertainty associated with tumor delineation. In our ongoing studies, we investigate training a model with all observers’ contours to reflect the uncertainty associated with the tumor segmentations.

Funding Agencies

CIHRNSERC

The Soybean High Density 'Forrest' by 'Williams 82' SNP-Based Genetic Linkage Map Identifies QTL and Candidate Genes for Seed Isoflavone Content

Isoflavones are secondary metabolites that are abundant in soybean and other legume seeds providing health and nutrition benefits for both humans and animals. The objectives of this study were to construct a single nucleotide polymorphism (SNP)-based genetic linkage map using the ‘Forrest’ by ‘Williams 82’ (F×W82) recombinant inbred line (RIL) population (n = 306); map quantitative trait loci (QTL) for seed daidzein, genistein, glycitein, and total isoflavone contents in two environments over two years (NC-2018 and IL-2020); identify candidate genes for seed isoflavone. The FXW82 SNP-based map was composed of 2075 SNPs and covered 4029.9 cM. A total of 27 QTL that control various seed isoflavone traits have been identified and mapped on chromosomes (Chrs.) 2, 4, 5, 6, 10, 12, 15, 19, and 20 in both NC-2018 (13 QTL) and IL-2020 (14 QTL). The six QTL regions on Chrs. 2, 4, 5, 12, 15, and 19 are novel regions while the other 21 QTL have been identified by other studies using different biparental mapping populations or genome-wide association studies (GWAS). A total of 130 candidate genes involved in isoflavone biosynthetic pathways have been identified on all 20 Chrs. And among them 16 have been identified and located within or close to the QTL identified in this study. Moreover, transcripts from four genes (Glyma.10G058200, Glyma.06G143000, Glyma.06G137100, and Glyma.06G137300) were highly abundant in Forrest and Williams 82 seeds. The identified QTL and four candidate genes will be useful in breeding programs to develop soybean cultivars with high beneficial isoflavone contents.

A comparison of structural features and vulnerability between government and nongovernment alcohol and other drug (AOD) treatment providers

OBJECTIVE

Both public (government-run), and not-for-profit (nongovernment) service providers provide alcohol and other drug (AOD) treatment services. Research has rarely studied the structural features of these providers, such as workforce characteristics, procurement arrangements, and funding security. The study reported here sought to document and analyze the differences between these two AOD treatment provider types in Australia.

METHODS

The study administered an online survey instrument targeted at managers of AOD treatment sites. The survey comprised three sections: (1) the service (e.g., treatment types); (2) workforce (e.g., total number of staff); and (3) funding and procurement arrangements (e.g., contract length). The study completed a total of 207 site surveys. The studied compared government and nongovernment services on structural features that may create a more or less sustainable or vulnerable service (funding arrangements, payment mechanisms, and contract length).

RESULTS

Government providers were more likely to provide medically oriented treatment types such as withdrawal management and pharmacotherapy, whereas nongovernment organization (NGO) providers were more likely to offer rehabilitation. Consistent with this, government services were more likely to employ medical professionals and nurses, indicative of a more medically oriented workforce, while NGO services were more likely to employ AOD workers, youth workers, peer workers, and counselors. Our data illustrate that NGO services were more likely to be subject to competitive tendering and to have shorter contract lengths, compared with government services, and overall to be more structurally vulnerable.

CONCLUSION

Despite the reliance on NGOs to provide the majority of specialist care (71% of all treatment episodes in Australia), these services are more vulnerable than their government counterparts. To ensure that a comprehensive suite of treatment services is available, procurement arrangements that support stability and security in nongovernment service providers and government service providers are essential.

Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing

We report characteristics of soybean genetic diversity and structure from the resequencing of 481 diverse soybean accessions, comprising 52 wild (Glycine soja) selections and 429 cultivated (Glycine max) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to identify the genetic structure, relationships, and linkage disequilibrium. We found evidence of distinct, mostly independent selection of lineages by particular geographic location. Among cultivated varieties, we identified numerous highly conserved regions, suggesting selection during domestication. Comparisons of these accessions against the whole U.S. germplasm genotyped with the SoySNP50K iSelect BeadChip revealed that over 95% of the re-sequenced accessions have a high similarity to their SoySNP50K counterparts. Probable errors in seed source or genotype tracking were also identified in approximately 5% of the accessions.

The importance of slow canopy wilting in drought tolerance in soybean

Slow canopy wilting (SW) is a water conservation trait controlled by quantitative trait loci (QTLs) in late maturity group soybeans [Glycine max (L.) Merr.]. Recently, two exotic (landraces) plant introductions (PI 567690 and PI 567731) were identified as new SW lines in early maturity groups. Here, we show that the two PIs share the same water conservation strategy of limited maximum transpiration rates as PI 416937. However, in contrast to PI 416937, the transpiration rates of these PIs were sensitive to an aquaporin inhibitor, indicating an independence between limited maximum transpiration and the lack of silver-sensitive aquaporins. Yield tests of selected recombinant inbred lines from two elite/exotic crosses provide direct evidence to support the benefit of SW in drought tolerance. Four SW QTLs mapped in a Pana×PI 567690 cross at multiple environments were found to be co-located with previous reports. Moreover, two new SW QTLs were mapped on chromosomes 6 and 10 from a Magellan×PI 567731 cross. These two QTLs explain the observed relatively large contributions of 20-30% and were confirmed in a near-isogenic background. These findings demonstrate the importance of SW in yield protection under drought and provide genetic resources for improving drought tolerance in early maturity group soybeans.

A major natural genetic variation associated with root system architecture and plasticity improves waterlogging tolerance and yield in soybean

Natural genetic variations in waterlogging tolerance are controlled by multiple genes mapped as quantitative trait loci (QTLs) in major crops, including soybean (Glycine max L.). In this research, 2 novel QTLs associated with waterlogging tolerance were mapped from an elite/exotic soybean cross. The subsequent research was focused on a major QTL (qWT_Gm03) with the tolerant allele from the exotic parent. This QTL was isolated into near-isogenic backgrounds, and its effects on waterlogging tolerance were validated in multiple environments. Fine mapping narrowed qWT_Gm03 into a genomic region of <380 Kbp excluding Rps1 gene for Phytophthora sojae resistance. The tolerant allele of qWT_Gm03 promotes root growth under nonstress conditions and favourable root plasticity under waterlogging, resulting in improved waterlogging tolerance, yield, and drought tolerance-related traits, possibly through more efficient water/nutrient uptakes. Meanwhile, involvement of auxin pathways was also identified in the regulation of waterlogging tolerance, as the genotypic differences of qWT_Gm03 in waterlogging tolerance and formation of adventitious/aerial roots can be complemented by an exogenous auxin-biosynthesis inhibitor. These findings provided genetic resources to address the urgent demand of improving waterlogging tolerance in soybean and revealed the determinant roles of root architecture and plasticity in the plant adaptation to waterlogging.

Session 3: Boosting primary and recurrent rectal cancer: how far can we push the radiotherapy envelope?

Neoadjuvant pelvic radiotherapy is widely used for patients with advanced rectal cancer. The trade-off between dose and response is well-established, yet little consensus remains on the precise methods of delivery and doses given in different scenarios. Professor Vuong reviews the evidence base and trial evidence on the escalation of radiotherapy dose and the methods of achieving this.

Molecular mapping and genomics of soybean seed protein: a review and perspective for the future

KEY MESSAGE

Genetic improvement of soybean protein meal is a complex process because of negative correlation with oil, yield, and temperature. This review describes the progress in mapping and genomics, identifies knowledge gaps, and highlights the need of integrated approaches. Meal protein derived from soybean [Glycine max (L) Merr.] seed is the primary source of protein in poultry and livestock feed. Protein is a key factor that determines the nutritional and economical value of soybean. Genetic improvement of soybean seed protein content is highly desirable, and major quantitative trait loci (QTL) for soybean protein have been detected and repeatedly mapped on chromosomes (Chr.) 20 (LG-I), and 15 (LG-E). However, practical breeding progress is challenging because of seed protein content's negative genetic correlation with seed yield, other seed components such as oil and sucrose, and interaction with environmental effects such as temperature during seed development. In this review, we discuss rate-limiting factors related to soybean protein content and nutritional quality, and potential control factors regulating seed storage protein. In addition, we describe advances in next-generation sequencing technologies for precise detection of natural variants and their integration with conventional and high-throughput genotyping technologies. A syntenic analysis of QTL on Chr. 15 and 20 was performed. Finally, we discuss comprehensive approaches for integrating protein and amino acid QTL, genome-wide association studies, whole-genome resequencing, and transcriptome data to accelerate identification of genomic hot spots for allele introgression and soybean meal protein improvement.

Phenolic compounds isolated from fermented blueberry juice decrease hepatocellular glucose output and enhance muscle glucose uptake in cultured murine and human cells

Background

We recently reported that blueberry juice fermented (FJ) with Serratia vaccinii bacterium has antidiabetic activities both in vivo and in vitro. The purpose of this project was to elucidate the effect of FJ on glucose homeostasis in liver and skeletal muscle cells and to identify active fractions/compounds responsible for this effect.

Methods

FJ was fractionated using standard chromatography procedures. Hepatic (H4IIE, HepG2) and skeletal muscle cells (C2C12) were treated with maximum non-toxic concentrations of FJ, fractions and isolated compounds thereof. Glucose-6-phosphatase (G6Pase) activity was measured using glucose oxidase method. To measure glucose uptake and glycogen synthase (GS) activity, radioactive assays were used.

Results

Fractionation of FJ yielded seven fractions. FJ and its phenolic fractions F2, F3-1 and F3-2 respectively inhibited G-6Pase by 31, 45, 51 and 26%; activated GS by 2.3-, 2.3-, 2.2- and 2-fold; and stimulated glucose uptake by 19, 25, 18 and 15%, as compared to DMSO vehicle control. Subfractionation of the active fractions yielded 4 compounds (catechol, chlorogenic, gallic and protocatechuic acid). Catechol, yielding the greatest bioactivity in G6Pase and glucose uptake assays, decreased G6Pase activity by 54%, increased GS by 2-fold and stimulated glucose uptake by 44% at 45.5 μM.

Conclusions

This study identifies novel potential antidiabetic compounds that can help standardize FJ.

Electronic supplementary material

The online version of this article (doi:10.1186/s12906-017-1650-2) contains supplementary material, which is available to authorized users.

Eastern Canadian Colorectal Cancer Consensus Conference 2013: Emerging Therapies in the Treatment of Pancreatic, Rectal, and Colorectal Cancers

The annual Eastern Canadian Colorectal Cancer Consensus Conference held in Montreal, Quebec, 17–19 October 2013, marked the 10-year anniversary of this meeting that is attended by leaders in medical, radiation, and surgical oncology. The goal of the attendees is to improve the care of patients affected by gastrointestinal malignancies. Topics discussed during the conference included pancreatic cancer, rectal cancer, and metastatic colorectal cancer.

Role of a polyphenol-enriched preparation on chemoprevention of mammary carcinoma through cancer stem cells and inflammatory pathways modulation

BACKGROUND

Naturally occurring polyphenolic compounds from fruits, particularly from blueberries, have been reported to be significantly involved in cancer chemoprevention and chemotherapy. Biotransformation of blueberry juice by Serratia vaccinii increases its polyphenolic content and endows it with anti-inflammatory properties.

METHODS

This study evaluated the effect of a polyphenol-enriched blueberry preparation (PEBP) and its non-fermented counterpart (NBJ), on mammary cancer stem cell (CSC) development in in vitro, in vivo and ex vivo settings. Effects of PEBP on cell proliferation, mobility, invasion, and mammosphere formation were measured in vitro in three cell lines: murine 4T1 and human MCF7 and MDA-MB-231. Ex vivo mammosphere formation, tumor growth and metastasis observations were carried out in a BALB/c mouse model.

RESULTS

Our research revealed that PEBP influence cellular signaling cascades of breast CSCs, regulating the activity of transcription factors and, consequently, inhibiting tumor growth in vivo by decreasing metastasis and controlling PI3K/AKT, MAPK/ERK, and STAT3 pathways, central nodes in CSC inflammatory signaling. PEBP significantly inhibited cell proliferation of 4T1, MCF-7 and MDA-MB-231. In all cell lines, PEBP reduced mammosphere formation, cell mobility and cell migration. In vivo, PEBP significantly reduced tumor development, inhibited the formation of ex vivo mammospheres, and significantly reduced lung metastasis.

CONCLUSIONS

This study showed that polyphenol enrichment of a blueberry preparation by fermentation increases its chemopreventive potential by protecting mice against tumor development, inhibiting the formation of cancer stem cells and reducing lung metastasis. Thus, PEBP may represent a novel complementary alternative medicine therapy and a source for novel therapeutic agents against breast cancer.

Identification and characterization of a stachyose synthase gene controlling reduced stachyose content in soybean

KEY MESSAGE

We identified and characterized a mutant of soybean stachyose synthase gene controlling reduced stachyose content which benefit the soybean seed composition breeding program in the future. It has been shown that in soybean, increased sucrose and reduced raffinose family oligosaccharides would have a positive impact on the world's feed industry by improving digestibility and feed efficiency. We searched for new sources of modified oligosaccharide content in a subset of the USDA Soybean Germplasm Collection and then identified plant introduction (PI) 603176A as having ultra-low stachyose content (0.5%). We identified a 33-bp deletion mutant in the putative stachyose synthase gene (STS gene, Glyma19g40550) of PI 603176A. A co-dominate indel marker was successfully developed from this 33-bp deletion area and was genetically mapped into two F 2:3 populations and a F 4:5 population, which associated with low stachyose content in the progeny lines. These observations provided strong evidence that the STS gene is responsible for stachyose biosynthesis in the soybean plant. Expression of the sts gene remained at the normal level, suggesting the loss of function in the gene is due to defective protein function. This gene-based perfect genetic marker for low stachyose content can be useful for marker-assisted selection in soybean molecular breeding programs.

Whole-genome gene expression profiling revealed genes and pathways potentially involved in regulating interactions of soybean with cyst nematode (Heterodera glycines Ichinohe)

BACKGROUND

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is the most devastating pathogen of soybean. Many gene expression profiling studies have been conducted to investigate the responses of soybean to the infection by this pathogen using primarily the first-generation soybean genome array that covered approximately 37,500 soybean transcripts. However, no study has been reported yet using the second-generation Affymetrix soybean whole-genome transcript array (Soybean WT array) that represents approximately 66,000 predicted soybean transcripts.

RESULTS

In the present work, the gene expression profiles of two soybean plant introductions (PIs) PI 437654 and PI 567516C (both resistant to multiple SCN HG Types) and cultivar Magellan (susceptible to SCN) were compared in the presence or absence of the SCN inoculum at 3 and 8 days post-inoculation using the Soybean WT array. Data analysis revealed that the two resistant soybean lines showed distinctive gene expression profiles from each other and from Magellan not only in response to the SCN inoculation, but also in the absence of SCN. Overall, 1,413 genes and many pathways were revealed to be differentially regulated. Among them, 297 genes were constitutively regulated in the two resistant lines (compared with Magellan) and 1,146 genes were responsive to the SCN inoculation in the three lines, with 30 genes regulated both constitutively and by SCN. In addition to the findings similar to those in the published work, many genes involved in ethylene, protein degradation, and phenylpropanoid pathways were also revealed differentially regulated in the present study. GC-rich elements (e.g., GCATGC) were found over-represented in the promoter regions of certain groups of genes. These have not been observed before, and could be new defense-responsive regulatory elements.

CONCLUSIONS

Different soybean lines showed different gene expression profiles in the presence and absence of the SCN inoculum. Both inducible and constitutive gene expression may contribute to resistance to multiple SCN HG Types in the resistant soybean PI lines. Ethylene, protein degradation, and phenylpropanoid pathways, as well as many other pathways reported previously, may play important roles in mediating the soybean-SCN interactions. The revealed genes, pathways, and promoter elements can be further explored to regulate or engineer soybean for resistance to SCN.

Integrating omic approaches for abiotic stress tolerance in soybean

Soybean production is greatly influenced by abiotic stresses imposed by environmental factors such as drought, water submergence, salt, and heavy metals. A thorough understanding of plant response to abiotic stress at the molecular level is a prerequisite for its effective management. The molecular mechanism of stress tolerance is complex and requires information at the omic level to understand it effectively. In this regard, enormous progress has been made in the omics field in the areas of genomics, transcriptomics, and proteomics. The emerging field of ionomics is also being employed for investigating abiotic stress tolerance in soybean. Omic approaches generate a huge amount of data, and adequate advancements in computational tools have been achieved for effective analysis. However, the integration of omic-scale information to address complex genetics and physiological questions is still a challenge. In this review, we have described advances in omic tools in the view of conventional and modern approaches being used to dissect abiotic stress tolerance in soybean. Emphasis was given to approaches such as quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS). Comparative genomics and candidate gene approaches are also discussed considering identification of potential genomic loci, genes, and biochemical pathways involved in stress tolerance mechanism in soybean. This review also provides a comprehensive catalog of available online omic resources for soybean and its effective utilization. We have also addressed the significance of phenomics in the integrated approaches and recognized high-throughput multi-dimensional phenotyping as a major limiting factor for the improvement of abiotic stress tolerance in soybean.

Effects of dna-dependent protein kinase inhibition by NU7026 on dna repair and cell survival in irradiated gastric cancer cell line N87

Repair of radiation-induced dna double-strand breaks is a key mechanism in cancer cell radio-resistance. The synthesized compound NU7026 specifically inhibits dna-dependent protein kinase (dna-pk) within the non-homologous end-joining repair mechanism. Earlier studies demonstrated increased radiosensitivity in dna-pk deficient cells compared with wild-type cells. In chronic leukemia cells, NU7026 appears to enhance the cytotoxic effect of chlorambucil. The radio-modifying effects of NU7026 on cell survival, cell cycle, apoptosis, and dna double-strand break repair have yet to be studied in gastric cancer cells.

METHODS

The gastric cancer cell line N87 was treated with 0 Gy or 4 Gy in the presence of NU7026 at a dose range of 0-20 μmol/L. Clonogenic assays were used to assess cell survival after treatment. Cell-cycle distribution was analyzed using propidium iodide with fluorescence-activated cell sorting. Apoptosis was detected using annexin-V and propidium iodide with fluorescence-activated cell sorting. The γH2AX assay was used to measure dna double-strand breaks.

RESULTS

Statistically significant increases in G2/M arrest were observed in N87 cells treated with radiation and NU7026 compared with those treated with radiation alone (p = 0.0004). Combined treatment also led to an increase in apoptosis (p = 0.01). At 24 hours, the γH2AX analysis revealed more dna double-strand breaks in N87 cells treated with radiation and NU7026 than in those treated with radiation alone (p = 0.04). Clonogenic assays demonstrated declining cell survival as both the radiation and the NU7026 dose increased. The dose enhancement factor at 0.1 survival fraction was 1.28 when N87 cells were treated with 4 Gy radiation and 5 μmol/L NU7026.

CONCLUSIONS

In gastric cancer cells, NU7026 appears to enhance the cytotoxic effect of irradiation as assessed by clonogenic assays. This increased cytotoxicity might be the result of an increase in dna double-strand breaks resulting in G2/M cell arrest and possibly higher levels of apoptosis.

The experience of pain and anxiety in rectal cancer patients during high-dose-rate brachytherapy

BACKGROUND

Pain and anxiety have been reported as primary concerns for patients with head-and-neck, gynecologic, and prostate cancers undergoing high dose rate (hdr) brachytherapy. However, almost no research has been published on the degree to which these symptoms are experienced by rectal cancer patients undergoing hdr brachytherapy. We conducted a pilot study examining the experiences of rectal cancer patients during hdr brachytherapy, specifically the intensity and trajectory of their anxiety and pain.

METHODS

Rectal cancer patients (n = 25) who received hdr brachytherapy treatment at a hospital in Montreal, Quebec, completed verbal analog scales for pain and anxiety at 4 time points over 4 treatment days.

RESULTS

On all 4 days, a subset of patients reported moderate-to-severe anxiety before applicator insertion. Pain increased significantly from the time patients were lying on the table to immediately after insertion of the applicator (p < 0.001). Insertion of the applicator appears to be the most painful part of the procedure, and although anxiety declined to below baseline after applicator removal, pain remained somewhat elevated. Some patients required conscious sedation; however, reports of moderate-to-severe pain were more frequent from patients who received pain medications than from patients who did not receive such medication (p < 0.05).

CONCLUSIONS

Most patients with rectal cancer tolerated hdr rectal brachytherapy well, although the procedure is stressful and painful for some. Insertion of the applicator was found to be the point of maximal pain, and medication was not always completely successful at alleviating the pain, suggesting that additional psychosocial interventions might be needed, with particular emphasis on the time of applicator insertion.

Pinpointing genes underlying the quantitative trait loci for root-knot nematode resistance in palaeopolyploid soybean by whole genome resequencing

The objective of this study was to use next-generation sequencing technologies to dissect quantitative trait loci (QTL) for southern root-knot nematode (RKN) resistance into individual genes in soybean. Two hundred forty-six recombinant inbred lines (RIL) derived from a cross between Magellan (susceptible) and PI 438489B (resistant) were evaluated for RKN resistance in a greenhouse and sequenced at an average of 0.19× depth. A sequence analysis pipeline was developed to identify and validate single-nucleotide polymorphisms (SNPs), infer the parental source of each SNP allele, and genotype the RIL population. Based on 109,273 phased SNPs, recombination events in RILs were identified, and a total of 3,509 bins and 3,489 recombination intervals were defined. About 50.8% of bins contain 1 to 10 genes. A linkage map was subsequently constructed by using bins as molecular markers. Three QTL for RKN resistance were identified. Of these, one major QTL was mapped to bin 10 of chromosome 10, which is 29.7 kb in size and harbors three true genes and two pseudogenes. Based on sequence variations and gene-expression analysis, the candidate genes underlying the major QTL for RKN resistance were pinpointed. They are Glyma10g02150 and Glyma10g02160, encoding a pectin methylesterase inhibitor and a pectin methylesterase inhibitor -pectin methylesterase, respectively. This QTL mapping approach not only combines SNP discovery, SNP validation, and genotyping, but also solves the issues caused by genome duplication and repetitive sequences. Hence, it can be widely used in crops with a reference genome to enhance QTL mapping accuracy.

Short-term outcome after neoadjuvant high-dose-rate endorectal brachytherapy or short-course external beam radiotherapy in resectable rectal cancer

AIM

Total mesorectal excision with preoperative radiotherapy reduces local recurrence in rectal cancer, but radiotherapy increases the risk of complications. This study compared the immediate postoperative outcome after external beam radiotherapy with outome after high-dose-rate endorectal brachytherapy (HDREBT).

METHOD

Patients (n = 318) treated with preoperative HDREBT (6.5 Gy, daily, over 4 days) followed by surgery 4-8 weeks later were matched with 318 patients from the Swedish Rectal Cancer Register treated with short-course radiotherapy (SCRT; 5 Gy, daily, over 5 days) and surgery in the subsequent week and with 318 patients who had surgery only (i.e. no preoperative radiotherapy; RT-) All 954 patients were followed for 30 days after surgery. Complications were divided into surgical, cardiovascular and infectious.

RESULTS

The SCRT group had fewer cardiovascular complications (3.1%) than did HDREBT (9.4%, P = 0.002) and RT- (7.2%, P = 0.03) groups. There was less perioperative bleeding in HDREBT patients (379.3 ml) than in SCRT (947.2 ml; P < 0.0001) or RT- (918.9 ml) patients, and the re-intervention rate was lower in HDREBT (4.1%) patients than in SCRT (14.2%; P = 0.005) and RT- (12.3%; P < 0.005) patients. The HDREBT group had fewer R2 resections than did the SCRT and RT- groups, but had a higher proportion of R0 resections compared with the RT- group (P = 0.03).

CONCLUSION

No major differences in postoperative complications were found. HDREBT patients had a higher rate of cardiovascular complications, but less perioperative bleeding and fewer re-interventions. A longer interval between radiotherapy and surgery may be beneficial for tumour regression and this could be reflected in the number of radical resections.

MicroRNA miR-30 family regulates non-attachment growth of breast cancer cells

BACKGROUND

A subset of breast cancer cells displays increased ability to self-renew and reproduce breast cancer heterogeneity. The characterization of these so-called putative breast tumor-initiating cells (BT-ICs) may open the road for novel therapeutic strategies. As microRNAs (miRNAs) control developmental programs in stem cells, BT-ICs may also rely on specific miRNA profiles for their sustained activity. To explore the notion that miRNAs may have a role in sustaining BT-ICs, we performed a comprehensive profiling of miRNA expression in a model of putative BT-ICs enriched by non-attachment growth conditions.

RESULTS

We found breast cancer cells grown under non-attachment conditions display a unique pattern of miRNA expression, highlighted by a marked low expression of miR-30 family members relative to parental cells. We further show that miR-30a regulates non-attachment growth. A target screening revealed that miR-30 family redundantly modulates the expression of apoptosis and proliferation-related genes. At least one of these targets, the anti-apoptotic protein AVEN, was able to partially revert the effect of miR-30a overexpression. Finally, overexpression of miR-30a in vivo was associated with reduced breast tumor progression.

CONCLUSIONS

miR30-family regulates the growth of breast cancer cells in non-attachment conditions. This is the first analysis of target prediction in a whole family of microRNAs potentially involved in survival of putative BT-ICs.