Integrating Association Mapping, Linkage Mapping, Fine Mapping with RNA Seq Conferring Seedling Vigor Improvement for Successful Crop Establishment in Deep Sown Direct-Seeded Rice

BACKGROUND

Ongoing large-scale shift towards direct seeded rice (DSR) necessitates a convergence of breeding and genetic approaches for its sustenance and harnessing natural resources and environmental benefits. Improving seedling vigour remains key objective for breeders working with DSR. The present study aims to understand the genetic control of seedling vigour in deep sown DSR. Combined genome-wide association mapping, linkage mapping, fine mapping, RNA-sequencing to identify candidate genes and validation of putative candidate genes were performed in the present study.

RESULTS

Significant phenotypic variations were observed among genotypes in both F3:4:5 and BC2F2:3 populations. The mesocotyl length showed significant positive correlation with %germination, root and shoot length. The 881 kb region on chromosome 7 reported to be associated with mesocotyl elongation. RNA-seq data and RT-PCR results identified and validated seven potential candidate genes. The four promising introgression lines free from linkage drag and with longer mesocotyl length, longer root length, semi-dwarf plant height have been identified.

CONCLUSION

The study will provide rice breeders (1) the pre breeding material in the form of anticipated DSR adapted introgression lines possessing useful traits and alleles improving germination under deep sown DSR field conditions (2) the base for the studies involving functional characterization of candidate genes. The development and utilization of improved introgression lines and molecular markers may play an important role in genomics-assisted breeding (GAB) during the pyramiding of valuable genes providing adaptation to rice under DSR. Our results offer a robust and reliable package that can contribute towards enhancing genetic gains in direct seeded rice breeding programs.

Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species

Citrus species among the most important and widely consumed fruit in the world due to Vitamin C, essential oil glands, and flavonoids. Highly variable simple sequence repeats (SSR) markers are one of the most informative and versatile molecular markers used in perennial tree genetic research. SSR survey of Citrus sinensis and Citrus maxima were identified perfect SSRs spanning nine chromosomes. Furthermore, we categorized all SSR motifs into three major classes based on their tract lengths. We designed and validated a class I SSRs in the C. sinensis and C. maxima genome through electronic polymerase chain reaction (ePCR) and found 83.89% in C. sinensis and 78.52% in C. maxima SSRs producing a single amplicon. Then, we selected extremely variable SSRs (> 40 nt) from the ePCR-verified class I SSRs and in silico validated across seven draft genomes of citrus, which provided us a subset of 84.74% in C. sinensis and 77.53% in C. maxima highly polymorphic SSRs. Out of these, 129 primers were validated on 24 citrus genotypes through wet-lab experiment. We found 127 (98.45%) polymorphic HvSSRs on 24 genotypes. The utility of the developed HvSSRs was demonstrated by analysing genetic diversity of 181 citrus genotypes using 17 HvSSRs spanning nine citrus chromosomes and were divided into 11 main groups through 17 HvSSRs. These chromosome-specific SSRs will serve as a powerful genomic tool used for future QTL mapping, molecular breeding, investigation of population genetic diversity, comparative mapping, and evolutionary studies among citrus and other relative genera/species.

Evaluation of Coliform and Faecal Coliform Bacteria in the Lakes of Broknes and Grovnes Peninsula, East Antarctica

More than 150 lakes on different peninsulas and islands are situated in the Larsemann Hills. The Larsemann Hills is an ice-free area and are located halfway between the Vestfold Hills and the Amery Ice Shelf on the southeastern coast of Prydz Bay, Princess Elizabeth Land, and East Antarctica. During 34th Indian Scientific Expedition to Antarctica (ISEA) from 2014 to 2015, twenty lake water samples in triplicates were collected from the Broknes & Grovnes peninsula. Coliform and fecal coliform bacteria were analyzed in these samples. Out of twenty, eleven lake water samples were found to be contaminated with coliform bacteria. However, fecal coliform bacteria were absent in all the lake water samples. Coliforms are found in the lakes of Broknes peninsula (P2 Lake & P3 Lake) and Grovnes peninsula (L1C NG, L1D NG, L1E NG, L7 NG, L7A NG, L7B NG, L2 SG, L4 SG & L5 SG). Antarctic lakes water is being polluted due to anthropogenic activities caused by various research activities and tourism. The present study confirms the presence of coliform bacteria in the lakes of East Antarctica which indicates an alarming situation and needs to be investigated further.

Type II papillary renal cell carcinoma with heterotrophic ossification: a case report

Heterotrophic ossification in tumours is an uncommon phenomenon. The presence of ossification in renal cell carcinomas is extremely rare. In this report, we present a unique case of type II papillary renal cell carcinoma associated with heterotrophic ossification.

Utilization of pelvic lymph node dissection in patients undergoing robot-assisted radical prostatectomy in India versus the United States - A Vattikuti Collective Quality Initiative database analysis

BACKGROUND

The utilization and extent of pelvic lymph node dissection (PLND) varies depending on the disease and practice patterns.

AIMS

This study compares practice patterns in utilization of PLND between Indian and United States (US) practices.

SETTINGS AND DESIGN

We focused on 415 patients (204 India; 211 US) prostate cancer patients treated with robot-assisted radical prostatectomy, between 2015 and 2016, within the Vattikuti Collective Quality Initiative database.

SUBJECTS AND METHODS

Utilization of PLND and number of nodes removed were evaluated for the entire cohort, and after stratifying for Country of treatment and D'Amico risk groups. Logistic regression tested the relationship between PLND and country of treatment, after adjusting for disease risk.

RESULTS

Indian patients had a higher risk distribution (D'Amico high-risk 53.4% in India vs. 27% in the US; P< 0.001) compared to their US counterparts. Overall, 193/204 (94.6%) Indian patients underwent PLND versus 181/211 (85.8%) US patients (P = 0.003). When stratified based on disease risk, PLND was performed more frequently in Indian patients with low-risk disease (81.0% vs. 41.4%,P= 0.008), but not in those with intermediate and high-risk disease. On multivariable analysis, Indian patients had a 2.57-fold higher probability of undergoing PLND than their US counterparts (P = 0.02). The analysis of the number of lymph nodes removed showed similar trends.

CONCLUSIONS

Indian patients are more likely to undergo PLND than US patients. This is, especially true for patients with low-risk disease, who are unlikely to benefit from this procedure. Efforts should focus on optimizing the utilization of PLND, and deliver it only when there is clinical indication.

Evaluation of the efficacy of a combination of diltiazem and periprostatic nerve block in pain control during transrectal ultrasonography-guided biopsy of the prostate

INTRODUCTION

The choice of analgesia during prostate biopsy remains controversial. The pain has dual origin: from the insertion of the probe as well as the biopsy itself. Periprostatic nerve block (PPNB) is currently the gold standard modality for decreasing pain of prostate biopsy but it does not alleviate the pain of probe insertion. A randomised controlled trial was performed to test the efficacy and safety of the combination of topical application of diltiazem gel and PPNB for pain control during transrectal ultrasonography guided prostate biopsy.

METHODS

A total of 73 patients who were to undergo their first prostate biopsy were randomised to receive either 2ml of 2% topical diltiazem gel or a placebo 15 minutes before the biopsy. All the patients then had a PPNB using 1% lignocaine. A ten- point visual analogue scale was used to record the pain immediately after the insertion of the probe and during the biopsy. Any adverse effects were also recorded.

RESULTS

There was no significant difference in the mean age and prostate volumes between the groups. There was a significantly lower mean pain score due to probe insertion in those patients who received topical diltiazem than in the placebo group (p<0.0001). There was no significant difference between the pain scores during the biopsy itself between the two groups.

CONCLUSIONS

Topical diltiazem significantly reduces the pain of probe insertion during prostate biopsy and can be used effectively as an adjuvant to PPNB.

Cystic schwannoma of the pelvis

Schwannomas are benign tumours that arise from the Schwann cells of nerve fibres. They commonly occur in the head and neck, mediastinum and extremities. They are extremely rare in the pelvis. These are usually slow-growing tumours and are often detected incidentally. Preoperative diagnosis is extremely difficult as there are no definitive signs on imaging. Aspiration biopsy is often inconclusive or misleading. Surgical excision is both diagnostic and therapeutic. As these tumours are often large in size, open excision is most commonly performed. We describe a case of a large, cystic schwannoma of the pelvis causing bladder outlet obstruction and bilateral hydroureteronephrosis. Complete surgical excision was performed laparoscopically.

Surgical reconstruction of penile stump in a patient with Klingsor syndrome

Self-mutilation of genitalia is an extremely rare entity, usually found in psychotic patients. Klingsor syndrome is a condition in which such an act is based upon religious delusions. The extent of genital mutilation can vary from superficial cuts to partial or total amputation of penis to total emasculation. The management of these patients is challenging. The aim of the treatment is restoration of the genital functionality. Microvascular reanastomosis of the phallus is ideal but it is often not possible due to the delay in seeking medical attention, non viability of the excised phallus or lack of surgical expertise. Hence, it is not unusual for these patients to end up with complete loss of the phallus and a perineal urethrostomy. We describe a patient with Klingsor syndrome who presented to us with near total penile amputation. The excised phallus was not viable and could not be used. The patient was managed with surgical reconstruction of the penile stump which was covered with loco-regional flaps. The case highlights that a functional penile reconstruction is possible in such patients even when microvascular reanastomosis is not feasible. This technique should be attempted before embarking upon perineal urethrostomy.

Persistence, degradation and leaching of coumaphos in soil

Dissipation, degradation and leaching of fresh 14C coumaphos, alkylated 14C coumaphos and aged residues of 14C coumaphos from vats were studied in alkaline sandy loam soil in soil columns in the field under subtropical conditions in Delhi for a year. Dissipation, degradation and bound residue formation was more in case of alkali treated coumaphos than fresh coumaphos. After 365 days total residues of fresh coumaphos accounted for 33.25% while that of alkali treated coumaphos was 19.12%. Bound residue formation was almost double in case of alkali treated coumaphos (18.95%) than fresh coumaphos (9.53%) after 150 days followed by release of bound residue in both the cases. The proportion of metabolites 4-methylumbelliferone, chlorferon and potasan collectively was 86.05% in fresh coumaphos extractable residues while the same was 91.74% in alkali treated coumaphos after 365 days. Aged residues from vats containing copper sulphate and buffer were found to be more persistent in soil as total residues remained were 95.58% in comparison with 83.09% total residues of aged residues from vats containing only buffer after 150 days of treatment. Copper sulphate seems to inhibit the degradatiion of coumaphos in soil by microorganisms. Chlorferon was the major metabolite in generally all the samples. Coumaphos did not leach below 10 cm in all the cases.