scholarly journals Combining conventional QTL analysis and whole-exome capture-based bulk-segregant analysis provides new genetic insights into tuber sprout elongation and dormancy release in a diploid potato population

Heredity ◽  
2021 ◽  
Author(s):  
Sanjeev Kumar Sharma ◽  
Karen McLean ◽  
Richard J. Colgan ◽  
Debbie Rees ◽  
Stephen Young ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Qtl Analysis ◽  
Bulk Segregant Analysis ◽  
Exome Capture ◽  
Dormancy Release ◽  
Diploid Potato ◽  
Growing Seasons ◽  
Whole Exome ◽  
Sprout Growth

AbstractTuber dormancy and sprouting are commercially important potato traits as long-term tuber storage is necessary to ensure year-round availability. Premature dormancy release and sprout growth in tubers during storage can result in a significant deterioration in product quality. In addition, the main chemical sprout suppressant chlorpropham has been withdrawn in Europe, necessitating alternative approaches for controlling sprouting. Breeding potato cultivars with longer dormancy and slower sprout growth is a desirable goal, although this must be tempered by the needs of the seed potato industry, where dormancy break and sprout vigour are required for rapid emergence. We have performed a detailed genetic analysis of tuber sprout growth using a diploid potato population derived from two highly heterozygous parents. A dual approach employing conventional QTL analysis allied to a combined bulk-segregant analysis (BSA) using a novel potato whole-exome capture (WEC) platform was evaluated. Tubers were assessed for sprout growth in storage at six time-points over two consecutive growing seasons. Genetic analysis revealed the presence of main QTL on five chromosomes, several of which were consistent across two growing seasons. In addition, phenotypic bulks displaying extreme sprout growth phenotypes were subjected to WEC sequencing for performing BSA. The combined BSA and WEC approach corroborated QTL locations and served to narrow the associated genomic regions, while also identifying new QTL for further investigation. Overall, our findings reveal a very complex genetic architecture for tuber sprouting and sprout growth, which has implications both for potato and other root, bulb and tuber crops where long-term storage is essential.

Identification of WDFY3 Neoantigens as Prognostic Markers in Longterm Survivors of Extrahepatic Cholangiocarcinoma

2020 ◽  
Vol 20 (11) ◽  
pp. 875-886
Author(s):  
Yingyi Wang ◽  
Bao Jin ◽  
Na Zhou ◽  
Zhao Sun ◽  
Jiayi Li ◽  
...  
Keyword(s):  
Antitumor Immunity ◽  
Prognostic Markers ◽  
Immune Cell ◽  
Neutrophil Infiltration ◽  
Computational Biophysics ◽  
Extrahepatic Cholangiocarcinoma ◽  
Whole Exome ◽  
Mutation Burden ◽  
Long Term Survivors

Background:: Neoantigens are newly formed antigens that have not been previously recognized by the immune system. They may arise from altered tumor proteins that form as a result of mutations. Although neoantigens have recently been linked to antitumor immunity in long-term survivors of cancers, such as melanoma and colorectal cancer, their prognostic and immune-modulatory role in many cancer types remains undefined. Objective: The purpose of this study is to identify prognostic markers for long-term extrahepatic cholangiocarcinoma (EHCC) survival. Methods: We investigated neoantigens in EHCC, a rare, aggressive cancer with a 5-year overall survival rate lower than 10%, using a combination of whole-exome sequencing (WES), RNA sequencing (RNA-seq), computational biophysics, and immunohistochemistry. Results: : Our analysis revealed a decreased neutrophil infiltration-related trend of high-quality neoantigen load with IC50 <500 nM (r=-0.445, P=0.043). Among 24 EHCC patients examined, we identified four long-term survivors with WDFY3 neoantigens and none with WDFY3 neoantigens in the short-term survivors. The WDFY3 neoantigens are associated with a lower infiltration of neutrophils (p=0.013), lower expression of CCL5 (p=0.025), CXCL9 (p=0.036) and TIGIT (p=0.016), and less favorable prognosis (p=0.030). In contrast, the prognosis was not significantly associated with tumor mutation burden, neoantigen load, or immune cell infiltration. Conclusion:: We suggest that the WDFY3 neoantigens may affect prognosis by regulating antitumor immunity and that the WDFY3 neoantigens may be harnessed as potential targets for immunotherapy of EHCC.

scholarly journals AB0994 NEW ALTERNATIVE IN THE TREATMENT OF PATIENT WITH MUTATION OF GEN LACC1

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 1790.2-1790
Author(s):  
R. M. Alcobendas ◽  
C. Quintana ◽  
J. Arostegui ◽  
C. Udaondo ◽  
S. Murias Loza ◽  
...  
Keyword(s):  
Chart Review ◽  
Loss Of Function ◽  
Acute Phase Reactants ◽  
Reactive Protein ◽  
Inflammatory Parameters ◽  
Whole Exome ◽  
Multiple Treatments ◽  
Clinical Chart ◽  
Clinical Worsening

Background:Few patients have been described in the literature with mutations in the Lacasa Domain containing one (LACC1) gene. Its clinical presentation usually associates sustained systemic inflammation associated with chronic polyarticular erosive arthritis. Until now, there have been multiple treatments described to try to control the disease, however, they are generally unsuccessful in the long term.Objectives:Describe the clinical course of a patient as well as the different treatments usedMethods:Clinical chart reviewResults:Female 18-year-old born from a consanguineous Moroccan couple. Mother, brother and sister with similar conditions. She started at 3 years with fever, anemia, intense elevation of acute phase reactants and symmetric polyarthritis (knees, elbows, carps, shoulders, hands and ankles). Subsequent whole exome sequencing identified c.128_129delGT mutation in the LACC1/FAMIN gene. During the course of her illness, she has received treatment with oral, intravenous and infiltrated corticosteroid, methotrexate and etanercept, without getting adequate control of the disease. In 2016, she started treatment with tocilizumab (8 mg / kg every two weeks), obtaining an acceptable control of the disease (requiring periodic infiltrations every 2-3 months due to persistent arthritis). Nonetheless, in April 2019, she consulted for clinical worsening of the arthritis and laboratory test (C reactive protein 99.7 mg / L, erythrosedimentation rate 53 mm / h, leukocytes 13,500/µL and neutrophils 10,930/µL). At that time, she discontinued therapy with tocilizumab and started tofacitinib 5 mg every 12 hours with good evolution. Since its introduction, it has not required joint infiltration again and the inflammatory parameters (persistently elevated previously) have normalized.Conclusion:The jak kinasa inhibitors may be a treatment option in those patients with bad response to conventional therapy.References:[1]Rabionet R, Remesal A, Mensa-Vilaró A, Murías S, Alcobendas R, González-Roca E, Ruiz-Ortiz E, Antón J, Iglesias E, Modesto C, Comas D, Puig A, Drechsel O, Ossowski S, Yagüe J, Merino R, Estivill X, Arostegui JI. Biallelic loss-of-function LACC1/FAMIN Mutations Presenting as Rheumatoid Factor-Negative Polyarticular Juvenile Idiopathic Arthritis. Sci Rep. 2019 Mar 14;9(1):4579Disclosure of Interests:None declared

scholarly journals A domestic cat whole exome sequencing resource for trait discovery

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alana R. Rodney ◽  
Reuben M. Buckley ◽  
Robert S. Fulton ◽  
Catrina Fronick ◽  
Todd Richmond ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Genetic Diseases ◽  
Domestic Cat ◽  
Whole Genome Sequence ◽  
Exome Capture ◽  
Single Nucleotide Variants ◽  
Whole Exome ◽  
Olfactory Receptor Genes ◽  
Feline Model

AbstractOver 94 million domestic cats are susceptible to cancers and other common and rare diseases. Whole exome sequencing (WES) is a proven strategy to study these disease-causing variants. Presented is a 35.7 Mb exome capture design based on the annotated Felis_catus_9.0 genome assembly, covering 201,683 regions of the cat genome. Whole exome sequencing was conducted on 41 cats with known and unknown genetic diseases and traits, of which ten cats had matching whole genome sequence (WGS) data available, used to validate WES performance. At 80 × mean exome depth of coverage, 96.4% of on-target base coverage had a sequencing depth > 20-fold, while over 98% of single nucleotide variants (SNVs) identified by WGS were also identified by WES. Platform-specific SNVs were restricted to sex chromosomes and a small number of olfactory receptor genes. Within the 41 cats, we identified 31 previously known causal variants and discovered new gene candidate variants, including novel missense variance for polycystic kidney disease and atrichia in the Peterbald cat. These results show the utility of WES to identify novel gene candidate alleles for diseases and traits for the first time in a feline model.

scholarly journals Genetic analysis of impaired trimethylamine metabolism using whole exome sequencing

2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Yiran Guo ◽  
Liang-Dar Hwang ◽  
Jiankang Li ◽  
Jason Eades ◽  
Chung Wen Yu ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Whole Exome

scholarly journals Whole Exome Sequencing of HIV-1 long-term non-progressors identifies rare variants in genes encoding innate immune sensors and signaling molecules

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Sara Konstantin Nissen ◽  
Mette Christiansen ◽  
Marie Helleberg ◽  
Kathrine Kjær ◽  
Sofie Eg Jørgensen ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Rare Variants ◽  
Signaling Molecules ◽  
Innate Immune ◽  
Whole Exome ◽  
Genes Encoding ◽  
Hiv 1

scholarly journals Longer Growing Seasons Cause Hydrological Regime Shifts in Central European Forests

Forests ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1656
Author(s):  
Petr Kupec ◽  
Jan Deutscher ◽  
Martyn Futter
Keyword(s):  
Regime Shift ◽  
Hydrological Regime ◽  
Annual Runoff ◽  
Order Effects ◽  
Runoff Generation ◽  
Central European ◽  
European Forests ◽  
Water Limitation ◽  
Growing Seasons

In this study, we present evidence for a hydrological regime shift in upland central European forests. Using a combination of long-term data, detailed field measurements and modelling, we show that there is a prolonged and persistent decline in annual runoff: precipitation ratios that is most likely linked to longer growing seasons. We performed a long term (1950–2018) water balance simulation for a Czech upland forest headwater catchment calibrated against measured streamflow and transpiration from deciduous and coniferous stands. Simulations were corroborated by long-term (1965–2018) borehole measurements and historical drought reports. A regime shift from positive to negative catchment water balances likely occurred in the early part of this century. Since 2007, annual runoff: precipitation ratios have been below the long-term average. Annual average temperatures have increased, but there have been no notable long term trends in precipitation. Since 1980, there has been a pronounced April warming, likely leading to earlier leaf out and higher annual transpiration, making water unavailable for runoff generation and/or soil moisture recharge. Our results suggest a regime shift due to second order effects of climate change where increased transpiration associated with a longer growing season leads to a shift from light to water limitation in central European forests. This will require new approaches to managing forests where water limitation has previously not been a problem.

scholarly journals Early queen joining and long‐term queen associations in polygyne colonies of an invasive wasp revealed by longitudinal genetic analysis

2021 ◽  
Author(s):  
Giulia Scarparo ◽  
Madison Sankovitz ◽  
Kevin J. Loope ◽  
Erin Wilson‐Rankin ◽  
Jessica Purcell
Keyword(s):  
Genetic Analysis ◽  
Queen Associations

Bi-directional exchange of ammonia above a corn crop canopy: from flux measurements to model parameterizations

2021 ◽  
Author(s):  
Alexander Moravek ◽  
Saumya Singh ◽  
Elizabeth Pattey ◽  
Amy Hdrina ◽  
Theodora Li ◽  
...  
Keyword(s):  
Atmospheric Transport ◽  
Fertilizer Application ◽  
Aerosol Formation ◽  
Crop Canopy ◽  
Crop Fields ◽  
Growing Seasons ◽  
Corn Crop ◽  
Stomatal Flux ◽  
Flux Measurements

&lt;p&gt;Emissions of ammonia (NH&lt;sub&gt;3&lt;/sub&gt;) from agriculture have a significant impact on the environment. Its atmospheric transport and subsequent deposition has been shown to alter nutrient-poor ecosystems thereby reducing biodiversity. As the most abundant base in the atmosphere, NH&lt;sub&gt;3&lt;/sub&gt; plays a key role in secondary aerosol formation impacting air quality and climate. Due to the lack of long term observations and challenges in performing NH&lt;sub&gt;3&lt;/sub&gt; flux measurements, large uncertainties exist in both emission quantification from fertilized crop fields and in the bi-directional exchange of NH&lt;sub&gt;3&lt;/sub&gt; with agroecosystems. We measured NH&lt;sub&gt;3&lt;/sub&gt; fluxes above a corn field using the eddy covariance technique together with a quantum cascade laser spectroscopy analyzer over two consecutive growing seasons in 2017 and 2018. We found that after initial NH&lt;sub&gt;3&lt;/sub&gt; emissions following fertilizer application, periods of both NH&lt;sub&gt;3&lt;/sub&gt; emission and deposition with similar flux magnitudes prevailed throughout the growing seasons (ranging approximately between &amp;#177;300 ng m&lt;sup&gt;-2&lt;/sup&gt; s&lt;sup&gt;-1&lt;/sup&gt;), highlighting the importance of the corn crop canopy for regulating the net NH&lt;sub&gt;3&lt;/sub&gt; exchange. To evaluate the underlying processes of the NH&lt;sub&gt;3&lt;/sub&gt; bi-directional exchange, a two-layer compensation point model was used. Based on the large range of environmental conditions encountered during the extensive flux measurements periods, the validity of different parameterizations could be assessed. In particular, processes regulating stomatal and non-stomatal flux pathways will be discussed.&lt;/p&gt;

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