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Genomic prediction of seasonal forage yield in perennial ryegrass

Grassland Research 2023年第3期2卷 167-181页

作者： Agnieszka Konkolewska steffie phang Patrick Conaghan Dan Milbourne Aonghus Lawlor Stephen Byrne Crop Science Department TeagascCarlowCo.CarlowIreland Insight SFI Research Centre for Data Analytics University College DublinDublinIreland VistaMilk SFI Research Centre FermoyCo.CorkIreland Grassland Science Research Department Animal and Grassland Research and Innovation CentreTeagascCarlowIreland

Background:Genomic selection has the potential to accelerate genetic gain in perennial ryegrass breeding,provided complex traits such as forage yield can be predicted with sufficient ***:In this study,we compared modelling approaches and feature selection strategies to evaluate the accuracy of genomic prediction models for seasonal forage yield ***:Overall,model selection had limited impact on predictive ability when using the full data *** a baseline genomic best linear unbiased prediction model,the highest mean predictive accuracy was obtained for spring grazing(0.78),summer grazing(0.62)and second cut silage(0.56).In terms of feature selection strategies,using uncorrelated single-nucleotide polymorphisms(SNPs)had no impact on predictive ability,allowing for a potential decrease of the data set *** a genome-wide association study,we found a significant SNP marker for spring grazing,located in the genic region annotated as coding for an enzyme responsible for fucosylation of xyloglucans—major components of the plant cell *** also presented an approach to increase interpretability of genomic prediction models with the use of Gene Ontology enrichment ***:Approaches for feature selection will be relevant in development of low-cost genotyping platforms in support of routine and cost-effective implementation of genomic selection.

关键词： forage yield genomic selection perennial ryegrass breeding

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Pooled genetic analysis in ultrasound measured non-alcoholic fatty liver disease in Indian subjects:A pilot study

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World Journal of Hepatology 2014年第6期6卷 435-442页

作者： Vishnubhotla Venkata Ravi Kanth Mitnala Sasikala Padaki Nagaraja Rao Urmila steffie Avanthi Kalashikam Rajender Rao Duvvuru Nageshwar Reddy Asian Healthcare Foundation Hyderabad 500082India Asian Institute of Gastroenterology Hyderabad 500082India Division of Endocrinology and Metabolism National Institute of NutritionTarnakaHyderabad 500082India

AIM: To investigate genetic susceptibility in Indian subjects with non-alcoholic fatty liver disease(NAFLD) by performing a pooled genetic ***: Study subjects(n = 306) were recruited and categorized into NAFLD and control groups based on ultrasound findings of fatty infiltration. Of the 306 individuals, 156 individuals had fatty infiltration and thus comprised the NAFLD group. One hundred and fifty(n = 150) individuals were normal, without fatty infiltration of the liver, comprising the control group. Blood samples, demographic and anthropometric data from the individuals were collected after obtaining informed consent. Anthropometric data, blood glucose, lipids and liver function tests were estimated using standard methods. Genome wide association stud-ies done to date on NAFLD were identified, 19 single nucleotide polymorphisms(SNPs) were selected from these studies that were reported to be significantly associated with NAFLD and genotyping was performed on the Sequenom platform. Student's t test for continuous variables and χ2 test was applied to variant carriers from both groups. Required corrections were applied as multiple testing was *** The mean age of the control group was 39.78 ± 10.83 and the NAFLD group was 36.63 ± 8.20 years. The waist circumference of males and females in the control and NAFLD groups were 80.13 ± 10.35; 81.77 ± 13.65 and 94.09 ± 10.53; 92.53 ± 8.27 respectively. The mean triglyceride and alanine transaminase(ALT) levels in the control and NAFLD groups were 135.18 ± 7.77; 25.39 ± 14.73 and 184.40 ± 84.31; 110.20 ± 67.05 respectively. When χ2 test was applied to the number of individuals carrying the variant risk alleles between the control and NAFLD group, a significant association was seen between rs738409 of the patatin-like phospholipase domain containing 3(PNPLA3) gene(P = 0.001), rs2073080 of the PARVB gene(P = 0.02), rs2143571 of SAMM50 gene(P = 0.05) and rs6487679 of the pregnancy zone protein(PZP) gene(P = 0.0

关键词： Non-alcoholic fatty liver disease Genome wide association studies Genetic association Hepatic steatosis Genotyping Single nucleotide polymorphisms Susceptibility

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Regional differences in genetic susceptibility to nonalcoholic liver disease in two distinct Indian ethnicities

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World Journal of Hepatology 2017年第26期9卷 1101-1107页

作者： Govardhan Bale Avanthi Urmila steffie Vishnubhotla Venkata Ravi Kanth Padaki Nagaraja Rao Mithun Sharma Mitnala Sasikala Duvvur Nageshwar Reddy Asian Healthcare Foundation Asian Institute of Gastroenterology

AIM To validate the association of variants in PNPLA3(rs2281135) and TM6SF2(rs58542926) genes with ultrasound detected non-alcoholic fatty liver disease(NAFLD).METHODS A total of 503 individuals with and without fatty infiltration were recruited. Fatty infiltration was confirmed based on ultrasound findings. Anthropometric data and blood samples were collected from the study group. DNA was isolated from peripheral blood, quality and quantity was assessed by gel electrophoresis and spectrophotometer respectively. Genotyping of the variants in PNPLA3 and TM6SF2 genes was carried out by employing taqman probes(C_15875080_10 for PNPLA3 and C_8946351_10 for TM6SF2 SNP) on real time PCR(Stepone-Lifetechnologies). Genotype data was tested for deviations from Hardy-Weinbergequilibrium. χ~2 test was used to analyze the statistical significance of the difference in genotype distribution of the studied variants in patients and controls and the strength of association was expressed as odds ratio(95%CI). A two-tailed P value of ≤ 0.05 was considered statistically significant. RESULTS The study group comprised of 503 individuals of which 256 had fatty infiltration and 247 without fatty infiltration and thus formed the patient and control groups respectively. As the patient group could be divided in to two distinct ethnicities(ancestral South Indians-ASI and North-East Indians-NEI), further recruitment of control cohort and association analyses was carried out based on ethnicities. Of the 256 with fatty infiltration 93 were ASI and 163 were NEI and of the 247 controls 138 were ASI and 109 were NEI. As expected, there were significant differences in the anthropometric and other clinical data between the control and the patient groups. However significant differences within the ethnicities were also noted. While rs2281135 in PNPLA3 gene was significantly associated(P = 0.03) with higher risk(odds 1.9, 95%CI: 1.5-3.14, P = 0.03) of NAFLD in NEI ethnicity, rs58542926 in TM6SF2 gene wa

关键词： Transmembrane 6 superfamily 2 Patatinlike phospholipase domain-containing protein 3 Fatty infiltration Genetic susceptibility Ethnicity Nonalcoholic fatty liver disease Cirrhosis Single nucleotide polymorphism

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SurePath、ThinPrep和传统细胞学3种方法常规筛查阴性后的宫颈癌发病率的研究：基于人群研究

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英国医学杂志中文版 2018年第3期21卷 177-177页

作者： Kirsten Rozemeijer steffie K Naber Corine Penning Lucy H Overbeek Caspar W N Looman Inge M C M de Kok Suzette M Matthijsse Matejka Rebolj Folkert J van Kemenade Marjolein van Ballegooijen 张雪芳王淑珍不详首都医科大学附属北京朝阳医院妇产科

摘要目的比较3种不同筛查方法即传统细胞学、液基细胞学（Sure Path和Thin Prep）检测阴性后72个月内宫颈癌的累积发病率。设计以人群为基础的回顾性队列研究。背景从2000年1月-2013年3月在荷兰全国范围内网络登记的有组织病理学或细... 详细信息

摘要目的比较3种不同筛查方法即传统细胞学、液基细胞学（Sure Path和Thin Prep）检测阴性后72个月内宫颈癌的累积发病率。设计以人群为基础的回顾性队列研究。背景从2000年1月-2013年3月在荷兰全国范围内网络登记的有组织病理学或细胞病理学情况的宫颈癌数据。

关键词：细胞学屏蔽学习人口癌症样品

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