Improvement of prediction ability for genomic selection of dairy cattle by including dominance effects. by Chuanyu Sun, Paul M VanRaden, John B Cole, Jeffrey R O'Connell

“…Additive and dominance variance components were estimated and then used to estimate additive and dominance effects of single nucleotide polymorphisms (SNPs). …”
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Mapping Quantitative Trait Loci (QTLs) for Reproductive Stage Salinity Tolerance in Rice by Yamini Deepthi Sugasi, Akanksha Srivastava, Jyothi Badri, Manish Pandey, Brajendra Parmar, Arun Kumar Singh, Polavarapu Bilhan Kavi Kishor, Ram Tilatoo

“…<i>qYLSt-12</i> with <b>an</b> LOD of 2.8 and a phenotypic variance (PV) of 6.4%, flanked by RM27940-RM27971, was identified for yield in moderate stress conditions. …”
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Uncovering the genetic basis of milk production traits in Mexican Holstein cattle based on individual markers and genomic windows. by José G Cortes-Hernández, Adriana García-Ruiz, Francisco Peñagaricano, Hugo H Montaldo, Felipe J Ruiz-López

“…The objective of this study was to evaluate the proportion of genetic variance explained by single nucleotide polymorphism markers, individually or clustered in 1, 2, and 5 Mb windows, for milk yield, fat yield, protein yield, fat content, protein content, and somatic cell score in Mexican Holstein cattle. …”
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Genome-wide identification and development of SSR molecular markers for genetic diversity studies in Ilex asprella by Jingchun Li, Jingchun Li, Changqian Quan, Rongchang Wei, Fan Wei, Qing Ma, Yuquan Huang, Meihua Xu, Danfeng Tang, Danfeng Tang

“…A total of 15 highly polymorphic primers were ultimately selected, including 13 dinucleotide primers and 2 trinucleotide primers. …”
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Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions. by Dmitry Shungin, Wei Q Deng, Tibor V Varga, Jian'an Luan, Evelin Mihailov, Andres Metspalu, GIANT Consortium, Andrew P Morris, Nita G Forouhi, Cecilia Lindgren, Patrik K E Magnusson, Nancy L Pedersen, Göran Hallmans, Audrey Y Chu, Anne E Justice, Mariaelisa Graff, Thomas W Winkler, Lynda M Rose, Claudia Langenberg, L Adrienne Cupples, Paul M Ridker, Nicholas J Wareham, Ken K Ong, Ruth J F Loos, Daniel I Chasman, Erik Ingelsson, Tuomas O Kilpeläinen, Robert A Scott, Reedik Mägi, Guillaume Paré, Paul W Franks

“…Phenotypic variance heterogeneity across genotypes at a single nucleotide polymorphism (SNP) may reflect underlying gene-environment (G×E) or gene-gene interactions. …”
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Genetic diversity and population structure analysis of Forsythia ovata, a Korean endemic, based on genotyping-by-sequencing. by Yoo-Bin Lee, Soonku So, Yoo-Jung Park, Halam Kang, Ha-Rim Lee, Jae-Hyeong Kim, Ho-Kwon Gwak, Kyung-Ah Kim, Kyeong-Sik Cheon

“…The analysis of molecular variance (AMOVA) results indicated that most genetic variation occurred within individuals, accounting for 86.66% of the total variance. …”
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Does ankylosing spondylitis exert a bidirectional influence on hypertension? A two-sample Mendelian randomization study by Weiran Hu, Kai Zhang, Guang Yang, Haoxu Wang, Yanzheng Gao

“…MR Egger regression, weighted median, inverse variance weighted, and weight mode methods were performed in the two-sample Mendelian randomization analysis. …”
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Mapping of the QTLs governing grain nutrients in wheat (Triticum aestivum L.) under nitrogen treatment using high-density SNP markers by Animireddy China Malakondaiah, Sudhir Kumar, Hari Krishna, Biswabiplab Singh, Sukumar Taria, Monika Dalal, R. Dhandapani, Lekshmy Sathee, Renu Pandey, Ranjeet Ranjan Kumar, Viswanathan Chinnusamy

“…According to recent studies, the optimum application of nitrogen (N) fertilizers can significantly enhance the micronutrient uptake and accumulation in wheat grains.MethodsThe aims of this study were to identify superior wheat recombinant inbred lines (RILs) of RAJ3765 × HD2329 with high nutrients in grain using the multi-trait genotype–ideotype distance index (MGIDI) and to identify quantitative trait loci (QTLs)/genes associated with grain nutrient content using a single-nucleotide polymorphism (SNP)-based genetic linkage map. The parents and their RIL population were grown under control and nitrogen-deficient (NT) conditions, and nutrient content was determined using inductively coupled plasma optical emission spectroscopy (ICP-OES).Results and discussionAnalysis of variance and descriptive statistics showed a significant difference among all the nutrients. …”
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Does uveitis increase the risk of age-related wet macular degeneration? A Mendelian randomization study by Rui-Hua Jing, Deng-Ke Zhou, Zhuo-Yan Yang, Zhao-Dan Ding, Jia-Hui Deng, Yao Xing, Xiao-Feng Chen

“…Besides, eight MR methods [inverse variance weighted (IVW), weighted median, MR-Egger regression, weighted mode, simple mode, robust adjusted profile score (RAPS), contamination inverse-variance weighted method, and debiased inverse-variance weighted method] were used to get the whole causal estimate for multiple instrumental single nucleotide polymorphism (SNPs). …”
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Chromosomal variations and genetic diversity in subpopulations of Senna alexandrina Mill. from Western Thar, India by Sunita Arora, Monika Vyas, Meena Barupal

“….), family Fabaceae which is known for its significant polymorphic variations. By observing chromosomal variances, we aimed to shed light on the underlying genetic variations responsible for the observed polymorphism. …”
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"Missing" G x E Variation Controls Flowering Time in Arabidopsis thaliana. by Eriko Sasaki, Pei Zhang, Susanna Atwell, Dazhe Meng, Magnus Nordborg

“…To identify the genetic polymorphisms underlying this variation, we conducted genome-wide scans using both SNPs and local variance components. …”
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Vitamin D levels and risk of type 1 diabetes: A Mendelian randomization study. by Despoina Manousaki, Adil Harroud, Ruth E Mitchell, Stephanie Ross, Vince Forgetta, Nicholas J Timpson, George Davey Smith, Constantin Polychronakos, J Brent Richards

“…In addition to the main analysis using inverse variance weighted MR, we applied 3 additional methods to control for pleiotropy (MR-Egger, weighted median, and mode-based estimate) and compared the respective MR estimates. …”
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Unveiling genetic basis of seedling emergence from deep soil depth under dry direct- seeded conditions in rice (Oryza sativa L.) by Vagish Mishra, Vagish Mishra, Shilpi Dixit, Shilpi Dixit, Swati Tyagi, Swati Tyagi, Challa Venkateswarlu, Challa Venkateswarlu, Pronob J. Paul, Pronob J. Paul, Anoop Kishor Singh Gurjar, Anoop Kishor Singh Gurjar, Shalabh Dixit, Nitika Sandhu, Smita Kurup, Arvind Kumar, Arvind Kumar, Pallavi Sinha, Pallavi Sinha, Vikas Kumar Singh, Vikas Kumar Singh, Uma Maheshwar Singh, Uma Maheshwar Singh

“…The mapping population was genotyped with mid-density SNP assay (1k-RiCA), and a linkage map was established with 414 polymorphic SNP markers. A total of 16 QTLs were identified for four traits, with phenotypic variance explained (PVE) ranging from 6.63% to 19.6% in the WS22. …”
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基于SSR分子标记的油棕遗传多样性 及群体遗传结构分析Analysis of genetic diversity and population genetic structure in oil palm based on SSR markers by 刘加能1,2，程秋如1,2，潘登浪1，李炜芳1，彭小芸1,2，周若茹1,2， 周丽霞3，曾宪海1,3，刘子凡1,2 LIU Jianeng1,2，CHENG Qiuru1,2，PAN Denglang1，LI Weifang1，PENG Xiaoyun1,2， ZHOU Ruoru1,2，ZHOU Lixia3，ZENG Xianhai1,3，LIU Zifan1,2

“…In order to provide reference for the exploration of excellent oil palm germplasm, 30 pairs of SSR primers were screened to detect and analyze the genetic diversity and population genetic structure of 605 oil palm germplasm resources.The results showed that the mean value of number of observed alleles (Na) was 11.933, the mean value of effective number of alleles (Ne) was 4.116, and the mean value of polymorphism information content (PIC) was 0.711 for the 30 pairs of SSR primers across all resources, indicating that SSR primers were highly polymorphic and rich in genetic diversity among germplasm. …”
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Assessment of the genetic diversity of cattle by marker genes of dairy productivity by Abramova M.V., Ilina A.V., Evdokimov E.G., Konovalov A.V., Mushtukova Yu.V.

“…Among the studied animals, the greatest genetic variance is accounted for by individual diversity - 82%. …”
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Cu²⁺ and Zn²⁺ Ions Affecting Biochemical Paths and DNA Methylation of Rye (<i>Secale cereale</i> L.) Anther Culture Influencing Plant Regeneration Efficiency by Wioletta Monika Dynkowska, Renata Orłowska, Piotr Waligórski, Piotr Tomasz Bednarek

“…Principal coordinate analysis explained 85% of the total variance based on sequence variation and 69% of the variance based on DNA methylation changes. …”
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Evaluation of the Association Between Postpartum Hemorrhage and Antidepressant Use: A Mendelian Randomization Study by Zhenzhen Chen, Qingqing Lv, Shiteng Lin, Wanlong Lin, Wei Zhuang

“…Results The analyses employed three sets of genetic tools, comprising two sets of 9 and 32 single nucleotide polymorphisms that are strongly associated with depression and another set of 26 single nucleotide polymorphisms that are associated with antidepressants. …”
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Pleiotropic Genes Affecting Milk Production, Fertility, and Health in Thai-Holstein Crossbred Dairy Cattle: A GWAS Approach by Akhmad Fathoni, Wuttigrai Boonkum, Vibuntita Chankitisakul, Sayan Buaban, Monchai Duangjinda

“…Genomic regions explaining at least 5% of the total genetic variance were selected for candidate gene analysis. …”
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Epigenetic age acceleration and allergic diseases: a bidirectional two-sample Mendelian randomization study by Junfang Sun, Guozhen Fan, Lixin Hu, Zheng Hai Qu, Hong Jiang

“…MR analysis was performed using inverse variance weighted, weighted median, and MR-Egger methods. …”
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Environment ensemble models for genomic prediction in common bean (Phaseolus vulgaris L.) by Isabella Chiaravallotti, Owen Pauptit, Valerio Hoyos‐Villegas

“…The optimized ensemble approach worked best for low‐variance locations because the model variance was reduced by averaging across submodels in the ensemble. …”
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