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4区生物学

Advances in Genetics Pub Date : 2019-01-01 DOI: 10.1016/s0065-2660(19)30019-7

引用次数: 0

Preface. 前言。

4区生物学

Advances in Genetics Pub Date : 2019-01-01 DOI: 10.1016/S0065-2660(19)30022-7

Dhavendra Kumar

引用次数: 0

Multi-omics approaches for strategic improvement of stress tolerance in underutilized crop species: A climate change perspective. 从气候变化的角度，利用多组学方法战略性地改善未充分利用作物物种的抗逆性。

4区生物学

Advances in Genetics Pub Date : 2019-01-01 Epub Date: 2019-02-20 DOI: 10.1016/bs.adgen.2019.01.001

Mehanathan Muthamilarasan, Nagendra Kumar Singh, Manoj Prasad

{"title":"Multi-omics approaches for strategic improvement of stress tolerance in underutilized crop species: A climate change perspective.","authors":"Mehanathan Muthamilarasan, Nagendra Kumar Singh, Manoj Prasad","doi":"10.1016/bs.adgen.2019.01.001","DOIUrl":"https://doi.org/10.1016/bs.adgen.2019.01.001","url":null,"abstract":"For several decades, researchers are working toward improving the \"major\" crops for better adaptability and tolerance to environmental stresses. However, little or no research attention is given toward neglected and underutilized crop species (NUCS) which hold the potential to ensure food and nutritional security among the ever-growing global population. NUCS are predominantly climate resilient, but their yield and quality are compromised due to selective breeding. In this context, the importance of omics technologies namely genomics, transcriptomics, proteomics, phenomics and ionomics in delineating the complex molecular machinery governing growth, development and stress responses of NUCS is underlined. However, gaining insights through individual omics approaches will not be sufficient to address the research questions, whereas integrating these technologies could be an effective strategy to decipher the gene function, genome structures, biological pathways, metabolic and regulatory networks underlying complex traits. Given this, the chapter enlists the importance of NUCS in food and nutritional security and provides an overview of deploying omics approaches to study the NUCS. Also, the chapter enumerates the status of crop improvement programs in NUCS and suggests implementing \"integrating omics\" for gaining a better understanding of crops' response to abiotic and biotic stresses.","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":"103 ","pages":"1-38"},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.adgen.2019.01.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37084325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 47

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4区生物学

Advances in Genetics Pub Date : 2019-01-01 DOI: 10.1016/s0065-2660(19)30017-3

引用次数: 0

Finding a cure for tuberous sclerosis complex: From genetics through to targeted drug therapies. 寻找治疗结节性硬化症的方法:从遗传学到靶向药物治疗。

4区生物学

Advances in Genetics Pub Date : 2019-01-01 Epub Date: 2018-12-20 DOI: 10.1016/bs.adgen.2018.11.003

Lauren J McEneaney, Andrew R Tee

引用次数: 19

Association mapping in plants in the post-GWAS genomics era. 后gwas基因组时代的植物关联图谱。

4区生物学

Advances in Genetics Pub Date : 2019-01-01 Epub Date: 2019-01-22 DOI: 10.1016/bs.adgen.2018.12.001

Pushpendra K Gupta, Pawan L Kulwal, Vandana Jaiswal

{"title":"Association mapping in plants in the post-GWAS genomics era.","authors":"Pushpendra K Gupta, Pawan L Kulwal, Vandana Jaiswal","doi":"10.1016/bs.adgen.2018.12.001","DOIUrl":"https://doi.org/10.1016/bs.adgen.2018.12.001","url":null,"abstract":"With the availability of DNA-based molecular markers during early 1980s and that of sophisticated statistical tools in late 1980s and later, it became possible to identify genomic regions that control a quantitative trait. The two methods used for this purpose included quantitative trait loci (QTL) interval mapping and genome-wide association mapping/studies (GWAS). Both these methods have their own merits and demerits, so that newer approaches were developed in order to deal with the demerits. We have now entered a post-GWAS era, where either the original data on individual genotypes are being used again keeping in view the results of GWAS or else summary statistics obtained through GWAS is subjected to further analysis. The first half of this review briefly deals with the approaches that were used for GWAS, the GWAS results obtained in some major crops (maize, wheat, rice, sorghum and soybean), their utilization for crop improvement and the improvements made to address the limitations of original GWA studies (computational demand, multiple testing and false discovery, rare marker alleles, etc.). These improvements included the development of multi-locus and multi-trait analysis, joint linkage association mapping, etc. Since originally GWA studies were used for mere identification of marker-trait association for marker-assisted selection, the second half of the review is devoted to activities in post-GWAS era, which include different methods that are being used for identification of causal variants and their prioritization (meta-analysis, pathway-based analysis, methylation QTL), functional characterization of candidate signals, gene- and gene-set based association mapping, GWAS using high dimensional data through machine learning, etc. The last section deals with popular resources available for GWAS in plants in the post-GWAS era and the implications of the results of post-GWAS for crop improvement.","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":"104 ","pages":"75-154"},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.adgen.2018.12.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37070548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 80

Preface. 前言。

4区生物学

Advances in Genetics Pub Date : 2019-01-01 DOI: 10.1016/S0065-2660(19)30010-0

Dhavendra Kumar

引用次数: 0

The role of inherited genetic variants in colorectal polyposis syndromes. 遗传变异在结直肠息肉病综合征中的作用。

4区生物学

Advances in Genetics Pub Date : 2019-01-01 Epub Date: 2019-01-22 DOI: 10.1016/bs.adgen.2018.11.002

E Short, J Sampson

{"title":"The role of inherited genetic variants in colorectal polyposis syndromes.","authors":"E Short, J Sampson","doi":"10.1016/bs.adgen.2018.11.002","DOIUrl":"https://doi.org/10.1016/bs.adgen.2018.11.002","url":null,"abstract":"Colorectal carcinoma (CRC) is the third most common cancer in men and the second most common cancer in women across the world. Most CRCs occur sporadically, but in 15-35% of cases, hereditary factors are important. Some patients with an inherited predisposition to CRC will be diagnosed with a \"genetic polyposis syndrome\" such as familial adenomatous polyposis (FAP), MUTYH-associated polyposis (MAP), polymerase proofreading associated polyposis (PPAP), NTHL1-associated polyposis, MSH3-associated polyposis or a hamartomatous polyposis syndrome. Individuals with ≥10 colorectal polyps have traditionally been referred for genetic diagnostic testing to identify APC and MUTYH mutations which cause FAP and MAP respectively. Mutations are found in most patients with >100 adenomas but in only a minority of those with 10-100 adenomas. The reasons that diagnostic laboratories are not identifying pathogenic variants include mutations occurring outside of the open reading frames of genes, individuals exhibiting generalized mosaicism and the involvement of additional genes. It is important to identify patients with an inherited polyposis syndrome, and to define the mutations causing their polyposis, so that the individuals and their relatives can be managed appropriately.","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":"103 ","pages":"183-217"},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.adgen.2018.11.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37246212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Series Page 系列页面

4区生物学

Advances in Genetics Pub Date : 2019-01-01 DOI: 10.1016/s0065-2660(19)30005-7

引用次数: 0

Understanding human DNA variants affecting pre-mRNA splicing in the NGS era. 了解NGS时代影响前mrna剪接的人类DNA变异。

4区生物学

Advances in Genetics Pub Date : 2019-01-01 Epub Date: 2019-01-17 DOI: 10.1016/bs.adgen.2018.09.002

Luiz Gustavo Dufner-Almeida, Ramon Torreglosa do Carmo, Cibele Masotti, Luciana Amaral Haddad

{"title":"Understanding human DNA variants affecting pre-mRNA splicing in the NGS era.","authors":"Luiz Gustavo Dufner-Almeida, Ramon Torreglosa do Carmo, Cibele Masotti, Luciana Amaral Haddad","doi":"10.1016/bs.adgen.2018.09.002","DOIUrl":"https://doi.org/10.1016/bs.adgen.2018.09.002","url":null,"abstract":"Pre-mRNA splicing, an essential step in eukaryotic gene expression, relies on recognition of short sequences on the primary transcript intron ends and takes place along transcription by RNA polymerase II. Exonic and intronic auxiliary elements may modify the strength of exon definition and intron recognition. Splicing DNA variants (SV) have been associated with human genetic diseases at canonical intron sites, as well as exonic substitutions putatively classified as nonsense, missense or synonymous variants. Their effects on mRNA may be modulated by cryptic splice sites associated to the SV allele, comprehending exon skipping or shortening, and partial or complete intron retention. As splicing mRNA outputs result from combinatorial effects of both intrinsic and extrinsic factors, in vitro functional assays supported by computational analyses are recommended to assist SV pathogenicity assessment for human Mendelian inheritance diseases. The increasing use of next-generating sequencing (NGS) targeting full genomic gene sequence has raised awareness of the relevance of deep intronic SV in genetic diseases and inclusion of pseudo-exons into mRNA. Finally, we take advantage of recent advances in sequencing and computational technologies to analyze alternative splicing in cancer. We explore the Catalog of Somatic Mutations in Cancer (COSMIC) to describe the proportion of splice-site mutations in cis and trans regulatory elements. Genomic data from large cohorts of different cancer types are increasingly available, in addition to repositories of normal and somatic genetic variations. These are likely to bring new insights to understanding the genetic control of alternative splicing by mapping splicing quantitative trait loci in tumors.","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":"103 ","pages":"39-90"},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.adgen.2018.09.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37246213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 25