Quantitative Trait Loci Mapping, Genome-wide Association Analysis, and Gene Expression of Salt Tolerance in Soybean

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ISBN 13 :
Total Pages : 270 pages
Book Rating : 4.:/5 (14 download)

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Book Synopsis Quantitative Trait Loci Mapping, Genome-wide Association Analysis, and Gene Expression of Salt Tolerance in Soybean by : Ailan Zeng

Download or read book Quantitative Trait Loci Mapping, Genome-wide Association Analysis, and Gene Expression of Salt Tolerance in Soybean written by Ailan Zeng and published by . This book was released on 2016 with total page 270 pages. Available in PDF, EPUB and Kindle. Book excerpt: Salt stress is a common abiotic stress causing yield reduction in soybean. There are differential responses, namely tolerance (excluder) and intolerance (includer), among soybean germplasm. However, the genetic and physiological mechanism for salt tolerance is not clear. Identification of novel QTL for salt tolerance and genes that are differentially expressed under salt stress would help elucidate the salt tolerance mechanism and facilitate the development of salt tolerant cultivars through marker assisted selection (MAS). The objectives of this study were to identify new QTL or genes responsible for salt tolerance using three approaches: QTL mapping, association analysis, and RNA sequencing (RNA-seq). A salt-sensitive cultivar, RA-452, was crossed with a salt-tolerant cultivar, Osage, to develop an F4-derived QTL mapping population. Composite interval mapping (CIM) analysis indicated that a major chloride (Cl-)-tolerant QTL was confirmed and narrowed down on Chr. 3 in both NaCl and KCl treatments, a novel Cl--tolerant QTL on Chr. 15 was identified in NaCl treatment, and a novel Cl--tolerant QTL on Chr. 13 was identified in KCl treatment. Based on the results from the screening of the RA-452 x Osage mapping population, two F4:6 lines with extreme responses, most tolerant and most sensitive, were selected for a time-course gene expression study. A total of 2374, 998, 1746, and 630 differentially expressed genes (DEGs) between salt-tolerant line and salt-sensitive line, were found at 0, 6, 12, and 24 h, respectively. The gene expression profiles of six genes including Glyma.02G228100, Glyma.03G031400, Glyma.04G180300, Glyma.04G180400, Glyma.05G204600, and Glyma.17G173200 were verified by qRT-PCR. In addition, a total of 283 diverse germplasm lines were obtained from the Germplasm Resource Information Network (GRIN) and screened for salt stress response in greenhouse. A total of 33,009 SNPs across 283 genotypes were employed in the association analysis with leaf chloride concentration and leaf chlorophyll concentration. Association analysis results confirmed the salt-tolerance QTL on Chr. 3 and revealed eight new putative QTL on Chr. 2, 7, 8, 10, 13, 14, 16, and 20. These QTL and linked SNP markers will be useful for MAS in breeding salt-tolerant soybean varieties.

Genome-wide Association Mapping Identifies QTLS and Candidate Genes for Salt Tolerance in Soybean

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ISBN 13 : 9781303275005
Total Pages : 228 pages
Book Rating : 4.2/5 (75 download)

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Book Synopsis Genome-wide Association Mapping Identifies QTLS and Candidate Genes for Salt Tolerance in Soybean by : Lei Huang

Download or read book Genome-wide Association Mapping Identifies QTLS and Candidate Genes for Salt Tolerance in Soybean written by Lei Huang and published by . This book was released on 2013 with total page 228 pages. Available in PDF, EPUB and Kindle. Book excerpt: Salinity is a common abiotic stress causing soybean yield loss worldwide. Use of tolerant cultivars is an effective and economic approach to coping with this stress. Toward this, research is needed to identify salt-tolerant germplasm and better understand the genetic and molecular basis of salt tolerance in soybean. The objectives of this study were to identify salt-tolerant genotypes, to search for SNPs and QTLs associated with salt tolerance, and to identify candidate salt tolerance genes. A total of 192 diverse soybean lines and cultivars were screened for salt tolerance in the greenhouse based on visual leaf scorch scores after 15--18 days of 120 ml NaCl stress, among which 94 were tolerant while 87 were sensitive. These genotypes were further genotyped using the SoySNP50K iSelect BeadChip with 52,041 single nucleotide polymorphism (SNP) markers, among which 37,281 SNPs were polymorphic with minor allele frequency (MAF) > 5% and present in 75% of all genotypes. Genome-wide association mapping showed that 62 SNP markers representing 6 genomic regions on Chromosomes 2, 3, 5, 6, 8, and 18, respectively were significantly associated with salt tolerance (P

Genetics, Genomics, and Breeding of Soybean

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Publisher : CRC Press
ISBN 13 : 1439844666
Total Pages : 388 pages
Book Rating : 4.4/5 (398 download)

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Book Synopsis Genetics, Genomics, and Breeding of Soybean by : Kristin Bilyeu

Download or read book Genetics, Genomics, and Breeding of Soybean written by Kristin Bilyeu and published by CRC Press. This book was released on 2016-04-19 with total page 388 pages. Available in PDF, EPUB and Kindle. Book excerpt: The soybean is an economically important leguminous seed crop for feed and food products that is rich in seed protein (about 40 percent) and oil (about 20 percent); it enriches the soil by fixing nitrogen in symbiosis with bacteria. Soybean was domesticated in northeastern China about 2500 BC and subsequently spread to other countries. The enormous

The Soybean Genome

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Publisher : Springer
ISBN 13 : 3319641980
Total Pages : 216 pages
Book Rating : 4.3/5 (196 download)

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Book Synopsis The Soybean Genome by : Henry T. Nguyen

Download or read book The Soybean Genome written by Henry T. Nguyen and published by Springer. This book was released on 2017-09-20 with total page 216 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book examines the application of soybean genome sequences to comparative, structural, and functional genomics. Since the availability of the soybean genome sequence has revolutionized molecular research on this important crop species, the book also describes how the genome sequence has shaped research on transposon biology and applications for gene identification, tilling and positional gene cloning. Further, the book shows how the genome sequence influences research in the areas of genetic mapping, marker development, and genome-wide association mapping for identifying important trait genes and soybean breeding. In closing, the economic and botanical aspects of the soybean are also addressed.

Soybean molecular breeding and genetics

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Publisher : Frontiers Media SA
ISBN 13 : 2832519229
Total Pages : 351 pages
Book Rating : 4.8/5 (325 download)

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Book Synopsis Soybean molecular breeding and genetics by : Guo-Liang Jiang

Download or read book Soybean molecular breeding and genetics written by Guo-Liang Jiang and published by Frontiers Media SA. This book was released on 2023-03-29 with total page 351 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Quantitative Trait Loci (QTL) for Salt Tolerance in Soybean and Physiological Response to Salt Stress During Early Growth Stage

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ISBN 13 :
Total Pages : 226 pages
Book Rating : 4.:/5 (14 download)

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Book Synopsis Quantitative Trait Loci (QTL) for Salt Tolerance in Soybean and Physiological Response to Salt Stress During Early Growth Stage by : Cindy Massiel Lopez Ramirez

Download or read book Quantitative Trait Loci (QTL) for Salt Tolerance in Soybean and Physiological Response to Salt Stress During Early Growth Stage written by Cindy Massiel Lopez Ramirez and published by . This book was released on 2016 with total page 226 pages. Available in PDF, EPUB and Kindle. Book excerpt: Soybean is a major cash crop used as a source of high-quality protein and oil. Salt stress is one of the main abiotic stresses causing significant yield losses in soybean, which is considered a moderately salt-sensitive crop. Breeding selection is a promising strategy to improve salt tolerance as soybean germplasm display wide variation in response to salinity stress. However, the physiological and genetic mechanisms for salt tolerance are not quite clear. The discovery of novel QTL/genes associated with salt tolerance facilitates the development of tolerant cultivars through marker-assisted selection (MAS). The objectives of this study were: 1) identify/confirm QTL associated with salt tolerance, and 2) evaluate progressive shoot ion accumulation in sensitive/tolerant genotypes and leaf physiological changes induced by salt stress during early growth stage. For the first objective, QTL mapping was performed using an F2:3 population from Jake (tolerant) x Ozark (sensitive). A major QTL was found on chromosome 3 linked to four SNP loci in the same genomic region previously reported, explaining 37% to 49% of the phenotypic variation in LSS, PDP, leaf chlorophyll and leaf chloride content. Additionally, a new minor QTL linked with two SNP markers was identified on chromosome 19 explaining 5% of leaf chlorophyll variation. These QTL and linked SNP markers will be useful in MAS for salt tolerance. For the second objective, two sensitive (Desha, Ozark) and two tolerant (Jake, Lee) cultivars were treated with NaCl and KCl at 80 mM and 120 mM from stage V1 to V5. The most adverse effects on tolerant and susceptible varieties, was caused by KCl compared to NaCl stress. Under KCl treatment, the tolerance capacity of the excluders was severely inhibited causing early death, while under NaCl stress, tolerant varieties were able to accumulate up to 2.3 and 3.8 times less leaf Cl- and leaf Na+, respectively, than the sensitive ones. Plant death occurred when shoot ion concentration reached 80,000 mg/kg and 18,000 mg/kg of Cl- and Na+, respectively, under 120 mM NaCl. Under 120 mM KCl, plants died when leaf Cl- content reached 120,000 mg/kg and leaf K+ content was over 100,000 mg/kg.

Genetics and Genomics of Soybean

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Publisher : Springer Science & Business Media
ISBN 13 : 0387722998
Total Pages : 405 pages
Book Rating : 4.3/5 (877 download)

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Book Synopsis Genetics and Genomics of Soybean by : Gary Stacey

Download or read book Genetics and Genomics of Soybean written by Gary Stacey and published by Springer Science & Business Media. This book was released on 2008-05-07 with total page 405 pages. Available in PDF, EPUB and Kindle. Book excerpt: Soybean genomics is of great interest as one of the most economically important crops and a major food source. This book covers recent advances in soybean genome research, including classical, RFLP, SSR, and SNP markers; genomic and cDNA libraries; functional genomics platforms; genetic and physical maps; and gene expression profiles. The book is for researchers and students in plant genetics and genomics, plant biology and pathology, agronomy, and food sciences.

Molecular Aspects of Plant Salinity Stress and Tolerance

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Publisher : MDPI
ISBN 13 : 3036513809
Total Pages : 286 pages
Book Rating : 4.0/5 (365 download)

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Book Synopsis Molecular Aspects of Plant Salinity Stress and Tolerance by : Jen-Tsung Chen

Download or read book Molecular Aspects of Plant Salinity Stress and Tolerance written by Jen-Tsung Chen and published by MDPI. This book was released on 2021-09-08 with total page 286 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the advances in plant salinity stress and tolerance, including mechanistic insights revealed using powerful molecular tools and multi-omics and gene functions studied by genetic engineering and advanced biotechnological methods. Additionally, the use of plant growth-promoting rhizobacteria in the improvement of plant salinity tolerance and the underlying mechanisms and progress in breeding for salinity-tolerant rice are comprehensively discussed. Clearly, the published data have contributed to the significant progress in expanding our knowledge in the field of plant salinity stress and the results are valuable in developing salinity-stress-tolerant crops; in benefiting their quality and productivity; and eventually, in supporting the sustainability of the world food supply.

Soybean Improvement

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Publisher : Springer Nature
ISBN 13 : 3031122321
Total Pages : 278 pages
Book Rating : 4.0/5 (311 download)

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Book Synopsis Soybean Improvement by : Shabir Hussain Wani

Download or read book Soybean Improvement written by Shabir Hussain Wani and published by Springer Nature. This book was released on 2022-10-17 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: Soybean (Glycine max L. (Merr)) is one of the most important crops worldwide. Soybean seeds are vital for both protein meal and vegetable oil. Soybean was domesticated in China, and since last 4-5 decades it has become one of the most widely grown crops around the globe. The crop is grown on an anticipated 6% of the world’s arable land, and since the 1970s, the area in soybean production has the highest percentage increase compared to any other major crop. It is a major crop in the United States, Brazil, China and Argentina and important in many other countries. The cultivated soybean has one wild annual relative, G. soja, and 23 wild perennial relatives. Soybean has spread to many Asian countries two to three thousand years ago, but was not known in the West until the 18th century. Among the various constraints responsible for decrease in soybean yields are the biotic and abiotic stresses which have recently increased as a result of changing climatic scenarios at global level. A lot of work has been done for cultivar development and germplasm enhancement through conventional plant breeding. This has resulted in development of numerous high yielding and climate resilient soybean varieties. Despite of this development, plant breeding is long-term by nature, resource dependent and climate dependent. Due to the advancement in genomics and phenomics, significant insights have been gained in the identification of genes for yield improvement, tolerance to biotic and abiotic stress and increased quality parameters in soybean. Molecular breeding has become routine and with the advent of next generation sequencing technologies resulting in SNP based molecular markers, soybean improvement has taken a new dimension and resulted in mapping of genes for various traits that include disease resistance, insect resistance, high oil content and improved yield. This book includes chapters from renowned potential soybean scientists to discuss the latest updates on soybean molecular and genetic perspectives to elucidate the complex mechanisms to develop biotic and abiotic stress resilience in soybean. Recent studies on the improvement of oil quality and yield in soybean have also been incorporated.

Mechanisms of Abiotic Stress Responses and Tolerance in Plants: Physiological, Biochemical and Molecular Interventions, volume II

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Publisher : Frontiers Media SA
ISBN 13 : 2832535755
Total Pages : 631 pages
Book Rating : 4.8/5 (325 download)

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Book Synopsis Mechanisms of Abiotic Stress Responses and Tolerance in Plants: Physiological, Biochemical and Molecular Interventions, volume II by : Shabir Hussain Wani

Download or read book Mechanisms of Abiotic Stress Responses and Tolerance in Plants: Physiological, Biochemical and Molecular Interventions, volume II written by Shabir Hussain Wani and published by Frontiers Media SA. This book was released on 2023-10-09 with total page 631 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Advances in Statistical Methods for the Genetic Dissection of Complex Traits in Plants

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Publisher : Frontiers Media SA
ISBN 13 : 2832543693
Total Pages : 278 pages
Book Rating : 4.8/5 (325 download)

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Book Synopsis Advances in Statistical Methods for the Genetic Dissection of Complex Traits in Plants by : Yuan-Ming Zhang

Download or read book Advances in Statistical Methods for the Genetic Dissection of Complex Traits in Plants written by Yuan-Ming Zhang and published by Frontiers Media SA. This book was released on 2024-01-26 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genome-wide association studies (GWAS) have been widely used in the genetic dissection of complex traits. However, there are still limits in current GWAS statistics. For example, (1) almost all the existing methods do not estimate additive and dominance effects in quantitative trait nucleotide (QTN) detection; (2) the methods for detecting QTN-by-environment interaction (QEI) are not straightforward and do not estimate additive and dominance effects as well as additive-by-environment and dominance-by-environment interaction effects, leading to unreliable results; and (3) no or too simple polygenic background controls have been employed in QTN-by-QTN interaction (QQI) detection. As a result, few studies of QEI and QQI for complex traits have been reported based on multiple-environment experiments. Recently, new statistical tools, including 3VmrMLM, have been developed to address these needs in GWAS. In 3VmrMLM, all the trait-associated effects, including QTN, QEI and QQI related effects, are compressed into a single effect-related vector, while all the polygenic backgrounds are compressed into a single polygenic effect matrix. These compressed parameters can be accurately and efficiently estimated through a unified mixed model analysis. To further validate these new GWAS methods, particularly 3VmrMLM, they should be rigorously tested in real data of various plants and a wide range of other species.

Biotechnology and Omics Approaches for Bioenergy Crops

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Publisher : Springer Nature
ISBN 13 : 9819949548
Total Pages : 298 pages
Book Rating : 4.8/5 (199 download)

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Book Synopsis Biotechnology and Omics Approaches for Bioenergy Crops by : Muhammad Aasim

Download or read book Biotechnology and Omics Approaches for Bioenergy Crops written by Muhammad Aasim and published by Springer Nature. This book was released on 2023-11-29 with total page 298 pages. Available in PDF, EPUB and Kindle. Book excerpt: This edited book summarizes the efforts made to develop sustainable bioenergy production through different generations. The topics included in the book cover information about different bioenergy crops, their classification and use as biofuel, agronomic practices to improve biomass yield, classic breeding techniques, genetic diversity, current status and future perspective of bioenergy crops in the omics era. It also discusses application of modern biotechnological and molecular biotechnological techniques for the improvement of bioenergy crops this having enhanced biomass and plant based products. The book explores growing biofuel crops and their impact on environment, bioethics and biosafety issues related to the modern approaches. Another important aspect is the incorporation of nanotechnology for bioenergy crops and biofuel production. All book chapters are contributed renowned researchers in their respective field. This is a unique book covering the bioeneragy crops in the modern omics era. The book is useful for the researchers and post-graduate students to guide them in the field of bioenergy crops.

Soybean Seed Composition

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Publisher : Springer Nature
ISBN 13 : 3030829065
Total Pages : 638 pages
Book Rating : 4.0/5 (38 download)

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Book Synopsis Soybean Seed Composition by : Moulay Abdelmajid Kassem

Download or read book Soybean Seed Composition written by Moulay Abdelmajid Kassem and published by Springer Nature. This book was released on 2022-01-10 with total page 638 pages. Available in PDF, EPUB and Kindle. Book excerpt: Soybean Seed Composition covers three decades of advances in quantitative trait loci (QTL) mapping of seed protein, oil, fatty acids, amino acids, sugars, mineral nutrients, isoflavones, lunasin, and other beneficial compounds. It opens with coverage of seed protein, oil, fatty acids, and amino acids and the effects that genetic and environmental factors have on them. Detailed discussion of QTL that control seed protein, oil, and fatty acids follows, and the book also covers seed amino acids, macronutrients, micronutrients, sugars, and other compounds that are key to selection for crop improvement. The book also provides an overview of two decades of QTL mapping of mineral deficiencies in soybean, which sheds light on the importance of a balanced mineral nutrition in soybean and other crops, elucidates salt stress tolerance QTL mapping, which is another challenge that faces soybean and other crop production worldwide. The importance of soybean seed isoflavones from their biosynthesis and quantification methods to locations and variations in seeds, roots, and leaves, to their QTL mapping is discussed, as well as providing key information on lunasin, a bioactive anticancer peptide in soybean seeds that will help farmers and breeders to develop soybean cultivars with improved seed isoflavones and lunasin content. The book will be of interest to graduate students, academics, and researchers in the fields of genetic and QTL mapping of important agronomic traits in soybean and other crops.

Genotyping by Sequencing for Crop Improvement

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Publisher : John Wiley & Sons
ISBN 13 : 1119745675
Total Pages : 404 pages
Book Rating : 4.1/5 (197 download)

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Book Synopsis Genotyping by Sequencing for Crop Improvement by : Humira Sonah

Download or read book Genotyping by Sequencing for Crop Improvement written by Humira Sonah and published by John Wiley & Sons. This book was released on 2022-03-29 with total page 404 pages. Available in PDF, EPUB and Kindle. Book excerpt: OGENOTYPING BY SEQUENCING FOR CROP IMPROVEMENT A thoroughly up-to-date exploration of genotyping-by-sequencing technologies and related methods in plant science In Genotyping by Sequencing for Crop Improvement, a team of distinguished researchers delivers an in-depth and current exploration of the latest advances in genotyping-by-sequencing (GBS) methods, the statistical approaches used to analyze GBS data, and its applications, including quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS) in crop improvement. This edited volume includes insightful contributions on a variety of relevant topics, like advanced molecular markers, high-throughput genotyping platforms, whole genome resequencing, QTL mapping with advanced mapping populations, analytical pipelines for GBS analysis, and more. The distinguished contributors explore traditional and advanced markers used in plant genotyping in extensive detail, and advanced genotyping platforms that cater to unique research purposes are discussed, as is the whole-genome resequencing (WGR) methodology. The included chapters also examine the applications of these technologies in several different crop categories, including cereals, pulses, oilseeds, and commercial crops. Genotyping by Sequencing for Crop Improvement also offers: A thorough introduction to molecular marker techniques and recent advancements in the technology Comprehensive explorations of the genotyping of seeds while preserving their viability, as well as advances in genomic selection Practical discussions of opportunities and challenges relating to high throughput genotyping in polyploid crops In-depth examinations of recent advances and applications of GBS, GWAS, and GS in cereals, pulses, oilseeds, millets, and commercial crops Perfect for practicing plant scientists with an interest in genotyping-by-sequencing technology, Genotyping by Sequencing for Crop Improvement will also earn a place in the libraries of researchers and students seeking a one-stop reference on the foundational aspects of – and recent advances in – genotyping-by-sequencing, genome-wide association studies, and genomic selection.

Genome-wide Analyses for Partial Resistance to Phytophthora Sojae Kaufmann and Gerdemann in Soybean (glycine Max L. Merr.) Populations from North America and the Republic of Korea

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ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (913 download)

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Book Synopsis Genome-wide Analyses for Partial Resistance to Phytophthora Sojae Kaufmann and Gerdemann in Soybean (glycine Max L. Merr.) Populations from North America and the Republic of Korea by : Rhiannon N. Schneider

Download or read book Genome-wide Analyses for Partial Resistance to Phytophthora Sojae Kaufmann and Gerdemann in Soybean (glycine Max L. Merr.) Populations from North America and the Republic of Korea written by Rhiannon N. Schneider and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Phytophthora root and stem rot of soybean (Glycine max) is caused by the oomycete pathogen Phytophthora sojae. This disease can be controlled by genetic resistance, but can cause devastating yield losses in fields planted with susceptible soybean cultivars and results in losses of around $300 million annually in the US. Partial resistance is considered to be more durable against P. sojae than race-specific resistance conferred by Rps genes and is theoretically effective against all races of this pathogen. Evaluation of a historical set of public cultivars representing 80 years of soybean breeding indicated that there have been genetic gains for partial resistance; however, these gains may have begun to plateau in the 1970s to early 1980s. Cultivars developed in Ohio generally have high levels of partial resistance to P. sojae; however, there is little known about the genetic regions associated with the partial resistance. Further improvement of increasing partial resistance could be achieved through the introgression of known quantitative trait loci (QTL) from plant introductions from the Republic of Korea (South Korea), which contain high levels of partial resistance. From an analysis of 1,398 plant introductions with a wide range of phenotypic expression of resistance, sixteen single nucleotide polymorphisms (SNPs) were associated with partial resistance to P. sojae. These SNPs were located in three genomic regions, or QTL, on chromosomes 3, 13, and 19. The QTL on chromosome 19 represented a novel locus, whereas the QTL on chromosomes 3 and 13 were coincident with previously identified QTL for partial resistance and/or Rps genes. In contrast, a genome-wide association study carried out in Ohio breeding lines was unable to detect any significant marker-trait associations, limiting the ability to use marker assisted selection to improve partial resistance in this population. However, genomic selection (GS) was shown to be a promising means of selection, with efficiencies relative to phenotypic selection of 0.5 to 1. Importantly, GS can be implemented through use of multi-trait indices which include yield. As exotic germplasm with high levels of partial resistance are identified, GS may be a valuable tool for utilizing exotic sources of partial resistance to P. sojae while maintaining or improving yield.

Statistical Methods for Integrating Quantitative Trait Loci Annotation in Post-gwas Analysis

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Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (14 download)

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Book Synopsis Statistical Methods for Integrating Quantitative Trait Loci Annotation in Post-gwas Analysis by : Kunling Huang

Download or read book Statistical Methods for Integrating Quantitative Trait Loci Annotation in Post-gwas Analysis written by Kunling Huang and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent advances in large-scale genome-wide association studies (GWAS) have highlighted the involvement of common genetic variants in complex traits and diseases. Data integration efforts linking GWAS signals with functional annotation data have provided insights into the genetic architecture of numerous human complex traits. For example, expression quantitative trait loci (eQTL) studies in relevant biological tissues provide gene candidates for complex diseases, which can be tested as therapeutic targets. Integrating multi-omics annotation data with GWAS association data brings in orthogonal information and improves the understanding of complex trait etiology. In this dissertation, we present two approaches to link genomic annotations to genotype-phenotype associations identified through GWAS. The two approaches both associate complex traits with genetically imputed molecular traits (i.e., gene expression levels and metabolite levels), and identify regulatory and metabolic machineries underlying a variety of complex traits.We start with integrating eQTLs with autism spectrum disorder (ASD) in parent-offspring trios by quantifying the transmission disequilibrium of genetically regulated gene expression from parents to offspring and performing transcriptome-wide association studies (TWAS). We identify transcription factor POU3F2 in our analysis. POU3F2 mainly expresses in developmental brain and the gene targets regulated by POU3F2 are enriched for known risk genes for ASD and loss-of-function de novo mutations in ASD probands. TWAS suggests that ASD genes affected by very rare mutations may be regulated by an unlinked transcription factor affected by common genetic variations. Next, we extend our TWAS framework to study the regulatory roles of metabolite quantitative trait loci (mQTL). We introduce metabolome-wide association study (MWAS), which integrates metabolomics data with genetics data. We benchmarked and optimized genetic prediction models for a total of 703 metabolites from cerebrospinal fluid, plasma, and urine, and performed a biobank-wide association scan between imputed metabolite levels and 530 complex traits in UK Biobank. We found a total of 1,311 significant metabolite-trait associations after performing Bonferroni correction across all tested associations. The significant MWAS results explain the difference in human body fat mass and body fat-free mass. In summary, we perform joint analysis on eQTL/mQTL data and complex trait GWAS to identify genes or metabolites relevant to complex traits. Our approaches improve our understanding of the phenotypic outcomes of non-coding genetic variations and may contribute to novel biomarker discovery, clinical diagnosis improvement, and therapeutics development.

Quantitative Trait Linkage Analysis of S.Cerevisiae Gene Expression Data

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Publisher :
ISBN 13 :
Total Pages : 268 pages
Book Rating : 4.:/5 ( download)

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Book Synopsis Quantitative Trait Linkage Analysis of S.Cerevisiae Gene Expression Data by : Xinping Cui

Download or read book Quantitative Trait Linkage Analysis of S.Cerevisiae Gene Expression Data written by Xinping Cui and published by . This book was released on 2002 with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt: