Natural variations and genome-wide association studies in crop plants pdf

Natural variations and genome-wide association studies in crop plants pdf
With the advent of rapid genotyping and next-generation sequencing technologies, genome-wide association study (GWAS) has become a routine strategy for decoding genotype-phenotype associations in many species.
A genome-wide association study (GWAS) is a new approach that involves rapidly scanning several hundred thousand (up to 5 millions) markers across the complete sets of DNA of many people to find genetic variations associated with a particular trait.
evolution in natural settings, descendent and antecedent conditions for crop plants are often both extant, providing opportunities for direct comparisons through crossing and …
use of natural variation in crop design and genome-wide selection (8, 30). ADVANCES IN CROP GENOME SEQUENCING The reference genome sequences of crops are the basis of crop genetic studies.
1 LARGE-SCALE BIOLOGY ARTICLE Genome-wide Association S. tudies. Reveal. the. Genetic. Basis. of. Ionomic. Variation. in. Rice. Meng. Yang. a, 1, Kai. Lu. a, d, 1
genome-wide association studies (GWAS), this analysis has iden- tified a comprehensive set of genes acting transcriptionally or post-transcriptionally in controlling seed protein composition.
crop breeding. Keywords: plant genetic resources; vegetable crops; horticulture; single nucleotide polymorphisms; genetic diversity; phenotyping; genome-wide association studies; genomic selection 1. The Use of Plant Genetic Resources in Vegetable Crop Improvement The main challenges for vegetable crop improvement are linked to the sustainable development of agriculture, food security
Genome-wide association studies (GWAS) have been even more successful in plants than in humans. Mapping approaches can be extended to dissect adaptive genetic variation from structured background variation in an ecological context. The genetic sources of phenotypic variation have been a …
Genome(Wide(Associa9on(Study((GWAS)((and(GBS(applica9on(in(Cereal(Crop(Plants(Definition of GWAS A genome-wide association study is defined as any study of genetic variation across the entire genome that is designed to identify genetic associations with observable traits (such as yield, height, disease) Association Mapping (AM) Linkage Disequilibrium mapping (LD mapping) Population …
Genome-wide association studies of five traits at the late booting stage measured by the RAP and five yield-related traits measured by the YTS. Certain loci were simultaneously detected for different traits.
On October 30th, the research group of Professor Tian Xingming from the Rice Science Team of the National Key Laboratory of Crop Genetic Improvement of our School of Life Science and Technology, published in the Plant Cell, “ Genetic basis of rice ionomic variation revealed by Genome-wide association studies“.
Recent studies, such as quantitative trait locus mapping, genome-wide association studies and whole-genome resequencing studies, have identified genes that are associated with the initial domestication and subsequent diversification of crops.
Abstract. In this chapter we will discuss genome wide association studies (GWAS) using SNP. GWAS present some challenges for biostatistics and bioinformatics—the sheer dimensionality of the data can create storage/retrieval and analysis problems.
Among all possible strategies using NGS data, we expect that genome-wide association studies (GWAS) have the most potential to revolutionize the field of phytopathology. In contrast to QTL mapping, GWAS use outbred populations to capture the standing genetic variation, thus characterizing the raw material for evolution. By examining the natural phenotypic and genetic variation, association
Salt is the major factor limiting crop productivity in saline soils and is controlled by various genes. The development of salt-tolerant rice through molecular breeding methods is important to meet the needs of rice breeding. We used 295 accessions to perform a genome-wide association study (GWAS
population for genome-wide association studies: theoretical consideration and genetic mapping of flowering traits in maize Hui Wang1, Cheng Xu1, Xiaogang Liu1, Zifeng Guo1, Xiaojie Xu 1, Shanhong Wang1, ChuanxiaoXie1, Wen-Xue Li1, Cheng Zou1 & Yunbi Xu1,2 Various types of populations have been used in genetics, genomics and crop improvement, including bi- and multi-parental populations …
Background. Improving the salt tolerance of direct-seeding rice at the seed germination stage is a major breeding goal in many Asian rice-growing countries, where seedlings must often establish in soils with a high salt content.
In genetics, a genome-wide association study (GWA study, or GWAS), also known as whole genome association study (WGA study, or WGAS), is an observational study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait.

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Population genomic and genome-wide association studies of
Genome Wide Association Studies SpringerLink
Studies (GWAS) Genome-wide Association Hands-on tutorial
Here, we first discuss crop genome studies and describe the development of sequencing-based genotyping and genome-wide association studies in crops. We then review sequencing-based crop domestication studies and offer a perspective on genomics-driven crop designs.
In addition, genome-wide association studies (GWAS) have been used to elucidate the genetic basis of agronomic traits in rice and maize . Nucleotide diversity scans ( 13 , 14 ) and association studies ( 5 , 15 ) have been carried out in sorghum, but the resolution and sensitivity of these studies has been limited by the small number of markers ( 14 ).
a Dep. of Agronomy, Iowa State Univ., Ames, IA 50011 b USDA-ARS, Corn Insects and Crop Genetics Research Unit, Dep. of Agronomy, Ames, IA 50011 c USDA-ARS, R.W. Holley Center for Agriculture and Health, Dep. of Plant Breeding and Genetics, Cornell Univ., Ithaca, NY 14853. Received 20 Jan. 2012
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Genetic Architecture of Natural Variation in Rice Chlorophyll Content Revealed by a Genome-Wide Association Study Quanxiu Wang 1, Weibo Xie , Hongkun Xing, Ju Yan, Xiangzhou Meng, Xinglei Li, Xiangkui Fu, Jiuyue Xu, Xingming Lian, Sibin Yu, Yongzhong Xing and Gongwei Wang* National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), …
Introduction to GWAS and MutMap for identification of
genome-wide association studies in plants Jie Luo The plant metabolome is the readout of plant physiological status and is regarded as the bridge between the genome and the phenome of plants. Unraveling the natural variation and the underlying genetic basis of plant metabolism has received increasing interest from plant biologists. Enabled by the recent advances in high-throughput profiling
Genome-wide association studies in plant pathosystems. Secondly, the 35 plant GWAS are not evenly distributed across the three classes of pathogenic organisms considered in this review (Table 1 ). Two thirds of the GWAS reported the mapping of resistance QTLs to fungal pathogens, whereas the remaining GWAS were split between bacterial pathogens ( n = 9) and oomycete pathogens ( n = 6).
Natural Variations and Genome-Wide Association Studies in Crop Plants Article· Literature Review in Annual Review of Plant Biology 65(1) · November 2013 with 482 Reads
Genome-wide association studies to dissect the genetic
First, due to breeders’ interest in incorporating natural genetic variation, crop GWAS tend to be conducted in large, diverse panels, providing lots of genetic variation to explore. Second, many of the selective agents that have shaped genetic diversity in crop plants are known, providing clear hypotheses to test. For example, maize has many fewer lateral branches than its wild progenitor
genome-wide association mapping. Most (58.5%) of the identified loci are supported Most (58.5%) of the identified loci are supported by expression QTLs, and …
Genome-Wide Association Studies Identified Three Independent Polymorphisms Associated with a-Tocopherol Content in Maize Kernels important crop plants, can not only better our understanding of the genetic mechanisms controlling tocopherol variations, but also provide invaluable information that may be applied directly to breeding. Maizeisanimportant sourceofanimalfeed,anditisalsoamain
Recently, genome-wide association studies have made significant contributions to facilitate the discovery of natural variation contributing to stress tolerance in crops. From these studies, the
Genome-wide association study (GWAS) has become a widely accepted strategy for decoding genotype-phenotype associations in many species thanks to advances in next-generation sequencing (NGS) technologies.
Over the last decade, genome-wide association studies (GWAS) have identified many loci controlling variation in quantitative traits in a variety of systems. In turn, increasingly sophisticated methods are being applied to population genomics datasets to infer the action of selection across the genome. Is it now possible to integrate population genetics and GWAS to evaluate which selective
the relatively high resolution of genome-wide association studies. Moreover, we detected Moreover, we detected novel significant associations on chromosomes 2, 3, and 6–10.
Genome Wide Study (GWAS) University of Pittsburgh
Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice Wanneng Yang1,2,3,4,*, Zilong Guo2,*,
Genome-wide Association Studies in Maize: Praise and Stargaze Yingjie Xiao 1 ,4, Haijun Liu , Liuji Wu2, Marilyn Warburton3 and Jianbing Yan1,* 1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
Through Genome-Wide Association Studies, we show that a large number of loci, including those that are involved in shattering in Arabidopsis, account for variation in shatter resistance in diverse B. napus germplasm. Our results indicate that genetic diversity for shatter resistance genes in B. napus is limited; many of the genes that might control this trait were not included during the
Status and Prospects of Association Mapping in Plants Chengsong Zhu, Michael Gore, Edward S. Buckler, and Jianming Yu* Abstract There is tremendous interest in using association mapping to identify genes responsible for quantitative variation of complex traits with agricultural and evolutionary importance. Recent advances in genomic technology, impetus to exploit natural diversity, and
The plant metabolome is the readout of plant physiological status and is regarded as the bridge between the genome and the phenome of plants. Unraveling the natural variation and the underlying genetic basis of plant metabolism has received increasing interest from plant biologists. – the bc principals vice principals association pdf association studies (GWAS), and pathway-level analysis to identify nine loci that impact the natural variation of seed carotenoids in Arabidopsis (Arabidopsis thaliana). ZEAXANTHIN EPOXIDASE (ZEP) was the major contributor to carotenoid
Appendix A Example QC Report for GWAS Data Over the following pages a fully automated quality control report for SNP data is illustrated. QC metrics are the same as those discussed in Chap.3.
Soybean exhibits natural variation in flower and seed coat colors via the deposition of various anthocyanin pigments in the respective tissues. Although pigmentation in seeds or flowers has been well dissected at molecular level in several plant
Yang, Jinliang, “Genome-wide association studies to dissect the genetic architecture of yield-related traits in maize and the genetic basis of heterosis” (2014). Graduate Theses and Dissertations . 14259.
Genome‐Wide Association Study (GWAS) Viji R. Avali Outline • Basic genetic concepts behind GWAS • Genotyping technologies and common study designs • Statistical concepts for GWAS analysis • Replication, interpretation and follow‐up of association results. 7/10/2014 2 Goal of GWAS • To use genetic risk factors to predict who is at risk • Identify the biological underpinnings of
Genomewide association studies (GWAS) that link molecular genetic information with phenotypic information have successfully been applied to detect causal mutations and to understand the genetic architecture of complex traits in both plants and animals, including humans (Rosenberg et al.
c Dep. of Plant, Soil and Microbial Sciences, Michigan State Univ., East Lansing, MI 48824 Abstract Genome-wide association studies (GWAS) are widely used in diploid species to study complex traits in diversity and breeding populations, but GWAS software tailored to autopolyploids is lacking.
Reference transcriptome assembly and annotation for perennial ryegrass Hiroshi Shinozuka, a Noel O.I. Cogan, a b German C. Spangenberg, a b John W. Forster a b a Agriculture Victoria, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia.
In the genomic era, whole genome sequencing combined with the development of statistical methods led to the emergence of Genome Wide Association (GWA) mapping, a powerful tool for detecting genomic regions associated with natural variation of disease resistance in both wild and cultivated plants. However, GWA mapping has been less employed for the detection of genetic variants associated …
Genome-wide association study (GWAS) is an effective method, which can associate phenotypes with genotypes in natural populations and reveal vast natural allelic variations and candidate genes based on linkage disequilibrium (LD), and have been widely used in crop plants, such as rice (Huang et al., 2010; Yano et al., 2016), maize (Li H. et al., 2013; Yang et al., 2014), and soybean (Zhang J
Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice. Authors: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China. Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques
Reference transcriptome assembly and annotation for
Natural Variations and Genome-Wide Association Studies in Crop Plants Natural Variations and Genome-Wide Association Studies in Crop Plants Huang, Xuehui; Han, Bin 2014-04-29 00:00:00 Natural variants of crops are generated from wild progenitor plants under both natural …
Here, we describe a genome-wide map of SNP variation, trace patterns of crop diffusion to diverse agroclimatic regions, and use GWAS to identify genes underlying natural variation in agroclimatic traits.
Introduction The genetic sources of phenotypic variation have been a major focus of both plant and animal studies aimed at identifying the causes of disease, improving agriculture
2010) analyses typically point to specific chromosomal sub‐regions, whereas the more recently developed genome‐wide association studies (GWASs) can identify precise chromosomal locations with the resolution to define specific genes or even polymorphisms within coding regions (Korte & …
Through Genome-Wide Association Studies, we show that a large number of loci, including those that are involved in shattering in Arabidopsis, account for variation in …
the plant genome november 2017 vol. 10, no. 3 1 of 14 original research Genome-Wide Association Mapping of Correlated Traits in Cassava: Dry Matter and Total Carotenoid Content
Seed size is variable within many plant species, and understanding the underlying genetic factors can provide insights into mechanisms of local environmental adaptation. Here we make use of the abundant genomic and germplasm resources available for rice (Oryza sativa) to perform a large-scale genome-wide association study (GWAS) of grain width.
potentially serve as candidates for studies of adaptive seed size variation in wild grass species. Key words: grain size, genome-wide association study (GWAS), General Linear Model (GLM), Mixed Linear Model (MLM), Oryza
The Plant Genome Abstract Original Research Software for
Genome-Wide Association Study Reveals Natural Variations
Genome‐wide association studies with proteomics data
genome-wide map of SNP variation, trace patterns of crop diffusion to diverse agroclimatic regions, and use GWAS to identify genes underlying natural variation in …
Genome-wide association studies (GWAS) have been even more successful in plants than in humans. Mapping approaches can be extended to dissect adaptive genetic variation from structured background variation in an ecological context.
(LD) and summarize published results on association studies in crop plant species. We give a list of different factors We give a list of different factors affecting LD, and discuss the current issues of LD research in plants.
ABSTRACT We investigated the natural variations in the flag leaf morphology of rice. We conducted a principal component analysis We conducted a principal component analysis based onnine flag leaf morphologytraits using103 accessions from the National Institute …
By combining genome-wide association mapping, linkage mapping in an experimental F2 population, and transgenic complementation, we reveal that HMA3 is the sole major locus responsible for the variation in leaf Cd accumulation we observe in this diverse population of A. thaliana accessions.
Abstract. Rice (Oryza sativa) is an important dietary source of both the essential micronutrients and the toxic trace elements to humans. The genetic basis underlying the variations in the mineral composition, the ionome, in rice remains largely unknown.
Metabolome-based genome-wide association study of maize
Development of a multiple-hybrid population for genome
Natural Variation in the Flag Leaf Morphology of Rice Due
Through Genome-Wide Association Studies, we show that a large number of loci, includ ing those that are involved in shattering in Arabidopsis, account for variation in …
High heritability and large variation of these traits was observed under drought stress in the natural population. A genome-wide association study (GWAS) of i-traits and traditional DR traits identified 470 association loci, some containing known DR-related genes. Of these 470 loci, 443 loci (94%) were identified using i-traits, 437 loci (93%) co-localized with previously reported DR-related
Introduction. Crop production is greatly influenced by environmental factors, such as temperature, photoperiod, and soil moisture. 1 One of the most important factors influencing plant growth is soil macronutrient uptake and utilization efficiency because plants cannot grow normally and survive without each of the macronutrients.
Hands-on tutorial to Genome-wide Association Studies (GWAS) Ümit Seren Exploring Plant Variation Data Workshop Jul. 1st-3rd 2015 trans-National Infrastructure for Plant Genomic Science
Genome-wide association study (GWAS) is a method for mapping the loci responsible for natural variations in a target phenotype by the identification of significantly associated genetic polymorphisms in a large population (Brachi et al., 2011; Weigel, 2012).
Genome-wide association studies in plants the missing

Genome-wide Association Studies in Maize cell.com

Genome-wide association study Wikipedia

Genome-wide association analysis identifies resistance

https://en.wikipedia.org/wiki/Association_Mapping
Genome-wide association study and gene set analysis for
american psychological association apa guidelines – Genome-Wide Association Studies Reveal Genetic Variation
genome wide association studies and genomic prediction
Association Genetics in Plant Pathogens Minding the Gap

Crop plants as models for understanding plant adaptation

Genome-wide association study of rice grain width variation

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Combining high-throughput phenotyping and genome-wide

Genome-wide association studies to dissect the genetic
Reference transcriptome assembly and annotation for

the plant genome november 2017 vol. 10, no. 3 1 of 14 original research Genome-Wide Association Mapping of Correlated Traits in Cassava: Dry Matter and Total Carotenoid Content
Genome-wide association studies in plant pathosystems. Secondly, the 35 plant GWAS are not evenly distributed across the three classes of pathogenic organisms considered in this review (Table 1 ). Two thirds of the GWAS reported the mapping of resistance QTLs to fungal pathogens, whereas the remaining GWAS were split between bacterial pathogens ( n = 9) and oomycete pathogens ( n = 6).
Genome-wide association study (GWAS) is a method for mapping the loci responsible for natural variations in a target phenotype by the identification of significantly associated genetic polymorphisms in a large population (Brachi et al., 2011; Weigel, 2012).
Among all possible strategies using NGS data, we expect that genome-wide association studies (GWAS) have the most potential to revolutionize the field of phytopathology. In contrast to QTL mapping, GWAS use outbred populations to capture the standing genetic variation, thus characterizing the raw material for evolution. By examining the natural phenotypic and genetic variation, association
Genome‐Wide Association Study (GWAS) Viji R. Avali Outline • Basic genetic concepts behind GWAS • Genotyping technologies and common study designs • Statistical concepts for GWAS analysis • Replication, interpretation and follow‐up of association results. 7/10/2014 2 Goal of GWAS • To use genetic risk factors to predict who is at risk • Identify the biological underpinnings of
Through Genome-Wide Association Studies, we show that a large number of loci, including those that are involved in shattering in Arabidopsis, account for variation in shatter resistance in diverse B. napus germplasm. Our results indicate that genetic diversity for shatter resistance genes in B. napus is limited; many of the genes that might control this trait were not included during the
In the genomic era, whole genome sequencing combined with the development of statistical methods led to the emergence of Genome Wide Association (GWA) mapping, a powerful tool for detecting genomic regions associated with natural variation of disease resistance in both wild and cultivated plants. However, GWA mapping has been less employed for the detection of genetic variants associated …
the relatively high resolution of genome-wide association studies. Moreover, we detected Moreover, we detected novel significant associations on chromosomes 2, 3, and 6–10.
Genome-wide Association Studies in Maize: Praise and Stargaze Yingjie Xiao 1 ,4, Haijun Liu , Liuji Wu2, Marilyn Warburton3 and Jianbing Yan1,* 1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
Introduction The genetic sources of phenotypic variation have been a major focus of both plant and animal studies aimed at identifying the causes of disease, improving agriculture
High heritability and large variation of these traits was observed under drought stress in the natural population. A genome-wide association study (GWAS) of i-traits and traditional DR traits identified 470 association loci, some containing known DR-related genes. Of these 470 loci, 443 loci (94%) were identified using i-traits, 437 loci (93%) co-localized with previously reported DR-related
Genome-Wide Association Studies Identified Three Independent Polymorphisms Associated with a-Tocopherol Content in Maize Kernels important crop plants, can not only better our understanding of the genetic mechanisms controlling tocopherol variations, but also provide invaluable information that may be applied directly to breeding. Maizeisanimportant sourceofanimalfeed,anditisalsoamain
Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice. Authors: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China. Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques
Genome(Wide(Associa9on(Study((GWAS)((and(GBS(applica9on(in(Cereal(Crop(Plants(Definition of GWAS A genome-wide association study is defined as any study of genetic variation across the entire genome that is designed to identify genetic associations with observable traits (such as yield, height, disease) Association Mapping (AM) Linkage Disequilibrium mapping (LD mapping) Population …
Abstract. In this chapter we will discuss genome wide association studies (GWAS) using SNP. GWAS present some challenges for biostatistics and bioinformatics—the sheer dimensionality of the data can create storage/retrieval and analysis problems.

32 Comments

  1. Author

    Among all possible strategies using NGS data, we expect that genome-wide association studies (GWAS) have the most potential to revolutionize the field of phytopathology. In contrast to QTL mapping, GWAS use outbred populations to capture the standing genetic variation, thus characterizing the raw material for evolution. By examining the natural phenotypic and genetic variation, association

    Genome-wide association studies to dissect the genetic

  2. Author

    population for genome-wide association studies: theoretical consideration and genetic mapping of flowering traits in maize Hui Wang1, Cheng Xu1, Xiaogang Liu1, Zifeng Guo1, Xiaojie Xu 1, Shanhong Wang1, ChuanxiaoXie1, Wen-Xue Li1, Cheng Zou1 & Yunbi Xu1,2 Various types of populations have been used in genetics, genomics and crop improvement, including bi- and multi-parental populations …

    Genome-wide association study and gene set analysis for
    Natural Variation in the Flag Leaf Morphology of Rice Due
    Genome-Wide Association Studies of Image Traits Reveal

  3. Author

    Recent studies, such as quantitative trait locus mapping, genome-wide association studies and whole-genome resequencing studies, have identified genes that are associated with the initial domestication and subsequent diversification of crops.

    Linkage disequilibrium genetic association mapping and
    Genome-Wide Association Studies In Plant Pathosystems
    What can genome‐wide association studies tell us about the

  4. Author

    Natural Variations and Genome-Wide Association Studies in Crop Plants Natural Variations and Genome-Wide Association Studies in Crop Plants Huang, Xuehui; Han, Bin 2014-04-29 00:00:00 Natural variants of crops are generated from wild progenitor plants under both natural …

    Genetic Basis of Natural Variation of Rice Ionomics Plantae
    Appendix A Example QC Report for GWAS Data Springer

  5. Author

    Hands-on tutorial to Genome-wide Association Studies (GWAS) Ümit Seren Exploring Plant Variation Data Workshop Jul. 1st-3rd 2015 trans-National Infrastructure for Plant Genomic Science

    Genome-Wide Delineation of Natural Variation for Pod

  6. Author

    Appendix A Example QC Report for GWAS Data Over the following pages a fully automated quality control report for SNP data is illustrated. QC metrics are the same as those discussed in Chap.3.

    Metabolite-based genome-wide association studies in plants
    genome wide association studies and genomic prediction
    Genome-wide association study of rice grain width variation

  7. Author

    genome-wide association studies in plants Jie Luo The plant metabolome is the readout of plant physiological status and is regarded as the bridge between the genome and the phenome of plants. Unraveling the natural variation and the underlying genetic basis of plant metabolism has received increasing interest from plant biologists. Enabled by the recent advances in high-throughput profiling

    Genome-wide Association Studies in Maize cell.com

  8. Author

    1 LARGE-SCALE BIOLOGY ARTICLE Genome-wide Association S. tudies. Reveal. the. Genetic. Basis. of. Ionomic. Variation. in. Rice. Meng. Yang. a, 1, Kai. Lu. a, d, 1

    Genome-Wide Association Studies In Plant Pathosystems

  9. Author

    Status and Prospects of Association Mapping in Plants Chengsong Zhu, Michael Gore, Edward S. Buckler, and Jianming Yu* Abstract There is tremendous interest in using association mapping to identify genes responsible for quantitative variation of complex traits with agricultural and evolutionary importance. Recent advances in genomic technology, impetus to exploit natural diversity, and

    Crop plants as models for understanding plant adaptation

  10. Author

    Reference transcriptome assembly and annotation for perennial ryegrass Hiroshi Shinozuka, a Noel O.I. Cogan, a b German C. Spangenberg, a b John W. Forster a b a Agriculture Victoria, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia.

    Crop Science Abstract dl.sciencesocieties.org

  11. Author

    potentially serve as candidates for studies of adaptive seed size variation in wild grass species. Key words: grain size, genome-wide association study (GWAS), General Linear Model (GLM), Mixed Linear Model (MLM), Oryza

    Natural Variations and Genome-Wide Association Studies in
    Genome-Wide Association Studies Reveal Genetic Variation
    ZEAXANTHIN EPOXIDASE Activity Potentiates Plant physiology

  12. Author

    use of natural variation in crop design and genome-wide selection (8, 30). ADVANCES IN CROP GENOME SEQUENCING The reference genome sequences of crops are the basis of crop genetic studies.

    Metabolome-genome-wide association study dissects genetic

  13. Author

    First, due to breeders’ interest in incorporating natural genetic variation, crop GWAS tend to be conducted in large, diverse panels, providing lots of genetic variation to explore. Second, many of the selective agents that have shaped genetic diversity in crop plants are known, providing clear hypotheses to test. For example, maize has many fewer lateral branches than its wild progenitor

    Genome-Wide Association Studies Reveal Genetic Variation
    Genome(Wide(Associa9on(Study( (GWAS)((and(GBS(applica9on

  14. Author

    Genome‐Wide Association Study (GWAS) Viji R. Avali Outline • Basic genetic concepts behind GWAS • Genotyping technologies and common study designs • Statistical concepts for GWAS analysis • Replication, interpretation and follow‐up of association results. 7/10/2014 2 Goal of GWAS • To use genetic risk factors to predict who is at risk • Identify the biological underpinnings of

    Reference transcriptome assembly and annotation for
    Population genomic and genome-wide association studies of

  15. Author

    Recent studies, such as quantitative trait locus mapping, genome-wide association studies and whole-genome resequencing studies, have identified genes that are associated with the initial domestication and subsequent diversification of crops.

    Natural Variations and Genome-Wide Association Studies in
    Genome-wide association studies in plants the missing

  16. Author

    Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice. Authors: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China. Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques

    REVIEW Genome-wide association studies in plants the
    “Population genomic and genome-wide association studies of
    Genetic Architecture of Natural Variation in Rice

  17. Author

    On October 30th, the research group of Professor Tian Xingming from the Rice Science Team of the National Key Laboratory of Crop Genetic Improvement of our School of Life Science and Technology, published in the Plant Cell, “ Genetic basis of rice ionomic variation revealed by Genome-wide association studies“.

    REVIEW Genome-wide association studies in plants the

  18. Author

    genome-wide association studies in plants Jie Luo The plant metabolome is the readout of plant physiological status and is regarded as the bridge between the genome and the phenome of plants. Unraveling the natural variation and the underlying genetic basis of plant metabolism has received increasing interest from plant biologists. Enabled by the recent advances in high-throughput profiling

    Introduction to GWAS and MutMap for identification of
    Metabolome-based genome-wide association study of maize

  19. Author

    Natural Variations and Genome-Wide Association Studies in Crop Plants Natural Variations and Genome-Wide Association Studies in Crop Plants Huang, Xuehui; Han, Bin 2014-04-29 00:00:00 Natural variants of crops are generated from wild progenitor plants under both natural …

    Metabolome-genome-wide association study dissects genetic
    Crop Science Abstract dl.sciencesocieties.org

  20. Author

    (LD) and summarize published results on association studies in crop plant species. We give a list of different factors We give a list of different factors affecting LD, and discuss the current issues of LD research in plants.

    Status and Prospects of Association Mapping in Plants
    Genome-Wide Association Studies Identify Heavy Metal
    Genome-Wide Association Studies Identified Three

  21. Author

    Appendix A Example QC Report for GWAS Data Over the following pages a fully automated quality control report for SNP data is illustrated. QC metrics are the same as those discussed in Chap.3.

    Genome-Wide Association Study Reveals Natural Variations
    Genome-Wide Delineation of Natural Variation for Pod
    Genome-wide Association Studies in Maize Praise and

  22. Author

    Genome-wide Association Studies in Maize: Praise and Stargaze Yingjie Xiao 1 ,4, Haijun Liu , Liuji Wu2, Marilyn Warburton3 and Jianbing Yan1,* 1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China

    Genome-Wide Association Study ScienceDirect.com

  23. Author

    Salt is the major factor limiting crop productivity in saline soils and is controlled by various genes. The development of salt-tolerant rice through molecular breeding methods is important to meet the needs of rice breeding. We used 295 accessions to perform a genome-wide association study (GWAS

    Crop plants as models for understanding plant adaptation

  24. Author

    Genome-wide association studies of five traits at the late booting stage measured by the RAP and five yield-related traits measured by the YTS. Certain loci were simultaneously detected for different traits.

    Genome-Wide Association Mapping of Correlated Traits in
    Genetic Basis of Natural Variation of Rice Ionomics Plantae

  25. Author

    Genome(Wide(Associa9on(Study((GWAS)((and(GBS(applica9on(in(Cereal(Crop(Plants(Definition of GWAS A genome-wide association study is defined as any study of genetic variation across the entire genome that is designed to identify genetic associations with observable traits (such as yield, height, disease) Association Mapping (AM) Linkage Disequilibrium mapping (LD mapping) Population …

    genome wide association studies and genomic prediction

  26. Author

    A genome-wide association study (GWAS) is a new approach that involves rapidly scanning several hundred thousand (up to 5 millions) markers across the complete sets of DNA of many people to find genetic variations associated with a particular trait.

    Population genomic and genome-wide association studies of
    Genome-wide Association Studies in Maize cell.com
    Increasing the power of genome wide association studies in

  27. Author

    The plant metabolome is the readout of plant physiological status and is regarded as the bridge between the genome and the phenome of plants. Unraveling the natural variation and the underlying genetic basis of plant metabolism has received increasing interest from plant biologists.

    Introduction to GWAS and MutMap for identification of
    Genome-wide delineation of natural variation for pod

  28. Author

    Over the last decade, genome-wide association studies (GWAS) have identified many loci controlling variation in quantitative traits in a variety of systems. In turn, increasingly sophisticated methods are being applied to population genomics datasets to infer the action of selection across the genome. Is it now possible to integrate population genetics and GWAS to evaluate which selective

    Genome-wide Association Studies in Maize cell.com

  29. Author

    Here, we describe a genome-wide map of SNP variation, trace patterns of crop diffusion to diverse agroclimatic regions, and use GWAS to identify genes underlying natural variation in agroclimatic traits.

    Natural Variations and Genome-Wide Association Studies in
    Metabolome-based genome-wide association study of maize

  30. Author

    genome-wide map of SNP variation, trace patterns of crop diffusion to diverse agroclimatic regions, and use GWAS to identify genes underlying natural variation in …

    Genome-wide delineation of natural variation for pod
    Genome-wide association study and gene set analysis for
    What can genome‐wide association studies tell us about the

  31. Author

    Reference transcriptome assembly and annotation for perennial ryegrass Hiroshi Shinozuka, a Noel O.I. Cogan, a b German C. Spangenberg, a b John W. Forster a b a Agriculture Victoria, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia.

    Genome-wide delineation of natural variation for pod
    Genome-Wide Association Studies Identify Heavy Metal

  32. Author

    Genome-wide association studies of five traits at the late booting stage measured by the RAP and five yield-related traits measured by the YTS. Certain loci were simultaneously detected for different traits.

    Genome Wide Association Studies SpringerLink

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