Status and prospects of genome-wide association studies in plants.

Published on Mar 1, 2021in The Plant Genome3.847
· DOI :10.1002/TPG2.20077
Laura E. Tibbs Cortes2
Estimated H-index: 2
(Iowa State University),
Zhiwu Zhang1
Estimated H-index: 1
(WSU: Washington State University)
+ 0 AuthorsJianming Yu49
Estimated H-index: 49
(Iowa State University)
Sources
Abstract
Genome-wide association studies (GWAS) have developed into a powerful and ubiquitous tool for the investigation of complex traits. In large part, this was fueled by advances in genomic technology, enabling us to examine genome-wide genetic variants across diverse genetic materials. The development of the mixed model framework for GWAS dramatically reduced the number of false positives compared with naive methods. Building on this foundation, many methods have since been developed to increase computational speed or improve statistical power in GWAS. These methods have allowed the detection of genomic variants associated with either traditional agronomic phenotypes or biochemical and molecular phenotypes. In turn, these associations enable applications in gene cloning and in accelerated crop breeding through marker assisted selection or genetic engineering. Current topics of investigation include rare-variant analysis, synthetic associations, optimizing the choice of GWAS model, and utilizing GWAS results to advance knowledge of biological processes. Ongoing research in these areas will facilitate further advances in GWAS methods and their applications.
Download
References123
Newest
#1Yunbi Xu (FOSU: Foshan University)H-Index: 54
#2Xiaogang Liu (CIMMYT: International Maize and Wheat Improvement Center)H-Index: 5
Last. Aimin Zhang (CAS: Chinese Academy of Sciences)H-Index: 1
view all 10 authors...
Abstract Although long term genetic gain has been achieved through increasing use of modern breeding methods and technologies, the rate of genetic gain needs to be accelerated to meet the human’s demand for agricultural products. In this regard, genomic selection (GS) has been considered most promising for genetic improvement of the complex traits controlled by many genes each with minor effects. Livestock scientists pioneered GS application largely due to livestock’s significantly higher indivi...
37 CitationsSource
#1Karl A. Kremling (Cornell University)H-Index: 11
#2Christine H. Diepenbrock (Cornell University)H-Index: 7
Last. Nonoy BandilloH-Index: 9
view all 5 authors...
Modern improvement of complex traits in agricultural species relies on successful associations of heritable molecular variation with observable phenotypes. Historically, this pursuit has primarily been based on easily measurable genetic markers. The recent advent of new technologies allows assaying and quantifying biological intermediates (hereafter endophenotypes) which are now readily measurable at a large scale across diverse individuals. The usefulness of endophenotypes for delineating the r...
25 CitationsSource
#1Hailin Pan (KIZ: Kunming Institute of Zoology)H-Index: 14
#2Theresa L. Cole (University of Otago)H-Index: 9
Last. Guojie ZhangH-Index: 76
view all 46 authors...
BACKGROUND: Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes close to the Cretaceous-Paleogene boundary (66 million years ago) and subsequently lost the ability to fly but enhanced their diving capabilities. With ∼20 species among 6 genera, penguins range from the tropical Galapagos Islands to the oceanic temperate forests of New Zealand, the...
91 CitationsSource
#1Torsten Pook (GAU: University of Göttingen)H-Index: 3
#2Martin Schlather (GAU: University of Göttingen)H-Index: 26
Last. Henner Simianer (GAU: University of Göttingen)H-Index: 8
view all 6 authors...
The concept of haplotype blocks has been shown to be useful in genetics. Fields of application range from the detection of regions under positive selection to statistical methods that make use of dimension reduction. We propose a novel approach (“HaploBlocker”) for defining and inferring haplotype blocks that focuses on linkage instead of the commonly used population-wide measures of linkage disequilibrium. We define a haplotype block as a sequence of genetic markers that has a predefined minimu...
14 CitationsSource
#1Lee T. Hickey (UQ: University of Queensland)H-Index: 23
#2Amber N. Hafeez (Norwich Research Park)H-Index: 2
Last. Brande B. H. Wulff (Norwich Research Park)H-Index: 32
view all 10 authors...
Crop improvements can help us to meet the challenge of feeding a population of 10 billion, but can we breed better varieties fast enough? Technologies such as genotyping, marker-assisted selection, high-throughput phenotyping, genome editing, genomic selection and de novo domestication could be galvanized by using speed breeding to enable plant breeders to keep pace with a changing environment and ever-increasing human population.
177 CitationsSource
#1Chenyong Miao (NU: University of Nebraska–Lincoln)H-Index: 10
#2Jinliang Yang (NU: University of Nebraska–Lincoln)H-Index: 13
Last. James C. Schnable (NU: University of Nebraska–Lincoln)H-Index: 32
view all 3 authors...
: Association studies use statistical links between genetic markers and the phenotype variation across many individuals to identify genes controlling variation in the target phenotype. However, this approach, particularly conducted on a genome-wide scale (GWAS), has limited power to identify the genes responsible for variation in traits controlled by complex genetic architectures. In this study, we employ real-world genotype datasets from four crop species with distinct minor allele frequency di...
15 CitationsSource
#1Erwang Chen (CAS: Chinese Academy of Sciences)H-Index: 3
#2Xuehui Huang (SHNU: Shanghai Normal University)H-Index: 29
Last. Bin Han (CAS: Chinese Academy of Sciences)H-Index: 72
view all 5 authors...
Here, we review recent progress in genetic and genomic studies of the diversity of Oryza species. In recent years, unlocking the genetic diversity of Oryza species has provided insights into the ge...
25 CitationsSource
#1Meng Huang (WSU: Washington State University)H-Index: 8
#2Xiaolei Liu (HAU: Huazhong Agricultural University)H-Index: 13
Last. Zhiwu Zhang (WSU: Washington State University)H-Index: 37
view all 5 authors...
: Big datasets, accumulated from biomedical and agronomic studies, provide the potential to identify genes that control complex human diseases and agriculturally important traits through genome-wide association studies (GWAS). However, big datasets also lead to extreme computational challenges, especially when sophisticated statistical models are employed to simultaneously reduce false positives and false negatives. The newly developed fixed and random model circulating probability unification (...
46 CitationsSource
#1Haijun Liu (HAU: Huazhong Agricultural University)H-Index: 40
#2Jianbing Yan (HAU: Huazhong Agricultural University)H-Index: 59
: 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. More than 1000 such studies over the last decade have revealed substantial genotype-phenotype associations in crops and provided unparalleled opportunities to probe functional genomics. Beyond the many 'hits' obtained, this review summarizes recent efforts to increase our understanding o...
62 CitationsSource
#2Pawan L. KulwalH-Index: 20
Last. Vandana Jaiswal (JNU: Jawaharlal Nehru University)H-Index: 13
view all 3 authors...
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 d...
27 CitationsSource
Cited By10
Newest
#1Merrick Lf (WSU: Washington State University)H-Index: 1
#2A. B. Burke (WSU: Washington State University)H-Index: 4
Last. Arron H. Carter (WSU: Washington State University)H-Index: 19
view all 4 authors...
Traits with an unknown genetic architecture make it difficult to create a useful bi-parental mapping population to characterize the genetic basis of the trait due to a combination of complex and pleiotropic effects. Seedling emergence of wheat (Triticum aestivum L.) from deep planting is a vital factor affecting stand establishment and grain yield, has a poorly understood genetic architecture, and is historically correlated with coleoptile length. The creation of bi-parental mapping populations ...
Source
#1Man Zhang (BFU: Beijing Forestry University)
#2Qingqing Yang (BFU: Beijing Forestry University)H-Index: 1
Last. Qixiang Zhang (BFU: Beijing Forestry University)H-Index: 22
view all 7 authors...
Prunus mume is one of the most important woody perennials for edible and ornamental use. Despite a substantial variation in the flowering phenology among the P. mume germplasm resources, the genetic control for flowering time remains to be elucidated. In this study, we examined five blooming time-related traits of 235 P. mume landraces for 2 years. Based on the phenotypic data, we performed genome-wide association studies, which included a combination of marker- and gene-based association tests,...
Source
#1Junghyun Shim (TTU: Texas Tech University)H-Index: 7
#2Nonoy Bandillo (NDSU: North Dakota State University)H-Index: 9
Last. Rosalyn B. Angeles-Shim (TTU: Texas Tech University)H-Index: 12
view all 3 authors...
The genetic uniformity of cultivated cotton as a consequence of domestication and modern breeding makes it extremely vulnerable to abiotic challenges brought about by major climate shifts. To sustain productivity amidst worsening agro-environments, future breeding objectives need to seriously consider introducing new genetic variation from diverse resources into the current germplasm base of cotton. Landraces are genetically heterogeneous, population complexes that have been primarily selected f...
Source
#1Xianran Li (Iowa State University)H-Index: 18
#2Tingting Guo (Iowa State University)H-Index: 9
Last. Jianming Yu (Iowa State University)H-Index: 49
view all 17 authors...
Abstract Identifying mechanisms and pathways involved in gene-environment interplay and phenotypic plasticity is a long-standing challenge. It is highly desirable to establish an integrated framework for complex trait dissection and prediction with an environmental dimension. A critical step was to identify an environmental index that is both biologically relevant and estimable for new environments. With extensive field-observed complex traits, environmental profiles, and genome-wide SNPs in thr...
2 CitationsSource
Source
#1Kimberly A. Reynolds (UTSW: University of Texas Southwestern Medical Center)H-Index: 11
#2Eduardo Rosa-Molinar (KU: University of Kansas)H-Index: 9
Last. A. Mark Settles (ARC: Ames Research Center)H-Index: 17
view all 6 authors...
The rapid expansion of genome sequence data is increasing the discovery of protein-coding genes across all domains of life. Annotating these genes with reliable functional information is necessary to understand evolution, to define the full biochemical space accessed by nature, and to identify target genes for biotechnology improvements. The vast majority of proteins are annotated based on sequence conservation with no specific biological, biochemical, genetic, or cellular function identified. R...
Source
#2Adam NunnH-Index: 1
Last. Stefan A. RensingH-Index: 60
view all 10 authors...
Bisulfite sequencing is a widely used technique for determining DNA methylation and its relationship with epigenetics, genetics, and environmental parameters. Various techniques were implemented for epigenome-wide association studies (EWAS) to reveal meaningful associations; however, there are only very few plant studies available to date. Here, we developed the EpiDiverse EWAS pipeline and tested it using two plant datasets, from P. abies (Norway spruce) and Q. lobata (valley oak). Hence, we pr...
Source
#1Idan Sabag (HUJI: Hebrew University of Jerusalem)
Last. Zvi PelegH-Index: 30
view all 3 authors...
Unrevealing the genetic makeup of crop morpho-agronomic traits is essential for improving yield quality and sustainability. Sesame (Sesamum indicum L.), one of the oldest oil-crops in the world, which despite its economical and agricultural importance, is an orphan crop-plant that undergone limited modern selection, thus, preserving wide genetic diversity. Here we harnessed this natural variation in a newly developed sesame panel (SCHUJI) to perform genome-wide association studies for morpho-agr...
Source
#1Zhiwu ZhangH-Index: 37
Last. Ben J. HayesH-Index: 83
view all 10 authors...
Source
#1Eiji Yamamoto (Meiji University)
#2Hiroshi Matsunaga (National Agriculture and Food Research Organization)H-Index: 13
Genotype-by-environment interactions (GEIs) are important for not only a precise understanding of genotype-phenotype relationships but also improving the environmental adaptability of crops. Although many formulae have been proposed to model GEI effects, a comprehensive comparison of their efficacy in genome-wide association studies (GWASs) has not been performed. Therefore, the advantages and disadvantages of the formulae are not well recognized. In this study, linear mixed models (LMMs) consis...
Source