Genome-wide Association Studies in Maize: Praise and Stargaze

Xiao, Yingjie; Liu, Haijun; Wu, Liuji; Warburton, Marilyn L.; Yan, Jianbing

doi:10.1016/j.molp.2016.12.008

Cited by 340 publications

(277 citation statements)

References 161 publications

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“…In contrast, QTL mapping in biparental populations derived from crosses between flint and popcorn lines has higher power to detect the effects of genomic regions carrying causal variants due to the lack of population structure in randomly derived mapping lines. The resolution of GWAS associations, however, can be much higher than typical QTL support intervals (Korte and Farlow, 2013; Xiao et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

Genomic‐Wide Association Study of Popping Expansion in Tropical Popcorn and Field Corn Germplasm

Senhorinho¹,

Coan²,

Marino

et al. 2019

Crop Science

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Popcorn is a popular snack food with higher grain value compared with “field corn” maize (Zea mays L.). In general, popcorn germplasm is less improved than common maize cultivars, with less favorable agronomic performance and greater susceptibility to pests, diseases, and lodging, especially in tropical environments. One approach to expanding and improving popcorn germplasm is to introduce favorable alleles for agronomic performance from field corn. If markers tagging quantitative trait loci (QTLs) associated with popping expansion were identified, they could be selected with markers to maintain popping expansion in breeding populations derived from crosses between field and popcorn germplasm. The objectives of this study were to identify single nucleotide polymorphism (SNP) markers and putative candidate genes associated with higher popping expansion in a diverse sample of popcorn and field corns relevant to Brazilian breeding programs. We applied a comprehensive genome‐wide association study (GWAS) for popping expansion, using 165,089 SNP markers in 183 inbred lines with 2 yr of trial data. Four SNPs were significantly associated with popping expansion, three of which were colocalized to previously reported meta‐QTLs, and one that was novel. Annotated genes closely linked to the associated SNPs were identified with functions related with starch content, which plays an important role in popping expansion quality. If these associations can be validated independently, they can be useful for breeders to select agronomically superior genotypes with greater popping expansion.

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Section: Discussionmentioning

confidence: 99%

Genomic‐Wide Association Study of Popping Expansion in Tropical Popcorn and Field Corn Germplasm

Senhorinho¹,

Coan²,

Marino

et al. 2019

Crop Science

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“…Selection of lines to be used in breeding programs can be optimized by understanding the genetic architecture of the trait, allowing breeders to better determine which elite lines to use in crosses (Massman et al, 2011; Xiao et al, 2017). A GWAS provides information such as the number of genes involved in controlling a trait and the effects of the SNP (Schmid and Bennewitz, 2017).…”

Section: Discussionmentioning

confidence: 99%

GWAS for Fusarium Head Blight Traits in a Soft Red Winter Wheat Mapping Panel

2019

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Fusarium head blight (FHB) is an important disease of wheat (Triticum aestivum L.) that has caused billions of dollars in losses in recent decades. Although a massive breeding effort has been undertaken on multiple continents, there are no wheat cultivars with immunity to the disease. Resistance is conditioned by multiple loci and is further complicated by the role of the environment in expression of the disease phenotype. The objectives of our study were (i) to evaluate the phenotypic response to FHB in a large, diverse soft red winter wheat mapping panel; and (ii) to identify promising quantitative trait loci (QTL) associated with FHB resistance based on a genome‐wide association study (GWAS). We evaluated the mapping panel in 2014–2015 and 2015–2016 in an irrigated, inoculated scab nursery near Lexington, KY. Traits evaluated were heading date, plant height, FHB rating, severity, incidence, index, Fusarium‐damaged kernels (FDK), and deoxynivalenol (DON). There were significant (p < 0.05) differences among genotypes for all traits measured. The GWAS (based on 2‐yr entry means) identified 16 significant (p < 0.001) single nucleotide polymorphisms (SNPs) associated with disease traits on multiple chromosomes. Single nucleotide polymorphism association ranged from −2.14 to 4.01% of the mean of a given trait. We detected SNPs associated with FDK and DON on chromosomes 4A, 5B and 6B, and these SNPs decreased DON levels by 1.5, 2.1 and 3.2 mg kg−1, respectively. Our study demonstrated that even small‐effect QTL can potentially decrease disease levels and thus be useful in breeding programs.

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“…For example, a nested association mapping populations (NAM) of maize, derived from crosses between a reference line and other founder inbreds, have been used in GWAS of developmental traits and resistance to pathogens with improved mapping resolution (Kump et al ., ; Poland et al ., ; Tian et al ., ; Li et al ., ; Wu et al ., ). However, the extremely unbalanced parental compositions might dilute the GWAS efficiency (Xiao et al ., ). To thoroughly intercross and effectively balance the contributions of all founder lines, the advanced generation intercross (MAGIC) populations of rice were established in various species (Kover et al ., ; Huang et al ., ; Bandillo et al ., ; Dell'Acqua et al ., ; Islam et al ., ).…”

Section: The Development Of Gwasmentioning

confidence: 97%

Metabolic GWAS‐based dissection of genetic bases underlying the diversity of plant metabolism

2018

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Plants have served as sources providing humans with metabolites for food and nutrition, biomaterials for living, and treatment for pain and disease. Plants produce a huge array of metabolites, with an immense diversity at both the population and individual levels. Dissection of the genetic bases for metabolic diversity has attracted increasing research attention. The concept of genome-wide association study (GWAS) was extended to studies on the diversity of plant metabolome that benefitted from the development of mass-spectrometry-based analytical systems and genome sequencing technologies. Metabolic genome-wide association study (mGWAS) is one of the most powerful tools for global identification of genetic determinants for diversity of plant metabolism. Recently, mGWAS has been performed for various species with continuous improvements, providing deeper insights into the genetic bases of metabolic diversity. In this review, we discuss fully the achievements to date and remaining challenges that are associated with both mGWAS and mGWAS-based multi-dimensional analysis. We begin with a summary of GWAS and its development based on statistical methods and populations. As variation in targeted traits is essential for GWAS, we review metabolic diversity and its rise at both the population and individual levels. Subsequently, the application of mGWAS for plants and its corresponding achievements are fully discussed. We address the current knowledge on mGWAS-based multi-dimensional analysis and emerging insights into the diversity of metabolism.

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Genome-wide Association Studies in Maize: Praise and Stargaze

Cited by 340 publications

References 161 publications

Genomic‐Wide Association Study of Popping Expansion in Tropical Popcorn and Field Corn Germplasm

Genomic‐Wide Association Study of Popping Expansion in Tropical Popcorn and Field Corn Germplasm

GWAS for Fusarium Head Blight Traits in a Soft Red Winter Wheat Mapping Panel

Metabolic GWAS‐based dissection of genetic bases underlying the diversity of plant metabolism

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