Genome-wide association study (GWAS) of resistance to head smut in maize

Ming, Wang; Yan, Jianbing; Zhao, Jiuran; Song, Wei; Zhang, Xiaobo; Xiao, Yanan; Zheng, Yanyan

doi:10.1016/j.plantsci.2012.08.004

Cited by 148 publications

(102 citation statements)

References 43 publications

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“…False-positive associations are indispensable when different models are used to detect genotype-phenotype associations in plant GWAS [31, 47, 66, 67]. Therefore, we compared six models for their ability to reduce the number of false positives in association mapping of this panel (Additional file 2: Figure S4), and found that the observed P -values fit best to the expected P -values using the K + PCA model (Additional file 2: Figure S5), suggesting that the K + PCA model was most efficient at controlling for false-positives, in accordance with previous reports [43, 47, 68, 69]. …”

Section: Discussionsupporting

confidence: 85%

Genome-wide association mapping and Identification of candidate genes for fatty acid composition in Brassica napus L. using SNP markers

Jia

et al. 2017

BMC Genomics

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Background B. napus (oilseed) is an important source of edible vegetable oil, and its nutritional and economic value is determined by its fatty acid composition and content.ResultsUsing the Brassica 60 K SNP array, we performed a genome-wide association study of fatty acid composition in a population of 520 genetically diverse oilseed accessions. Using the PCA + K model in TASSEL 5.2.1, we identified 62 genomic regions that were significantly associated with the composition of seven fatty acids, and five consensus regions that mapped to the A2, A8, A9, C1, and C3 chromosomes, respectively, of the Brassica napus Darmor-bzh genome. We then identified 24 orthologs of the functional candidate genes involved in fatty acid biosynthesis, excluding BnaA.FAE1 and BnaC.FAE1 on the A8 and C3 homologous genome blocks, which are known to have critical roles in the fatty acid biosynthesis pathway, and potential orthologs of these genes (e.g., LACS9, KCR1, FAB1, LPAT4, KCS17, CER4, TT16, and ACBP5).ConclusionsOur results demonstrate the power of association mapping in identifying genes of interest in B. napus and provide insight into the genetic basis of fatty acid biosynthesis in B. napus. Furthermore, our findings may facilitate marker-based breeding efforts aimed at improving fatty acid composition and quality in B. napus.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3607-8) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 85%

Genome-wide association mapping and Identification of candidate genes for fatty acid composition in Brassica napus L. using SNP markers

Jia

et al. 2017

BMC Genomics

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“…As maize has high genetic diversity and rapid LD decay, GWAS has been successfully used to analyse the genetic architecture of many complex traits, such as resistance to head smut31, oil biosynthesis32, seedling root development33, and resistance to northern corn leaf blight34. In the present study, 57 SNPs related to 43 genes were detected in association with resistance to FSR.…”

Section: Discussionmentioning

confidence: 65%

Dissecting the genetic architecture of Fusarium verticillioides seed rot resistance in maize by combining QTL mapping and genome-wide association analysis

Jun

Zhou

et al. 2017

Sci Rep

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Fusarium verticillioides can be transmitted via seeds and cause systemic infection in maize (Zea mays L.); its mycotoxin has harmful effects on animal and human health. We combined QTL mapping in recombinant inbred line (RIL) populations with a genome-wide association study (GWAS) of 217 diverse maize lines using 224,152 single nucleotide polymorphisms (SNPs) under controlled conditions to determine the genetic architecture of F. verticillioides seed rot (FSR) resistance. Our study identified 8 quantitative trait loci (QTLs) and 43 genes associated with 57 SNPs that were correlated with FSR resistance through linkage mapping and GWAS, respectively. Among these, there were three candidate genes, namely GRMZM2G0081223, AC213654.3_FG004, and GRMZM2G099255, which were detected in both linkage mapping and GWAS. Furthermore, the near-isogenic lines (NILs) containing GRMZM2G0081223, which also had a susceptible parent background, were found to have a significantly improved level of resistance. In addition, the expression profile of the three candidate genes revealed that they all respond to the infection following inoculation with F. verticillioides. These genetic analyses indicate that FSR resistance is controlled by loci with minor effect, and the polymerization breeding of lines with beneficial alleles and candidate genes could improve FSR resistance in maize.Maize is one of the most important cereals in the world due to its high yield potential and its high demand for use as food, feed, and for industrial purposes. Maize is subject to a variety of biotic and abiotic stresses during its lifetime, which can significantly affect final yield and quality. The planting area for maize in China is 37.07 million hectares, of which the Huang-Huai-Hai region accounts for 39%. In this region, the incidence of soil-borne diseases in maize has increased over the years, which coincides with increases in the use of cultivation systems such as double cropping, no-tillage, and straw returned. Fusarium verticillioides (formerly Fusarium moniliforme), which is a commonly-found soil-borne fungal species, can be transmitted to seeds and cause systemic infection in maize 1 . Previous studies have confirmed that seeds infected with F. verticillioides are a source of root and stalk infection 2 . In addition, the fungus can be transmitted from the planted seed through to the developing kernels via the mature plant 1,[3][4][5] . The diseases caused by F. verticillioides include seedling blight, stalk rot, root rot, kernel rot, ear rot, and seed rot 5,6 . F. verticillioides infection can result in decreased grain yields, poor grain quality, and contamination by the mycotoxin fumonisin 7 . The fumonisins produced by F. verticillioides are known to cause a variety of diseases when ingested by animals, and have been implicated in human carcinogenesis and neural tube defects, as well as in plant diseases 6 .

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“…Maize husk constitutes the leafy outer of ear and protects cob from dehydration and pathogen infection [2, 3, 10]. Therefore, the husk morphogenesis must be delicately coordinated with ear growth and development.…”

Section: Discussionmentioning

confidence: 99%

“…In the past decades, the husk surrounding the ear of maize has gained extensive attentions due to its special characters, such as operating a partial C 3 photosynthetic pathway in contrast to stem leaves [1], the proper tightness and coverage protecting the ear infected from diseases [2, 3], and directly or indirectly providing plentiful sources of anthocyanin and fibre for nutritional or industrial production [4, 5]. The husk leaf area is positively correlated with the amount of cell-wall components such as the hemicellulose and cellulose fractions [6].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study (GWAS) reveals the genetic architecture of four husk traits in maize

Cui

Luo

et al. 2016

BMC Genomics

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BackgroundMaize (Zea mays) husk referring to the leafy outer enclosing the ear, plays an important role in grain production by directly contributing photosynthate and protecting ear from pathogen infection. Although the physiological functions related to husk have been extensively studied, little is known about its morphological variation and genetic basis in natural population.ResultsHere we utilized a maize association panel including 508 inbred lines with tropical, subtropical and temperate backgrounds to decipher the genetic architecture attributed to four husk traits, i.e. number of layers, length, width and thickness. Evaluating the phenotypic diversity at two different environments showed that four traits exhibit broadly natural variations and moderate levels of heritability with 0.64, 0.74, 0.49 and 0.75 for number, length, width and thickness, respectively. Diversity analysis indicated that different traits have dissimilar responses to subpopulation effects. A series of significantly positive or negative correlations between husk phenotypes and other agronomic traits were identified, indicating that husk growth is coordinated with other developmental processes. Combining husk traits with about half of a million of single nucleotide polymorphisms (SNPs) via genome-wide association study revealed a total of 9 variants significantly associated with traits at P < 1.04 × 10-5, which are implicated in multiple functional categories, such as cellular trafficking, transcriptional regulation and metabolism.ConclusionsThese results provide instrumental information for understanding the genetic basis of husk development, and further studies on identified candidate genes facilitate to illuminate molecular pathways regulating maize husk growth.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3229-6) contains supplementary material, which is available to authorized users.

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Genome-wide association study (GWAS) of resistance to head smut in maize

Cited by 148 publications

References 43 publications

Genome-wide association mapping and Identification of candidate genes for fatty acid composition in Brassica napus L. using SNP markers

Genome-wide association mapping and Identification of candidate genes for fatty acid composition in Brassica napus L. using SNP markers

Dissecting the genetic architecture of Fusarium verticillioides seed rot resistance in maize by combining QTL mapping and genome-wide association analysis

Genome-wide association study (GWAS) reveals the genetic architecture of four husk traits in maize

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