rMVP: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated tool for Genome-Wide Association Study

Yin, Lilin; Zhang, Haohao; Tang, Zhenshuang; Xu, Jingya; Ding, Yin; Zhang, Zhiwu; Yuan, Xiaohui; Zhu, Mengjin; Zhao, Shuhong; Li, Xinyun

doi:10.1101/2020.08.20.258491

Cited by 67 publications

(34 citation statements)

References 28 publications

(31 reference statements)

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“…Candidate genes located within an LD block near a peak SNP were identified and analyzed. Manhattan plots of the GWAS were drawn using the cmplot package (Yin, 2019) and qqman (Turner, 2017) in r 3.6.0 (R Core Team, 2019).…”

Section: Methodsmentioning

confidence: 99%

Identification of a candidate gene associated with isoflavone content in soybean seeds using genome‐wide association and linkage mapping

Zhao

et al. 2020

The Plant Journal

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Isoflavone, a secondary metabolite produced by Glycine max (L.) Merr. (soybean), is valuable for human and plant health. The genetic architecture of soybean isoflavone content remains unclear, however, despite several mapping studies. We generated genomic data for 200 soybean cultivars and 150 recombinant inbred lines (RILs) to localize putative loci associated with soybean seed isoflavone content. Using a genome-wide association study (GWAS), we identified 87 single-nucleotide polymorphisms (SNPs) that were significantly associated with isoflavone concentration. Using linkage mapping, we identified 37 quantitative trait loci (QTLs) underlying the content of four isoflavones found in the RILs. A major locus on chromosome 8 (qISO8-1) was co-located by both the GWAS and linkage mapping. qISO8-1 was fine mapped to a 99.5-kb region, flanked by SSR_08_1651 and SSR_08_1656, in a BC 2 F 5 population. GmMPK1, encoding a mitogenactivated protein kinase, was identified as the causal gene in qISO8-1, and two natural GmMPK1 polymorphisms were significantly associated with isoflavone content. Overexpression of GmMPK1 in soybean hairy roots resulted in increased isoflavone concentrations. Overexpressing GmMPK1 in transgenic soybeans had greater resistance to Phytophthora root rot, suggesting that GmMPK1 might increase soybean resistance to biotic stress by influencing isoflavone content. Our results not only increase our understanding of the genetic architecture of soybean seed isoflavone content, but also provide a framework for the future marker-assisted breeding of high isoflavone content in soybean cultivars.

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Section: Methodsmentioning

confidence: 99%

Identification of a candidate gene associated with isoflavone content in soybean seeds using genome‐wide association and linkage mapping

Zhao

et al. 2020

The Plant Journal

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“…We used likelihood ratio P values from the GEMMA output files because likelihood ratio test makes fewer approximations compared to the Wald’s test. Manhattan and QQ-plots were drawn using rMVP package 66 in R version 3.6.1 in RStudio version 1.2.1335.…”

Section: Methodsmentioning

confidence: 99%

Natural variation in Arabidopsis thaliana rosette area unveils new genes involved in plant development

González

Butković

Rivarez

et al. 2020

Sci Rep

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Growth is a complex trait influenced by multiple genes that act at different moments during the development of an organism. This makes it difficult to spot its underlying genetic mechanisms. Since plant growth is intimately related to the effective leaf surface area (ELSA), identifying genes controlling this trait will shed light on our understanding of plant growth. To find new genes with a significant contribution to plant growth, here we used the natural variation in Arabidopsis thaliana to perform a genome-wide association study of ELSA. To do this, the projected rosette area of 710 worldwide distributed natural accessions was measured and analyzed using the genome-wide efficient mixed model association algorithm. From this analysis, ten genes were identified having SNPs with a significant association with ELSA. To validate the implication of these genes into A. thaliana growth, six of them were further studied by phenotyping knock-out mutant plants. It was observed that rem1.2, orc1a, ppd1, and mcm4 mutants showed different degrees of reduction in rosette size, thus confirming the role of these genes in plant growth. Our study identified genes already known to be involved in plant growth but also assigned this role, for the first time, to other genes.

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“…Association analysis for each trait on each SNP with an MAF larger than 0.05 was performed using a single-locus mixed linear model (MLM) implemented in GEMMA[40] (which corrects confounding by population structure and the relatedness matrix). The GWAS results were displayed using a Manhattan plot and a QQ-plot created with the R package CMplot[41]. A clump based method implemented in PLINK[39] was used to reduce a false peak and to detect real SALs.…”

Section: Methodsmentioning

confidence: 99%

Resequencing 250 soybean accessions: new insights into genes associated with agronomic traits and genetic networks

Yang

Yan

Jiang

et al. 2021

Preprint

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Limited knowledge on genomic diversity and the functional genes associated with soybean variety traits has resulted in slow breeding progress. We sequenced the genome of 250 soybean landraces and cultivars from China, America and Europe, and investigated their population structure, genetic diversity and architecture and selective sweep regions of accessions. We identified five novel agronomically important genes and studied the effects of functional mutations in respective genes. We found candidate genes GSTT1, GL3 and GSTL3 associated with isoflavone content, CKX3 associated with yield traits, and CYP85A2 associated with both architecture and yield traits. Our phenotype-gene network analysis revealed that hub nodes play a role in complex phenotypic associations. In this work, we describe novel agronomic trait associated genes and a complex genetic network, providing a valuable resource for future soybean molecular breeding.

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rMVP: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated tool for Genome-Wide Association Study

Cited by 67 publications

References 28 publications

Identification of a candidate gene associated with isoflavone content in soybean seeds using genome‐wide association and linkage mapping

Identification of a candidate gene associated with isoflavone content in soybean seeds using genome‐wide association and linkage mapping

Natural variation in Arabidopsis thaliana rosette area unveils new genes involved in plant development

Resequencing 250 soybean accessions: new insights into genes associated with agronomic traits and genetic networks

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