Transcriptome and GWAS analyses reveal candidate gene for seminal root length of maize seedlings under drought stress

Guo, Jian; Li, Chunhui; Zhang, Xiaoqiong; Li, Yongxiang; Zhang, Dengfeng; Shi, Yunsu; Song, Yifu; Yu, Li; Yang, Deguang; Wang, Tianyu

doi:10.1016/j.plantsci.2019.110380

Cited by 105 publications

(71 citation statements)

References 80 publications

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“…Recently, the method of integrating GWAS and RNA-seq has been widely adopted to predict candidate genes. For example, a method combining GWAS results with linked DEGs and co-expression network analysis was used to identify seven candidate genes that respond to drought stress in maize [ 28 ]. We identified 10 candidate genes related to seed germination at low temperatures through this method.…”

Section: Discussionmentioning

confidence: 99%

Identification of candidate tolerance genes to low-temperature during maize germination by GWAS and RNA-seq approaches

Zhang

et al. 2020

BMC Plant Biol

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Background Maize ( Zea mays L.) is one of the main agricultural crops with the largest yield and acreage in the world. However, maize germplasm is very sensitive to low temperatures, mainly during germination, and low temperatures significantly affect plant growth and crop yield. Therefore, the identification of genes capable of increasing tolerance to low temperature has become necessary. Results In this study, fourteen phenotypic traits related to seed germination were used to assess the genetic diversity of maize through genome-wide association study (GWAS). A total of 30 single-nucleotide polymorphisms (SNPs) linked to low-temperature tolerance were detected (−log10( P ) > 4), fourteen candidate genes were found to be directly related to the SNPs, further additional 68 genes were identified when the screen was extended to include a linkage disequilibrium (LD) decay distance of r 2 ≥ 0.2 from the SNPs. RNA-sequencing (RNA-seq) analysis was then used to confirm the linkage between the candidate gene and low-temperature tolerance. A total of ten differentially expressed genes (DEGs) (|log 2 fold change (FC)| ≥ 0.585, P < 0.05) were found within the set distance of LD decay ( r 2 ≥ 0.2). Among these genes, the expression of six DEGs was verified using qRT-PCR. Zm00001d039219 and Zm00001d034319 were putatively involved in ‘mitogen activated protein kinase (MAPK) signal transduction’ and ‘fatty acid metabolic process’, respectively, based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Thus, these genes appeared to be related to low-temperature signal transduction and cell membrane fluidity. Conclusion Overall, by integrating the results of our GWAS and DEG analysis of low-temperature tolerance during germination in maize, we were able to identify a total of 30 SNPs and 82 related candidate genes, including 10 DEGs, two of which were involved in the response to tolerance to low temperature. Functional analysis will provide valuable information for understanding the genetic mechanism of low-temperature tolerance during germination in maize.

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Section: Discussionmentioning

confidence: 99%

Identification of candidate tolerance genes to low-temperature during maize germination by GWAS and RNA-seq approaches

Zhang

et al. 2020

BMC Plant Biol

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“…Paralogous gene pairs and their ratios of the number of nonsynonymous substitutions per nonsynonymous substitution site to the number of synonymous substitutions per synonymous substitution site (Ka/Ks) were retrieved from a recent publication from our group [28]. Divergence times (in million years ago, mya) were calculated using DT = Ks / (2 × 6.1 × 1e−9) × 1e−6 mya [29].…”

Section: Phylogenetic Reconstruction Gene Duplication and Selection mentioning

confidence: 99%

Pathogenesis-related protein 1 (PR-1) genes in soybean: genome-wide identification, structural analysis and expression profiling under multiple biotic and abiotic stresses

Almeida‐Silva

Venancio

2021

Preprint

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Plant pathogenesis-related (PR) proteins are a large group of proteins, classified in 17 families, that are induced by pathological conditions. Here, we characterized the soybean PR-1 (GmPR-1) gene repertoire at the sequence, structural and expression levels. We found 24 GmPR-1 genes, clustered in two phylogenetic groups. GmPR-1 genes are under strong purifying selection, particularly those that emerged by tandem duplications. GmPR-1 promoter regions are abundant in cis-regulatory elements associated with major stress-related transcription factor families, namely WRKY, ERF, HD-Zip, C2H2, NAC, and GATA. We observed that 23 GmPR-1 genes are induced by stress conditions or exclusively expressed upon stress. We explored 1972 transcriptome samples, including 26 stress conditions, revealing that most GmPR-1 genes are differentially expressed in a plethora of biotic and abiotic stresses. Our findings highlight stress-responsive GmPR-1 genes with potential biotechnological applications, such as the development of transgenic lines with increased resistance to biotic and abiotic stresses.

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“…Combination of GWAS, WGCNA, and differential expression analysis has been reported as an efficient way to acquire crucial genes in maize, rice, soybean, carrot, and other crops (Li et al 2017;Que et al 2018;Wang et al 2019a;Guo et al 2020). We identified four persistent and eight stage-specific crucial candidate genes related to root development by integrating GWAS, WGCNA and differential expression analysis in rapeseed.…”

Section: Efficient Discovery Of Candidate Genes By Combining Gwas Wgcna and Differential Expression Analysismentioning

confidence: 99%

“…To breed the crops with better RSA, a large number of studies have focused on variations in root architecture in many crops, such as rice, wheat, maize, soybean, and rapeseed (Burton et al 2014;Song et al 2016a;Beyer et al 2019;Wang et al 2019b;Guo et al 2020). Several studies have identified hundreds of root QTL in controlled environments or in the field (Song et al 2016b;Wang et al 2017Wang et al , 2019aWang et al , 2019b.…”

Section: Introductionmentioning

confidence: 99%

“…Functional candidate genes related to root development were identified at different developmental stages in crops by WGCNA, including DcMYB113, which was reported to regulate anthocyanin transport in carrot root (Xu et al 2020), and three hub genes (GRMZM2G477658, GRMZM2G15536, and GRMZM2G072121) played a possible role in maize root formation and growth through the division and/or elongation of cells (Hwang et al 2018). Recently, the combination of GWAS, transcriptome sequencing, and/or WGCNA has been turned out to be a rapid and efficient approach to identifying crucial candidate genes regulating root development (Li et al 2017;Que et al 2018;Wang et al 2019a;Guo et al 2020). For example, OsNal1 and OsJAZ1 located in the peak SNPs have been confirmed to facilitate the root development in rice (Li et al 2017).…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Association Study and Transcriptome Analysis Reveal Key Genes Affecting Root Growth Dynamics In Rapeseed

Wang

Kuang

et al. 2021

Preprint

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Root growth is a dynamic process mediated by interactive genetic factors and environmental cues. Seven root-related traits and two shoot-related traits in 280 Brassica napus accessions at five continuous vegetative stages were measured to establish the genetic basis of root growth in rapeseed. The persistent and stage-specific genetic mechanisms were revealed by root dynamic analysis. Sixteen persistent and 32 stage-specific quantitative trait loci (QTL) clusters were identified through genome-wide association study (GWAS). Root samples with contrasting (slow and fast) growth rates throughout investigated stages and those with obvious stage-specific changes in growth rates were subjected to transcriptome analysis. The former identified 367 differentially expressed genes (DEGs) with persistently differential expressions throughout root development that were significantly enriched in GO terms of energy metabolism and response to biotic or abiotic stress, whereas the later identified 485 stage-specific DEGs with different expressions at corresponding stage that were enriched in GO terms of nitrogen metabolism. By integrating GWAS, weighted gene co-expression network analysis (WGCNA), and differential expression analysis, four and eight candidate genes less than 100 kb away from peak SNPs of QTL clusters were identified as key persistent and stage-specific genetic factors, respectively. The homologs of 3 genes ( BnaA03g52990D , BnaA06g37280D, and BnaA09g07580D ) out of 12 candidate genes have been reported to regulate root development in previous studies. Our results provide new insights into the temporal genetic mechanisms of root growth by identifying key candidate QTL/genes in rapeseed.

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Transcriptome and GWAS analyses reveal candidate gene for seminal root length of maize seedlings under drought stress

Cited by 105 publications

References 80 publications

Identification of candidate tolerance genes to low-temperature during maize germination by GWAS and RNA-seq approaches

Identification of candidate tolerance genes to low-temperature during maize germination by GWAS and RNA-seq approaches

Pathogenesis-related protein 1 (PR-1) genes in soybean: genome-wide identification, structural analysis and expression profiling under multiple biotic and abiotic stresses

Genome-Wide Association Study and Transcriptome Analysis Reveal Key Genes Affecting Root Growth Dynamics In Rapeseed

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