Genome-wide analysis of the transcriptional response to drought stress in root and leaf of common bean

Pereira, Wendell Jacinto; Melo, Arthur Tavares de Oliveira; Coelho, Alexandre Siqueira Guedes; Rodrigues, Fabiana Aparecida; Mamidi, Sujan; Alencar, Sérgio Amorim de; Lanna, Anna Cristina; Valdisser, P. A. M. R.; Brondani, C.; Nascimento-Júnior, Ivanildo Ramalho do; Borba, T. C. de O.; Vianello, R. P.

doi:10.1590/1678-4685-gmb-2018-0259

Cited by 22 publications

(15 citation statements)

References 118 publications

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“…For the SNPs from DArTseq, the estimates of marker reproducibility (99.8%) and call rate (94%) were close and consistent with those previously reported ( Cruz et al, 2013 ; Ren et al, 2015 ), thus indicating the quality and reliability of this set of SNPs. Using the CaptureSeq, we reported the identification and genotyping of 3,166 SNPs located inside or in close proximity to 3,304 (65.42%) annotated protein-coding genes associated with drought tolerance ( Pereira et al, 2020 ) along the common bean genome. Despite a reduced number of SNPs targeted, this strategy represents a real possibility to explore the polymorphism in gene regions of interest, enabling the mapping of the set of isoforms for association analysis.…”

Section: Discussionmentioning

confidence: 99%

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Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress

Valdisser

Müller

Filho³

et al. 2020

Front. Plant Sci.

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Drought stress is an important abiotic factor limiting common bean yield, with great impact on the production worldwide. Understanding the genetic basis regulating beans’ yield and seed weight (SW) is a fundamental prerequisite for the development of superior cultivars. The main objectives of this work were to conduct genome-wide marker discovery by genotyping a Mesoamerican panel of common bean germplasm, containing cultivated and landrace accessions of broad origin, followed by the identification of genomic regions associated with productivity under two water regimes using different genome-wide association study (GWAS) approaches. A total of 11,870 markers were genotyped for the 339 genotypes, of which 3,213 were SilicoDArT and 8,657 SNPs derived from DArT and CaptureSeq. The estimated linkage disequilibrium extension, corrected for structure and relatedness (r2sv), was 98.63 and 124.18 kb for landraces and breeding lines, respectively. Germplasm was structured into landraces and lines/cultivars. We carried out GWASs for 100-SW and yield in field environments with and without water stress for 3 consecutive years, using single-, segment-, and gene-based models. Higher number of associations at high stringency was identified for the SW trait under irrigation, totaling ∼185 QTLs for both single- and segment-based, whereas gene-based GWASs showed ∼220 genomic regions containing ∼650 genes. For SW under drought, 18 QTLs were identified for single- and segment-based and 35 genes by gene-based GWASs. For yield, under irrigation, 25 associations were identified, whereas under drought the total was 10 using both approaches. In addition to the consistent associations detected across experiments, these GWAS approaches provided important complementary QTL information (∼221 QTLs; 650 genes; r2 from 0.01% to 32%). Several QTLs were mined within or near candidate genes playing significant role in productivity, providing better understanding of the genetic mechanisms underlying these traits and making available molecular tools to be used in marker-assisted breeding. The findings also allowed the identification of genetic material (germplasm) with better yield performance under drought, promising to a common bean breeding program. Finally, the availability of this highly diverse Mesoamerican panel is of great scientific value for the analysis of any relevant traits in common bean.

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Section: Discussionmentioning

confidence: 99%

“…A set of 5,293 differentially expressed genes under drought stress ( Pereira et al, 2020 ) were initially used as target regions of the genome. The target capture (CaptureSeq) methodology was carried out by the company RAPiD Genomics (Gainesville, FL, United States).…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress

Valdisser

Müller

Filho³

et al. 2020

Front. Plant Sci.

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“…The majority of drought-related unigenes in this study were classified under different families of transcription factors (TFs) such as AP2/ERF, NAC, bZIP, DBP, MYB, HB-HD-ZIP, WRK, B3->B3, C2C2->C2C2-GATA, C3H, and bHLH, which were identified at all studied time points except for the first time point of drought stress. It was reported that TFs are considered as early activated genes that are targeted by phosphatases and PKs 63 . Among the active TFs, WRKY are largely up-regulated and known to be involved in drought stress defense pathways in plants [64][65][66] , and the members of AP2-EREBP TFs family are also shown to be highly up-regulated.…”

Section: Discussionmentioning

confidence: 99%

RNA-sequencing analysis revealed genes associated drought stress responses of different durations in hexaploid sweet potato

Arisha

Ahmad

Tang

et al. 2020

Sci Rep

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Purple-fleshed sweet potato (PFSP) is an important food crop, as it is a rich source of nutrients and anthocyanin pigments. Drought has become a major threat to sustainable sweetpotato production, resulting in huge yield losses. Therefore, the present study was conducted to identify drought stressresponsive genes using next-generation (NGS) and third-generation sequencing (TGS) techniques. Five cDNA libraries were constructed from seedling leaf segments treated with a 30% solution of polyethylene glycol (PEG-6000) for 0, 1, 6, 12, and 48 h for second-generation sequencing. Leaf samples taken from upper third of sweet potato seedlings after 1, 6, 12, and 48 h of drought stress were used for the construction of cDNA libraries for third-generation sequencing; however, leaf samples from untreated plants were collected as controls. A total of 184,259,679 clean reads were obtained using second and third-generation sequencing and then assembled into 17,508 unigenes with an average length of 1,783 base pairs. Out of 17,508 unigenes, 642 (3.6%) unigenes failed to hit any homologs in any databases, which might be considered novel genes. A total of 2, 920, 1578, and 2,418 up-regulated unigenes and 3,834, 2,131, and 3,337 down-regulated unigenes from 1 h, 6 h, 12 h, and 48 h library were identified, respectively in drought stress versus control. In addition, after 6, 12, and 48 h of drought stress, 540 up-regulated unigenes, 486 down-regulated unigenes and 414 significantly differentially expressed unigenes were detected. It was found that several gene families including Basic Helix-loop-helix (bHLH), basic leucine zipper (bZIP), Cystein2/Histidine2 (C2H2), C3H, Ethylene-responsive transcription factor (ERF), Homo domain-leucine zipper (HD-ZIP), MYB, NAC (NAM, ATAF1/2, and CUC2), Thiol specific antioxidant and WRKY showed responses to drought stress. In total, 17,472 simple sequence repeats and 510,617 single nucleotide polymorphisms were identified based on transcriptome sequencing of the PFSP. About 96.55% of the obtained sequences are not available online in sweet potato genomics resources. Therefore, it will enrich annotated sweet potato gene sequences and enhance understanding of the mechanisms of drought tolerance through genetic manipulation. Moreover, it represents a sequence resource for genetic and genomic studies of sweet potato. Purple-fleshed sweet potato (PFSP) (Ipomoea batatas (L.) Lam.) is a type of sweet potato, which has purple skin and flesh color of the storage roots due to the large accumulation of anthocyanin pigments 1. It is a root crop widely grown in some Asian and African countries (i.e. China, India, and Kenya). Sweet potato is regarded as the seventh most important food crop. It is among the crops which generate large amounts of food per unit area per unit time 2. Furthermore, it is considered to be a cheap source of energy, carbohydrates, vitamin, potassium, iron, fiber, and protein 3 .

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“…The expression le data indicated that PvXIP1;2 transcript levels were strongly induced by drought stress (Wu et al, 2014;Pereira et al, 2020). To verify the expression data, we performed quantitative real-time RT-qPCR using RNA isolated from drought-treated common bean, and the results con rmed the expression data (Fig.…”

Section: Expression Patterns Of Pvxip1;2mentioning

confidence: 67%

Genetic Dissection of Drought Resistance of Common Bean at the Seedling Stage by Genome-wide Association Study

Chang

Wang

et al. 2021

Preprint

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A variety of adverse conditions, including drought stress, severely affect common bean production. Molecular breeding for drought resistance has been proposed as an effective and practical way to improve the drought resistance of common bean. A genome-wide association analysis was conducted to identify drought-related loci based on survival rates at the seedling stage using a natural population consisting of 400 common bean accessions and 3832340 SNPs. The coefficient of variation ranged from 40.90% to 56.22% for survival rates in three independent experiments. A total of 12 associated loci containing 89 significant SNPs were identified for survival rates at the seedling stage. Four loci overlapped in the region of the QTLs reported to be associated with drought resistance. According to the expression profiles, gene annotations and references of the functions of homologous genes in Arabidopsis, 39 genes were considered potential candidate genes selected from 199 genes annotated within all associated loci. A stable locus (Locus_10) was identified on chromosome 11, which contained LEA, aquaporin, and proline-rich protein genes. We further confirmed the drought-related function of an aquaporin (PvXIP1;2) located at Locus_10 by expression pattern analysis, phenotypic analysis of PvXIP1;2-overexpressing Arabidopsis and Agrobacterium rhizogenes-mediated hairy root transformation systems, indicating that the association results can facilitate the efficient identification of genes related to drought resistance. These loci and their candidate genes provide a foundation for crop improvement via breeding for drought resistance in common bean.

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Genome-wide analysis of the transcriptional response to drought stress in root and leaf of common bean

Cited by 22 publications

References 118 publications

Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress

Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress

RNA-sequencing analysis revealed genes associated drought stress responses of different durations in hexaploid sweet potato

Genetic Dissection of Drought Resistance of Common Bean at the Seedling Stage by Genome-wide Association Study

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