Genome-wide association study (GWAS) reveals genetic loci of lead (Pb) tolerance during seedling establishment in rapeseed (Brassica napus L.)

Zhang, Fugui; Xiao, Xin; Xu, Kun; Cheng, Xi; Xie, Ting; Hu, Jihong; Wu, Xiaoming

doi:10.1186/s12864-020-6558-4

Cited by 14 publications

(2 citation statements)

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“…A recent GWA study in wheat identified five loci ( qSCd−1A , qSCd−1D , qZn−2B1 , qZn−2B2 , and qFe−6D) associated with Cd stress tolerance ( Safdar et al, 2020a ). Analysis of a large collection of rapeseed accessions identified four QTLs and underlying candidate genes, including GSTUs, BCATs, UBP13, TBR , and HIPP01 , responsible for Pb tolerance ( Zhang et al, 2020a ). GWAS investigation on rice grains for Fe and Zn traces have identified novel marker-trait associations with a phenotypic variation of 2.1–53%, which could be helpful to identify candidate genes for improving Fe and Zn tolerance ( Bollinedi et al, 2020 ).…”

Section: Seven-(omics)-based Approaches To Improve Toxic Metals/metalloids Tolerance In Plantsmentioning

confidence: 99%

Advances in “Omics” Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants

et al. 2022

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Food safety has emerged as a high-urgency matter for sustainable agricultural production. Toxic metal contamination of soil and water significantly affects agricultural productivity, which is further aggravated by extreme anthropogenic activities and modern agricultural practices, leaving food safety and human health at risk. In addition to reducing crop production, increased metals/metalloids toxicity also disturbs plants’ demand and supply equilibrium. Counterbalancing toxic metals/metalloids toxicity demands a better understanding of the complex mechanisms at physiological, biochemical, molecular, cellular, and plant level that may result in increased crop productivity. Consequently, plants have established different internal defense mechanisms to cope with the adverse effects of toxic metals/metalloids. Nevertheless, these internal defense mechanisms are not adequate to overwhelm the metals/metalloids toxicity. Plants produce several secondary messengers to trigger cell signaling, activating the numerous transcriptional responses correlated with plant defense. Therefore, the recent advances in omics approaches such as genomics, transcriptomics, proteomics, metabolomics, ionomics, miRNAomics, and phenomics have enabled the characterization of molecular regulators associated with toxic metal tolerance, which can be deployed for developing toxic metal tolerant plants. This review highlights various response strategies adopted by plants to tolerate toxic metals/metalloids toxicity, including physiological, biochemical, and molecular responses. A seven-(omics)-based design is summarized with scientific clues to reveal the stress-responsive genes, proteins, metabolites, miRNAs, trace elements, stress-inducible phenotypes, and metabolic pathways that could potentially help plants to cope up with metals/metalloids toxicity in the face of fluctuating environmental conditions. Finally, some bottlenecks and future directions have also been highlighted, which could enable sustainable agricultural production.

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Section: Seven-(omics)-based Approaches To Improve Toxic Metals/metalloids Tolerance In Plantsmentioning

confidence: 99%

Advances in “Omics” Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants

et al. 2022

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“…One of them is the genome-wide association study (GWAs), used to connect plant phenotypes with candidate marker genes. This tool has lately been used to describe nine potential candidate genes related to the Pb-tolerance in Brassica napus (Zhang et al, 2020). Using the GWAs approach, we aim to improve the fragmentary picture of genes responsible for Pb tolerance taking advantage of the variability present in natural accessions of A. thaliana.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Study Reveals Key Genes for Differential Lead Accumulation and Tolerance in Natural Arabidopsis thaliana Accessions

et al. 2021

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Soil contamination by lead (Pb) has become one of the major ecological threats to the environment. Understanding the mechanisms of Pb transport and deposition in plants is of great importance to achieve a global Pb reduction. We exposed a collection of 360 Arabidopsis thaliana natural accessions to a Pb-polluted soil. Germination rates, growth, and leaf Pb concentrations showed extensive variation among accessions. These phenotypic data were subjected to genome wide association studies (GWAs) and we found a significant association on chromosome 1 for low leaf Pb accumulation. Genes associated with significant SNP markers were evaluated and we selected EXTENSIN18 (EXT18) and TLC (TRAM-LAG1-CLN8) as candidates for having a role in Pb homeostasis. Six Pb-tolerant accessions, three of them exhibiting low leaf Pb content, and three of them with high leaf Pb content; two Pb-sensitive accessions; two knockout T-DNA lines of GWAs candidate genes (ext18, tlc); and Col-0 were screened under control and high-Pb conditions. The relative expression of EXT18, TLC, and other genes described for being involved in Pb tolerance was also evaluated. Analysis of Darwinian fitness, root and leaf ionome, and TEM images revealed that Pb-tolerant accessions employ two opposing strategies: (1) low translocation of Pb and its accumulation into root cell walls and vacuoles, or (2) high translocation of Pb and its efflux to inactive organelles or intracellular spaces. Plants using the first strategy exhibited higher expression of EXT18 and HMA3, thicker root cell walls and Pb vacuolar sequestration, suggesting that these genes may contribute to the deposition of Pb in the roots. On the other hand, plants translocating high amounts of Pb showed upregulation of TLC and ABC transporters, indicating that these plants were able to properly efflux Pb in the aerial tissues. We conclude that EXT18 and TLC upregulation enhances Pb tolerance promoting its sequestration: EXT18 favors the thickening of the cell walls improving Pb accumulation in roots and decreasing its toxicity, while TLC facilitates the formation of dictyosome vesicles and the Pb encapsulation in leaves. These findings are relevant for the design of phytoremediation strategies and environment restoration.

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Genome‐Wide Association Studies of Important Agronomic Traits in Brassica napus : What We Have Learned and Where We Are Headed

Liu

Wang

Yang

et al. 2022

Annual Plant Reviews Online

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Oilseed rape ( Brassica napus L.; B. napus ) is one of the main oil crops in China as well as in the world. Genome‐wide association studies (GWAS) have revolutionised the field of complex agronomic traits. In B. napus, these include seed yield and yield‐related traits, seed oil content, and abiotic and biotic stress‐tolerance traits over the past decade in which hundreds of thousands to millions of genetic variants across the genomes of hundreds of individuals have been tested to identify genotype–phenotype associations. In this review, we assess the current status of GWAS in terms of genotypes, phenotypes, statistical models, and candidate genes for these agronomic traits in B. napus . Post‐GWAS, the combination of QTL mapping, transcriptomics, and new statistical methods, has allowed us to identify candidate genes associated with specific agronomic traits. In addition, we can use diverse populations, increase the population size, or look for rare variants and structural variations of B. napus by whole‐genome sequencing to minimise the ‘missing heritability’ effects. These approaches are essential for uncovering the genetic mechanisms defining or regulating complex agronomic traits and the delivery of molecular marker‐assisted breeding in B. napus to breed new varieties that are higher yielding but resilient to our changing climate.

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Genome-wide association study (GWAS) reveals genetic loci of lead (Pb) tolerance during seedling establishment in rapeseed (Brassica napus L.)

Cited by 14 publications

References 82 publications

Advances in “Omics” Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants

Advances in “Omics” Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants

Genome-Wide Association Study Reveals Key Genes for Differential Lead Accumulation and Tolerance in Natural Arabidopsis thaliana Accessions

Genome‐Wide Association Studies of Important Agronomic Traits in Brassica napus : What We Have Learned and Where We Are Headed

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