Genome-wide association study identifies novel loci and candidate genes for drought stress tolerance in rapeseed

Shahzad, Ali; Qian, Minchao; Sun, Bangyang; Mahmood, Umer; Li, Shengting; Fan, Yonghai; Chang, Wei; Dai, Lishi; Zhu, Hong; Li, Jiana; Qu, Cunmin; Lu, Kun

doi:10.1016/j.ocsci.2021.01.002

Cited by 15 publications

(6 citation statements)

References 65 publications

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“…These frightening projections indicate that crops would experience heat stress and a rise in the frequency of droughts during their growing seasons ( Rustgi et al., 2021 ; Raza et al., 2022b ). Furthermore, climatic changes will probably increase the intensity of both single and combination abiotic stresses, including drought ( Shahzad et al., 2021 ), cold, heat, salinity, and submergence ( Anwar et al., 2021 ). Abiotic stresses are expected to worsen with the predicted climate-change scenarios by increasing the prevalence and severity of insects, pests, and pathogens as well as weed species proliferation and beneficial soil bacteria, as well as endangering essential plant pollinators ( Zenda et al., 2021 ).…”

Section: Challenges and Future Perspectivementioning

confidence: 99%

Multi-omics revolution to promote plant breeding efficiency

Mahmood

Li²,

Fan³

et al. 2022

Front. Plant Sci.

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Crop production is the primary goal of agricultural activities, which is always taken into consideration. However, global agricultural systems are coming under increasing pressure from the rising food demand of the rapidly growing world population and changing climate. To address these issues, improving high-yield and climate-resilient related-traits in crop breeding is an effective strategy. In recent years, advances in omics techniques, including genomics, transcriptomics, proteomics, and metabolomics, paved the way for accelerating plant/crop breeding to cope with the changing climate and enhance food production. Optimized omics and phenotypic plasticity platform integration, exploited by evolving machine learning algorithms will aid in the development of biological interpretations for complex crop traits. The precise and progressive assembly of desire alleles using precise genome editing approaches and enhanced breeding strategies would enable future crops to excel in combating the changing climates. Furthermore, plant breeding and genetic engineering ensures an exclusive approach to developing nutrient sufficient and climate-resilient crops, the productivity of which can sustainably and adequately meet the world’s food, nutrition, and energy needs. This review provides an overview of how the integration of omics approaches could be exploited to select crop varieties with desired traits.

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Section: Challenges and Future Perspectivementioning

confidence: 99%

Multi-omics revolution to promote plant breeding efficiency

Mahmood

Li²,

Fan³

et al. 2022

Front. Plant Sci.

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“…The GWAS analysis identified 139 linked SNPs with water loss ratio, of which, 13 were significant SNPs. Four putative candidate genes BnaC09.RPS6, BnaC09.MATE, BnaA10.PPD5, and BnaC09.Histone was identified involved in DS tolerance in rapeseed (Shahzad et al, 2021). In a recent study, Varshney et al (2019) resequenced the whole genome of 429 chickpea lines collected from 45 countries.…”

Section: Genome-wide Association Studiesmentioning

confidence: 99%

Developing drought‐smart, ready‐to‐grow future crops

Raza

Mubarik²,

Sharif

et al. 2022

The Plant Genome

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Breeding crop plants with increased yield potential and improved tolerance to stressful environments is critical for global food security. Drought stress (DS) adversely affects agricultural productivity worldwide and is expected to rise in the coming years. Therefore, it is vital to understand the physiological, biochemical, molecular, and ecological mechanisms associated with DS. This review examines recent advances in plant responses to DS to expand our understanding of DS-associated mechanisms. Suboptimal water sources adversely affect crop growth and yields through physical impairments, physiological disturbances, biochemical modifications, and molecular adjustments. To control the devastating effect of DS in crop plants, it is important to understand its consequences, mechanisms, and the agronomic and genetic basis of DS for sustainable production. In addition to plant responses, we highlight several mitigation options such as omics approaches, transgenics breeding, genome editing, and biochemical to mechanical methods (foliar treatments, seed priming, and conventional agronomic practices). Further, we have

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“…(2015) analyzed 66 rapeseed accessions under drought conditions and identified 16 single-nucleotide polymorphisms (SNPs) significantly associated with water stress-related responses. Recently, Shahzad et al. (2021) identified 139 SNPs associated with the water loss ratio using GWAS in 264 rapeseed accessions at the full-bloom stage, of which four were related to putative candidate genes (CGs) involved in drought tolerance in rapeseed.…”

Section: Introductionmentioning

confidence: 99%

Integration of genome-wide association studies, metabolomics, and transcriptomics reveals phenolic acid- and flavonoid-associated genes and their regulatory elements under drought stress in rapeseed flowers

Salami,

Heidari,

Batley

et al. 2024

Front. Plant Sci.

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IntroductionBiochemical and metabolic processes help plants tolerate the adverse effects of drought. In plants accumulating bioactive compounds, understanding the genetic control of the biosynthesis of biochemical pathways helps the discovery of candidate gene (CG)–metabolite relationships.MethodsThe metabolic profile of flowers in 119 rapeseed (Brassica napus) accessions was assessed over two irrigation treatments, one a well-watered (WW) condition and the other a drought stress (DS) regime. We integrated information gained from 52,157 single-nucleotide polymorphism (SNP) markers, metabolites, and transcriptomes to identify linked SNPs and CGs responsible for the genetic control of flower phenolic compounds and regulatory elements.ResultsIn a genome-wide association study (GWAS), of the SNPs tested, 29,310 SNPs were qualified to assess the population structure and linkage disequilibrium (LD), of which several SNPs for radical scavenging activity (RSA) and total flavanol content (TFLC) were common between the two irrigation conditions and pleiotropic SNPs were found for chlorogenic and coumaric acids content. The principal component analysis (PCA) and stepwise regression showed that chlorogenic acid and epicatechin in WW and myricetin in DS conditions were the most important components for RSA. The hierarchical cluster analysis (HCA) showed that vanillic acid, myricetin, gallic acid, and catechin were closely associated in both irrigation conditions. Analysis of GWAS showed that 60 CGs were identified, of which 18 were involved in stress-induced pathways, phenylpropanoid pathway, and flavonoid modifications. Of the CGs, PAL1, CHI, UGT89B1, FLS3, CCR1, and CYP75B137 contributed to flavonoid biosynthetic pathways. The results of RNA sequencing (RNA-seq) revealed that the transcript levels of PAL, CHI, and CYP75B137 known as early flavonoid biosynthesis-related genes and FLS3, CCR1, and UGT89B1 related to the later stages were increased during drought conditions. The transcription factors (TFs) NAC035 and ERF119 related to flavonoids and phenolic acids were upregulated under drought conditions.DiscussionThese findings expand our knowledge on the response mechanisms to DS, particularly regarding the regulation of key phenolic biosynthetic genes in rapeseed. Our data also provided specific linked SNPs for marker-assisted selection (MAS) programs and CGs as resources toward realizing metabolomics-associated breeding of rapeseed.

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Genome-wide association study identifies novel loci and candidate genes for drought stress tolerance in rapeseed

Cited by 15 publications

References 65 publications

Multi-omics revolution to promote plant breeding efficiency

Multi-omics revolution to promote plant breeding efficiency

Developing drought‐smart, ready‐to‐grow future crops

Integration of genome-wide association studies, metabolomics, and transcriptomics reveals phenolic acid- and flavonoid-associated genes and their regulatory elements under drought stress in rapeseed flowers

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