Genome-wide association study identifies GhSAL1 affects cold tolerance at the seedling emergence stage in upland cotton (Gossypium hirsutum L.)

Shen, Qian; Zhang, Siping; Ge, Changwei; Liu, Shaodong; Chen, Jing; Liu, Ruihua; Ma, Huijuan; Song, Meizhen; Pang, Chaoyou

doi:10.1007/s00122-023-04317-x

Cited by 15 publications

(7 citation statements)

References 67 publications

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“…Plant SAL1s have been extensively reported to be involved in phytohormones (Ishiga et al, 2017) (e.g., ABA, salicylic acid, jasmonic acid, and auxin) and stresses (Jia et al, 2019) such as Fusarium graminearum (Yu et al, 2015), salt (Chen et al, 2011), drought (Abdallah et al, 2022), cold (Shen et al, 2023), high light (Estavillo et al, 2011), oxidative stress (Chan et al, 2016), and cadmium (Xi et al, 2016). Due to its distinct effects on different cellular processes, the underlying molecular mechanisms of SAL1 in stress responses appears to be complex (Jia et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

“…Transient silencing of SAL1 and loss-of-function mutants led to enhanced drought tolerance in T. aestivum (Manmathan et al, 2013; Abdallah et al, 2022) and Arabidopsis thaliana (Wilson et al, 2009; Estavillo et al, 2011), while OsSAL1 overexpression plants were severely impaired in drought tolerance of rice (Liu et al, 2023). Additionally, GhSAL1 improved cold tolerance via inositol 1,4,5-triphosphate-Ca 2+ signaling pathway in cotton ( Gossypium hirsutum ) (Shen et al, 2023). Our previous study showed that C. richardii SAL1 (CrSAL1) and its byproduct 3’-phosphoadenosine-5’-phosphate (PAP) function as chloroplast stress signals and participated in the abscisic acid (ABA) signaling pathway for drought response and stomatal regulation (Zhao et al, 2019), but CrSAL1 was not functionally verified through genetic engineering in C. richardii .…”

Section: Introductionmentioning

confidence: 99%

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Efficient Gene Editing and Overexpression of Gametophyte Transformation in a Model Fern

Jiang,

Deng,

Babla

et al. 2024

Preprint

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The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-related nuclease (Cas) system allows precise and easy editing of genes in many plant species. However, this system has not yet been applied to any fern species due to the complex characteristics of fern genomes, genetics and physiology. Here, we established, for the first time, a protocol for gametophyte-based screening single-guide RNAs (sgRNAs) with high efficiency for CRISPR/Cas-mediated gene editing in a model fern species, Ceratopteris richardii. We utilized the C. richardii Actin promoter to drive sgRNA expression and enhanced CaMV 35S promoter to drive the expression of Streptococcus pyogenes Cas9 in this CRISPR-mediated editing system, which was employed to successfully edit a few genes (e.g., nucleotidase/phosphatase 1, CrSAL1; Cryptochrome 4, CRY4) and CrPDS, encoding a phytoene desaturase protein that resulted in an albino phenotype in C. richardii. Knockout of CrSAL1 resulted in significantly reduced stomatal conductance (gs), leaf transpiration rate (E), stomatal/pore length, and abscisic acid (ABA)-induced reactive oxygen species (ROS) accumulation in guard cells. Moreover, CrSAL1 overexpressing plants showed significantly increased net photosynthetic rate (A), gs, E and intrinsic water use efficiency (iWUE) as well as most of the stomatal traits and ROS production in guard cells compared to those in the wild-type (WT) plants. Taken together, the optimized CRISPR/Cas9 system provides a useful tool for functional genomics in a model fern species, allowing the exploration of fern gene functions for evolutionary biology, herbal medicine discovery and agricultural applications.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Efficient Gene Editing and Overexpression of Gametophyte Transformation in a Model Fern

Jiang,

Deng,

Babla

et al. 2024

Preprint

View full text Add to dashboard Cite

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“…Another GWAS analysis in rice focused on the seedling stage response to CS and chilling acclimation identified 235 SNPs (120 and 88 for relative shoot fresh weight under CS and chilling acclimation, respectively) and 11 and 12 QTL for CS and chilling acclimation, respectively (Li et al, 2022a). A GWAS study investigated phenotypic and physiological parameters at the seedling emergence stage in 200 cotton accessions from five ecological distributions under constant chilling (CC) and diurnal variation in chilling (DVC) identified 575 significantly associated SNPs and 35 stable QTL, with five each associated with traits under CC and DVC stress and 25 co‐associated (Shen et al, 2023a). Another recent GWAS study coupled with RNA‐seq in 351 core rice germplasm under three temperature conditions detected 54, 59, and 21 QTL (total 134 QTL) associated with normal, CS, and chilling acclimation conditions, respectively (Khatab et al, 2022).…”

Section: Omics‐driven Breeding For Temperature‐smart Plantsmentioning

confidence: 99%

Temperature‐smart plants: A new horizon with omics‐driven plant breeding

Raza,

Bashir,

Khare

et al. 2024

Physiologia Plantarum

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The adverse effects of mounting environmental challenges, including extreme temperatures, threaten the global food supply due to their impact on plant growth and productivity. Temperature extremes disrupt plant genetics, leading to significant growth issues and eventually damaging phenotypes. Plants have developed complex signaling networks to respond and tolerate temperature stimuli, including genetic, physiological, biochemical, and molecular adaptations. In recent decades, omics tools and other molecular strategies have rapidly advanced, offering crucial insights and a wealth of information about how plants respond and adapt to stress. This review explores the potential of an integrated omics‐driven approach to understanding how plants adapt and tolerate extreme temperatures. By leveraging cutting‐edge omics methods, including genomics, transcriptomics, proteomics, metabolomics, miRNAomics, epigenomics, phenomics, and ionomics, alongside the power of machine learning and speed breeding data, we can revolutionize plant breeding practices. These advanced techniques offer a promising pathway to developing climate‐proof plant varieties that can withstand temperature fluctuations, addressing the increasing global demand for high‐quality food in the face of a changing climate.

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“…Squared Pearson correlation coe cients (r 2 ) were calculated between pairwise SNPs using TASSEL version 5.0, utilizing the full matrix option to estimate the degree of linkage disequilibrium (LD) of the whole genome, as well as of the A, B, and D subgenomes (Shen et al, 2023). The LD decay curves were obtained by plotting the average pairwise correlation coe cient at the same chromosomal distance against the physical distance, and the con dence intervals for the QTL were de ned as the intersection of the curve with the LD threshold (r 2 = 0.2).…”

Section: Linkage Disequilibrium and Kinship Analysismentioning

confidence: 99%

Identification of genetic loci and candidate genes underlying freezing tolerance in wheat seedlings

Pan,

Nie,

Gao

et al. 2024

Theor Appl Genet

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Frost damage restricts wheat growth, development, and geographical distribution. However, the genetic mechanism of freezing tolerance (FT) remains unclear. Here, we evaluated FT phenotypes of 245 wheat varieties (lines) and genotyped them using a Wheat 90K array. The association analysis showed that ten stable loci were signi cantly associated with FT (P < 1 × 10-4), and explained 6.45-26.33% of the phenotypic variation. In particular, the major locus QFT.ahau-7B.2 was consistently related to all nine sets of FT phenotypic data. Based on ve cleaved ampli ed polymorphic sequence (CAPS) markers closely linked to QFT.ahau-7B.2, we narrowed down the target region to the 566.13-566.63 Mb interval on chromosome 7B, in which four candidate genes were annotated. Of these, only TaRPM1-7BL exhibited consistent differential expression after low temperature treatment between freezing-tolerant and freezingsensitive varieties. The results of cloning and whole-exome capture sequencing indicated that there were two main haplotypes for TaRPM1-7BL, including freezing-tolerant Hap1 and freezing-sensitive Hap2.Based on the representative SNP (+2556, A/G), leading to an amino acid change in the NBS domain, a CAPS marker (CAPS-TaRPM1-7BL) was developed and validated in 431 wheat varieties (lines) and 318 F2 lines derived from the cross of 'Annong 9267' (freezing-tolerant) × 'Yumai 9' (freezing-sensitive).Subsequently, the TaRPM1-7BL gene was silenced in 'Yumai 9' by virus-induced gene silencing (VIGS), and these silenced wheat seedlings exhibited enhanced FT phenotypes, suggesting that TaRPM1-7BL negatively regulates FT. These ndings are valuable for understanding the complex genetic basis of FT in wheat. Key messageTen stable loci for freezing tolerance (FT) in wheat were detected by association analysis. The candidate gene TaRPM1-7BL underlying the major locus QFT.ahau-7B.2 was identi ed and validated.

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Genome-wide association study identifies GhSAL1 affects cold tolerance at the seedling emergence stage in upland cotton (Gossypium hirsutum L.)

Cited by 15 publications

References 67 publications

Efficient Gene Editing and Overexpression of Gametophyte Transformation in a Model Fern

Efficient Gene Editing and Overexpression of Gametophyte Transformation in a Model Fern

Temperature‐smart plants: A new horizon with omics‐driven plant breeding

Identification of genetic loci and candidate genes underlying freezing tolerance in wheat seedlings

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