Genome-Wide Association Study for Non-Photochemical Quenching Traits in Oryza sativa L.

Wei, Youbo; Liu, Sicheng; Xiong, Dongliang; Xiong, Zhuang; Zhang, Zuolin; Wang, Fei; Huang, Jianliang

doi:10.3390/agronomy12123216

Cited by 4 publications

(3 citation statements)

References 43 publications

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“…Despite the challenges associated with GBS, it is still a cost-effective, high-throughput, and minimally invasive method, making it suitable for large-scale studies of diverse crop populations. GBS can capture rare and low-frequency genetic variants that may not be detected by other genotyping methods, providing a more comprehensive view of the genetic architecture underlying BLB resistance [29,60,97].…”

Section: Discussionmentioning

confidence: 99%

“…Variant were called using the Genome Analysis Toolkit (GATK) software v 4.2.3.0 [42,58] where SNPs and insertions-deletions (indels) were named using the GVCF analysis, and variants were grouped using GATK's CombineGVCFs function [59]. The joint call step was then performed using genotypeGVCFs of the GATK software [60], followed by SNP extraction using SelectVariantsGATK based on the reference genome.…”

Section: Genotyping Preparationmentioning

confidence: 99%

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Genome-Wide Association Study Using Genotyping by Sequencing for Bacterial Leaf Blight Resistance Loci in Local Thai Indica Rice

Danaisilichaichon

Vejchasarn²,

Patarapuwadol

et al. 2023

Agronomy

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Bacterial leaf blight (BLB) is a devastating disease caused by Xanthomonas oryzae pv. oryzae (Xoo), which poses a significant threat to global rice production. In this study, a genome-wide association study (GWAS) was conducted using the genotyping-by-sequencing (GBS) approach to identify candidate single nucleotide polymorphisms (SNPs) associated with BLB resistance genes. The study utilized 200 indica rice accessions inoculated with seven distinct Xoo isolates and filtered highly significant SNPs using a minor allele frequency (MAF) of >5% and a call rate of 75%. Four statistical models were used to explore potential SNPs associated with BLB resistance, resulting in the identification of 32 significant SNPs on chromosomes 1–8 and 12 in the rice genome. Additionally, 179 genes were located within ±100 kb of the SNP region, of which 49 were selected as candidate genes based on their known functions in plant defense mechanisms. Several candidate genes were identified, including two genes in the same linkage disequilibrium (LD) decay as the well-known BLB resistance gene (Xa1). These findings represent a valuable resource for conducting further functional studies and developing novel breeding strategies to enhance the crop’s resistance to this disease.

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Section: Discussionmentioning

confidence: 99%

Section: Genotyping Preparationmentioning

confidence: 99%

Genome-Wide Association Study Using Genotyping by Sequencing for Bacterial Leaf Blight Resistance Loci in Local Thai Indica Rice

Danaisilichaichon

Vejchasarn²,

Patarapuwadol

et al. 2023

Agronomy

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“…Both crops and wild species exhibit substantial natural variation in NPQ (Jung and Niyogi 2009;Rungrat et al 2019;Gamba et al 2022;Wei et al 2022). A study of the maximum NPQ induction in rice (Oryza sativa) identified 33 loci, including the rice ortholog of PSBS (Wang et al 2017).…”

Section: Introductionmentioning

confidence: 99%

Comparative GWAS identifies a role for Mendel’s green pea gene in the nonphotochemical quenching kinetics of sorghum, maize, and arabidopsis

Sahay,

Shrestha,

Dias

et al. 2023

Preprint

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Photosynthetic organisms must cope with rapid fluctuations in light intensity. Nonphotochemical quenching (NPQ) enables the dissipation of excess light energy as heat under high light conditions, whereas its relaxation under low light maximizes photosynthetic productivity. We quantified variation in NPQ kinetics across a large sorghum (Sorghum bicolor) association panel in four environments, uncovering significant genetic control for NPQ. A genome-wide association study (GWAS) identified 20 unique regions in the sorghum genome associated with NPQ. We detected strong signals from the sorghum ortholog of Arabidopsis thaliana SUPPRESSOR OF VARIEGATION3 (SVR3) involved in plastid nucleus signaling and tolerance to cold. By integrating GWAS results for NPQ across maize (Zea mays) and sorghum association panels, we identified a second gene, NON-YELLOWING 1 (NYE1), originally identified by Gregor Mendel in pea (Pisum sativum) and involved in the degradation of photosynthetic pigments in light-harvesting complexes, along with OUTER ENVELOPE PROTEIN 37 (OEP37), that encodes a transporter in chloroplast envelope. Analysis of nye1 insertion alleles in A. thaliana confirmed the effect of this gene on NPQ kinetics across monocots and eudicots. We extended our comparative genomics GWAS framework across the entire maize and sorghum genomes, identifying four additional loci involved in NPQ kinetics. These results provide a baseline for engineering crops with improved NPQ kinetics and increasing the accuracy and speed of candidate gene identification for GWAS in species with high linkage disequilibrium.

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MWCNTs Alleviated saline-alkali stress by optimizing photosynthesis and sucrose metabolism in rice seedling

Xu,

Liu,

et al. 2023

Plant Signaling & Behavior

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Saline and alkali stress affects the growth and development, survival rate, and final yield of rice, while new nano materials can have a positive effect on rice growth. In order to investing the effects of carboxymethyl multi walled carbon nanotubes (MWCNTs) on the growth and development of rice seedlings under salt alkali stress, rice seedlings were cultured using rice variety “Songjing 3” using nutrient solution water culture method. The effects of MWCNTs on water absorption capacity, leaf photosynthesis, and sucrose metabolism of rice seedlings under 50 mmol/L saline-alkali stress (1NaCl: 9Na 2 SO 4 : 9NaHCO 3 : 1Na 2 CO 3 ) conditions were investigated. The results showed that MWCNTs can improve the water use ability of roots and leaves, especially the water absorption ability of roots, which provides a guarantee for the improvement of rice biomass and the enhancement of leaf photosynthetic capacity under adverse conditions. After treatment with MWCNTs, the photosynthetic rate (P n ), stomatal conductance (g s ), and transpiration rate (T r ) of leaves increased significantly, and the photochemical quenching value (qP), photochemical quantum efficiency value ( F v / F m ), and electron transfer rate value (ETR) of chlorophyll fluorescence parameters increased significantly, which is beneficial to the improvement of the PSII photosynthetic system. MWCNTs treatment promoted the increase of photosynthetic pigment content in leaves under salt and alkali stress, improved the ratio of Chla and Chlb parameters, increased the activities of key photosynthetic enzymes (RUBPCase and PEPCase) in leaves, increased the value of total lutein cycle pool (VAZ), and significantly enhanced the deepoxidation effect of lutein cycle (DEPS), which can effectively alleviate the stomatal and non stomatal constraints on leaf photosynthesis caused by salt and alkali stress. MWCNTs treatment significantly enhanced the activities of sucrose phosphate synthase (SPS) and sucrose synthase (SS) under salt and alkali stress, and decreased the activities of soluble acid invertase (SAInv) and alkaline/neutral invertase (A/N-Inv), indicating that MWCNTs promoted sucrose synthesis while inhibiting sucrose decomposition, thereby promoting sucrose accumulation in rice leaves. This study can provide theoretical and experimental basis for the application of MWCNTs to the production of rice under salt and alkali stress, and can find a new way for rice production in saline and alkaline lands.

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Genome-Wide Association Study for Non-Photochemical Quenching Traits in Oryza sativa L.

Cited by 4 publications

References 43 publications

Genome-Wide Association Study Using Genotyping by Sequencing for Bacterial Leaf Blight Resistance Loci in Local Thai Indica Rice

Genome-Wide Association Study Using Genotyping by Sequencing for Bacterial Leaf Blight Resistance Loci in Local Thai Indica Rice

Comparative GWAS identifies a role for Mendel’s green pea gene in the nonphotochemical quenching kinetics of sorghum, maize, and arabidopsis

MWCNTs Alleviated saline-alkali stress by optimizing photosynthesis and sucrose metabolism in rice seedling

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