Combining GWAS, Genome-Wide Domestication and a Transcriptomic Analysis Reveals the Loci and Natural Alleles of Salt Tolerance in Rice (Oryza sativa L.)

Lv, Yang; Ma, Jie; Hua, Wei; Xiao, Fang; Wang, Yueying; Jahan, Noushin; Hazman, Mohamed; Qian, Qian; Shang, Lianguang; Guo, Longbiao

doi:10.3389/fpls.2022.912637

Cited by 24 publications

(13 citation statements)

References 111 publications

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“…Soil salinity increase is mainly owed to improper irrigation practices and limited fresh water irrigation [75]. Many farmers have had to use mixed saline water for irrigating their crops cultivated in the fertile soil of the Nile Delta and Valley, practices that imposed negative effects on both soil properties and crop productivity.…”

Section: Practical Implications Of This Studymentioning

confidence: 99%

Effect of Biochar Application to Fertile Soil on Tomato Crop Production under Saline Irrigation Regime

et al. 2022

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Biochar application is a promising sustainable strategy for enhancing soil properties thus crop production. However, biochar application to soil certainly alters its biological and physical properties, and could require extra costs. Therefore, biochar suitability to agroecosystems must be proactively estimated. The advantage of biochar addition to poor fertile or weathered soils has been well studies, however, its feasibility to fertile soil under low quality (saline) irrigation water was not frequently studied. Consequently, this work investigates the hypothesis of whether the application of biochar at a rate of 4.8 tons/ha to fertile soil (Nile Valley, Giza, Egypt) would ameliorate the negative effects of saline irrigation regime (3000 ppm) on tomato crop and soil. The results of two seasons experiments showed that saline irrigation significantly reduced tomato crop yield by an average reduction ratio of 51%, and biochar addition could not compensate such reduction. Furthermore, biochar did not reduce accumulated Na+ in fruits or roots. Tomato fruits produced from biochar-added soil were lower in TSS levels (41.7% reduction ratio) yet larger in diameter by approximately 1.5-fold increase. Interestingly, biochar addition into soil greatly promotes the length of stem-borne lateral roots and elevates the expression of LeNR (encodes nitrate reductase enzyme) in leaves yet under fresh irrigation regime. For soil properties, biochar application enhanced the soil properties under either saline or fresh water irrigation conditions. Collectively, it is assumed that biochar application to fertile soil in Nile Valley of Egypt could not alleviate tomato fruits yield reduction affected by applied saline irrigation regime.

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Section: Practical Implications Of This Studymentioning

confidence: 99%

Effect of Biochar Application to Fertile Soil on Tomato Crop Production under Saline Irrigation Regime

et al. 2022

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“…In addition, transcriptomic sequencing provides a high-throughput approach to identifying differentially expressed genes (DEG) at the whole genome level. The combination of transcriptome and genome-wide association analysis has been confirmed to be an effective method for identifying causative or candidate genes regulating complicated quantitative traits ( Li et al., 2021 ; Liu et al., 2021 ; Lv et al., 2022 ; Tan et al., 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Genetic dissection of branch architecture in oilseed rape (Brassica napus L.) germplasm

Wang

Wang²,

An³

et al. 2022

Front. Plant Sci.

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Branch architecture is an important factor influencing rapeseed planting density, mechanized harvest, and yield. However, its related genes and regulatory mechanisms remain largely unknown. In this study, branch angle (BA) and branch dispersion degree (BD) were used to evaluate branch architecture. Branch angle exhibited a dynamic change from an increase in the early stage to a gradual decrease until reaching a stable state. Cytological analysis showed that BA variation was mainly due to xylem size differences in the vascular bundle of the branch junction. The phenotypic analysis of 327 natural accessions revealed that BA in six environments ranged from 24.3° to 67.9°, and that BD in three environments varied from 4.20 cm to 21.4 cm, respectively. A total of 115 significant loci were detected through association mapping in three models (MLM, mrMLM, and FarmCPU), which explained 0.53%-19.4% of the phenotypic variations. Of them, 10 loci were repeatedly detected in different environments and models, one of which qBAD.A03-2 was verified as a stable QTL using a secondary segregation population. Totally, 1066 differentially expressed genes (DEGs) were identified between branch adaxial- and abaxial- sides from four extremely large or small BA/BD accessions through RNA sequencing. These DEGs were significantly enriched in the pathways related to auxin biosynthesis and transport as well as cell extension such as indole alkaloid biosynthesis, other glycan degradation, and fatty acid elongation. Four known candidate genes BnaA02g16500D (PIN1), BnaA03g10430D (PIN2), BnaC03g06250D (LAZY1), and BnaC06g20640D (ARF17) were identified by both GWAS and RNA-seq, all of which were involved in regulating the asymmetric distribution of auxins. Our identified association loci and candidate genes provide a theoretical basis for further study of gene cloning and genetic improvement of branch architecture.

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“…Since this initial observation, various studies have shown increased DHPD transcription in rice under abiotic stress ( Shankar et al., 2016 ; Zhou et al., 2016 ; Li et al., 2018 ). DHPD is one of seven genes that were simultaneously selected for salt tolerance during domestication of rice, that were identified by Lv et al. (2022) in transcriptomics and genome wide association studies of wild and domesticated Asian and African rice.…”

Section: Discussionmentioning

confidence: 99%

“…Since this initial observation, various studies have shown increased DHPD transcription in rice under abiotic stress (Shankar et al, 2016;Zhou et al, 2016;Li et al, 2018). DHPD is one of seven genes that were simultaneously selected for salt tolerance during domestication of rice, that were identified by Lv et al (2022) in transcriptomics and genome wide association studies of wild and domesticated Asian and African rice. Narsai and coworkers found that in rice, DHPD was one of 10% -14% of differentially expressed genes upregulated in response to salt and drought that was also upregulated in A. thaliana (Narsai et al, 2010).…”

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confidence: 99%

New Insights into rice pyrimidine catabolic enzymes

Lopez

Narvaez-Ortiz²,

Rincon‐Benavides³

et al. 2023

Front. Plant Sci.

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IntroductionRice is a primary global food source, and its production is affected by abiotic stress, caused by climate change and other factors. Recently, the pyrimidine reductive catabolic pathway, catalyzed by dihydropyrimidine dehydrogenase (DHPD), dihydropyrimidinase (DHP) and β-ureidopropionase (β-UP), has emerged as a potential participant in the abiotic stress response of rice.MethodsThe rice enzymes were produced as recombinant proteins, and two were kinetically characterized. Rice dihydroorotate dehydrogenase (DHODH), an enzyme of pyrimidine biosynthesis often confused with DHPD, was also characterized. Salt-sensitive and salt-resistant rice seedlings were subjected to salt stress (24 h) and metabolites in leaves were determined by mass spectrometry.ResultsThe OsDHPD sequence was homologous to the C-terminal half of mammalian DHPD, conserving FMN and uracil binding sites, but lacked sites for Fe/S clusters, FAD, and NADPH. OsDHPD, truncated to eliminate the chloroplast targeting peptide, was soluble, but inactive. Database searches for polypeptides homologous to the N-terminal half of mammalian DHPD, that could act as co-reductants, were unsuccessful. OsDHODH exhibited kinetic parameters similar to those of other plant DHODHs. OsDHP, truncated to remove a signal sequence, exhibited a kcat/Km = 3.6 x 103 s-1M-1. Osb-UP exhibited a kcat/Km = 1.8 x 104 s-1M-1. Short-term salt exposure caused insignificant differences in the levels of the ureide intermediates dihydrouracil and ureidopropionate in leaves of salt-sensitive and salt-resistant plants. Allantoin, a ureide metabolite of purine catabolism, was found to be significantly higher in the resistant cultivar compared to one of the sensitive cultivars.DiscussionOsDHP, the first plant enzyme to be characterized, showed low kinetic efficiency, but its activity may have been affected by truncation. Osb-UP exhibited kinetic parameters in the range of enzymes of secondary metabolism. Levels of two pathway metabolites were similar in sensitive and resistant cultivars and appeared to be unaffected by short-term salt exposure.”

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Combining GWAS, Genome-Wide Domestication and a Transcriptomic Analysis Reveals the Loci and Natural Alleles of Salt Tolerance in Rice (Oryza sativa L.)

Cited by 24 publications

References 111 publications

Effect of Biochar Application to Fertile Soil on Tomato Crop Production under Saline Irrigation Regime

Effect of Biochar Application to Fertile Soil on Tomato Crop Production under Saline Irrigation Regime

Genetic dissection of branch architecture in oilseed rape (Brassica napus L.) germplasm

New Insights into rice pyrimidine catabolic enzymes

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