Comparative transcriptome analysis reveals a rapid response to phosphorus deficiency in a phosphorus-efficient rice genotype

Prodhan, M. Asaduzzaman; Pariasca‐Tanaka, Juan; Ueda, Yoshiaki; Hayes, Patrick E.; Wissuwa, Matthias

doi:10.1038/s41598-022-13709-w

Cited by 7 publications

(2 citation statements)

References 63 publications

(70 reference statements)

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“…The most TFs were detected in the DEGs of Qd11 (361), followed by Zh13 (261), and the least TFs were detected in DEGs of Nm, with only 19 ( Table S4 ). Similar results were observed in the comparative transcriptome analysis of rice ( Prodhan et al., 2022 ) and sorghum ( Zhang et al., 2019 ). This suggests that phosphorus-efficient varieties express more enzymes in response to low phosphorus.…”

Section: Discussionsupporting

confidence: 84%

Global transcriptomic analysis reveals candidate genes associated with different phosphorus acquisition strategies among soybean varieties

Yang

Chen

et al. 2022

Front. Plant Sci.

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IntroductionSoybean adapts to phosphorus-deficient soils through three important phosphorus acquisition strategies, namely altered root conformation, exudation of carboxylic acids, and symbiosis with clumping mycorrhizal fungi. However, the trade-offs and regulatory mechanisms of these three phosphorus acquisition strategies in soybean have not been researched.MethodsIn this study, we investigated the responses of ten different soybean varieties to low soil phosphorus availability by determining biomass, phosphorus accumulation, root morphology, exudation, and mycorrhizal colonization rate. Furthermore, the molecular regulatory mechanisms underlying root phosphorus acquisition strategies were examined among varieties with different low-phosphorus tolerance using transcriptome sequencing and weighted gene co-expression network analysis.Results and discussionThe results showed that two types of phosphorus acquisition strategies—“outsourcing” and “do-it-yourself”—were employed by soybean varieties under low phosphorus availability. The “do-it-yourself” varieties, represented by QD11, Zh30, and Sd, obtained sufficient phosphorus by increasing their root surface area and secreting carboxylic acids. In contrast, the “outsourcing” varieties, represented by Zh301, Zh13, and Hc6, used increased symbiosis with mycorrhizae to obtain phosphorus owing to their large root diameters. Transcriptome analysis showed that the direction of acetyl-CoA metabolism could be the dividing line between the two strategies of soybean selection. ERF1 and WRKY1 may be involved in the regulation of phosphorus acquisition strategies for soybeans grown under low P environments. These findings will enhance our understanding of phosphorus acquisition strategies in soybeans. In addition, they will facilitate the development of breeding strategies that are more flexible to accommodate a variety of production scenarios in agriculture under low phosphorus environments.BackgroundAssociation of gastric atrophy or cancer with levels of serum pepsinogens, gastrin-17 and anti-Helicobacter pylori IgG antibody have been extensively studied. However, the association of serum pepsinogen and gastrin-17 with H. pylori infection has not been studied in a large population.

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Section: Discussionsupporting

confidence: 84%

Global transcriptomic analysis reveals candidate genes associated with different phosphorus acquisition strategies among soybean varieties

Yang

Chen

et al. 2022

Front. Plant Sci.

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“…Shoots were oven-dried for 3 days at 70°C and weighed. A subsample of 0.2 g was used for acid digestion in a 3:1 mixture of HNO 3 and HClO 4 and subjected to determination of tissue P concentrations using the molybdenum blue method as previously described (Prodhan et al 2022).…”

Section: Variation In Lateral Root Traits Between Parental Genotypesmentioning

confidence: 99%

Novel QTL for Lateral Root Density and Length improve Phosphorus Uptake in Rice (Oryza sativa L.)

Dinh

Ueda

González

et al. 2023

Preprint

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The rice root system consists of two types of lateral roots, indeterminate larger L-types capable of further branching, and determinate, short, unbranched S-types. L-type laterals correspond to the typical lateral roots of cereals whereas S-type laterals are unique to rice. Both types contribute to nutrient and water uptake and genotypic variation for density and length of these laterals could be exploited in rice improvement to enhance adaptations to nutrient and water-limited environments. Our objectives were to determine how best to screen for lateral root density and length and to identify markers linked to genotypic variation for these traits. Using different growing media showed that screening in nutrient solution exposed genotypic variation for S-type and L-type density, but only the lateral roots of soil-grown plants varied for their lengths. A QTL mapping population developed from parents contrasting for lateral root traits was grown in a low-P field, roots were sampled, scanned and density and length of lateral roots measured. One QTL each was detected for L-type density (LDC), S-type density on crown root (SDC), S-type density on L-type (SDL), S-type length on L-type (SLL), and crown root number (RNO). The QTL for LDC on chromosome 5 had a major effect, accounting for 46% of the phenotypic variation. This strong positive effect was confirmed in additional field experiments, showing that lines with the donor parent allele at qLDC5 had 50% higher LDC. Investigating the contribution of lateral root traits to P uptake using stepwise regressions indicated LDC and RNO were most influential, followed by SDL. Simulating effects of allelic differences of main QTL in a P uptake model confirmed that qLDC5 was most effective in improving P uptake followed by qRNO9 for RNO and qSDL9 for S-type lateral density on L-type laterals. Pyramiding qLDC5 with qRNO9 and qSDL9 is possible given that trade-offs between traits were not detected. Phenotypic selection for the RNO trait during variety development would be feasible, however, the costs of doing so reliably for lateral root density traits is prohibitive and markers identified here therefore provide the first opportunity to incorporate such traits into a breeding program.

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Physiological evidence that nitrate use positively correlates with internal phosphorus utilization efficiency and phosphorus uptake efficiency in rice (Oryza sativa L.)

Ueda

Wissuwa²

2022

Plant Soil

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Comparative transcriptome analysis reveals a rapid response to phosphorus deficiency in a phosphorus-efficient rice genotype

Cited by 7 publications

References 63 publications

Global transcriptomic analysis reveals candidate genes associated with different phosphorus acquisition strategies among soybean varieties

Global transcriptomic analysis reveals candidate genes associated with different phosphorus acquisition strategies among soybean varieties

Novel QTL for Lateral Root Density and Length improve Phosphorus Uptake in Rice (Oryza sativa L.)

Physiological evidence that nitrate use positively correlates with internal phosphorus utilization efficiency and phosphorus uptake efficiency in rice (Oryza sativa L.)

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