Phenylalanine ammonia-lyase family is closely associated with response to phosphate deficiency in rice

Gho, Yun-Shil; Kim, Sang-jin; Jung, Ki‐Hong

doi:10.1007/s13258-019-00879-7

Cited by 32 publications

(22 citation statements)

References 36 publications

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“…Both expression and sequence analysis indicates that OsPAL2 and OsPAL4 influence grain yield in test hybrid. Thus phenyl propanoid pathway and PAL genes in particular are at centre stage of not only broad spectrum disease 74 , pest resistance 72 and tolerance to abiotic stress 75 but also for increasing grain yield.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide transcriptome profile of rice hybrids with and without Oryza rufipogon introgression reveals candidate genes for yield

Guttikonda

Thummala

Agarwal

et al. 2020

Sci Rep

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In this study, we compared genome-wide transcriptome profile of two rice hybrids, one with (test hybrid IR79156A/IL50-13) and the other without (control hybrid IR79156A/KMR3) O. rufipogon introgressions to identify candidate genes related to grain yield in the test hybrid. IL50-13 (Chinsurah Nona2 IET21943) the male parent (restorer) used in the test hybrid, is an elite BC 4 f 8 introgression line of KMR3 with O. rufipogon introgressions. We identified 2798 differentially expressed genes (DEGs) in flag leaf and 3706 DEGs in panicle. Overall, 78 DEGs were within the major yield QTL qyld2.1 and 25 within minor QTL qyld8.2. The DEGs were significantly (p < 0.05) enriched in starch synthesis, phenyl propanoid pathway, ubiquitin degradation and phytohormone related pathways in test hybrid compared to control hybrid. Sequence analysis of 136 DEGs from KMR3 and IL50-13 revealed 19 DEGs with SNP/InDel variations. Of the 19 DEGs only 6 showed both SNP and InDel variations in exon regions. Of these, two DEGs within qyld2.1, Phenylalanine ammonia-lyase (PAL) (Os02t0626400-01, OsPAL2) showed 184 SNPs and 11 InDel variations and Similar to phenylalanine ammonia-lyase (Os02t0627100-01, OsPAL4) showed 205 SNPs and 13 InDel variations. Both PAL genes within qyld2.1 and derived from O. rufipogon are high priority candidate genes for increasing grain yield in rice. Rice (Oryza sativa) is an important food crop providing 20% of daily calories to more than 50 percent of global population. Nearly 90% of rice is produced and consumed in Asia. The continuous increase in human population, especially in Asia, poses a major challenge to food security. Therefore, enhancing grain yield is the primary thrust area of plant breeders. Hybrid rice can help increase productivity by 10-20% more than conventional varieties 1. Currently, the highest-yielding rice hybrids are developed from inter-subspecific crosses between indica and japonica 2-5. Wild species have been used to breed parental lines for yield improvement in derived rice hybrids 6-10. Flag leaf is the most essential functional organ to produce a large proportion of photo-assimilates that are stored in grains 11,12. It is estimated that it contributes around 32.3% of total carbohydrates during grain filling 13. The panicle morphology also directly affects the number and size of seeds and also determines grain yield in rice 14-16. Flag leaf and panicles have been used previously at different developmental stages to unravel gene expression in pollen development and genetic networks that control panicle branching and architecture 17,18. The spatial and temporal expression profiles of genes during 19 vegetative and reproductive stages of organ development were analysed to identify stage-preferential/stage-specific genes in IR64 variety and anther-specific genes in Pusa Basmati1 variety 19,20. A whole-genome oligonucleotide microarray of super hybrid LYP9 (Liangyoupeijiu) and its parents 9311 and PA64s in 7 different tissues showed that differentially expressed genes for energy metabolism i...

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Section: Discussionmentioning

confidence: 99%

Genome-wide transcriptome profile of rice hybrids with and without Oryza rufipogon introgression reveals candidate genes for yield

Guttikonda

Thummala

Agarwal

et al. 2020

Sci Rep

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“…Low-Pi lowers the capacity to process incoming light and enhances starch accumulation in chloroplasts, thereby leading to photoinhibition [72,73]. Within the category of genes that were signi cantly down-regulated, most of them were related to stress and defense responses (Additional le 8); for instance, uncharacterized protein (HORVU2Hr1G030090, -6.50), oxalate oxidase (-4.41) [74], beta-sesquiphellandrene synthase (-3.41), glutamate carboxypeptidase (-3.17), chalcone synthase (-3.05) [75], or caleosin-like protein (-2.95) ( Fig. 5C).…”

Section: Identi Cation Of Barley Genes Responsive To Pi-starvationmentioning

confidence: 99%

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

Sega

Kruszka

Bielewicz

et al. 2020

Preprint

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Background: Small RNAs (sRNAs) are 20–30 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration triggers plant responses to balance the internal Pi level. Results: In this study, we describe Pi-starvation-responsive small RNAs and transcriptome changes in barley (Hordeum vulgare L.) using Next-Generation Sequencing (NGS) RNA-Seq data derived from three different types of NGS libraries: (i) small RNAs, (ii) degraded RNAs, and (iii) functional mRNAs. We find that differentially and significantly expressed miRNAs (DEMs, p-value < 0.05) are represented by 162 (44.88 % of total differentially expressed small RNAs) molecules in shoot and 138 (7.14 %) in root; mainly various miR399 and miR827 isomiRs. The remaining small RNAs (i.e., those without perfect match to reference sequences deposited in miRBase) are considered as differentially expressed other sRNAs (DESs, p-value Bonferroni correction < 0.05). In roots, a more abundant and diverse set of other sRNAs (DESs, 1796 unique sequences, 0.13 % from total unique reads obtained under low-Pi) contributes more to the compensation of low-Pi stress than that in shoots (DESs, 199 unique sequences, 0.01 %). More than 80 % of differentially expressed other sRNAs are up-regulated in both organs. Additionally, in barley shoots, up-regulation of small RNAs is accompanied by strong induction of two nucleases (S1/P1 endonuclease and 3’-5’ exonuclease). This suggests that most small RNAs may be generated upon endonucleolytic cleavage to increase the internal Pi pool. Transcriptomic profiling of Pi-starved barley shoots identifies 98 differentially expressed genes (DEGs). A majority of the DEGs possess characteristic Pi-responsive cis-regulatory elements (P1BS and/or PHO element), located mostly in the proximal promoter regions. GO analysis shows that the discovered DEGs primarily alter plant defense, plant stress response, nutrient mobilization, or pathways involved in the gathering and recycling of phosphorus from organic pools.Conclusions: Our results provide comprehensive data to demonstrate complex responses at the RNA level in barley to maintain Pi homeostasis and indicate that barley adapts to Pi-starvation through elicitation of RNA degradation. Novel P-responsive genes were selected as putative candidates to overcome low-Pi stress in barley plants.

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“…Therefore, PAL is involved in the biosynthesis of a wide range of secondary metabolites including lignin, flavonoids, tannins, and many other less-studied benzene compounds and phenolic glycosides that play many essential physiological roles in plant growth, development and adaptations (MacDonald and D'Cunha 2007;Vogt 2010). Numerous studies have suggested the essential role of PAL in protecting plants from environmental stressors such as drought (Guo and Wang 2009;Khakdan et al 2018), salinity (Gao et al 2008), extreme temperatures (Olsen et al 2008), nutrient deficiency (Olsen et al 2008;Gho et al 2020) and waterlogging (Nguyen et al 2016). This makes it an excellent inducer that triggers reactions aimed at increasing plant resistance to multiple stresses.…”

Section: Introductionmentioning

confidence: 99%

Molecular characterisation of

Feng

Huang

Zhang

et al. 2022

Crop & Pasture Science

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Phenylalanine ammonia lyase (PAL) is the first enzyme in the phenylpropanoid pathway and plays a critical role in plant growth, development and stress defence. However, there have been few reports of the PAL gene family in lucerne (also known as alfalfa, Medicago sativa L.), one of the most important forage legume species worldwide. In this study, we report that PAL in lucerne is encoded by a family of seven genes: MsPAL1–MsPAL7. Furthermore, a comprehensive genome-wide bioinformatics analysis of the MsPAL gene family is presented, including chromosomal locations, phylogenetic relationships, gene structures and conserved motifs. The cis-elements and potential biological functions of these genes were investigated, revealing the potential roles of MsPAL members in response to various stresses. RT-qPCR results showed that the expression of MsPAL6 was significantly upregulated under both salinity- and waterlogging-stress conditions. Other MsPAL members such as MsPAL1 and MsPAL2 were downregulated under saline conditions and upregulated significantly after waterlogging stress. Our findings provide useful information for further practical analyses and for the genetic improvement of abiotic stress tolerance of lucerne.

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Phenylalanine ammonia-lyase family is closely associated with response to phosphate deficiency in rice

Cited by 32 publications

References 36 publications

Genome-wide transcriptome profile of rice hybrids with and without Oryza rufipogon introgression reveals candidate genes for yield

Genome-wide transcriptome profile of rice hybrids with and without Oryza rufipogon introgression reveals candidate genes for yield

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

Molecular characterisation of

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