Genome-Wide Analysis of the PYL Gene Family and Identification of PYL Genes That Respond to Abiotic Stress in Brassica napus

Di, Feifei; Jian, Hongju; Wang, Tengyue; Chen, Xueping; Ding, Yiran; Du, Hongwu; Lu, Kun; Li, Jiana; Liu, Liezhao

doi:10.3390/genes9030156

Cited by 69 publications

(53 citation statements)

References 51 publications

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“…The members of a gene family, having significant similarities in both structure and function, encode similar protein products. However, they are usually located at different positions on the same chromosome or on different chromosomes, each with different regulatory patterns and functions 39 . In our previous study, the two members of the BoaPDS gene family in Chinese kale (BaPDS1 and BaPDS2) played different and indispensable roles, and their functions were partially complementary 20 .…”

Section: Discussionmentioning

confidence: 99%

Color-related chlorophyll and carotenoid concentrations of Chinese kale can be altered through CRISPR/Cas9 targeted editing of the carotenoid isomerase gene BoaCRTISO

et al. 2020

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The carotenoid isomerase gene (BoaCRTISO) of Chinese kale was targeted and edited using the CRISPR/Cas9 system in the present study. The results showed a high mutation rate (81.25%), and 13 crtiso mutants were obtained. Only two types of mutations, insertions and replacements, were found. Both the total and individual carotenoid and chlorophyll concentrations of the biallelic and homozygous mutants were reduced, and the total levels declined by 11.89–36.33%. The color of the biallelic and homozygous mutants changed from green to yellow, likely reflecting a reduction in the color-masking effect of chlorophyll on carotenoids. The expression levels of most carotenoid and chlorophyll biosynthesis-related genes, including CRTISO, were notably lower in the mutants than in the WT plants. In addition, the functional differences between members of this gene family were discussed. In summary, these findings indicate that CRISPR/Cas9 is a promising technique for the quality improvement of Chinese kale and other Brassica vegetables.

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Section: Discussionmentioning

confidence: 99%

Color-related chlorophyll and carotenoid concentrations of Chinese kale can be altered through CRISPR/Cas9 targeted editing of the carotenoid isomerase gene BoaCRTISO

et al. 2020

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“…To date, their expression profiles in various tissues have been revealed substantial differences among PYL genes for many plants. For example, some PYLs respectively displayed relatively higher levels in seeds of soybean, the callus of B. rapa , and the latex of rubber tree than other tissues [ 23 , 24 , 40 , 41 ]. Moreover, most OsPYLs were expressed in all organs of rice, OsPYL3 and OsPYL5 were predominantly expressed in leaves, and OsPYL1 in roots [ 42 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification of the ABA Receptors Genes and Their Response to Abiotic Stress in Apple

Hou

Huo

et al. 2020

Plants

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The pyrabactin resistance (PYR)/PYR1-like (PYL)/regulatory components of ABA receptor (RCAR) (known as PYLs for short) have been identified and characterized as the ABA receptors in some plants. However, little is known about the details regarding PYL family genes in the apple (Malusdomestica). In this study, we identified 13 apple PYLs, termed MdPYL1-13, which could be classified into four groups according to structural features of the amino acid sequence. The gene structures and conserved motifs analysis found that the majority of MdPYLs had a similar number of exons and similar conserved motif profile in the same group. In addition, 11 gene pairs were identified to exhibit synteny by synteny analysis between the apple and Arabidopsis. Furthermore, we investigated MdPYLs transcript level in various organs of the red-fleshed apple (Malussieversii f. Neidzwetzkyana (Dieck) Langenf) ‘Xinjiang No.1’. The results suggested all MdPYLs within group I were expressed at relatively higher levels in all of the organs tested. However, the genes of group IV had little or no variation. Additionally, we found various hormone and stress-related cis-elements in the promoters of MdPYLs by analyzing cis-elements. Therefore, the expression levels of all MdPYLs were further detected under ABA, PEG, salt, and cold stresses in ‘Xinjiang No.1’ seedlings. We found that all MdPYLs except for MdPYL11 were upregulated by ABA treatment, 10 genes were upregulated by PEG treatment, 12 genes were upregulated by NaCl treatment, and six genes were upregulated by cold treatment (4 °C) while seven genes were downregulated. Thus, these MdPYLs might be involved in the defense against abiotic stresses. In addition, the interaction between 13 MdPYLs and two 2C protein phosphatases in the apple (MdPP2C65 and MdPP2C72) was investigated in yeast two-hybrid assays. These results suggested that MdPYLs may bind to MdPP2C65 and MdPP2C72 in different manners and with different intensity. Our studies provide useful information for further investigating and researching the regulatory mechanisms of PYL family genes in response to abiotic stresses in the apple.

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“…Most of these miRNAs identified have been implicated in stress responsiveness and development (Additional file 8). In an earlier study with Brassica napus, 26 miRNAs targeting 11 BnPYL genes were identified, and predicted that 10 members of miR169 target BnPYL1-4 [85]. For better understanding, each OsPYL gene targeted by different miRNAs is depicted by different colour and shape (Fig.…”

Section: Regulation Of Gene Expressionmentioning

confidence: 99%

Genome-wide identification and characterization of ABA receptor PYL gene family in rice

et al. 2020

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Background Abscisic acid (ABA), a key phytohormone that controls plant growth and stress responses, is sensed by the pyrabactin resistance 1(PYR1)/PYR1-like (PYL)/regulatory components of the ABA receptor (RCAR) family of proteins. Comprehensive information on evolution and function of PYL gene family in rice (Oryza sativa) needs further investigation. This study made detailed analysis on evolutionary relationship between PYL family members, collinearity, synteny, gene structure, protein motifs, cis-regulatory elements (CREs), SNP variations, miRNAs targeting PYLs and expression profiles in different tissues and stress responses. Results Based on sequence homology with Arabidopsis PYL proteins, we identified a total of 13 PYLs in rice (BOP clade) and maize (PACCMAD clade), while other members of BOP (wheat – each diploid genome, barley and Brachypodium) and PACCMAD (sorghum and foxtail millet) have 8-9 PYLs. The phylogenetic analysis divided PYLs into three subfamilies that are structurally and functionally conserved across species. Gene structure and motif analysis of OsPYLs revealed that members of each subfamily have similar gene and motif structure. Segmental duplication appears be the driving force for the expansion of PYLs, and the majority of the PYLs underwent evolution under purifying selection in rice. 32 unique potential miRNAs that might target PYLs were identified in rice. Thus, the predicted regulation of PYLs through miRNAs in rice is more elaborate as compared with B. napus. Further, the miRNAs identified to in this study were also regulated by stresses, which adds additional layer of regulation of PYLs. The frequency of SAPs identified was higher in indica cultivars and were predominantly located in START domain that participate in ABA binding. The promoters of most of the OsPYLs have cis-regulatory elements involved in imparting abiotic stress responsive expression. In silico and q-RT-PCR expression analyses of PYL genes revealed multifaceted role of ABARs in shaping plant development as well as abiotic stress responses. Conclusion The predicted miRNA mediated regulation of OsPYLs and stress regulated expression of all OsPYLs, at least, under one stress, lays foundation for further validation and fine tuning ABA receptors for stress tolerance without yield penalty in rice.

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Genome-Wide Analysis of the PYL Gene Family and Identification of PYL Genes That Respond to Abiotic Stress in Brassica napus

Cited by 69 publications

References 51 publications

Color-related chlorophyll and carotenoid concentrations of Chinese kale can be altered through CRISPR/Cas9 targeted editing of the carotenoid isomerase gene BoaCRTISO

Color-related chlorophyll and carotenoid concentrations of Chinese kale can be altered through CRISPR/Cas9 targeted editing of the carotenoid isomerase gene BoaCRTISO

Genome-Wide Identification of the ABA Receptors Genes and Their Response to Abiotic Stress in Apple

Genome-wide identification and characterization of ABA receptor PYL gene family in rice

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