Identification and characterization ofS-RNasegenes in apple rootstock and the diversity ofS-RNasesinMalusspecies

Kim, Hoy Taek; Moriya, Shigeki; Okada, Kazuma; Abe, Kazuyuki; Park, Jong In; Yamamoto, Takatsugu; Nou, Ill Sup

doi:10.5010/jpb.2016.43.1.49

Cited by 6 publications

(2 citation statements)

References 36 publications

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“…For the first time, CCD-like (CCDL), a new member of the CCD family, was found in tomatoes (Cheng et al, 2022). The retinal pigment epithelium membrane protein (RPE65) domain is found in all CCD genes (Kiser, 2022), which is typical of enzymes involved in carotenoid cleavage (Kim et al, 2016). The CCD gene family has been found and studied in several plant species, including Arabidopsis (Chernys and Zeevaart, 2000).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and in-silico expression analysis of carotenoid cleavage oxygenases gene family in Oryza sativa (rice) in response to abiotic stress

Haider,

Sami,

Shafiq

et al. 2023

Front. Plant Sci.

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Rice constitutes a foundational cereal and plays a vital role in the culinary sector. However, the detriments of abiotic stress on rice quality and productivity are noteworthy. Carotenoid cleavage oxygenases (CCO) hold vital importance as they enable the particular breakdown of carotenoids and significantly contribute towards the growth and response to abiotic stress in rice. Due to the insufficient information regarding rice CCOs and their potential role in abiotic stress, their utilization in stress-resistant genetic breeding remains limited. The current research identified 16 CCO genes within the Oryza sativa japonica group. These OsCCO genes can be bifurcated into three categories based on their conserved sequences: NCEDs (9-Cis-epoxycarotenoid dioxygenases), CCDs (Carotenoid cleavage dioxygenases) and CCD-like (Carotenoid cleavage dioxygenases-like). Conserved motifs were found in the OsCCO gene sequence via MEME analysis and multiple sequence alignment. Stress-related cis-elements were detected in the promoter regions of OsCCOs genes, indicating their involvement in stress response. Additionally, the promoters of these genes had various components related to plant light, development, and hormone responsiveness, suggesting they may be responsive to plant hormones and involved in developmental processes. MicroRNAs play a pivotal role in the regulation of these 16 genes, underscoring their significance in rice gene regulation. Transcriptome data analysis suggests a tissue-specific expression pattern for rice CCOs. Only OsNCED6 and OsNCED10 significantly up-regulated during salt stress, as per RNA seq analyses. CCD7 and CCD8 levels were also higher in the CCD group during the inflorescence growth stage. This provides insight into the function of rice CCOs in abiotic stress response and identifies possible genes that could be beneficial for stress-resistant breeding.

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Section: Introductionmentioning

confidence: 99%

Genome-wide identification and in-silico expression analysis of carotenoid cleavage oxygenases gene family in Oryza sativa (rice) in response to abiotic stress

Haider,

Sami,

Shafiq

et al. 2023

Front. Plant Sci.

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“…The S-RNase is always expressed in the pistil, but when the S-allele of the pollen is not the same as either of the two S-alleles expressed in the pistil, the S-RNases are inactivated by at least two genes specifically expressed in pollen -S-locus F-box Brother genes (Sassa et al 2007). To date, 57 S-alleles of the Malus S-locus encoding a different S-RNase have been identified (Kim et al 2016).…”

Section: Introductionmentioning

confidence: 99%

Self-incompatibility alleles in important genotypes for apple breeding in Brazil

Brancher

Hawerroth

Kvitschal

et al. 2020

Crop Breed. Appl. Biotechnol.

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Characterization of 25 full-length S-RNase alleles, including flanking regions, from a pool of resequenced apple cultivars

et al. 2018

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Data obtained from Illumina resequencing of 63 apple cultivars were used to obtain full-length S-RNase sequences using a strategy based on both alignment and de novo assembly of reads. The reproductive biology of apple is regulated by the S-RNase-based gametophytic self-incompatibility system, that is genetically controlled by the single, multi-genic and multi-allelic S locus. Resequencing of apple cultivars provided a huge amount of genetic data, that can be aligned to the reference genome in order to characterize variation to a genome-wide level. However, this approach is not immediately adaptable to the S-locus, due to some peculiar features such as the high degree of polymorphism, lack of colinearity between haplotypes and extensive presence of repetitive elements. In this study we describe a dedicated procedure aimed at characterizing S-RNase alleles from resequenced cultivars. The S-genotype of 63 apple accessions is reported; the full length coding sequence was determined for the 25 S-RNase alleles present in the 63 resequenced cultivars; these included 10 previously incomplete sequences (S , S , S , S , S , S , S , S , S and S ). Moreover, sequence divergence clearly suggests that alleles S and S , proposed to be neutral variants of the same alleles, should be instead considered different specificities. The promoter sequences have also been analyzed, highlighting regions of homology conserved among all the alleles.

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Identification and characterization ofS-RNasegenes in apple rootstock and the diversity ofS-RNasesinMalusspecies

Cited by 6 publications

References 36 publications

Genome-wide identification and in-silico expression analysis of carotenoid cleavage oxygenases gene family in Oryza sativa (rice) in response to abiotic stress

Genome-wide identification and in-silico expression analysis of carotenoid cleavage oxygenases gene family in Oryza sativa (rice) in response to abiotic stress

Self-incompatibility alleles in important genotypes for apple breeding in Brazil

Characterization of 25 full-length S-RNase alleles, including flanking regions, from a pool of resequenced apple cultivars

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