Genome‑wide identification and molecular characterization of cysteine protease genes in rice

Marjohn C. Niño,Me‑Sun Kim,Kwon-Kyoo Kang,조용구 한국식물생명공학회 2020 Plant biotechnology reports Vol.14 No.1

Cysteine protease activity comprises the majority of proteolytic activities in plants. They are involved in almost every facet of the plant’s development. Accumulating evidence indicates multiple roles of this protease type in response to biotic and abiotic stress. To understand the regulations and functions of cysteine protease in rice, its evolutionary and structural evidence was uncovered in this study. Using MEROPS, a peptidase database, the 74 rice cysteine proteases belonging to six families were queried. Each of these families represents distinct proteolytic enzyme; C1 is a papain-like protease, C2 is a calpain- 2-type, C12 is an ubiquitinyl hydrolase-L1 enzyme, C13 is legumain, C14 is a caspase-1 type, and C15 is a pyroglutamyl peptidase 1 enzyme type. Evolutionary expansion attributed to gene duplication and diversification was particularly evident in C1 family which showed the highest number (n = 53) of members, most of which contained the highest number and most variable introns and motifs, whereas families C13, C14, and C15 had only a few members which all contained lesser number and variation of intron and motif. Out of 74 total cysteine protease gene members, 73 were globular proteins and 55 were predicted as stable proteins. Spatial expression assay of selected C1 members showed that LOC_Os01g73980 and LOC_Os05g01810 were highly expressed in the stem and leaves, while LOC_Os02g27030 was constitutively expressed in all tissues. The expression of LOC_Os01g73980 and LOC_Os05g01810 was also highly activated by salinity stress, while LOC_Os02g27030 was activated by both salinity and heat. LOC_Os05g01810 overexpression transgenic rice exhibited moderate tolerance to salinity stress, which provides interesting clues on biological functions of these genes in rice.

Low-Affinity Cation Transporter 1 Improves Salt Stress Tolerance in Japonica Rice

Marjohn C. Niño,Franz Marielle Nogoy,강권규,조용구 한국육종학회 2018 Plant Breeding and Biotechnology Vol.6 No.1

Plants adapt to hostile environmental condition through specialized cellular processes which require coordinatedregulation of multiple transport mechanisms. Low-affinity cation transporter (LCT) 1 is a membrane transporter gene exclusive only tomembers of the grass family, and the rice genome contained only one copy of the gene. Accumulating evidence highlighted theimportant role of this gene in the regulation of various cations transport into the plant cells including heavy metals. To furthercharacterize the role of this membrane transporter in planta, we overexpressed the OsLCT1 in japonica rice using CaMV 35S andscreened the transgenic plants for high salt toxicity at the seedling stage. A striking difference in the phenotype ofOsLCT1-overexpression plants and the wild-type was observed at seven days after treatment, where transgenic plants exhibitedmoderate tolerance reaction to salinity stress. Our findings suggest that OsLCT1 gene can be useful to develop new resistant varietiesagainst salinity stress.

Overexpression of rice premnaspirodiene oxygenase reduces the infection rate of Xanthomonas oryzae pv. oryzae

Marjohn C. Niño,송재영,Franz Marielle Nogoy,김미선,정유진,강권규,노일섭,조용구 한국식물생명공학회 2016 JOURNAL OF PLANT BIOTECHNOLOGY Vol.43 No.4

Plants utilize cytochrome P450, a large superfamily of heme-containing mono-oxygenases, in the synthesis of lignins, UV protectants, pigments, defense compounds, fatty acids, hormones, and signaling molecules. Despite the overwhelming assortment of rice P450 accession numbers in the database, their functional studies are lacking. So far, there is no evidence involving rice P450 in disease immunity. Most of our understanding has been based on other plant systems that are mostly dicot. In this study, we isolated the cytochrome P450 (OsCYP71) in rice, and screened the gene using gain-of-function technique. The full-length cDNA of OsCYP71 was constitutively overexpressed using the 35S promoter. We then explored the functions of OsCYP71 in the rice - Xanthomonas oryzae pv. oryzae pathosystem. Using the gene expression assays, we demonstrate the interesting correlation of PR gene activation and the magnitude of resistance in P450-mediated immunity.

Plant microRNAs in molecular breeding

Franz Marielle Nogoy,Marjohn C. Niño,송재영,정유진,강권규,노일섭,조용구 한국식물생명공학회 2018 Plant biotechnology reports Vol.12 No.1

MicroRNAs are small, endogenous, non-coding RNAs found in plants, animals, and in some viruses, which negatively regulate the expression of genes by promoting the degradation of target mRNAs or by translation inhibition. Ever since the discovery of miRNAs, its biology, mechanisms, and functions were extensively studied in the past two decades. Plant and animal miRNAs both regulate target mRNAs, but they differ in scope of complementarity to their target mRNA. Plant microRNAs are known to play essential roles in a wide array of plant development. To date, there are many studies giving evidence that the regulation of miRNA levels can reprogram plant responses to abiotic (physical environment) and biotic stresses (pathogen and herbivore). Most of these studies were first carried out in the model plant Arabidopsis thaliana. Recently, the trend of miRNA research is furthering its role in crop breeding and its evolutionary origin. In this review, we presented the dynamic biogenesis of microRNAs, the diverse functions of miRNAs in plants, and experimental designs used in studying microRNAs in plants, and most importantly, we presented the applications of microRNA-based technology to improve the resistance of crops in abiotic and biotic stresses.

Overexpression of UGE1 from Brassica rapa enhances yield and tolerance to drought in transgenic rice

Hye Jung Lee,Sailila E. Abdula,Marjohn C. Niño,Kwon-Kyoo Kang,Illsup Nou,Yong-Gu Cho 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07

UDP-glucose 4-epimerase (UGE) catalyzes the reversible conversion of UDP-glucose to UDP-galactose. To understand the biological function of UGE from Brassica rapa, the gene hereinafter referred to as was cloned and overexpressed into Japonica rice cv. Gopum. Transcriptional profiling showed that the is specific to stem of rice plant. Morphological evaluation of the overexpression lines revealed altered phenotype characters particularly in panicle length, number of productive tillers and filled spikelets which account for an increase in yield. This remarkable agronomic performance was ascribed to higher photosynthetic rate complemented with higher CO2 assimilation. Interestingly, BrUGE1 did not only improve plant fitness under optimal condition but also under water deficit stress. The enhanced drought tolerance may be due to the induction of soluble sugar which may act as osmolyte to compensate dehydration during drought stress.

Application and utilization of marker assisted selection for biotic stress resistance in hybrid rice (Oryza sativa L.)

송재영,Sothea Ouk,Franz Marielle Nogoy,Marjohn C. Niño,권순욱,하운구,강권규,조용구 한국식물생명공학회 2016 JOURNAL OF PLANT BIOTECHNOLOGY Vol.43 No.3

Development of disease resistant plant is one of the important objectives in rice breeding programs because biotic stresses can adversely affect rice growth and yield losses. This study was conducted to identify lines with multiple-resistance genes to biotic stress among 173 hybrid rice breeding lines and germplasms using DNA-based markers. Our results showed that one hybrid rice line [IR98161-2- 1-1-k1-3 (IR86409-3-1-1-1-1-1/IRBB66)] possessed 5 bacterial blight resistance genes (Xa4, xa5, Xa7, Xa13 and Xa21) while two hybrid rice lines [IR98161-2-1-1-k1-2 (IR86409- 3-1-1-1-1-1/IRBB66) and 7292s (IR75589-31-27-8-33S(S1)/ IR102758B)] possessed 3 bacterial blight resistance genes (Xa4, Xa7 and Xa21, and Xa3, Xa4 and xa5). Molecular survey on rice blast disease revealed that most of these lines had two different resistant genes. Only 11 lines possessed Pib, Pi-5, and Pi-ta. In addition, we further surveyed the distribution of insect resistant genes, such as Bph1, Bph18(t), and Wbph. Three hybrid breeding lines [IR98161-2-1-1-k1-3 (IR86409-3-1-1-1-1-1/IRBB66), IR98161-2-1-1-k1-2 (IR86409- 3-1-1-1-1-1/IRBB66), and 7292s (IR75589-31-27-8-33S(S1) /IR102758B)] contained all three resistance genes. Finally, we obtained four hybrid rice breeding lines and germplasms [IR98161-2-1-1-k1-2 (IR86409-3-1-1-1-1-1/IRBB66), Damm- Noeub Khmau, 7290s, and 7292s (IR75589-31-27-8-33S(S1)/ IR102758B)] possessing six-gene combination. They are expected to provide higher level of multiple resistance to biotic stress. This study is important for genotyping hybrid rice with resistance to diverse diseases and pests. Results obtained in this study suggest that identification of pyramided resistance genes is very important for screening hybrid rice breeding lines and germplasms accurately for disease and pest resistance. We will expand their cultivation safely through bioassays against diseases, pests, and disaster in its main export countries.

Genetic Characterization of BADH2 in Philippine Aromatic Rice Cultivars

( Dindo A. Tabanao ),( Rafael B. Navarro ),( Reneth A. Millas ),( Marjohn C. Niño ) 한국육종학회 2021 Plant Breeding and Biotechnology Vol.9 No.3

Fragrance is considered one of the most highly valued grain quality traits in rice, yet its genetic basis among Philippine cultivars, especially traditional accessions, is unknown. This study characterized the fragrance gene Betaine aldehyde dehydrogenase isoform 2 (BADH2) in selected Philippine aromatic rice cultivars at the DNA, transcript, and phenotypic level. DNA fragment length analysis showed that eight out of 18 cultivars were positive for badh2.1, an allele responsible for the accumulation of 2-acetyl-1-pyrroline (2AP), the marker compound for fragrance in rice. DNA sequence alignment of nine cultivars confirmed the absence of 8 base pairs (bp) and three single nucleotide polymorphism (SNPs) in exon 7 in Dinorado White, Saigorot, and Salanay, while revealing several other nucleotide variations in other coding regions and immediate upstream region of the gene. The BADH2 gene expression profile showed that aromatic cultivars have varying lower amounts of the BADH2 mRNA than the non-aromatic cultivars. Results in 2AP analysis showed significant discrepancies in 2AP levels among cultivars during wet and dry season, which may be due to some possible factors such as sequence variation in the coding regions of BADH2, affecting gene expression, and environmental factors such as exposure to stress or postharvest processes. Overall, results have shown that aroma production among the Philippine aromatic cultivars was not due to just one genetic mechanism. Further investigation regarding analysis at the protein level, characterization of regulatory mechanisms in gene expression, and finding new genes that may be involved in the production of aroma must be pursued.