Diverse chromosomal rearrangements induced by Ac/Ds at the OsRLG5 locus in regenerated rice plants

Yuan Hu Xuan,박순주,조준현,김태호,한창덕 한국식물학회 2015 Journal of Plant Biology Vol.58 No.5

Closely-located transposable elements (TEs) can induce chromosomal breakage and rearrangements via alternative transposition (AT) reactions. Our previous study showed that diverse chromosomal rearrangements were induced by two inversely-oriented Ds elements at the OsRLG5 (Oryza sativa receptor-like kinase gene 5) locus in regenerated rice plants. Here, several novel chromosomal rearrangements were identified in a population of tissue culture regenerants, and their proposed Ac/Ds-transposition mechanisms were discussed. In the first type of event, AT was induced by the same Ds element on each of two sister chromatids and resulted in the inversion of genomic DNA flanking the Ds element. In the second type of event, DNA segments of the inter-transposon segment (ITS) region were deleted or inverted. This novel local rearrangement likely resulted from an AT reaction of two directly-oriented Ds elements located on the same chromatid. The 5' and 3' termini of two Ds elements were re-inserted into two different sites inside the ITS, which generated the subsequent deletion and inversion. In the third type of event, two inversely-oriented Ds elements induced homologous recombination and chromosomal translocation. Together, these results showed the diversity of Ac/Ds-mediated chromosomal rearrangements and demonstrated the utility of the experimental system for examining the mechanisms underlying Ac/Ds AT reactions.

<i>Ac/Ds</i> -induced chromosomal rearrangements in rice genomes

Xuan, Yuan Hu,Zhang, Jianbo,Peterson, Thomas,Han, Chang-deok Landes Bioscience 2012 Mobile genetic elements Vol.2 No.2

<P>A closely-linked pair of <I>Ac/Ds</I> elements induces chromosomal rearrangements in Arabidopsis and maize. This report summarizes the <I>Ac</I>/<I>Ds</I> systems that generate an exceptionally high frequency of chromosomal rearrangements in rice genomes. From a line containing a single <I>Ds</I> element inserted at the <I>OsRLG5</I> locus, plants containing a closely-linked pair of inversely-oriented <I>Ds</I> elements were obtained at 1% frequency among the population regenerated from tissue culture. Subsequent regeneration of the lines containing <I>cis</I>-paired <I>Ds</I> elements via tissue culture led to a high frequency (35.6%) of plants containing chromosomal rearrangements at the <I>OsRLG5</I> locus. Thirty-four rearrangement events were characterized, revealing diverse chromosomal aberrations including deletions, inversions and duplications. Many rearrangements could be explained by sister chromatid transposition (SCT) and homologous recombination (HR), events previously demonstrated in Arabidopsis and maize. In addition, novel events were detected and presumably generated via a new alternative transposition mechanism. This mechanism, termed single chromatid transposition (SLCT), resulted in juxtaposed inversions and deletions on the same chromosome. This study demonstrated that the <I>Ac</I>/<I>Ds</I> system coupled with tissue culture-mediated plant regeneration could induce higher frequencies and a greater diversity of chromosomal rearrangements than previously reported. </P><P> Understanding transposon-induced chromosomal rearrangements can provide new insights into the relationship between transposable elements and genome evolution, as well as a means to perform chromosomal engineering for crop improvement. Rice is a staple cereal crop worldwide. Complete genome sequencing and rich genetic resources are great advantages for the study of the genomic complexity induced by transposable elements.<SUP>1</SUP><SUP>–</SUP><SUP>2</SUP> The combination of tissue culture with genetic lines carrying a pair of closely located <I>Ac/Ds</I> elements greatly increases the frequency and diversity of rearrangements in rice genomes. The methodology and its efficiency and significance are briefly summarized.</P>

Transposon <i>Ac/Ds</i> -induced chromosomal rearrangements at the rice <i>OsRLG5</i> locus

Xuan, Yuan Hu,Piao, Hai Long,Je, Byoung Il,Park, Soon Ju,Park, Su Hyun,Huang, Jin,Zhang, Jian Bo,Peterson, Thomas,Han, Chang-deok Oxford University Press 2011 Nucleic acids research Vol.39 No.22

<P>Previous studies have shown that pairs of closely-linked <I>Ac/Ds</I> transposable elements can induce various chromosomal rearrangements in plant genomes. To study chromosomal rearrangements in rice, we isolated a line (<I>OsRLG5-161)</I> that contains two inversely-oriented <I>Ds</I> insertions in <I>OsRLG5</I> (<I>Oryza sativa</I> Receptor like kinase Gene 5). Among approximately 300 plants regenerated from <I>OsRLG5-161</I> heterozygous seeds, 107 contained rearrangements including deletions, duplications and inversions of various sizes. Most rearrangements were induced by previously identified alternative transposition mechanism. Furthermore, we also detected a new class of rearrangements that contain juxtaposed inversions and deletions on the same chromosome. We propose that these novel alleles were generated by a previously unreported type of alternative transposition reactions involving the 5′ and 3′ termini of two inversely-oriented <I>Ds</I> elements located on the same chromatid. Finally, 11% of rearrangements contained inversions resulting from homologous recombination between the two inverted <I>Ds</I> elements in <I>OsRLG5-161</I>. The high frequency inheritance and great variety of rearrangements obtained suggests that the rice regeneration system results in a burst of transposition activity and a relaxation of the controls which normally limit the transposition competence of individual <I>Ds</I> termini. Together, these results demonstrate a greatly enlarged potential of the <I>Ac/Ds</I> system for plant chromosome engineering.</P>

Study on Phenotypes and Agronomical utility of a Rice GT1 (grassy tillers 1, OsGT1) Homologue

Vikranth Kumar,Yuan Hu Xuan,Byoung Il Je,Soon Ju Park,Jin Huang,Jing Miao Liu,Ryza A. Priatama,Vimal Raj K,Sung Hoon Kim,Jin-hee Jeong,Chang-deok Han 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07

Enhancing yield has been a major challenge of agriculture. In rice, tiller number is one of the important biomass and yield components. A maize mutant grassy tillers1 (gt1) increases lateral branches in maize. The GT1 gene encodes a class I homeodomain leucine zipper (HD-Zip) protein. In maize, the gt1 expression is induced by shading and is dependent on the activity of teosinte branched1 (tb1), a major domestication locus controlling tillering and lateral branching. To estimate the biological role and agricultural utility of gt1 in rice, rice homologue (OsGT1) has been isolated and its overexpressors and RNAi lines were generated. Field data showed that OsGT1 overexpressors reduced tillers and panicles while RNAi lines increased them, compared to wild type. Shade signal is an important factor in determining lateral branching. To understand the relationship between OsGT1 and shade avoidance, plants have been grown under 50% shading in the field. Also, double genetic combinations with phytochrome mutants (phyA, B, and C) are being examining for tillering phenotype. These ongoing researches will provide insights in determining the action of OsGT1 on branching and shade avoidance in rice.

Transcriptome analysis of rice leaves in response to Rhizoctonia solani infection and reveals a novel regulatory mechanism

De Peng Yuan,Xiao Feng Xu,Hong Woo-Jong,Si Ting Wang,Xin Tong Jia,Yang Liu,Shuang Li,Zhi Min Li,Qian Sun,Qiong Mei,Shuai Li,정기홍,Song Hong Wei,Yuan Hu Xuan 한국식물생명공학회 2020 Plant biotechnology reports Vol.14 No.5

Sheath blight disease (ShB) severely afects rice production; however, the details of defense against ShB remain unclear. To understand the rice defense mechanism against ShB, an RNA sequencing analysis was performed using Rhizoctonia solani inoculated rice leaves after 48 h of inoculation. Among them, 3417 genes were upregulated and 2532 were downregulated when compared with the control group (>twofold or<1/2). In addition, the diferentially expressed genes were classifed via Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and MapMan analyses. Fifty-nine GO terms and seven KEGG pathways were signifcantly enriched. A MapMan analysis demonstrated that the phytohormone and metabolic pathways were signifcantly altered. Interestingly, the expression levels of 359 transcription factors, including WRKY, MYB, and NAC family members, as well as 239 transporter genes, including ABC, MFS, and SWEET, were signifcantly changed in response to R. solani AG1-IA inoculation. Additionally, OsWRKY53 and OsAKT1 negatively regulate the defense response in rice against R. solani via gain of function study for OsWRKY53 and loss of function study for OsAKT1, respectively. Furthermore, several diferentially expressed genes contain R. solani-responsive cis acting regulatory elements in their promoter regions. Taken together, our analyses provide valuable information for the additional study of the defense mechanisms against ShB, and the candidate genes identifed in this study will be useful resource for future breeding to enhance resistance against ShB.

OsCIPK31, a CBL-Interacting Protein Kinase Is Involved in Germination and Seedling Growth under Abiotic Stress Conditions in Rice Plants

Piao, Hai-long,Xuan, Yuan-hu,Park, Su-Hyun,Je, Byoung-Il,Park, Soon-Ju,Park, Sung-Han,Kim, Chul-Min,Huang, Jin,Wang, Guo Kui,Kim, Min-Jung,Kang, Sang-Mo,Lee, In-Jung,Kwon, Taek-Ryoun,Kim, Yong-Hwan,Ye Korean Society for Molecular and Cellular Biology 2010 Molecules and cells Vol.30 No.1

Calcineurin B-like protein-interacting protein kinases (CIPKs) are a group of typical Ser/Thr protein kinases that mediate calcium signals. Extensive studies using Arabidopsis plants have demonstrated that many calcium signatures that activate CIPKs originate from abiotic stresses. However, there are few reports on the functional demonstration of CIPKs in other plants, especially in grasses. In this study, we used a loss-of-function mutation to characterize the function of the rice CIPK gene OsCIPK31. Exposure to high concentrations of NaCl or mannitol effected a rapid and transient enhancement of OsCIPK31 expression. These findings were observed only in the light. However, longer exposure to most stresses resulted in downregulation of OsCIPK31 expression in both the presence and absence of light. To determine the physiological roles of OsCIPK31 in rice plants, the sensitivity of oscipk31::Ds, which is a transposon Ds insertion mutant, to abiotic stresses was examined during germination and seedling stages. oscipk31::Ds mutants exhibited hypersensitive phenotypes to ABA, salt, mannitol, and glucose. Compared with wild-type rice plants, mutants exhibited retarded germination and slow seedling growth. In addition, oscipk31::Ds seedlings exhibited enhanced expression of several stress-responsive genes after exposure to these abiotic stresses. However, the expression of ABA metabolic genes and the endogenous levels of ABA were not altered significantly in the oscipk31::Ds mutant. This study demonstrated that rice plants use OsCIPK31 to modulate responses to abiotic stresses during the seed germination and seedling stages and to modulate the expression of stress-responsive genes.

IDD10 is Involved in the Interaction between NH4+ and Auxin Signaling in Rice Roots

Chang-Deok Han,Yuan Hu Xuan,Vikranth Kumar,Xiao Feng Zhu,Byoung Il Je,Chul Min Kim,Jin Huang,Jun Hyeon Cho,Gihwan Yi 한국식물학회 2018 Journal of Plant Biology Vol.61 No.2

NH4+ is an important nitrogen resource for rice plantsin paddy soil. Therefore, it is likely that NH4+-triggered plantgrowth interacts with phytohormone-mediated developmentalmechanisms. Our previous transcriptomic analysis revealedthat many genes involved in auxin signaling and efflux aresensitive to NH4+. In the current study, we found that NH4+treatment causes a delayed gravity response in rice roots. Tofurther elucidate the interlocking relationship between NH4+and auxin signaling during root development, we utilizedmutants and overexpressors of a key NH4+ signaling transcriptionfactor INDETERMINATE DOMAIN 10 (IDD10), encoding atranscription factor that regulates the expression of NH4+uptake and N-assimilation genes. We obtained several linesof evidence that auxin affects NH4+-mediated gene expressionand root development in rice plants via IDD10. First, thegravity response was delayed in idd10 roots and acceleratedin IDD10 overexpressor (IDD10 OX) roots in the absenceand (especially) presence of NH4+. Second, idd10 plantsshowed strong root coiling only in the presence of NH4+. However, treatment of 1-N-naphthylphthalamic acid (NPA),a polar auxin transport inhibitor suppressed the NH4+-specific root phenotype of idd10. Third, the expression ofNH4+-responsive auxin-related genes was affected in idd10and IDD10 overexpressors. Finally, IDD10 expression wasinduced by IAA and suppressed by NPA. These findingssuggest that the gene expression patterns and phenotypestriggered by NH4+ are influenced by the actions of auxinduring root development, pointing to a regulatory circuitbetween NH4+ and auxin signaling that functions in rootdevelopment in rice.

OsCIPK31, a CBL-Interacting Protein Kinase Is Involved in Germination and Seedling Growth under Abiotic Stress Conditions in Rice Plants

Hai-long Piao,Yuan-hu Xuan,Su Hyun Park,제병일,Soon Ju Park,Sung Han Park,김철민,Jin Huang,Guo Kui Wang,김민정,강상모,이인중,Taek-Ryoun Kwon,Yong Hwan Kim,Un-sang Yeo,이기환,손대영,한창덕 한국분자세포생물학회 2010 Molecules and cells Vol.30 No.1

Calcineurin B-like protein-interacting protein kinases (CIPKs) are a group of typical Ser/Thr protein kinases that mediate calcium signals. Extensive studies using Arabi-dopsis plants have demonstrated that many calcium sig-natures that activate CIPKs originate from abiotic stresses. However, there are few reports on the functional demon-stration of CIPKs in other plants, especially in grasses. In this study, we used a loss-of-function mutation to charac-terize the function of the rice CIPK gene OsCIPK31. Expo-sure to high concentrations of NaCl or mannitol effected a rapid and transient enhancement of OsCIPK31 expression. These findings were observed only in the light. However, longer exposure to most stresses resulted in down-regulation of OsCIPK31 expression in both the presence and absence of light. To determine the physiological roles of OsCIPK31 in rice plants, the sensitivity of oscipk31::Ds, which is a transposon Ds insertion mutant, to abiotic stresses was examined during germination and seedling stages. oscipk31::Ds mutants exhibited hypersensitive phenotypes to ABA, salt, mannitol, and glucose. Com-pared with wild-type rice plants, mutants exhibited re-tarded germination and slow seedling growth. In addition, oscipk31::Ds seedlings exhibited enhanced expression of several stress-responsive genes after exposure to these abiotic stresses. However, the expression of ABA meta-bolic genes and the endogenous levels of ABA were not altered significantly in the oscipk31::Ds mutant. This study demonstrated that rice plants use OsCIPK31 to modulate responses to abiotic stresses during the seed germination and seedling stages and to modulate the expression of stress-responsive genes.

Analysis of Intragenic Ds Transpositions and Excision Events Generating Novel Allelic Variation in Rice

박순주,한창덕,Hai Long Piao,Yuan-hu Xuan,박성한,제병일,김철민,이은진,박수현,류병찬,이곤호,이기환,남민희,여운상,이명철,윤도원,은무영 한국분자세포생물학회 2006 Molecules and cells Vol.21 No.2

Analysis of intragenic Ds transpositions and excision events generating novel allelic variation in rice.

Park, Soon Ju,Piao, Hai Long,Xuan, Yuan-hu,Park, Sung Han,Je, Byoung Il,Kim, Chul Min,Lee, Eun Jin,Park, Soo Hyun,Ryu, ByeongChan,Lee, Kon Ho,Lee, Gi Hwan,Nam, Min Hee,Yeo, Un Sang,Lee, Myung Chul,Yun Korean Society for Molecular Biology 2006 Molecules and cells Vol.21 No.2

<P>Even though Ac/Ds gene-tagging systems have been established in many higher plants, maize is the only major plant in which short-distance transposition of Ac/Ds has been utilized to probe gene function. This study was performed to evaluate the efficiency of obtaining new alleles and functional revertants from Ds insertion loci in rice. By analyzing 1,580 plants and the progeny of selected lines, the insertion sites and orientations of Ds elements within 16 new heritable alleles of three rice loci were identified and characterized. Intragenic transposition was detected in both directions from the original insertion sites. The closest interval was 35 bp. Three of the alleles had two Ds elements in cis configuration in the same transcription units. We also analyzed the excision footprints of intragenic and extragenic transpositions in Ds-inserted alleles at 5 loci. The 134 footprints obtained from different plants revealed predominant patterns. Ds excision at each locus left a predominant footprint at frequencies of 30-75%. Overall, 66% of the footprints were 7-bp additions. In addition, 16% of the excisions left 0-, 3-, 6-, and 9-bp additions with the potential of conserving reading frame.</P>