• The Plant Pathology Journal
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• v.21 no.4
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• pp.334-342
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• 2005

The prototype Chlorella virus PBCV-l encodes 11 tRNA genes and over 350 protein-encoding genes in its 330 kbp genome. Initial attempts to overexpress the recombinant A189/192R protein, a putative virus attachment protein, in E. coli strain BL21(DE3) SI were unsuccessful, and multiple protein bands were detected on Western blots. However, the full-length A189/192R recombinant protein or fragments derived from it were detected when they were expressed in E. coli BL21 CodonPlus (DE3) RIL, which contains extra tRNAs. Codon usage analysis of the a189/192r gene showed highly biased usage of the AGA and AVA codons compared to genes encoded by E. coli and Chlorella. In addition, there were biases of XXA/U($56\%$) and XXG/ C($44\%$) in the codons recognized by the viral tRNAs, which correspond to the codon usage bias in the PBCV-1 genome of XXA/U ($63\%$) over those ending in XXC/G ($37\%$). Analysis of the codon usage in the major capsid protein and DNA polymerase showed preferential usage of codons that can be recognized by the viral tRNAs. The Asn (AAC) and Lys (AAG) codons whose corresponding tRNA genes are duplicated in the tRNA gene cluster were the most abundant (i.e., preferred) codons in these two proteins. The tRNA genes encoded in the PBCV-l genome seem to play a very important role during the synthesis of viral proteins through supplementing the tRNAs that are frequently used in viral proteins, but are rare in the host cells. In addition, these tRNAs would help the virus to adapt to a wide range of hosts by providing tRNAs that are rare in the host cells.

• Korean Journal of Breeding Science
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• v.40 no.3
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• pp.291-294
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• 2008

Amylogram properties such as peak viscosity, hot viscosity, cool viscosity, breakdown, pasting consistency and setback were investigated by the Rapid Visco Analyzer and interpreted by the relationship among amylogram properties according to the varietal groups classified by the rapidity of grain filling (RGF) which was calculated by the percentage of grain weight at 15 days after heading to 40 days after heading. The 164 rice recombinant inbred lines from the cross of Milyang23 and Gihobyeo were used to get the basic information regarding the amylogram properties. The used recombinant inbred lines could be grouped into 4 varietal groups such as slow maturing (less than 40% of RGF), mid-slow maturing (41-60% of RGF),mid-fast maturing (61-80% of RGF), and fast maturing (more than 81% of RGF) groups based on the RGF. The peak viscosity and setback showed regular tendency according to the varietal groups classified by the RGF. Positive significant correlations were found between pasting consistency and setback, however negative significant correlations were found between breakdown and setback in all varietal groups.

• Korean Journal of Breeding Science
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• v.40 no.1
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• pp.48-53
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• 2008

This study presents a case study designed to compare the selection efficiency between phenotypic selection (PS) and marker-assisted selection (MAS) in breeding of resistance lines to brown planthopper (BPH). The efficiency between PS and MAS were compared with four population such as the $F_2$, RILs ($F_6$), DH, and backcrosse ($BC_6F_5$) population, derived from a cross 'Samgang / Nagdong'. The resistance lines were selected using two markers, RM28493 and BpE18-3, related to BPH resistance were screened as resistance lines over 95% in PS. The costs required for BPH screening in the MAS system account for approximately 32% of the total costs of PS. The period needed to select the resistance plants was 30 days in PS and 7 days in MAS. Based on the results, we could establish the breeding system for selection of BPH resistance lines by MAS.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2020.12a
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• pp.64-64
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• 2020

Bakanae disease, caused by several Fusarium species, imposes serious limitations to the productivity of rice across the globe. The incidence of this disease has been shown to increase, particularly in major rice-growing countries. Thus, the use of high resistant rice cultivars offers a comparative advantage, such as being cost effective, and could be preferred to the use of fungicides. In this research, we used a tropical japonica rice variety, Zenith, a bakanae disease resistant line selected as donor parent. A RIL population (F_8:9) composed of 180 lines generated from a cross between Ilpum and Zenith was used. In primary mapping, a QTL was detected on the short arm of chromosome 1, covering about 3.5 Mb region flanked by RM1331 and RM3530 markers. The resistance QTL, qBK1^Z, explained about 30.93% of the total phenotype variation (PVE, logarith of the odds (LOD) of 13.43). Location of qBK1^Z was further narrowed down to 730 kb through fine mapping using additional RM markers, including those previously reported and developed by Sid markers. Furthermore, there is a growing need to improving resistance to bakanae disease and promoting breeding efficiency using MAS from qBK1^Z region. The new QTL, qBK1^Z, developed by the current study is expected to be used as foundation to promoting breeding efficiency with an enhanced resistance against bakanae disease. Moreover, this study provides useful information for developing resistant rice lines carrying single or multiple major QTLs using gene pyramiding approach and marker-assisted breeding.

• Korean Journal of Breeding Science
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• v.40 no.4
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• pp.408-413
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• 2008

Rice blast resistance is considered one of the most important traits in rice breeding and the disease, caused by Magnaporthe grisea Barr, has brought significant crop losses annually. Moreover, breakdown of resistance normally occurs in two to five years after cultivar release, thus a more durable resistance is needed for better control of this disease. We developed a new variety, Keumo3, which showed strong resistance to leaf blast. It was tested in 2003 to 2007 at fourteen blast nursery sites covering entire rice-growing regions of South Korea. It showed resistance reactions in 12 regions and moderate in 2 regions without showing susceptible reactions. Durability test by sequential planting method indicated that this variety had better resistance. Results showed that Keumo3 was incompatible against 19 blast isolates with the exception of KI101 by artificial inoculation. To understand the genetic control of blast resistance in rice cultivar Keumo3 and facilitate its utilization, recombinant inbred lines (RIL) consisting of 290 F5 lines derived from Akidagomachi/Keumo3 were analyzed and genotyped with Pizt InDel marker zt56591. The recombination value between the marker allele of zt56591 and bioassay data of blast nursery test was 1.1%. These results indicated that MAS can be applied in selecting breeding populations for blast resistance using zt56591 as DNA marker.

• Horticultural Science & Technology
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• v.28 no.4
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• pp.664-671
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• 2010

A genetic linkage map was constructed using 188 $F_9$ RILs derived from a cross between $Solanum$ $lycopersicum$ H7996 (resistant to bacterial wilt) and $S.$ $pimpinellifolium$ WVa700 (highly susceptible to bacterial wilt). The map consisted of 361 markers including 260 DArTs, 74 AFLPs, 4 RFLPs, 1 SNP, and 22 SSRs. The resulting linkage map was comprised of 13 linkage groups covering 2042.7 cM. The genetic linkage map had an average map distance between markers of 5.7 cM, with an average DArT marker density of 1/7.9 cM. Based on the distribution of anchor SSR markers, 11 linkage groups were assigned to 10 chromosomes of tomato except chromosomes 5 and 12. The DArT markers were distributed across the genome in a similar way as other markers and showed the highest frequency of clustering (38.8%) at ${\leq}$ 0.5 cM intervals between adjacent markers, which is 3 times higher than AFLPs (13.5%). The present study is the first utilization of DArT markers in tomato linkage map construction.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.51 no.3
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• pp.259-268
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• 2006

Miniature inverted transposable elements (MITEs) are abundant genomic components in plant including rice. MITE-transposon display (MITE-TD) is an Amplified Fragment Length Polymorphism (AFLP)-related technique based on MITE sequence. In this study, we used the MITE-AFLP for the analysis of diversity and relation-ship of the 114 japonica accessions. Of the several MITEs, the mPing family was applied to detect polymorphisms based on PCR amplification. The BfaI adaptor primer and the specific primer derived from mPing terminal inverted repeat (TIR) region were used to PCR amplification of 114 accessions. Nine primer pairs produced a total of 160 polymorphic bands. PIC values of the polymorphic bands generated by nine primer pairs ranged from 0.269 (BfaI + ACT) to 0.426 (BfaI + T). Each accession revealed a distinct fingerprint with two primer combinations, BfaI + G and BfaI + C. Cluster analysis using marker-based genetic similarity classified 114 accessions into five groups. MITE-AFLP markers were genetically mapped using a population of 80 BILs (BC1F7) derived from a cross between the rice accessions, Milyang 23 and Hapcheonaengmi 3. Eight of the markers produced with the primer pair BfaI + 0 were mapped on chromosomes 1, 2, 4, 5, 7, and 9. Considering that one MITE-AFLP marker on chromosome 7 was tightly linked to the Rc gene, the MITE-AFLP markers will be useful for gene tagging and molecular cloning.

• Molecules and Cells
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• v.24 no.1
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• pp.83-94
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• 2007

During monocarpic senescence in higher plants, functional stay-green delays leaf yellowing, maintaining photosynthetic competence, whereas nonfunctional stay-green retains leaf greenness without sustaining photosynthetic activity. Thus, functional stay-green is considered a beneficial trait that can increase grain yield in cereal crops. A stay-green japonica rice 'SNU-SG1' had a good seed-setting rate and grain yield, indicating the presence of a functional stay-green genotype. SNU-SG1 was crossed with two regular cultivars to determine the inheritance mode and identify major QTLs conferring stay-green in SNU-SG1. For QTL analysis, linkage maps with 100 and 116 DNA marker loci were constructed using selective genotyping with $F_2$ and RIL (recombinant inbred line) populations, respectively. Molecular marker-based QTL analyses with both populations revealed that the functional stay-green phenotype of SNU-SG1 is regulated by several major QTLs accounting for a large portion of the genetic variation. Three main-effect QTLs located on chromosomes 7 and 9 were detected in both populations and a number of epistatic-effect QTLs were also found. The amount of variation explained by several digenic interactions was larger than that explained by main-effect QTLs. Two main-effect QTLs on chromosome 9 can be considered the target loci that most influence the functional stay-green in SNU-SG1. The functional stay-green QTLs may help develop low-input high-yielding rice cultivars by QTL-marker-assisted breeding with SNU-SG1.

• Journal of Life Science
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• v.14 no.5
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• pp.821-828
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• 2004

The increasing apparent photosynthetic rate per leaf area may improve seed yield in soybean. Leaf area, length and width are related to the photosynthetic capability of the plant. In this study, two populations derived from the cross of Keunolkong, Shinpaldalkong and Iksanl0 were evaluated with simple sequence repeat (SSR) markers to identify length, width and length/width ratio of leaf. Leaf length/width ratio were significantly negative correlation with leaf width in K/S and K/I populations. In the K/S population, two minor QTLs for leaf length (LL) were found on LG Dlb+W and 1. Two QTLs on LG J and L were related to LL in K/I population. Two and three minor QTLs were identified in leaf width with total phenotypic variation of 13% and 18.04 in K/S and K/I populations, respectively. The leaf length/width ratio, two QTLs on LG I and L, and three QTLs on LG Cl, E and L were related to K/S and K/I populations, respectively. Thus it is assumed that the leaf traits are very much dependent on the genotype used and different breeding approach should be considered for the selection of favorite leaf traits in soybean breeding programs.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.98-98
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• 2017

Leaf senescence is the process of aging in plants. Chlorophyll degradation during leaf senescence has the important role translocating nutrients from leaves to storage organs. The functional stay-green with slow leaf yellowing and photosynthesis activity maintenance has been considered one of strategy for increasing crop productivity. Here, we have identified two QTLs on chromosome 9 and 10 for leaf senescence with chlorophyll content of RIL population derived from a cross between Hanareum 2, early leaf senescence Indica-type variety, and Unkwang, delayed leaf senescence Japonica variety. Among these QTLs, we chose qPLS1 QTL on chromosome 9 for further study. qPLS1 was found to explain 14.4% of the total phenotypic variation with 11.2 of LOD score. Through fine-mapping approach, qPLS1 QTL locus was narrowed down to about 25kb in the marker interval between In/del-4-7-9 and In/del-5-9-4. There are 3 genes existed within 25kb of qPLS1 locus: LOC_Os09g36200, LOC_Os09g36210, and LOC_Os09g36220. Among these genes, transcript level of LOC_Os09g36200 was increased during the leaf senescence stage and the expression level of LOC_Os09g36200 in Indica was higher than in Japonica. Finally, we chose LOC_Os09g36200 as candidate gene and renamed it as OsPLS1-In and OsPLS1-Jp from Indica- and Japonica-type rice, respectively. OsPLS1-In and OsPLS1-Jp overexpressing transgenic plants showed both early leaf senescence phenotype. These results indicate that OsPLS1 functions in chlorophyll degradation and the difference of expression level of OsPLS1 cause the difference of leaf senescence between Indica and Japonica in rice.