• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.280-280
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• 2022

Tiller angle, defined as the angle between the main stem and its side tillers, is one of the main target traits selected inbreeding to achieve the ideal plant type and increase rice yield. Therefore, the discovery and identification of tiller angle-related genes can provide architecture and yield. In the present work, using QTL analysis hence a total of 8 quantitative trait loci (QTLs) were detected based on the phenotype data of tiller angle and tiller crown width in two years. Among them, four QTLs (qTA9, qCW9, qTA9-1, qCW9-1) were overlapped at marker interval RM6235-RM24288 on chromosome 9 with a large effect value regarded as stable major QTL. Twenty tiller angle-related genes were selected from the target region and the relative gene expression levels were checked in five compact type lines, five spreading type lines, and their parental lines. Finally, OsSA URq9 which belongs auxin-responsive SMALL AUXIN UP RNA (SAUR) protein family was selected as a target gene. Overall, this work will help broaden our understanding of the genetic control of tiller angle and tiller crown width, and this study provides both a good theoretical basis and a new genetic resource for the breeding of ideal-type rice.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.283-283
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• 2022

Abiotic stresses such as high/low temperature, drought, salinity, and submergence directly or indirectly influence the physiological status and molecular mechanisms of rice which badly affect yield. Especially, the low temperature causes harmful influences in the overall process of rice growth such as uneven germination and the establishment of seedlings, which has become one of the main limiting factors affecting rice production in the world. It is of great significance to find the candidate genes controlling low-temperature tolerance during seed germination and study their functions for breeding new rice cultivars with immense low-temperature tolerance during seed germination. In this study, 120 lines of Cheongcheong/Nagdong double haploid population were used for quantitative trait locus analysis of low-temperature germinability. The results showed significant difference in germination under low different temperature conditions. In total, 4 QTLs were detected on chromosome 3, 6, and 8. A total of 41 genes were identified from all the 4 QTLs, among them, 25 genes were selected by gene function annotation and further screened through quantitative real time polymerase chain reaction. Based on gene function annotation and level of expression under low-temperature, our study suggested OsGPq3 gene as a candidate gene controlling viviparous germination, ABA and GA signaling under low-temperature. This study will provide a theoretical basis for marker-assisted breeding.

• 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.

• Microbiology and Biotechnology Letters
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• v.47 no.4
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• pp.667-672
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• 2019

We compared two integration systems for stable expression of heterologous genes in Saccharomyces cerevisiae. A Candida glabrata-derived gene was used as the selective marker for the Cre/loxP system, and XYLP, XYLB, GRE3, and XYL2 genes were used as model heterologous genes and ligated into the universal pRS-CMT vector. The resulting pRS-XylP, pRS-XylB, pRS-Gre3, and pRS-Xyl2 plasmids were sequentially integrated into yeast chromosome VII by four integration processes (marker rescue and gene integration). The four introduced genes were successfully expressed. Further, the pRS-PBG2 plasmid harboring expression cassettes for the four genes was constructed for one-step integration. The four genes that were introduced were stably maintained as a gene cluster and were simultaneously expressed. The one-step integration was more effective for the simultaneous integration and expression of the four genes related to xylan/xylose metabolism. This method will enable the generation of a useful biosystem through appropriate use of gene integration methods.

• 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.

• Horticultural Science & Technology
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• v.33 no.4
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• pp.566-574
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• 2015

Yellow or transparent fruit peel color is caused by the accumulation or lack of naringenin chalcone (NG, C) in fruit peel and determines the red or pink appearance of tomato fruit, respectively. NGC biosynthesis is regulated by the SlMYB12 gene of the Y locus on chromosome 1, and DNA markers derived from SlMYB12 would be useful for marker-assisted selection (MAS) of tomato fruit color. To develop a gene-based marker, 4.9 kb of the SlMYB12 gene including a potential promoter region was sequenced from the red-fruited (YY) line 'FCR' and pink-fruited (yy) line 'FCP'. Sequence alignment of these SlMYB12 alleles revealed no sequence variations between 'FCR' and 'FCP'. To identify SlMYB12-linked single nucleotide polymorphisms (SNPs), 'FCR' and 'FCP' were genotyped using a SolCAP Tomato SNP array and CAPS markers (CAPS-456, 531, 13762, and 38123) were developed from the four SNPs (solcap_snp_sl_456, 531, 13762, and 38123) most closely flanking the SlMYB12. These CAPS markers were mapped using $F_2$ plants derived from 'FCR' ${\times}$ 'FCP'. The map positions of the fruit peel color locus (Y) were CAPS-13762 (0 cM) - 456 (11.09 cM) - Y (15.71 cM) - 38123 (17.82 cM) - 531 (30.86 cM), and the DNA sequence of SlMYB12 was physically anchored in the middle of CAPS-456 and CAPS-38123, indicating that fruit peel color in domesticated tomato is controlled by SlMYB12. A total of 64 SolCAP tomato germplasms were evaluated for their fruit peel color and SNPs located between solcap_snp_sl_456 and 38123. Seven SNPs that were detected in this interval were highly conserved for pink-fruited accessions and specific to transparent fruit peel traits, as depicted by a phenetic tree of 64 accessions based on the seven SNPs.

• Korean Journal of Breeding Science
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• v.43 no.5
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• pp.464-469
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• 2011

Virus diseases often cause serious damage to rice production in Asia. The lack of information on virus resistance genes has been a major obstacle for the breeding of resistant varieties. In order to identify DNA marker associated with resistance against rice stripe virus (RSV), the quantitative trait locus (QTL) was carried out using advanced backcross population developed from a cross between RSV-resistant tongil type cultivar Shinkwang and susceptible japonica cultivar Ilpum. A RSV resistance QTL $qSTV11^{SG}$ explaining 44.2% of the phenotypic variation was identified on chromosome 11 of Tongil type rice cultivar 'Shingwang'. $qSTV11^{SG}$ was tightly linked to DNA marker RM6897. The RM6897 divided as resistance type allele and susceptible type alleles. Twenty seven resistant varieties showed the resistant-type allele and 23 susceptible varieties were susceptible-type allele to the marker of RM6897. This results and the molecular markers presented here may be useful in rice breeding for improving RSV resistance in japonica rice.

• Journal of Animal Science and Technology
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• v.46 no.4
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• pp.537-546
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• 2004

Adiponectin is adipocyte complement-related protein which is highly specialized to play important roles in metabolic and honnonal processes. This protein, called GBP-28, AdipoQ, and Acrp30, is encoded by the adipose most abundant gene transcript 1 (APM1) which locates on human chromosome 3q27 and mouse chromosome 16. In order to determine chromosomal localization of the porcine APM1, we carried out PCR analysis using somatic cell hybrid panel as well as porcine whole genome radiation hybrid (RH) panel. The result showed that the porcine APM1 located on chromosome 13q41 or 13q46-49. These locations were further investigated with the two point analysis of RH panel, revealed the most significant linked marker (LOD score 20.29) being SIAT1 (8 cRs away), where the fat-related QTL located. From the SSCP analysis of APM1 using 8 pig breeds, two distinct SSCP types were detected from K~ native and Korean wild pigs. The determined sequences in Korean native and Korean wild pigs showed that two nucleotide positions (T672C and C705G) were substituted. The primary sequence of the porcine APM1 has 79 to 87% identity with those of human, mouse, and bovine APM1. The domain structures of the porcine APM1 such as signal sequence, hypervariable region, collagenous region. and globular domain are also similar to those of mammalian genes.

• Journal of Plant Biotechnology
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• v.29 no.3
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• pp.151-159
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• 2002

Genetic map and molecular marker have a great importance in improving and facilitating crop breeding program as well as in genome analysis and map-based cloning of genes representing desirable characters. This study aimed at developing RAPD markers and constructing a genetic linkage map using 82 BC$_1$F$_1$individuals originated from the cross between '835' and B$_2$in radish (Raphanus sativus L.). One of the parents for genetic linkage map construction, '835'(P$_1$) of egg type is susceptible to Fusarium wilt and have medium resistance to virus infection and the other parent, B$_2$(P$_2$) of round type, is susceptible to Fusarium wilt and virus, Screening of 394 RAPD primers in BC$_1$F$_1$) population resulted in selecting 128 polymorphic markers which displayed 1:1 segregation pattern. Two markers failed to display 1:1 segregation and showed the segregation ratio skewed to maternal genotype. Selected markers were categorized into 14 linkage group based on LOD score represented by MAPMAKER/EXP program. Five groups composed of single marker among them were excluded from the linkage map, and consequently, the remaining groups are well matched with the number of radish chromosome (n＝9). The linkage map constructed with 128 markers covers 1,688.3 cM and the average distance between markers was 13.8 cM. For developing STS marker, we determined the partial nucleotide sequence of OPE10 marker at both ends and designed a oligonucleotide primer pair based on this sequence. STS PCR using the primer pair displayed a single, clear band of which segregation is perfectly matched with that of OPE10 marker. This implies that RAPD markers could readily convert into clear and reliable STS markers.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.60 no.4
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• pp.448-457
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• 2015

Developing rice lines with various amylose contents is necessary to diverse usages of rice in terms of raw materials for processed food production, and thereby to promote rice consumption in Korea. A rice mutant line, 'Namil(SA)-dull1' was established through sodium azide mutagenesis on 'Namil', a non-glutinous Korean Japonica rice cultivar. Namil(SA)-dull1' had dull endosperm characteristics and the evaluated amylose content was 12.2%. A total of 94 F2 progenies from a cross between 'Namil(SA)-dull1' and 'Milyang23', a non-glutinous Tongil-type rice cultivar, was used for genetic studies on the endosperm amylose content. Association analyses, between marker genotypes of 53 SSR anchor markers and evaluated amylose contents of each 94 F2:3 seeds, initially localized rice chromosome 6 as the harboring place for the modified allele(s) directing low amylose content of 'Namil(SA)-dull1'. By increasing SSR marker density on the putative chromosomal region followed by association analyses, the target region was narrowed down 0.94 Mbp segment, expanding from 28.95 Mbp to 29.89 Mbp, on rice chromosome 6 pseudomolecule. Among the SSR loci, RM7555 explained 84.2% of total variation of amylose contents in the $F_2$ population. Further physical mapping on the target region directing low amylose content of 'Namil(SA)-dull1' would increase the breeding efficiency in developing promising rice cultivars with various endosperm characteristics.