Sang-Nag ahn - Academia.edu (original) (raw)

Papers by Sang-Nag ahn

Research paper thumbnail of Terminal repeat retrotransposon in miniature (TRIM) as DNA markers in Brassica relatives

Molecular Genetics and Genomics, 2007

We have developed a display system using a unique sequence of terminal repeat retrotransposon in ... more We have developed a display system using a unique sequence of terminal repeat retrotransposon in miniature (TRIM) elements, which were recently identified from gene-rich regions of Brassica rapa. The technique, named TRIM display, is based on modification of the AFLP technique using an adapter primer for the restriction fragments of BfaI and a primer derived from conserved terminal repeat sequences

Research paper thumbnail of Article : QTLs for Domestication-related and Agronomic Traits in Temperate Japonica Weedy Rice

This study was conducted to identify the genetic basis of the domestication-related traits in wee... more This study was conducted to identify the genetic basis of the domestication-related traits in weedy rice. An RIL population consisting of 80 lines was developed from a cross between the japonica weedy rice, Hapcheonaengmi 3 and the Tongiltype cultivar Milyang 23. The population was genotyped with 132 DNA markers, providing an average interval size of 11.0cM, and also evaluated for 20 traits related to domestication and agricultural performance. A total of 48 QTLs and two loci associated with qualitative variation for pericarp and base coloration were identified using single point and interval analysis. The number of QTLs per trait ranged from one to six. These 48 QTLs were located in 27 intervals distributed on 11 chromosomes except for chromosome 12. The results indicated that most domestication-related traits clustered in chromosomal blocks, and the positions of many of these clusters were consistent with those reported in previous studies. Phenotypic variation associated with eac...

Research paper thumbnail of Mapping Quantitative Trait Loci for Grain Weight, gw5 and Ratooning Ability using ILs from a Cross between Oryza sativa and O. rufipogon

Research paper thumbnail of Characteristics of β-Carotene Rice Developed using Marker-Assisted Selection

Research paper thumbnail of Introgression for agronomic traits from Oryza grandiglumis into rice, O. sativa

Research paper thumbnail of Natural variation in rice ascorbate peroxidase gene APX9 is associated with a yield-enhancing QTL cluster

Journal of Experimental Botany

We previously identified a cluster of yield-related quantitative trait loci (QTLs) including plan... more We previously identified a cluster of yield-related quantitative trait loci (QTLs) including plant height in CR4379, a near-isogenic line from a cross between Oryza sativa spp. japonica cultivar ‘Hwaseong’ and the wild relative Oryza rufipogon. Map-based cloning and transgenic approaches revealed that APX9, which encodes an l-ascorbate peroxidase 4, is associated with this cluster. A 3 bp InDel was observed leading to the addition of a valine in Hwaseong compared with O. rufipogon. APX9-overexpressing transgenic plants in the Hwaseong background were taller than Hwaseong. Consistent with these results, APX9 T-DNA insertion mutants in the japonica cultivar Dongjin were shorter. These results confirm that APX9 is the causal gene for the QTL cluster. Sequence analysis of APX9 from 303 rice accessions revealed that the 3 bp InDel clearly differentiates japonica (APX9HS) and O. rufipogon (APX9OR) alleles. indica accessions shared both alleles, suggesting that APX9HS was introgressed into...

Research paper thumbnail of Genetic Structure and Geographical Differentiation of Traditional Rice (Oryza sativa L.) from Northern Vietnam

Plants

Northern Vietnam is one of the most important centers of genetic diversity for cultivated rice. O... more Northern Vietnam is one of the most important centers of genetic diversity for cultivated rice. Over thousands of years of cultivation, natural and artificial selection has preserved many traditional rice landraces in northern Vietnam due to its geographic situation, climatic conditions, and many ethnic groups. These local landraces serve as a rich source of genetic variation—an important resource for future crop improvement. In this study, we determined the genetic diversity and population structure of 79 rice landraces collected from northern Vietnam and 19 rice accessions collected from different countries. In total, 98 rice accessions could be differentiated into japonica and indica with moderate genetic diversity and a polymorphism information content of 0.382. Moreover, we found that genetic differentiation was related to geographical regions with an overall PhiPT (analog of fixation index FST) value of 0.130. We also detected subspecies-specific markers to classify rice (Oryz...

Research paper thumbnail of A Coordinated Suite of Wild-Introgression Lines in Indica and Japonica Elite Backgrounds

Frontiers in Plant Science

Rice, Oryza sativa L., is a cultivated, inbreeding species that serves as the staple food for the... more Rice, Oryza sativa L., is a cultivated, inbreeding species that serves as the staple food for the largest number of people on earth. It has two strongly diverged varietal groups, Indica and Japonica, which result from a combination of natural and human selection. The genetic divergence of these groups reflects the underlying population structure of their wild ancestors, and suggests that a pre-breeding strategy designed to take advantage of existing genetic, geographic and ecological substructure may provide a rational approach to the utilization of crop wild ancestors in plant improvement. Here we describe the coordinated development of six introgression libraries (n = 63 to 81 lines per library) in both Indica (cv. IR64) and Japonica (cv. Cybonnet) backgrounds using three bio-geographically diverse wild donors representing the Oryza rufipogon Species Complex from China, Laos and Indonesia. The final libraries were genotyped using an Infinium 7K rice SNP array (C7AIR) and analyzed ...

Research paper thumbnail of Genetic Analysis of Anthocyanin Pigmentation in Sterile Lemma and Apiculus in Rice

Plant Breeding and Biotechnology

Genetic analysis of genes that regulate the color pigmentation of sterile lemma and apiculus has ... more Genetic analysis of genes that regulate the color pigmentation of sterile lemma and apiculus has been conducted. "Josaengjado" has small and round grains with purple leaf, sterile lemma and apiculus. In the F2 population from a cross between Josaengjado and Daeribbyeo 1, 246 and 182 plants exhibited purple and straw-white sterile lemma, respectively. It fitted a 9:7 segregation ratio indicating that two complementary genes control the pigmentation in sterile lemma and apiculus. Genetic analysis was performed using the F2:3 and KASP (Kompetitive Allele-Specific PCR) markers. Genes for the coloration of leaf sheath, ligule, sterile lemma, and apiculus were detected on chromosomes 1 and 6. Sequence comparison showed a single nucleotide substitution C (Josaengjado) to A (Daeribbyeo 1) in the second exon of the Rd gene on chromosome 1 leading to a premature stop in Daeribbyeo 1. In C1, a 3-bp deletion in the second exon was detected in Daeribbyeo 1. Haplotype analysis was performed in the Rd and C1 genes of the 78 rice accessions. 78 accessions were divided into 14 groups. A total of 11 and 1 mutation sites were detected in OsC1 and Rd, respectively. The haplotype analysis also confirmed that two complementary genes, Rd and OsC1 are necessary to express anthocyanin pigmentation in sterile lemma and apiculus. To our knowledge, this is the first report to identify genes for the coloration of sterile lemma in rice.

Research paper thumbnail of Characterization of Quantitative Trait Loci for Germination and Coleoptile Length under Low-Temperature Condition Using Introgression Lines Derived from an Interspecific Cross in Rice

Genes

Previously, five putative quantitative trait loci (QTLs) for low-temperature germination (LTG) ha... more Previously, five putative quantitative trait loci (QTLs) for low-temperature germination (LTG) have been detected using 96 BC3F8 lines derived from an interspecific cross between the Korean japonica cultivar “Hwaseong” and Oryza rufipogon. In the present study, two introgression lines, CR1517 and CR1518, were used as parents to detect additional QTLs and analyze interactions among QTLs for LTG. The F2 population (154 plants) along with parental lines, Hwaseong and O. rufipogon, were evaluated for LTG and coleoptile length under low-temperature conditions (13 °C). Among five QTLs for LTG, two major QTLs, qLTG1 and qLTG3, were consistently detected at 6 and 7 days after incubation. Three minor QTLs were detected on chromosomes 8 and 10. Two QTLs, qLTG10.1 and qLTG10.2, showing linkage on chromosome 10, exerted opposite effects with the Hwaseong allele at qLTG10.2 and the O. rufipogon allele at qLTG10.1 respectively, in turn, increasing LTG. Interactions among QTLs were not significant...

Research paper thumbnail of Characterization of a New qLTG3–1 Allele for Low-temperature Germinability in Rice from the Wild Species Oryza rufipogon

Rice

Background Rice (Oryza sativa L.) is generally sensitive to low temperatures, and in production s... more Background Rice (Oryza sativa L.) is generally sensitive to low temperatures, and in production systems that use direct-seeding, low-temperature germinability (LTG) is a desired trait. Previously, the QTLs, qLTG1 and qLTG3, that control LTG, were mapped using the BC4F8 population, which is a cross of Korean elite cultivar Hwaseong and O. rufipogon (IRGC 105491). We have characterized and analyzed the interaction between the two QTLs, by crossing TR20 that has O. rufipogon alleles at qLTG1 and qLTG3 in a Hwaseong background, with Hwaseong, to develop an F2 population. Results The F2 plants with both qLTG1 and qLTG3 alleles from O. rufipogon showed higher LTG scores, than the plants with only qLTG1 or qLTG3. No significant interaction between the qLTG1 and qLTG3 was observed, indicating that they may regulate LTG via different pathways. Based on its location, qLTG3 appears to be allelic with qLTG3–1, a major QTL known to control LTG. To investigate the genetic differences between the ...

Research paper thumbnail of A RING-Type E3 Ubiquitin Ligase, OsGW2, Controls Chlorophyll Content and Dark-Induced Senescence in Rice

International Journal of Molecular Sciences

Leaf senescence is the final stage of plant development. Many internal and external factors affec... more Leaf senescence is the final stage of plant development. Many internal and external factors affect the senescence process in rice (Oryza sativa L.). In this study, we identified qCC2, a major quantitative trait locus (QTL) for chlorophyll content using a population derived from an interspecific cross between O. sativa (cv. Hwaseong) and Oryza grandiglumis. The O. grandiglumis allele at qCC2 increased chlorophyll content and delayed senescence. GW2 encoding E3 ubiquitin ligase in the qCC2 region was selected as a candidate for qCC2. To determine if GW2 is allelic to qCC2, a gw2-knockout mutant (gw2-ko) was examined using a dark-induced senescence assay. gw2-ko showed delayed leaf senescence in the dark with down-regulated expression of senescence-associated genes (SAGs) and chlorophyll degradation genes (CDGs). The association of the GW2 genotype with the delayed senescence phenotype was confirmed in an F2 population. RNA-seq analysis was conducted to investigate 30-day-old leaf tran...

Research paper thumbnail of Analysis of QTL responsible for grain iron and zinc content in doubled haploid lines of rice ( Oryza sativa ) derived from an intra ‐japonica cross

Research paper thumbnail of Sequencing and Comparative Analysis of the Chloroplast Genome of Angelica polymorpha and the Development of a Novel Indel Marker for Species Identification

Molecules

The genus Angelica (Apiaceae) comprises valuable herbal medicines. In this study, we determined t... more The genus Angelica (Apiaceae) comprises valuable herbal medicines. In this study, we determined the complete chloroplast (CP) genome sequence of A. polymorpha and compared it with that of Ligusticum officinale (GenBank accession no. NC039760). The CP genomes of A. polymorpha and L. officinale were 148,430 and 147,127 bp in length, respectively, with 37.6% GC content. Both CP genomes harbored 113 unique functional genes, including 79 protein-coding, four rRNA, and 30 tRNA genes. Comparative analysis of the two CP genomes revealed conserved genome structure, gene content, and gene order. However, highly variable regions, sufficient to distinguish between A. polymorpha and L. officinale, were identified in hypothetical chloroplast open reading frame1 (ycf1) and ycf2 genic regions. Nucleotide diversity (Pi) analysis indicated that ycf4–chloroplast envelope membrane protein (cemA) intergenic region was highly variable between the two species. Phylogenetic analysis revealed that A. polymo...

Research paper thumbnail of Characterization of the Spikelet Number per Panicle QTL qSPP7 Using a Nearly Isogenic Line Derived from an Interspecific Cross in Rice

Plant Breeding and Biotechnology

Previously, we mapped the qSPP7 QTL affecting the number of spikelets per panicle (SPP) on rice c... more Previously, we mapped the qSPP7 QTL affecting the number of spikelets per panicle (SPP) on rice chromosome 7 using near-isogenic line (NIL WH29001) derived from an interspecific cross between the japonica 'Hwaseong' and Oryza minuta. In the present study, we confirmed this QTL using progeny derived from a cross between IL102, a WH29001 sister line and Hwaseong. Genetic analysis determined that qSPP7 was located between a KASP marker KJ07-049 and RM21605. The O. minuta segment on chromosome 7 introgressed into the Hwaseong background was associated with an increase in SPP. The panicle structure of IL102 revealed that not only the number of SPP increased significantly, but also the number of branches per panicle increased as compared to Hwaseong suggesting that the donor allele of qSPP7 promotes branching in the genetic background of Hwaseong. Linkage analysis indicated that qEhd1 on chromosome 10 is involved in the difference in heading date of IL102 and Hwaseong. Experiments under 3 different day length conditions revealed that IL102 always showed earlier heading and higher SPP as compared to Hwaseong indicating that the effect of qSPP7 in the Hwaseong background was not dependent on photoperiod, and SPP increased in proportion to the number of days to heading.

Research paper thumbnail of A New High-yielding Rice Variety ‘Hwaweon 7’ with Lodging Tolerance

Korean Journal of Breeding Science

'Hwaweon 7' was developed from a cross between the African upland cultivar, 'Moroberekan' and 'Il... more 'Hwaweon 7' was developed from a cross between the African upland cultivar, 'Moroberekan' and 'Ilpumbyeo' based on marker-aided backcross selection. The recurrent parent, Ilpumbyeo is a high grain quality cultivar with medium to late maturity. Hwaweon 7 is nearly isogenic to Ilpumbyeo except a small Moroberekan introgressed segment on chromosome 6 harboring genes related with spikelets per panicle and internode diameter. The preliminary and replicated yield trial was conducted at Chungnam National University and Chungcheongnamdo Agricultural Research & Extension (CARES), Yesan in 2010 and 2011. The local adaptability test was carried out by the National Seed Management Office (NSMO) in 2012 and 2013. This cultivar was registered to NSMO with a cultivar designated as "Hwaweon7". This cultivar averaged 80cm in culm length and has a medium growth duration. Milled rice of "Hwaweon7" is translucent and the grain quality traits are comparable to those of the recurrent parent. The average yield potential of Hwaweon 7 in grain was about 6.48 MT/ha at the ordinary fertilizer level for two years about 5.1% higher than that of Ilpumbyeo due to increase in spikelets per panicle. This variety is tolerant to lodging and the tolerance is due to the APO1 gene controlling the base internode diameter on chromosome 6 introgressed from the donor parent, Moroberekan. The Apo1 gene would be useful in enhancing resistance to lodging in rice breeding program.

Research paper thumbnail of A New High-yielding Rice Variety developed from an Interspecific cross, ‘Hwaweon 6’

Korean Journal of Breeding Science

Hwaweon 6' was developed from a cross between 'Hwaseongbyeo' and a wild species, Oryza minuta L. ... more Hwaweon 6' was developed from a cross between 'Hwaseongbyeo' and a wild species, Oryza minuta L. (Acc. No. 101154) based on marker-assisted selection and backcrossing. The recurrent parent 'Hwaseongbyeo' is a high grain quality cultivar with medium maturity. Hwaweon 6 is nearly isogenic to Hwaseongbyeo except a small O. minuta introgressed segment on chromosome 7 harboring genes related with spikelets per panicle. The preliminary and replicated yield trial was conducted at Chungnam National University and Chungcheongnamdo Agricultural Research & Extension (CARES), Yesan in 2009 and 2010. The local adaptability test was carried out by the National Seed Management Office (NSMO) in 2011 and 2012. This cultivar was registered to NSMO with a cultivar designated as Hwaweon 6. This cultivar averaged 80cm in culm length and has a medium growth duration. Milled rice of Hwaweon 6 is translucent and the grain quality traits are comparable to those of the recurrent parent. The average yield potential of Hwaweon 6 in grain was about 6.57 MT/ha at the ordinary fertilizer level for two years about 3.0% higher than that of Hwaseongbyeo due to an introgression of the quantitative trait locus (QTL) for spikelets per panicle (qSPP7) from O. minuta. This variety is comparable to Hwaseongbyeo in low temperature germinability and cold tolerance. The qSPP7 QTL would be useful in enhancing yield potential in rice breeding program.

Research paper thumbnail of Fine mapping and candidate gene analysis of the quantitative trait locus gw8.1 associated with grain length in rice

Research paper thumbnail of Genetic Analysis of Seedling Traits Regulated by Light in Weedy Rice

Plant Breeding and Biotechnology

The Korean weedy rice, PBR (photoblastic rice) was reported to have light-inducible seed germinat... more The Korean weedy rice, PBR (photoblastic rice) was reported to have light-inducible seed germination (photoblastism) and long mesocotyl. In previous studies, we mapped two QTL each for photoblastism and mesocotyl length using progeny from a cross between Ilpumbyeo and PBR. One F8 line CR7124 having photoblastism and long mesocotyl, was chosen and crossed to Ilpumbyeo to produce 95 F3 lines for QTL mapping. Germination percentage of CR7124 and Ilpumbyeo was 3.3 ± 2.4% and 91.7 ± 7.1%, respectively in the dark condition. 95 F3 lines ranged from 28.6% to 100% in germination. For mesocotyl, Ilpumbyeo and PBR elongated up to 1.5 mm and 18.5 mm, respectively whereas 95 F3 lines ranged from 0.9 mm to 16.3 mm. The mesocotyl length showed highly negative significant correlation with germination rate in dark condition (r = 0.70, P ＜ 0.0001). QTL mapping using 95 F3 lines confirmed the linkage of two QTL for photoblastism and mesocotyl length on chromosome 1. Eight F4 lines with different PBR chromosome segments in the target region were used for substitution mapping of pbr1 and qMel-1. It appears that qMel-1 was located in the interval RM11252-RM7419, a region of approximately 4.7 Mb. pbr1 was located in the interval between RM7202 and RM11729. Although further fine mapping of two QTL is necessary to know the relationship of these two traits, these results together with the highly significant correlation between two traits indicate that two QTL are linked. DNA markers linked to these QTLs would be useful in facilitating the selection of lines with enhanced mesocotyl elongation.

Research paper thumbnail of Genetic Analysis and Mapping of Genes for Culm Length and Internode Diameter in Progeny from an Interspecific Cross in Rice

Plant Breeding and Biotechnology

In this study, two near-isogenic lines (NILs) were selected from a series of chromosome segment s... more In this study, two near-isogenic lines (NILs) were selected from a series of chromosome segment substitution lines developed from an interspecific cross between Oryza sativa ssp. japonica cultivar 'Hwaseongbyeo' as a recipient parent and wild rice (Oryza grandiglumis) as the donor parent. Compared with Hwaseongbyeo control, one NIL (CR222) had reduced plant height and the other NIL (CR7501) displayed thicker basal and first internodes leading to increased lodging tolerance in the field condition. QTL analysis using progeny from crosses between Hwaseongbyeo and the NILs indicated that QTL for culm length and internode diameter leading to erect panicle were located on chromosomes 1 and 2, respectively. The major QTL for culm length on chromosome 1 was allelic to sd1 locus and the NIL showed the same sequence as the sd1 mutant cultivar 'Reimei'. The QTL for the internode diameter was delimited to a 1-Mbp region on chromosome 2 and this QTL region harbors GW2 gene controlling grain width. The NIL with thick internode trait showed no undesirable pleiotropic effects and therefore has potential value for rice breeding for increasing lodging resistance.

Research paper thumbnail of Terminal repeat retrotransposon in miniature (TRIM) as DNA markers in Brassica relatives

Molecular Genetics and Genomics, 2007

We have developed a display system using a unique sequence of terminal repeat retrotransposon in ... more We have developed a display system using a unique sequence of terminal repeat retrotransposon in miniature (TRIM) elements, which were recently identified from gene-rich regions of Brassica rapa. The technique, named TRIM display, is based on modification of the AFLP technique using an adapter primer for the restriction fragments of BfaI and a primer derived from conserved terminal repeat sequences

Research paper thumbnail of Article : QTLs for Domestication-related and Agronomic Traits in Temperate Japonica Weedy Rice

This study was conducted to identify the genetic basis of the domestication-related traits in wee... more This study was conducted to identify the genetic basis of the domestication-related traits in weedy rice. An RIL population consisting of 80 lines was developed from a cross between the japonica weedy rice, Hapcheonaengmi 3 and the Tongiltype cultivar Milyang 23. The population was genotyped with 132 DNA markers, providing an average interval size of 11.0cM, and also evaluated for 20 traits related to domestication and agricultural performance. A total of 48 QTLs and two loci associated with qualitative variation for pericarp and base coloration were identified using single point and interval analysis. The number of QTLs per trait ranged from one to six. These 48 QTLs were located in 27 intervals distributed on 11 chromosomes except for chromosome 12. The results indicated that most domestication-related traits clustered in chromosomal blocks, and the positions of many of these clusters were consistent with those reported in previous studies. Phenotypic variation associated with eac...

Research paper thumbnail of Mapping Quantitative Trait Loci for Grain Weight, gw5 and Ratooning Ability using ILs from a Cross between Oryza sativa and O. rufipogon

Research paper thumbnail of Characteristics of β-Carotene Rice Developed using Marker-Assisted Selection

Research paper thumbnail of Introgression for agronomic traits from Oryza grandiglumis into rice, O. sativa

Research paper thumbnail of Natural variation in rice ascorbate peroxidase gene APX9 is associated with a yield-enhancing QTL cluster

Journal of Experimental Botany

We previously identified a cluster of yield-related quantitative trait loci (QTLs) including plan... more We previously identified a cluster of yield-related quantitative trait loci (QTLs) including plant height in CR4379, a near-isogenic line from a cross between Oryza sativa spp. japonica cultivar ‘Hwaseong’ and the wild relative Oryza rufipogon. Map-based cloning and transgenic approaches revealed that APX9, which encodes an l-ascorbate peroxidase 4, is associated with this cluster. A 3 bp InDel was observed leading to the addition of a valine in Hwaseong compared with O. rufipogon. APX9-overexpressing transgenic plants in the Hwaseong background were taller than Hwaseong. Consistent with these results, APX9 T-DNA insertion mutants in the japonica cultivar Dongjin were shorter. These results confirm that APX9 is the causal gene for the QTL cluster. Sequence analysis of APX9 from 303 rice accessions revealed that the 3 bp InDel clearly differentiates japonica (APX9HS) and O. rufipogon (APX9OR) alleles. indica accessions shared both alleles, suggesting that APX9HS was introgressed into...

Research paper thumbnail of Genetic Structure and Geographical Differentiation of Traditional Rice (Oryza sativa L.) from Northern Vietnam

Plants

Northern Vietnam is one of the most important centers of genetic diversity for cultivated rice. O... more Northern Vietnam is one of the most important centers of genetic diversity for cultivated rice. Over thousands of years of cultivation, natural and artificial selection has preserved many traditional rice landraces in northern Vietnam due to its geographic situation, climatic conditions, and many ethnic groups. These local landraces serve as a rich source of genetic variation—an important resource for future crop improvement. In this study, we determined the genetic diversity and population structure of 79 rice landraces collected from northern Vietnam and 19 rice accessions collected from different countries. In total, 98 rice accessions could be differentiated into japonica and indica with moderate genetic diversity and a polymorphism information content of 0.382. Moreover, we found that genetic differentiation was related to geographical regions with an overall PhiPT (analog of fixation index FST) value of 0.130. We also detected subspecies-specific markers to classify rice (Oryz...

Research paper thumbnail of A Coordinated Suite of Wild-Introgression Lines in Indica and Japonica Elite Backgrounds

Frontiers in Plant Science

Rice, Oryza sativa L., is a cultivated, inbreeding species that serves as the staple food for the... more Rice, Oryza sativa L., is a cultivated, inbreeding species that serves as the staple food for the largest number of people on earth. It has two strongly diverged varietal groups, Indica and Japonica, which result from a combination of natural and human selection. The genetic divergence of these groups reflects the underlying population structure of their wild ancestors, and suggests that a pre-breeding strategy designed to take advantage of existing genetic, geographic and ecological substructure may provide a rational approach to the utilization of crop wild ancestors in plant improvement. Here we describe the coordinated development of six introgression libraries (n = 63 to 81 lines per library) in both Indica (cv. IR64) and Japonica (cv. Cybonnet) backgrounds using three bio-geographically diverse wild donors representing the Oryza rufipogon Species Complex from China, Laos and Indonesia. The final libraries were genotyped using an Infinium 7K rice SNP array (C7AIR) and analyzed ...

Research paper thumbnail of Genetic Analysis of Anthocyanin Pigmentation in Sterile Lemma and Apiculus in Rice

Plant Breeding and Biotechnology

Genetic analysis of genes that regulate the color pigmentation of sterile lemma and apiculus has ... more Genetic analysis of genes that regulate the color pigmentation of sterile lemma and apiculus has been conducted. "Josaengjado" has small and round grains with purple leaf, sterile lemma and apiculus. In the F2 population from a cross between Josaengjado and Daeribbyeo 1, 246 and 182 plants exhibited purple and straw-white sterile lemma, respectively. It fitted a 9:7 segregation ratio indicating that two complementary genes control the pigmentation in sterile lemma and apiculus. Genetic analysis was performed using the F2:3 and KASP (Kompetitive Allele-Specific PCR) markers. Genes for the coloration of leaf sheath, ligule, sterile lemma, and apiculus were detected on chromosomes 1 and 6. Sequence comparison showed a single nucleotide substitution C (Josaengjado) to A (Daeribbyeo 1) in the second exon of the Rd gene on chromosome 1 leading to a premature stop in Daeribbyeo 1. In C1, a 3-bp deletion in the second exon was detected in Daeribbyeo 1. Haplotype analysis was performed in the Rd and C1 genes of the 78 rice accessions. 78 accessions were divided into 14 groups. A total of 11 and 1 mutation sites were detected in OsC1 and Rd, respectively. The haplotype analysis also confirmed that two complementary genes, Rd and OsC1 are necessary to express anthocyanin pigmentation in sterile lemma and apiculus. To our knowledge, this is the first report to identify genes for the coloration of sterile lemma in rice.

Research paper thumbnail of Characterization of Quantitative Trait Loci for Germination and Coleoptile Length under Low-Temperature Condition Using Introgression Lines Derived from an Interspecific Cross in Rice

Genes

Previously, five putative quantitative trait loci (QTLs) for low-temperature germination (LTG) ha... more Previously, five putative quantitative trait loci (QTLs) for low-temperature germination (LTG) have been detected using 96 BC3F8 lines derived from an interspecific cross between the Korean japonica cultivar “Hwaseong” and Oryza rufipogon. In the present study, two introgression lines, CR1517 and CR1518, were used as parents to detect additional QTLs and analyze interactions among QTLs for LTG. The F2 population (154 plants) along with parental lines, Hwaseong and O. rufipogon, were evaluated for LTG and coleoptile length under low-temperature conditions (13 °C). Among five QTLs for LTG, two major QTLs, qLTG1 and qLTG3, were consistently detected at 6 and 7 days after incubation. Three minor QTLs were detected on chromosomes 8 and 10. Two QTLs, qLTG10.1 and qLTG10.2, showing linkage on chromosome 10, exerted opposite effects with the Hwaseong allele at qLTG10.2 and the O. rufipogon allele at qLTG10.1 respectively, in turn, increasing LTG. Interactions among QTLs were not significant...

Research paper thumbnail of Characterization of a New qLTG3–1 Allele for Low-temperature Germinability in Rice from the Wild Species Oryza rufipogon

Rice

Background Rice (Oryza sativa L.) is generally sensitive to low temperatures, and in production s... more Background Rice (Oryza sativa L.) is generally sensitive to low temperatures, and in production systems that use direct-seeding, low-temperature germinability (LTG) is a desired trait. Previously, the QTLs, qLTG1 and qLTG3, that control LTG, were mapped using the BC4F8 population, which is a cross of Korean elite cultivar Hwaseong and O. rufipogon (IRGC 105491). We have characterized and analyzed the interaction between the two QTLs, by crossing TR20 that has O. rufipogon alleles at qLTG1 and qLTG3 in a Hwaseong background, with Hwaseong, to develop an F2 population. Results The F2 plants with both qLTG1 and qLTG3 alleles from O. rufipogon showed higher LTG scores, than the plants with only qLTG1 or qLTG3. No significant interaction between the qLTG1 and qLTG3 was observed, indicating that they may regulate LTG via different pathways. Based on its location, qLTG3 appears to be allelic with qLTG3–1, a major QTL known to control LTG. To investigate the genetic differences between the ...

Research paper thumbnail of A RING-Type E3 Ubiquitin Ligase, OsGW2, Controls Chlorophyll Content and Dark-Induced Senescence in Rice

International Journal of Molecular Sciences

Leaf senescence is the final stage of plant development. Many internal and external factors affec... more Leaf senescence is the final stage of plant development. Many internal and external factors affect the senescence process in rice (Oryza sativa L.). In this study, we identified qCC2, a major quantitative trait locus (QTL) for chlorophyll content using a population derived from an interspecific cross between O. sativa (cv. Hwaseong) and Oryza grandiglumis. The O. grandiglumis allele at qCC2 increased chlorophyll content and delayed senescence. GW2 encoding E3 ubiquitin ligase in the qCC2 region was selected as a candidate for qCC2. To determine if GW2 is allelic to qCC2, a gw2-knockout mutant (gw2-ko) was examined using a dark-induced senescence assay. gw2-ko showed delayed leaf senescence in the dark with down-regulated expression of senescence-associated genes (SAGs) and chlorophyll degradation genes (CDGs). The association of the GW2 genotype with the delayed senescence phenotype was confirmed in an F2 population. RNA-seq analysis was conducted to investigate 30-day-old leaf tran...

Research paper thumbnail of Analysis of QTL responsible for grain iron and zinc content in doubled haploid lines of rice ( Oryza sativa ) derived from an intra ‐japonica cross

Research paper thumbnail of Sequencing and Comparative Analysis of the Chloroplast Genome of Angelica polymorpha and the Development of a Novel Indel Marker for Species Identification

Molecules

The genus Angelica (Apiaceae) comprises valuable herbal medicines. In this study, we determined t... more The genus Angelica (Apiaceae) comprises valuable herbal medicines. In this study, we determined the complete chloroplast (CP) genome sequence of A. polymorpha and compared it with that of Ligusticum officinale (GenBank accession no. NC039760). The CP genomes of A. polymorpha and L. officinale were 148,430 and 147,127 bp in length, respectively, with 37.6% GC content. Both CP genomes harbored 113 unique functional genes, including 79 protein-coding, four rRNA, and 30 tRNA genes. Comparative analysis of the two CP genomes revealed conserved genome structure, gene content, and gene order. However, highly variable regions, sufficient to distinguish between A. polymorpha and L. officinale, were identified in hypothetical chloroplast open reading frame1 (ycf1) and ycf2 genic regions. Nucleotide diversity (Pi) analysis indicated that ycf4–chloroplast envelope membrane protein (cemA) intergenic region was highly variable between the two species. Phylogenetic analysis revealed that A. polymo...

Research paper thumbnail of Characterization of the Spikelet Number per Panicle QTL qSPP7 Using a Nearly Isogenic Line Derived from an Interspecific Cross in Rice

Plant Breeding and Biotechnology

Previously, we mapped the qSPP7 QTL affecting the number of spikelets per panicle (SPP) on rice c... more Previously, we mapped the qSPP7 QTL affecting the number of spikelets per panicle (SPP) on rice chromosome 7 using near-isogenic line (NIL WH29001) derived from an interspecific cross between the japonica 'Hwaseong' and Oryza minuta. In the present study, we confirmed this QTL using progeny derived from a cross between IL102, a WH29001 sister line and Hwaseong. Genetic analysis determined that qSPP7 was located between a KASP marker KJ07-049 and RM21605. The O. minuta segment on chromosome 7 introgressed into the Hwaseong background was associated with an increase in SPP. The panicle structure of IL102 revealed that not only the number of SPP increased significantly, but also the number of branches per panicle increased as compared to Hwaseong suggesting that the donor allele of qSPP7 promotes branching in the genetic background of Hwaseong. Linkage analysis indicated that qEhd1 on chromosome 10 is involved in the difference in heading date of IL102 and Hwaseong. Experiments under 3 different day length conditions revealed that IL102 always showed earlier heading and higher SPP as compared to Hwaseong indicating that the effect of qSPP7 in the Hwaseong background was not dependent on photoperiod, and SPP increased in proportion to the number of days to heading.

Research paper thumbnail of A New High-yielding Rice Variety ‘Hwaweon 7’ with Lodging Tolerance

Korean Journal of Breeding Science

'Hwaweon 7' was developed from a cross between the African upland cultivar, 'Moroberekan' and 'Il... more 'Hwaweon 7' was developed from a cross between the African upland cultivar, 'Moroberekan' and 'Ilpumbyeo' based on marker-aided backcross selection. The recurrent parent, Ilpumbyeo is a high grain quality cultivar with medium to late maturity. Hwaweon 7 is nearly isogenic to Ilpumbyeo except a small Moroberekan introgressed segment on chromosome 6 harboring genes related with spikelets per panicle and internode diameter. The preliminary and replicated yield trial was conducted at Chungnam National University and Chungcheongnamdo Agricultural Research & Extension (CARES), Yesan in 2010 and 2011. The local adaptability test was carried out by the National Seed Management Office (NSMO) in 2012 and 2013. This cultivar was registered to NSMO with a cultivar designated as "Hwaweon7". This cultivar averaged 80cm in culm length and has a medium growth duration. Milled rice of "Hwaweon7" is translucent and the grain quality traits are comparable to those of the recurrent parent. The average yield potential of Hwaweon 7 in grain was about 6.48 MT/ha at the ordinary fertilizer level for two years about 5.1% higher than that of Ilpumbyeo due to increase in spikelets per panicle. This variety is tolerant to lodging and the tolerance is due to the APO1 gene controlling the base internode diameter on chromosome 6 introgressed from the donor parent, Moroberekan. The Apo1 gene would be useful in enhancing resistance to lodging in rice breeding program.

Research paper thumbnail of A New High-yielding Rice Variety developed from an Interspecific cross, ‘Hwaweon 6’

Korean Journal of Breeding Science

Hwaweon 6' was developed from a cross between 'Hwaseongbyeo' and a wild species, Oryza minuta L. ... more Hwaweon 6' was developed from a cross between 'Hwaseongbyeo' and a wild species, Oryza minuta L. (Acc. No. 101154) based on marker-assisted selection and backcrossing. The recurrent parent 'Hwaseongbyeo' is a high grain quality cultivar with medium maturity. Hwaweon 6 is nearly isogenic to Hwaseongbyeo except a small O. minuta introgressed segment on chromosome 7 harboring genes related with spikelets per panicle. The preliminary and replicated yield trial was conducted at Chungnam National University and Chungcheongnamdo Agricultural Research & Extension (CARES), Yesan in 2009 and 2010. The local adaptability test was carried out by the National Seed Management Office (NSMO) in 2011 and 2012. This cultivar was registered to NSMO with a cultivar designated as Hwaweon 6. This cultivar averaged 80cm in culm length and has a medium growth duration. Milled rice of Hwaweon 6 is translucent and the grain quality traits are comparable to those of the recurrent parent. The average yield potential of Hwaweon 6 in grain was about 6.57 MT/ha at the ordinary fertilizer level for two years about 3.0% higher than that of Hwaseongbyeo due to an introgression of the quantitative trait locus (QTL) for spikelets per panicle (qSPP7) from O. minuta. This variety is comparable to Hwaseongbyeo in low temperature germinability and cold tolerance. The qSPP7 QTL would be useful in enhancing yield potential in rice breeding program.

Research paper thumbnail of Fine mapping and candidate gene analysis of the quantitative trait locus gw8.1 associated with grain length in rice

Research paper thumbnail of Genetic Analysis of Seedling Traits Regulated by Light in Weedy Rice

Plant Breeding and Biotechnology

The Korean weedy rice, PBR (photoblastic rice) was reported to have light-inducible seed germinat... more The Korean weedy rice, PBR (photoblastic rice) was reported to have light-inducible seed germination (photoblastism) and long mesocotyl. In previous studies, we mapped two QTL each for photoblastism and mesocotyl length using progeny from a cross between Ilpumbyeo and PBR. One F8 line CR7124 having photoblastism and long mesocotyl, was chosen and crossed to Ilpumbyeo to produce 95 F3 lines for QTL mapping. Germination percentage of CR7124 and Ilpumbyeo was 3.3 ± 2.4% and 91.7 ± 7.1%, respectively in the dark condition. 95 F3 lines ranged from 28.6% to 100% in germination. For mesocotyl, Ilpumbyeo and PBR elongated up to 1.5 mm and 18.5 mm, respectively whereas 95 F3 lines ranged from 0.9 mm to 16.3 mm. The mesocotyl length showed highly negative significant correlation with germination rate in dark condition (r = 0.70, P ＜ 0.0001). QTL mapping using 95 F3 lines confirmed the linkage of two QTL for photoblastism and mesocotyl length on chromosome 1. Eight F4 lines with different PBR chromosome segments in the target region were used for substitution mapping of pbr1 and qMel-1. It appears that qMel-1 was located in the interval RM11252-RM7419, a region of approximately 4.7 Mb. pbr1 was located in the interval between RM7202 and RM11729. Although further fine mapping of two QTL is necessary to know the relationship of these two traits, these results together with the highly significant correlation between two traits indicate that two QTL are linked. DNA markers linked to these QTLs would be useful in facilitating the selection of lines with enhanced mesocotyl elongation.

Research paper thumbnail of Genetic Analysis and Mapping of Genes for Culm Length and Internode Diameter in Progeny from an Interspecific Cross in Rice

Plant Breeding and Biotechnology

In this study, two near-isogenic lines (NILs) were selected from a series of chromosome segment s... more In this study, two near-isogenic lines (NILs) were selected from a series of chromosome segment substitution lines developed from an interspecific cross between Oryza sativa ssp. japonica cultivar 'Hwaseongbyeo' as a recipient parent and wild rice (Oryza grandiglumis) as the donor parent. Compared with Hwaseongbyeo control, one NIL (CR222) had reduced plant height and the other NIL (CR7501) displayed thicker basal and first internodes leading to increased lodging tolerance in the field condition. QTL analysis using progeny from crosses between Hwaseongbyeo and the NILs indicated that QTL for culm length and internode diameter leading to erect panicle were located on chromosomes 1 and 2, respectively. The major QTL for culm length on chromosome 1 was allelic to sd1 locus and the NIL showed the same sequence as the sd1 mutant cultivar 'Reimei'. The QTL for the internode diameter was delimited to a 1-Mbp region on chromosome 2 and this QTL region harbors GW2 gene controlling grain width. The NIL with thick internode trait showed no undesirable pleiotropic effects and therefore has potential value for rice breeding for increasing lodging resistance.