• Molecules and Cells
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• v.37 no.2
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• pp.149-160
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• 2014

Plant breeders have focused on improving plant architecture as an effective means to increase crop yield. Here, we identify the main-effect quantitative trait loci (QTLs) for plant shape-related traits in rice (Oryza sativa) and find candidate genes by applying whole genome re-sequencing of two parental cultivars using next-generation sequencing. To identify QTLs influencing plant shape, we analyzed six traits: plant height, tiller number, panicle diameter, panicle length, flag leaf length, and flag leaf width. We performed QTL analysis with 178 $F_7$ recombinant inbred lines (RILs) from a cross of japonica rice line 'SNU-SG1' and indica rice line 'Milyang23'. Using 131 molecular markers, including 28 insertion/deletion markers, we identified 11 main- and 16 minor-effect QTLs for the six traits with a threshold LOD value > 2.8. Our sequence analysis identified fifty-four candidate genes for the main-effect QTLs. By further comparison of coding sequences and meta-expression profiles between japonica and indica rice varieties, we finally chose 15 strong candidate genes for the 11 main-effect QTLs. Our study shows that the whole-genome sequence data substantially enhanced the efficiency of polymorphic marker development for QTL fine-mapping and the identification of possible candidate genes. This yields useful genetic resources for breeding high-yielding rice cultivars with improved plant architecture.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.43 no.4
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• pp.250-253
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• 1998

Somaclonal variation was observed in the field on doubled haploid plants derived from single pollen of a rice cultivar "Hwaseongbyeo". The variations of seven quantitative traits including plant height and one qualitative trait (pubescence) in 436 lines ($R_2$ generation) were analyzed. The number of lines which fell beyond the boundaries of the 95% confidence intervals of the check variety, Hwaseongbyeo was checked for each quantitative trait, and of those fertility showed the highest variation frequency (85.6%), followed by plant height (77.5%), flag leaf length (66.5%), grains per panicle (42.2%), days to heading (34.5%), panicle length (30.7%) and panicles per hill (22.7%). And the variations of quantitative traits except days to flowering appeared to move in the negative direction compared to "Hwaseongbyeo". Variability within lines was also observed for quantitative and qualitative traits. Twenty-nine $R_2$ lines (7%) segregated for pubescence and 130 $R_2$ lines (30%) showed variation with regard to fertility. This suggests that mutations usually occur before diploidization. Twenty-nine $R_2$ lines representing a wide spectrum of variation were chosen for RAPD analysis. The number of lines showing DNA polymorphism compared to Hwaseongbyeo ranged 0 from to 10 according to the primer used and this seems to indicate that specific loci have highly mutable genomic site.utable genomic site.

• Korean Journal of Breeding Science
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• v.43 no.1
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• pp.68-80
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• 2011

This study was conducted to investigate characteristics and variations of rice panicle traits for breeding temperate japonica varieties adapted to tropical environment. Eleven panicle traits were investigated from nine Korean rice varieties cultivated in Korea and wet season of the Philippines. Tested cultivars were composed of six temperate japonica varieties, three Tongil-type varieties, and one indica variety bred in the Philippines. The number of spikelets on secondary rachis branches (SRBs) was the most variable trait in both environments, while the mean number of spikelets on a primary rachis branch (PRB) was the least variable. Compared with PRB-related traits, SRB traits showed higher correlation with the number of spikelets per panicle. Compared with the plants grown in Korea, the number of spikelets on SRBs, the number of SRBs, spikelets, and rachis branches per panicle were decreased more than other traits in the Philippines. According to path analysis, the number of spikelets on SRBs per panicle affects the number of spikelets per panicle more than the number of spikelets on PRBs per panicle. Climatic factors such as growth duration, cumulative mean temperature, and integrated solar radiation were highly correlated with the relative rate of number of spikelets per panicle. To breed temperate japonica rice varieties adapted to tropical environment, it would be important to select lines which maintain proper growth duration and spikelets on SRBs in target region.

• Korean Journal of Breeding Science
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• v.40 no.4
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• pp.414-421
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• 2008

We conducted a QTL analysis of agronomic traits using 117 $BC_3F_5$ and $BC_3F_6$ lines developed from a cross between Ilpumbyeo and Moroberekan. Genotypes of 117 $BC_3F_5$ lines were determined using 134 simple sequence repeat (SSR) markers. A total of 832 Moroberekan chromosome segments with 410 homozygous and 422 heterozygous, respectively, were detected, and the genetic distance of introgression segments ranged from 0.5 cm to 112.1 cm. A linkage map constructed using 134 SSR markers was employed to characterize quantitative trait loci (QTL). The 117 $BC_3F_5$ and $BC_3F_6$ lines were evaluated for seven agronomic traits at two locations in 2006 and 2007 and at one location in 2007. A total of 26 QTLs were identified for seven traits including days to heading, and the phenotypic variance explained by each QTL ranged from 9.2% to 24.2%. Moroberekan alleles contributed positive effects in the Ilpumbyeo background at eleven QTL loci including panicle length and spikelets per panicle. Five QTLs, two for days to heading and one each for culm length, panicle length and spikelets per panicle were consistently detected in every occasions indicating that these QTLs are stable. Among them, two QTLs, spp6 for spikelets per panicle and pl6 for paniclel length were localized in the similar region. Increase in spikelets per panicle at this locus might be due to the increase in panicle length, because both traits were associated with increase in spikelets per panicle and panicle length due to the presence of the Moroberekan allele. These Moroberekan QTLs might be useful in breeding programs to develop high-yielding cultivars.

• Journal of Plant Biotechnology
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• v.30 no.3
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• pp.227-232
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• 2003

Radiation technique has been used to develope mutant rice. Suwon 345 rice seeds were irradiated with 250 Gy gamma ray. Morphological characteristics of the variants in M$_{8}$ generation were observed and random amplified polymorphic DNA(RAPD) analysis was carried out. Plant height, panicle length, 1,000 grain weight and lodging were very different in mutants compared with donor cultivar. RAPD analysis showed that polymorphic bands were presented in several primers of the mutants. In comparison with original variety, variants were classified into four group through UPGMA analysis. A group has mutation trait in panicle length, B group in plant height and C group in 1,000 grain weight. Among mutants, no. 46 and 147 was ranked as salt tolerance and the malonaldehyde content of these mutants was more increased than that of original variety. Valuable mutants obtained will be useful for developing new cultivars and for studing gene function in molecular level.l.

• Journal of Plant Biotechnology
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• v.44 no.4
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• pp.356-363
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• 2017

ARice is an important staple food in the world and rice yield is one of the main traits for rice breeding. Several genes involved in increasing the yield have been identified through map-based gene cloning within natural variations in rice. These identified genes are good targets for introducing a genetic trait in molecular breeding. Here, we chose five genes reported to be involved in increasing grain number per panicle in rice; Gn1a, dep1, Apo1, Ghd7, and Nal1. We developed In/Del markers for Gn1a, and dep1, Apo1, and applied the reported SNP markers for Ghd7 and Nal1. We were easily able to examine the genotype of each gene on agarose gel. We tested the genotypes on 479 rice resources that we held with evaluated molecular markers. According to the genotype of each gene, rice resources were divided into 13 haplotypes, and most of the Indica and Japonica varieties were included in haplotypes 1 and 13, respectively. When we examined the effect of each gene on grain number per panicle and panicle number per plant, panicle number per plant in the yield negative allele group for each gene was reduced by approximately 0.3 to 0.8 compared to that in the yield positive allele group. However, the number of yield positive alleles for each gene was higher by about 21 to 27 grains per panicle than that of yield negative alleles. Although most of the varieties were grouped in haplotypes 1 and 13, we believe that this genotype information with evaluated molecular markers will be useful in rice breeding for increasing the yield with grain number per panicle.

• Korean Journal of Agricultural Science
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• v.38 no.2
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• pp.199-204
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• 2011

This study was conducted to map quantitative trait loci (QTLs) related to drought stress tolerance. An introgression line population derived from a cross, "Ilpum" / "Moroberekan" was used in this study. $F_1$ plants were backcrossed three times to Ilpum to produce $BC_3F_1$ plants. These plants were advanced by selfing for four generation and a total of 117 $BC_3F_5$ introgression lines were developed. These lines were evaluated for percent seed set and spikelets per panicle under the control (field) and drought condition. To identify QTLs related to drought tolerance, 134 SSR markers showing polymorph isms between the parents were genotyped for the 117 $BC_3F_5$ lines. A total of 6 QTLs associated with drought stress were detected on chromosomes 1, 3, 4, 7 and 10. These include two QTLs for phenotypic acceptability, two QTLs for percent seed set ($R^2$ = 19.0 - 20.9%), and two QTLs for spikelets per panicle ($R^2$ = 22.3 - 23.10%). The Moroberekan alleles at three loci contributed the positive effect for drought tolerance. The SSR markers linked to drought stress tolerance can not only facilitate the selection of valuable genes from Moroberekan, but also allow identification of lines with drought tolerance.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.44 no.1
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• pp.86-94
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• 1999

A set of rice recombinant inbred lines was developed from a cross between a Tongil type variety, Nonganbyeo, and an indica variety, BG276, by the single seed descent method. The number of the lines in the population was 272. All the agronomic characters studied except ADV (alkali-digestion value) showed continuous variation among the RILs, implying that their inheritance mode should be quantitative. The patterns of the variation in the RILs were either normal or skewed distribution. ADVs of RILs were segregated into two groups with 1:1 ratio, indicating that ADVs in this KIL population might be controlled by one major gene. Transgressive variations were also observed in all characters. Heritability values of the characters varied from 0.488 in brown/rough rice ratio to 0.895 in alkali-digestion value. In the analysis of genotypic and phenotypic correlations, the character of yield was positively correlated with 8 different agronomic characters. The number of panicles per hill was negatively correlated with culm length, panicle length, and number of spikelets per panicle. Grain length was positively correlated with grain width, grain thickness, grain length/width ratio, white belly, ADV, and amylose. However, grain length/width ratio was negatively correlated with grain width. White core was also negatively correlated with white belly and ADV.

• Korean Journal of Agricultural Science
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• v.49 no.3
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• pp.483-493
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• 2022

It is important to improve the efficiency of plant breeding and crop yield to fulfill increasing food demands. In plant phenotyping studies, the capability to correlate morphological traits such as plant height, stem diameter, leaf length, leaf width, leaf angle and size of panicle of the plants has an important role. However, manual phenotyping of plants is prone to human errors and is labor intensive and time-consuming. Hence, it is important to develop techniques that measure plant phenotypic traits accurately and rapidly. The aim of this study was to determine the feasibility of point cloud data based on a 3D light detection and ranging (LiDAR) system for plant phenotyping. The obtained results were then verified through manually acquired data from the sorghum samples. This study measured the plant height, plant crown diameter and the panicle height and diameter. The R² of each trait was 0.83, 0.94, 0.90, and 0.90, and the root mean square error (RMSE) was 6.8 cm, 1.82 cm, 5.7 mm, and 7.8 mm, respectively. The results showed good correlation between the point cloud data and manually acquired data for plant phenotyping. The results indicate that the 3D LiDAR system has potential to measure the phenotypes of sorghum in a rapid and accurate way.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.252-252
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• 2022

Genotype-by-environment interaction (GEI) refers to the comparative response of genotypes to different environments conditions. Thus, understanding GEI is a fundamental component for selecting superior genotypes for breeding programs. The significance of utilizing early maturing cultivars not only provides flexibility in planting dates, but also serves as an effective strategy to reduce methane emission from the paddy fields. In this study, we conducted multi-environment trials (METs) to evaluate yield-related traits such as culm length, panicle length, panicle number, spikelet per plant, and thousand grain weight. A total of eighty-one Korean commercial rice cultivars categorized as early maturing cultivars, were cultivated in three regions, two planting seasons for two years. The genotype main effect plus genotype-by-environment interaction (GGE) biplot analysis of yield-related traits and grain yield explained 70.02-91.24% of genotype plus GEI variation, and exhibited various patterns of mega-environment delineation, discriminating ability, representativeness, and genotype rankings across the planting seasons and environments. Moreover, simultaneous selection using weighted average of absolute scores from the singular value decomposition (WAASB) and multi-trait stability index (MTSI) revealed six highly recommended genotypes with high stability and crop productivity. The winning genotypes under specific environment can be utilized as useful genetic materials to develop regional specialty cultivars, and recommended genotypes can be used as elite climate-resilient parents to improve yield-potential and reduce methane emission as part to accomplish carbon-neutrality.