Fast and accurate selection is essential for breeding to cope with rapid climate changes and a steeply increasing population. Consequently, technologies for high-throughput phenotyping (HTP) are emerging. These technologies, unlike conventional phenotyping methods, enable us to evaluate agronomic traits in a fast and massive manner. Thus, the HTP facility was built to acquire and analyze crop images using RGB sensors at the National Institute of Agricultural Sciences, Republic of Korea. By testing various conditions to acquire images, we determined the conditions for phenotyping using the RGB sensor as follows: exposure 30,000 ms, gamma 75, and gain 100 using LED lights in a blue background. Based on this condition, images from 96 individual plants of rice Dongjin cultivar were obtained every week to measure plant height and shoot area, which are directly associated with yield. The results obtained from the image analysis were compared with the manually collected results. The r² value between the projected plant height obtained from image analysis and the plant height obtained from manual measurement was 0.989. Furthermore, the r² value between the projected shoot area obtained from image analysis and the shoot area obtained from manual measurement was 0.981. These results show that image analysis is highly reliable and can be used for crop phenotyping. Therefore, we expect that the new method we developed will be used for breeding in the near future.

A dwarf mutant rice line was selected from an Ac/Ds insertion mutant population and named dwf1. The phenotype of F₁ and F₂ plants derived from a cross between dwf1 and Dongjin indicated that a single recessive gene is responsible for the mutant phenotype, and we named this gene dwf1. Resequencing of the dwf1 line and Dongjin (wild type) revealed 42,386 homozygous single nucleotide polymorphisms (SNPs) between dwf1 line and Dongjin. MutMap analysis was performed by sequencing a DNA pool prepared from 100 mutant type plants in the dwf1/Dongjin F₂ population, and it was found that the dwf1 gene was located in the 23 ~ 30 Mbp region on chromosome 4. In this region, we found a non-synonymous SNP in the Os04g0469800 gene, which was reported as D11 gene encoding a cytochrome P450 family protein involved in the biosynthesis of brassinosteroids (BRs). This SNP was regarded as the causative SNP for the dwf1 phenotype, and the dwf1 gene is a novel allele of D11. We performed mapping of the dwf1 gene with five SNP markers on chromosome 4 with 190 dwf1/Dongjin F₂ plants. The phenotype of F₂ plants was completely co-segregated with genotypes of the J10402 marker, which was developed based on the non-synonymous SNP in the D11 gene. These results will contribute to the study of the molecular biological functions of the D11 gene and BRs.

Perilla is an oilseed crop cultivated in Korea since ancient times. Due to the high α-linolenic acid content in perilla, perilla seed oil can easily become rancid. α-Linolenic acid is synthesized by two enzymes, endoplasmic reticulum-localized Δ15 desaturase (FAD3) and chloroplast-localized Δ15 desaturase (FAD7) in vivo. In order to lower the α-linolenic acid content of the seed oil without disturbing plant growth, we tried to suppress the expression of only the FAD3 gene using RNA interference, whilst maintaining the expression of the FAD7 gene. Seventeen transgenic plants with herbicide (Basta™) resistance were obtained by Agrobacterium-mediated transformation using hypocotyls of perilla plants. The transgenic plants were firstly confirmed by treatment with 0.3% (v/v) Basta™ herbicide, and the expression of FAD3 was measured by Northern blot analysis. The α-linolenic acid content was 10-20%, 30-40%, and 60% in two, seven, and three of the twelve T₁ transgenic perilla plants which had enough seeds to be analyzed for fatty acid composition, respectively. Analysis of the fatty acid composition of T₂ progeny seeds from T₁ plants with the lowest α-linolenic acid content showed that the homozygous lines had 6-10% α-linolenic acid content and the heterozygous lines had 20-26% α-linolenic acid content. It is expected that the reduction in α-linolenic acid content in perilla seed oil will prevent rancidity and can be utilized for the production of high-value functional ingredients such as high γ-linolenic acid.

Gayabyeo, a Tongil-type rice variety, has been known to be resistant to the brown planthopper (BPH) in Korea. For genetic analysis of BPH resistance of Gayabyeo, we developed an F2 and F3 population derived from a cross between Gayabyeo and Taebaegbyeo which is a Tongil-type BPH susceptible rice variety. Based on the previously detected 284,501 putative SNPs between Gayabyeo and Taebaegbyeo, 99 cleaved amplified polymorphic sequences (CAPS) markers were developed, and they have been used for genotyping 180 F2 plants. By comparison of resequencing data of Gayabyeo and the sequences of already reported BPH resistance genes (Bph3, BPH9, Bph14, BPH18, BPH26), it was revealed that Gayabyeo has Bph3 and BPH26 resistance genes. Two InDel markers, Bph3IND and BPH26IND, were developed, which can be used as selection markers in breeding program aiming at introducing BPH resistance genes of Gayabyeo into Korean high quality japonica rice varieties. In addition, BPH bioassay was performed with 180 F3 lines for BPH resistance QTL analysis. Two major QTLs were found on chromosome 4 and 12. The regions of these two QTLs included Bph3 and BPH26, which also supported that Gayabyeo has Bph3 and BPH26 resistance genes. These results would be useful in accelerating development of various BPH-resistant high quality japonica rice varieties in Korea.

As a first step of mapping genes conferring resistance to the brown planthopper, Nilaparvata lugens Stål, in Gayabyeo using a population derived from a cross between Gayabyeo and Taebaegbyeo, we performed the whole genome resequencing of these two Tongil-type rice varieties. The amount of raw sequence data was about 18.5X10⁹ bp and 17.9X10⁹ bp in Gayabyeo and Taebaegbyeo, respectively. After quality trimming and read mapping onto Nipponbare reference genome sequence, 9.3X10⁹ bp was mapped in Gayabyeo with mapping depth of 25.0X, and 9.5X10⁹ bp was mapped in Taebaegbyeo with mapping depth of 25.5X. Between Gayabyeo and Nipponbare, 1,585,880 SNPs were detected, while 1,416,898 SNPs were detected between Taebaegbyeo and Nipponbare. Between Gayabyeo and Taebaegbyeo, 284,501 SNPs were detected. Among the SNPs between Gayabyeo and Taebaegbyeo, 21.2% were in genic region and 78.8% were in intergenic region. In CDS region, 15,924 SNPs were detected, among which synonymous SNPs covered 47.3% and non-synonymous SNPs covered 52.7%. We designed Cleaved Amplified Polymorphic Sequences (CAPS) markers with SNPs in the restriction enzyme recognition sites, and 20 CAPS markers were tested. Of the 20 markers, 19 markers showed polymorphism and one marker showed monomorphism between Gayabyeo and Taebaegbyeo. It is expected that sufficient DNA markers for mapping genes with a population derived from a cross between Gayabyeo and Taebaegbyeo can be developed based on the results of the study.