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 F_2:3 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.

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• Genetic dissection and transcriptomic analysis of a novel high‐tillering phenotype in rice derived from weedy rice (Hapcheonaengmi3) and Tongil‐type Rice (Milyang23)
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• Identification of a novel mutant allele of the LIKE EARLY STARVATION 1 gene in rice (Oryza sativa L.) using QTL-seq
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• Spontaneous mutation in OsABCI8 caused an albino rice mutant induced by transplanting
  Kyu-Chan Shim, Yun-A Jeon, Hyun-Sook Lee, Sang-Nag Ahn, Inkyu Park
  Scientific Reports.2025;[Epub]     CrossRef
• Genetic analysis and gene mapping of the purple glume tip trait in rice (Oryza sativa)
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• A Frameshift Mutation in the Mg-Chelatase I Subunit Gene OsCHLI Is Associated with a Lethal Chlorophyll-Deficient, Yellow Seedling Phenotype in Rice
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  Plants.2023; 12(15): 2831.     CrossRef
• Identification of QTLs for Cold Tolerance at Seedling Stage Using a Population Derived from an Inter-specific Cross in Rice
  Kyu-Chan Shim, Yeo-Tae Yun, Ju-Won Kang, Sang-Nag Ahn
  Plant Breeding and Biotechnology.2022; 10(4): 282.     CrossRef

Quantitative trait loci (QTLs) for the starch-related traits amylose content (AC) and resistant starch (RS) content have received much attention due to the potential benefits of grains high in these starch levels. In this study, QTLs associated with AC and RS content were identified using 92 recombinant inbred lines (RILs) developed from a cross between two closely related japonica cultivars ‘Dodamssal’ and ‘Hwayeong’. One QTL on chromosome 2 for RS content and 2 QTLs for AC on chromosomes 2 and 6 were detected. The F₂ population derived from a cross between Hwayeong and two selected RILs were used to analyze the interaction between starch branching enzyme 3 (SBE3) and granule-bound starch synthase 1 (GBSS1). The combined effect of SBE3 and GBSS1 in the F₂ population suggested that these two genes behaved in an additive manner in increasing AC. Haplotype analysis based on two SNPs in GBSS1 classified 117 rice accessions into three groups. At the first SNP site, all indica, Korean landrace, and weedy rice accessions had the Wx^a allele at the 5ʹ splice site of intron 1, whereas japonica accessions had the mutated Wx^b allele. This suggests that this splice-donor mutation is prevalent in japonica cultivars, but rare or absent in landrace and weedy rice cultivars. Landrace or weedy rice accessions harboring the Wx^a allele could be employed in breeding programs to manipulate AC in cultivated japonica rice considering the difficulty and time to introduce desirable indica traits into japonica due to reproductive barriers.

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• Quality Characteristics of Rice-Based Ice Creams with Different Amylose Contents
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• Molecular Breeding of Zheyou810, an Indica–Japonica Hybrid Rice Variety with Superior Quality and High Yield
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  Kyu-Chan Shim, Cheryl Adeva, Ju-Won Kang, Ngoc Ha Luong, Hyun-Sook Lee, Jun-Hyeon Cho, HyunJung Kim, Thomas H. Tai, Sang-Nag Ahn
  Frontiers in Plant Science.2022;[Epub]     CrossRef
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  Cheryl Adeva, Yeo-Tae Yun, Kyu-Chan Shim, Ngoc Ha Luong, Hyun-Sook Lee, Ju-Won Kang, Hyun-Jung Kim, Sang-Nag Ahn
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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.

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• Assessment of mutant rice genotypes on growth cycle length and response to reduced water availability
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Low-temperature germinability (LTG) is an important trait for rice direct seeding at temperate and high-altitude region. Previously, five QTLs (quantitative trait loci) for LTG were detected using an interspecific cross population between the Korea japonica cultivar Hwaseong and Oryza rufipogon (IRGSP#105491). O. rufipogon alleles at all loci increased the germination rate at the 13°C condition. In this study, we tried to confirm and fine-map qLTG1 located on the short arm of chromosome 1. To map the qLTG1, two introgression lines, TR5 and TR20 were crossed to Hwaseong to develop F_2:3 populations. QTL analysis confirmed the existence of the qLTG1 and it explained 55.5% and 29.9% of phenotypic variation in two populations, respectively. Substitution mapping using informative recombinant lines indicated that qLTG1 was located in 167-kb region between two SSR markers RM10310 and RM10326. This segment harbored 18 genes with nine of them were annotated with specific gene function. In addition, the O. rufipogon introgression in this region was associated with an increase in spikelets per panicle in the Hwaseong background. The results strongly indicate that the O. rufipogon alleles will be a valuable source of genes in improving japonica rice for low-temperature germinability and yield. To our knowledge, this is the first report to fine-map qLTG1 associated with LTG in rice considering that no QTL for LTG has not been reported near this QTL region from other biparental populations.

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• Genetic dissection and transcriptomic analysis of a novel high‐tillering phenotype in rice derived from weedy rice (Hapcheonaengmi3) and Tongil‐type Rice (Milyang23)
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  Scientific Reports.2025;[Epub]     CrossRef
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• A Frameshift Mutation in the Mg-Chelatase I Subunit Gene OsCHLI Is Associated with a Lethal Chlorophyll-Deficient, Yellow Seedling Phenotype in Rice
  Kyu-Chan Shim, Yuna Kang, Jun-Ho Song, Ye Jin Kim, Jae Kwang Kim, Changsoo Kim, Thomas H. Tai, Inkyu Park, Sang-Nag Ahn
  Plants.2023; 12(15): 2831.     CrossRef
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  PeerJ.2023; 11: e14690.     CrossRef
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  Food and Energy Security.2023;[Epub]     CrossRef
• Interaction of starch branching enzyme 3 and granule-bound starch synthase 1 alleles increases amylose content and alters physico-chemical properties in japonica rice (Oryza sativa L.)
  Kyu-Chan Shim, Cheryl Adeva, Ju-Won Kang, Ngoc Ha Luong, Hyun-Sook Lee, Jun-Hyeon Cho, HyunJung Kim, Thomas H. Tai, Sang-Nag Ahn
  Frontiers in Plant Science.2022;[Epub]     CrossRef
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  Sun Ha Kim, Shi-Dong Ji, Hyun-Sook Lee, Yun-A Jeon, Kyu-Chan Shim, Cheryl Adeva, Ngoc Ha Luong, Pingrong Yuan, Hyun-Jung Kim, Thomas H. Tai, Sang-Nag Ahn
  Frontiers in Plant Science.2022;[Epub]     CrossRef
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  Sun Ha Kim, Kyu-Chan Shim, Hyun-Sook Lee, Yun-A Jeon, Cheryl Adeva, Ngoc Ha Luong, Sang-Nag Ahn
  Frontiers in Plant Science.2022;[Epub]     CrossRef
• Identification of QTLs for Cold Tolerance at Seedling Stage Using a Population Derived from an Inter-specific Cross in Rice
  Kyu-Chan Shim, Yeo-Tae Yun, Ju-Won Kang, Sang-Nag Ahn
  Plant Breeding and Biotechnology.2022; 10(4): 282.     CrossRef
• Mapping QTLs controlling low-temperature germinability in rice by using single segment substitution lines derived from 4 AA-genome species of wild rice
  Ruiqin Pei, Zhengao Zhang, Mingchuan Huang, Guangshan Hou, Jijing Luo, Haitao Zhu, GuiFu Liu, Xuelin Fu, Guiquan Zhang, Shaokui Wang
  Euphytica.2021;[Epub]     CrossRef
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  Yun-A Jeon, Hyun-Sook Lee, Sun-Ha Kim, Kyu-Chan Shim, Ju-Won Kang, Hyun-Jung Kim, Thomas H Tai, Sang-Nag Ahn, Christine Foyer
  Journal of Experimental Botany.2021; 72(12): 4254.     CrossRef
• Deployment of wild relatives for genetic improvement in rice (Oryza sativa)
  Kiran B. Gaikwad, Naveen Singh, Parampreet Kaur, Sushma Rani, Prashanth Babu H, Kuldeep Singh, Sang Nag Ahn
  Plant Breeding.2021; 140(1): 23.     CrossRef
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  Mirjalol Akhtamov, Cheryl Adeva, Kyu-Chan Shim, Hyun-Sook Lee, Sun Ha Kim, Yun-A Jeon, Ngoc Ha Luong, Ju-Won Kang, Ji-Yoon Lee, Sang-Nag Ahn
  Genes.2020; 11(10): 1200.     CrossRef
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  Kyu-Chan Shim, Sun Ha Kim, Hyun-Sook Lee, Cheryl Adeva, Yun-A Jeon, Ngoc Ha Luong, Woo-Jin Kim, Mirjalol Akhtamov, Yong-Jin Park, Sang-Nag Ahn
  Rice.2020;[Epub]     CrossRef
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  Kyu-Chan Shim, Sun Ha Kim, Yun-A Jeon, Hyun-Sook Lee, Cheryl Adeva, Ju-Won Kang, Hyun-Jung Kim, Thomas H Tai, Sang-Nag Ahn
  International Journal of Molecular Sciences.2020; 21(5): 1704.     CrossRef

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.

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• Brassinosteroid biosynthesis gene OsD2 is associated with low-temperature germinability in rice
  Sun Ha Kim, Kyu-Chan Shim, Hyun-Sook Lee, Yun-A Jeon, Cheryl Adeva, Ngoc Ha Luong, Sang-Nag Ahn
  Frontiers in Plant Science.2022;[Epub]     CrossRef
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  Min‐Gyoung Shin, Maizura Ithnin, Wendy T. Vu, Katialisa Kamaruddin, Ting Ngoot Chin, Zulkifli Yaakub, Peter L. Chang, Kandha Sritharan, Sergey Nuzhdin, Rajinder Singh
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Grain size is one of the most important factors determining grain yield in rice breeding. In previous studies, we constructed high-density maps for two quantitative trait loci (QTL) for grain weight, tgw2 and gw9.1, using progeny derived from crosses between the japonica cultivar Hwaseong and Oryza grandiglumis, and Hwaseong and O. rufipogon (IRGC 105491), respectively. The wild alleles contributed an increase in grain weight at these two loci. We developed an F₂ population (146 plants) by crossing two near isogenic lines (NILs) harboring tgw2 and gw9.1 to know how they interact in the near isogenic background. Simple sequence repeat markers tightly linked to two QTL were used to check the genotype of the F₂ population. Based on the genotype at two loci, 146 F₂ plants were classified into 9 groups with a combination of three genotypes at each two loci. Two gene interaction was not significant (P=0.99) in the F₂. Homozygous plants with wild alleles at two loci showed significantly higher 1,000 grain weight than plants with a single QTL in the F₂ and F₃. These results indicate that two QTLs act additively in distinct or complementary pathways in controlling GW. Gene expression analysis was also performed to know the relationship of the gw9.1 QTL with three major grain size genes with Hwaseong and two NILs plants at the transcription level. The results from this study provide insight into grain size regulation in rice and are likely to be useful for marker aided selection for grain size.

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