A total of 857 rice breed lines were used to evaluate rice blast resistance. Frequency of leaf spot index was skewed to the right of the 1-9 scale in bar plot, with a score of 7 showing the highest frequency. The average spot index score of 857 breed lines was 5.33. Associations showing higher than the threshold of ‒log10(P) = 5.17 were detected as significant associations. Significantly associated single nucleotide polymorphism (SNP) markers located within ± 250 kb on the lead SNP position was designated to one QTL locus of lead SNP markers. Five association loci were detected. Two associated QTLs detected on Chr. 4 were designated as qRB4.1 and qRB422, explaining 17.8% and 14.3% of total phenotypic variations, respectively. Associated QTLs detected on Chr. 1, 11, and 12 (one each) designated as qRB1, qRB11 and qRB12 explained 44.6%, 9.09%, and 13.7% of total phenotypic variations, respectively. We compared previously reported QTLs. The location of qRB4.2 was overlapped with the previously reported QTL for blast field resistance. The location of qRB12 was also overlapped with the field resistance leaf blast. The other one, qRB4.1, was overlapped with bacterial blight resistance.

Citations

Citations to this article as recorded by  

• Genome-Wide Association Study of Body Conformation Traits in Tashi Goats (Capra hircus)
  Rong Yang, Di Zhou, Xiaoshan Tan, Zhonghai Zhao, Yanli Lv, Xingzhou Tian, Liqun Ren, Yan Wang, Jun Li, Yongju Zhao, Jipan Zhang
  Animals.2024; 14(8): 1145.     CrossRef
• Genome-Wide Association Study of Submergence Tolerance in Rice (Oryza sativa L.)
  Seong-Gyu Jang, Backki Kim, Yongchul Kim, Soon-Wook Kwon
  Plant Breeding and Biotechnology.2023; 11(1): 25.     CrossRef

Bakanae disease is an important fungal disease caused by Gibberella fujikuroi. The outbreak of rice bakanae disease causes the most important problems for rice producing countries and affects almost all known rice cultivars. Identifying balance disease resistance in Korean Rice Landrace with diverse genetic sources is important for efficient breeding. In this study, we tried to find out useful genetic resources for bakanae resistant cultivar. The result suggested highly strong 3 varieties (‘IT010631’, ‘IT009118’ and ‘IT009221’.) to be used in breeding program. Additionally, we applied reported marker related qFfR1 bakanae disease to accessions which showed strong resistance. It is expected that these resources can be used to develop useful cultivars for each trait. Especially, accessions showed strong resistance in this study have different genotype with reported resistant resources, they would be used to find other genes related to bakanae resistance.

Citations

Citations to this article as recorded by  

• Genome-Wide Association Study to identify Bakanae disease resistance-related QTLs carrying novel candidate genes in rice (Oryza sativa L.)
  Yuting Zeng, Fang-Yuan Cao, Ah-Rim Lee, Dongryung Lee, Backki Kim, Soon-Wook Kwon
  npj Science of Plants.2025;[Epub]     CrossRef
• Current insights on rice (Oryza sativa L.) bakanae disease and exploration of its management strategies
  Chinnannan Karthik, Qingyao Shu
  Journal of Zhejiang University-SCIENCE B.2023; 24(9): 755.     CrossRef
• Evaluation of Major Rice Varieties for Bakanae Disease Resistance in Korea
  Sais-Beul Lee, Ju-Won Kang, Ji-Yoon Lee, Gi-Un Seong, Youngho Kwon, So-Myeong Lee, Nkulu Rolly Kabang, Jun-Hyeon Cho, Seong-Hwan Oh, Dongjin Shin, Jong-Hee Lee, Ki-Won Oh, Dong-Soo Park
  Korean Journal of Breeding Science.2023; 55(2): 103.     CrossRef

Rice is a temperature-sensitive crop, its yield is severely affected by low temperature, especially cold stress at the seedling stage will delay heading. To understand the genetic basis of cold tolerance, we evaluated the cold tolerance at the seedling stage of 136 rice accessions. To evaluate cold tolerance, we treated rice seedlings with cold water irrigation for ten days and scored the cold tolerance on a 1-9 scale, based on their low-temperature response and subsequent recovery. The genome-wide association study for cold tolerance revealed seven QTLs on chromosomes 1, 3, 6, 7, 10, and 12. The genomic region of the qCWS7 on chromosome 7 overlapped with a previously reported QTL associated with cold tolerance in the germinating stage. Similarly, qCWS1-1, qCWS1-2, qCWS3, qCWS6, and qCWS10 overlapped with a previously reported QTL associated with drought-stress tolerance. Subsequent bioinformatic and haplotype analyses suggested that five candidate genes affect cold tolerance: Os01g0228600 encoding a cytosolic hydroxypyruvate reductase, Os03g0115000 encoding a cupredoxin domain containing protein, Os06g0612800 encoding a stress-associated protein (SAP) gene family, Os12g0552500 encoding a universal stress protein (USP), and Os10g0482900 encoding a thioredoxin fold domain containing protein.

Citations

Citations to this article as recorded by  

• Analysis of quantitative trait loci and candidate gene exploration associated with cold tolerance in rice (Oryza sativa L.) during the seedling stage
  Sumin Jo, Seong-Gyu Jang, Sais-Beul Lee, Ji-Yoon Lee, Jun-Hyeon Cho, Ju-Won Kang, Yeongho Kwon, So-Myeong Lee, Dong-Soo Park, Soon-Wook Kwon, Jong-Hee Lee
  Frontiers in Plant Science.2025;[Epub]     CrossRef
• Genome-wide Association Study for Cold Tolerance at Seedling Stage Using a Core Collection of Korean Rice
  Sa-Eun Park, Ngoc Ha Luong, Sang-Nag Ahn, Kyu-Chan Shim
  Journal of Agriculture & Life Science.2025; 59(2): 13.     CrossRef
• Predicting the influence of extreme temperatures on grain production in the Middle-Lower Yangtze Plains using a spatially-aware deep learning model
  Zijun Mu, Junfei Xia
  PeerJ.2024; 12: e18234.     CrossRef

Pre-harvest sprouting (PHS) is one of the important traits that not only cause serious economic issues but also lead to reduction in grain quality and yield in rice (Oryza sativa L.). To analyze the quantitative trait loci (QTLs) for PHS tolerance, we evaluated PHS, seed dormancy (SD), and low-temperature germination (LTG) of 88 F_2:3 populations and their parental lines. Genotypic analysis was performed by using 441 single nucleotide polymorphisms (SNPs) detected from re-sequencing data. Seed dormancy (SD) and low-temperature germination (LTG) were identified to exhibit a positive correlation with PHS. Under the field condition, two major QTLs for PHS, qPHS1-1^FC and qPHS1-2^FC were identified on chromosome 1. Under the growth chamber condition, qPHS1-1^GC and qPHS1-2^GC had the same regions on chromosome 1. QTLs of SD and LTG (qSD1-1, qSD1-2, qLTG1-1, and qLTG1-2) had the same regions; these results suggested that candidate QTLs demonstrate pleiotropy about PHS, SD, and LTG. The major QTLs detected in this study are hypothesized to provide an important resource for molecular breeding and gain a better understanding of the genetics of traits in rice.

Citations

Citations to this article as recorded by  

• Integrated physiological, genetic, and environmental insights into pre-harvest sprouting in cereal for climate-resilient breeding
  Trung Quoc Nguyen, Gioi Huy Dong, Nguyen LV, Thao Duc Le, Nguyen Nguyen Chuong, Weiqiang Li, Ha Duc Chu, Cuong Ngoc Duong, Lam-Son Phan Tran
  Seed Biology.2026;[Epub]     CrossRef
• Mapping QTLs for PHS resistance and development of a deep learning model to measure PHS rate in japonica rice
  Soojin Jun, Mi Hyun Cho, Hyoja Oh, Younguk Kim, Dong Kyung Yoon, Myeongjin Kang, Hwayoung Kim, Seon‐Hwa Bae, Song Lim Kim, Jeongho Baek, HwangWeon Jeong, Jae Il Lyu, Gang‐Seob Lee, Changsoo Kim, Hyeonso Ji
  The Plant Genome.2025;[Epub]     CrossRef
• Whole-genome meta-analysis coupled with haplotype analysis reveal new genes and functional haplotypes conferring pre-harvest sprouting in rice
  Kelvin Dodzi Aloryi, Nnaemeka Emmanuel Okpala, Mawuli Korsi Amenyogbe, Daniel Bimpong, Benjamin Karikari, Hong Guo, Semiu Folaniyi Bello, Selorm Akaba, Akwasi Yeboah, Abdul Razak Ahmed, Patrick Maada Ngegba, Nabieu Kamara, Juliet Nkiruku Anyanwu, Danielle
  BMC Plant Biology.2025;[Epub]     CrossRef
• QTL Analysis for Pre-Harvest Sprouting and Low-Temperature Germinability Using Recombinant Inbred Lines Derived from a Cross between ‘Chamdongjin’ and ‘Younghojinmi’
  Hyun-Su Park, Jeonghwan Seo, Heyonso Ji, Gileung Lee, Chang-Min Lee, Jae-Ryoung Park, Songhee Park, Keon-Mi Lee, Mina Jin, O-Young Jeong
  Korean Journal of Breeding Science.2024; 56(2): 79.     CrossRef
• Discovery of Genomic Regions and Candidate Genes for Awn Length Using QTL-seq in Rice (Oryza sativa L.)
  Dongryung Lee, Hongjia Zhang, Yuting Zeng, Backki Kim, Soon-Wook Kwon
  Plant Breeding and Biotechnology.2023; 11(4): 271.     CrossRef
• Fine-Mapping Analysis of the Genes Associated with Pre-Harvest Sprouting Tolerance in Rice (Oryza sativa L.)
  Seong-Gyu Jang, Backki Kim, Insoo Choi, Joohyun Lee, Tae-Ho Ham, Soon-Wook Kwon
  Agronomy.2023; 13(3): 818.     CrossRef
• QTL mapping and improvement of pre-harvest sprouting resistance using japonica weedy rice
  Chang-Min Lee, Hyun-Su Park, Man-Kee Baek, O-Young Jeong, Jeonghwan Seo, Suk-Man Kim
  Frontiers in Plant Science.2023;[Epub]     CrossRef
• Application of CRISPR/Cas9 Genome Editing System to Reduce the Pre- and Post-Harvest Yield Losses in Cereals
  Thumadath Palayullaparambil Ajeesh Krishna, Theivanayagam Maharajan, Stanislaus Antony Ceasar
  The Open Biotechnology Journal.2022;[Epub]     CrossRef
• Seed Dormancy and Pre-Harvest Sprouting in Rice—An Updated Overview
  Soo-In Sohn, Subramani Pandian, Thamilarasan Senthil Kumar, Yedomon Ange Bovys Zoclanclounon, Pandiyan Muthuramalingam, Jayabalan Shilpha, Lakkakula Satish, Manikandan Ramesh
  International Journal of Molecular Sciences.2021; 22(21): 11804.     CrossRef