Amylose content is a key factor affecting the eating and cooking qualities of rice. In our previous study, protein disulfide isomerase like 1-1 (PDIL1-1) on chromosome 11 was a candidate gene for amylose content (AC) trait. Based on whole genome sequencing, polymorphisms were identified between Dodamssal and Hwayeong on PDIL1-1. In this study, the association of PDIL1-1 on AC was characterized. Haplotype analysis of 79 KNU accessions highlighted the presence of allelic patterns identifiable by the sequence variants between Dodamssal and Hwayeong. Identified SNPs and InDel were used to develop gene-based molecular markers for PDIL1-1. The 29 F₂ plants and 160 Korean japonica cultivars were classified into two and three groups, respectively, based on the G/A SNP at position -4973180 and ATTCG/G at position -4974161. Our findings revealed that the G/A SNP at position -4973180 of PDIL1-1 plays a role in regulating the AC in japonica rice. This suggested that PDIL1-1 would be useful for fine-tuning the rice AC. To our knowledge, no studies of the allelic variation of the PDIL1-1 gene regulating AC have been reported worldwide. Furthermore, no research had reported the development of PDIL1-1 gene-based molecular markers.

Cold stress is one of the serious abiotic stresses for stable rice production especially in high-latitude temperate region and high-altitude tropical area. Improving cold tolerance at seedling stage led stable seedling growth with yield stability. In this study, QTLs for cold tolerance at seedling stage were identified using the 96 introgression lines (ILs) derived from an inter-specific cross between Hwaseong (Oryza sativa) and Oryza rufipogon. Three QTLs were detected and the O. rufipogon alleles at two QTL (qCTS1 and qCTS12) improved cold tolerance in the Hwaseong genetic background whereas the O. rufipogon allele at qCTS10 on chromosome 10 decreased cold tolerance. Among these three QTLs, a major QTL qCTS12 explained 27.5% of phenotypic variation. Fine-mapping indicated that qCTS12 was different from those QTL reported in previous studies based on the map location suggesting that qCTS12 might be a new allele and is not associated with deleterious genes such fertility reduction. Among the 96 introgression lines, two lines, CR60 and CR61 were selected based on enhanced cold tolerance at seedling stage. qCTS12, therefore, provides a valuable allele for breeding rice with improved cold tolerance.

Citations

Citations to this article as recorded by  

• Stage-specific screening reveals differential resilience response to cold stress in rice
  Fahamida Akter, Partha S. Biswas, Abul Kalam Mohammad Aminul Islam, Mohammad Sharif Raihan, Md. Mizanur Rahman, Khandakar Md. Iftekharuddaula, Mohammad Rafiqul Islam, John Damien Platten, Md Ashrafuzzaman
  PLOS One.2026; 21(4): e0338290.     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
• Identification of QTLs Related to Plant Growth at Low Temperatures in the Seedling Stage of Tongil Type Rice after Transplanting
  Seong-Gyu Jang, Ji-Yoon Lee, Ju-Won Kang, Youngho Kwon, So-Myeong Lee, Sais-Beul Lee, Jun-Hyeon Cho, Dong-Soo Park, Jong-Hee Lee, Soon-Wook Kwon, Sumin Jo
  Korean Journal of Breeding Science.2024; 56(3): 225.     CrossRef

We conducted transcriptome profiling analysis of O. glaberrima root using RNA-Seq at the control (OCR) and 100 mM NaCl treatment (OTR) at two time points (6 and 24 hours after treatment) to detect genes induced by salt stress. RNA-Seq analysis generated 102,690,698 sequence reads representing 30,388 predicted transcripts including 6,189 unannotated in Rice Annotation Project database. A total of 539 and 424 of differentially expressed genes (DEGs) were detected between OCR_6hours vs OTR_6hours and between OCR_24hours vs OTR_24hours, respectively (P < 0.001, q < 0.05). Among these DEGs, 262 genes showed constant differential expression at both 6 hours and 24 hours, and these included a bHLH containing protein, WRKY transcription factor, serine/threonine kinase, R2R3 MYB protein, and amino acid transporters. Interestingly, an enhanced seedling salt tolerant introgression line IL55 from a cross between a salt sensitive indica cultivar “Milyang23” and O. glaberrima harbors one DEG, Os02g0787300 encoding a mitogen activated protein kinase kinase (MAPKK) on chromosome 2. Analysis of the salt tolerance of the F_2:3 lines from a cross between IL55 and Milyang23 indicated that the O. glaberrima segment on chromosome 2 containing the MAPKK gene was responsible for better shoot growth under salt stress at the seedling stage. The salt inducible genes will be evaluated in introgression lines (ILs) to understand whether the expression of these genes is associated with salt tolerance in ILs having the Milyang23 genetic background. Transcriptome sequence information in this study may be useful for developing DNA markers linked to salinity tolerance for MAS breeding.

Citations

Citations to this article as recorded by  

• Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages
  Taikui Zhang, Weichen Huang, Lin Zhang, De-Zhu Li, Ji Qi, Hong Ma
  Nature Communications.2024;[Epub]     CrossRef
• Grain protein function prediction based on self-attention mechanism and bidirectional LSTM
  Jing Liu, Xinghua Tang, Xiao Guan
  Briefings in Bioinformatics.2023;[Epub]     CrossRef

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.

Citations

Citations to this article as recorded by  

• Genetic dissection and transcriptomic analysis of a novel high‐tillering phenotype in rice derived from weedy rice (Hapcheonaengmi3) and Tongil‐type Rice (Milyang23)
  Kyu‐Chan Shim, Donghyun Jeon, Yun‐A Jeon, Cheryl Adeva, Hyun‐Sook Lee, Ju‐Won Kang, Sa‐Eun Park, Sang‐Nag Ahn, Inkyu Park
  The Plant Genome.2026;[Epub]     CrossRef
• Identification of a novel mutant allele of the LIKE EARLY STARVATION 1 gene in rice (Oryza sativa L.) using QTL-seq
  Kyu-Chan Shim, HyunJung Kim, Mi-Ra Yoon, Sung-Ho Na, Sa-Eun Park, Sang-Nag Ahn, Thomas H Tai, J Holland
  G3: Genes, Genomes, Genetics.2026;[Epub]     CrossRef
• 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)
  Gang Jin, Zhongquan Cai, Yanxi Chen, Ying Ling, Liping Wang, Deyuan Mo
  Crop Breeding and Applied Biotechnology.2024;[Epub]     CrossRef
• T-DNA insertion mutants of Arabidopsis DA1 orthologous genes displayed altered plant height and yield-related traits in rice (O. sativa L.)
  Kyu-Chan Shim, Ngoc Ha Luong, Thomas H. Tai, Gyu-Ri Lee, Sang-Nag Ahn, Inkyu Park
  Genes & Genomics.2024; 46(4): 451.     CrossRef
• 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
• 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.

Citations

Citations to this article as recorded by  

• Improved Processing Quality in a tongil-type Waxy Rice Cultivar Associated with a Rare granule-bound starch synthase I Allele
  Seong-Gyu Jang, Ji-Min Kim, Ji-Yoon Lee, Jun-Hyeon Cho, Youngho Kwon, So-Myeong Lee, Jisu Choi, Ju-Won Kang, Jong-Min Jeong, Jong-Hee Lee, Dong-Soo Park, Soon-Wook Kwon, Sumin Jo
  Korean Journal of Breeding Science.2026; 58(2): 123.     CrossRef
• Evaluation of glycemic response and starch digestibility in Korean rice toward the development of low GI rice
  Chang-Min Lee, O-Young Jeong, Hyun-Su Park, Jeonghwan Seo, Songhee Park, Keon-Mi Lee, Mina Jin, Il-Ryong Choi, Jae-Hyuk Han
  Frontiers in Plant Science.2025;[Epub]     CrossRef
• Evolution and association analysis of SSIIIa in rice landraces of Yunnan Province
  Xia Li, Xiaomeng Yang, Li’e Yang, Hafiz Ghulam Muhu-Din Ahmed, Chunlian Yao, Jiazhen Yang, Luxiang Wang, Tao Yang, Xiaoying Pu, Yawen Zeng
  Biologia.2024; 79(7): 2203.     CrossRef
• Allelic Diversity at Protein Disulfide Isomerase Like 1-1 (PDIL1-1) Gene is Associated with Amylose Content in Japonica Rice
  Cheryl Adeva, Ju-Won Kang, Kyu-Chan Shim, Ngoc Ha Luong, Hyun-Sook Lee, Jong-Hee Lee, Sang-Nag Ahn
  Plant Breeding and Biotechnology.2023; 11(1): 56.     CrossRef
• Quality Characteristics of Rice-Based Ice Creams with Different Amylose Contents
  Gi-Un Seong, Ji-Yoon Kim, Jung-Soo Kim, Sae-Ul Jeong, Jun-Hyeon Cho, Ji-Yoon Lee, Sais-Beul Lee, Nkulu-Rolly Kabange, Dong-Soo Park, Kwang-Deog Moon, Ju-Won Kang
  Foods.2023; 12(7): 1518.     CrossRef
• Molecular Breeding of Zheyou810, an Indica–Japonica Hybrid Rice Variety with Superior Quality and High Yield
  Jian Song, Yongtao Cui, Honghuan Fan, Liqun Tang, Jianjun Wang
  Agriculture.2023; 13(9): 1807.     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
• QTL Mapping of Mineral Element Contents in Rice Using Introgression Lines Derived from an Interspecific Cross
  Cheryl Adeva, Yeo-Tae Yun, Kyu-Chan Shim, Ngoc Ha Luong, Hyun-Sook Lee, Ju-Won Kang, Hyun-Jung Kim, Sang-Nag Ahn
  Agronomy.2022; 13(1): 76.     CrossRef
• Evaluation of Hardness and Retrogradation of Cooked Rice Based on Its Pasting Properties Using a Novel RVA Testing
  Sumiko Nakamura, Junji Katsura, Yasuhiro Maruyama, Ken’ichi Ohtsubo
  Foods.2021; 10(5): 987.     CrossRef

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.

Citations

Citations to this article as recorded by  

• Assessment of mutant rice genotypes on growth cycle length and response to reduced water availability
  Luis Herminio Chairez Tejeda, Raymond Joseph, Eduardo Venske, Viviane Kopp da Luz, Andrés Eloy Chacón-Ortiz, Ariano Martins de Magalhães Júnior, Luciano Carlos da Maia, Antonio Costa de Oliveira, Camila Pegoraro
  Scientia Agricola.2024;[Epub]     CrossRef
• Molecular Breeding of Zheyou810, an Indica–Japonica Hybrid Rice Variety with Superior Quality and High Yield
  Jian Song, Yongtao Cui, Honghuan Fan, Liqun Tang, Jianjun Wang
  Agriculture.2023; 13(9): 1807.     CrossRef
• Genetic Structure and Geographical Differentiation of Traditional Rice (Oryza sativa L.) from Northern Vietnam
  Ngoc Ha Luong, Le-Hung Linh, Kyu-Chan Shim, Cheryl Adeva, Hyun-Sook Lee, Sang-Nag Ahn
  Plants.2021; 10(10): 2094.     CrossRef

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.

Citations

Citations to this article as recorded by  

• Genetic dissection and transcriptomic analysis of a novel high‐tillering phenotype in rice derived from weedy rice (Hapcheonaengmi3) and Tongil‐type Rice (Milyang23)
  Kyu‐Chan Shim, Donghyun Jeon, Yun‐A Jeon, Cheryl Adeva, Hyun‐Sook Lee, Ju‐Won Kang, Sa‐Eun Park, Sang‐Nag Ahn, Inkyu Park
  The Plant Genome.2026;[Epub]     CrossRef
• Prebreeding using untapped rice genetic resources: linking the gap between biodiversity and crop improvement
  Santhosh Venna, Divya Balakrishnan, P. K. Singh, B. Arun, Suneetha Kota, S. Amurutha Rao, Naresh Kumar Sahu, S.V. SaiPrasad, R. M. Sundaram
  Journal of Crop Science and Biotechnology.2026; 29(3): 371.     CrossRef
• 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
• Cold-Tolerance Candidate Gene Identification in Maize Germination Using BSA, Transcriptome and Metabolome Profiling
  Cheng Wang, Nan Hao, Yueming Li, Nan Sun, Liwei Wang, Yusheng Ye
  Agronomy.2025; 15(5): 1067.     CrossRef
• Genome-Wide Identification and Expression Analysis Unveil the Involvement of the Cold Shock Protein (CSP) Gene Family in Cotton Hypothermia Stress
  Yejun Yang, Ting Zhou, Jianglin Xu, Yongqiang Wang, Yuanchun Pu, Yunfang Qu, Guoqing Sun
  Plants.2024; 13(5): 643.     CrossRef
• 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
• Genome-wide identification and expression reveal the involvement of the FCS-like zinc finger (FLZ) gene family in Gossypium hirsutum at low temperature
  JunDuo Wang, Zhiqiang Li, Yajun Liang, Juyun Zheng, Zhaolong Gong, Guohui Zhou, Yuhui Xu, Xueyuan Li
  PeerJ.2023; 11: e14690.     CrossRef
• Identification of QTLs and candidate genes for rice seed germinability under low temperature using high‐density genetic mapping and RNA‐seq
  Jing Yang, Aie Chen, Ji Wei, Jifen Xu, Shengnan Chen, Wei Tang, Jing Liu, Hongyang Wang
  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
• A Novel Embryo Phenotype Associated With Interspecific Hybrid Weakness in Rice Is Controlled by the MADS-Domain Transcription Factor OsMADS8
  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
• 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
• 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
• Natural variation in rice ascorbate peroxidase gene APX9 is associated with a yield-enhancing QTL cluster
  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
• Characterization of Quantitative Trait Loci for Germination and Coleoptile Length under Low-Temperature Condition Using Introgression Lines Derived from an Interspecific Cross in Rice
  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
• Characterization of a New qLTG3–1 Allele for Low-temperature Germinability in Rice from the Wild Species Oryza rufipogon
  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
• A RING-Type E3 Ubiquitin Ligase, OsGW2, Controls Chlorophyll Content and Dark-Induced Senescence in Rice
  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.

Citations

Citations to this article as recorded by  

• Identification of QTLs for internode length and diameter associated with lodging resistance in rice
  Qiuyun Lin, Ping Gan, Yujie Zhou, Yuehui Lin, Zhenyu Xie, Wei Hu
  Frontiers in Plant Science.2025;[Epub]     CrossRef
• Characterization of QTLs for diameter in panicle neck and substitution mapping of qDPN5/qVBN5.2 and qVBN6 in rice (Oryza sativa L.)
  Ha Thi Le Nguyen, Ami Yoshiura, Shao-Hui Zheng, Daisuke Fujita
  Breeding Science.2024; 74(4): 337.     CrossRef
• Strong culm: a crucial trait for developing next-generation climate-resilient rice lines
  Pritam Kanti Guha, Nakul D. Magar, Madhavilatha Kommana, Kalyani M. Barbadikar, B. Suneel, C. Gokulan, D. Vijay Lakshmi, Hitendra Kumar Patel, Ramesh V. Sonti, R. M. Sundaram, Maganti Sheshu Madhav
  Physiology and Molecular Biology of Plants.2024; 30(4): 665.     CrossRef
• Mapping of QTLs for Yield Traits Using F2:3:4 Populations Derived From Two Alien Introgression Lines Reveals qTGW8.1 as a Consistent QTL for Grain Weight From Oryza nivara
  Kavitha Beerelli, Divya Balakrishnan, Krishnam Raju Addanki, Malathi Surapaneni, Venkateswara Rao Yadavalli, Sarla Neelamraju
  Frontiers in Plant Science.2022;[Epub]     CrossRef
• 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
• Fine-Mapping of a Major Quantitative Trait Locusq2ID1for Rice Stem Diameter
  Ye-Ji Lee, Yeisoo Yu, Hyeonso Ji, Gang-Sub Lee, Nam-In Hyung, Keunpyo Lee, Tae-Ho Kim
  Plant Breeding and Biotechnology.2021; 9(4): 298.     CrossRef
• Association mapping analysis of oil palm interspecific hybrid populations and predicting phenotypic values via machine learning algorithms
  Min‐Gyoung Shin, Maizura Ithnin, Wendy T. Vu, Katialisa Kamaruddin, Ting Ngoot Chin, Zulkifli Yaakub, Peter L. Chang, Kandha Sritharan, Sergey Nuzhdin, Rajinder Singh
  Plant Breeding.2021; 140(6): 1150.     CrossRef

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.

Citations

Citations to this article as recorded by  

• Analysis of Yield- and Quality-Related Traits of Risotto Rice Varieties in a Korean Environment
  Songhee Park, Jeonghwan Seo, Chang-Min Lee, Jae-Ryoung Park, Keonmi Lee, O-Young Jeong, Youngjun Mo, Hyun-Su Park
  Korean Journal of Breeding Science.2025; 57(1): 13.     CrossRef
• QTL Analysis Related to Grain Size Using the Population Derived from a Cross Between Hopum and Basmati 370
  Da-Eun Im, Seong-Gyu Jang, Backki Kim, Jeonghwan Seo, D. S. Kishor, Hee-Jong Koh, Soon-Wook Kwon
  Korean Journal of Breeding Science.2023; 55(2): 118.     CrossRef
• QTL-by-QTL, QTL-by-environment, and QTL-by-QTL-by-environment interactions of loci controlling grain length in rice
  Tsuneo Kato, Akira Horibata
  Euphytica.2022;[Epub]     CrossRef

This study was initiated to identify quantitative trait loci (QTL) involved in root system development by measuring root length and weight of rice seedlings grown in hydroponic culture condition. Growth conditions for estimating the root elongation were set up to supply NH₄⁺ as a single nitrogen source. Four rice accessions and 40 introgression lines (ILs) derived from a cross between ‘Ilpumbyeo’, a temperate japonica variety, and ‘Moroberekan’, a tropical japonica accession, were used to detect QTL for two root traits of seedlings grown in 0, 250 and 500 μM NH₄⁺. Seven chromosomal regions were found to be involved in root elongation. The qRW6 QTL detected on the long-arm of chromosome 6 promoted root weight and the ‘Moroberekan’ allele at this QTL was associated with enhanced root weight at 250 μM NH₄⁺ concentration. The Moroberekan alleles were beneficial at all loci except for qRW4 at which the Ilpumbyeo allele increased root weight under 0, 250 and 500 μM NH₄⁺. A field trial was conducted for selected four ILs to know whether the introgressed Moroberekan segments harboring the beneficial QTL were associated with effects on other agronomic traits. No significant difference was detected between four ILs and Ilpumbyeo for days to heading and culm length. Two lines showed significant difference from Ilpumbyeo in spikelets per panicle and 1,000 grain weight, and the difference might be attributed to the Moroberekan segment on chromosome 6. Our QTL results indicate that the Moroberekan introgression on chromosome 6 flanked by RM162-RM3430 has the potential to enhance root traits and yield potential in the temperate japonica background.

Citations

Citations to this article as recorded by  

• Identification of shoot and root genomic regions in response to nitrogen deficiency tolerance in rice through the use of rice back cross recombinant inbred lines (BRILs)
  Abdul Malik Solangi, Hira Khanzada, Ghulam Mustafa Wassan, Adnan Rasheed, Ayaz Ali Keerio, Huijie Li, Saba Khanzada, Muhammad Faheem, Mashooq Ali Laghari, Jianmin Bian, Xiaohua Pan, Ziming Wu
  Journal of Plant Biochemistry and Biotechnology.2023; 32(1): 40.     CrossRef
• Genome-wide association study and transcriptome analysis reveal new QTL and candidate genes for nitrogen‐deficiency tolerance in rice
  Qing Li, Xueli Lu, Changjian Wang, Lan Shen, Liping Dai, Jinli He, Long Yang, Peiyuan Li, Yifeng Hong, Qiang Zhang, Guojun Dong, Jiang Hu, Guangheng Zhang, Deyong Ren, Zhenyu Gao, Longbiao Guo, Qian Qian, Li Zhu, Dali Zeng
  The Crop Journal.2022; 10(4): 942.     CrossRef
• Pinpointing genomic regions associated with root system architecture in rice through an integrative meta-analysis approach
  Parisa Daryani, Hadi Darzi Ramandi, Sara Dezhsetan, Raheleh Mirdar Mansuri, Ghasem Hosseini Salekdeh, Zahra-Sadat Shobbar
  Theoretical and Applied Genetics.2022; 135(1): 81.     CrossRef
• Mapping of quantitative trait loci for root elongation in rice ( Oryza sativa L.) treated with various nitrogen sources and concentrations
  Kazuhiro Sasaki, Mitsuhiro Obara
  Soil Science and Plant Nutrition.2022; 68(4): 454.     CrossRef
• Root Branching and Nutrient Efficiency: Status and Way Forward in Root and Tuber Crops
  Luis O. Duque, Arthur Villordon
  Frontiers in Plant Science.2019;[Epub]     CrossRef
• RDWN6XB, a major quantitative trait locus positively enhances root system architecture under nitrogen deficiency in rice
  Galal Bakr Anis, Yingxin Zhang, Anowerul Islam, Yue Zhang, Yongrun Cao, Weixun Wu, Liyong Cao, Shihua Cheng
  BMC Plant Biology.2019;[Epub]     CrossRef

Studies were initiated for two consecutive years to examine the effects of transplanting date on the yield and quality of early maturing rice cultivars and to select rice cultivars capable of adapting to early transplanting in the middle plain area. The experiment was laid out in a split-plot design with 3 replications. The main plots consisted of two transplanting dates viz. early (25th of April) and ordinary (25th of May), with sub-plots containing eight cultivars. For early transplanting the mean temperature at the grain filling stage was lower than for ordinary transplanting, while the rice grain quality traits and palatability values were improved. Early transplanting results in 11 days earlier heading, higher head rice yield and lower milled rice yield than ordinary transplanting. Significant differences among the eight cultivars tested in this study were observed for most traits. Among cultivars, ‘Joami’ demonstrated the highest palatability. ‘Joami’ also performed better in head rice ratio and head rice yield than ‘Unkwang’, which is widely cultivated in the middle plain area. Palatability value (PV) showed significant positive correlations with head rice ratio (HR) and amylose content (AC), and negative correlations with chalky rice ratio (CR) and protein content (PC). Mean temperature (MT) was positively correlated with CR and PC, and negatively correlated with HR and AC. The highest positive and negative correlations among the rice quality traits were observed between HR and AC (r = 0.734), and HR and CR (r = −0.944), respectively. Based on the research findings, ‘Joami’ is suitable for early transplanting for cultivation in the Chungnam plain area.

Citations

Citations to this article as recorded by  

• Effect of Nitrogen Application Methods on Yield and Grain Quality of an Extremely Early Maturing Rice Variety
  Yeotae Yun, Gyucheol Kim, Giwon Cho, Youngju Lee, Tugsang Yun, Hakhun Kim
  Agriculture.2023; 13(4): 832.     CrossRef
• Effect of Transplanting Date on Agronomic and Grain Quality Traits Using Early-Maturing Rice Varieties
  Yeotae Yun, Gyucheol Kim, Giwon Cho, Tugsang Yun
  Agronomy.2023; 13(5): 1195.     CrossRef
• “Yeoreumi,” an Early Maturing Rice Cultivar Adaptable for Early-Transplanting Cultivation in the Chungnam Plain Area
  Yeotae Yun, Gyucheol Kim, Giwon Cho, Chongtae Chung, Tugsang Yun
  Korean Journal of Breeding Science.2022; 54(4): 405.     CrossRef
• ‘Bbareumi’, an Extremely Early-Maturing Rice Cultivar Adaptable for Early Transplanting, in the Chungnam Plain Area
  Yeotae Yun, Chongtae Chung, Gyucheol Kim, Tugsang Yun
  Korean Journal of Breeding Science.2022; 54(3): 238.     CrossRef
• Changes in Growth and Quality Traits According to Transplanting Dates using ‘Bbareumi’, an Extremely Early Maturing Rice Cultivar, in the Chungnam Plain Area
  Yeotae Yun, Gyucheol Kim, Giwon Cho, Tugsang Yun
  Korean Journal of Breeding Science.2022; 54(4): 305.     CrossRef
• Development of an expert vision-based system for inspecting rice quality indices
  S.H. Payman, A. Bakhshipour, H. Zareiforoush
  Quality Assurance and Safety of Crops & Foods.2018; 10(1): 103.     CrossRef

Grain weight (GW) is one of the most important targets for grain yield in rice breeding. In previous studies, two quantitative trait loci (QTLs) for grain weight, tgw2 and gw8.1, were identified using progeny derived from crosses between the japonica cultivar Hwaseong and Oryza grandiglumis, and between Hwaseong and O. rufipogon (IRGC 105491), respectively. The wild alleles increased GW at two loci. An F₂ population (186 plants) was developed by crossing two near isogenic lines (NILs) harboring tgw2 and gw8.1 to test their interaction. Simple sequence repeat (SSR) markers tightly linked to the two QTLs were used to check the genotype of the F₂ population. Based on the genotype at the two loci, tgw2 and gw8.1, the F₂ plants were classified into 9 groups with a combination of three genotypes at each of the two loci. Two-way ANOVA revealed no interaction between the 2 QTLs in the F₂ population. The 1,000 grain weight (TGW) of homozygous plants with wild alleles at the two loci was significantly higher than that of plants with a single QTL in the F₂ and F₃ lines. These results indicate that two QTLs act additively, in distinct or complementary pathways, to control grain weight. Based on these results, it is desirable to pyramid the two QTLs into a single line, since the double-QTL line displayed further increase of TGW in the Hwaseong background.

Citations

Citations to this article as recorded by  

• QTL Analysis Related to Grain Size Using the Population Derived from a Cross Between Hopum and Basmati 370
  Da-Eun Im, Seong-Gyu Jang, Backki Kim, Jeonghwan Seo, D. S. Kishor, Hee-Jong Koh, Soon-Wook Kwon
  Korean Journal of Breeding Science.2023; 55(2): 118.     CrossRef
• QTL-by-QTL, QTL-by-environment, and QTL-by-QTL-by-environment interactions of loci controlling grain length in rice
  Tsuneo Kato, Akira Horibata
  Euphytica.2022;[Epub]     CrossRef
• Fine mapping and candidate gene analysis of the quantitative trait locus gw8.1 associated with grain length in rice
  Yun-Joo Kang, Kyu-Chan Shim, Hyun-Sook Lee, Yun-A Jeon, Sun-Ha Kim, Ju-Won Kang, Yeo-Tae Yun, In-Kyu Park, Sang-Nag Ahn
  Genes & Genomics.2018; 40(4): 389.     CrossRef
• Estimation of additive and epistatic gene effects of doubled haploid lines of winter oilseed rape (Brassica napus L.)
  Jan Bocianowski, Kamila Nowosad, Agnieszka Dobrzycka, Joanna Wolko
  Euphytica.2017;[Epub]     CrossRef
• Path analysis and estimation of additive and epistatic gene effects of barley SSD lines
  Jan Bocianowski, Katarzyna Górczak, Kamila Nowosad, Wojciech Rybiński, Dariusz Piesik
  Journal of Integrative Agriculture.2016; 15(9): 1983.     CrossRef

Although traditional rice varieties and wild rice species exhibit vast genetic diversity, the transfer of useful genes to modern varieties is often hampered by linkage drag. In this study, the previously identified blast resistance locus Pi45(t) from a cross between ‘Ilpumbyeo’ and ‘Moroberekan’ was linked to the spreading-type panicle caused by the SPR3 locus. Using InDel4 and RM17579 linked to the Pi45(t) and the SPR3, respectively, the distance between the two loci was estimated to be 6.9cM. This suggests a tight, yet incomplete linkage and provides the opportunity to utilize Pi45(t) in breeding programs without including SPR3. Two groups based on the genotype at the SPR3 locus were assembled; the CLosed Panicle (CLP) and SPReading panicle (SPR) groups, with lines which were homozygous for the Ilpumbyeo and Moroberekan alleles, respectively. A comparison between the traits of CLP and SPR groups revealed a decrease in 1000-grain weight and length and an increase in spikelets per panicle and secondary branches in the SPR group. This complicates selection against SPR3 as it is not clear whether these quantitative trait loci are linked to either SPR3 or Pi45(t). Re-evaluation of these traits using lines recombinant at the two loci would be necessary to clarify this issue.

Citations

Citations to this article as recorded by  

• Directional upgrading of brown planthopper resistance in an elite rice cultivar by precise introgression of two resistance genes using genomics-based breeding
  Hongbo Wang, Yi Gao, Fangming Mao, Lizhong Xiong, Tongmin Mou
  Plant Science.2019; 288: 110211.     CrossRef

Low-temperature stress is an important factor controlling the growth and development of rice (Oryza sativa L.) in temperate region. In this study, a molecular linkage map consisting of 136 SSR markers was employed to identify QTL associated with cold tolerance at the seedling stage. 80 recombinant inbred lines (RILs) from an intersubspecific cross between Milyang23 (O. sativa ssp. Indica) and Hapcheonaengmi3, a japonica weedy rice and the parents were evaluated for leaf discoloration and SAPD value of seedlings. Rice plants were grown for 15 days in the low-temperature condition (13/20°C day/night) and the control condition (25/20°C day/night) in the growth chamber. The degree of leaf discoloration showed a highly significant correlation with the SPAD value in the low-temperature plot (r = −0.708, P < 0.0001). A total of four QTLs for SPAD were identified and the phenotypic variance explained by each QTL ranged from 5.4 to 16.0%. Two QTLs detected in the control condition were located on chromosomes 2 and 5, respectively. Two QTL on chromosomes 1 and 4 were detected at the low-temperature condition and Hapcheonaengmi3 alleles increased the SPAD values at these loci. Substitution mapping was conducted to delimit the position of qSPA-4 using introgression lines derived from the same cross. Results indicated that qSPA-4 was located in a 810-Kb region flanked by RM16333 and RM16368. The results indicated that Hapcheonaengmi3 contains QTL alleles that are likely to improve cold tolerance of Indica rice.

Citations

Citations to this article as recorded by  

• Integrating RNA-Seq and linkage mapping to identify and characterize qESCT2, a cold tolerance QTL at the early seedling stage in rice
  Wenqiang Liu, Zuwu Chen, Liang Guo, Zheng Dong, Biaoren Yang, Licheng Liu, Sanxiong Liu, Xiaowu Pan
  Frontiers in Plant Science.2025;[Epub]     CrossRef
• Genome‐wide association study for traits related to cold tolerance and recovery during seedling stage in rice
  Khushboo Rastogi, Sumeet P. Mankar, Endang M. Septiningsih
  Crop Science.2025;[Epub]     CrossRef
• Genetic Foundation of Leaf Senescence: Insights from Natural and Cultivated Plant Diversity
  Phan Phuong Thao Doan, Hue Huong Vuong, Jeongsik Kim
  Plants.2024; 13(23): 3405.     CrossRef
• Advances and opportunities in unraveling cold‐tolerance mechanisms in the world's primary staple food crops
  Sofora Jan, Sachin Rustgi, Rutwik Barmukh, Asif B. Shikari, Brenton Leske, Amanuel Bekuma, Darshan Sharma, Wujun Ma, Upendra Kumar, Uttam Kumar, Abhishek Bohra, Rajeev K. Varshney, Reyazul Rouf Mir
  The Plant Genome.2024;[Epub]     CrossRef
• Effects of Cold Temperature and Acclimation on Cold Tolerance and Cannabinoid Profiles of Cannabis sativa L. (Hemp)
  Andrei Galic, Heather Grab, Nicholas Kaczmar, Kady Maser, William B. Miller, Lawrence B. Smart
  Horticulturae.2022; 8(6): 531.     CrossRef
• Phenotypic and Molecular Characterization of Rice Genotypes’ Tolerance to Cold Stress at the Seedling Stage
  Nasira Akter, Partha Sarathi Biswas, Md. Abu Syed, Nasrin Akter Ivy, Amnah Mohammed Alsuhaibani, Ahmed Gaber, Akbar Hossain
  Sustainability.2022; 14(9): 4871.     CrossRef
• Screening of rice germplasms (Oryza sativa L.) for seedling stage cold tolerance utilizing morphological and molecular markers
  Brijesh Kumar Singh, Monoj Sutradhar, Chayanika Lahkar, Amit Kumar Singh, N.G. Tombisana Meetei, Nirmal Mandal
  Ecological Genetics and Genomics.2022; 24: 100128.     CrossRef
• QTL mapping and validation of a segment responsible for early-seedling cold tolerance in rice
  Wenqiang Liu, Xiaowu Pan, Haibo Xiong, Fenglin Huang, Yonghong Duan, Yongchao Li, Jun Min, Sanxiong Liu, Licheng Liu, Xiucai Wei, Wenjin Zhao, Xiaoxiang Li
  Euphytica.2020;[Epub]     CrossRef
• Identification of main-effect quantitative trait loci (QTLs) for low-temperature stress tolerance germination- and early seedling vigor-related traits in rice (Oryza sativa L.)
  S. Najeeb, J. Ali, A. Mahender, Y.L. Pang, J. Zilhas, V. Murugaiyan, Lakshminarayana R. Vemireddy, Z. Li
  Molecular Breeding.2020;[Epub]     CrossRef
• Amelioration of cold-induced oxidative stress by exogenous 24-epibrassinolide treatment in grapevine seedlings: Toward regulating the ascorbate–glutathione cycle
  Ze-Ya Chen, Yu-Ting Wang, Xing-Bo Pan, Zhu-Mei Xi
  Scientia Horticulturae.2019; 244: 379.     CrossRef
• Mapping and validation of QTLs for cold tolerance at seedling stage in rice from an indica cultivar Habiganj Boro VI (Hbj.BVI)
  Partha S. Biswas, Hasina Khatun, Nomita Das, Md. Mahathir Sarker, M. Anisuzzaman
  3 Biotech.2017;[Epub]     CrossRef
• Overexpression of BrCIPK1 Gene Enhances Abiotic Stress Tolerance by Increasing Proline Biosynthesis in Rice
  Sailila E. Abdula, Hye-Jung Lee, Hojin Ryu, Kwon Kyoo Kang, Illsup Nou, Mark E. Sorrells, Yong-Gu Cho
  Plant Molecular Biology Reporter.2016; 34(2): 501.     CrossRef
• Mapping of quantitative trait loci for cold tolerance at the early seedling stage in landrace rice Xiang 743
  Wenqiang Liu, Tingting Lu, Yongchao Li, Xiaowu Pan, Yonghong Duan, Jun Min, Xiqin Fu, Xinnian Sheng, Junzhi Xiao, Sanxiong Liu, Jiang Tan, Yi Yao, Xiaoxiang Li
  Euphytica.2015; 201(3): 401.     CrossRef
• Development of low-temperature germinability markers for evaluation of rice (Oryza sativa L.) germplasm
  Do Yoon Hyun, Gi An Lee, Man Jung Kang, Diana Burkart-Waco, Sang Ic Kim, Jae Yoon Kim, Myung Chul Lee, Jae Gyun Gwag, Yeon Gyu Kim, Thomas H. Tai
  Molecular Breeding.2015;[Epub]     CrossRef