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Yoon DK, Choi I, Won YJ, Shin Y, Cheon KS, Oh H, Lee C, Lee S, Cho MH, Jun S, Kim Y, Kim SL, Baek J, Jeong H, Lyu JI, Lee GS, Kim KH, Ji H. QTL Mapping of Tiller Number in Korean Japonica Rice Varieties. Genes (Basel) 2023; 14:1593. [PMID: 37628644 PMCID: PMC10454613 DOI: 10.3390/genes14081593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/25/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Tiller number is an important trait associated with yield in rice. Tiller number in Korean japonica rice was analyzed under greenhouse conditions in 160 recombinant inbred lines (RILs) derived from a cross between the temperate japonica varieties Odae and Unbong40 to identify quantitative trait loci (QTLs). A genetic map comprising 239 kompetitive allele-specific PCR (KASP) and 57 cleaved amplified polymorphic sequence markers was constructed. qTN3, a major QTL for tiller number, was identified at 132.4 cm on chromosome 3. This QTL was also detected under field conditions in a backcross population; thus, qTN3 was stable across generations and environments. qTN3 co-located with QTLs associated with panicle number per plant and culm diameter, indicating it had pleiotropic effects. The qTN3 regions of Odae and Unbong40 differed in a known functional variant (4 bp TGTG insertion/deletion) in the 5' UTR of OsTB1, a gene underlying variation in tiller number and culm strength. Investigation of variation in genotype and tiller number revealed that varieties with the insertion genotype had lower tiller numbers than those with the reference genotype. A high-resolution melting marker was developed to enable efficient marker-assisted selection. The QTL qTN3 will therefore be useful in breeding programs developing japonica varieties with optimal tiller numbers for increased yield.
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Affiliation(s)
- Dong-Kyung Yoon
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Inchan Choi
- Department of Agricultural Engineering, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54875, Republic of Korea;
| | - Yong Jae Won
- Cheorwon Branch, National Institute of Crop Science, Rural Development Administration (RDA), Cheorwon 24010, Republic of Korea;
| | - Yunji Shin
- Genecell Biotech Inc., Wanju 55322, Republic of Korea;
| | - Kyeong-Seong Cheon
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Republic of Korea;
| | - Hyoja Oh
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Chaewon Lee
- Department of Central Area Crop Science, National Institute of Crop Science, Rural Development Administration (RDA), Suwon 16429, Republic of Korea;
| | - Seoyeon Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Mi Hyun Cho
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Soojin Jun
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Yeongtae Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Song Lim Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Jeongho Baek
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - HwangWeon Jeong
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Jae Il Lyu
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Gang-Seob Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Kyung-Hwan Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
| | - Hyeonso Ji
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea; (D.-K.Y.); (H.O.); (S.L.); (M.H.C.); (S.J.); (Y.K.); (S.L.K.); (J.B.); (H.J.); (J.I.L.); (G.-S.L.); (K.-H.K.)
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Lee CM, Park HS, Baek MK, Jeong OY, Seo J, Kim SM. QTL mapping and improvement of pre-harvest sprouting resistance using japonica weedy rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1194058. [PMID: 37342139 PMCID: PMC10277695 DOI: 10.3389/fpls.2023.1194058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 04/25/2023] [Indexed: 06/22/2023]
Abstract
The stability of cultivation and production in terms of crop yield has been threatened by climate change due to global warming. Pre-harvest sprouting (PHS) is a threat to crops, especially staple foods, including rice, because of reductions in yield and quality. To address the problem of precocious germination before harvest, we performed quantitative trait loci (QTL) analysis for PHS using F8 RILs populations derived from japonica weedy rice in Korea. QTL analysis revealed that two stable QTLs, qPH7 and qPH2, associated with PHS resistance were identified on chromosomes 7 and 2, respectively, explaining approximately 38% of the phenotypic variation. The QTL effect in the tested lines significantly decreased the degree of PHS, based on the number of QTLs included. Through fine mapping for main QTL qPH7, the region for the PHS was found to be anchored within 23.575-23.785 Mbp on chromosome 7 using 13 cleaved amplified sequence (CAPS) markers. Among 15 open reading frames (ORFs) within the detected region, one ORF, Os07g0584366, exhibited upregulated expression in the resistant donor, which was approximately nine times higher than that of susceptible japonica cultivars under PHS-inducing conditions. Japonica lines with QTLs related to PHS resistance were developed to improve the characteristics of PHS and design practical PCR-based DNA markers for marker-assisted backcrosses of many other PHS-susceptible japonica cultivars.
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Affiliation(s)
- Chang-Min Lee
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Hyun-Su Park
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Man-Kee Baek
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - O-Young Jeong
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Jeonghwan Seo
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Suk-Man Kim
- Department of Ecological & Environmental System, Kyungpook National University, Sangju, Republic of Korea
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Chen D, Zou W, Zhang M, Liu J, Chen L, Peng T, Ye G. Genome-Wide Association Study for Seed Dormancy Using Re-Sequenced Germplasm under Multiple Conditions in Rice. Int J Mol Sci 2023; 24:ijms24076117. [PMID: 37047087 PMCID: PMC10094323 DOI: 10.3390/ijms24076117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/08/2023] [Accepted: 03/17/2023] [Indexed: 04/14/2023] Open
Abstract
Seed dormancy is a key factor used to determine seed germination in rice production. So far, only a few genes controlling seed dormancy have been reported, and the genetic mechanism of rice seed dormancy is still elusive. In this study, a population of 195 diverse re-sequenced accessions from 40 countries was evaluated for the seed germination rate (GR) without dormancy breaking (WDB) as a control and under dry heating (DH) and gibberellic acid (GA) treatments, as dormancy breaking agents to identify QTLs for seed dormancy. Phenotypic assessment revealed that these accessions had abundant variations in seed dormancy. GWAS using 1,120,223 high-quality single nucleotide polymorphisms (SNPs) and a mixed linear model (MLM) incorporating both principal components (PCs) and kinship (K) identified 30 QTLs on 10 chromosomes, accounting for 7.3-20.4% of the phenotypic variance in GR. Ten of the QTLs were located in the regions of previously reported QTLs, while the rest were novel ones. Thirteen high-confidence candidate genes were predicted for the four QTLs detected in two or three conditions (qGR4-4, qGR4-5, qGR8 and qGR11-4) and one QTL with a large effect (qGR3). These genes were highly expressed during seed development and were significantly regulated by various hormone treatments. This study provides new insights into the genetic and molecular basis of rice seed dormancy/germination. The accessions with moderate and strong dormancy and markers for the QTLs and candidate genes are useful for attaining a proper level of seed dormancy.
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Affiliation(s)
- Dandan Chen
- Key Laboratory of Rice Biology in Henan Province, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wenli Zou
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Mingpei Zhang
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Jindong Liu
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Liang Chen
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Ting Peng
- Key Laboratory of Rice Biology in Henan Province, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Guoyou Ye
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Rice Breeding Innovations Platform, International Rice Research Institute (IRRI), Metro Manila 1301, Philippines
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Liu D, Zeng M, Wu Y, Du Y, Liu J, Luo S, Zeng Y. Comparative transcriptomic analysis provides insights into the molecular basis underlying pre-harvest sprouting in rice. BMC Genomics 2022; 23:771. [PMID: 36434522 PMCID: PMC9701047 DOI: 10.1186/s12864-022-08998-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Pre-harvest sprouting (PHS) is one of the most serious rice production constraints in areas where prolonged rainfall occurs during harvest. However, the molecular mechanisms of transcriptional regulation underlying PHS remain largely unknown. RESULTS In the current study, comparative transcriptome analyses were performed to characterize the similarities and differences between two rice varieties: PHS-sensitive Jiuxiangzhan (JXZ) and PHS-resistant Meixiangxinzhan (MXXZ). The physiological experimental results indicated that PHS causes a significant decrease in starch content and, in contrast, a significant increase in soluble sugar content and amylase activity. The extent of change in these physiological parameters in the sensitive variety JXZ was greater than that in the resistant variety MXXZ. A total of 9,602 DEGs were obtained from the transcriptome sequencing data, and 5,581 and 4,021 DEGs were identified in JXZ and MXXZ under high humidity conditions, respectively. The KEGG pathway enrichment analysis indicated that many DEGs under high humidity treatment were mainly linked to plant hormone signal transduction, carbon metabolism, starch and sucrose metabolism, and phenylpropanoid biosynthesis. Furthermore, the number of upregulated genes involved in these pathways was much higher in JXZ than in MXXZ, while the number of downregulated genes was higher in MXXZ than in JXZ. These results suggest that the physiological and biochemical processes of these pathways are more active in the PHS-sensitive JXZ than in the PHS-resistant MXXZ. CONCLUSION Based on these results, we inferred that PHS in rice results from altered phytohormone regulation, more active carbon metabolism and energy production, and enhanced phenylpropanoid biosynthesis. Our study provides a theoretical foundation for further elucidation of the complex regulatory mechanism of PHS in rice and the molecular breeding of PHS-resistant rice varieties.
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Affiliation(s)
- Dong Liu
- grid.411859.00000 0004 1808 3238Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Mingyang Zeng
- grid.411859.00000 0004 1808 3238Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Yan Wu
- grid.411859.00000 0004 1808 3238Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Yanli Du
- grid.411859.00000 0004 1808 3238Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Jianming Liu
- grid.411859.00000 0004 1808 3238Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Shaoqiang Luo
- grid.411859.00000 0004 1808 3238Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Yongjun Zeng
- grid.411859.00000 0004 1808 3238Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045 China
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Lee C, Cheon KS, Shin Y, Oh H, Jeong YM, Jang H, Park YC, Kim KY, Cho HC, Won YJ, Baek J, Cha YS, Kim SL, Kim KH, Ji H. Development and Application of a Target Capture Sequencing SNP-Genotyping Platform in Rice. Genes (Basel) 2022; 13:genes13050794. [PMID: 35627177 PMCID: PMC9141132 DOI: 10.3390/genes13050794] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/25/2022] Open
Abstract
The development of efficient, robust, and high-throughput SNP genotyping platforms is pivotal for crop genetics and breeding. Recently, SNP genotyping platforms based on target capture sequencing, which is very flexible in terms of the number of SNP markers, have been developed for maize, cassava, and fava bean. We aimed to develop a target capture sequencing SNP genotyping platform for rice. A target capture sequencing panel containing 2565 SNPs, including 1225 SNPs informative for japonica and 1339 SNPs informative for indica, was developed. This platform was used in diversity analysis of 50 rice varieties. Of the 2565 SNP markers, 2341 (91.3%) produced useful polymorphic genotype data, enabling the production of a phylogenetic tree of the 50 varieties. The mean number of markers polymorphic between any two varieties was 854. The platform was used for QTL mapping of preharvest sprouting (PHS) resistance in an F8 recombinant inbred line population derived from the cross Odae × Joun. A genetic map comprising 475 markers was constructed, and two QTLs for PHS resistance were identified on chromosomes 4 and 11. This system is a powerful tool for rice genetics and breeding and will facilitate QTL studies and gene mapping, germplasm diversity analysis, and marker-assisted selection.
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Affiliation(s)
- Chaewon Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
- Department of Crop Science and Biotechnology, Chonbuk National University, Jeonju 54896, Korea
| | - Kyeong-Seong Cheon
- Division of Forest Tree Improvement and Biotechnology, Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Korea;
| | - Yunji Shin
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
- Genecell Biotech Inc., Wanju, 55322, Korea
| | - Hyoja Oh
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
| | - Young-Min Jeong
- Seed Industry Promotion Center, Korea Agriculture Technology Promotion Agency (KOAT), Gimje 54324, Korea;
| | - Hoon Jang
- CELEMICS, Seoul 08506, Korea; (H.J.); (Y.-C.P.)
| | | | - Kyung-Yun Kim
- INSILICOGEN, Yongin 16954, Korea; (K.-Y.K.); (H.-C.C.)
| | - Hang-Chul Cho
- INSILICOGEN, Yongin 16954, Korea; (K.-Y.K.); (H.-C.C.)
| | - Yong-Jae Won
- Cheorwon Branch, National Institute of Crop Science, Rural Development Administration (RDA), Cheorwon 24010, Korea;
| | - Jeongho Baek
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
| | - Young-Soon Cha
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
| | - Song-Lim Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
| | - Kyung-Hwan Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
| | - Hyeonso Ji
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
- Correspondence: ; Tel.: +82-63-238-4657
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Seed Dormancy and Pre-Harvest Sprouting in Rice-An Updated Overview. Int J Mol Sci 2021; 22:ijms222111804. [PMID: 34769234 PMCID: PMC8583970 DOI: 10.3390/ijms222111804] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/14/2022] Open
Abstract
Pre-harvest sprouting is a critical phenomenon involving the germination of seeds in the mother plant before harvest under relative humid conditions and reduced dormancy. As it results in reduced grain yield and quality, it is a common problem for the farmers who have cultivated the rice and wheat across the globe. Crop yields need to be steadily increased to improve the people’s ability to adapt to risks as the world’s population grows and natural disasters become more frequent. To improve the quality of grain and to avoid pre-harvest sprouting, a clear understanding of the crops should be known with the use of molecular omics approaches. Meanwhile, pre-harvest sprouting is a complicated phenomenon, especially in rice, and physiological, hormonal, and genetic changes should be monitored, which can be modified by high-throughput metabolic engineering techniques. The integration of these data allows the creation of tailored breeding lines suitable for various demands and regions, and it is crucial for increasing the crop yields and economic benefits. In this review, we have provided an overview of seed dormancy and its regulation, the major causes of pre-harvest sprouting, and also unraveled the novel avenues to battle pre-harvest sprouting in cereals with special reference to rice using genomics and transcriptomic approaches.
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Ji H, Shin Y, Lee C, Oh H, Yoon IS, Baek J, Cha YS, Lee GS, Kim SL, Kim KH. Genomic Variation in Korean japonica Rice Varieties. Genes (Basel) 2021; 12:genes12111749. [PMID: 34828355 PMCID: PMC8623644 DOI: 10.3390/genes12111749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/24/2021] [Accepted: 10/28/2021] [Indexed: 11/27/2022] Open
Abstract
Next-generation sequencing technologies have enabled the discovery of numerous sequence variations among closely related crop varieties. We analyzed genome resequencing data from 24 Korean temperate japonica rice varieties and discovered 954,233 sequence variations, including 791,121 single nucleotide polymorphisms (SNPs) and 163,112 insertions/deletions (InDels). On average, there was one variant per 391 base-pairs (bp), a variant density of 2.6 per 1 kbp. Of the InDels, 10,860 were longer than 20 bp, which enabled conversion to markers resolvable on an agarose gel. The effect of each variant on gene function was predicted using the SnpEff program. The variants were categorized into four groups according to their impact: high, moderate, low, and modifier. These groups contained 3524 (0.4%), 27,656 (2.9%), 24,875 (2.6%), and 898,178 (94.1%) variants, respectively. To test the accuracy of these data, eight InDels from a pre-harvest sprouting resistance QTL (qPHS11) target region, four highly polymorphic InDels, and four functional sequence variations in known agronomically important genes were selected and successfully developed into markers. These results will be useful to develop markers for marker-assisted selection, to select candidate genes in map-based cloning, and to produce efficient high-throughput genome-wide genotyping systems for Korean temperate japonica rice varieties.
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Genome-Wide Identification and Expression Analysis of OsbZIP09 Target Genes in Rice Reveal Its Mechanism of Controlling Seed Germination. Int J Mol Sci 2021; 22:ijms22041661. [PMID: 33562219 PMCID: PMC7915905 DOI: 10.3390/ijms22041661] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/30/2021] [Accepted: 02/03/2021] [Indexed: 01/01/2023] Open
Abstract
Seed dormancy and germination are key events in plant development and are critical for crop production, and defects in seed germination or the inappropriate release of seed dormancy cause substantial losses in crop yields. Rice is the staple food for more than half of the world's population, and preharvest sprouting (PHS) is one of the most severe problems in rice production, due to a low level of seed dormancy, especially under warm and damp conditions. Therefore, PHS leads to yield loss and a decrease in rice quality and vitality. We reveal that mutation of OsbZIP09 inhibited rice PHS. Analysis of the expression of OsbZIP09 and its encoded protein sequence and structure indicated that OsbZIP09 is a typical bZIP transcription factor that contains conserved bZIP domains, and its expression is induced by ABA. Moreover, RNA sequencing (RNA-seq) and DNA affinity purification sequencing (DAP-seq) analyses were performed and 52 key direct targets of OsbZIP09 were identified, including OsLOX2 and Late Embryogenesis Abundant (LEA) family genes, which are involved in controlling seed germination. Most of these key targets showed consistent changes in expression in response to abscisic acid (ABA) treatment and OsbZIP09 mutation. The data characterize a number of key target genes that are directly regulated by OsbZIP09 and contribute to revealing the molecular mechanism that underlies how OsbZIP09 controls rice seed germination.
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Cheon KS, Jeong YM, Oh H, Oh J, Kang DY, Kim N, Lee E, Baek J, Kim SL, Choi I, Yoon IS, Kim KH, Won YJ, Cho YI, Han JH, Ji H. Development of 454 New Kompetitive Allele-Specific PCR (KASP) Markers for Temperate japonica Rice Varieties. PLANTS 2020; 9:plants9111531. [PMID: 33182649 PMCID: PMC7698039 DOI: 10.3390/plants9111531] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/04/2020] [Accepted: 11/07/2020] [Indexed: 12/02/2022]
Abstract
Temperate japonica rice varieties exhibit wide variation in the phenotypes of several important agronomic traits, including disease resistance, pre-harvest sprouting resistance, plant architecture, and grain quality, indicating the presence of genes contributing to favorable agronomic traits. However, gene mapping and molecular breeding has been hampered as a result of the low genetic diversity among cultivars and scarcity of polymorphic DNA markers. Single nucleotide polymorphism (SNP)-based kompetitive allele-specific PCR (KASP) markers allow high-throughput genotyping for marker-assisted selection and quantitative trait loci (QTL) mapping within closely related populations. Previously, we identified 740,566 SNPs and developed 771 KASP markers for Korean temperate japonica rice varieties. However, additional markers were needed to provide sufficient genome coverage to support breeding programs. In this study, the 740,566 SNPs were categorized according to their predicted impacts on gene function. The high-impact, moderate-impact, modifier, and low-impact groups contained 703 (0.1%), 20,179 (2.7%), 699,866 (94.5%), and 19,818 (2.7%) SNPs, respectively. A subset of 357 SNPs from the high-impact group was selected for initial KASP marker development, resulting in 283 polymorphic KASP markers. After incorporation of the 283 markers with the 771 existing markers in a physical map, additional markers were developed to fill genomic regions with large gaps between markers, and 171 polymorphic KASP markers were successfully developed from 284 SNPs. Overall, a set of 1225 KASP markers was produced. The markers were evenly distributed across the rice genome, with average marker density of 3.3 KASP markers per Mbp. The 1225 KASP markers will facilitate QTL/gene mapping and marker-assisted selection in temperate japonica rice breeding programs.
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Affiliation(s)
- Kyeong-Seong Cheon
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Young-Min Jeong
- Seed Industry Promotion Center, Foundation of Agri. Tech. Commercialization & Transfer (FACT), Gimje 54324, Korea;
| | - Hyoja Oh
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Jun Oh
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Do-Yu Kang
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Nyunhee Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Eungyeong Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Jeongho Baek
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Song Lim Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Inchan Choi
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - In Sun Yoon
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Kyung-Hwan Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Yong Jae Won
- Cheorwon Branch, National Institute of Crop Science, Rural Development Administration (RDA), Cheorwon 24010, Korea;
| | - Young-il Cho
- Seed Business Team, Department of Seed Services, Foundation of Agri. Tech. Commercialization & Transfer (FACT), Iksan 54667, Korea;
| | - Jung-Heon Han
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
| | - Hyeonso Ji
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (K.-S.C.); (H.O.); (J.O.); (D.-Y.K.); (N.K.); (E.L.); (J.B.); (S.L.K.); (I.C.); (I.S.Y.); (K.-H.K.); (J.-H.H.)
- Correspondence:
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