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Yin M, Tong X, Yang J, Cheng Y, Zhou P, Li G, Wang Y, Ying J. Dissecting the Genetic Basis of Yield Traits and Validation of a Novel Quantitative Trait Locus for Grain Width and Weight in Rice. Plants (Basel) 2024; 13:770. [PMID: 38592774 PMCID: PMC10975080 DOI: 10.3390/plants13060770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 04/11/2024]
Abstract
Grain yield in rice is a complex trait and it is controlled by a number of quantitative trait loci (QTL). To dissect the genetic basis of rice yield, QTL analysis for nine yield traits was performed using an F2 population containing 190 plants, which was developed from a cross between Youyidao (YYD) and Sanfenhe (SFH), and each plant in the population evaluated with respect to nine yield traits. In this study, the correlations among the nine yield traits were analyzed. The grain yield per plant positively correlated with six yield traits, except for grain length and grain width, and showed the highest correlation coefficient of 0.98 with the number of filled grains per plant. A genetic map containing 133 DNA markers was constructed and it spanned 1831.7 cM throughout 12 chromosomes. A total of 36 QTLs for the yield traits were detected on nine chromosomes, except for the remaining chromosomes 5, 8, and 9. The phenotypic variation was explained by a single QTL that ranged from 6.19% to 36.01%. Furthermore, a major QTL for grain width and weight, qGW2-1, was confirmed to be newly identified and was narrowed down to a relatively smaller interval of about ~2.94-Mb. Collectively, we detected a total of 36 QTLs for yield traits and a major QTL, qGW2-1, was confirmed to control grain weight and width, which laid the foundation for further map-based cloning and molecular design breeding in rice.
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Affiliation(s)
| | | | | | | | | | | | | | - Jiezheng Ying
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China; (M.Y.); (J.Y.); (Y.C.); (P.Z.); (G.L.); (Y.W.)
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Yang T, Dong J, Zhao J, Zhang L, Zhou L, Yang W, Ma Y, Wang J, Fu H, Chen J, Li W, Hu H, Jiang X, Liu Z, Liu B, Zhang S. Genome-wide association mapping combined with gene-based haplotype analysis identify a novel gene for shoot length in rice (Oryza sativa L.). Theor Appl Genet 2023; 136:251. [PMID: 37985474 PMCID: PMC10661777 DOI: 10.1007/s00122-023-04497-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/27/2023] [Indexed: 11/22/2023]
Abstract
KEY MESSAGE Genome-wide association mapping revealed a novel QTL for shoot length across multiple environments. Its causal gene, LOC_Os01g68500, was identified firstly through gene-based haplotype analysis, gene expression and knockout transgenic verification. Strong seedling vigor is an important breeding target for rice varieties used in direct seeding. Shoot length (SL) is one of the important traits associated with seedling vigor characterized by rapid growth of seedling, which enhance seedling emergence. Therefore, mining genes for SL and conducting molecular breeding help to develop varieties for direct seeding. However, few QTLs for SL have been fine mapped or cloned so far. In this study, a genome-wide association study of SL was performed in a diverse rice collection consisting of 391 accessions in two years, using phenotypes generated by different cultivation methods according to the production practice, and a total of twenty-four QTLs for SL were identified. Among them, the novel QTL qSL-1f on chromosome 1 could be stably detected across all three cultivation methods in the whole population and indica subpopulation. Through gene-based haplotype analysis of the annotated genes within the putative region of qSL-1f, and validated by gene expression and knockout transgenic experiments, LOC_Os01g68500 (i.e., Os01g0913100 in RAP-DB) was identified as the causal gene for SL, which has a single-base variation (C-to-A transversion) in its CDS region, resulting in the significant difference in SL of rice. LOC_Os01g68500 encodes a DUF538 (Domain of unknown function) containing protein, and the function of DUF538 protein gene on rice seedling growth is firstly reported in this study. These results provide a new clue for exploring the molecular mechanism regulating SL, and promising gene source for the molecular breeding in rice.
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Affiliation(s)
- Tifeng Yang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jingfang Dong
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Longting Zhang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Lian Zhou
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Wu Yang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Yamei Ma
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jian Wang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Hua Fu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jiansong Chen
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Wenhui Li
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Haifei Hu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Xianya Jiang
- Yangjiang Institute of Agricultural Science, Yangjiang, 529500, China
| | - Ziqiang Liu
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Bin Liu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Shaohong Zhang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Xu Y, Bai L, Liu M, Liu Y, Peng S, Hu P, Wang D, Liu Q, Yan S, Gao L, Wang X, Ning Y, Zuo S, Zheng W, Liu S, Xiang W, Wang G, Kang H. Identification of two novel rice S genes through combination of association and transcription analyses with gene-editing technology. Plant Biotechnol J 2023; 21:1628-1641. [PMID: 37154202 PMCID: PMC10363757 DOI: 10.1111/pbi.14064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 04/04/2023] [Accepted: 04/16/2023] [Indexed: 05/10/2023]
Abstract
Traditional rice blast resistance breeding largely depends on utilizing typical resistance (R) genes. However, the lack of durable R genes has prompted rice breeders to find new resistance resources. Susceptibility (S) genes are potential new targets for resistance genetic engineering using genome-editing technologies, but identifying them is still challenging. Here, through the integration of genome-wide association study (GWAS) and transcriptional analysis, we identified two genes, RNG1 and RNG3, whose polymorphisms in 3'-untranslated regions (3'-UTR) affected their expression variations. These polymorphisms could serve as molecular markers to identify rice blast-resistant accessions. Editing the 3'-UTRs using CRISPR/Cas9 technology affected the expression levels of two genes, which were positively associated with rice blast susceptibility. Knocking out either RNG1 or RNG3 in rice enhanced the rice blast and bacterial blight resistance, without impacting critical agronomic traits. RNG1 and RNG3 have two major genotypes in diverse rice germplasms. The frequency of the resistance genotype of these two genes significantly increased from landrace rice to modern cultivars. The obvious selective sweep flanking RNG3 suggested it has been artificially selected in modern rice breeding. These results provide new targets for S gene identification and open avenues for developing novel rice blast-resistant materials.
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Affiliation(s)
- Yuchen Xu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and College of AgronomyHunan Agricultural UniversityChangshaHunanChina
| | - Lu Bai
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Minghao Liu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Yanchen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Shasha Peng
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and College of AgronomyHunan Agricultural UniversityChangshaHunanChina
| | - Pei Hu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Dan Wang
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and College of AgronomyHunan Agricultural UniversityChangshaHunanChina
| | - Qi Liu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Shuangyong Yan
- Tianjin Key Laboratory of Crop Genetic BreedingTianjin Crop Research Institute, Tianjin Academy of Agriculture SciencesTianjinChina
| | - Lijun Gao
- Guangxi Crop Genetic Improvement and Biotechnology LaboratoryGuangxi Academy of Agricultural SciencesNanningChina
| | - Xuli Wang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Shimin Zuo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular BreedingAgricultural College of Yangzhou UniversityYangzhouChina
| | - Wenjing Zheng
- Rice Research Institute of Liaoning Province, Liaoning Academy of Agricultural SciencesShenyangChina
| | - Shiming Liu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Wensheng Xiang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Guo‐Liang Wang
- Department of Plant PathologyOhio State UniversityColumbusOhioUSA
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
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Xu Y, Yan S, Jiang S, Bai L, Liu Y, Peng S, Chen R, Liu Q, Xiao Y, Kang H. Identification of a Rice Leaf Width Gene Narrow Leaf 22 ( NAL22) through Genome-Wide Association Study and Gene Editing Technology. Int J Mol Sci 2023; 24:ijms24044073. [PMID: 36835485 PMCID: PMC9962836 DOI: 10.3390/ijms24044073] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Rice leaf width (RLW) is a crucial determinant of photosynthetic area. Despite the discovery of several genes controlling RLW, the underlying genetic architecture remains unclear. In order to better understand RLW, this study conducted a genome-wide association study (GWAS) on 351 accessions from the rice diversity population II (RDP-II). The results revealed 12 loci associated with leaf width (LALW). In LALW4, we identified one gene, Narrow Leaf 22 (NAL22), whose polymorphisms and expression levels were associated with RLW variation. Knocking out this gene in Zhonghua11, using CRISPR/Cas9 gene editing technology, resulted in a short and narrow leaf phenotype. However, seed width remained unchanged. Additionally, we discovered that the vein width and expression levels of genes associated with cell division were suppressed in nal22 mutants. Gibberellin (GA) was also found to negatively regulate NAL22 expression and impact RLW. In summary, we dissected the genetic architecture of RLW and identified a gene, NAL22, which provides new loci for further RLW studies and a target gene for leaf shape design in modern rice breeding.
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Affiliation(s)
- Yuchen Xu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shuangyong Yan
- Tianjin Key Laboratory of Crop Genetic Breeding, Tianjin Crop Research Institute, Tianjin Academy of Agriculture Sciences, Tianjin 300112, China
| | - Su Jiang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Lu Bai
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yanchen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shasha Peng
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Rubin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qi Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yinghui Xiao
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence:
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Yen KS, Sundar LS, Chao Y. Foliar Application of Rhodopseudomonas palustris Enhances the Rice Crop Growth and Yield under Field Conditions. Plants 2022; 11:2452. [PMID: 36235318 PMCID: PMC9614608 DOI: 10.3390/plants11192452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/09/2022] [Accepted: 09/17/2022] [Indexed: 11/17/2022]
Abstract
Anthropogenic activities causing climate change and other environmental effects are lowering crop yield by deteriorating the growing environment for crops. Rice, a globally important cereal crop, is under production threat due to climate change and land degradation. This research aims to sustainably improve rice growth and yield by using Rhodopseudomonas palustris, a plant growth-promoting bacteria that has recently gained much attention in crop production. The experiment was set up in two fields, one as a control and the other as a PNSB-treated field. The foliar application of treatment was made fortnightly until the end of the vegetative stage. Data on the growth, yield, and antioxidant enzymes were collected weekly. The results of this experiment indicate no significant differences in the plant height, root volume, average grain per panicle, biological yield, grain fertility, and antioxidant enzyme activity between the PNSB-treated and untreated plants. However, a significant increase in the tiller number, leaf chlorophyll content and lodging resistance were noted with PNSB treatment. Likewise, PNSB-treatment significantly increased root length (25%), root dry weight (57%), productive tillers per plants (26%), average grains per plant (38%), grain yield (33%), 1000 grain weight (1.6%), and harvest index (41%). Hence, from this research, it can be concluded that foliar application of PNSB on rice crops under field conditions improves crop growth and yield, although it does not affect antioxidant enzyme activity.
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Li D, Zhang F, Pinson SRM, Edwards JD, Jackson AK, Xia X, Eizenga GC. Assessment of Rice Sheath Blight Resistance Including Associations with Plant Architecture, as Revealed by Genome-Wide Association Studies. Rice (N Y) 2022; 15:31. [PMID: 35716230 PMCID: PMC9206596 DOI: 10.1186/s12284-022-00574-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Sheath blight (ShB) disease caused by Rhizoctonia solani Kühn, is one of the most economically damaging rice (Oryza sativa L.) diseases worldwide. There are no known major resistance genes, leaving only partial resistance from small-effect QTL to deploy for cultivar improvement. Many ShB-QTL are associated with plant architectural traits detrimental to yield, including tall plants, late maturity, or open canopy from few or procumbent tillers, which confound detection of physiological resistance. RESULTS To identify QTL for ShB resistance, 417 accessions from the Rice Diversity Panel 1 (RDP1), developed for association mapping studies, were evaluated for ShB resistance, plant height and days to heading in inoculated field plots in Arkansas, USA (AR) and Nanning, China (NC). Inoculated greenhouse-grown plants were used to evaluate ShB using a seedling-stage method to eliminate effects from height or maturity, and tiller (TN) and panicle number (PN) per plant. Potted plants were used to evaluate the RDP1 for TN and PN. Genome-wide association (GWA) mapping with over 3.4 million SNPs identified 21 targeted SNP markers associated with ShB which tagged 18 ShB-QTL not associated with undesirable plant architecture traits. Ten SNPs were associated with ShB among accessions of the Indica subspecies, ten among Japonica subspecies accessions, and one among all RDP1 accessions. Across the 18 ShB QTL, only qShB4-1 was not previously reported in biparental mapping studies and qShB9 was not reported in the GWA ShB studies. All 14 PN QTL overlapped with TN QTL, with 15 total TN QTL identified. Allele effects at the five TN QTL co-located with ShB QTL indicated that increased TN does not inevitably increase disease development; in fact, for four ShB QTL that overlapped TN QTL, the alleles increasing resistance were associated with increased TN and PN, suggesting a desirable coupling of alleles at linked genes. CONCLUSIONS Nineteen accessions identified as containing the most SNP alleles associated with ShB resistance for each subpopulation were resistant in both AR and NC field trials. Rice breeders can utilize these accessions and SNPs to develop cultivars with enhanced ShB resistance along with increased TN and PN for improved yield potential.
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Affiliation(s)
- Danting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang, Jiangxi, China
| | - Shannon R M Pinson
- USDA Dale Bumpers National Rice Research Center, 2890 Highway 130 East, Stuttgart, AR, 72160, USA.
| | - Jeremy D Edwards
- USDA Dale Bumpers National Rice Research Center, 2890 Highway 130 East, Stuttgart, AR, 72160, USA
| | - Aaron K Jackson
- USDA Dale Bumpers National Rice Research Center, 2890 Highway 130 East, Stuttgart, AR, 72160, USA
| | - Xiuzhong Xia
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Georgia C Eizenga
- USDA Dale Bumpers National Rice Research Center, 2890 Highway 130 East, Stuttgart, AR, 72160, USA.
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8
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Biernaskie JM. Kin selection theory and the design of cooperative crops. Evol Appl 2022; 15:1555-1564. [DOI: 10.1111/eva.13418] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Jay M. Biernaskie
- Department of Crop Genetics, John Innes Centre, Norwich Research Park Norwich UK
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9
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Zhao DD, Park JR, Jang YH, Kim EG, Du XX, Farooq M, Yun BJ, Kim KM. Identification of One Major QTL and a Novel Gene OsIAA17q5 Associated with Tiller Number in Rice Using QTL Analysis. Plants (Basel) 2022; 11:538. [PMID: 35214873 PMCID: PMC8875189 DOI: 10.3390/plants11040538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/16/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Rice tillers are one of the most important traits for the yield and development of rice, although little is known about its mode of inheritance. Tiller numbers were recorded every 7 days a total of nine times, starting 30 days after transplantation. Quantitative trait locus (QTL) based analysis on a set of double haploid population derivatives of a cross between the Cheongcheong and Nagdong varieties identified a major effect of locus RM18130-RM3381 on chromosome 5, which was expressed in eight different growth stages. Within the target region RM18130-RM3381 (physical distance: 2.08 Mb), 61 candidate genes were screened by annotation. Among the candidate genes, Os05g0230700 (named OsIAA17q5), which belongs to the family of auxin-responsive genes, was selected as a target. Auxin promotes cell division and meristem maintenance and is an effective plant regulator which influences plant growth and development by altering the expression of various genes. OsIAA17q5 is expected to control the number of tillers. The present study provides further understanding of the basic genetic mechanisms that selectively express the control of tiller numbers in different growth stages, as well as provides valuable information for future research aimed at cloning the target gene. These results may contribute to developing a comprehensive understanding of the basic genetic processes regulating the developmental behavior of tiller numbers in rice.
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Affiliation(s)
- Dan-Dan Zhao
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea; (D.-D.Z.); (J.-R.P.); (Y.-H.J.); (E.-G.K.); (M.F.)
| | - Jae-Ryoung Park
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea; (D.-D.Z.); (J.-R.P.); (Y.-H.J.); (E.-G.K.); (M.F.)
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea
| | - Yoon-Hee Jang
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea; (D.-D.Z.); (J.-R.P.); (Y.-H.J.); (E.-G.K.); (M.F.)
| | - Eun-Gyeong Kim
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea; (D.-D.Z.); (J.-R.P.); (Y.-H.J.); (E.-G.K.); (M.F.)
| | - Xiao-Xuan Du
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Korea;
- Biosafety Division, National Institute of Agricultural Science, Jeonju 54874, Korea
| | - Muhammad Farooq
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea; (D.-D.Z.); (J.-R.P.); (Y.-H.J.); (E.-G.K.); (M.F.)
| | - Byoung-Ju Yun
- School of Electronics Engineering, College of IT Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Korea
| | - Kyung-Min Kim
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea; (D.-D.Z.); (J.-R.P.); (Y.-H.J.); (E.-G.K.); (M.F.)
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Korea;
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10
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Kulkarni SR, Balachandran SM, Ulaganathan K, Balakrishnan D, Prasad ASH, Rekha G, Kousik MBVN, Hajira SK, Kale RR, Aleena D, Anila M, Punniakoti E, Dilip T, Pranathi K, Das MA, Shaik M, Chaitra K, Sinha P, Sundaram RM. Mapping novel QTLs for yield related traits from a popular rice hybrid KRH-2 derived doubled haploid (DH) population. 3 Biotech 2021; 11:513. [PMID: 34926111 DOI: 10.1007/s13205-021-03045-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 10/29/2021] [Indexed: 11/30/2022] Open
Abstract
A doubled haploid (DH) population consisting of 125 DHLs derived from the popular rice hybrid, KRH-2 (IR58025A/KMR3R) was utilized for Quantitative Trait Loci (QTL) mapping to identify novel genomic regions associated with yield related traits. A genetic map was constructed with 126 polymorphic SSR and EST derived markers, which were distributed across rice genome. QTL analysis using inclusive composite interval mapping (ICIM) method identified a total of 24 major and minor effect QTLs. Among them, twelve major effect QTLs were identified for days to fifty percent flowering (qDFF12-1), total grain yield/plant (qYLD3-1 and qYLD6-1), test (1,000) grain weight (qTGW6-1 and qTGW7-1), panicle weight (qPW9-1), plant height (qPH12-1), flag leaf length (qFLL6-1), flag leaf width (qFLW4-1), panicle length (qPL3-1 and qPL6-1) and biomass (qBM4-1), explaining 29.95-56.75% of the phenotypic variability with LOD scores range of 2.72-16.51. Chromosomal regions with gene clusters were identified on chromosome 3 for total grain yield/plant (qYLD3-1) and panicle length (qPL3-1) and on chromosome 6 for total grain yield/plant (qYLD6-1), flag leaf length (qFLL6-1) and panicle length (qPL6-1). Majority of the QTLs identified were observed to be co-localized with the previously reported QTL regions. Five novel, major effect QTLs associated with panicle weight (qPW9-1), plant height (qPH12-1), flag leaf width (qFLW4-1), panicle length (qPL3-1) and biomass (qBM4-1) and three novel minor effect QTLs for panicle weight (qPW3-1 and qPW8-1) and fertile grains per panicle (qFGP5-1) were identified. These QTLs can be used in breeding programs aimed to yield improvement after their validation in alternative populations. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03045-7.
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Affiliation(s)
- Swapnil Ravindra Kulkarni
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - S M Balachandran
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - K Ulaganathan
- Centre for Plant Molecular Biology (CPMB), Osmania University, Hyderabad, 500007 India
| | - Divya Balakrishnan
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - A S Hari Prasad
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - G Rekha
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - M B V N Kousik
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - S K Hajira
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - Ravindra Ramarao Kale
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - D Aleena
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - M Anila
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - E Punniakoti
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - T Dilip
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - K Pranathi
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - M Ayyappa Das
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - Mastanbee Shaik
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - K Chaitra
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - Pragya Sinha
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - R M Sundaram
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
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11
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Wang D, Liu Z, Xiao Y, Liu X, Chen Y, Zhang Z, Kang H, Wang X, Jiang S, Peng S, Tan X, Zhang D, Liu Y, Wang GL, Li C. Association Mapping and Functional Analysis of Rice Cold Tolerance QTLs at the Bud Burst Stage. Rice (N Y) 2021; 14:98. [PMID: 34825994 PMCID: PMC8626552 DOI: 10.1186/s12284-021-00538-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
Cold tolerance at the bud burst stage (CTB) is a key trait for direct-seeded rice. Although quantitative trait loci (QTL) affecting CTB in rice have been mapped using traditional linkage mapping and genome-wide association study (GWAS) methods, the underlying genes remain unknown. In this study, we evaluated the CTB phenotype of 339 cultivars in the Rice Diversity Panel II (RDP II) collection. GWAS identified four QTLs associated with CTB (qCTBs), distributed on chromosomes 1-3. Among them, qCTB-1-1 overlaps with Osa-miR319b, a known cold tolerance micro RNA gene. The other three qCTBs have not been reported. In addition, we characterised the candidate gene OsRab11C1 for qCTB-1-2 that encodes a Rab protein belonging to the small GTP-binding protein family. Overexpression of OsRab11C1 significantly reduced CTB, while gene knockout elevated CTB as well as cold tolerance at the seedling stage, suggesting that OsRab11C1 negatively regulates rice cold tolerance. Molecular analysis revealed that OsRab11C1 modulates cold tolerance by suppressing the abscisic acid signalling pathway and proline biosynthesis. Using RDP II and GWAS, we identified four qCTBs that are involved in CTB and determined the function of the candidate gene OsRab11C1 in cold tolerance. Our results demonstrate that OsRab11C1 is a negative regulator of cold tolerance and knocking out of the gene by genome-editing may provide enhanced cold tolerance in rice.
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Affiliation(s)
- Dan Wang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China.
| | - Zhuo Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yinghui Xiao
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Xionglun Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yue Chen
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Zhuo Zhang
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xuli Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Su Jiang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Shasha Peng
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Xinqiu Tan
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Deyong Zhang
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Yong Liu
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Guo-Liang Wang
- Department of Plant Pathology, The Ohio State University, Columbus, 43210, USA.
| | - Chenggang Li
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
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12
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Ren M, Huang M, Qiu H, Chun Y, Li L, Kumar A, Fang J, Zhao J, He H, Li X. Genome-Wide Association Study of the Genetic Basis of Effective Tiller Number in Rice. Rice (N Y) 2021; 14:56. [PMID: 34170442 PMCID: PMC8233439 DOI: 10.1186/s12284-021-00495-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/17/2021] [Indexed: 05/14/2023]
Abstract
BACKGROUND Effective tiller number (ETN) has a pivotal role in determination of rice (Oryza sativa L.) grain yield. ETN is a complex quantitative trait regulated by both genetic and environmental factors. Despite multiple tillering-related genes have been cloned previously, few of them have been utilized in practical breeding programs. RESULTS In this study, we conducted a genome-wide association study (GWAS) for ETN using a panel of 490 rice accessions derived from the 3 K rice genomes project. Thirty eight ETN-associated QTLs were identified, interestingly, four of which colocalized with the OsAAP1, DWL2, NAL1, and OsWRKY74 gene previously reported to be involved in rice tillering regulation. Haplotype (Hap) analysis revealed that Hap5 of OsAAP1, Hap3 and 6 of DWL2, Hap2 of NAL1, and Hap3 and 4 of OsWRKY74 are favorable alleles for ETN. Pyramiding favorable alleles of all these four genes had more enhancement in ETN than accessions harboring the favorable allele of only one gene. Moreover, we identified 25 novel candidate genes which might also affect ETN, and the positive association between expression levels of the OsPILS6b gene and ETN was validated by RT-qPCR. Furthermore, transcriptome analysis on data released on public database revealed that most ETN-associated genes showed a relatively high expression from 21 days after transplanting (DAT) to 49 DAT and decreased since then. This unique expression pattern of ETN-associated genes may contribute to the transition from vegetative to reproductive growth of tillers. CONCLUSIONS Our results revealed that GWAS is a feasible way to mine ETN-associated genes. The candidate genes and favorable alleles identified in this study have the potential application value in rice molecular breeding for high ETN and grain yield.
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Affiliation(s)
- Mengmeng Ren
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Minghan Huang
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325 Shandong China
| | - Haiyang Qiu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yan Chun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Lu Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Ashmit Kumar
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jingjing Fang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jinfeng Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hang He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325 Shandong China
| | - Xueyong Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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13
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Wu F, Luo X, Wang L, Wei Y, Li J, Xie H, Zhang J, Xie G. Genome-Wide Association Study Reveals the QTLs for Seed Storability in World Rice Core Collections. Plants (Basel) 2021; 10:plants10040812. [PMID: 33924151 PMCID: PMC8074387 DOI: 10.3390/plants10040812] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 11/30/2022]
Abstract
Seed storability is a main agronomically important trait to assure storage safety of grain and seeds in rice. Although many quantitative trait loci (QTLs) and associated genes for rice seed storability have been identified, the detailed genetic mechanisms of seed storability remain unclear in rice. In this study, a genome-wide association study (GWAS) was performed in 456 diverse rice core collections from the 3K rice genome. We discovered the new nine QTLs designated as qSS1-1, qSS1-2, qSS2-1, qSS3-1, qSS5-1, qSS5-2, qSS7-1, qSS8-1, and qSS11-1. According to the analysis of the new nine QTLs, our results could well explain the reason why seed storability of indica subspecies was superior to japonica subspecies in rice. Among them, qSS1-2 and qSS8-1 were potentially co-localized with a known associated qSS1/OsGH3-2 and OsPIMT1, respectively. Our results also suggest that pyramiding breeding of superior alleles of these associated genes will lead to new varieties with improved seed storability in the future.
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Affiliation(s)
- Fangxi Wu
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China; (F.W.); (X.L.); (Y.W.); (H.X.)
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi Luo
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China; (F.W.); (X.L.); (Y.W.); (H.X.)
| | - Lingqiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (L.W.); (J.L.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yidong Wei
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China; (F.W.); (X.L.); (Y.W.); (H.X.)
| | - Jianguo Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (L.W.); (J.L.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Huaan Xie
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China; (F.W.); (X.L.); (Y.W.); (H.X.)
| | - Jianfu Zhang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China; (F.W.); (X.L.); (Y.W.); (H.X.)
- Correspondence: (J.Z.); (G.X.)
| | - Guosheng Xie
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (J.Z.); (G.X.)
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Su J, Xu K, Li Z, Hu Y, Hu Z, Zheng X, Song S, Tang Z, Li L. Genome-wide association study and Mendelian randomization analysis provide insights for improving rice yield potential. Sci Rep 2021; 11:6894. [PMID: 33767346 DOI: 10.1038/s41598-021-86389-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 03/11/2021] [Indexed: 01/31/2023] Open
Abstract
Rice yield per plant has a complex genetic architecture, which is mainly determined by its three component traits: the number of grains per panicle (GPP), kilo-grain weight (KGW), and tillers per plant (TP). Exploring ideotype breeding based on selection for genetically less complex component traits is an alternative route for further improving rice production. To understand the genetic basis of the relationship between rice yield and component traits, we investigated the four traits of two rice hybrid populations (575 + 1495 F1) in different environments and conducted meta-analyses of genome-wide association study (meta-GWAS). In total, 3589 significant loci for three components traits were detected, while only 3 loci for yield were detected. It indicated that rice yield is mainly controlled by minor-effect loci and hardly to be identified. Selecting quantitative trait locus/gene affected component traits to further enhance yield is recommended. Mendelian randomization design is adopted to investigate the genetic effects of loci on yield through component traits and estimate the genetic relationship between rice yield and its component traits by these loci. The loci for GPP or TP mainly had a positive genetic effect on yield, but the loci for KGW with different direction effects (positive effect or negative effect). Additionally, TP (Beta = 1.865) has a greater effect on yield than KGW (Beta = 1.016) and GPP (Beta = 0.086). Five significant loci for component traits that had an indirect effect on yield were identified. Pyramiding superior alleles of the five loci revealed improved yield. A combination of direct and indirect effects may better contribute to the yield potential of rice. Our findings provided a rationale for using component traits as indirect indices to enhanced rice yield, which will be helpful for further understanding the genetic basis of yield and provide valuable information for improving rice yield potential.
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15
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Zhao S, Jang S, Lee YK, Kim DG, Jin Z, Koh HJ. Genetic Basis of Tiller Dynamics of Rice Revealed by Genome-Wide Association Studies. Plants (Basel) 2020; 9:plants9121695. [PMID: 33276582 PMCID: PMC7761586 DOI: 10.3390/plants9121695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 11/16/2022]
Abstract
A tiller number is the key determinant of rice plant architecture and panicle number and consequently controls grain yield. Thus, it is necessary to optimize the tiller number to achieve the maximum yield in rice. However, comprehensive analyses of the genetic basis of the tiller number, considering the development stage, tiller type, and related traits, are lacking. In this study, we sequence 219 Korean rice accessions and construct a high-quality single nucleotide polymorphism (SNP) dataset. We also evaluate the tiller number at different development stages and heading traits involved in phase transitions. By genome-wide association studies (GWASs), we detected 20 significant association signals for all traits. Five signals were detected in genomic regions near known candidate genes. Most of the candidate genes were involved in the phase transition from vegetative to reproductive growth. In particular, HD1 was simultaneously associated with the productive tiller ratio and heading date, indicating that the photoperiodic heading gene directly controls the productive tiller ratio. Multiple linear regression models of lead SNPs showed coefficients of determination (R2) of 0.49, 0.22, and 0.41 for the tiller number at the maximum tillering stage, productive tiller number, and productive tiller ratio, respectively. Furthermore, the model was validated using independent japonica rice collections, implying that the lead SNPs included in the linear regression model were generally applicable to the tiller number prediction. We revealed the genetic basis of the tiller number in rice plants during growth, By GWASs, and formulated a prediction model by linear regression. Our results improve our understanding of tillering in rice plants and provide a basis for breeding high-yield rice varieties with the optimum the tiller number.
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Affiliation(s)
- Shuyu Zhao
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (S.Z.); (S.J.); (Y.K.L.)
- Department of Agronomy, College of Agriculture, Northeast Agricultural University, Harbin 150030, China;
| | - Su Jang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (S.Z.); (S.J.); (Y.K.L.)
| | - Yoon Kyung Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (S.Z.); (S.J.); (Y.K.L.)
| | - Dong-Gwan Kim
- Department of Bioindustry and Bioresource Engineering, Department of Molecular Biology and Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea;
| | - Zhengxun Jin
- Department of Agronomy, College of Agriculture, Northeast Agricultural University, Harbin 150030, China;
| | - Hee-Jong Koh
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (S.Z.); (S.J.); (Y.K.L.)
- Correspondence:
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Tanase DM, Gosav EM, Neculae E, Costea CF, Ciocoiu M, Hurjui LL, Tarniceriu CC, Maranduca MA, Lacatusu CM, Floria M, Serban IL. Genetic Basis of Tiller Dynamics of Rice Revealed by Genome-Wide Association Studies. Nutrients 2020; 12:nu12123719. [PMID: 33276482 PMCID: PMC7760723 DOI: 10.3390/nu12123719] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022] Open
Abstract
A tiller number is the key determinant of rice plant architecture and panicle number and consequently controls grain yield. Thus, it is necessary to optimize the tiller number to achieve the maximum yield in rice. However, comprehensive analyses of the genetic basis of the tiller number, considering the development stage, tiller type, and related traits, are lacking. In this study, we sequence 219 Korean rice accessions and construct a high-quality single nucleotide polymorphism (SNP) dataset. We also evaluate the tiller number at different development stages and heading traits involved in phase transitions. By genome-wide association studies (GWASs), we detected 20 significant association signals for all traits. Five signals were detected in genomic regions near known candidate genes. Most of the candidate genes were involved in the phase transition from vegetative to reproductive growth. In particular, HD1 was simultaneously associated with the productive tiller ratio and heading date, indicating that the photoperiodic heading gene directly controls the productive tiller ratio. Multiple linear regression models of lead SNPs showed coefficients of determination (R2) of 0.49, 0.22, and 0.41 for the tiller number at the maximum tillering stage, productive tiller number, and productive tiller ratio, respectively. Furthermore, the model was validated using independent japonica rice collections, implying that the lead SNPs included in the linear regression model were generally applicable to the tiller number prediction. We revealed the genetic basis of the tiller number in rice plants during growth, By GWASs, and formulated a prediction model by linear regression. Our results improve our understanding of tillering in rice plants and provide a basis for breeding high-yield rice varieties with the optimum the tiller number.
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Affiliation(s)
- Daniela Maria Tanase
- Department of Internal Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700111 Iasi, Romania; (D.M.T.); (M.F.)
- Internal Medicine Clinic, “St. Spiridon” County Clinical Emergency Hospital Iasi, 700115 Iasi, Romania
| | - Evelina Maria Gosav
- Department of Internal Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700111 Iasi, Romania; (D.M.T.); (M.F.)
- Internal Medicine Clinic, “St. Spiridon” County Clinical Emergency Hospital Iasi, 700115 Iasi, Romania
- Correspondence:
| | - Ecaterina Neculae
- Department of Gastroenterology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania;
- Institute of Gastroenterology and Hepatology, “St. Spiridon” County Clinical Emergency Hospital Iasi, 700111 Iasi, Romania
| | - Claudia Florida Costea
- Department of Ophthalmology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania;
- 2nd Ophthalmology Clinic, “Nicolae Oblu” Emergency Clinical Hospital, 700309 Iași, Romania
| | - Manuela Ciocoiu
- Department of Pathophysiology, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania;
| | - Loredana Liliana Hurjui
- Department of Morpho-Functional Sciences II, Physiology Discipline, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (L.L.H.); (M.A.M.); (I.L.S.)
- Hematology Laboratory, “St. Spiridon” County Clinical Emergency Hospital, 700111 Iasi, Romania
| | - Claudia Cristina Tarniceriu
- Department of Morpho-Functional Sciences I, Discipline of Anatomy, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania;
- Hematology Clinic, “St. Spiridon” County Clinical Emergency Hospital, 700111 Iasi, Romania
| | - Minela Aida Maranduca
- Department of Morpho-Functional Sciences II, Physiology Discipline, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (L.L.H.); (M.A.M.); (I.L.S.)
| | - Cristina Mihaela Lacatusu
- Unit of Diabetes, Nutrition and Metabolic Diseases, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania;
- Clinical Center of Diabetes, Nutrition and Metabolic Diseases, “St. Spiridon” County Clinical Emergency Hospital, 700111 Iasi, Romania
| | - Mariana Floria
- Department of Internal Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700111 Iasi, Romania; (D.M.T.); (M.F.)
- Internal Medicine Clinic, Emergency Military Clinical Hospital, 700483 Iasi, Romania
| | - Ionela Lacramioara Serban
- Department of Morpho-Functional Sciences II, Physiology Discipline, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (L.L.H.); (M.A.M.); (I.L.S.)
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Ma X, Li F, Zhang Q, Wang X, Guo H, Xie J, Zhu X, Ullah Khan N, Zhang Z, Li J, Li Z, Zhang H. Genetic architecture to cause dynamic change in tiller and panicle numbers revealed by genome-wide association study and transcriptome profile in rice. Plant J 2020; 104:1603-1616. [PMID: 33058400 DOI: 10.1111/tpj.15023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 09/24/2020] [Accepted: 10/02/2020] [Indexed: 05/27/2023]
Abstract
Panicle number (PN) is one of the three yield components in rice. As one of the most unstable traits, the dynamic change in tiller number (DCTN) may determine the final PN. However, the genetic basis of DCTN and its relationship with PN remain unclear. Here, 377 deeply re-sequenced rice accessions were used to perform genome-wide association studies (GWAS) for tiller/PN. It was found that the DCTN pattern rather than maximum tiller number or effective tiller ratio is the determinant factor of high PN. The DCTN pattern that affords more panicles exhibits a period of stable tillering peak between 30 and 45 days after transplant (called DT30 and DT45, respectively), which was believed as an ideal pattern contributing to the steady transition from tiller development to panicle development (ST-TtP). Consistently, quantitative trait loci (QTL) expressed near DT30-DT45 were especially critical to the rice DCTN and in supporting the ST-TtP. The spatio-temporal expression analysis showed that the expression pattern of keeping relatively high expression in root at 24:00 (R24-P2) from about DT30 to DT45 is a typical expression pattern of cloned tiller genes, and the candidate genes with R24-P2 can facilitate the prediction of PN. Moreover, gene OsSAUR27 was identified by an integrated approach combining GWAS, bi-parental QTL mapping and transcription. These findings related to the genetic basis underlying the DCTN will provide the genetic theory in making appropriate decisions on field management, and in developing new varieties with high PN and ideal dynamic plant architecture.
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Affiliation(s)
- Xiaoqian Ma
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Fengmei Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- School of Life Science and Technology, Xinxiang University, Henan, 453003, China
| | - Quan Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xueqiang Wang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Haifeng Guo
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jianyin Xie
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiaoyang Zhu
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Najeeb Ullah Khan
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhanying Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jinjie Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Hongliang Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
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Yang T, Zhou L, Zhao J, Dong J, Liu Q, Fu H, Mao X, Yang W, Ma Y, Chen L, Wang J, Bai S, Zhang S, Liu B. The Candidate Genes Underlying a Stably Expressed QTL for Low Temperature Germinability in Rice (Oryza sativa L.). Rice (N Y) 2020; 13:74. [PMID: 33074410 PMCID: PMC7573065 DOI: 10.1186/s12284-020-00434-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/07/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND Direct seeding is an efficient cultivation technique in rice. However, poor low temperature germinability (LTG) of modern rice cultivars limits its application. Identifying the genes associated with LTG and performing molecular breeding is the fundamental way to address this issue. However, few LTG QTLs have been fine mapped and cloned so far. RESULTS In the present study, the LTG evaluation of 375 rice accessions selected from the Rice Diversity Panel 2 showed that there were large LTG variations within the population, and the LTG of Indica group was significantly higher than that of Japonica and Aus groups (p < 0.01). In total, eleven QTLs for LTG were identified through genome-wide association study (GWAS). Among them, qLTG_sRDP2-3/qLTG_JAP-3, qLTG_AUS-3 and qLTG_sRDP2-12 are first reported in the present study. The QTL on chromosome 10, qLTG_sRDP2-10a had the largest contribution to LTG variations in 375 rice accessions, and was further validated using single segment substitution line (SSSL). The presence of qLTG_sRDP2-10a could result in 59.8% increase in LTG under 15 °C low temperature. The expression analysis of the genes within qLTG_sRDP2-10a region indicated that LOC_Os10g22520 and LOC_Os10g22484 exhibited differential expression between the high and low LTG lines. Further sequence comparisons revealed that there were insertion and deletion sequence differences in the promoter and intron region of LOC_Os10g22520, and an about 6 kb variation at the 3' end of LOC_Os10g22484 between the high and low LTG lines, suggesting that the sequence variations of the two genes could be the cause for their differential expression in high and low LTG lines. CONCLUSION Among the 11 QTLs identified in this study, qLTG_sRDP2-10a could also be detected in other three studies using different germplasm under different cold environments. Its large effect and stable expression make qLTG_sRDP2-10a particularly valuable in rice breeding. The two genes, LOC_Os10g22484 and LOC_Os10g22520, were considered as the candidate genes underlying qLTG_sRDP2-10a. Our results suggest that integrating GWAS and SSSL can facilitate identification of QTL for complex traits in rice. The identification of qLTG_sRDP2-10a and its candidate genes provide a promising source for gene cloning of LTG and molecular breeding for LTG in rice.
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Affiliation(s)
- Tifeng Yang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Lian Zhou
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Jingfang Dong
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Qing Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Hua Fu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Xingxue Mao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Wu Yang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Yamei Ma
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Luo Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Jian Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Song Bai
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Shaohong Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Bin Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
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Xu X, Ye J, Yang Y, Zhang M, Xu Q, Feng Y, Yuan X, Yu H, Wang Y, Yang Y, Wei X. Genome-Wide Association Study of Rice Rooting Ability at the Seedling Stage. Rice (N Y) 2020; 13:59. [PMID: 32833069 PMCID: PMC7445215 DOI: 10.1186/s12284-020-00420-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/10/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Rice rooting ability is a complex agronomical trait that displays heterosis and plays an important role in rice growth and production. Only a few quantitative trait loci (QTLs) have been identified by bi-parental population. More genes or QTLs are required to dissect the genetic architecture of rice rooting ability. RESULTS To characterize the genetic basis for rice rooting ability, we used a natural rice population, genotyped by a 90 K single nucleotide polymorphism (SNP) array, to identify the loci associated with rooting-related traits through the genome-wide association study (GWAS). Population structure analysis divided the natural population into two subgroups: indica and japonica. We measured four traits for evaluating rice rooting ability, namely root growth ability (RGA), maximum root length (MRL), root length (RL), and root number (RN). Using the association study in three panels consisting of one for the full population, one for indica, and one for japonica, 24 SNPs associated with rooting ability-related traits were identified. Through comparison of the relative expression levels and DNA sequences between germplasm with extreme phenotypes, results showed that LOC_Os05g11810 had non-synonymous variations at the coding region, which may cause differences in root number, and that the expression levels of LOC_Os04g09900 and LOC_Os04g10060 are closely associated with root length variation. CONCLUSIONS Through evaluation of the rice rooting ability-related traits and the association mapping, we provided useful information for understanding the genetic basis of rice rooting ability and also identified some candidate genes and molecular markers for rice root breeding.
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Affiliation(s)
- Xin Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Junhua Ye
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yingying Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Mengchen Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Qun Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yue Feng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Xiaoping Yuan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Hanyong Yu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yiping Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yaolong Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
| | - Xinghua Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
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