1
|
Xu Q, Jiang J, Jing C, Hu C, Zhang M, Li X, Shen J, Hai M, Zhang Y, Wang D, Dang X. Genome-wide association mapping of quantitative trait loci for chalkiness-related traits in rice ( Oryza sativa L.). Front Genet 2024; 15:1423648. [PMID: 39050253 PMCID: PMC11266141 DOI: 10.3389/fgene.2024.1423648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/07/2024] [Indexed: 07/27/2024] Open
Abstract
Grain chalkiness directly affects the commercial value of rice. Genes related to chalkiness reported thus far have been discovered in mutants, but it has not been identified whether these genes can be used to improve rice quality by breeding. Therefore, discovering more quantitative trait loci (QTLs) or genes related to chalkiness in the rice germplasm is necessary. This study entails a genome-wide association study on the degree of endosperm chalkiness (DEC) and percentage of grains with chalkiness (PGWC) by combining 1.2 million single-nucleotide polymorphisms (SNPs) with the phenotypic data of 173 rice accessions. Thirteen QTLs for DEC and nine for PGWC were identified, of which four were detected simultaneously for both DEC and PGWC; further, qDEC11/qPGWC11 was identified as the major QTL. By combining linkage disequilibrium analysis and SNP information, LOC_Os11g10170 was identified as the candidate gene for DEC. There were significant differences among the haplotypes of LOC_Os11g10170, and the Hap 1 of LOC_Os11g10170 was observed to reduce the DEC by 6.19%. The qRT-PCR results showed that the gene expression levels in accessions with high DEC values were significantly higher than those in accessions with low DEC values during days 21-42 after flowering, with a maximum at 28 days. These results provide molecular markers and germplasm resources for genetic improvement of the chalkiness-related traits in rice.
Collapse
Affiliation(s)
- Qing Xu
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Jianhua Jiang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Chunyu Jing
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
- College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Changmin Hu
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
- College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Mengyuan Zhang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
- College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Xinru Li
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
- College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Jiaming Shen
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
- College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Mei Hai
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
- College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Ying Zhang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Dezheng Wang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Xiaojing Dang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
| |
Collapse
|
2
|
Hu C, Li X, Zhang M, Jing C, Hai M, Shen J, Xu Q, Dang X, Shi Y, Liu E, Jiang J. Identifying the Quantitative Trait Locus and Candidate Genes of Traits Related to Milling Quality in Rice via a Genome-Wide Association Study. PLANTS (BASEL, SWITZERLAND) 2024; 13:1324. [PMID: 38794395 PMCID: PMC11124788 DOI: 10.3390/plants13101324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024]
Abstract
Milling quality directly affects production efficiency in rice, which is closely related to the brown rice recovery (BRR), the milled rice recovery (MRR) and the head milled rice recovery (HMRR). The present study investigated these three traits in 173 germplasms in two environments, finding abundant phenotypic variation. Three QTLs for BRR, two for MRR, and three for HMRR were identified in a genome-wide association study, five of these were identified in previously reported QTLs and three were newly identified. By combining the linkage disequilibrium (LD) analyses, the candidate gene LOC_Os05g08350 was identified. It had two haplotypes with significant differences and Hap 2 increased the BRR by 4.40%. The results of the qRT-PCR showed that the expression of LOC_Os05g08350 in small-BRR accessions was significantly higher than that in large-BRR accessions at Stages 4-5 of young panicle development, reaching the maximum value at Stage 5. The increase in thickness of the spikelet hulls of the accession carrying LOC_Os05g08350TT occurred due to an increase in the cell width and the cell numbers in cross-sections of spikelet hulls. These results help to further clarify the molecular genetic mechanism of milling-quality-related traits and provide genetic germplasm materials for high-quality breeding in rice.
Collapse
Affiliation(s)
- Changmin Hu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xinru Li
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Mengyuan Zhang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Chunyu Jing
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Mei Hai
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Jiaming Shen
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Qing Xu
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiaojing Dang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Erbao Liu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Jianhua Jiang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| |
Collapse
|
3
|
Sachdeva S, Singh R, Maurya A, Singh VK, Singh UM, Kumar A, Singh GP. New insights into QTNs and potential candidate genes governing rice yield via a multi-model genome-wide association study. BMC PLANT BIOLOGY 2024; 24:124. [PMID: 38373874 PMCID: PMC10877931 DOI: 10.1186/s12870-024-04810-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/08/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND Rice (Oryza sativa L.) is one of the globally important staple food crops, and yield-related traits are prerequisites for improved breeding efficiency in rice. Here, we used six different genome-wide association study (GWAS) models for 198 accessions, with 553,229 single nucleotide markers (SNPs) to identify the quantitative trait nucleotides (QTNs) and candidate genes (CGs) governing rice yield. RESULTS Amongst the 73 different QTNs in total, 24 were co-localized with already reported QTLs or loci in previous mapping studies. We obtained fifteen significant QTNs, pathway analysis revealed 10 potential candidates within 100kb of these QTNs that are predicted to govern plant height, days to flowering, and plot yield in rice. Based on their superior allelic information in 20 elite and 6 inferior genotypes, we found a higher percentage of superior alleles in the elite genotypes in comparison to inferior genotypes. Further, we implemented expression analysis and enrichment analysis enabling the identification of 73 candidate genes and 25 homologues of Arabidopsis, 19 of which might regulate rice yield traits. Of these candidate genes, 40 CGs were found to be enriched in 60 GO terms of the studied traits for instance, positive regulator metabolic process (GO:0010929), intracellular part (GO:0031090), and nucleic acid binding (GO:0090079). Haplotype and phenotypic variation analysis confirmed that LOC_OS09G15770, LOC_OS02G36710 and LOC_OS02G17520 are key candidates associated with rice yield. CONCLUSIONS Overall, we foresee that the QTNs, putative candidates elucidated in the study could summarize the polygenic regulatory networks controlling rice yield and be useful for breeding high-yielding varieties.
Collapse
Grants
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
Collapse
Affiliation(s)
- Supriya Sachdeva
- Division of Genomic Resources, ICAR-NBPGR, Pusa, New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-NBPGR, Pusa, New Delhi, India.
| | - Avantika Maurya
- Division of Genomic Resources, ICAR-NBPGR, Pusa, New Delhi, India
| | - Vikas K Singh
- International Rice Research Institute (IRRI), South Asia Hub, ICRISAT, Hyderabad, India
| | - Uma Maheshwar Singh
- International Rice Research Institute (IRRI), South Asia Regional Centre (ISARC), Varanasi, India
| | - Arvind Kumar
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | | |
Collapse
|
4
|
Sachdeva S, Singh R, Maurya A, Singh VK, Singh UM, Kumar A, Singh GP. Multi-model genome-wide association studies for appearance quality in rice. FRONTIERS IN PLANT SCIENCE 2024; 14:1304388. [PMID: 38273959 PMCID: PMC10808671 DOI: 10.3389/fpls.2023.1304388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024]
Abstract
Improving the quality of the appearance of rice is critical to meet market acceptance. Mining putative quality-related genes has been geared towards the development of effective breeding approaches for rice. In the present study, two SL-GWAS (CMLM and MLM) and three ML-GWAS (FASTmrEMMA, mrMLM, and FASTmrMLM) genome-wide association studies were conducted in a subset of 3K-RGP consisting of 198 rice accessions with 553,831 SNP markers. A total of 594 SNP markers were identified using the mixed linear model method for grain quality traits. Additionally, 70 quantitative trait nucleotides (QTNs) detected by the ML-GWAS models were strongly associated with grain aroma (AR), head rice recovery (HRR, %), and percentage of grains with chalkiness (PGC, %). Finally, 39 QTNs were identified using single- and multi-locus GWAS methods. Among the 39 reliable QTNs, 20 novel QTNs were identified for the above-mentioned three quality-related traits. Based on annotation and previous studies, four functional candidate genes (LOC_Os01g66110, LOC_Os01g66140, LOC_Os07g44910, and LOC_Os02g14120) were found to influence AR, HRR (%), and PGC (%), which could be utilized in rice breeding to improve grain quality traits.
Collapse
Affiliation(s)
- Supriya Sachdeva
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Avantika Maurya
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, International Crop Reseach Institute for Semi Arid Tropics (ICRISAT), Hyderabad, India
| | - Uma Maheshwar Singh
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, India
| | - Arvind Kumar
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Gyanendra Pratap Singh
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| |
Collapse
|
5
|
Jiang J, Song S, Hu C, Jing C, Xu Q, Li X, Zhang M, Hai M, Shen J, Zhang Y, Wang D, Dang X. QTL Detection and Candidate Gene Identification for Eating and Cooking Quality Traits in Rice ( Oryza sativa L.) via a Genome-Wide Association Study. Int J Mol Sci 2024; 25:630. [PMID: 38203801 PMCID: PMC10779416 DOI: 10.3390/ijms25010630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/25/2023] [Accepted: 12/30/2023] [Indexed: 01/12/2024] Open
Abstract
The eating and cooking quality (ECQ) directly affects the taste of rice, being closely related to factors such as gelatinization temperature (GT), gel consistency (GC) and amylose content (AC). Mining the quantitative trait loci (QTLs), and gene loci controlling ECQ-related traits is vital. A genome-wide association study on ECQ-related traits was conducted, combining 1.2 million single nucleotide polymorphisms (SNPs) with the phenotypic data of 173 rice accessions. Two QTLs for GT, one for GC and five for AC were identified, of which two were found in previously reported genes, and six were newly found. There were 28 positional candidate genes in the region of qAC11. Based on a linkage disequilibrium (LD) analysis, three candidate genes were screened within the LD region associated with AC. There were significant differences between the haplotypes of LOC_Os11g10170, but no significant differences were found for the other two genes. The qRT-PCR results showed that the gene expression levels in the accessions with high ACs were significantly larger than those in the accessions with low ACs at 35d and 42d after flowering. Hap 2 and Hap 3 of LOC_Os11g10170 reduced the AC by 13.09% and 10.77%, respectively. These results provide a theoretical and material basis for improving the ECQ of rice.
Collapse
Affiliation(s)
- Jianhua Jiang
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Shaojie Song
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Changmin Hu
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Chunyu Jing
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Qing Xu
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xinru Li
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Mengyuan Zhang
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Mei Hai
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Jiaming Shen
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Ying Zhang
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Dezheng Wang
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiaojing Dang
- Anhui Province Key Laboratory of Rice Genetics and Breeding (Rice Research Institute), Anhui Academy of Agricultural Sciences, Hefei 230031, China
| |
Collapse
|
6
|
Liu H, Zeng B, Zhao J, Yan S, Wan J, Cao Z. Genetic Research Progress: Heat Tolerance in Rice. Int J Mol Sci 2023; 24:ijms24087140. [PMID: 37108303 PMCID: PMC10138502 DOI: 10.3390/ijms24087140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/28/2023] [Accepted: 04/02/2023] [Indexed: 04/29/2023] Open
Abstract
Heat stress (HS) caused by high-temperature weather seriously threatens international food security. Indeed, as an important food crop in the world, the yield and quality of rice are frequently affected by HS. Therefore, clarifying the molecular mechanism of heat tolerance and cultivating heat-tolerant rice varieties is urgent. Here, we summarized the identified quantitative trait loci (Quantitative Trait Loci, QTL) and cloned rice heat tolerance genes in recent years. We described the plasma membrane (PM) response mechanisms, protein homeostasis, reactive oxygen species (ROS) accumulation, and photosynthesis under HS in rice. We also explained some regulatory mechanisms related to heat tolerance genes. Taken together, we put forward ways to improve heat tolerance in rice, thereby providing new ideas and insights for future research.
Collapse
Affiliation(s)
- Huaqing Liu
- Rice National Engineering Research Center (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
- Jiangxi Research and Development Center of Super Rice, Nanchang 330200, China
| | - Bohong Zeng
- Jiangxi Research and Development Center of Super Rice, Nanchang 330200, China
| | - Jialiang Zhao
- Jiangxi Research and Development Center of Super Rice, Nanchang 330200, China
| | - Song Yan
- Jiangxi Research and Development Center of Super Rice, Nanchang 330200, China
| | - Jianlin Wan
- Jiangxi Research and Development Center of Super Rice, Nanchang 330200, China
| | - Zhibin Cao
- Rice National Engineering Research Center (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
- Jiangxi Research and Development Center of Super Rice, Nanchang 330200, China
| |
Collapse
|
7
|
Boulanger HG, Guo W, Monteiro LDFR, Calixto CPG. Co-expression network of heat-response transcripts: A glimpse into how splicing factors impact rice basal thermotolerance. Front Mol Biosci 2023; 10:1122201. [PMID: 36818043 PMCID: PMC9932781 DOI: 10.3389/fmolb.2023.1122201] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
To identify novel solutions to improve rice yield under rising temperatures, molecular components of thermotolerance must be better understood. Alternative splicing (AS) is a major post-transcriptional mechanism impacting plant tolerance against stresses, including heat stress (HS). AS is largely regulated by splicing factors (SFs) and recent studies have shown their involvement in temperature response. However, little is known about the splicing networks between SFs and AS transcripts in the HS response. To expand this knowledge, we constructed a co-expression network based on a publicly available RNA-seq dataset that explored rice basal thermotolerance over a time-course. Our analyses suggest that the HS-dependent control of the abundance of specific transcripts coding for SFs might explain the widespread, coordinated, complex, and delicate AS regulation of critical genes during a plant's inherent response to extreme temperatures. AS changes in these critical genes might affect many aspects of plant biology, from organellar functions to cell death, providing relevant regulatory candidates for future functional studies of basal thermotolerance.
Collapse
Affiliation(s)
- Hadrien Georges Boulanger
- Université Paris-Saclay, Gif-sur-Yvette, France,École Nationale Supérieure d'Informatique pour l'Industrie et l’Entreprise, Evry-Courcouronnes, France,Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Wenbin Guo
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | | | - Cristiane Paula Gomes Calixto
- Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, Brazil,*Correspondence: Cristiane Paula Gomes Calixto,
| |
Collapse
|