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Daryani P, Amirbakhtiar N, Soorni J, Loni F, Darzi Ramandi H, Shobbar ZS. Uncovering the Genomic Regions Associated with Yield Maintenance in Rice Under Drought Stress Using an Integrated Meta-Analysis Approach. RICE (NEW YORK, N.Y.) 2024; 17:7. [PMID: 38227151 DOI: 10.1186/s12284-024-00684-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 01/03/2024] [Indexed: 01/17/2024]
Abstract
The complex trait of yield is controlled by several quantitative trait loci (QTLs). Given the global water deficit issue, the development of rice varieties suitable for non-flooded cultivation holds significant importance in breeding programs. The powerful approach of Meta-QTL (MQTL) analysis can be used for the genetic dissection of complicated quantitative traits. In the current study, a comprehensive MQTL analysis was conducted to identify consistent QTL regions associated with drought tolerance and yield-related traits under water deficit conditions in rice. In total, 1087 QTLs from 134 rice populations, published between 2000 to 2021, were utilized in the analysis. Distinct MQTL analysis of the relevant traits resulted in the identification of 213 stable MQTLs. The confidence interval (CI) for the detected MQTLs was between 0.12 and 19.7 cM. The average CI of the identified MQTLs (4.68 cM) was 2.74 times narrower compared to the average CI of the initial QTLs. Interestingly, 63 MQTLs coincided with SNP peak positions detected by genome-wide association studies for yield and drought tolerance-associated traits under water deficit conditions in rice. Considering the genes located both in the QTL-overview peaks and the SNP peak positions, 19 novel candidate genes were introduced, which are associated with drought response index, plant height, panicle number, biomass, and grain yield. Moreover, an inclusive MQTL analysis was performed on all the traits to obtain "Breeding MQTLs". This analysis resulted in the identification of 96 MQTLs with a CI ranging from 0.01 to 9.0 cM. The mean CI of the obtained MQTLs (2.33 cM) was 4.66 times less than the mean CI of the original QTLs. Thirteen MQTLs fulfilling the criteria of having more than 10 initial QTLs, CI < 1 cM, and an average phenotypic variance explained greater than 10%, were designated as "Breeding MQTLs". These findings hold promise for assisting breeders in enhancing rice yield under drought stress conditions.
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Affiliation(s)
- Parisa Daryani
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Nazanin Amirbakhtiar
- National Plant Gene Bank of Iran, Seed and Plant Improvement Institute (SPII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Jahad Soorni
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Fatemeh Loni
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Hadi Darzi Ramandi
- Department of Plant Production and Genetics, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran.
| | - Zahra-Sadat Shobbar
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
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Wang X, Li X, Luo X, Tang S, Wu T, Wang Z, Peng Z, Xia Q, Yu C, Xiao Y. Identification, Fine Mapping and Application of Quantitative Trait Loci for Grain Shape Using Single-Segment Substitution Lines in Rice ( Oryza sativa L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:892. [PMID: 36840239 PMCID: PMC9966618 DOI: 10.3390/plants12040892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Quantitative trait loci (QTLs) and HQTL (heterosis QTLs) for grain shape are two major genetic factors of grain yield and quality in rice (Oryza sativa L.). Although many QTLs for grain shape have been reported, only a few are applied in production. In this study, 54 QTLs for grain shape were detected on 10 chromosomes using 33 SSSLs (single-segment substitution lines) and methods of statistical genetics. Among these, 23 exhibited significant positive additive genetic effects, including some novel QTLs, among which qTGW4-(1,2), qTGW10-2, and qTGW10-3 were three QTLs newly found in this study and should be paid more attention. Moreover, 26 HQTLs for grain shape were probed. Eighteen of these exhibited significant positive dominant genetic effects. Thirty-three QTLs for grain shape were further mapped using linkage analysis. Most of the QTLs for grain shape produced pleiotropic effects, which simultaneously controlled multiple appearance traits of grain shape. Linkage mapping of the F2 population derived from sub-single-segment substitution lines further narrowed the interval harbouring qTGW10-3 to 75.124 kb between PSM169 and RM25753. The candidate gene was identified and could be applied to breeding applications by molecular marker-assisted selection. These identified QTLs for grain shape will offer additional insights for improving grain yield and quality in rice breeding.
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Affiliation(s)
- Xiaoling Wang
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Bioscience and Biotechnology & San Ya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xia Li
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Xin Luo
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Shusheng Tang
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Ting Wu
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Zhiquan Wang
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Zhiqin Peng
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Qiyu Xia
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Bioscience and Biotechnology & San Ya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Chuanyuan Yu
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Yulong Xiao
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
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Current Advances and Future Prospects for Molecular Research for Agronomically Important Traits in Rice. Int J Mol Sci 2022; 23:ijms23147531. [PMID: 35886876 PMCID: PMC9316905 DOI: 10.3390/ijms23147531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/02/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
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Du XX, Park JR, Wang XH, Jang YH, Kim EG, Lee GS, Kim KM. Applying HPLC to Screening QTLs for BLB Resistance in Rice. PLANTS 2021; 10:plants10102145. [PMID: 34685953 PMCID: PMC8537431 DOI: 10.3390/plants10102145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/27/2021] [Accepted: 10/08/2021] [Indexed: 11/28/2022]
Abstract
Bacterial leaf blight (BLB) is caused by Xanthomonas oryzae pv. oryzae and is a major cause of rice yield reductions around the world. When diseased, plants produce a variety of metabolites to resist pathogens. In this study, the various defense metabolites were quantified using high-performance liquid chromatography (HPLC) after Xoo inoculation in a 120 Cheongcheong/Nagdong double haploid (CNDH) population. Quantitative trait locus (QTL) mapping was conducted using the concentration of the plant defense metabolites. HPLC analyzes the concentration of substances according to the severity of disease symptoms. Searching for BLB resistance candidate genes by applying this analysis method is very effective when mapping related genes. These resistance genes can be mapped directly to the causative pathogens. A total of 17 metabolites were detected by means of HPLC analysis after Xoo inoculation in the 120 CNDH population. QTL mapping of the metabolite concentrations resulted in the detection of the BLB resistance candidate gene, OsWRKYq6, in RM3343 of chromosome 6. OsWRKYq6 has a very high homology sequence with WRKY transcription factor 39, and when inoculated with Xoo, the relative expression level of the resistant population was higher than that of the susceptible population. Resistance genes have previously been detected using only phenotypic change data. In this study, resistance candidate genes were detected using the concentration of metabolites produced in plants after inoculation with pathogens. This newly developed analysis method can be used to effectively detect and identify genes directly involved in disease resistance for future studies.
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Affiliation(s)
- Xiao-Xuan Du
- Biosafety Division, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea;
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Korea;
| | - Jae-Ryoung Park
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Korea;
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea; (Y.-H.J.); (E.-G.K.)
| | - Xiao-Han Wang
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 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; (Y.-H.J.); (E.-G.K.)
| | - Eun-Gyeong Kim
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea; (Y.-H.J.); (E.-G.K.)
| | - Gang-Seob Lee
- Biosafety Division, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea;
- Correspondence: (G.-S.L.); (K.-M.K.); Tel.: +82-63-238-4714 (G.-S.L.); +82-53-950-5711 (K.-M.K.)
| | - Kyung-Min Kim
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea; (Y.-H.J.); (E.-G.K.)
- Correspondence: (G.-S.L.); (K.-M.K.); Tel.: +82-63-238-4714 (G.-S.L.); +82-53-950-5711 (K.-M.K.)
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