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Dipta B, Sood S, Mangal V, Bhardwaj V, Thakur AK, Kumar V, Singh B. KASP: a high-throughput genotyping system and its applications in major crop plants for biotic and abiotic stress tolerance. Mol Biol Rep 2024; 51:508. [PMID: 38622474 DOI: 10.1007/s11033-024-09455-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 03/18/2024] [Indexed: 04/17/2024]
Abstract
Advances in plant molecular breeding have resulted in the development of new varieties with superior traits, thus improving the crop germplasm. Breeders can screen a large number of accessions without rigorous and time-consuming phenotyping by marker-assisted selection (MAS). Molecular markers are one of the most imperative tools in plant breeding programmes for MAS to develop new cultivars possessing multiple superior traits. Single nucleotide polymorphisms (SNPs) are ideal for MAS due to their low cost, low genotyping error rates, and reproducibility. Kompetitive Allele Specific PCR (KASP) is a globally recognized technology for SNP genotyping. KASP is an allele-specific oligo extension-based PCR assay that uses fluorescence resonance energy transfer (FRET) to detect genetic variations such as SNPs and insertions/deletions (InDels) at a specific locus. Additionally, KASP allows greater flexibility in assay design, which leads to a higher success rate and the capability to genotype a large population. Its versatility and ease of use make it a valuable tool in various fields, including genetics, agriculture, and medical research. KASP has been extensively used in various plant-breeding applications, such as the identification of germplasm resources, quality control (QC) analysis, allele mining, linkage mapping, quantitative trait locus (QTL) mapping, genetic map construction, trait-specific marker development, and MAS. This review provides an overview of the KASP assay and emphasizes its validation in crop improvement related to various biotic and abiotic stress tolerance and quality traits.
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Affiliation(s)
- Bhawna Dipta
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India
| | - Salej Sood
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India.
| | - Vikas Mangal
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India
| | - Vinay Bhardwaj
- ICAR-National Research Centre on Seed Spices, Tabiji, Ajmer, Rajasthan, 305206, India
| | - Ajay Kumar Thakur
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India
| | - Brajesh Singh
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India
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Anilkumar C, Muhammed Azharudheen TP, Sah RP, Sunitha NC, Devanna BN, Marndi BC, Patra BC. Gene based markers improve precision of genome-wide association studies and accuracy of genomic predictions in rice breeding. Heredity (Edinb) 2023; 130:335-345. [PMID: 36792661 PMCID: PMC10163052 DOI: 10.1038/s41437-023-00599-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/17/2023] Open
Abstract
It is hypothesized that the genome-wide genic markers may increase the prediction accuracy of genomic selection for quantitative traits. To test this hypothesis, a set of candidate gene-based markers for yield and grain traits-related genes cloned across the rice genome were custom-designed. A multi-model, multi-locus genome-wide association study (GWAS) was performed using new genic markers developed to test their effectiveness for gene discovery. Two multi-locus models, FarmCPU and mrMLM, along with a single-locus mixed linear model (MLM), identified 28 significant marker-trait associations. These associations revealed novel causative alleles for grain weight and pleiotropic associations with other traits. For instance, the marker YD91 derived from the gene OsAAP3 on chromosome 1 was consistently associated with grain weight, while the gene has a significant effect on grain yield. Furthermore, nine genomic selection methods, including regression-based and machine learning-based models, were used to predict grain weight using a leave-one-out five-fold cross-validation approach to optimize the genomic selection model with genic markers. Among nine prediction models, Kernel Hilbert Space Regression (RKHS) is the best among regression-based models, and Random Forest Regression (RFR) is the best among machine learning-based models. Genomic prediction accuracies with and without GWAS significant markers were compared to assess the effectiveness of markers. The rapid decreases in prediction accuracy upon dropping GWAS significant markers indicate the effectiveness of new genic markers in genomic selection. Apart from that, the candidate gene-based markers were found to be more effective in genomic selection programs for better accuracy.
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Zhang B, Ma L, Wu B, Xing Y, Qiu X. Introgression Lines: Valuable Resources for Functional Genomics Research and Breeding in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:863789. [PMID: 35557720 PMCID: PMC9087921 DOI: 10.3389/fpls.2022.863789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/01/2022] [Indexed: 05/14/2023]
Abstract
The narrow base of genetic diversity of modern rice varieties is mainly attributed to the overuse of the common backbone parents that leads to the lack of varied favorable alleles in the process of breeding new varieties. Introgression lines (ILs) developed by a backcross strategy combined with marker-assisted selection (MAS) are powerful prebreeding tools for broadening the genetic base of existing cultivars. They have high power for mapping quantitative trait loci (QTLs) either with major or minor effects, and are used for precisely evaluating the genetic effects of QTLs and detecting the gene-by-gene or gene-by-environment interactions due to their low genetic background noise. ILs developed from multiple donors in a fixed background can be used as an IL platform to identify the best alleles or allele combinations for breeding by design. In the present paper, we reviewed the recent achievements from ILs in rice functional genomics research and breeding, including the genetic dissection of complex traits, identification of elite alleles and background-independent and epistatic QTLs, analysis of genetic interaction, and genetic improvement of single and multiple target traits. We also discussed how to develop ILs for further identification of new elite alleles, and how to utilize IL platforms for rice genetic improvement.
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Affiliation(s)
- Bo Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Ling Ma
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Bi Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Xianjin Qiu
- College of Agriculture, Yangtze University, Jingzhou, China
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Shin NH, Han JH, Vo KTX, Seo J, Navea IP, Yoo SC, Jeon JS, Chin JH. Development of a Temperate Climate-Adapted indica Multi-stress Tolerant Rice Variety by Pyramiding Quantitative Trait Loci. RICE (NEW YORK, N.Y.) 2022; 15:22. [PMID: 35397732 PMCID: PMC8994804 DOI: 10.1186/s12284-022-00568-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
Successful cultivation of rice (Oryza sativa L.) in many Asian countries requires submergence stress tolerance at the germination and early establishment stages. Two quantitative trait loci, Sub1 (conferring submergence tolerance) and AG1 (conferring anaerobic germination), were recently pyramided into a single genetic background, without compromising any desirable agronomic traits, leading to the development of Ciherang-Sub1 + AG1 (CSA). However, little research has been conducted to enhance plant tolerance to abiotic stress (submergence) and biotic stress (rice blast), which occur in a damp climate following flooding. The BC2F5 breeding line was phenotypically characterized using the AvrPi9 isolate. The biotic and abiotic stress tolerance of selected lines was tested under submergence stress and anaerobic germination conditions, and lines tolerant to each stress condition were identified through phenotypic and gene expression analyses. The Ciherang-Sub1 + AG1 + Pi9 (CSA-Pi9) line showed similar agronomic performance to its recurrent parent, CSA, but had significantly reduced chalkiness in field trials conducted in temperate regions. Unexpectedly, the CSA-Pi9 line also showed salinity tolerance. Thus, the breeding line newly developed in this study, CSA-Pi9, functioned under stress conditions, in which Sub1, AG1, and Pi9 play a role and had superior grain quality traits compared to its recurrent parent in temperate regions. We speculate that CSA-Pi9 will enable the establishment of climate-resilient rice cropping systems, particularly in East Asia.
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Affiliation(s)
- Na-Hyun Shin
- Department of Integrative Biological Sciences and Industry, College of Life Sciences, Sejong University, Seoul, 05006, Korea
| | - Jae-Hyuk Han
- Department of Integrative Biological Sciences and Industry, College of Life Sciences, Sejong University, Seoul, 05006, Korea
| | - Kieu Thi Xuan Vo
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Gyeonggi-do, 17104, Korea
| | - Jeonghwan Seo
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463, Korea
- Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, Korea
| | - Ian Paul Navea
- Department of Integrative Biological Sciences and Industry, College of Life Sciences, Sejong University, Seoul, 05006, Korea
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Banos, Philippines
| | - Soo-Cheul Yoo
- Department of Plant Life and Environmental Science, Hankyong National University, Anseong, Gyeonggi-do, 17579, Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Gyeonggi-do, 17104, Korea.
| | - Joong Hyoun Chin
- Department of Integrative Biological Sciences and Industry, College of Life Sciences, Sejong University, Seoul, 05006, Korea.
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Beerelli K, Balakrishnan D, Addanki KR, Surapaneni M, Rao Yadavalli V, Neelamraju S. Mapping of QTLs for Yield Traits Using F 2:3:4 Populations Derived From Two Alien Introgression Lines Reveals qTGW8.1 as a Consistent QTL for Grain Weight From Oryza nivara. FRONTIERS IN PLANT SCIENCE 2022; 13:790221. [PMID: 35356124 PMCID: PMC8959756 DOI: 10.3389/fpls.2022.790221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
Wild introgressions play a crucial role in crop improvement by transferring important novel alleles and broadening allelic diversity of cultivated germplasm. In this study, two stable backcross alien introgression lines 166s and 14s derived from Swarn/Oryza nivara IRGC81848 were used as parents to generate populations to map quantitative trait loci (QTLs) for yield-related traits. Field evaluation of yield-related traits in F2, F3, and F4 population was carried out in normal irrigated conditions during the wet season of 2015 and dry seasons of 2016 and 2018, respectively. Plant height, tiller number, productive tiller number, total dry matter, and harvest index showed a highly significant association to single plant yield in F2, F3, and F4. In all, 21, 30, and 17 QTLs were identified in F2, F2:3, and F2:4, respectively, for yield-related traits. QTLs qPH6.1 with 12.54% phenotypic variance (PV) in F2, qPH1.1 with 13.01% PV, qTN6.1 with 10.08% PV in F2:3, and qTGW6.1 with 15.19% PV in F2:4 were identified as major effect QTLs. QTLs qSPY4.1 and qSPY6.1 were detected for grain yield in F2 and F2:3 with PV 8.5 and 6.7%, respectively. The trait enhancing alleles of QTLs qSPY4.1, qSPY6.1, qPH1.1, qTGW6.1, qTGW8.1, qGN4.1, and qTDM5.1 were from O. nivara. QTLs of the yield contributing traits were found clustered in the same chromosomal region. qTGW8.1 was identified in a 2.6 Mb region between RM3480 and RM3452 in all three generations with PV 6.1 to 9.8%. This stable and consistent qTGW8.1 allele from O. nivara can be fine mapped for identification of causal genes. From this population, lines C212, C2124, C2128, and C2143 were identified with significantly higher SPY and C2103, C2116, and C2117 had consistently higher thousand-grain weight values than both the parents and Swarna across the generations and are useful in gene discovery for target traits and further crop improvement.
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Affiliation(s)
- Kavitha Beerelli
- National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, India
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - Divya Balakrishnan
- National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Krishnam Raju Addanki
- National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, India
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - Malathi Surapaneni
- National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | | | - Sarla Neelamraju
- National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, India
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Yu S, Ali J, Zhou S, Ren G, Xie H, Xu J, Yu X, Zhou F, Peng S, Ma L, Yuan D, Li Z, Chen D, Zheng R, Zhao Z, Chu C, You A, Wei Y, Zhu S, Gu Q, He G, Li S, Liu G, Liu C, Zhang C, Xiao J, Luo L, Li Z, Zhang Q. From Green Super Rice to green agriculture: Reaping the promise of functional genomics research. MOLECULAR PLANT 2022; 15:9-26. [PMID: 34883279 DOI: 10.1016/j.molp.2021.12.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 06/13/2023]
Abstract
Producing sufficient food with finite resources to feed the growing global population while having a smaller impact on the environment has always been a great challenge. Here, we review the concept and practices of Green Super Rice (GSR) that have led to a paradigm shift in goals for crop genetic improvement and models of food production for promoting sustainable agriculture. The momentous achievements and global deliveries of GSR have been fueled by the integration of abundant genetic resources, functional gene discoveries, and innovative breeding techniques with precise gene and whole-genome selection and efficient agronomic management to promote resource-saving, environmentally friendly crop production systems. We also provide perspectives on new horizons in genomic breeding technologies geared toward delivering green and nutritious crop varieties to further enhance the development of green agriculture and better nourish the world population.
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Affiliation(s)
- Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jauhar Ali
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Shaochuan Zhou
- Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Guangjun Ren
- Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Huaan Xie
- Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jianlong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinqiao Yu
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Fasong Zhou
- China National Seed Group Co., Ltd, Beijing, China
| | - Shaobing Peng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Liangyong Ma
- China National Rice Research Institute, Hangzhou, China
| | | | - Zefu Li
- Anhui Academy of Agricultural Sciences, Hefei, China
| | - Dazhou Chen
- Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | | | | | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Aiqing You
- Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yu Wei
- Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Susong Zhu
- Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Qiongyao Gu
- Yunnan Academy of Agricultural Sciences, Kunming, China
| | | | - Shigui Li
- Sichuan Agricultural University, Chengdu, China
| | - Guifu Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Changhua Liu
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Chaopu Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai, China.
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
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7
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Radha B, Sunitha NC, Sah RP, T P MA, Krishna GK, Umesh DK, Thomas S, Anilkumar C, Upadhyay S, Kumar A, Ch L N M, S B, Marndi BC, Siddique KHM. Physiological and molecular implications of multiple abiotic stresses on yield and quality of rice. FRONTIERS IN PLANT SCIENCE 2022; 13:996514. [PMID: 36714754 PMCID: PMC9874338 DOI: 10.3389/fpls.2022.996514] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 12/05/2022] [Indexed: 05/12/2023]
Abstract
Abiotic stresses adversely affect rice yield and productivity, especially under the changing climatic scenario. Exposure to multiple abiotic stresses acting together aggravates these effects. The projected increase in global temperatures, rainfall variability, and salinity will increase the frequency and intensity of multiple abiotic stresses. These abiotic stresses affect paddy physiology and deteriorate grain quality, especially milling quality and cooking characteristics. Understanding the molecular and physiological mechanisms behind grain quality reduction under multiple abiotic stresses is needed to breed cultivars that can tolerate multiple abiotic stresses. This review summarizes the combined effect of various stresses on rice physiology, focusing on grain quality parameters and yield traits, and discusses strategies for improving grain quality parameters using high-throughput phenotyping with omics approaches.
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Affiliation(s)
- Beena Radha
- Department of Plant Physiology, Kerala Agricultural University-College of Agriculture, Vellayani, Thiruvananthapuram, Kerala, India
| | | | - Rameswar P Sah
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Md Azharudheen T P
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - G K Krishna
- Department of Plant Physiology, Kerala Agricultural University-College of Agriculture, Thrissur, Kerala, India
| | - Deepika Kumar Umesh
- Mulberry Breeding & Genetics Section, Central Sericultural Research and Training Institute-Berhampore, Central Silk Board, Murshidabad, West Bengal, India
| | - Sini Thomas
- Department of Plant Physiology, Kerala Agricultural University-Regional Agricultural Research Station, Kumarakom, Kerala, India
| | - Chandrappa Anilkumar
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Sameer Upadhyay
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Awadhesh Kumar
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Manikanta Ch L N
- Department of Plant Physiology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Behera S
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Bishnu Charan Marndi
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Kadambot H M Siddique
- The University of Western Australia Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
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Sandhu N, Pruthi G, Prakash Raigar O, Singh MP, Phagna K, Kumar A, Sethi M, Singh J, Ade PA, Saini DK. Meta-QTL Analysis in Rice and Cross-Genome Talk of the Genomic Regions Controlling Nitrogen Use Efficiency in Cereal Crops Revealing Phylogenetic Relationship. Front Genet 2021; 12:807210. [PMID: 34992638 PMCID: PMC8724540 DOI: 10.3389/fgene.2021.807210] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
The phenomenal increase in the use of nitrogenous fertilizers coupled with poor nitrogen use efficiency is among the most important threats to the environment, economic, and social health. During the last 2 decades, a number of genomic regions associated with nitrogen use efficiency (NUE) and related traits have been reported by different research groups, but none of the stable and major effect QTL have been utilized in the marker-assisted introgression/pyramiding program. Compiling the data available in the literature could be very useful in identifying stable and major effect genomic regions associated with the root and NUE-related trait improving the rice grain yield. In the present study, we performed meta-QTL analysis on 1,330 QTL from 29 studies published in the past 2 decades. A total of 76 MQTL with a stable effect over different genetic backgrounds and environments were identified. The significant reduction in the confidence interval of the MQTL compared to the initial QTL resulted in the identification of annotated and putative candidate genes related to the traits considered in the present study. A hot spot region associated with correlated traits on chr 1, 4, and 8 and candidate genes associated with nitrate transporters, nitrogen content, and ammonium uptake on chromosomes 2, 4, 6, and 8 have been identified. The identified MQTL, putative candidate genes, and their orthologues were validated on our previous studies conducted on rice and wheat. The research-based interventions such as improving nitrogen use efficiency via identification of major genomic regions and candidate genes can be a plausible, simple, and low-cost solution to address the challenges of the crop improvement program.
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Affiliation(s)
| | | | | | | | - Kanika Phagna
- Indian Institute of Science Education and Research, Berhampur, India
| | - Aman Kumar
- Punjab Agricultural University, Ludhiana, India
| | - Mehak Sethi
- Punjab Agricultural University, Ludhiana, India
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9
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Shariatipour N, Heidari B, Tahmasebi A, Richards C. Comparative Genomic Analysis of Quantitative Trait Loci Associated With Micronutrient Contents, Grain Quality, and Agronomic Traits in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:709817. [PMID: 34712248 PMCID: PMC8546302 DOI: 10.3389/fpls.2021.709817] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/06/2021] [Indexed: 05/02/2023]
Abstract
Comparative genomics and meta-quantitative trait loci (MQTLs) analysis are important tools for the identification of reliable and stable QTLs and functional genes controlling quantitative traits. We conducted a meta-analysis to identify the most stable QTLs for grain yield (GY), grain quality traits, and micronutrient contents in wheat. A total of 735 QTLs retrieved from 27 independent mapping populations reported in the last 13 years were used for the meta-analysis. The results showed that 449 QTLs were successfully projected onto the genetic consensus map which condensed to 100 MQTLs distributed on wheat chromosomes. This consolidation of MQTLs resulted in a three-fold reduction in the confidence interval (CI) compared with the CI for the initial QTLs. Projection of QTLs revealed that the majority of QTLs and MQTLs were in the non-telomeric regions of chromosomes. The majority of micronutrient MQTLs were located on the A and D genomes. The QTLs of thousand kernel weight (TKW) were frequently associated with QTLs for GY and grain protein content (GPC) with co-localization occurring at 55 and 63%, respectively. The co- localization of QTLs for GY and grain Fe was found to be 52% and for QTLs of grain Fe and Zn, it was found to be 66%. The genomic collinearity within Poaceae allowed us to identify 16 orthologous MQTLs (OrMQTLs) in wheat, rice, and maize. Annotation of promising candidate genes (CGs) located in the genomic intervals of the stable MQTLs indicated that several CGs (e.g., TraesCS2A02G141400, TraesCS3B02G040900, TraesCS4D02G323700, TraesCS3B02G077100, and TraesCS4D02G290900) had effects on micronutrients contents, yield, and yield-related traits. The mapping refinements leading to the identification of these CGs provide an opportunity to understand the genetic mechanisms driving quantitative variation for these traits and apply this information for crop improvement programs.
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Affiliation(s)
- Nikwan Shariatipour
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Bahram Heidari
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Ahmad Tahmasebi
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Christopher Richards
- USDA ARS National Laboratory for Genetic Resources Preservation, Fort Collins, CO, United States
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10
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Sevanthi AM, Sinha SK, V S, Rani M, Saini MR, Kumari S, Kaushik M, Prakash C, K V, Singh GP, Mohapatra T, Mandal PK. Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in Rice. RICE (NEW YORK, N.Y.) 2021; 14:49. [PMID: 34089405 PMCID: PMC8179884 DOI: 10.1186/s12284-021-00487-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 05/05/2021] [Indexed: 05/19/2023]
Abstract
We report here the genome-wide changes resulting from low N (N-W+), low water (N+W-)) and dual stresses (N-W-) in root and shoot tissues of two rice genotypes, namely, IR 64 (IR64) and Nagina 22 (N22), and their association with the QTLs for nitrogen use efficiency. For all the root parameters, except for root length under N-W+, N22 performed better than IR64. Chlorophyll a, b and carotenoid content were higher in IR64 under N+W+ treatment and N-W+ and N+W- stresses; however, under dual stress, N22 had higher chlorophyll b content. While nitrite reductase, glutamate synthase (GS) and citrate synthase assays showed better specific activity in IR64, glutamate dehydrogenase showed better specific activity in N22 under dual stress (N-W-); the other N and C assimilating enzymes showed similar but low specific activities in both the genotypes. A total of 8926 differentially expressed genes (DEGs) were identified compared to optimal (N+W+) condition from across all treatments. While 1174, 698 and 903 DEGs in IR64 roots and 1197, 187 and 781 in N22 roots were identified, nearly double the number of DEGs were found in the shoot tissues; 3357, 1006 and 4005 in IR64 and 4004, 990 and 2143 in N22, under N-W+, N+W- and N-W- treatments, respectively. IR64 and N22 showed differential expression in 15 and 11 N-transporter genes respectively, under one or more stress treatments, out of which four showed differential expression also in N+W- condition. The negative regulators of N- stress, e.g., NIGT1, OsACTPK1 and OsBT were downregulated in IR64 while in N22, OsBT was not downregulated. Overall, N22 performed better under dual stress conditions owing to its better root architecture, chlorophyll and porphyrin synthesis and oxidative stress management. We identified 12 QTLs for seed and straw N content using 253 recombinant inbred lines derived from IR64 and N22 and a 5K SNP array. The QTL hotspot region on chromosome 6 comprised of 61 genes, of which, five were DEGs encoding for UDP-glucuronosyltransferase, serine threonine kinase, anthocyanidin 3-O-glucosyltransferase, and nitrate induced proteins. The DEGs, QTLs and candidate genes reported in this study can serve as a major resource for both rice improvement and functional biology.
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Affiliation(s)
| | - Subodh Kumar Sinha
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Sureshkumar V
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Manju Rani
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Manish Ranjan Saini
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Sapna Kumari
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Megha Kaushik
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Chandra Prakash
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Venkatesh K
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - G P Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Trilochan Mohapatra
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
- Indian Council of Agricultural Research, Krishi Bhavan, New Delhi, 110001, India
| | - Pranab Kumar Mandal
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.
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11
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Shen C, Chen K, Cui Y, Chen J, Mi X, Zhu S, Zhu Y, Ali J, Ye G, Li Z, Xu J. QTL Mapping and Favorable Allele Mining of Nitrogen Deficiency Tolerance Using an Interconnected Breeding Population in Rice. Front Genet 2021; 12:616428. [PMID: 33889173 PMCID: PMC8056011 DOI: 10.3389/fgene.2021.616428] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/04/2021] [Indexed: 02/04/2023] Open
Abstract
Nitrogen is one of the most important nutrients for rice growth and development. Breeding of nitrogen deficiency tolerance (NDT) variety is considered to be the most economic measure to solve the constrain of low nitrogen stress on grain yield in rice. An interconnected breeding (IB) population of 497 lines developed using Huanghuazhan (HHZ) as the recurrent parent and eight elite lines as the donor parents were tested for five traits including grain yield, biomass, harvest index, thousand grain weight, and spikelet fertility under two nitrogen treatments in three growing seasons. Association analysis using 7,388 bins generated by sequencing identified a total of 14, 14, and 12 QTLs for the five traits under low nitrogen (LN), normal nitrogen (NN), and LN/NN conditions, respectively, across three seasons. Favorable alleles were dissected for the 40 QTLs at the 10 NDT regions, and OM1723 was considered as the most important parent with the highest frequency of favorable alleles contributing to NDT-related traits. Six superior lines all showed significantly higher GY in LN environments and similar GY under NN environments except for H10. Substitution mapping using near-isogenic introgression lines delimited the qTGW2-1, which was identified on chromosome 2 under LN, NN, and LN/NN conditions into two QTLs, which were located in the two regions of about 200 and 350 kb with different favorable alleles. The bins 16, 1301, 1465, 1486, 3464, and 6249 harbored the QTLs for NDT detected in this study, and the QTLs/genes previously identified for NDT or nitrogen use efficiency (NUE) could be used for enhancing NDT and NUE by marker-assisted selection (MAS).
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Affiliation(s)
- Congcong Shen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kai Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yanru Cui
- College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Jiantao Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xuefei Mi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shuangbin Zhu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yajun Zhu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jauhar Ali
- International Rice Research Institute, Los Baños, Philippines
| | - Guoyou Ye
- International Rice Research Institute, Los Baños, Philippines
| | - Zhikang Li
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianlong Xu
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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12
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Reddy SH, Singhal RK, DaCosta MVJ, Kambalimath SK, Rajanna MP, Muthurajan R, Sevanthi AM, Mohapatra T, Sarla N, Chinnusamy V, S GK, Singh AK, Singh NK, Sharma RP, Pathappa N, Sheshshayee SM. Leaf mass area determines water use efficiency through its influence on carbon gain in rice mutants. PHYSIOLOGIA PLANTARUM 2020; 169:194-213. [PMID: 31912892 DOI: 10.1111/ppl.13062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 06/10/2023]
Abstract
Saving water and enhancing rice productivity are consensually the most important research goals globally. While increasing canopy cover would enhance growth rates by higher photosynthetic carbon gain, an accompanied increase in transpiration would have a negative impact on saving water as well as for sustainability under water-limited conditions. Increased water use efficiency (WUE) by virtue of higher carbon assimilatory capacity can significantly circumvent this trade-off. Here, we report leaf mass area (LMA) has an important canopy architecture trait which when combined with superior carboxylation efficiency (CE) would achieve higher water productivity in rice. A set of 130 ethyl methanesulfonate induced mutants of an upland cultivar Nagina-22 (N22), was screened for leaf morphological traits leading to the identification of mutants differing in LMA. The wild-type, N22, along with a selected low-LMA (380-4-3) and two high-LMA mutants (392-9-1 and 457-1-3), all with comparable total leaf area, were raised under well-watered (100% Field Capacity (FC)) and water-limited (60% FC) conditions. Low Δ13 C and a higher RuBisCO content in high-LMA mutants indicated higher carboxylation efficiency, leading to increased carbon gain. Single parent backcross populations developed by crossing high and the low-LMA mutants with N22, separately, were screened for LMA, Δ13 C and growth traits. Comparison of dry matter accumulation per unit leaf area among the progenies differing in LMA and Δ13 C reiterated the association of LMA with CE. Results illustrated that high-LMA when combined with higher CE (low Δ13 C) lead to increased WUE and growth rates.
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Affiliation(s)
| | - Rajesh Kumar Singhal
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
| | | | | | | | - Raveendran Muthurajan
- Center for Plant Molecular Biology, Tamil Nadu Agricultural University, Coimbatore, India
| | | | | | | | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Gopala Krishnan S
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ashok Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | | | | - Sreeman M Sheshshayee
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
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13
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Yu S, Ali J, Zhang C, Li Z, Zhang Q. Genomic Breeding of Green Super Rice Varieties and Their Deployment in Asia and Africa. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1427-1442. [PMID: 31915875 PMCID: PMC7214492 DOI: 10.1007/s00122-019-03516-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/17/2019] [Indexed: 05/22/2023]
Abstract
KEY MESSAGE The "Green Super Rice" (GSR) project aims to fundamentally transform crop production techniques and promote the development of green agriculture based on functional genomics and breeding of GSR varieties by whole-genome breeding platforms. Rice (Oryza sativa L.) is one of the leading food crops of the world, and the safe production of rice plays a central role in ensuring food security. However, the conflicts between rice production and environmental resources are becoming increasingly acute. For this reason, scientists in China have proposed the concept of Green Super Rice for promoting resource-saving and environment-friendly rice production, while still achieving a yield increase and quality improvement. GSR is becoming one of the major goals for agricultural research and crop improvement worldwide, which aims to mine and use vital genes associated with superior agronomic traits such as high yield, good quality, nutrient efficiency, and resistance against insects and stresses; establish genomic breeding platforms to breed and apply GSR; and set up resource-saving and environment-friendly cultivation management systems. GSR has been introduced into eight African and eight Asian countries and has contributed significantly to rice cultivation and food security in these countries. This article mainly describes the GSR concept and recent research progress, as well as the significant achievements in GSR breeding and its application.
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Affiliation(s)
- Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jauhar Ali
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Chaopu Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
- College of Agronomy, Anhui Agricultural University, Hefei, China.
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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14
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Liu C, Ding S, Zhang A, Hong K, Jiang H, Yang S, Ruan B, Zhang B, Dong G, Guo L, Zeng D, Qian Q, Gao Z. Development of nutritious rice with high zinc/selenium and low cadmium in grains through QTL pyramiding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:349-359. [PMID: 31957138 DOI: 10.1111/jipb.12909] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
Enriching zinc (Zn) and selenium (Se) levels, while reducing cadmium (Cd) concentration in rice grains is of great benefit for human diet and health. Large natural variations in grain Zn, Se, and Cd concentrations in different rice accessions enable Zn/Se-biofortification and Cd-minimization through molecular breeding. Here, we report the development of new elite varieties by pyramiding major quantitative trait loci (QTLs) that significantly contribute to high Zn/Se and low Cd accumulation in grains. A chromosome segment substitution line CSSLGCC7 with the PA64s-derived GCC7 allele in the 93-11 background, exhibited steadily higher Mn and lower Cd concentrations in grains than those of 93-11. This elite chromosome segment substitution line (CSSL) was used as the core breeding material to cross with CSSLs harboring other major QTLs for essential mineral elements, especially CSSLGZC6 for grain Zn concentration and CSSLGSC5 for grain Se concentration. The CSSLGCC7+GZC6 and CSSLGCC7+GSC5 exhibited lower Cd concentration with higher Zn and Se concentrations in grains, respectively. Our study thus provides elite materials for rice breeding targeting high Zn/Se and low Cd concentrations in grains.
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Affiliation(s)
- Chaolei Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Shilin Ding
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Anpeng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Kai Hong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Hongzhen Jiang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Shenglong Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Banpu Ruan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Bin Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
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15
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Najeeb S, Ali J, Mahender A, Pang Y, Zilhas J, Murugaiyan V, Vemireddy LR, Li Z. Identification of main-effect quantitative trait loci (QTLs) for low-temperature stress tolerance germination- and early seedling vigor-related traits in rice ( Oryza sativa L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2020; 40:10. [PMID: 31975784 PMCID: PMC6944268 DOI: 10.1007/s11032-019-1090-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 12/12/2019] [Indexed: 05/09/2023]
Abstract
An attempt was made in the current study to identify the main-effect and co-localized quantitative trait loci (QTLs) for germination and early seedling growth traits under low-temperature stress (LTS) conditions in rice. The plant material used in this study was an early backcross population of 230 introgression lines (ILs) in BCIF7 generation derived from the Weed Tolerant Rice-1 (WTR-1) (as the recipient) and Haoannong (HNG) (as the donor). Genetic analyses of LTS tolerance revealed a total of 27 main-effect quantitative trait loci (M-QTLs) mapped on 12 chromosomes. These QTLs explained more than 10% of phenotypic variance (PV), and average PV of 12.71% while employing 704 high-quality SNP markers. Of these 27 QTLs distributed on 12 chromosomes, 11 were associated with low-temperature germination (LTG), nine with low-temperature germination stress index (LTGS), five with root length stress index (RLSI), and two with biomass stress index (BMSI) QTLs, shoot length stress index (SLSI) and root length stress index (RLSI), seven with seed vigor index (SVI), and single QTL with root length (RL). Among them, five significant major QTLs (qLTG(I) 1 , qLTGS(I) 1-2 , qLTG(I) 5 , qLTGS(I) 5 , and qLTG(I) 7 ) mapped on chromosomes 1, 5, and 7 were associated with LTG and LTGS traits and the PV explained ranged from 16 to 23.3%. The genomic regions of these QTLs were co-localized with two to six QTLs. Most of the QTLs were growth stage-specific and found to harbor QTLs governing multiple traits. Eight chromosomes had more than four QTLs and were clustered together and designated as promising LTS tolerance QTLs (qLTTs), as qLTT 1 , qLTT 2 , qLTT 3 , qLTT 5 , qLTT 6 , qLTT 8 , qLTT 9 , and qLTT 11 . A total of 16 putative candidate genes were identified in the major M-QTLs and co-localized QTL regions distributed on different chromosomes. Overall, these significant genomic regions of M-QTLs are responsible for multiple traits and this suggested that these could serve as the best predictors of LTS tolerance at germination and early seedling growth stages. Furthermore, it is necessary to fine-map these regions and to find functional markers for marker-assisted selection in rice breeding programs for cold tolerance.
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Affiliation(s)
- S. Najeeb
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Science & Technology (SKAUST), Khudwani, Kashmir 190025 India
| | - J. Ali
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
| | - A. Mahender
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
| | - Y.L. Pang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018 People’s Republic of China
| | - J. Zilhas
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
| | - V. Murugaiyan
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
- Plant Nutrition, Institute of Crop Sciences and Resource Conservation (INRES), University of Bonn, 53012 Bonn, Germany
| | - Lakshminarayana R. Vemireddy
- Department of Genetics and Plant Breeding, Sri Venkateswara Agricultural College, Acharya NG Ranga Agricultural University, Tirupati, Andhra Pradesh 517502 India
| | - Z. Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081 People’s Republic of China
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16
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Mahender A, Ali J, Prahalada GD, Sevilla MAL, Balachiranjeevi CH, Md J, Maqsood U, Li Z. Genetic dissection of developmental responses of agro-morphological traits under different doses of nutrient fertilizers using high-density SNP markers. PLoS One 2019; 14:e0220066. [PMID: 31335882 PMCID: PMC6650078 DOI: 10.1371/journal.pone.0220066] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 07/07/2019] [Indexed: 11/19/2022] Open
Abstract
The production and productivity of rice (Oryza sativa L.) are primarily influenced by the application of the critical nutrients nitrogen (N), phosphorus (P), and potassium (K). However, excessive application of these fertilizers is detrimental to the environment and increases the cost of production. Hence, there is a need to develop varieties that simultaneously increase yields under both optimal and suboptimal rates of fertilizer application by maximizing nutrient use efficiency (NuUE). To unravel the hidden genetic variation and understand the molecular and physiological mechanisms of NuUE, three different mapping populations (MPs; BC1F5) derived from three donors (Haoannong, Cheng-Hui 448, and Zhong 413) and recipient Weed Tolerant Rice 1 were developed. A total of three favorable agronomic traits (FATs) were considered as the measure of NuUE. Analysis of variance and descriptive statistics indicated the existence of genetic variation for NuUE and quantitative inheritance of FATs. The genotypic data from single-nucleotide polymorphism (SNP) markers from Tunable Genotyping-By-Sequencing (tGBS) and phenotypic values were used for locating the genomic regions conferring NuUE. A total of 19 quantitative trait loci (QTLs) were detected, out of which 11 QTLs were putative on eight chromosomes, which individually explained 17.02% to 34.85% of the phenotypic variation. Notably, qLC-II_1 and qLC-II_11 detected at zero fertilizer application showed higher performance for LC under zero percentage of NPK fertilizer. The remarkable findings of the present study are that the detected QTLs were associated in building tolerance to low/no nutrient application and six candidate genes on chromosomes 2 and 5 within these putative QTLs were found associated with low nutrient tolerance and related to several physiological and metabolic pathways involved in abiotic stress tolerance. The identified superior introgressed lines (ILs) and trait-associated genetic regions can be effectively used in marker-assisted selection (MAS) for NuUE breeding programs.
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Affiliation(s)
- Anumalla Mahender
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - Jauhar Ali
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
- * E-mail:
| | - G. D. Prahalada
- Strategic Innovation Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - Ma. Anna Lynn Sevilla
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - C. H. Balachiranjeevi
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - Jamaloddin Md
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Manila, Philippines
| | - Umer Maqsood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Pakistan
| | - Zhikang Li
- Chinese Academy of Agricultural Sciences, Haidian District, P.R. China
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17
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Liang Y, Meng L, Lin X, Cui Y, Pang Y, Xu J, Li Z. QTL and QTL networks for cold tolerance at the reproductive stage detected using selective introgression in rice. PLoS One 2018; 13:e0200846. [PMID: 30222760 PMCID: PMC6141068 DOI: 10.1371/journal.pone.0200846] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 05/17/2018] [Indexed: 11/18/2022] Open
Abstract
Low temperature stress is one of the major abiotic stresses limiting the productivity of Geng (japonica) rice grown the temperate regions as well as in tropical high lands worldwide. To develop rice varieties with improved cold tolerance (CT) at the reproductive stage, 84 BC2 CT introgression lines (ILs) were developed from five populations through backcross breeding. These CT ILs plus 310 random ILs from the same BC populations were used for dissecting genetic networks underlying CT in rice by detecting QTLs and functional genetic units (FGUs) contributing to CT. Seventeen major QTLs for CT were identified using five selective introgression populations and the method of segregation distortion. Of them, three QTLs were confirmed using the random populations and seven others locate in the regions with previously reported CT QTLs/genes. Using multi-locus probability tests and linkage disequilibrium (LD) analyses, 46 functional genetic units (FGUs) (37 single loci and 9 association groups or AGs) distributed in 37 bins (~20%) across the rice genome for CT were detected. Together, each of the CT loci (bins) was detected in 1.7 populations, including 18 loci detected in two or more populations. Putative genetic networks (multi-locus structures) underlying CT were constructed based on strong non-random associations between or among donor alleles at the unlinked CT loci/FGUs identified in the CT ILs, suggesting the presence of strong epistasis among the detected CT loci. Our results demonstrated the power and usefulness of using selective introgression for simultaneous improvement and genetic dissection of complex traits such as CT in rice.
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Affiliation(s)
- Yuntao Liang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Lijun Meng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiuyun Lin
- Rice Research Institute, Jilin Academy of Agricultural Sciences, Jilin, China
| | - Yanru Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunlong Pang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianlong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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18
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Ali J, Jewel ZA, Mahender A, Anandan A, Hernandez J, Li Z. Molecular Genetics and Breeding for Nutrient Use Efficiency in Rice. Int J Mol Sci 2018; 19:E1762. [PMID: 29899204 PMCID: PMC6032200 DOI: 10.3390/ijms19061762] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/26/2018] [Accepted: 06/01/2018] [Indexed: 11/17/2022] Open
Abstract
In the coming decades, rice production needs to be carried out sustainably to keep the balance between profitability margins and essential resource input costs. Many fertilizers, such as N, depend primarily on fossil fuels, whereas P comes from rock phosphates. How long these reserves will last and sustain agriculture remains to be seen. Therefore, current agricultural food production under such conditions remains an enormous and colossal challenge. Researchers have been trying to identify nutrient use-efficient varieties over the past few decades with limited success. The concept of nutrient use efficiency is being revisited to understand the molecular genetic basis, while much of it is not entirely understood yet. However, significant achievements have recently been observed at the molecular level in nitrogen and phosphorus use efficiency. Breeding teams are trying to incorporate these valuable QTLs and genes into their rice breeding programs. In this review, we seek to identify the achievements and the progress made so far in the fields of genetics, molecular breeding and biotechnology, especially for nutrient use efficiency in rice.
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Affiliation(s)
- Jauhar Ali
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines.
| | - Zilhas Ahmed Jewel
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines.
| | - Anumalla Mahender
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines.
| | - Annamalai Anandan
- ICAR-National Rice Research Institute, Cuttack, Odisha 753006, India.
| | - Jose Hernandez
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, Laguna 4031, Philippines.
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, China.
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Tao Y, Niu Y, Wang Y, Chen T, Naveed SA, Zhang J, Xu J, Li Z. Genome-wide association mapping of aluminum toxicity tolerance and fine mapping of a candidate gene for Nrat1 in rice. PLoS One 2018; 13:e0198589. [PMID: 29894520 PMCID: PMC5997306 DOI: 10.1371/journal.pone.0198589] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 05/22/2018] [Indexed: 11/30/2022] Open
Abstract
Aluminum (Al) stress is becoming the major limiting factor in crop production in acidic soils. Rice has been reported as the most Al-tolerant crop and the capacity of Al toxicity tolerance is generally evaluated by comparing root growth under Al stress. Here, we performed an association mapping of Al toxicity tolerance using a core collection of 211 indica rice accessions with 700 K high quality SNP data. A total of 21 putative QTL affecting shoot height (SH), root length (RL), shoot fresh weight (SFW), shoot dry weight (SDW), root dry weight (RDW) and shoot water content (SWC) were identified at seedling stage, including three QTL detected only under control condition, eight detected only under Al stress condition, ten simultaneously detected in both control and Al stress conditions, and seven were identified by stress tolerance index of their corresponding traits. Total of 21 candidate genes for 7 important QTL regions associated with Al toxicity tolerance were identified based on combined haplotype analysis and functional annotation, and the most likely candidate gene(s) for each important QTL were also discussed. Also a candidate gene Nrat1 on chromosome 2 was further fine-mapped using BSA-seq and linkage analysis in the F2 population derived from the cross of Al tolerant accession CC105 and super susceptible accession CC180. A new non-synonymous SNP variation was observed at Nrat1 between CC105 and CC180, which resulted in an amino-acid substitution from Ala (A) in CC105 to Asp (D) in CC180. Haplotype analysis of Nrat1 using 327 3K RGP accessions indicated that minor allele variations in aus and indica subpopulations decreased Al toxicity tolerance in rice. The candidate genes identified in this study provide valuable information for improvement of Al toxicity tolerance in rice. Our research indicated that minor alleles are important for QTL mapping and its application in rice breeding when natural gene resources are used.
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Affiliation(s)
- Yonghong Tao
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanan Niu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yun Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianxiao Chen
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shahzad Amir Naveed
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Jianlong Xu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Institute of Breeding and Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Institute of Breeding and Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, China
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