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Bhandari A, Sandhu N, Bartholome J, Cao-Hamadoun TV, Ahmadi N, Kumari N, Kumar A. Genome-Wide Association Study for Yield and Yield Related Traits under Reproductive Stage Drought in a Diverse indica-aus Rice Panel. RICE (NEW YORK, N.Y.) 2020; 13:53. [PMID: 32761553 PMCID: PMC7410978 DOI: 10.1186/s12284-020-00406-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/02/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Reproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for ten agronomic traits including yield and yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers. RESULTS The study identified a total of 219 significant MTAs for 10 traits and candidate gene analysis within a 200 kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related and other agronomic traits except for flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought. CONCLUSION These results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.
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Affiliation(s)
- Aditi Bhandari
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- Banasthali Vidyapith, Banasthali, 304022, India
| | - Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- Punjab Agricultural University, Ludhiana, 141004, India
| | - Jérôme Bartholome
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | - Tuong-Vi Cao-Hamadoun
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | - Nourollah Ahmadi
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | | | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines.
- IRRI South Asia Regional Centre, Varanasi, 221006, India.
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Varshney RK, Sinha P, Singh VK, Kumar A, Zhang Q, Bennetzen JL. 5Gs for crop genetic improvement. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:190-196. [PMID: 32005553 PMCID: PMC7450269 DOI: 10.1016/j.pbi.2019.12.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/22/2019] [Accepted: 12/03/2019] [Indexed: 05/20/2023]
Abstract
Here we propose a 5G breeding approach for bringing much-needed disruptive changes to crop improvement. These 5Gs are Genome assembly, Germplasm characterization, Gene function identification, Genomic breeding (GB), and Gene editing (GE). In our view, it is important to have genome assemblies available for each crop and a deep collection of germplasm characterized at sequencing and agronomic levels for identification of marker-trait associations and superior haplotypes. Systems biology and sequencing-based mapping approaches can be used to identify genes involved in pathways leading to the expression of a trait, thereby providing diagnostic markers for target traits. These genes, markers, haplotypes, and genome-wide sequencing data may be utilized in GB and GE methodologies in combination with a rapid cycle breeding strategy.
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Affiliation(s)
- Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
| | - Pallavi Sinha
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Vikas K Singh
- International Rice Research Institute, South Asia Hub, ICRISAT, Hyderabad, 502324, India
| | - Arvind Kumar
- IRRI South Asia Regional Center, NSRTC Campus, G.T. Road, Collectry Farm, P.O. Industrial Estate, Varanasi, 221006, India
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Seo J, Lee SM, Han JH, Shin NH, Lee YK, Kim B, Chin JH, Koh HJ. Characterization of the Common Japonica-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice ( Oryza sativa L.). Genes (Basel) 2020; 11:genes11050562. [PMID: 32443496 PMCID: PMC7290844 DOI: 10.3390/genes11050562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 01/18/2023] Open
Abstract
The inter-subspecific crossing between indica and japonica subspecies in rice have been utilized to improve the yield potential of temperate rice. In this study, a comparative study of the genomic regions in the eight high-yielding varieties (HYVs) was conducted with those of the four non-HYVs. The Next-Generation Sequencing (NGS) mapping on the Nipponbare reference genome identified a total of 14 common genomic regions of japonica-originated alleles. Interestingly, the HYVs shared japonica-originated genomic regions on nine chromosomes, although they were developed through different breeding programs. A panel of 94 varieties was classified into four varietal groups with 38 single nucleotide polymorphism (SNP) markers from 38 genes residing in the japonica-originated genomic regions and 16 additional trait-specific SNPs. As expected, the japonica-originated genomic regions were only present in the japonica (JAP) and HYV groups, except for Chr4-1 and Chr4-2. The Wx gene, located within Chr6-1, was present in the HYV and JAP variety groups, while the yield-related genes were conserved as indica alleles in HYVs. The japonica-originated genomic regions and alleles shared by HYVs can be employed in molecular breeding programs to further develop the HYVs in temperate rice.
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Affiliation(s)
- Jeonghwan Seo
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea; (J.S.); (S.-M.L.); (Y.K.L.); (B.K.)
| | - So-Myeong Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea; (J.S.); (S.-M.L.); (Y.K.L.); (B.K.)
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, Korea
| | - Jae-Hyuk Han
- Department of Integrative Biological Sciences and Industry, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006, Korea; (J.-H.H.); (N.-H.S.)
| | - Na-Hyun Shin
- Department of Integrative Biological Sciences and Industry, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006, Korea; (J.-H.H.); (N.-H.S.)
| | - Yoon Kyung Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea; (J.S.); (S.-M.L.); (Y.K.L.); (B.K.)
| | - Backki Kim
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea; (J.S.); (S.-M.L.); (Y.K.L.); (B.K.)
| | - Joong Hyoun Chin
- Department of Integrative Biological Sciences and Industry, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006, Korea; (J.-H.H.); (N.-H.S.)
- Correspondence: (J.H.C.); (H.-J.K.)
| | - Hee-Jong Koh
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea; (J.S.); (S.-M.L.); (Y.K.L.); (B.K.)
- Correspondence: (J.H.C.); (H.-J.K.)
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Xu P, Yang J, Ma Z, Yu D, Zhou J, Tao D, Li Z. Identification and Validation of Aerobic Adaptation QTLs in Upland Rice. Life (Basel) 2020; 10:life10050065. [PMID: 32423169 PMCID: PMC7281610 DOI: 10.3390/life10050065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/30/2020] [Accepted: 05/13/2020] [Indexed: 12/23/2022] Open
Abstract
The aerobic adaptation of upland rice is considered as the key genetic difference between upland rice and lowland rice. Genetic dissection of the aerobic adaptation is important as the basis for improving drought tolerance and terrestrial adaptation by using the upland rice. We raised BC1-BC3 introgression lines (ILs) in lowland rice Minghui 63 (MH63) background. The QTLs of yield and yield-related traits were detected based on ILs under the aerobic and lowland environments, and then the yield-related QTLs were identified in a backcrossed inbred population of BC4F5 under aerobic condition. We further verified phenotypes of QTL near-isogenic lines. Finally, three QTLs responsible for increasing yield in aerobic environment were detected by multiple locations and generations, which were designated as qAER1, qAER3, and qAER9 (QTL of aerobic adaptation). The qAER1 and qAER9 were fine-mapped. We found that qAER1 and qAER9 controlled plant height and heading date, respectively; while both of them increased yields simultaneously by suitable plant height and heading date without delay in the aerobic environment. The phenotypic differences between lowland rice and upland rice in the aerobic environment further supported the above results. We pyramided the two QTLs as corresponding molecular modules in the irrigated lowland rice MH63 background, and successfully developed a new upland rice variety named as Zhongkexilu 2. This study will lay the foundation for using aerobic adaptation QTLs in rice breeding programs and for further cloning the key genes involved in aerobic adaptation.
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Affiliation(s)
- Peng Xu
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China;
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (J.Y.); (Z.M.); (D.Y.)
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China;
| | - Jun Yang
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (J.Y.); (Z.M.); (D.Y.)
| | - Zhenbing Ma
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (J.Y.); (Z.M.); (D.Y.)
| | - Diqiu Yu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (J.Y.); (Z.M.); (D.Y.)
| | - Jiawu Zhou
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China;
| | - Dayun Tao
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China;
- Correspondence: (D.T.); (Z.L.); Tel.: +86-871-6589-3754 (D.T.); +86-10-6273-1414 (Z.L.)
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China;
- Correspondence: (D.T.); (Z.L.); Tel.: +86-871-6589-3754 (D.T.); +86-10-6273-1414 (Z.L.)
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Hua K, Zhang J, Botella JR, Ma C, Kong F, Liu B, Zhu JK. Perspectives on the Application of Genome-Editing Technologies in Crop Breeding. MOLECULAR PLANT 2019; 12:1047-1059. [PMID: 31260812 DOI: 10.1016/j.molp.2019.06.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/23/2019] [Accepted: 06/24/2019] [Indexed: 05/20/2023]
Abstract
Most conventional and modern crop-improvement methods exploit natural or artificially induced genetic variations and require laborious characterization of the progenies of multiple generations derived from time-consuming genetic crosses. Genome-editing systems, in contrast, provide the means to rapidly modify genomes in a precise and predictable way, making it possible to introduce improvements directly into elite varieties. Here, we describe the range of applications available to agricultural researchers using existing genome-editing tools. In addition to providing examples of genome-editing applications in crop breeding, we discuss the technical and social challenges faced by breeders using genome-editing tools for crop improvement.
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Affiliation(s)
- Kai Hua
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jinshan Zhang
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jose Ramon Botella
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Changle Ma
- Shandong Provincial Key Lab of Plant Stress, School of Life Sciences, Shandong Normal University, Jinan, China
| | - Fanjiang Kong
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Baohui Liu
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA.
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