1
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Kabade PG, Dixit S, Singh UM, Alam S, Bhosale S, Kumar S, Singh SK, Badri J, Varma NRG, Chetia S, Singh R, Pradhan SK, Banerjee S, Deshmukh R, Singh SP, Kalia S, Sharma TR, Singh S, Bhardwaj H, Kohli A, Kumar A, Sinha P, Singh VK. SpeedFlower: a comprehensive speed breeding protocol for indica and japonica rice. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1051-1066. [PMID: 38070179 PMCID: PMC11022788 DOI: 10.1111/pbi.14245] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/10/2023] [Accepted: 11/13/2023] [Indexed: 04/18/2024]
Abstract
To increase rice yields and feed billions of people, it is essential to enhance genetic gains. However, the development of new varieties is hindered by longer generation times and seasonal constraints. To address these limitations, a speed breeding facility has been established and a robust speed breeding protocol, SpeedFlower is developed that allows growing 4-5 generations of indica and/or japonica rice in a year. Our findings reveal that a high red-to-blue (2R > 1B) spectrum ratio, followed by green, yellow and far-red (FR) light, along with a 24-h long day (LD) photoperiod for the initial 15 days of the vegetative phase, facilitated early flowering. This is further enhanced by 10-h short day (SD) photoperiod in the later stage and day and night temperatures of 32/30 °C, along with 65% humidity facilitated early flowering ranging from 52 to 60 days at high light intensity (800 μmol m-2 s-1). Additionally, the use of prematurely harvested seeds and gibberellic acid treatment reduced the maturity duration by 50%. Further, SpeedFlower was validated on a diverse subset of 198 rice accessions from 3K RGP panel encompassing all 12 distinct groups of Oryza sativa L. classes. Our results confirmed that using SpeedFlower one generation can be achieved within 58-71 days resulting in 5.1-6.3 generations per year across the 12 sub-groups. This breakthrough enables us to enhance genetic gain, which could feed half of the world's population dependent on rice.
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Affiliation(s)
- Pramod Gorakhanath Kabade
- International Rice Research InstituteLos BanosPhilippines
- IRRI South Asia Regional CentreVaranasiIndia
- Banaras Hindu University (BHU)VaranasiUttar PradeshIndia
| | - Shilpi Dixit
- International Rice Research InstituteLos BanosPhilippines
- IRRI South Asia Regional CentreVaranasiIndia
| | - Uma Maheshwar Singh
- International Rice Research InstituteLos BanosPhilippines
- IRRI South Asia Regional CentreVaranasiIndia
| | - Shamshad Alam
- International Rice Research InstituteLos BanosPhilippines
- IRRI South Asia HubHyderabadIndia
| | | | - Sanjay Kumar
- Banaras Hindu University (BHU)VaranasiUttar PradeshIndia
| | | | - Jyothi Badri
- Indian Institute of Rice Research (IIRR)HyderabadTelanganaIndia
| | | | - Sanjay Chetia
- Assam Agricultural University (AAU)TitabarAssamIndia
| | - Rakesh Singh
- National Bureau of Plant Genetic Resources (NBPGR)New DelhiIndia
| | | | - Shubha Banerjee
- Indira Gandhi Krishi Vishwavidyalaya (IGKV)RaipurChhattisgarhIndia
| | - Rupesh Deshmukh
- National Agri‐Food Biotechnology Institute (NABI)Mohali, ChandigarhIndia
- Present address:
Central University of Haryana (CUH)MahendragarhHaryanaIndia
| | | | - Sanjay Kalia
- Department of Biotechnology (DBT)CGO ComplexNew DelhiIndia
| | | | - Sudhanshu Singh
- International Rice Research InstituteLos BanosPhilippines
- IRRI South Asia Regional CentreVaranasiIndia
| | - Hans Bhardwaj
- International Rice Research InstituteLos BanosPhilippines
| | - Ajay Kohli
- International Rice Research InstituteLos BanosPhilippines
| | - Arvind Kumar
- International Rice Research InstituteLos BanosPhilippines
- IRRI South Asia Regional CentreVaranasiIndia
- Present address:
International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruTelanganaIndia
| | - Pallavi Sinha
- International Rice Research InstituteLos BanosPhilippines
- IRRI South Asia HubHyderabadIndia
| | - Vikas Kumar Singh
- International Rice Research InstituteLos BanosPhilippines
- IRRI South Asia Regional CentreVaranasiIndia
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2
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Henry A. A step forward in breeding for ratooning ability in rice. MOLECULAR PLANT 2024; 17:368-369. [PMID: 38238998 DOI: 10.1016/j.molp.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/07/2023] [Accepted: 01/12/2024] [Indexed: 02/19/2024]
Affiliation(s)
- Amelia Henry
- Rice Breeding Innovations Department, International Rice Research Institute, Los Baños, Laguna, Philippines.
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3
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Khanna A, Anumalla M, Ramos J, Cruz MTS, Catolos M, Sajise AG, Gregorio G, Dixit S, Ali J, Islam MR, Singh VK, Rahman MA, Khatun H, Pisano DJ, Bhosale S, Hussain W. Genetic gains in IRRI's rice salinity breeding and elite panel development as a future breeding resource. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:37. [PMID: 38294550 PMCID: PMC10830834 DOI: 10.1007/s00122-024-04545-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 01/05/2024] [Indexed: 02/01/2024]
Abstract
KEY MESSAGE Estimating genetic gains and formulating a future salinity elite breeding panel for rice pave the way for developing better high-yielding salinity tolerant lines with enhanced genetic gains. Genetic gain is a crucial parameter to check the breeding program's success and help optimize future breeding strategies for enhanced genetic gains. To estimate the genetic gains in IRRI's salinity breeding program and identify the best genotypes based on high breeding values for grain yield (kg/ha), we analyzed the historical data from the trials conducted in the IRRI, Philippines and Bangladesh. A two-stage mixed-model approach accounting for experimental design factors and a relationship matrix was fitted to obtain the breeding values for grain yield and estimate genetic trends. A positive genetic trend of 0.1% per annum with a yield advantage of 1.52 kg/ha was observed in IRRI, Philippines. In Bangladesh, we observed a genetic gain of 0.31% per annum with a yield advantage of 14.02 kg/ha. In the released varieties, we observed a genetic gain of 0.12% per annum with a 2.2 kg/ha/year yield advantage in the IRRI, Philippines. For the Bangladesh dataset, a genetic gain of 0.14% per annum with a yield advantage of 5.9 kg/ha/year was observed in the released varieties. Based on breeding values for grain yield, a core set of the top 145 genotypes with higher breeding values of > 2400 kg/ha in the IRRI, Philippines, and > 3500 kg/ha in Bangladesh with a reliability of > 0.4 were selected to develop the elite breeding panel. Conclusively, a recurrent selection breeding strategy integrated with novel technologies like genomic selection and speed breeding is highly required to achieve higher genetic gains in IRRI's salinity breeding programs.
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Affiliation(s)
- Apurva Khanna
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Mahender Anumalla
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Joie Ramos
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Ma Teresa Sta Cruz
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Margaret Catolos
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Andres Godwin Sajise
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Glenn Gregorio
- Southeast Asian Regional Center for Graduate Study and Research in Agriculture (SEARCA) and University of Philippines, 4031, Los Baños, Laguna, Philippines
| | - Shalabh Dixit
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Jauhar Ali
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Md Rafiqul Islam
- IRRI South Asia Regional Center (IRRI-SA Hub), Hyderabad, Telangana, 502324, India
| | - Vikas Kumar Singh
- IRRI South Asia Regional Center (IRRI-SA Hub), Hyderabad, Telangana, 502324, India
| | - Md Akhlasur Rahman
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur, 1701, Bangladesh
| | - Hasina Khatun
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur, 1701, Bangladesh
| | - Daniel Joseph Pisano
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Sankalp Bhosale
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines
| | - Waseem Hussain
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), 4031, Los Baños, Laguna, Philippines.
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4
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Seck F, Covarrubias-Pazaran G, Gueye T, Bartholomé J. Realized Genetic Gain in Rice: Achievements from Breeding Programs. RICE (NEW YORK, N.Y.) 2023; 16:61. [PMID: 38099942 PMCID: PMC10724102 DOI: 10.1186/s12284-023-00677-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/10/2023] [Indexed: 12/18/2023]
Abstract
Genetic improvement is crucial for ensuring food security globally. Indeed, plant breeding has contributed significantly to increasing the productivity of major crops, including rice, over the last century. Evaluating the efficiency of breeding strategies necessitates a quantification of this progress. One approach involves assessing the genetic gain achieved through breeding programs based on quantitative traits. This study aims to provide a theoretical understanding of genetic gain, summarize the major results of genetic gain studies in rice breeding, and suggest ways of improving breeding program strategies and future studies on genetic gain. To achieve this, we present the concept of genetic gain and the essential aspects of its estimation. We also provide an extensive literature review of genetic gain studies in rice (Oryza sativa L.) breeding programs to understand the advances made to date. We reviewed 29 studies conducted between 1999 and 2023, covering different regions, traits, periods, and estimation methods. The genetic gain for grain yield, in particular, showed significant variation, ranging from 1.5 to 167.6 kg/ha/year, with a mean value of 36.3 kg/ha/year. This translated into a rate of genetic gain for grain yield ranging from 0.1% to over 3.0%. The impact of multi-trait selection on grain yield was clarified by studies that reported genetic gains for other traits, such as plant height, days to flowering, and grain quality. These findings reveal that while breeding programs have achieved significant gains, further improvements are necessary to meet the growing demand for rice. We also highlight the limitations of these studies, which hinder accurate estimations of genetic gain. In conclusion, we offer suggestions for improving the estimation of genetic gain based on quantitative genetic principles and computer simulations to optimize rice breeding strategies.
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Affiliation(s)
- Fallou Seck
- Rice Breeding Innovation Platform, International Rice Research Institute, DAPO Box7777, Metro Manila, Philippines
- University Iba Der Thiam of Thiès, GrandStanding, Thiès, Senegal
| | - Giovanny Covarrubias-Pazaran
- Rice Breeding Innovation Platform, International Rice Research Institute, DAPO Box7777, Metro Manila, Philippines
| | - Tala Gueye
- University Iba Der Thiam of Thiès, GrandStanding, Thiès, Senegal
| | - Jérôme Bartholomé
- CIRAD, UMR AGAP, Cali, Colombia.
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
- Alliance Bioversity-CIAT, Cali, Colombia.
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5
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Pereira de Castro A, Breseghello F, Furtini IV, Utumi MM, Pereira JA, Cao TV, Bartholomé J. Population improvement via recurrent selection drives genetic gain in upland rice breeding. Heredity (Edinb) 2023; 131:201-210. [PMID: 37407693 PMCID: PMC10462700 DOI: 10.1038/s41437-023-00636-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
One of the main challenges of breeding programs is to identify superior genotypes from a large number of candidates. By gradually increasing the frequency of favorable alleles in the breeding population, recurrent selection improves the population mean for target traits, increasing the chance to identify promising genotypes. In rice, population improvement through recurrent selection has been used very little to date, except in Latin America. At Embrapa (Brazilian Agricultural Research Corporation), the upland rice breeding program is conducted in two phases: population improvement followed by product development. In this study, the CNA6 population, evaluated over five cycles (3 to 7) of selection, including 20 field trials, was used to assess the realized genetic gain. A high rate of genetic gain was observed for grain yield, at 215 kg.ha-1 per cycle or 67.8 kg.ha-1 per year (3.08%). The CNA6 population outperformed the controls only for the last cycle, with a yield difference of 1128 kg.ha-1. An analysis of the product development pipeline, based on 29 advanced yield trials with lines derived from cycles 3 to 6, showed that lines derived from the CNA6 population had high grain yield, but did not outperform the controls. These results demonstrate that the application of recurrent selection to a breeding population with sufficient genetic variability can result in significant genetic gains for quantitative traits, such as grain yield. The integration of this strategy into a two-phase breeding program also makes it possible to increase quantitative traits while selecting for other traits of interest.
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Affiliation(s)
| | | | | | | | | | - Tuong-Vi Cao
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR AGAP Institut, F-34398, Montpellier, France
| | - Jérôme Bartholomé
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR AGAP Institut, F-34398, Montpellier, France
- Alliance Bioversity-CIAT, Cali, Colombia
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6
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McNally KL, Henry A. Tools for using the International Rice Genebank to breed for climate-resilient varieties. PLoS Biol 2023; 21:e3002215. [PMID: 37410801 PMCID: PMC10353781 DOI: 10.1371/journal.pbio.3002215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/18/2023] [Indexed: 07/08/2023] Open
Abstract
Traditional rice varieties have been critical for developing improved stress-tolerant rice varieties. Tools to analyze the genome sequences of traditional varieties are accelerating the identification and deployment of genes conferring climate change resilience.
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Affiliation(s)
- Kenneth L. McNally
- Rice Breeding Innovations Department, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Amelia Henry
- Rice Breeding Innovations Department, International Rice Research Institute, Los Baños, Laguna, Philippines
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7
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Singh AK, Ponnuswamy R, Srinivas Prasad M, Sundaram RM, Hari Prasad AS, Senguttuvel P, Kempa Raju KB, Sruthi K. Improving blast resistance of maintainer line DRR 9B by transferring broad spectrum resistance gene Pi2 by marker assisted selection in rice. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:253-262. [PMID: 36819122 PMCID: PMC9930015 DOI: 10.1007/s12298-023-01291-y] [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: 01/18/2022] [Revised: 01/31/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Hybrid rice technology offers great promise to further enhance rice production and productivity for global food security. Improving hybrid rice parental lines is the first step in developing heterotic rice hybrids. To improve resistance against blast disease, a maintainer line DRR 9B was fortified with a major broad-spectrum blast resistance gene Pi2 through marker-assisted selection. The rice blast caused by Magnaporthe oryzae is a major disease and can cause severe yield losses upto 100%. The NILs of Samba Mahsuri namely BA-23-11-89-12-168 possessing Pi2 was utilized as a donor parent. The PCR-based molecular marker tightly linked to Pi2 gene was used for the foreground selection at BC1F1 generation. The molecular marker tightly linked to the major fertility restorer gene Rf4 was used for negative selection (i.e., selection of plants possessing non fertility restoring alleles) at BC1F1 generation to identify maintainer lines. The positive plants with Rf4 gene were added to the restorer pool for restorer line development. At each stage, MAS for Pi2 coupled with stringent phenotypic selection for agro-morphological and grain quality traits were exercised. At BC1F3 generation, one hundred families were screened against blast disease at uniform blast nursery (UBN) and selected resistant lines were advanced to next generations. In the BC1F5 generation plants were subjected to agro-morphological evaluation for yield and yield-contributing traits. The selected plants at BC1F5 generation were crossed with DRR 9A to assess the maintainer ability of blast resistance lines and for further CMS line conversion for hybrid rice breeding for developing blast resistance rice hybrids.
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Affiliation(s)
- Arun Kumar Singh
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana India
| | - Revathi Ponnuswamy
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana India
| | - M. Srinivas Prasad
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana India
| | - R. M. Sundaram
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana India
| | - A. S. Hari Prasad
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana India
| | - P. Senguttuvel
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana India
| | - K. B. Kempa Raju
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana India
| | - K. Sruthi
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana India
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8
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Eckardt NA, Ainsworth EA, Bahuguna RN, Broadley MR, Busch W, Carpita NC, Castrillo G, Chory J, DeHaan LR, Duarte CM, Henry A, Jagadish SVK, Langdale JA, Leakey ADB, Liao JC, Lu KJ, McCann MC, McKay JK, Odeny DA, Jorge de Oliveira E, Platten JD, Rabbi I, Rim EY, Ronald PC, Salt DE, Shigenaga AM, Wang E, Wolfe M, Zhang X. Climate change challenges, plant science solutions. THE PLANT CELL 2023; 35:24-66. [PMID: 36222573 PMCID: PMC9806663 DOI: 10.1093/plcell/koac303] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g. heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.
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Affiliation(s)
| | - Elizabeth A Ainsworth
- USDA ARS Global Change and Photosynthesis Research Unit, Urbana, Illinois 61801, USA
| | - Rajeev N Bahuguna
- Centre for Advanced Studies on Climate Change, Dr Rajendra Prasad Central Agricultural University, Samastipur 848125, Bihar, India
| | - Martin R Broadley
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Nicholas C Carpita
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Gabriel Castrillo
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Joanne Chory
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | | | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Amelia Henry
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - S V Krishna Jagadish
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas 79410, USA
| | - Jane A Langdale
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Andrew D B Leakey
- Department of Plant Biology, Department of Crop Sciences, and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - James C Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Kuan-Jen Lu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Maureen C McCann
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - John K McKay
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Damaris A Odeny
- The International Crops Research Institute for the Semi-Arid Tropics–Eastern and Southern Africa, Gigiri 39063-00623, Nairobi, Kenya
| | | | - J Damien Platten
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
| | - Ellen Youngsoo Rim
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
- Innovative Genomics Institute, Berkeley, California 94704, USA
| | - David E Salt
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alexandra M Shigenaga
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Marnin Wolfe
- Auburn University, Dept. of Crop Soil and Environmental Sciences, College of Agriculture, Auburn, Alabama 36849, USA
| | - Xiaowei Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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9
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Biswas PS, Ahmed MME, Afrin W, Rahman A, Shalahuddin AKM, Islam R, Akter F, Syed MA, Sarker MRA, Ifterkharuddaula KM, Islam MR. Enhancing genetic gain through the application of genomic selection in developing irrigated rice for the favorable ecosystem in Bangladesh. Front Genet 2023; 14:1083221. [PMID: 36911402 PMCID: PMC9992429 DOI: 10.3389/fgene.2023.1083221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/18/2023] [Indexed: 02/24/2023] Open
Abstract
Increasing selection differential and decreasing cycle time, the rate of genetic improvement can be accelerated. Creating and capturing higher genetic with higher accuracy within the shortest possible time is the prerequisite for enhancing genetic gain for any trait. Comprehensive yield testing at multi-locations at early generations together with the shortest line fixation time can expedite the rapid recycling of parents in the breeding program through recurrent selection. Genomic selection is efficient in capturing high breeding value individuals taking additive genetic effects of all genes into account with and without extensive field testing, thus reducing breeding cycle time enhances genetic gain. In the Bangladesh Rice Research Institute, GS technology together with the trait-specific marker-assisted selection at the early generation of RGA-derived breeding lines showed a prediction accuracy of 0.454-0.701 with 0.989-2.623 relative efficiency over the four consecutive years of exercise. This study reports that the application of GS together with trait-specific MAS has expedited the yield improvement by 117 kg ha-1·year-1, which is around seven-fold larger than the baseline annual genetic gain and shortened the breeding cycle by around 1.5 years from the existing 4.5 years.
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Affiliation(s)
- Partha S Biswas
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - M M Emam Ahmed
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - Wazifa Afrin
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - Anisar Rahman
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - A K M Shalahuddin
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - Rafiqul Islam
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - Fahamida Akter
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - Md Abu Syed
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - Md Ruhul Amin Sarker
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - K M Ifterkharuddaula
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
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10
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Rahman NMF, Malik WA, Kabir MS, Baten MA, Hossain MI, Paul DNR, Ahmed R, Biswas PS, Rahman MC, Rahman MS, Iftekharuddaula KM, Hadasch S, Schmidt P, Islam MR, Rahman MA, Atlin GN, Piepho HP. 50 years of rice breeding in Bangladesh: genetic yield trends. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:18. [PMID: 36680594 PMCID: PMC9867671 DOI: 10.1007/s00122-023-04260-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
To assess the efficiency of genetic improvement programs, it is essential to assess the genetic trend in long-term data. The present study estimates the genetic trends for grain yield of rice varieties released between 1970 and 2020 by the Bangladesh Rice Research Institute. The yield of the varieties was assessed from 2001-2002 to 2020-2021 in multi-locations trials. In such a series of trials, yield may increase over time due to (i) genetic improvement (genetic trend) and (ii) improved management or favorable climate change (agronomic/non-genetic trend). In both the winter and monsoon seasons, we observed positive genetic and non-genetic trends. The annual genetic trend for grain yield in both winter and monsoon rice varieties was 0.01 t ha-1, while the non-genetic trend for both seasons was 0.02 t ha-1, corresponding to yearly genetic gains of 0.28% and 0.18% in winter and monsoon seasons, respectively. The overall percentage yield change from 1970 until 2020 for winter rice was 40.96%, of which 13.91% was genetic trend and 27.05% was non-genetic. For the monsoon season, the overall percentage change from 1973 until 2020 was 38.39%, of which genetic and non-genetic increases were 8.36% and 30.03%, respectively. Overall, the contribution of non-genetic trend is larger than genetic trend both for winter and monsoon seasons. These results suggest that limited progress has been made in improving yield in Bangladeshi rice breeding programs over the last 50 years. Breeding programs need to be modernized to deliver sufficient genetic gains in the future to sustain Bangladeshi food security.
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Affiliation(s)
| | - Waqas Ahmed Malik
- Institute of Crop Science, Biostatistics Unit, University of Hohenheim, Fruwirthstrasse 23, 70599, Stuttgart, Germany.
| | | | - Md Azizul Baten
- Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | | | | | - Rokib Ahmed
- Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | | | | | | | | | - Steffen Hadasch
- Institute of Crop Science, Biostatistics Unit, University of Hohenheim, Fruwirthstrasse 23, 70599, Stuttgart, Germany
| | - Paul Schmidt
- Institute of Crop Science, Biostatistics Unit, University of Hohenheim, Fruwirthstrasse 23, 70599, Stuttgart, Germany
| | | | | | | | - Hans-Peter Piepho
- Institute of Crop Science, Biostatistics Unit, University of Hohenheim, Fruwirthstrasse 23, 70599, Stuttgart, Germany
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Introgression of tsv1 improves tungro disease resistance of a rice variety BRRI dhan71. Sci Rep 2022; 12:18820. [PMID: 36335190 PMCID: PMC9637097 DOI: 10.1038/s41598-022-23413-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
Rice Tungro disease poses a threat to rice production in Asia. Marker assisted backcross breeding is the most feasible approach to address the tungro disease. We targeted to introgress tungro resistance locus tsv1 from Matatag 1 into a popular but tungro susceptible rice variety of Bangladesh, BRRI dhan71. The tsv1 locus was traced using two tightly linked markers RM336 and RM21801, and background genotyping was carried out using 7 K SNPs. A series of three back crosses followed by selfing resulted in identification of plants similar to BRRI dhan71. The background recovery varied at 91-95% with most of the lines having 95%. The disease screening of the lines showed moderate to high level of tungro resistance with a disease index score of ≤ 5. Introgression Lines (ILs) had medium slender grain type, and head rice recovery (59.2%), amylose content (20.1%), gel consistency (40.1 mm) and gelatinization temperature were within the acceptable range. AMMI and Kang's stability analysis based on multi-location data revealed that multiple selected ILs outperformed BRRI dhan71 across the locations. IR144480-2-2-5, IR144483-1-2-4, IR144484-1-2-2 and IR144484-1-2-5 are the most promising lines. These lines will be further evaluated and nominated for varietal testing in Bangladesh.
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Khanna A, Anumalla M, Catolos M, Bhosale S, Jarquin D, Hussain W. Optimizing predictions in IRRI's rice drought breeding program by leveraging 17 years of historical data and pedigree information. FRONTIERS IN PLANT SCIENCE 2022; 13:983818. [PMID: 36204059 PMCID: PMC9530897 DOI: 10.3389/fpls.2022.983818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
Prediction models based on pedigree and/or molecular marker information are now an inextricable part of the crop breeding programs and have led to increased genetic gains in many crops. Optimization of IRRI's rice drought breeding program is crucial for better implementation of selections based on predictions. Historical datasets with precise and robust pedigree information have been a great resource to help optimize the prediction models in the breeding programs. Here, we leveraged 17 years of historical drought data along with the pedigree information to predict the new lines or environments and dissect the G × E interactions. Seven models ranging from basic to proposed higher advanced models incorporating interactions, and genotypic specific effects were used. These models were tested with three cross-validation schemes (CV1, CV2, and CV0) to assess the predictive ability of tested and untested lines in already observed environments and tested lines in novel or new environments. In general, the highest prediction abilities were obtained when the model accounting interactions between pedigrees (additive) and environment were included. The CV0 scheme (predicting unobserved or novel environments) reveals very low predictive abilities among the three schemes. CV1 and CV2 schemes that borrow information from the target and correlated environments have much higher predictive abilities. Further, predictive ability was lower when predicting lines in non-stress conditions using drought data as training set and/or vice-versa. When predicting the lines using the data sets under the same conditions (stress or non-stress data sets), much better prediction accuracy was obtained. These results provide conclusive evidence that modeling G × E interactions are important in predictions. Thus, considering G × E interactions would help to build enhanced genomic or pedigree-based prediction models in the rice breeding program. Further, it is crucial to borrow the correlated information from other environments to improve prediction accuracy.
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Affiliation(s)
- Apurva Khanna
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Mahender Anumalla
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Margaret Catolos
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Sankalp Bhosale
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Diego Jarquin
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Waseem Hussain
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
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Vinarao R, Proud C, Snell P, Fukai S, Mitchell J. Genomic Regions and Floral Traits Contributing to Low Temperature Tolerance at Young Microspore Stage in a Rice ( Oryza sativa L.) Recombinant Inbred Line Population of Sherpa/IRAT109. FRONTIERS IN PLANT SCIENCE 2022; 13:873677. [PMID: 35574104 PMCID: PMC9100824 DOI: 10.3389/fpls.2022.873677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
Aerobic rice production (AP) consumes less water compared to flooded systems. Developing genotypes and identifying genomic regions associated with low temperature (LT) tolerance at the young microspore stage (YMS) is imperative for AP, particularly for temperate regions. Using a recombinant inbred line population derived from the Australian LT tolerant variety Sherpa, experiments were conducted to map and dissect quantitative trait loci (QTL) associated with spikelet sterility (SS) after exposure to LT and to investigate floral traits contributing to the development of lower SS. Significant genotypic variation for SS was observed in the population after exposure to LT at YMS. Three genomic regions associated with SS, qYMCT3, qYMCT4, and qYMCT8.1 were identified in chromosomes 3, 4, and 8 respectively, using multiple QTL models explaining 22.4% of the genotypic variation. Introgression of the favorable allele from qYMCT3 was estimated to reduce SS by up to 15.4%. A co-locating genomic region with qYMCT3, qDTHW3.1 was identified as the major QTL affecting days to heading and explained as much as 44.7% of the genotypic variation. Whole-genome sequence and bioinformatic analyses demonstrated OsMADS50 as the candidate gene for qYMCT3/qDTHW3.1 and to our knowledge, this was the first attempt in connecting the role of OsMADS50 in both LT and flowering in rice. Differential sets selected for extreme SS showed LT tolerant genotype group produced higher total pollen per spikelet resulting in a higher number of dehisced anthers and pollen on stigma and eventually, lower SS than THE sensitive group. The relationship between these key floral traits with SS was induced only after exposure to LT and was not observed in warm ideal temperature conditions. Identification of elite germplasm with favorable QTL allele and combinations, gene cloning, and pyramiding with additional high-value QTL for key traits should empower breeders to develop AP adapted genotypes for temperate growing regions, and ultimately produce climate-resilient rice.
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Affiliation(s)
- Ricky Vinarao
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Christopher Proud
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Peter Snell
- Department of Primary Industries, Yanco Agricultural Institute, Yanco, NSW, Australia
| | - Shu Fukai
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jaquie Mitchell
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
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