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Kapoor C, Anamika, Mukesh Sankar S, Singh SP, Singh N, Kumar S. Omics-driven utilization of wild relatives for empowering pre-breeding in pearl millet. PLANTA 2024; 259:155. [PMID: 38750378 DOI: 10.1007/s00425-024-04423-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 04/25/2024] [Indexed: 05/23/2024]
Abstract
MAIN CONCLUSION Pearl millet wild relatives harbour novel alleles which could be utilized to broaden genetic base of cultivated species. Genomics-informed pre-breeding is needed to speed up introgression from wild to cultivated gene pool in pearl millet. Rising episodes of intense biotic and abiotic stresses challenge pearl millet production globally. Wild relatives provide a wide spectrum of novel alleles which could address challenges posed by climate change. Pre-breeding holds potential to introgress novel diversity in genetically narrow cultivated Pennisetum glaucum from diverse gene pool. Practical utilization of gene pool diversity remained elusive due to genetic intricacies. Harnessing promising traits from wild pennisetum is limited by lack of information on underlying candidate genes/QTLs. Next-Generation Omics provide vast scope to speed up pre-breeding in pearl millet. Genomic resources generated out of draft genome sequence and improved genome assemblies can be employed to utilize gene bank accessions effectively. The article highlights genetic richness in pearl millet and its utilization with a focus on harnessing next-generation Omics to empower pre-breeding.
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Affiliation(s)
- Chandan Kapoor
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Anamika
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - S Mukesh Sankar
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, 673012, India
| | - S P Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Nirupma Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sudhir Kumar
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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Horsnell R, Leigh FJ, Wright TIC, Burridge AJ, Ligeza A, Przewieslik-Allen AM, Howell P, Uauy C, Edwards KJ, Bentley AR. A wheat chromosome segment substitution line series supports characterization and use of progenitor genetic variation. THE PLANT GENOME 2024; 17:e20288. [PMID: 36718796 DOI: 10.1002/tpg2.20288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/20/2022] [Indexed: 06/18/2023]
Abstract
Genome-wide introgression and substitution lines have been developed in many plant species, enhancing mapping precision, gene discovery, and the identification and exploitation of variation from wild relatives. Created over multiple generations of crossing and/or backcrossing accompanied by marker-assisted selection, the resulting introgression lines are a fixed genetic resource. In this study we report the development of spring wheat (Triticum aestivum L.) chromosome segment substitution lines (CSSLs) generated to systematically capture genetic variation from tetraploid (T. turgidum ssp. dicoccoides) and diploid (Aegilops tauschii) progenitor species. Generated in a common genetic background over four generations of backcrossing, this is a base resource for the mapping and characterization of wheat progenitor variation. To facilitate further exploitation the final population was genetically characterized using a high-density genotyping array and a range of agronomic and grain traits assessed to demonstrate the potential use of the populations for trait localization in wheat.
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Affiliation(s)
- Richard Horsnell
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
| | - Fiona J Leigh
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
| | - Tally I C Wright
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
| | | | - Aleksander Ligeza
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
| | | | - Philip Howell
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Alison R Bentley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
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Zhao N, Yuan R, Usman B, Qin J, Yang J, Peng L, Mackon E, Liu F, Qin B, Li R. Detection of QTLs Regulating Six Agronomic Traits of Rice Based on Chromosome Segment Substitution Lines of Common Wild Rice ( Oryza rufipogon Griff.) and Mapping of qPH1.1 and qLMC6.1. Biomolecules 2022; 12:biom12121850. [PMID: 36551278 PMCID: PMC9775987 DOI: 10.3390/biom12121850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Wild rice is a primary source of genes that can be utilized to generate rice cultivars with advantageous traits. Chromosome segment substitution lines (CSSLs) are consisting of a set of consecutive and overlapping donor chromosome segments in a recipient's genetic background. CSSLs are an ideal genetic population for mapping quantitative traits loci (QTLs). In this study, 59 CSSLs from the common wild rice (Oryza rufipogon Griff.) accession DP15 under the indica rice cultivar (O. sativa L. ssp. indica) variety 93-11 background were constructed through multiple backcrosses and marker-assisted selection (MAS). Through high-throughput whole genome re-sequencing (WGRS) of parental lines, 12,565 mapped InDels were identified and designed for polymorphic molecular markers. The 59 CSSLs library covered 91.72% of the genome of common wild rice accession DP15. The DP15-CSSLs displayed variation in six economic traits including grain length (GL), grain width (GW), thousand-grain weight (TGW), grain length-width ratio (GLWR), plant height (PH), and leaf margin color (LMC), which were finally attributed to 22 QTLs. A homozygous CSSL line and a purple leave margin CSSL line were selected to construct two secondary genetic populations for the QTLs mapping. Thus, the PH-controlling QTL qPH1.1 was mapped to a region of 4.31-Mb on chromosome 1, and the LMC-controlling QTL qLMC6.1 was mapped to a region of 370-kb on chromosome 6. Taken together, these identified novel QTLs/genes from common wild rice can potentially promote theoretical knowledge and genetic applications to rice breeders worldwide.
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Affiliation(s)
- Neng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Ruizhi Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Babar Usman
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Jiaming Qin
- Maize Research Institute, Guangxi Academy of Agricultural Science, Nanning 530007, China
| | - Jinlian Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Liyun Peng
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Enerand Mackon
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
- Correspondence:
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Yadav OP, Gupta SK, Govindaraj M, Sharma R, Varshney RK, Srivastava RK, Rathore A, Mahala RS. Genetic Gains in Pearl Millet in India: Insights Into Historic Breeding Strategies and Future Perspective. FRONTIERS IN PLANT SCIENCE 2021; 12:645038. [PMID: 33859663 DOI: 10.3389/fpls.2021.64503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/19/2021] [Indexed: 05/27/2023]
Abstract
Pearl millet (Pennisetum glaucum R. Br.) is an important staple and nutritious food crop in the semiarid and arid ecologies of South Asia (SA) and Sub-Saharan Africa (SSA). In view of climate change, depleting water resources, and widespread malnutrition, there is a need to accelerate the rate of genetic gains in pearl millet productivity. This review discusses past strategies and future approaches to accelerate genetic gains to meet future demand. Pearl millet breeding in India has historically evolved very comprehensively from open-pollinated varieties development to hybrid breeding. Availability of stable cytoplasmic male sterility system with adequate restorers and strategic use of genetic resources from India and SSA laid the strong foundation of hybrid breeding. Genetic and cytoplasmic diversification of hybrid parental lines, periodic replacement of hybrids, and breeding disease-resistant and stress-tolerant cultivars have been areas of very high priority. As a result, an annual yield increase of 4% has been realized in the last three decades. There is considerable scope to further accelerate the efforts on hybrid breeding for drought-prone areas in SA and SSA. Heterotic grouping of hybrid parental lines is essential to sustain long-term genetic gains. Time is now ripe for mainstreaming of the nutritional traits improvement in pearl millet breeding programs. New opportunities are emerging to improve the efficiency and precision of breeding. Development and application of high-throughput genomic tools, speed breeding, and precision phenotyping protocols need to be intensified to exploit a huge wealth of native genetic variation available in pearl millet to accelerate the genetic gains.
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Affiliation(s)
| | - S K Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Mahalingam Govindaraj
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Rajan Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Rakesh K Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - A Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
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Pujarula V, Pusuluri M, Bollam S, Das RR, Ratnala R, Adapala G, Thuraga V, Rathore A, Srivastava RK, Gupta R. Genetic Variation for Nitrogen Use Efficiency Traits in Global Diversity Panel and Parents of Mapping Populations in Pearl Millet. FRONTIERS IN PLANT SCIENCE 2021; 12:625915. [PMID: 33613608 PMCID: PMC7893144 DOI: 10.3389/fpls.2021.625915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/11/2021] [Indexed: 05/09/2023]
Abstract
Nitrogen (N) is one of the primary macronutrients required for crop growth and yield. This nutrient is especially limiting in the dry and low fertility soils where pearl millet [Pennisetum glaucum (L.) R. Br] is typically grown. Globally, pearl millet is the sixth most important cereal grown by subsistence farmers in the arid and semi-arid regions of sub-Saharan Africa and the Indian subcontinent. Most of these agro-ecologies have low N in the root zone soil strata. Therefore, there is an immense need to identify lines that use nitrogen efficiently. A set of 380 diverse pearl millet lines consisting of a global diversity panel (345), parents of mapping populations (20), and standard checks (15) were evaluated in an alpha-lattice design with two replications, 25 blocks, a three-row plot for 11 nitrogen use efficiency (NUE) related traits across three growing seasons (Summer 2017, Rainy 2017, and Summer 2018) in an N-depleted precision field under three different N levels (0%-N0, 50%-N50, 100%-N100 of recommended N, i.e., 100 kg ha-1). Analysis of variance revealed significant genetic variation for NUE-related traits across treatments and seasons. Nitrogen in limited condition (N0) resulted in a 27.6 and 17.6% reduction in grain yield (GY) and dry stover yield (DSY) compared to N50. Higher reduction in GY and DSY traits by 24.6 and 23.6% were observed under N0 compared to N100. Among the assessed traits, GY exhibited significant positive correlations with nitrogen utilization efficiency (NUtE) and nitrogen harvest index (NHI). This indicated the pivotal role of N remobilization to the grain in enhancing yield levels. Top 25 N-insensitive (NIS-top grain yielders) and N-sensitive (NS-poor grain yielders) genotypes were identified under low N conditions. Out of 25 NIS lines, nine genotypes (IP 10820, IP 17720, ICMB 01222-P1, IP 10379, ICMB 89111-P2, IP 8069, ICMB 90111-P2, ICMV IS89305, and ICMV 221) were common with the top 25 lines for N100 level showing the genotype plasticity toward varying N levels. Low N tolerant genotypes identified from the current investigation may help in the identification of genomic regions responsible for NUE and its deployment in pearl millet breeding programs through marker-assisted selection (MAS).
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Affiliation(s)
| | | | | | | | | | | | | | | | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
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Yadav OP, Gupta SK, Govindaraj M, Sharma R, Varshney RK, Srivastava RK, Rathore A, Mahala RS. Genetic Gains in Pearl Millet in India: Insights Into Historic Breeding Strategies and Future Perspective. FRONTIERS IN PLANT SCIENCE 2021; 12:645038. [PMID: 33859663 PMCID: PMC8042313 DOI: 10.3389/fpls.2021.645038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/19/2021] [Indexed: 05/09/2023]
Abstract
Pearl millet (Pennisetum glaucum R. Br.) is an important staple and nutritious food crop in the semiarid and arid ecologies of South Asia (SA) and Sub-Saharan Africa (SSA). In view of climate change, depleting water resources, and widespread malnutrition, there is a need to accelerate the rate of genetic gains in pearl millet productivity. This review discusses past strategies and future approaches to accelerate genetic gains to meet future demand. Pearl millet breeding in India has historically evolved very comprehensively from open-pollinated varieties development to hybrid breeding. Availability of stable cytoplasmic male sterility system with adequate restorers and strategic use of genetic resources from India and SSA laid the strong foundation of hybrid breeding. Genetic and cytoplasmic diversification of hybrid parental lines, periodic replacement of hybrids, and breeding disease-resistant and stress-tolerant cultivars have been areas of very high priority. As a result, an annual yield increase of 4% has been realized in the last three decades. There is considerable scope to further accelerate the efforts on hybrid breeding for drought-prone areas in SA and SSA. Heterotic grouping of hybrid parental lines is essential to sustain long-term genetic gains. Time is now ripe for mainstreaming of the nutritional traits improvement in pearl millet breeding programs. New opportunities are emerging to improve the efficiency and precision of breeding. Development and application of high-throughput genomic tools, speed breeding, and precision phenotyping protocols need to be intensified to exploit a huge wealth of native genetic variation available in pearl millet to accelerate the genetic gains.
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Affiliation(s)
- Om Parkash Yadav
- ICAR-Central Arid Zone Research Institute, Jodhpur, India
- *Correspondence: Om Parkash Yadav
| | - S. K. Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Mahalingam Govindaraj
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Rajan Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - A. Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
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Lu X, Zhou Z, Yuan Z, Zhang C, Hao Z, Wang Z, Li M, Zhang D, Yong H, Han J, Li X, Weng J. Genetic Dissection of the General Combining Ability of Yield-Related Traits in Maize. FRONTIERS IN PLANT SCIENCE 2020; 11:788. [PMID: 32793248 PMCID: PMC7387702 DOI: 10.3389/fpls.2020.00788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/18/2020] [Indexed: 05/27/2023]
Abstract
Maize yield components including row number, kernel number per row, kernel thickness, kernel width, kernel length, 100-kernel weight, and volume weight affect grain yield directly. Previous studies mainly focused on dissecting the genetic basis of per se performances for yield-related traits, but the genetic basis of general combining ability (GCA) for these traits is still unclear. In the present study, 328 RILs were crossed as males to two testers according to the NCII mating design, resulting in a hybrid panel composed of 656 hybrids. Both the hybrids and parental lines were evaluated in four environments in 2015 and 2016. Correlation analysis showed the performances of GCA effects were significantly correlated to the per se performances of RILs for all yield-related traits (0.17 ≤ r ≤ 0.64, P > 0.01). Only 17 of 95 QTL could be detected for both per se performances of RILs and GCA effects for eight yield-related traits. The QTL qKN7-1 and qHKW1-3, which could explain more than 10% of the variation in the GCA effects of KN and HKW, were also detected for per se performances for the traits. The pleiotropic loci qRN3-1 and qRN6, which together explained 14.92% of the observed variation in GCA effects for RN, were associated with the GCA effects of KW and HKW, but not with per se performances for these traits. In contrast, Incw1, which was related to seed weight in maize, was mapped to the region surrounding MK2567 at the qHKW5-2 locus, but no GCA effect was detected. The QTL identified in present study for per se performances and corresponding GCA effects for yield-related traits might be useful for maize hybrid breeding.
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Affiliation(s)
- Xin Lu
- College of Agriculture, Northeast Agricultural University, Harbin, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiqiang Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhaohui Yuan
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Chaoshu Zhang
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Zhuanfang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhenhua Wang
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Degui Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongjun Yong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jienan Han
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinhai Li
- College of Agriculture, Northeast Agricultural University, Harbin, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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