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Jadhav Y, Thakur NR, Ingle KP, Ceasar SA. The role of phenomics and genomics in delineating the genetic basis of complex traits in millets. PHYSIOLOGIA PLANTARUM 2024; 176:e14349. [PMID: 38783512 DOI: 10.1111/ppl.14349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/22/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024]
Abstract
Millets, comprising a diverse group of small-seeded grains, have emerged as vital crops with immense nutritional, environmental, and economic significance. The comprehension of complex traits in millets, influenced by multifaceted genetic determinants, presents a compelling challenge and opportunity in agricultural research. This review delves into the transformative roles of phenomics and genomics in deciphering these intricate genetic architectures. On the phenomics front, high-throughput platforms generate rich datasets on plant morphology, physiology, and performance in diverse environments. This data, coupled with field trials and controlled conditions, helps to interpret how the environment interacts with genetics. Genomics provides the underlying blueprint for these complex traits. Genome sequencing and genotyping technologies have illuminated the millet genome landscape, revealing diverse gene pools and evolutionary relationships. Additionally, different omics approaches unveil the intricate information of gene expression, protein function, and metabolite accumulation driving phenotypic expression. This multi-omics approach is crucial for identifying candidate genes and unfolding the intricate pathways governing complex traits. The review highlights the synergy between phenomics and genomics. Genomically informed phenotyping targets specific traits, reducing the breeding size and cost. Conversely, phenomics identifies promising germplasm for genomic analysis, prioritizing variants with superior performance. This dynamic interplay accelerates breeding programs and facilitates the development of climate-smart, nutrient-rich millet varieties and hybrids. In conclusion, this review emphasizes the crucial roles of phenomics and genomics in unlocking the genetic enigma of millets.
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Affiliation(s)
- Yashoda Jadhav
- International Crops Research Institutes for the Semi-Arid Tropics, Patancheru, TS, India
| | - Niranjan Ravindra Thakur
- International Crops Research Institutes for the Semi-Arid Tropics, Patancheru, TS, India
- Vasantrao Naik Marathwada Agricultural University, Parbhani, MS, India
| | | | - Stanislaus Antony Ceasar
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Kochi, KL, India
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Dominguez DLE, Cavagnaro JB, Ros JP, Le AT, Chung YS, Cavagnaro PF. Genetic diversity for drought tolerance in the native forage grass Trichloris crinita and possible morpho-physiological mechanisms involved. FRONTIERS IN PLANT SCIENCE 2023; 14:1235923. [PMID: 37600198 PMCID: PMC10435868 DOI: 10.3389/fpls.2023.1235923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023]
Abstract
Introduction The use of drought tolerant genotypes is one of the main strategies proposed for coping with the negative effects of global warming in dry lands. Trichloris crinita is a native forage grass occupying extensive arid and semi-arid regions in the American continent, and used for range grazing and revegetation of degraded lands. Methods To identify drought-tolerant genotypes and possible underlying physiological mechanisms, this study investigated drought tolerance in 21 genetically diverse T. crinita genotypes under natural field conditions. The accessions were grown under irrigated (control) and drought conditions for 84 days after initiation of the drought treatment (DAIDT), which coincided with flowering initiation. Various morpho-physiological traits were monitored, including total-, foliage-, and root biomass yield, dry matter partitioning to individual plant organs (roots, leaves, stems, and panicles), total leaf area, chlorophyll content, photochemical efficiency of photosystem II, stomatal conductance, and number of panicles per plant. Results and discussion Broad and significant variation (p<0.001) was found among the accessions for all the traits. Three highly tolerant and three very sensitive accessions were identified as the most contrasting materials, and their responses to drought stress were confirmed over two years of experiments. Under prolonged drought conditions (84 DAIDT), the tolerant accessions were generally more productive than the rest for all the biomass yield components analyzed, and this was associated with a postponed and more attenuated decrease in variables related to the plant photosynthetic activity, such as stomatal conductance, chlorophyll content, and photochemical efficiency. In contrast to previous findings, our data indicate no direct relationship between drought tolerance and the level of aridity in the accessions natural habitats, but rather suggest genetic heterogeneity and ample variation for drought tolerance in T. crinita natural populations derived from a particular location or environment. Also, having low total and forageable biomass yield, or increased biomass allocation to the roots (i.e., lower foliage/root ratio), under optimal water availability, were not associated with greater drought tolerance. The drought-tolerant accessions identified are of value for future genetic research and breeding programs, and as forage for range grazing and revegetation in arid regions.
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Affiliation(s)
- Deolindo Luis Esteban Dominguez
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo, Lujan de Cuyo, Mendoza, Argentina
| | - Juan Bruno Cavagnaro
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo, Lujan de Cuyo, Mendoza, Argentina
| | - Juana Panasiti Ros
- Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Lujan de Cuyo, Mendoza, Argentina
| | - Anh Tuan Le
- Department of Plant Resources and Environment, Jeju National University, Jeju, Republic of Korea
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, Republic of Korea
| | - Pablo Federico Cavagnaro
- Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Lujan de Cuyo, Mendoza, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Nacional de Tecnología Agropecuaria (INTA) Agricultural Experimental Station Mendoza (EEA Mendoza), Lujan de Cuyo, Mendoza, Argentina
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Devos KM, Qi P, Bahri BA, Gimode DM, Jenike K, Manthi SJ, Lule D, Lux T, Martinez-Bello L, Pendergast TH, Plott C, Saha D, Sidhu GS, Sreedasyam A, Wang X, Wang H, Wright H, Zhao J, Deshpande S, de Villiers S, Dida MM, Grimwood J, Jenkins J, Lovell J, Mayer KFX, Mneney EE, Ojulong HF, Schatz MC, Schmutz J, Song B, Tesfaye K, Odeny DA. Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet. Nat Commun 2023; 14:3694. [PMID: 37344528 DOI: 10.1038/s41467-023-38915-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/19/2023] [Indexed: 06/23/2023] Open
Abstract
Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a 'poor man's crop', finger millet has regained attention over the past decade for its climate resilience and the nutritional qualities of its grain. To bring finger millet breeding into the 21st century, here we present the assembly and annotation of a chromosome-scale reference genome. We show that this ~1.3 million years old allotetraploid has a high level of homoeologous gene retention and lacks subgenome dominance. Population structure is mainly driven by the differential presence of large wild segments in the pericentromeric regions of several chromosomes. Trait mapping, followed by variant analysis of gene candidates, reveals that loss of purple coloration of anthers and stigma is associated with loss-of-function mutations in the finger millet orthologs of the maize R1/B1 and Arabidopsis GL3/EGL3 anthocyanin regulatory genes. Proanthocyanidin production in seed is not affected by these gene knockouts.
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Affiliation(s)
- Katrien M Devos
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA.
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA.
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
| | - Peng Qi
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Bochra A Bahri
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Pathology, University of Georgia, Griffin, GA, 30223, USA
| | - Davis M Gimode
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, P.O. Box 39063-00623, Nairobi, Kenya
| | - Katharine Jenike
- Departments of Computer Science, Biology and Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Samuel J Manthi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, P.O. Box 39063-00623, Nairobi, Kenya
- Department of Horticulture, University of Georgia, Athens, GA, 30602, USA
| | - Dagnachew Lule
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Oromia Agricultural Research Institute, P.O. Box 81265, Addis Ababa, Ethiopia
- Ethiopian Agricultural Transformation Agency, Addis Ababa, Bole, Ethiopia
| | - Thomas Lux
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Liliam Martinez-Bello
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
- UR Ventures, University of Rochester, Rochester, NY, 14627, USA
| | - Thomas H Pendergast
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Dipnarayan Saha
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- ICAR-Central Research Institute for Jute and Allied Fibers, Kolkata, West Bengal, 700120, India
| | - Gurjot S Sidhu
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Hao Wang
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Hallie Wright
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Jianxin Zhao
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Santosh Deshpande
- ICRISAT, Patancheru, 502 324, T.S., India
- Hytech Seed India Pvt. Ltd., Ravalkol Village, Medcahl-Malkajgiri Dist-, 501 401, Hubballi, T.S, India
| | - Santie de Villiers
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, 80108, Kenya
- Pwani University Biosciences Research Center (PUBReC), Kilifi, 80108, Kenya
| | - Mathews M Dida
- Department of Crop and Soil Science, Maseno University, P.O. 333, Maseno, Kenya
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - John Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Emmarold E Mneney
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar Es Salaam, Tanzania
- Biotechnology Society of Tanzania, P.O. Box 10257, Dar es Salaam, Tanzania
| | - Henry F Ojulong
- ICRISAT, Matopos Research Station, P.O. Box 776, Bulawayo, Zimbabwe
| | - Michael C Schatz
- Departments of Computer Science, Biology and Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Bo Song
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Bio and Emerging Technology Institute, Addis Ababa, Ethiopia
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, P.O. Box 39063-00623, Nairobi, Kenya
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