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Kasule F, Diack O, Mbaye M, Kakeeto R, Econopouly BF. Genomic resources, opportunities, and prospects for accelerated improvement of millets. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:273. [PMID: 39565376 PMCID: PMC11579216 DOI: 10.1007/s00122-024-04777-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 10/28/2024] [Indexed: 11/21/2024]
Abstract
KEY MESSAGE Genomic resources, alongside the tools and expertise required to leverage them, are essential for the effective improvement of globally significant millet crop species. Millets are essential for global food security and nutrition, particularly in sub-Saharan Africa and South Asia. They are crucial in promoting nutrition, climate resilience, economic development, and cultural heritage. Despite their critical role, millets have historically received less investment in developing genomic resources than major cereals like wheat, maize, and rice. However, recent advancements in genomics, particularly next-generation sequencing technologies, offer unprecedented opportunities for rapid improvement in millet crops. This review paper provides an overview of the status of genomic resources in millets and in harnessing the recent opportunities in artificial intelligence to address challenges in millet crop improvement to boost productivity, nutrition, and end quality. It emphasizes the significance of genomics in tackling global food security issues and underscores the necessity for innovative breeding strategies to translate genomics and AI into effective breeding strategies for millets.
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Affiliation(s)
- Faizo Kasule
- Interdepartmental Genetics and Genomics (IGG), Iowa State University, Ames, IA, 50011, USA
| | - Oumar Diack
- Centre National de Recherches Agronomiques de Bambey (CNRA), Institut Sénégalais de Recherches Agricoles (ISRA), BP 53, Bambey, Sénégal
| | - Modou Mbaye
- Centre d'Etude Régional Pour L'Amélioration de L'Adaptation À La Sécheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, BP 3320, Thiès, Sénégal
| | - Ronald Kakeeto
- National Agricultural Research Organization (NARO), National Semi-Arid Resources Research Institute (NaSARRI), P.O. Box 56, Soroti, Uganda
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Chandra T, Jaiswal S, Tomar RS, Iquebal MA, Kumar D. Realizing visionary goals for the International Year of Millet (IYoM): accelerating interventions through advances in molecular breeding and multiomics resources. PLANTA 2024; 260:103. [PMID: 39304579 DOI: 10.1007/s00425-024-04520-0] [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: 05/01/2024] [Accepted: 08/30/2024] [Indexed: 09/22/2024]
Abstract
MAIN CONCLUSION Leveraging advanced breeding and multi-omics resources is vital to position millet as an essential "nutricereal resource," aligning with IYoM goals, alleviating strain on global cereal production, boosting resilience to climate change, and advancing sustainable crop improvement and biodiversity. The global challenges of food security, nutrition, climate change, and agrarian sustainability demand the adoption of climate-resilient, nutrient-rich crops to support a growing population amidst shifting environmental conditions. Millets, also referred to as "Shree Anna," emerge as a promising solution to address these issues by bolstering food production, improving nutrient security, and fostering biodiversity conservation. Their resilience to harsh environments, nutritional density, cultural significance, and potential to enhance dietary quality index made them valuable assets in global agriculture. Recognizing their pivotal role, the United Nations designated 2023 as the "International Year of Millets (IYoM 2023)," emphasizing their contribution to climate-resilient agriculture and nutritional enhancement. Scientific progress has invigorated efforts to enhance millet production through genetic and genomic interventions, yielding a wealth of advanced molecular breeding technologies and multi-omics resources. These advancements offer opportunities to tackle prevailing challenges in millet, such as anti-nutritional factors, sensory acceptability issues, toxin contamination, and ancillary crop improvements. This review provides a comprehensive overview of molecular breeding and multi-omics resources for nine major millet species, focusing on their potential impact within the framework of IYoM. These resources include whole and pan-genome, elucidating adaptive responses to abiotic stressors, organelle-based studies revealing evolutionary resilience, markers linked to desirable traits for efficient breeding, QTL analysis facilitating trait selection, functional gene discovery for biotechnological interventions, regulatory ncRNAs for trait modulation, web-based platforms for stakeholder communication, tissue culture techniques for genetic modification, and integrated omics approaches enabled by precise application of CRISPR/Cas9 technology. Aligning these resources with the seven thematic areas outlined by IYoM catalyzes transformative changes in millet production and utilization, thereby contributing to global food security, sustainable agriculture, and enhanced nutritional consequences.
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Affiliation(s)
- Tilak Chandra
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Rukam Singh Tomar
- Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, 110012, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India.
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
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Vetriventhan M, Upadhyaya HD, Deshpande S, Johnson MS, Wallace JG, Victor A, Naresh D, Rayaprolu L, Singh K, Mayes S. Genome-wide assessment of population structure and association mapping for agronomic and grain nutritional traits in proso millet (Panicum miliaceum L.). Sci Rep 2024; 14:21920. [PMID: 39300236 DOI: 10.1038/s41598-024-72319-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Accepted: 09/05/2024] [Indexed: 09/22/2024] Open
Abstract
Proso millet is an important but under-researched and underutilized crop with the potential to become a future smart crop because of its climate-resilient features and high nutrient content. Assessing diversity and marker-trait associations are essential to support the genomics-assisted improvement of proso millet. This study aimed to assess the population structure and diversity of a proso millet diversity panel and identify marker-trait associations for agronomic and grain nutrient traits. In this study, genome-wide single nucleotide polymorphisms (SNPs) were identified by mapping raw genotyping-by-sequencing (GBS) data onto the proso millet genome, resulting in 5621 quality-filtered SNPs in 160 diverse accessions. The modified Roger's Distance assessment indicated an average distance of 0.268 among accessions, with the race miliaceum exhibiting the highest diversity and ovatum the lowest. Proso millet germplasm diversity was structured according to geographic centers of origin and domestication. Genome-wide association mapping identified 40 marker-trait associations (MTAs), including 34 MTAs for agronomic traits and 6 for grain nutrients; 20 of these MTAs were located within genes. Favourable alleles and phenotypic values were estimated for all MTAs. This study provides valuable insights into the population structure and diversity of proso millet, identified marker-trait associations, and reported favourable alleles and their phenotypic values for supporting genomics-assisted improvement efforts in proso millet.
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Affiliation(s)
- Mani Vetriventhan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India.
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
- University of Georgia, Athens, GA, 30605, USA
| | - Santosh Deshpande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
- Hytech Seed India Private Limited, Hyderabad, India
| | - Matthew S Johnson
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA, USA
| | - Jason G Wallace
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA, USA
- Department of Crop and Soil Science, University of Georgia, Athens, GA, USA
| | - Allan Victor
- Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - D Naresh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
| | - Laavanya Rayaprolu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
- Wageningen University and Research, Wageningen, The Netherlands
| | - Kuldeep Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
| | - Sean Mayes
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
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4
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Reinman T, Braden J, Miller ND, Murphy KM. Mineral, seed morphology, and agronomic characteristics of proso millet grown in the inland Pacific Northwest. Front Nutr 2024; 11:1394136. [PMID: 39323567 PMCID: PMC11422230 DOI: 10.3389/fnut.2024.1394136] [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: 03/01/2024] [Accepted: 07/31/2024] [Indexed: 09/27/2024] Open
Abstract
Climate change increases stressors that will challenge the resiliency of global agricultural production. Just three crops, wheat, maize, and rice, are estimated to sustain 50% of the caloric demand of the world population, meaning that significant loss of any of these crops would threaten global food security. However, increasing cropping system diversity can create a more resilient food system. One crop that could add diversity to wheat-dominated cropping systems in the inland Pacific Northwest is proso millet, a climate-resilient, small-seeded cereal crop that is highly water efficient, able to grow in low fertility soils, and has a desirable nutritional profile. Proso millet shows potential for adoption in this region due to its short growing season, compatibility with regional equipment, and environmental requirements, however US cultivars have been developed for the Great Plains and little research has been conducted outside of this region. To better understand the potential for adoption in the inland PNW, seven commercially available varieties were planted in a researcher-run trial in Pullman, WA and in a series of producer-run trials across the region in 2022. Samples were analyzed for mineral concentration (Zn, Fe, Cu, Mn, Mg, Ca, P, and K), seed morphology phenotypes (seed area, seed eccentricity, thousand seed weight, and seed color), and agronomic phenotypes (grain yield, plant height, days to heading, days to maturity, and percent emergence). Varieties from the researcher-run trial showed significant differences for all traits excluding percent emergence. Samples from producer-run trials showed differences by location for concentration of all minerals and for all seed morphology traits but were not analyzed for agronomic phenotypes. Samples from producer-run trials showed no difference by variety for mineral concentration but showed varietal differences for all seed morphology phenotypes. Most minerals were positively correlated with one another (0.28 < r < 0.92). Grain yield was negatively correlated with Zn (r = -0.55, p < 0.01) and was positively correlated with plant height (r = 0.62, p < 0.001), seed area (r = 0.45, p < 0.05), and thousand seed weight (r = 0.45, p < 0.05). Results from this study can inform variety selection for stakeholders interested in adopting proso millet in the inland PNW and can support future proso millet breeding efforts, particularly in this region.
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Affiliation(s)
- Tayler Reinman
- Sustainable Seed Systems Lab, Department of Crop and Soil Science, Washington States University, Pullman, WA, United States
| | - Jessica Braden
- Sustainable Seed Systems Lab, Department of Crop and Soil Science, Washington States University, Pullman, WA, United States
| | - Nathan Daniel Miller
- Spalding Lab, Department of Botany, University of Wisconsin, Madison, WI, United States
| | - Kevin M Murphy
- Sustainable Seed Systems Lab, Department of Crop and Soil Science, Washington States University, Pullman, WA, United States
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Botkin J, Medina C, Park S, Poudel K, Cha M, Lee Y, Prom LK, Curtin SJ, Xu Z, Ahn E. Analyzing Medicago spp. seed morphology using GWAS and machine learning. Sci Rep 2024; 14:17588. [PMID: 39080407 PMCID: PMC11289399 DOI: 10.1038/s41598-024-67790-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/16/2024] [Indexed: 08/02/2024] Open
Abstract
Alfalfa is widely recognized as an important forage crop. To understand the morphological characteristics and genetic basis of seed morphology in alfalfa, we screened 318 Medicago spp., including 244 Medicago sativa subsp. sativa (alfalfa) and 23 other Medicago spp., for seed area size, length, width, length-to-width ratio, perimeter, circularity, the distance between the intersection of length & width (IS) and center of gravity (CG), and seed darkness & red-green-blue (RGB) intensities. The results revealed phenotypic diversity and correlations among the tested accessions. Based on the phenotypic data of M. sativa subsp. sativa, a genome-wide association study (GWAS) was conducted using single nucleotide polymorphisms (SNPs) called against the Medicago truncatula genome. Genes in proximity to associated markers were detected, including CPR1, MON1, a PPR protein, and Wun1(threshold of 1E-04). Machine learning models were utilized to validate GWAS, and identify additional marker-trait associations for potentially complex traits. Marker S7_33375673, upstream of Wun1, was the most important predictor variable for red color intensity and highly important for brightness. Fifty-two markers were identified in coding regions. Along with strong correlations observed between seed morphology traits, these genes will facilitate the process of understanding the genetic basis of seed morphology in Medicago spp.
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Affiliation(s)
- Jacob Botkin
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Cesar Medina
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Sunchung Park
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture- Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, 20705, USA
| | - Kabita Poudel
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Minhyeok Cha
- Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Yoonjung Lee
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Louis K Prom
- United States Department of Agriculture- Agricultural Research Service, Southern Plains Agricultural Research Center, 2765 F & B Road, College Station, TX, 77845, USA
| | - Shaun J Curtin
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
- Plant Science Research Unit, United States Department of Agriculture- Agricultural Research Service, St. Paul, MN, 55108, USA
- Center for Plant Precision Genomics, University of Minnesota, St. Paul, MN, 55108, USA
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, 55108, USA
| | - Zhanyou Xu
- Plant Science Research Unit, United States Department of Agriculture- Agricultural Research Service, St. Paul, MN, 55108, USA.
| | - Ezekiel Ahn
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture- Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, 20705, USA.
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Matías J, Rodríguez MJ, Carrillo-Vico A, Casals J, Fondevilla S, Haros CM, Pedroche J, Aparicio N, Fernández-García N, Aguiló-Aguayo I, Soler-Rivas C, Caballero PA, Morte A, Rico D, Reguera M. From 'Farm to Fork': Exploring the Potential of Nutrient-Rich and Stress-Resilient Emergent Crops for Sustainable and Healthy Food in the Mediterranean Region in the Face of Climate Change Challenges. PLANTS (BASEL, SWITZERLAND) 2024; 13:1914. [PMID: 39065441 PMCID: PMC11281201 DOI: 10.3390/plants13141914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/08/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024]
Abstract
In the dynamic landscape of agriculture and food science, incorporating emergent crops appears as a pioneering solution for diversifying agriculture, unlocking possibilities for sustainable cultivation and nutritional bolstering food security, and creating economic prospects amid evolving environmental and market conditions with positive impacts on human health. This review explores the potential of utilizing emergent crops in Mediterranean environments under current climate scenarios, emphasizing the manifold benefits of agricultural and food system diversification and assessing the impact of environmental factors on their quality and consumer health. Through a deep exploration of the resilience, nutritional value, and health impacts of neglected and underutilized species (NUS) such as quinoa, amaranth, chia, moringa, buckwheat, millet, teff, hemp, or desert truffles, their capacity to thrive in the changing Mediterranean climate is highlighted, offering novel opportunities for agriculture and functional food development. By analysing how promoting agricultural diversification can enhance food system adaptability to evolving environmental conditions, fostering sustainability and resilience, we discuss recent findings that underscore the main benefits and limitations of these crops from agricultural, food science, and health perspectives, all crucial for responsible and sustainable adoption. Thus, by using a sustainable and holistic approach, this revision analyses how the integration of NUS crops into Mediterranean agrifood systems can enhance agriculture resilience and food quality addressing environmental, nutritional, biomedical, economic, and cultural dimensions, thereby mitigating the risks associated with monoculture practices and bolstering local economies and livelihoods under new climate scenarios.
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Affiliation(s)
- Javier Matías
- Agrarian Research Institute “La Orden-Valdesequera” of Extremadura (CICYTEX), 06187 Guadajira (Badajoz), Spain;
| | - María José Rodríguez
- Technological Institute of Food and Agriculture of Extremadura (INTAEX-CICYTEX), Avda. Adolfo Suárez s/n, 06007 Badajoz, Spain;
| | - Antonio Carrillo-Vico
- Instituto de Biomedicina de Sevilla, IBiS/Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Seville, Spain;
- Departamento de Bioquímica Médica y Biología Molecular e Inmunología, Facultad de Medicina, Universidad de Sevilla, 41009 Seville, Spain
| | - Joan Casals
- Fundació Miquel Agustí/HorPTA, Department of Agri-Food Engineering and Biotechnology, Universitat Politècnica de Catalunya (UPC)-BarcelonaTech, 08860 Castelldefels, Spain;
| | - Sara Fondevilla
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas, Avda. Menéndez Pidal s/n, 14004 Córdoba, Spain;
| | - Claudia Mónika Haros
- Cereal Group, Institute of Agrochemistry and Food Technology (IATA-CSIC), Av. Agustín Escardino 7, Parque Científico, 46980 Valencia, Spain;
| | - Justo Pedroche
- Group of Plant Proteins, Instituto de la Grasa, CSIC. Ctra. de Utrera Km. 1, 41013 Seville, Spain;
| | - Nieves Aparicio
- Agro-Technological Institute of Castilla y León (ITACyL), Ctra. Burgos Km. 119, 47071 Valladolid, Spain;
| | - Nieves Fernández-García
- Department of Abiotic Stress and Plant Pathology, Centro de Edafología y Biología Aplicada del Segura (CSIC), Campus Universitario de Espinardo, 30100 Murcia, Spain;
| | - Ingrid Aguiló-Aguayo
- Postharvest Programme, Institute of Agrifood Research and Technology (IRTA), Parc Agrobiotech Lleida, Parc de Gardeny, Edifici Fruitcentre, 25003 Lleida, Spain;
| | - Cristina Soler-Rivas
- Departamento de Producción y Caracterización de Nuevos Alimentos, Institute of Food Science Research-CIAL (UAM+CSIC), Campus de Cantoblanco, Universidad Autónoma de Madrid, C/Nicolas Cabrera 9, 28049 Madrid, Spain;
- Sección Departamental de Ciencias de la Alimentación, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Pedro A. Caballero
- Food Technology, Department of Agriculture and Forestry Engineering, Universidad de Valladolid, 34004 Palencia, Spain;
| | - Asunción Morte
- Departamento Biología Vegetal, Facultad de Biología, Campus Universitario de Espinardo, Universidad de Murcia, 30100 Murcia, Spain;
| | - Daniel Rico
- Department of Medicine, Dermatology and Toxicology, Universidad de Valladolid, Av. Ramón y Cajal, 7, 47005 Valladolid, Spain;
| | - María Reguera
- Departamento de Biología, Campus de Cantoblanco, Universidad Autónoma de Madrid, C/Darwin 2, 28049 Madrid, Spain
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Khound R, Rajput SG, Schnable JC, Vetriventhan M, Santra DK. Genome-wide association study reveals marker-trait associations for major agronomic traits in proso millet (Panicum miliaceum L.). PLANTA 2024; 260:44. [PMID: 38963439 DOI: 10.1007/s00425-024-04465-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
MAIN CONCLUSION The pilot-scale genome-wide association study in the US proso millet identified twenty marker-trait associations for five morpho-agronomic traits identifying genomic regions for future studies (e.g. molecular breeding and map-based cloning). Proso millet (Panicum miliaceum L.) is an ancient grain recognized for its excellent water-use efficiency and short growing season. It is an indispensable part of the winter wheat-based dryland cropping system in the High Plains of the USA. Its grains are endowed with high nutritional and health-promoting properties, making it increasingly popular in the global market for healthy grains. There is a dearth of genomic resources in proso millet for developing molecular tools to complement conventional breeding for developing high-yielding varieties. Genome-wide association study (GWAS) is a widely used method to dissect the genetics of complex traits. In this pilot study of the first-ever GWAS in the US proso millet, 71 globally diverse genotypes of 109 the US proso millet core collection were evaluated for five major morpho-agronomic traits at two locations in western Nebraska, and GWAS was conducted to identify single nucleotide polymorphisms (SNPs) associated with these traits. Analysis of variance showed that there was a significant difference among the genotypes, and all five traits were also found to be highly correlated with each other. Sequence reads from genotyping-by-sequencing (GBS) were used to identify 11,147 high-quality bi-allelic SNPs. Population structure analysis with those SNPs showed stratification within the core collection. The GWAS identified twenty marker-trait associations (MTAs) for the five traits. Twenty-nine putative candidate genes associated with the five traits were also identified. These genomic regions can be used to develop genetic markers for marker-assisted selection in proso millet breeding.
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Affiliation(s)
- Rituraj Khound
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Santosh G Rajput
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
- Dryland Genetics Inc, Ames, IA, USA
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Mani Vetriventhan
- Genebank, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Dipak K Santra
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA.
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Lu Q, Zhao H, Zhang Z, Bai Y, Zhao H, Liu G, Liu M, Zheng Y, Zhao H, Gong H, Chen L, Deng X, Hong X, Liu T, Li B, Lu P, Wen F, Wang L, Li Z, Li H, Li H, Zhang L, Ma W, Liu C, Bai Y, Xin B, Chen J, E L, Lai J, Song W. Genomic variation in weedy and cultivated broomcorn millet accessions uncovers the genetic architecture of agronomic traits. Nat Genet 2024; 56:1006-1017. [PMID: 38658793 DOI: 10.1038/s41588-024-01718-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 03/15/2024] [Indexed: 04/26/2024]
Abstract
Large-scale genomic variations are fundamental resources for crop genetics and breeding. Here we sequenced 1,904 genomes of broomcorn millet to an average of 40× sequencing depth and constructed a comprehensive variation map of weedy and cultivated accessions. Being one of the oldest cultivated crops, broomcorn millet has extremely low nucleotide diversity and remarkably rapid decay of linkage disequilibrium. Genome-wide association studies identified 186 loci for 12 agronomic traits. Many causative candidate genes, such as PmGW8 for grain size and PmLG1 for panicle shape, showed strong selection signatures during domestication. Weedy accessions contained many beneficial variations for the grain traits that are largely lost in cultivated accessions. Weedy and cultivated broomcorn millet have adopted different loci controlling flowering time for regional adaptation in parallel. Our study uncovers the unique population genomic features of broomcorn millet and provides an agronomically important resource for cereal crops.
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Affiliation(s)
- Qiong Lu
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
| | - Hainan Zhao
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
- Frontiers Science Center for Molecular Design Breeding (Ministry of Education), China Agricultural University, Beijing, People's Republic of China
| | - Zhengquan Zhang
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
| | - Yuhe Bai
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
| | - Haiming Zhao
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
| | - Guoqing Liu
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, People's Republic of China
| | - Minxuan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Yunxiao Zheng
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
| | - Haiyue Zhao
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
| | - Huihui Gong
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
| | - Lingwei Chen
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
| | - Xizhen Deng
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
| | - Xiangde Hong
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
| | - Tianxiang Liu
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
| | - Baichuan Li
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
| | - Ping Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Feng Wen
- Tongliao Agricultural and Animal Husbandry Research Institute, Tongliao, People's Republic of China
| | - Lun Wang
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, People's Republic of China
| | - Zhijiang Li
- Institute of Crop Resources Research, Heilongjiang Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Hai Li
- High Latitude Crops Institute, Shanxi Agricultural University, Datong, People's Republic of China
| | - Haiquan Li
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, People's Republic of China
| | - Like Zhang
- National Agricultural Technology Extension & Service Center, Beijing, People's Republic of China
| | - Wenhui Ma
- National Agricultural Technology Extension & Service Center, Beijing, People's Republic of China
| | - Chunqing Liu
- National Agricultural Technology Extension & Service Center, Beijing, People's Republic of China
| | - Yan Bai
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
- National Agricultural Technology Extension & Service Center, Beijing, People's Republic of China
| | - Beibei Xin
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
| | - Jian Chen
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
| | - Lizhu E
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
| | - Jinsheng Lai
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
- Frontiers Science Center for Molecular Design Breeding (Ministry of Education), China Agricultural University, Beijing, People's Republic of China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, People's Republic of China
- Sanya Institute of China Agricultural University, Sanya, People's Republic of China
| | - Weibin Song
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China.
- Frontiers Science Center for Molecular Design Breeding (Ministry of Education), China Agricultural University, Beijing, People's Republic of China.
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, People's Republic of China.
- Sanya Institute of China Agricultural University, Sanya, People's Republic of China.
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9
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Jiang Y, Dong L, Li H, Liu Y, Wang X, Liu G. Genetic linkage map construction and QTL analysis for plant height in proso millet (Panicum miliaceum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:78. [PMID: 38466414 DOI: 10.1007/s00122-024-04576-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/06/2024] [Indexed: 03/13/2024]
Abstract
KEY MESSAGE A genetic linkage map representing proso millet genome was constructed with SSR markers, and a major QTL corresponding to plant height was mapped on chromosome 14 of this map. Proso millet (Panicum miliaceum L.) has the lowest water requirements of all cultivated cereal crops. However, the lack of a genetic map and the paucity of genomic resources for this species have limited the utility of proso millet for detailed genetic studies and hampered genetic improvement programs. In this study, 97,317 simple sequence repeat (SSR) markers were developed based on the genome sequence of the proso millet landrace Longmi 4. Using some of these markers in conjunction with previously identified SSRs, an SSR-based linkage map for proso millet was successfully constructed using a large mapping population (316 F2 offspring). In total, 186 SSR markers were assigned to 18 linkage groups corresponding to the haploid chromosomes. The constructed map had a total length of 3033.42 centimorgan (cM) covering 78.17% of the assembled reference genome. The length of the 18 linkage groups ranged from 88.89 cM (Chr. 15) to 274.82 cM (Chr. 16), with an average size of 168.17 cM. To our knowledge, this is the first genetic linkage map for proso millet based on SSR markers. Plant height is one of the most important traits in crop improvement. A major QTL was repeatedly detected in different environments, explaining 8.70-24.50% of the plant height variations. A candidate gene affecting auxin biosynthesis and transport, and ROS homeostasis regulation was predicted. Thus, the linkage map and QTL analysis provided herein will promote the development of gene mining and molecular breeding in proso millet.
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Affiliation(s)
- Yanmiao Jiang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China
| | - Li Dong
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China
| | - Haiquan Li
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China
| | - Yanan Liu
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China
| | - Xindong Wang
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Guoqing Liu
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China.
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China.
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10
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Chen J, Liu Y, Liu M, Guo W, Wang Y, He Q, Chen W, Liao Y, Zhang W, Gao Y, Dong K, Ren R, Yang T, Zhang L, Qi M, Li Z, Zhao M, Wang H, Wang J, Qiao Z, Li H, Jiang Y, Liu G, Song X, Deng Y, Li H, Yan F, Dong Y, Li Q, Li T, Yang W, Cui J, Wang H, Zhou Y, Zhang X, Jia G, Lu P, Zhi H, Tang S, Diao X. Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet. Nat Genet 2023; 55:2243-2254. [PMID: 38036791 PMCID: PMC10703678 DOI: 10.1038/s41588-023-01571-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/17/2023] [Indexed: 12/02/2023]
Abstract
Broomcorn millet (Panicum miliaceum L.) is an orphan crop with the potential to improve cereal production and quality, and ensure food security. Here we present the genetic variations, population structure and diversity of a diverse worldwide collection of 516 broomcorn millet genomes. Population analysis indicated that the domesticated broomcorn millet originated from its wild progenitor in China. We then constructed a graph-based pangenome of broomcorn millet based on long-read de novo genome assemblies of 32 representative accessions. Our analysis revealed that the structural variations were highly associated with transposable elements, which influenced gene expression when located in the coding or regulatory regions. We also identified 139 loci associated with 31 key domestication and agronomic traits, including candidate genes and superior haplotypes, such as LG1, for panicle architecture. Thus, the study's findings provide foundational resources for developing genomics-assisted breeding programs in broomcorn millet.
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Affiliation(s)
- Jinfeng Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Yang Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Minxuan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenlei Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yongqiang Wang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weiyao Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yi Liao
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Wei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanzhu Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kongjun Dong
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Ruiyu Ren
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Tianyu Yang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Liyuan Zhang
- Chifeng Academy of Agricultural and Animal Husbandry Sciences, Chifeng, China
| | - Mingyu Qi
- Chifeng Academy of Agricultural and Animal Husbandry Sciences, Chifeng, China
| | - Zhiguang Li
- Chifeng Academy of Agricultural and Animal Husbandry Sciences, Chifeng, China
| | - Min Zhao
- Chifeng Academy of Agricultural and Animal Husbandry Sciences, Chifeng, China
| | - Haigang Wang
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, China
| | - Junjie Wang
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, China
| | - Zhijun Qiao
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, China
| | - Haiquan Li
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Yanmiao Jiang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Guoqing Liu
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Xiaoqiang Song
- High Latitude Crops Institute to Shanxi Academy, Shanxi Agricultural University (Shanxi Academy of Agricultural Sciences), Datong, China
| | - Yarui Deng
- High Latitude Crops Institute to Shanxi Academy, Shanxi Agricultural University (Shanxi Academy of Agricultural Sciences), Datong, China
| | - Hai Li
- High Latitude Crops Institute to Shanxi Academy, Shanxi Agricultural University (Shanxi Academy of Agricultural Sciences), Datong, China
| | - Feng Yan
- Qiqihar Sub-academy of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Yang Dong
- Qiqihar Sub-academy of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Qingquan Li
- Qiqihar Sub-academy of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Tao Li
- Institute of Crop Sciences, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Wenyao Yang
- Institute of Crop Sciences, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Jianghui Cui
- College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Hongru Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yongfeng Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ping Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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11
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Kheya SA, Talukder SK, Datta P, Yeasmin S, Rashid MH, Hasan AK, Anwar MP, Islam AA, Islam AM. Millets: The future crops for the tropics - Status, challenges and future prospects. Heliyon 2023; 9:e22123. [PMID: 38058626 PMCID: PMC10695985 DOI: 10.1016/j.heliyon.2023.e22123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 10/26/2023] [Accepted: 11/05/2023] [Indexed: 12/08/2023] Open
Abstract
Millets are small-grained nutritious minor cereal crops that are resistant to different abiotic stresses resulting from climate change. Despite their many benefits, millets have received limited attention in agricultural research, policies, and markets. Considering the importance of millets, recently the government many tropical countries including India and Bangladesh give more emphasis to millets cultivation and improvement. Moreover, Food and Agricultural Organization of the United Nations (FAO) declared 2023 to be the "International Years of Millets". In these connections, a details and updated review of the pros and cons of millets cultivation and its improvement in this region warrant due attention. The review therefore, examines the potential and main barriers to the adoption and promotion of millet cultivation in this region. These include limited research and development efforts, inadequate infrastructure and inputs, weak market linkages and demand, and insufficient awareness and knowledge about millets' nutritional and environmental benefits. This review also highlighted the prospects and strategies for scaling up millet cultivation in this region especially in Bangladesh. These include increasing public and private investment in research and extension services, strengthening farmers' organizations and market linkages, promoting millet-based value chains and products, and integrating millets into nation's food policy. The review concludes that millets might support equitable and sustainable agricultural growth, which would contribute to global food and nutritional security and could help attain the sustainable development goals (SDGs). However, achieving this potential will require concerted efforts from multiple stakeholders, including farmers, researchers and policymakers. The review emphasizes the need for a multi-disciplinary and multi-stakeholder approach that prioritizes innovation, inclusiveness, and sustainability. Lastly, the review highlights more investigation into the socioeconomic, environmental, and nutritional effects of millet production in this region with special emphasis on Bangladesh in order to support evidence-based policies and practices.
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Affiliation(s)
- Sinthia Afsana Kheya
- Department of Agronomy, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Shishir Kanti Talukder
- Department of Agronomy, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Prantika Datta
- Department of Soil Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Sabina Yeasmin
- Department of Agronomy, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Md. Harun Rashid
- Department of Agronomy, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Ahmed Khairul Hasan
- Department of Agronomy, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Md. Parvez Anwar
- Department of Agronomy, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - A.K.M. Aminul Islam
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - A.K.M. Mominul Islam
- Department of Agronomy, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
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12
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Naithani S, Deng CH, Sahu SK, Jaiswal P. Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes. Biomolecules 2023; 13:1403. [PMID: 37759803 PMCID: PMC10527062 DOI: 10.3390/biom13091403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/29/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
The availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution and build clade-specific pan-genomes of several crops. The pan-genomes of crops constructed from various cultivars, accessions, landraces, and wild ancestral species represent a compendium of genes and structural variations and allow researchers to search for the novel genes and alleles that were inadvertently lost in domesticated crops during the historical process of crop domestication or in the process of extensive plant breeding. Fortunately, many valuable genes and alleles associated with desirable traits like disease resistance, abiotic stress tolerance, plant architecture, and nutrition qualities exist in landraces, ancestral species, and crop wild relatives. The novel genes from the wild ancestors and landraces can be introduced back to high-yielding varieties of modern crops by implementing classical plant breeding, genomic selection, and transgenic/gene editing approaches. Thus, pan-genomic represents a great leap in plant research and offers new avenues for targeted breeding to mitigate the impact of global climate change. Here, we summarize the tools used for pan-genome assembly and annotations, web-portals hosting plant pan-genomes, etc. Furthermore, we highlight a few discoveries made in crops using the pan-genomic approach and future potential of this emerging field of study.
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Affiliation(s)
- Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;
| | - Cecilia H. Deng
- Molecular & Digital Breeing Group, New Cultivar Innovation, The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand;
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China;
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;
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13
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Pandey S, Singh A, Jaiswal P, Singh MK, Meena KR, Singh SK. The potentialities of omics resources for millet improvement. Funct Integr Genomics 2023; 23:210. [PMID: 37355501 DOI: 10.1007/s10142-023-01149-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023]
Abstract
Millets are nutrient-rich (nutri-rich) cereals with climate resilience attributes. However, its full productive potential is not realized due to the lack of a focused yield improvement approach, as evidenced by the available literature. Also, the lack of well-characterized genomic resources significantly limits millet improvement. But the recent availability of genomic data and advancement in omics tools has shown its enormous potential to enhance the efficiency and precision faced by conventional breeding in millet improvement. The development of high throughput genotyping platforms based on next-generation sequencing (NGS) has provided a low-cost method for genomic information, specifically for neglected nutri-rich cereals with the availability of a limited number of reference genome sequences. NGS has created new avenues for millet biotechnological interventions such as mutation-based study, GWAS, GS, and other omics technologies. The simultaneous discovery of high-throughput markers and multiplexed genotyping platform has aggressively aided marker-assisted breeding for millet improvement. Therefore, omics technology offers excellent opportunities to explore and combine useful variations for targeted traits that could impart high nutritional value to high-yielding cultivars under changing climatic conditions. In millet improvement, an in-depth account of NGS, integrating genomics data with different biotechnology tools, is reviewed in this context.
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Affiliation(s)
- Saurabh Pandey
- Department of Agricultural, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Ashutosh Singh
- Centre for Advanced Studies on Climate Change, RPCAU, Pusa, Samastipur, Bihar, 848125, India.
| | - Priyanka Jaiswal
- Lovely Professional University, Jalandhar - Delhi G.T. Road, Phagwara, Punjab, 144411, India
| | - Mithilesh Kumar Singh
- Department of Genetics and Plant Breeding, RPCAU, Pusa, Samastipur, Bihar, 848125, India
| | - Khem Raj Meena
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Kishangarh, Rajasthan, 305817, India
| | - Satish Kumar Singh
- Department of Genetics and Plant Breeding, RPCAU, Pusa, Samastipur, Bihar, 848125, India
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14
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Kumar SR, Tangsrianugul N, Suphantharika M. A Review on Isolation, Characterization, Modification, and Applications of Proso Millet Starch. Foods 2023; 12:2413. [PMID: 37372623 DOI: 10.3390/foods12122413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/12/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023] Open
Abstract
Proso millet starch (PMS) as an unconventional and underutilized millet starch is becoming increasingly popular worldwide due to its health-promoting properties. This review summarizes research progress in the isolation, characterization, modification, and applications of PMS. PMS can be isolated from proso millet grains by acidic, alkaline, or enzymatic extraction. PMS exhibits typical A-type polymorphic diffraction patterns and shows polygonal and spherical granular structures with a granule size of 0.3-17 µm. PMS is modified by chemical, physical, and biological methods. The native and modified PMS are analyzed for swelling power, solubility, pasting properties, thermal properties, retrogradation, freeze-thaw stability, and in vitro digestibility. The improved physicochemical, structural, and functional properties and digestibility of modified PMS are discussed in terms of their suitability for specific applications. The potential applications of native and modified PMS in food and nonfood products are presented. Future prospects for research and commercial use of PMS in the food industry are also highlighted.
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Affiliation(s)
- Simmi Ranjan Kumar
- Department of Biotechnology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand
| | - Nuttinee Tangsrianugul
- Department of Biotechnology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand
| | - Manop Suphantharika
- Department of Biotechnology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand
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15
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Francis N, Rajasekaran R, Rajagopalan VR, Bakya SV, Muthurajan R, Kumar AG, Alagarswamy S, Krishnamoorthy I, Thiyagarajan C. Molecular characterization and SNP identification using genotyping-by-sequencing in high-yielding mutants of proso millet. FRONTIERS IN PLANT SCIENCE 2023; 14:1108203. [PMID: 37275247 PMCID: PMC10233037 DOI: 10.3389/fpls.2023.1108203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 04/07/2023] [Indexed: 06/07/2023]
Abstract
Proso millet (Panicummiliaceum L.) is a short-duration C4 crop that is drought tolerant and nutritionally rich and can grow well in marginal lands. Though the crop has many climate-resilient traits like tolerance to drought and heat, its yield is lower than that of common cereals like rice, wheat, and maize. Being an underutilized crop, the molecular resources in the crop are limited. The main aim of the present study was to develop and characterize contrasting mutants for yield and generate functional genomic information for the trait in proso millet. Gamma irradiation-induced mutant population was screened to identify high-yielding mutants, which were evaluated up to M4 generation. One mutant with a dense panicle and high yield (ATL_hy) and one with a lax panicle and low yield (ATL_ly) along with the wild type were sequenced using the genotyping-by-sequencing approach. The variants detected as single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels) were annotated against the reference genome of proso millet. Bioinformatic analyses using the National Center for Biotechnology Information (NCBI) and UniProt databases were performed to elucidate genetic information related to the SNP variations. A total of 25,901, 30,335, and 31,488 SNPs, respectively, were detected in the wild type, ATL_hy mutants, and ATL_ly mutants. The total number of functional SNPs identified in high-yielding and low-yielding mutants was 84 and 171, respectively. Two functional SNPs in the high-yielding mutant (ATL_hy) and one in the low-yielding mutant (ATL_ly) corresponded to the gene coding for "E3 ubiquitin-protein ligase UPL7". Pathway mapping of the functional SNPs identified that two SNPs in ATL_ly were involved in the starch biosynthetic pathway coding for the starch synthase enzyme. This information can be further used in identifying genes responsible for various metabolic processes in proso millet and in designing useful genetic markers.
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Affiliation(s)
- Neethu Francis
- Department of Genetics and Plant Breeding, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India
| | - Ravikesavan Rajasekaran
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India
| | - Veera Ranjani Rajagopalan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - S. Vinothini Bakya
- Department of Genetics and Plant Breeding, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India
| | | | | | - Senthil Alagarswamy
- Department of Crop Physiology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Iyanar Krishnamoorthy
- Department of Millets, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India
| | - Chitdeshwari Thiyagarajan
- Department of Soil Science and Agricultural Chemistry, Tamil Nadu Agricultural University, Coimbatore, India
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16
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Lydia Pramitha J, Ganesan J, Francis N, Rajasekharan R, Thinakaran J. Revitalization of small millets for nutritional and food security by advanced genetics and genomics approaches. Front Genet 2023; 13:1007552. [PMID: 36699471 PMCID: PMC9870178 DOI: 10.3389/fgene.2022.1007552] [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: 07/30/2022] [Accepted: 12/07/2022] [Indexed: 01/12/2023] Open
Abstract
Small millets, also known as nutri-cereals, are smart foods that are expected to dominate food industries and diets to achieve nutritional security. Nutri-cereals are climate resilient and nutritious. Small millet-based foods are becoming popular in markets and are preferred for patients with celiac and diabetes. These crops once ruled as food and fodder but were pushed out of mainstream cultivation with shifts in dietary habits to staple crops during the green revolution. Nevertheless, small millets are rich in micronutrients and essential amino acids for regulatory activities. Hence, international and national organizations have recently aimed to restore these lost crops for their desirable traits. The major goal in reviving these crops is to boost the immune system of the upcoming generations to tackle emerging pandemics and disease infestations in crops. Earlier periods of civilization consumed these crops, which had a greater significance in ethnobotanical values. Along with nutrition, these crops also possess therapeutic traits and have shown vast medicinal use in tribal communities for the treatment of diseases like cancer, cardiovascular disease, and gastrointestinal issues. This review highlights the significance of small millets, their values in cultural heritage, and their prospects. Furthermore, this review dissects the nutritional and therapeutic traits of small millets for developing sustainable diets in near future.
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Affiliation(s)
- J. Lydia Pramitha
- Karunya Institute of Technology and Sciences, Coimbatore, India,*Correspondence: J. Lydia Pramitha,
| | - Jeeva Ganesan
- Tamil Nadu Agricultural University, Coimbatore, India
| | - Neethu Francis
- Karunya Institute of Technology and Sciences, Coimbatore, India
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17
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Khound R, Sun G, Mural RV, Schnable JC, Santra DK. SNP discovery in proso millet ( Panicum miliaceum L.) using low-pass genome sequencing. PLANT DIRECT 2022; 6:e447. [PMID: 36176305 PMCID: PMC9470529 DOI: 10.1002/pld3.447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 06/07/2023]
Abstract
Domesticated ~10,000 years ago in northern China, Proso millet (Panicum miliaceum L.) is a climate-resilient and human health-promoting cereal crop. The genome size of this self-pollinated allotetraploid is 923 Mb. Proso millet seeds are an important part of the human diet in many countries. In the USA, its use is restricted to the birdseed and pet food market. Proso millet is witnessing gradual demand in the global human health and wellness food market owing to its health-promoting properties such as low glycemic index and gluten-free. The breeding efforts for developing improved proso millet cultivars are hindered by the dearth of genomic resources available to researchers. The publication of the reference genome and availability of cost-effective NGS methodologies could lead to the identification of high-quality genetic variants, which can be incorporated into breeding pipelines. Here, we report the identification of single-nucleotide polymorphisms (SNPs) by low-pass (1×) genome sequencing of 85 diverse proso millet accessions from 23 different countries. The 2 × 150 bp Illumina paired-end reads generated after sequencing were aligned to the proso millet reference genome. The resulting sequence alignment information was used to call SNPs. We obtained 972,863 bi-allelic SNPs after quality filtering of the raw SNPs. These SNPs were used to assess the population structure and phylogenetic relationships among the accessions. Most of the accessions were found to be highly inbred with heterozygosity ranging between .05 and .20. Principal component analysis (PCA) showed that PC1 (principal component) and PC2 explained 19% of the variability in the population. PCA also clustered all the genotypes into three groups. A neighbor-joining tree clustered the genotypes into four distinct groups exhibiting diverse representation within the population. The SNPs identified in our study could be used for molecular breeding and genetics research (e.g., genetic and association mapping, and population genetics) in proso millet after proper validation.
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Affiliation(s)
- Rituraj Khound
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
- UNL Panhandle Research and Extension CenterScottsbluffNEUSA
| | - Guangchao Sun
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
- Center for Plant Science InnovationUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Ravi V. Mural
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
- Center for Plant Science InnovationUniversity of Nebraska‐LincolnLincolnNEUSA
| | - James C. Schnable
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
- Center for Plant Science InnovationUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Dipak K. Santra
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
- UNL Panhandle Research and Extension CenterScottsbluffNEUSA
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Chapman MA, He Y, Zhou M. Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security. THE NEW PHYTOLOGIST 2022; 234:1583-1597. [PMID: 35318683 PMCID: PMC9994440 DOI: 10.1111/nph.18021] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/22/2022] [Indexed: 04/14/2023]
Abstract
Underutilized crops are, by definition, under-researched compared to staple crops yet come with traits that may be especially important given climate change and the need to feed a globally increasing population. These crops are often stress-tolerant, and this combined with unique and beneficial nutritional profiles. Whilst progress is being made by generating reference genome sequences, in this Tansley Review, we show how this is only the very first step. We advocate that going 'beyond a reference genome' should be a priority, as it is only at this stage one can identify the specific genes and the adaptive alleles that underpin the valuable traits. We sum up how population genomic and pangenomic approaches have led to the identification of stress- and disease-tolerant alleles in staple crops and compare this to the small number of examples from underutilized crops. We also demonstrate how previously underutilized crops have benefitted from genomic advances and that many breeding targets in underutilized crops are often well studied in staple crops. This cross-crop population-level resequencing could lead to an understanding of the genetic basis of adaptive traits in underutilized crops. This level of investment may be crucial for fully understanding the value of these crops before they are lost.
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Affiliation(s)
- Mark A. Chapman
- Biological SciencesUniversity of SouthamptonLife Sciences Building 85, Highfield CampusSouthamptonSO17 1BJUK
| | - Yuqi He
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
| | - Meiliang Zhou
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
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19
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Wilson ML, VanBuren R. Leveraging millets for developing climate resilient agriculture. Curr Opin Biotechnol 2022; 75:102683. [DOI: 10.1016/j.copbio.2022.102683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 12/16/2021] [Accepted: 01/03/2022] [Indexed: 01/31/2023]
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Ajeesh Krishna TP, Maharajan T, Ceasar SA. Improvement of millets in the post-genomic era. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:669-685. [PMID: 35465206 PMCID: PMC8986959 DOI: 10.1007/s12298-022-01158-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 02/23/2022] [Accepted: 03/01/2022] [Indexed: 05/16/2023]
Abstract
Millets are food and nutrient security crops in the semi-arid tropics of developing countries. Crop improvement using modern tools is one of the priority areas of research in millets. The whole-genome sequence (WGS) of millets provides new insight into understanding and studying the genes, genome organization and genomic-assisted improvement of millets. The WGS of millets helps to carry out genome-wide comparison and co-linearity studies among millets and other cereal crops. This approach might lead to the identification of genes underlying biotic and abiotic stress tolerance in millets. The available genome sequence of millets can be used for SNP identification, allele discovery, association and linkage mapping, identification of valuable candidate genes, and marker-assisted breeding (MAB) programs. Next generation sequencing (NGS) technology provides opportunities for genome-assisted breeding (GAB) through genomic selection (GS) and genome-wide association studies (GAWS) for crop improvement. Clustered, regularly interspaced, short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) genome editing (GE) system provides new opportunities for millet improvement. In this review, we discuss the details on the WGS available for millets and highlight the importance of utilizing such resources in the post-genomic era for millet improvement. We also draw inroads on the utilization of various approaches such as GS, GWAS, functional genomics, gene validation and GE for millet improvement. This review might be helpful for understanding the developments in the post-genomic era of millet improvement.
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Affiliation(s)
- T P Ajeesh Krishna
- Department of Biosciences, Rajagiri College of Social Sciences, 683104 Kochi, Kerala India
| | - T Maharajan
- Department of Biosciences, Rajagiri College of Social Sciences, 683104 Kochi, Kerala India
| | - S Antony Ceasar
- Department of Biosciences, Rajagiri College of Social Sciences, 683104 Kochi, Kerala India
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