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Bulut M, Wendenburg R, Bitocchi E, Bellucci E, Kroc M, Gioia T, Susek K, Papa R, Fernie AR, Alseekh S. A comprehensive metabolomics and lipidomics atlas for the legumes common bean, chickpea, lentil and lupin. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1152-1171. [PMID: 37285370 DOI: 10.1111/tpj.16329] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/09/2023] [Accepted: 05/24/2023] [Indexed: 06/09/2023]
Abstract
Legumes represent an important component of human and livestock diets; they are rich in macro- and micronutrients such as proteins, dietary fibers and polyunsaturated fatty acids. Whilst several health-promoting and anti-nutritional properties have been associated with grain content, in-depth metabolomics characterization of major legume species remains elusive. In this article, we used both gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) to assess the metabolic diversity in the five legume species commonly grown in Europe, including common bean (Phaseolus vulgaris), chickpea (Cicer arietinum), lentil (Lens culinaris), white lupin (Lupinus albus) and pearl lupin (Lupinus mutabilis), at the tissue level. We were able to detect and quantify over 3400 metabolites covering major nutritional and anti-nutritional compounds. Specifically, the metabolomics atlas includes 224 derivatized metabolites, 2283 specialized metabolites and 923 lipids. The data generated here will serve the community as a basis for future integration to metabolomics-assisted crop breeding and facilitate metabolite-based genome-wide association studies to dissect the genetic and biochemical bases of metabolism in legume species.
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Affiliation(s)
- Mustafa Bulut
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Regina Wendenburg
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, Ancona, 60131, Italy
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, Ancona, 60131, Italy
| | - Magdalena Kroc
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, Poznan, 60-479, Poland
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, 85100, Italy
| | - Karolina Susek
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, Poznan, 60-479, Poland
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, Ancona, 60131, Italy
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center for Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center for Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
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Alseekh S, Karakas E, Zhu F, Wijesingha Ahchige M, Fernie AR. Plant biochemical genetics in the multiomics era. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4293-4307. [PMID: 37170864 PMCID: PMC10433942 DOI: 10.1093/jxb/erad177] [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: 12/13/2022] [Accepted: 05/09/2023] [Indexed: 05/13/2023]
Abstract
Our understanding of plant biology has been revolutionized by modern genetics and biochemistry. However, biochemical genetics can be traced back to the foundation of Mendelian genetics; indeed, one of Mendel's milestone discoveries of seven characteristics of pea plants later came to be ascribed to a mutation in a starch branching enzyme. Here, we review both current and historical strategies for the elucidation of plant metabolic pathways and the genes that encode their component enzymes and regulators. We use this historical review to discuss a range of classical genetic phenomena including epistasis, canalization, and heterosis as viewed through the lens of contemporary high-throughput data obtained via the array of approaches currently adopted in multiomics studies.
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Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Esra Karakas
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070 Wuhan, China
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
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Arca M, Gouesnard B, Mary-Huard T, Le Paslier MC, Bauland C, Combes V, Madur D, Charcosset A, Nicolas SD. Genotyping of DNA pools identifies untapped landraces and genomic regions to develop next-generation varieties. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1123-1139. [PMID: 36740649 DOI: 10.1111/pbi.14022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 01/18/2023] [Indexed: 05/27/2023]
Abstract
Landraces, that is, traditional varieties, have a large diversity that is underexploited in modern breeding. A novel DNA pooling strategy was implemented to identify promising landraces and genomic regions to enlarge the genetic diversity of modern varieties. As proof of concept, DNA pools from 156 American and European maize landraces representing 2340 individuals were genotyped with an SNP array to assess their genome-wide diversity. They were compared to elite cultivars produced across the 20th century, represented by 327 inbred lines. Detection of selective footprints between landraces of different geographic origin identified genes involved in environmental adaptation (flowering times, growth) and tolerance to abiotic and biotic stress (drought, cold, salinity). Promising landraces were identified by developing two novel indicators that estimate their contribution to the genome of inbred lines: (i) a modified Roger's distance standardized by gene diversity and (ii) the assignation of lines to landraces using supervised analysis. It showed that most landraces do not have closely related lines and that only 10 landraces, including famous landraces as Reid's Yellow Dent, Lancaster Surecrop and Lacaune, cumulated half of the total contribution to inbred lines. Comparison of ancestral lines directly derived from landraces with lines from more advanced breeding cycles showed a decrease in the number of landraces with a large contribution. New inbred lines derived from landraces with limited contributions enriched more the haplotype diversity of reference inbred lines than those with a high contribution. Our approach opens an avenue for the identification of promising landraces for pre-breeding.
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Affiliation(s)
- Mariangela Arca
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Brigitte Gouesnard
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Tristan Mary-Huard
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Cyril Bauland
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Valérie Combes
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Delphine Madur
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Alain Charcosset
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Stéphane D Nicolas
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
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Tagiakas RI, Avdikos ID, Goula A, Koutis K, Nianiou-Obeidat I, Mavromatis AG. Characterization and evaluation of Greek tomato landraces for productivity and fruit quality traits related to sustainable low-input farming systems. FRONTIERS IN PLANT SCIENCE 2022; 13:994530. [PMID: 36578333 PMCID: PMC9791058 DOI: 10.3389/fpls.2022.994530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Tomato is one of the most important horticultural species all over the world, having high level of consumption and employing many people, both in the primary sector (farmers) and in the secondary sector (traders, seed companies and processors). Nowadays, the use of commercial tomato F1 hybrids tends to prevail because of high yield potential and homogeneity of fruits which are often characterized by lack of quality and sensory characteristics. In contrast, tomato landraces have outstanding quality traits, such as high concentration of antioxidants and organoleptic compounds, as well as often include desirable genes in their genome for adaptability, plasticity, response to low-input conditions, and high fruit nutritional value. Thus, they are appropriate material in the use of sustainable agricultural management systems or as gene donors for the development of new type of tomato cultivars suitable for low-input farming systems. The present experimental study refers to 22 Greek tomato landraces and two commercial cultivars (cv. Macedonia and the F1 hybrid Formula) used as controls, which were characterized by phenotypical markers and evaluated under low-input sustainable farming conditions. Specifically, during this research, measurements were taken regarding yield potential (early production, number of fruits per plant, fruit weight, total yield) and fruit quality traits, such as physicochemical characteristics (pH, acidity, and soluble solid components - Brixο) also according to nutritional value (content of ascorbic acid, lycopene, total carotenoids, and total phenolics) of tomato fruits. In the most promising landraces (cv. Milo Chalkidiki, cv. Eratiras, cv. Lotos, cv. Aspros lotos, cv. Pantaroza, cv. Karabola and cv. Kardia Vodiou), having comparable yield and fruit quality traits with commercial cultivars, intrapopulation "Pure line selection" method, under low-input farming conditions was applied for two years. Following this approach, we succeed to determine the level of yield potential and provide information for the nutritive value and utilization of typical tomato landraces, improving their yield and fruit quality traits, following a mild intrapopulation selection under low-input farming conditions. This data pipeline is expected to be of interest for organic farmers and processors of high nutritive tomato products, with low carbon footprint for the environment.
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Affiliation(s)
- R. I. Tagiakas
- Aristotle University, Lab of Genetics and Plant Breeding, School of Agriculture, Thessaloniki, Greece
| | - I. D. Avdikos
- International Hellenic University, Lab of Horticulture, Thessaloniki, Greece
| | - A. Goula
- Aristotle University, Lab of Food Engineering and Processing, School of Agriculture, Thessaloniki, Greece
| | - K. Koutis
- Aegilops, Network for Biodiversity, Volos, Greece
| | - Irini Nianiou-Obeidat
- Aristotle University, Lab of Genetics and Plant Breeding, School of Agriculture, Thessaloniki, Greece
| | - A. G. Mavromatis
- Aristotle University, Lab of Genetics and Plant Breeding, School of Agriculture, Thessaloniki, Greece
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Jian L, Yan J, Liu J. De Novo Domestication in the Multi-Omics Era. PLANT & CELL PHYSIOLOGY 2022; 63:1592-1606. [PMID: 35762778 DOI: 10.1093/pcp/pcac077] [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: 01/14/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Most cereal crops were domesticated within the last 12,000 years and subsequently spread around the world. These crops have been nourishing the world by supplying a primary energy and nutrient source, thereby playing a critical role in determining the status of human health and sustaining the global population. Here, we review the major challenges of future agriculture and emphasize the utilization of wild germplasm. De novo domestication is one of the most straightforward strategies to manipulate domestication-related and/or other genes with known function, and thereby introduce desired traits into wild plants. We also summarize known causal variations and their corresponding pathways in order to better understand the genetic basis of crop evolution, and how this knowledge could facilitate de novo domestication. Indeed knowledge-driven de novo domestication has great potential for the development of new sustainable crops that have climate-resilient high yield with low resource input and meet individual nutrient needs. Finally, we discuss current opportunities for and barriers to knowledge-driven de novo domestication.
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Affiliation(s)
- Liumei Jian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Bohra A, Tiwari A, Kaur P, Ganie SA, Raza A, Roorkiwal M, Mir RR, Fernie AR, Smýkal P, Varshney RK. The Key to the Future Lies in the Past: Insights from Grain Legume Domestication and Improvement Should Inform Future Breeding Strategies. PLANT & CELL PHYSIOLOGY 2022; 63:1554-1572. [PMID: 35713290 PMCID: PMC9680861 DOI: 10.1093/pcp/pcac086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/09/2022] [Accepted: 06/15/2022] [Indexed: 05/11/2023]
Abstract
Crop domestication is a co-evolutionary process that has rendered plants and animals significantly dependent on human interventions for survival and propagation. Grain legumes have played an important role in the development of Neolithic agriculture some 12,000 years ago. Despite being early companions of cereals in the origin and evolution of agriculture, the understanding of grain legume domestication has lagged behind that of cereals. Adapting plants for human use has resulted in distinct morpho-physiological changes between the wild ancestors and domesticates, and this distinction has been the focus of several studies aimed at understanding the domestication process and the genetic diversity bottlenecks created. Growing evidence from research on archeological remains, combined with genetic analysis and the geographical distribution of wild forms, has improved the resolution of the process of domestication, diversification and crop improvement. In this review, we summarize the significance of legume wild relatives as reservoirs of novel genetic variation for crop breeding programs. We describe key legume features, which evolved in response to anthropogenic activities. Here, we highlight how whole genome sequencing and incorporation of omics-level data have expanded our capacity to monitor the genetic changes accompanying these processes. Finally, we present our perspective on alternative routes centered on de novo domestication and re-domestication to impart significant agronomic advances of novel crops over existing commodities. A finely resolved domestication history of grain legumes will uncover future breeding targets to develop modern cultivars enriched with alleles that improve yield, quality and stress tolerance.
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Affiliation(s)
- Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Abha Tiwari
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kalyanpur, Kanpur 208024, India
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Showkat Ahmad Ganie
- Department of Biotechnology, Visva-Bharati, Santiniketan, Santiniketan Road, Bolpur 731235, India
| | - Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China
| | - Manish Roorkiwal
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), UAE University, Sheik Khalifa Bin Zayed Street, Al Ain, Abu Dhabi 15551, UAE
| | - Reyazul Rouf Mir
- Division of Genetics & Plant Breeding, Faculty of Agriculture, SKUAST, Shalimar, Srinagar 190025, India
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacky University, Křížkovského 511/8, Olomouc 78371, Czech Republic
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Metabolomics and Chemoinformatics in Agricultural Biotechnology Research: Complementary Probes in Unravelling New Metabolites for Crop Improvement. BIOLOGY 2022; 11:biology11081156. [PMID: 36009783 PMCID: PMC9405339 DOI: 10.3390/biology11081156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/16/2022] [Accepted: 07/28/2022] [Indexed: 11/25/2022]
Abstract
Simple Summary The world is facing an overarching threat to food security, particularly in developing nations. The issue is further exacerbated by the apparent impacts of biotic and abiotic stresses driving down crop yields and productivity. Conventional strategies to improve yields and sustain productivity have been employed, including plant breeding for favourable and resilient agronomic traits. However, the efficacy and success rates of these methods are declining, partly due to the rapid changes in climate variability and the emergence of new and resistant phytopathogens. Additionally, the process of creating new and improved transgenic varieties of crops is long and can be expensive. Thus, new and innovative technologies are required for crop improvement. This review explores recent advances in the science of metabolomics and chemoinformatics, which have presented an avenue for rapid and robust analysis; moreover, it explores the elucidation of the complex plant metabolome, providing the opportunity to decipher the reactionary mechanisms of plants to the surrounding environment through their metabolic activity. As such, specific metabolites can, thus, be selected as biomarkers for crop improvement based on their functional characteristics under varying environmental conditions (growth, development, and defence). This new knowledge can enhance breeding practices through rapid and robust metabolic engineering techniques for sustainable agriculture. Abstract The United Nations (UN) estimate that the global population will reach 10 billion people by 2050. These projections have placed the agroeconomic industry under immense pressure to meet the growing demand for food and maintain global food security. However, factors associated with climate variability and the emergence of virulent plant pathogens and pests pose a considerable threat to meeting these demands. Advanced crop improvement strategies are required to circumvent the deleterious effects of biotic and abiotic stress and improve yields. Metabolomics is an emerging field in the omics pipeline and systems biology concerned with the quantitative and qualitative analysis of metabolites from a biological specimen under specified conditions. In the past few decades, metabolomics techniques have been extensively used to decipher and describe the metabolic networks associated with plant growth and development and the response and adaptation to biotic and abiotic stress. In recent years, metabolomics technologies, particularly plant metabolomics, have expanded to screening metabolic biomarkers for enhanced performance in yield and stress tolerance for metabolomics-assisted breeding. This review explores the recent advances in the application of metabolomics in agricultural biotechnology for biomarker discovery and the identification of new metabolites for crop improvement. We describe the basic plant metabolomics workflow, the essential analytical techniques, and the power of these combined analytical techniques with chemometrics and chemoinformatics tools. Furthermore, there are mentions of integrated omics systems for metabolomics-assisted breeding and of current applications.
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Singh M, Avtar R, Kumar N, Punia R, Pal A, Lakra N, Kumari N, Kumar D, Naruka A, Bishnoi M, Khedwal RS, Choudhary RR, Singh A, Meena RK, Dhillon A, Singh VK. Genetic Analysis for Resistance to Sclerotinia Stem Rot, Yield and Its Component Traits in Indian Mustard [ Brassica juncea (L.) Czern & Coss.]. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050671. [PMID: 35270141 PMCID: PMC8912491 DOI: 10.3390/plants11050671] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/17/2022] [Accepted: 02/23/2022] [Indexed: 06/12/2023]
Abstract
Understanding the mode of gene action that controls seed yield and Sclerotinia stem rot resistance in Indian mustard is critical for boosting yield potential. In a line × tester mating design, ten susceptible lines and four resistant testers were used to conduct genetic analysis. The significance of general combining ability (GCA) and specific combining ability (SCA) variances revealed that both additive and non-additive gene actions were involved in the inheritance of Sclerotinia stem rot resistance and yield attributing traits. In addition to 1000-seed weight and number of primary and secondary branches/plant, the genotypes RH 1569 (line) and DRMR 2035 (tester) appeared to be the strongest general combiners for Sclerotinia stem rot resistance. RH 1657 × EC 597317 was the only cross among several that demonstrated a significant desired SCA value for Sclerotinia rot resistance. Regarding SCA effects for yield and component traits, the cross RH 1658 × EC 597328 performed best, with a non-significant but acceptable negative SCA effect for resistance. DRMR 2035, RH 1222-28, RH 1569, RH 1599-41, RH 1657, RH 1658, and EC 597328 are promising genotypes to use as parents in future heterosis breeding and for obtaining populations with high yield potential and greater resistance to Sclerotinia stem rot disease in Indian mustard, based on GCA effects of parents, per se performance, and SCA effects of hybrids. Days to 50% flowering, number of primary branches/plant, main shoot length, and 1000-seed weight all had a high genotypic coefficient of variability (GCV), broad-sense heritability (h2bs), and genetic advance as percent of the mean (GAM) values, as well as significant and desirable correlations and direct effects on seed yield. As a result, these traits have been recognized as the most critical selection criterion for Indian mustard breeding programs.
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Affiliation(s)
- Manjeet Singh
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Ram Avtar
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Neeraj Kumar
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Rakesh Punia
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Ajay Pal
- Department of Biochemistry, CCS Haryana Agricultural University, Hisar 125004, India;
| | - Nita Lakra
- Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, Hisar 125004, India;
| | - Nisha Kumari
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Dalip Kumar
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Anu Naruka
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Mahavir Bishnoi
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Rajbir Singh Khedwal
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Raju Ram Choudhary
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Anoop Singh
- Department of Botany, Maharshi Dayanand University, Rohtak 124001, India;
| | - Ravindra Kumar Meena
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Ankit Dhillon
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Vivek K. Singh
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
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9
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Diversity: current and prospective secondary metabolites for nutrition and medicine. Curr Opin Biotechnol 2021; 74:164-170. [PMID: 34942505 DOI: 10.1016/j.copbio.2021.11.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/28/2021] [Accepted: 11/29/2021] [Indexed: 12/11/2022]
Abstract
Plants have been used as sources of food, feed and medicine for millennia. The ever-increasing population has, however, dramatically increased the burden on our arable land to meet nutritional demand. Concomitantly, and in part due to poor nutrition, we are faced with massive increases in chronic diseases, meaning the need for medicine has also increased. Here, we look back on research in these areas, surveying the polyphenols as a case study for health-conferring metabolites. We conclude that the tools that will allow us to breed more nutritious crops are all at hand. We stress that collaboration between plant and medical research needs to be intensified in order to improve our understanding of the bioactivities. In doing so, we attempt to draw a roadmap for the use of plants for mid-21st Century human health.
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Kallow S, Panis B, Vu DT, Vu TD, Paofa J, Mertens A, Swennen R, Janssens SB. Maximizing genetic representation in seed collections from populations of self and cross-pollinated banana wild relatives. BMC PLANT BIOLOGY 2021; 21:415. [PMID: 34503446 PMCID: PMC8431884 DOI: 10.1186/s12870-021-03142-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/06/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Conservation of plant genetic resources, including the wild relatives of crops, plays an important and well recognised role in addressing some of the key challenges faced by humanity and the planet including ending hunger and biodiversity loss. However, the genetic diversity and representativeness of ex situ collections, especially that contained in seed collections, is often unknown. This limits meaningful assessments against conservation targets, impairs targeting of future collecting and limits their use. We assessed genetic representation of seed collections compared to source populations for three wild relatives of bananas and plantains. Focal species and sampling regions were M. acuminata subsp. banksii (Papua New Guinea), M. balbisiana (Viet Nam) and M. maclayi s.l. (Bougainville, Papua New Guinea). We sequenced 445 samples using suites of 16-20 existing and newly developed taxon-specific polymorphic microsatellite markers. Samples of each species were from five populations in a region; 15 leaf samples from different individuals and 16 seed samples from one infructescence ('bunch') were analysed for each population. RESULTS Allelic richness of seeds compared to populations was 51, 81 and 93% (M. acuminata, M. balbisiana and M. maclayi respectively). Seed samples represented all common alleles in populations but omitted some rarer alleles. The number of collections required to achieve the 70% target of the Global Strategy for Plant Conservation was species dependent, relating to mating systems. Musa acuminata populations had low heterozygosity and diversity, indicating self-fertilization; many bunches were needed (> 15) to represent regional alleles to 70%; over 90% of the alleles from a bunch are included in only two seeds. Musa maclayi was characteristically cross-fertilizing; only three bunches were needed to represent regional alleles; within a bunch, 16 seeds represent alleles. Musa balbisiana, considered cross-fertilized, had low genetic diversity; seeds of four bunches are needed to represent regional alleles; only two seeds represent alleles in a bunch. CONCLUSIONS We demonstrate empirical measurement of representation of genetic material in seeds collections in ex situ conservation towards conservation targets. Species mating systems profoundly affected genetic representation in seed collections and therefore should be a primary consideration to maximize genetic representation. Results are applicable to sampling strategies for other wild species.
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Affiliation(s)
- Simon Kallow
- Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium.
- Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium.
- Royal Botanic Gardens Kew, Millennium Seed Bank, Wakehurst, Ardingly, Sussex, RH17 6TN, UK.
| | - Bart Panis
- Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
- Bioversity International, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Dang Toan Vu
- Plant Resources Center, Ankhanh, Hoaiduc, Hà Noi, Viet Nam
| | - Tuong Dang Vu
- Plant Resources Center, Ankhanh, Hoaiduc, Hà Noi, Viet Nam
| | - Janet Paofa
- National Agricultural Research Institute, Laloki, Port Moresby, 121, Papua New Guinea
| | - Arne Mertens
- Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
- Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium
- Department of Biology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 31, 3001, Leuven, Belgium
| | - Rony Swennen
- Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
- International Institute of Tropical Agriculture, Plot 15B Naguru East Road, Upper Naguru, 7878, Kampala, Uganda
| | - Steven B Janssens
- Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium
- Department of Biology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 31, 3001, Leuven, Belgium
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11
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Athinodorou F, Foukas P, Tsaniklidis G, Kotsiras A, Chrysargyris A, Delis C, Kyratzis AC, Tzortzakis N, Nikoloudakis N. Morphological Diversity, Genetic Characterization, and Phytochemical Assessment of the Cypriot Tomato Germplasm. PLANTS (BASEL, SWITZERLAND) 2021; 10:1698. [PMID: 34451743 PMCID: PMC8401825 DOI: 10.3390/plants10081698] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/14/2021] [Accepted: 08/17/2021] [Indexed: 01/07/2023]
Abstract
Tomato (Solanum lycopersicum L.) is considered one of the most valuable and versatile vegetable crops globally and also serves as a significant model species for fruit developmental biology. Despite its significance, a severe genetic bottleneck and intense selection of genotypes with specific qualitative traits have resulted in the prevalence of a restricted number of (geno)types, also causing a lack of diversity across widespread cultivated types. As a result, the re-emergence of landraces as well as traditional and heirloom varieties is largely acknowledged as a countermeasure to restore phenotypic, phytochemical and genetic diversity while enriching the aroma/taste tomato palette. On those grounds, the Cypriot tomato germplasm was assessed and characterized. Ten landrace accessions were evaluated under greenhouse conditions and data were collected for 24 IPGRI discrete phenotypic traits. Grouping of accessions largely reflected the fruit shape and size; four different fruit types were recorded across accessions (flattened, heart-shaped, rounded and highly rounded). Moreover, a single run panel consisting of ten SSRs was developed and applied in order to genetically characterize 190 Cypriot genotypes and foreign heirloom varieties. Based on genetic indexes it was established that tomato landraces have a rather low level of heterogeneity and genetic variation. Finally, mineral and phytochemical analyses were conducted in order to estimate biochemical attributes (total phenolics, ascorbic acid, lycopene, β-carotene, total soluble content, titratable acidity) across genotypes; thus, ascertaining that the Cypriot panel has a high nutritional value. Due to the thermo-drought adaptation and tolerance of these genotypes, the current study serves as a roadmap for future breeding efforts in order to incorporate desirable traits or develop novel tomato lines combining resilience and alimentary value.
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Affiliation(s)
- Filio Athinodorou
- Department of Agricultural Science, Biotechnology and Food Science, Cyprus University of Technology, Limassol 3036, Cyprus; (F.A.); (P.F.); (A.C.); (N.T.)
| | - Petros Foukas
- Department of Agricultural Science, Biotechnology and Food Science, Cyprus University of Technology, Limassol 3036, Cyprus; (F.A.); (P.F.); (A.C.); (N.T.)
| | - Georgios Tsaniklidis
- Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization ELGO-DIMITRA, Mesa Katsabas, 71307 Heraklion, Greece;
| | - Anastasios Kotsiras
- Department of Agricultural Technology, School of Agricultural Technology and Food Technology and Nutrition, University of Peloponnese, 24100 Kalamata, Greece; (A.K.); (C.D.)
| | - Antonios Chrysargyris
- Department of Agricultural Science, Biotechnology and Food Science, Cyprus University of Technology, Limassol 3036, Cyprus; (F.A.); (P.F.); (A.C.); (N.T.)
| | - Costas Delis
- Department of Agricultural Technology, School of Agricultural Technology and Food Technology and Nutrition, University of Peloponnese, 24100 Kalamata, Greece; (A.K.); (C.D.)
| | - Angelos C. Kyratzis
- Vegetable Crop Sector, Agricultural Research Institute—Ministry of Agriculture, Rural Development and Environment, Nicosia 1516, Cyprus;
| | - Nikolaos Tzortzakis
- Department of Agricultural Science, Biotechnology and Food Science, Cyprus University of Technology, Limassol 3036, Cyprus; (F.A.); (P.F.); (A.C.); (N.T.)
| | - Nikolaos Nikoloudakis
- Department of Agricultural Science, Biotechnology and Food Science, Cyprus University of Technology, Limassol 3036, Cyprus; (F.A.); (P.F.); (A.C.); (N.T.)
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12
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Abstract
Tremendous chemical diversity is the hallmark of plants and is supported by highly complex biochemical machinery. Plant metabolic enzymes originated and were transferred from eukaryotic and prokaryotic ancestors and further diversified by the unprecedented rates of gene duplication and functionalization experienced in land plants. Unlike microbes, which have frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO2 and have experienced very few, if any, gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner and on existing networks under various evolutionary constraints. This review aims to take a broader view of plant metabolic evolution and lay a framework to further explore evolutionary mechanisms of the complex metabolic network. Understanding the underlying metabolic and genetic constraints is also an empirical prerequisite for rational engineering and redesigning of plant metabolic pathways.
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Affiliation(s)
- Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany;
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13
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Wu X, Liang Y, Gao H, Wang J, Zhao Y, Hua L, Yuan Y, Wang A, Zhang X, Liu J, Zhou J, Meng X, Zhang D, Lin S, Huang X, Han B, Li J, Wang Y. Enhancing rice grain production by manipulating the naturally evolved cis-regulatory element-containing inverted repeat sequence of OsREM20. MOLECULAR PLANT 2021; 14:997-1011. [PMID: 33741527 DOI: 10.1016/j.molp.2021.03.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/19/2021] [Accepted: 03/14/2021] [Indexed: 05/05/2023]
Abstract
Grain number per panicle (GNP) is an important agronomic trait that contributes to rice grain yield. Despite its importance in rice breeding, the molecular mechanism underlying GNP regulation remains largely unknown. In this study, we identified a previously unrecognized regulatory gene that controls GNP in rice, Oryza sativa REPRODUCTIVE MERISTEM 20 (OsREM20), which encodes a B3 domain transcription factor. Through genetic analysis and transgenic validation we found that genetic variation in the CArG box-containing inverted repeat (IR) sequence of the OsREM20 promoter alters its expression level and contributes to GNP variation among rice varieties. Furthermore, we revealed that the IR sequence regulates OsREM20 expression by affecting the direct binding of OsMADS34 to the CArG box within the IR sequence. Interestingly, the divergent pOsREM20IR and pOsREM20ΔIR alleles were found to originate from different Oryza rufipogon accessions, and were independently inherited into the japonica and indica subspecies, respectively, during domestication. Importantly, we demonstrated that IR sequence variations in the OsREM20 promoter can be utilized for germplasm improvement through either genome editing or traditional breeding. Taken together, our study characterizes novel genetic variations responsible for GNP diversity in rice, reveals the underlying molecular mechanism in the regulation of agronomically important gene expression, and provides a promising strategy for improving rice production by manipulating the cis-regulatory element-containing IR sequence.
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Affiliation(s)
- Xiaowei Wu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Liang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Hengbin Gao
- College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Jiyao Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Zhao
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Lekai Hua
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yundong Yuan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ahong Wang
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Xiaohui Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiafan Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Zhou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangbing Meng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dahan Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shaoyang Lin
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Bin Han
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yonghong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China; College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China.
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14
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Alseekh S, Scossa F, Wen W, Luo J, Yan J, Beleggia R, Klee HJ, Huang S, Papa R, Fernie AR. Domestication of Crop Metabolomes: Desired and Unintended Consequences. TRENDS IN PLANT SCIENCE 2021; 26:650-661. [PMID: 33653662 DOI: 10.1016/j.tplants.2021.02.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 05/02/2023]
Abstract
The majority of the crops and vegetables of today were domesticated from their wild progenitors within the past 12 000 years. Considerable research effort has been expended on characterizing the genes undergoing positive and negative selection during the processes of crop domestication and improvement. Many studies have also documented how the contents of a handful of metabolites have been altered during human selection, but we are only beginning to unravel the true extent of the metabolic consequences of breeding. We highlight how crop metabolomes have been wittingly or unwittingly shaped by the processes of domestication, and highlight how we can identify new targets for metabolite engineering for the purpose of de novo domestication of crop wild relatives.
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Affiliation(s)
- Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), 00178 Rome, Italy
| | - Weiwei Wen
- Key laboratory of Horticultural Plant Biology (MOE),College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Hubei, Wuhan 430070, China
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University Hubei, Wuhan 430070, China; College of Tropical Crops, Hainan University, Haikou, Hainan, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University Hubei, Wuhan 430070, China
| | - Romina Beleggia
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-, CI), 71122 Foggia, Italy
| | - Harry J Klee
- Horticultural Sciences, University of Florida, Gainesville, FL, USA
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture - Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria.
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15
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Scossa F, Alseekh S, Fernie AR. Integrating multi-omics data for crop improvement. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153352. [PMID: 33360148 DOI: 10.1016/j.jplph.2020.153352] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 05/26/2023]
Abstract
Our agricultural systems are now in urgent need to secure food for a growing world population. To meet this challenge, we need a better characterization of plant genetic and phenotypic diversity. The combination of genomics, transcriptomics and metabolomics enables a deeper understanding of the mechanisms underlying the complex architecture of many phenotypic traits of agricultural relevance. We review the recent advances in plant genomics to see how these can be integrated with broad molecular profiling approaches to improve our understanding of plant phenotypic variation and inform crop breeding strategies.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Golm, Germany; Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), 00178, Rome, Italy.
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Golm, Germany; Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Golm, Germany; Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria.
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16
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Arca M, Mary-Huard T, Gouesnard B, Bérard A, Bauland C, Combes V, Madur D, Charcosset A, Nicolas SD. Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array. FRONTIERS IN PLANT SCIENCE 2021; 11:568699. [PMID: 33488638 PMCID: PMC7817617 DOI: 10.3389/fpls.2020.568699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/12/2020] [Indexed: 05/13/2023]
Abstract
Genebanks harbor original landraces carrying many original favorable alleles for mitigating biotic and abiotic stresses. Their genetic diversity remains, however, poorly characterized due to their large within genetic diversity. We developed a high-throughput, cheap and labor saving DNA bulk approach based on single-nucleotide polymorphism (SNP) Illumina Infinium HD array to genotype landraces. Samples were gathered for each landrace by mixing equal weights from young leaves, from which DNA was extracted. We then estimated allelic frequencies in each DNA bulk based on fluorescent intensity ratio (FIR) between two alleles at each SNP using a two step-approach. We first tested either whether the DNA bulk was monomorphic or polymorphic according to the two FIR distributions of individuals homozygous for allele A or B, respectively. If the DNA bulk was polymorphic, we estimated its allelic frequency by using a predictive equation calibrated on FIR from DNA bulks with known allelic frequencies. Our approach: (i) gives accurate allelic frequency estimations that are highly reproducible across laboratories, (ii) protects against false detection of allele fixation within landraces. We estimated allelic frequencies of 23,412 SNPs in 156 landraces representing American and European maize diversity. Modified Roger's genetic Distance between 156 landraces estimated from 23,412 SNPs and 17 simple sequence repeats using the same DNA bulks were highly correlated, suggesting that the ascertainment bias is low. Our approach is affordable, easy to implement and does not require specific bioinformatics support and laboratory equipment, and therefore should be highly relevant for large-scale characterization of genebanks for a wide range of species.
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Affiliation(s)
- Mariangela Arca
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
| | - Tristan Mary-Huard
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
| | - Brigitte Gouesnard
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Aurélie Bérard
- Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux, Evry-Courcouronnes, France
| | - Cyril Bauland
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
| | - Valérie Combes
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
| | - Delphine Madur
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
| | - Alain Charcosset
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
| | - Stéphane D. Nicolas
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
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17
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Hübner S, Kantar MB. Tapping Diversity From the Wild: From Sampling to Implementation. FRONTIERS IN PLANT SCIENCE 2021; 12:626565. [PMID: 33584776 PMCID: PMC7873362 DOI: 10.3389/fpls.2021.626565] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/07/2021] [Indexed: 05/05/2023]
Abstract
The diversity observed among crop wild relatives (CWRs) and their ability to flourish in unfavorable and harsh environments have drawn the attention of plant scientists and breeders for many decades. However, it is also recognized that the benefit gained from using CWRs in breeding is a potential rose between thorns of detrimental genetic variation that is linked to the trait of interest. Despite the increased interest in CWRs, little attention was given so far to the statistical, analytical, and technical considerations that should guide the sampling design, the germplasm characterization, and later its implementation in breeding. Here, we review the entire process of sampling and identifying beneficial genetic variation in CWRs and the challenge of using it in breeding. The ability to detect beneficial genetic variation in CWRs is strongly affected by the sampling design which should be adjusted to the spatial and temporal variation of the target species, the trait of interest, and the analytical approach used. Moreover, linkage disequilibrium is a key factor that constrains the resolution of searching for beneficial alleles along the genome, and later, the ability to deplete linked deleterious genetic variation as a consequence of genetic drag. We also discuss how technological advances in genomics, phenomics, biotechnology, and data science can improve the ability to identify beneficial genetic variation in CWRs and to exploit it in strive for higher-yielding and sustainable crops.
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Affiliation(s)
- Sariel Hübner
- Galilee Research Institute (MIGAL), Tel-Hai College, Qiryat Shemona, Israel
- *Correspondence: Sariel Hübner,
| | - Michael B. Kantar
- Department of Tropical Plant and Soil Sciences, University of Hawai’i at Mânoa, Honolulu, HI, United States
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18
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Tamburino R, Sannino L, Cafasso D, Cantarella C, Orrù L, Cardi T, Cozzolino S, D’Agostino N, Scotti N. Cultivated Tomato ( Solanum lycopersicum L.) Suffered a Severe Cytoplasmic Bottleneck during Domestication: Implications from Chloroplast Genomes. PLANTS 2020; 9:plants9111443. [PMID: 33114641 PMCID: PMC7692331 DOI: 10.3390/plants9111443] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/13/2022]
Abstract
In various crops, genetic bottlenecks occurring through domestication can limit crop resilience to biotic and abiotic stresses. In the present study, we investigated nucleotide diversity in tomato chloroplast genome through sequencing seven plastomes of cultivated accessions from the Campania region (Southern Italy) and two wild species among the closest (Solanum pimpinellifolium) and most distantly related (S. neorickii) species to cultivated tomatoes. Comparative analyses among the chloroplast genomes sequenced in this work and those available in GenBank allowed evaluating the variability of plastomes and defining phylogenetic relationships. A dramatic reduction in genetic diversity was detected in cultivated tomatoes, nonetheless, a few de novo mutations, which still differentiated the cultivated tomatoes from the closest wild relative S. pimpinellifolium, were detected and are potentially utilizable as diagnostic markers. Phylogenetic analyses confirmed that S. pimpinellifolium is the closest ancestor of all cultivated tomatoes. Local accessions all clustered together and were strictly related with other cultivated tomatoes (S. lycopersicum group). Noteworthy, S. lycopersicum var. cerasiforme resulted in a mixture of both cultivated and wild tomato genotypes since one of the two analyzed accessions clustered with cultivated tomato, whereas the other with S. pimpinellifolium. Overall, our results revealed a very reduced cytoplasmic variability in cultivated tomatoes and suggest the occurrence of a cytoplasmic bottleneck during their domestication.
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Affiliation(s)
- Rachele Tamburino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy; (R.T.); (L.S.)
| | - Lorenza Sannino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy; (R.T.); (L.S.)
| | - Donata Cafasso
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy; (D.C.); (S.C.)
| | - Concita Cantarella
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy; (C.C.); (T.C.); (N.D.)
| | - Luigi Orrù
- CREA Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d’Arda (PC), Italy;
| | - Teodoro Cardi
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy; (C.C.); (T.C.); (N.D.)
| | - Salvatore Cozzolino
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy; (D.C.); (S.C.)
| | - Nunzio D’Agostino
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy; (C.C.); (T.C.); (N.D.)
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 133, 80055 Portici (NA), Italy
| | - Nunzia Scotti
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy; (R.T.); (L.S.)
- Correspondence: ; Tel.: +39-0812-53-9482
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Hyeon H, Xu JL, Kim JK, Choi Y. Comparative metabolic profiling of cultivated and wild black soybeans reveals distinct metabolic alterations associated with their domestication. Food Res Int 2020; 134:109290. [PMID: 32517920 DOI: 10.1016/j.foodres.2020.109290] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/15/2020] [Accepted: 05/01/2020] [Indexed: 12/26/2022]
Abstract
Generally, cultivated black soybean (CBS) has been used as a major source of various nutrients for humans and animals. To assess the metabolic alterations induced by domestication in soybean, we performed a comprehensive metabolite profiling of 56 soybean varieties, including 28 CBS and 28 wild black soybean (WBS) varieties. A total of 48 metabolites were characterized, including 45 primary and 3 secondary metabolites, from CBS and WBS. The results of principal component analysis and hierarchical cluster analysis (HCA) revealed significant metabolic differences between CBS and WBS that were closely related to metabolic pathways. The results indicate that flavonoids correlated positively with phenylalanine, a precursor for phenylpropanoid biosynthesis; the contents of flavonoids and phenylpropanoids were higher in WBS. Pathway analysis revealed that CBS contained large amounts of TCA cycle intermediates, amino acids, and fatty acids as a result of increased energy metabolism, amino acid metabolism, and seed filling. The projection to latent structure method, using the partial least squares method, was applied to predict the flavonoid content in soybean seed, which indicated that sucrose, threonic acid, citric acid, and fatty acids are important in predicting the antioxidant content of samples. This work will provide important information for designing new soybean cultivars with enhanced nutritional and agricultural traits.
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Affiliation(s)
- Hyejin Hyeon
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Jiu Liang Xu
- Natural Product Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Republic of Korea; College of Resources and Environmental Sciences; National Academy of Agriculture Green Development; School of Agriculture Green Development, China Agricultural University, 100193 Beijing, China
| | - Jae Kwang Kim
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea.
| | - Yongsoo Choi
- Natural Product Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Republic of Korea; Department of Biological Chemistry, University of Science and Technology, Youseng-gu, Daejeon 305-350, Republic of Korea.
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20
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Tohge T, Scossa F, Wendenburg R, Frasse P, Balbo I, Watanabe M, Alseekh S, Jadhav SS, Delfin JC, Lohse M, Giavalisco P, Usadel B, Zhang Y, Luo J, Bouzayen M, Fernie AR. Exploiting Natural Variation in Tomato to Define Pathway Structure and Metabolic Regulation of Fruit Polyphenolics in the Lycopersicum Complex. MOLECULAR PLANT 2020; 13:1027-1046. [PMID: 32305499 DOI: 10.1016/j.molp.2020.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 02/01/2020] [Accepted: 04/11/2020] [Indexed: 05/10/2023]
Abstract
While the structures of plant primary metabolic pathways are generally well defined and highly conserved across species, those defining specialized metabolism are less well characterized and more highly variable across species. In this study, we investigated polyphenolic metabolism in the lycopersicum complex by characterizing the underlying biosynthetic and decorative reactions that constitute the metabolic network of polyphenols across eight different species of tomato. For this purpose, GC-MS- and LC-MS-based metabolomics of different tissues of Solanum lycopersicum and wild tomato species were carried out, in concert with the evaluation of cross-hybridized microarray data for MapMan-based transcriptomic analysis, and publicly available RNA-sequencing data for annotation of biosynthetic genes. The combined data were used to compile species-specific metabolic networks of polyphenolic metabolism, allowing the establishment of an entire pan-species biosynthetic framework as well as annotation of the functions of decoration enzymes involved in the formation of metabolic diversity of the flavonoid pathway. The combined results are discussed in the context of the current understanding of tomato flavonol biosynthesis as well as a global view of metabolic shifts during fruit ripening. Our results provide an example as to how large-scale biology approaches can be used for the definition and refinement of large specialized metabolism pathways.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192 Japan
| | - Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, via Ardeatina 546 00178 Rome, Italy
| | - Regina Wendenburg
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Pierre Frasse
- Université de Toulouse, INP-ENSA Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan 31326, France
| | - Ilse Balbo
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Mutsumi Watanabe
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192 Japan
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Institute of Plant Systems Biology, 4000 Plovdiv, Bulgaria
| | - Sagar Sudam Jadhav
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jay C Delfin
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192 Japan
| | - Marc Lohse
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Patrick Giavalisco
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Max Planck Institute for Biology of Ageing, Joseph Stelzmann Strasse 9b, 50931 Cologne, Germany
| | - Bjoern Usadel
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Institute of Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52056 Aachen, Germany
| | - Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Institute of Plant Systems Biology, 4000 Plovdiv, Bulgaria
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Mondher Bouzayen
- Université de Toulouse, INP-ENSA Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan 31326, France
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Institute of Plant Systems Biology, 4000 Plovdiv, Bulgaria.
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21
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Fantini E, Facella P. Cryptochromes in the field: how blue light influences crop development. PHYSIOLOGIA PLANTARUM 2020; 169:336-346. [PMID: 32175597 DOI: 10.1111/ppl.13088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/03/2020] [Accepted: 03/11/2020] [Indexed: 05/02/2023]
Abstract
Light is a pivotal environmental element capable of influencing multiple physiological processes across the entire plant life cycle. Over the course of their evolution, plants have developed several families of photoreceptors such as phytochromes, phototropins, ultraviolet (UV) resistance locus 8 and cryptochromes (crys), in order to sense light stimuli and respond to their changes. Numerous genetic studies have demonstrated that functional alterations to these photoreceptors cause a change in important agronomical traits. In particular, crys, which absorb UVA/blue light, can influence seed germination, flowering induction, plant architecture, fruit metabolic content and resistance to biotic and abiotic stresses. In the years to come, the rising temperatures and alterations to precipitation patterns generated by climate change will present a dramatic challenge for our agricultural system, with its few varieties characterized by a narrow genetic pool derived from artificial selection. Here, we review the main roles of crys in determining important agronomic traits in crops, we discuss the opportunities of using these photoreceptors as genetic targets for tuning plant physiological responses to environmental change, and the molecular strategies used so far to manipulate this family of photoreceptors.
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Affiliation(s)
- Elio Fantini
- Agenzia Nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile (ENEA), Trisaia Research Center, 75026, Rotondella (Matera), Italy
| | - Paolo Facella
- Agenzia Nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile (ENEA), Trisaia Research Center, 75026, Rotondella (Matera), Italy
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22
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Tomato Phenotypic Diversity Determined by Combined Approaches of Conventional and High-Throughput Tomato Analyzer Phenotyping. PLANTS 2020; 9:plants9020197. [PMID: 32033402 PMCID: PMC7076427 DOI: 10.3390/plants9020197] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 11/18/2022]
Abstract
Morphological variation in vegetative and fruit traits is a key determinant in unraveling phenotypic diversity. This study was designed to assess phenotypic diversity in tomatoes and examine intra- and intervarietal groups’ variability using 28 conventional descriptors (CDs) and 47 Tomato Analyzer (TA) descriptors related to plant and fruit morphometry. Comprehensive phenotyping of 150 accessions representing 21 countries discerned noticeable variability for CD vegetative traits and TA quantified fruit features, such as shape, size, and color. Hierarchical cluster analysis divided the accessions into 10 distinct classes based on fruit shape and size. Multivariate analysis was used to assess divergence in variable traits among populations. Eight principal components with an eigenvalue >1 were identified by factor analysis, which contributed 87.5% variation to the total cumulative variance with the first two components contributing 32.0% and 18.1% variance, respectively. The relationship between vegetative and fruit descriptors was explained by respective CD and TA correlation networks. There was a strong positive correlation between fruit shape and size whereas negative correlations were between fruit shape index, internal eccentricity, and proximal end shape. The combined approach of CD and TA phenotyping allowed us to unravel the phenotypic diversity of vegetative and reproductive trait variation evaluated at pre- and post-harvest stages.
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23
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Liu J, Fernie AR, Yan J. The Past, Present, and Future of Maize Improvement: Domestication, Genomics, and Functional Genomic Routes toward Crop Enhancement. PLANT COMMUNICATIONS 2020; 1:100010. [PMID: 33404535 PMCID: PMC7747985 DOI: 10.1016/j.xplc.2019.100010] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/07/2019] [Accepted: 11/22/2019] [Indexed: 05/14/2023]
Abstract
After being domesticated from teosinte, cultivated maize (Zea mays ssp. mays) spread worldwide and now is one of the most important staple crops. Due to its tremendous phenotypic and genotypic diversity, maize also becomes to be one of the most widely used model plant species for fundamental research, with many important discoveries reported by maize researchers. Here, we provide an overview of the history of maize domestication and key genes controlling major domestication-related traits, review the currently available resources for functional genomics studies in maize, and discuss the functions of most of the maize genes that have been positionally cloned and can be used for crop improvement. Finally, we provide some perspectives on future directions regarding functional genomics research and the breeding of maize and other crops.
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Affiliation(s)
- Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding author
| | - Alisdair R. Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding author
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24
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Mazzucotelli E, Sciara G, Mastrangelo AM, Desiderio F, Xu SS, Faris J, Hayden MJ, Tricker PJ, Ozkan H, Echenique V, Steffenson BJ, Knox R, Niane AA, Udupa SM, Longin FCH, Marone D, Petruzzino G, Corneti S, Ormanbekova D, Pozniak C, Roncallo PF, Mather D, Able JA, Amri A, Braun H, Ammar K, Baum M, Cattivelli L, Maccaferri M, Tuberosa R, Bassi FM. The Global Durum Wheat Panel (GDP): An International Platform to Identify and Exchange Beneficial Alleles. FRONTIERS IN PLANT SCIENCE 2020; 11:569905. [PMID: 33408724 PMCID: PMC7779600 DOI: 10.3389/fpls.2020.569905] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 11/24/2020] [Indexed: 05/04/2023]
Abstract
Representative, broad and diverse collections are a primary resource to dissect genetic diversity and meet pre-breeding and breeding goals through the identification of beneficial alleles for target traits. From 2,500 tetraploid wheat accessions obtained through an international collaborative effort, a Global Durum wheat Panel (GDP) of 1,011 genotypes was assembled that captured 94-97% of the original diversity. The GDP consists of a wide representation of Triticum turgidum ssp. durum modern germplasm and landraces, along with a selection of emmer and primitive tetraploid wheats to maximize diversity. GDP accessions were genotyped using the wheat iSelect 90K SNP array. Among modern durum accessions, breeding programs from Italy, France and Central Asia provided the highest level of genetic diversity, with only a moderate decrease in genetic diversity observed across nearly 50 years of breeding (1970-2018). Further, the breeding programs from Europe had the largest sets of unique alleles. LD was lower in the landraces (0.4 Mbp) than in modern germplasm (1.8 Mbp) at r 2 = 0.5. ADMIXTURE analysis of modern germplasm defined a minimum of 13 distinct genetic clusters (k), which could be traced to the breeding program of origin. Chromosome regions putatively subjected to strong selection pressure were identified from fixation index (F st ) and diversity reduction index (DRI) metrics in pairwise comparisons among decades of release and breeding programs. Clusters of putative selection sweeps (PSW) were identified as co-localized with major loci controlling phenology (Ppd and Vrn), plant height (Rht) and quality (gliadins and glutenins), underlining the role of the corresponding genes as driving elements in modern breeding. Public seed availability and deep genetic characterization of the GDP make this collection a unique and ideal resource to identify and map useful genetic diversity at loci of interest to any breeding program.
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Affiliation(s)
- Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Giuseppe Sciara
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Anna M. Mastrangelo
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, Foggia, Italy
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, Bergamo, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Steven S. Xu
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, Fargo, ND, United States
| | - Justin Faris
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, Fargo, ND, United States
| | - Matthew J. Hayden
- Agriculture Victoria, Agribio, Centre for AgriBiosciences, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Penny J. Tricker
- School of Agriculture, Food and Wine, Faculty of Sciences, Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Hakan Ozkan
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Turkey
| | - Viviana Echenique
- Centro de Recursos Naturales Renovables de la Zona Semiárida, Departamento de Agronomía, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas, Bahía Blanca, Argentina
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Ron Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Abdoul A. Niane
- International Center for Agricultural Research in the Dry Areas, Beirut, Lebanon
| | - Sripada M. Udupa
- International Center for Agricultural Research in the Dry Areas, Beirut, Lebanon
| | | | - Daniela Marone
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, Foggia, Italy
| | - Giuseppe Petruzzino
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, Foggia, Italy
| | - Simona Corneti
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Danara Ormanbekova
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Curtis Pozniak
- Plant Sciences and Crop Development Center, University of Saskatchewan, Saskatoon, SK, Canada
| | - Pablo F. Roncallo
- Centro de Recursos Naturales Renovables de la Zona Semiárida, Departamento de Agronomía, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas, Bahía Blanca, Argentina
| | - Diane Mather
- School of Agriculture, Food and Wine, Faculty of Sciences, Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Jason A. Able
- School of Agriculture, Food and Wine, Faculty of Sciences, Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Ahmed Amri
- International Center for Agricultural Research in the Dry Areas, Beirut, Lebanon
| | - Hans Braun
- Plant Sciences and Crop Development Center, University of Saskatchewan, Saskatoon, SK, Canada
| | - Karim Ammar
- International Maize and Wheat Improvement Center, Texcoco de Mora, Mexico
| | - Michael Baum
- International Center for Agricultural Research in the Dry Areas, Beirut, Lebanon
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Filippo M. Bassi
- International Center for Agricultural Research in the Dry Areas, Beirut, Lebanon
- *Correspondence: Filippo M. Bassi,
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25
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Bogdanova VS. Genetic and Molecular Genetic Basis of Nuclear-Plastid Incompatibilities. PLANTS (BASEL, SWITZERLAND) 2019; 9:E23. [PMID: 31878042 PMCID: PMC7020172 DOI: 10.3390/plants9010023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/18/2019] [Accepted: 12/20/2019] [Indexed: 01/21/2023]
Abstract
Genetic analysis of nuclear-cytoplasm incompatibilities is not straightforward and requires an elaborated experimental design. A number of species have been genetically studied, but notable advances in genetic mapping of nuclear loci involved in nuclear-plastid incompatibility have been achieved only in wheat and pea. This review focuses on the study of the genetic background underlying nuclear-plastid incompatibilities, including cases where the molecular genetic basis of such incompatibility has been unveiled, such as in tobacco, Oenothera, pea, and wheat.
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Affiliation(s)
- Vera S Bogdanova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
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26
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Wang X, Zhang X, Yang J, Liu X, Song Y, Wang Z. Genetic variation assessment of stacked-trait transgenic maize via conventional breeding. BMC PLANT BIOLOGY 2019; 19:346. [PMID: 31391002 PMCID: PMC6686426 DOI: 10.1186/s12870-019-1956-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/31/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND The safety assessment and control of stacked transgenic crops is increasingly important due to continuous crop development and is urgently needed in China. The genetic stability of foreign genes and unintended effects are the primary problems encountered in safety assessment. Omics techniques are useful for addressing these problems. The stacked transgenic maize variety 12-5 × IE034, which has insect-resistant and glyphosate-tolerant traits, was developed via a breeding stack using 12-5 and IE034 as parents. Using 12-5 × IE034, its parents (12-5 and IE034), and different maize varieties as materials, we performed proteomic profiling, molecular characterization and a genetic stability analysis. RESULTS Our results showed that the copy number of foreign genes in 12-5 × IE034 is identical to that of its parents 12-5 and IE034. Foreign genes can be stably inherited over different generations. Proteomic profiling analysis found no newly expressed proteins in 12-5 × IE034, and the differences in protein expression between 12 and 5 × IE034 and its parents were within the range of variation of conventional maize varieties. The expression levels of key enzymes participating in the shikimic acid pathway which is related to glyphosate tolerance of 12-5 × IE034 were not significantly different from those of its parents or five conventional maize varieties, which indicated that without selective pressure by glyphosate, the introduced EPSPS synthase is not has a pronounced impact on the synthesis of aromatic amino acids in maize. CONCLUSIONS Stacked-trait development via conventional breeding did not have an impact on the genetic stability of T-DNA, and the impact of stacked breeding on the maize proteome was less significant than that of genotypic differences. The results of this study provide a theoretical basis for the development of a safety assessment approach for stacked-trait transgenic crops in China.
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Affiliation(s)
- Xujing Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, 12 Zhuangguancun South Street, Beijing, 100081 China
| | - Xin Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, 12 Zhuangguancun South Street, Beijing, 100081 China
| | - Jiangtao Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, 12 Zhuangguancun South Street, Beijing, 100081 China
| | - Xiaojing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, 12 Zhuangguancun South Street, Beijing, 100081 China
| | - Yaya Song
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, 12 Zhuangguancun South Street, Beijing, 100081 China
| | - Zhixing Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, 12 Zhuangguancun South Street, Beijing, 100081 China
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27
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Fernie AR, Yan J. De Novo Domestication: An Alternative Route toward New Crops for the Future. MOLECULAR PLANT 2019; 12:615-631. [PMID: 30999078 DOI: 10.1016/j.molp.2019.03.016] [Citation(s) in RCA: 171] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 05/19/2023]
Abstract
Current global agricultural production must feed over 7 billion people. However, productivity varies greatly across the globe and is under threat from both increased competitions for land and climate change and associated environmental deterioration. Moreover, the increase in human population size and dietary changes are putting an ever greater burden on agriculture. The majority of this burden is met by the cultivation of a very small number of species, largely in locations that differ from their origin of domestication. Recent technological advances have raised the possibility of de novo domestication of wild plants as a viable solution for designing ideal crops while maintaining food security and a more sustainable low-input agriculture. Here we discuss how the discovery of multiple key domestication genes alongside the development of technologies for accurate manipulation of several target genes simultaneously renders de novo domestication a route toward crops for the future.
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Affiliation(s)
- Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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28
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Fang C, Luo J, Wang S. The Diversity of Nutritional Metabolites: Origin, Dissection, and Application in Crop Breeding. FRONTIERS IN PLANT SCIENCE 2019; 10:1028. [PMID: 31475024 PMCID: PMC6706459 DOI: 10.3389/fpls.2019.01028] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/23/2019] [Indexed: 05/21/2023]
Abstract
The chemical diversity of plants is very high, and plant-based foods provide almost all the nutrients necessary for human health, either directly or indirectly. With advancements in plant metabolomics studies, the concept of nutritional metabolites has been expanded and updated. Because the concentration of many nutrients is usually low in plant-based foods, especially those from crops, metabolome-assisted breeding techniques using molecular markers associated with the synthesis of nutritional metabolites have been developed and used to improve nutritional quality of crops. Here, we review the origins of the diversity of nutrient metabolites from a genomic perspective and the role of gene duplication and divergence. In addition, we systematically review recent advances in the metabolomic and genetic basis of metabolite production in major crops. With the development of genome sequencing and metabolic detection technologies, multi-omic integrative analysis of genomes, transcriptomes, and metabolomes has greatly facilitated the deciphering of the genetic basis of metabolic pathways and the diversity of nutrient metabolites. Finally, we summarize the application of nutrient diversity in crop breeding and discuss the future development of a viable alternative to metabolome-assisted breeding techniques that can be used to improve crop nutrient quality.
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Affiliation(s)
- Chuanying Fang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
| | - Jie Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Shouchuang Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- *Correspondence: Shouchuang Wang,
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Zhang S, Yu H, Wang K, Zheng Z, Liu L, Xu M, Jiao Z, Li R, Liu X, Li J, Cui X. Detection of major loci associated with the variation of 18 important agronomic traits between Solanum pimpinellifolium and cultivated tomatoes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:312-323. [PMID: 29738097 DOI: 10.1111/tpj.13952] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 04/13/2018] [Indexed: 06/08/2023]
Abstract
Wild species can be used to improve various agronomic traits in cultivars; however, a limited understanding of the genetic basis underlying the morphological differences between wild and cultivated species hinders the integration of beneficial traits from wild species. In the present study, we generated and sequenced recombinant inbred lines (RILs, 201 F10 lines) derived from a cross between Solanum pimpinellifolium and Solanum lycopersicum tomatoes. Based on a high-resolution recombination bin map to uncover major loci determining the phenotypic variance between wild and cultivated tomatoes, 104 significantly associated loci were identified for 18 agronomic traits. On average, these loci explained ~39% of the phenotypic variance of the RILs. We further generated near-isogenic lines (NILs) for four identified loci, and the lines exhibited significant differences for the associated traits. We found that two loci could improve the flower number and inflorescence architecture in the cultivar following introgression of the wild-species alleles. These findings allowed us to construct a trait-locus network to help explain the correlations among different traits based on the pleiotropic or linked loci. Our results provide insights into the morphological changes between wild and cultivated tomatoes, and will help to identify key genes governing important agronomic traits for the molecular selection of elite tomato varieties.
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Affiliation(s)
- Shuaibin Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hong Yu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ketao Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zheng Zheng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Huayuan Road 116, Zhengzhou, 450002, Henan, China
| | - Lei Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Meng Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhicheng Jiao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ren Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiyan Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xia Cui
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Klopsch R, Witzel K, Artemyeva A, Ruppel S, Hanschen FS. Genotypic Variation of Glucosinolates and Their Breakdown Products in Leaves of Brassica rapa. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:5481-5490. [PMID: 29746112 DOI: 10.1021/acs.jafc.8b01038] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
An in-depth glucosinolate (GLS) profiling was performed on a core collection of 91 Brassica rapa accessions, representing diverse morphotypes of heterogeneous geographical origin, to better understand the natural variation in GLS accumulation and GLS breakdown product formation. Leaves of the 91 B. rapa accessions were analyzed for their GLS composition by UHPLC-DAD and the corresponding breakdown products by GC-MS. Fifteen different GLSs were identified, and aliphatic GLSs prevailed regarding diversity and concentration. Twenty-three GLS breakdown products were identified, among them nine isothiocyanates, ten nitriles, and four epithionitriles. Epithionitriles were the prevailing breakdown products due to the high abundance of alkenyl GLSs. The large scale data set allowed the identification of correlations in abundance of specific GLSs or of GLS breakdown products. Discriminant function analysis identified subspecies with high levels of similarity in the acquired metabolite profiles. In general, the five main subspecies grouped significantly in terms of their GLS profiles.
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Affiliation(s)
- Rebecca Klopsch
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1 , 14979 Großbeeren , Germany
| | - Katja Witzel
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1 , 14979 Großbeeren , Germany
| | - Anna Artemyeva
- N.I.Vavilov Institute of Plant Genetic Resources, Bolshaya Morskaya Street 42-44 , 190000 St. Petersburg , Russia
- Agrophysical Research Institute, Grazhdanskiy prospect 14 , 195220 St. Petersburg , Russia
| | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1 , 14979 Großbeeren , Germany
| | - Franziska S Hanschen
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1 , 14979 Großbeeren , Germany
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Manganaris GA, Goulas V, Mellidou I, Drogoudi P. Antioxidant Phytochemicals in Fresh Produce: Exploitation of Genotype Variation and Advancements in Analytical Protocols. Front Chem 2018; 5:95. [PMID: 29468146 PMCID: PMC5807909 DOI: 10.3389/fchem.2017.00095] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/24/2017] [Indexed: 01/27/2023] Open
Abstract
Horticultural commodities (fruit and vegetables) are the major dietary source of several bioactive compounds of high nutraceutical value for humans, including polyphenols, carotenoids and vitamins. The aim of the current review was dual. Firstly, toward the eventual enhancement of horticultural crops with bio-functional compounds, the natural genetic variation in antioxidants found in different species and cultivars/genotypes is underlined. Notably, some landraces and/or traditional cultivars have been characterized by substantially higher phytochemical content, i.e., small tomato of Santorini island (cv. "Tomataki Santorinis") possesses appreciably high amounts of ascorbic acid (AsA). The systematic screening of key bioactive compounds in a wide range of germplasm for the identification of promising genotypes and the restoration of key gene fractions from wild species and landraces may help in reducing the loss of agro-biodiversity, creating a healthier "gene pool" as the basis of future adaptation. Toward this direction, large scale comparative studies in different cultivars/genotypes of a given species provide useful insights about the ones of higher nutritional value. Secondly, the advancements in the employment of analytical techniques to determine the antioxidant potential through a convenient, easy and fast way are outlined. Such analytical techniques include electron paramagnetic resonance (EPR) and infrared (IR) spectroscopy, electrochemical, and chemometric methods, flow injection analysis (FIA), optical sensors, and high resolution screening (HRS). Taking into consideration that fruits and vegetables are complex mixtures of water- and lipid-soluble antioxidants, the exploitation of chemometrics to develop "omics" platforms (i.e., metabolomics, foodomics) is a promising tool for researchers to decode and/or predict antioxidant activity of fresh produce. For industry, the use of optical sensors and IR spectroscopy is recommended to estimate the antioxidant activity rapidly and at low cost, although legislation does not allow its correlation with health claims.
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Affiliation(s)
- George A. Manganaris
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Lemesos, Cyprus
| | - Vlasios Goulas
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Lemesos, Cyprus
| | - Ifigeneia Mellidou
- Hellenic Agricultural Organization ‘Demeter’, Institute of Plant Breeding and Genetic Resources, Thessaloniki, Greece
| | - Pavlina Drogoudi
- Hellenic Agricultural Organization ‘Demeter’, Department of Deciduous Fruit Trees, Institute of Plant Breeding and Genetic Resources, Naoussa, Greece
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Abstract
Plant metabolic studies have traditionally focused on the role and regulation of the enzymes catalyzing key reactions within specific pathways. Within the past 20 years, reverse genetic approaches have allowed direct determination of the effects of the deficiency, or surplus, of a given protein on the biochemistry of a plant. In parallel, top-down approaches have also been taken, which rely on screening broad, natural genetic diversity for metabolic diversity. Here, we compare and contrast the various strategies that have been adopted to enhance our understanding of the natural diversity of metabolism. We also detail how these approaches have enhanced our understanding of both specific and global aspects of the genetic regulation of metabolism. Finally, we discuss how such approaches are providing important insights into the evolution of plant secondary metabolism.
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Affiliation(s)
- Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany;
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany;
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Kang J, Li J, Gao S, Tian C, Zha X. Overexpression of the leucine-rich receptor-like kinase gene LRK2 increases drought tolerance and tiller number in rice. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1175-1185. [PMID: 28182328 PMCID: PMC5552483 DOI: 10.1111/pbi.12707] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 01/29/2017] [Accepted: 01/30/2017] [Indexed: 05/18/2023]
Abstract
Drought represents a key limiting factor of global crop distribution. Receptor-like kinases play major roles in plant development and defence responses against stresses such as drought. In this study, LRK2, which encodes a leucine-rich receptor-like kinase, was cloned and characterized and found to be localized on the plasma membrane in rice. Promoter-GUS analysis revealed strong expression in tiller buds, roots, nodes and anthers. Transgenic plants overexpressing LRK2 exhibited enhanced tolerance to drought stress due to an increased number of lateral roots compared with the wild type at the vegetative stage. Moreover, ectopic expression of LRK2 seedlings resulted in increased tiller development. Yeast two-hybrid screening and bimolecular fluorescence complementation (BiFC) indicated a possible interaction between LRK2 and elongation factor 1 alpha (OsEF1A) in vitro. These results suggest that LRK2 functions as a positive regulator of the drought stress response and tiller development via increased branch development in rice. These findings will aid our understanding of branch regulation in other grasses and support improvements in rice genetics.
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Affiliation(s)
- Junfang Kang
- College of Chemistry and Life SciencesZhejiang Normal UniversityJinhuaChina
| | - Jianmin Li
- College of Chemistry and Life SciencesZhejiang Normal UniversityJinhuaChina
| | - Shuang Gao
- College of Chemistry and Life SciencesZhejiang Normal UniversityJinhuaChina
| | - Chao Tian
- College of Chemistry and Life SciencesZhejiang Normal UniversityJinhuaChina
| | - Xiaojun Zha
- College of Chemistry and Life SciencesZhejiang Normal UniversityJinhuaChina
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Gascuel Q, Diretto G, Monforte AJ, Fortes AM, Granell A. Use of Natural Diversity and Biotechnology to Increase the Quality and Nutritional Content of Tomato and Grape. FRONTIERS IN PLANT SCIENCE 2017; 8:652. [PMID: 28553296 PMCID: PMC5427129 DOI: 10.3389/fpls.2017.00652] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/10/2017] [Indexed: 05/18/2023]
Abstract
Improving fruit quality has become a major goal in plant breeding. Direct approaches to tackling fruit quality traits specifically linked to consumer preferences and environmental friendliness, such as improved flavor, nutraceutical compounds, and sustainability, have slowly been added to a breeder priority list that already includes traits like productivity, efficiency, and, especially, pest and disease control. Breeders already use molecular genetic tools to improve fruit quality although most advances have been made in producer and industrial quality standards. Furthermore, progress has largely been limited to simple agronomic traits easy-to-observe, whereas the vast majority of quality attributes, specifically those relating to flavor and nutrition, are complex and have mostly been neglected. Fortunately, wild germplasm, which is used for resistance against/tolerance of environmental stresses (including pathogens), is still available and harbors significant genetic variation for taste and health-promoting traits. Similarly, heirloom/traditional varieties could be used to identify which genes contribute to flavor and health quality and, at the same time, serve as a good source of the best alleles for organoleptic quality improvement. Grape (Vitis vinifera L.) and tomato (Solanum lycopersicum L.) produce fleshy, berry-type fruits, among the most consumed in the world. Both have undergone important domestication and selection processes, that have dramatically reduced their genetic variability, and strongly standardized fruit traits. Moreover, more and more consumers are asking for sustainable production, incompatible with the wide range of chemical inputs. In the present paper, we review the genetic resources available to tomato/grape breeders, and the recent technological progresses that facilitate the identification of genes/alleles of interest within the natural or generated variability gene pool. These technologies include omics, high-throughput phenotyping/phenomics, and biotech approaches. Our review also covers a range of technologies used to transfer to tomato and grape those alleles considered of interest for fruit quality. These include traditional breeding, TILLING (Targeting Induced Local Lesions in Genomes), genetic engineering, or NPBT (New Plant Breeding Technologies). Altogether, the combined exploitation of genetic variability and innovative biotechnological tools may facilitate breeders to improve fruit quality tacking more into account the consumer standards and the needs to move forward into more sustainable farming practices.
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Affiliation(s)
- Quentin Gascuel
- Laboratory of Plant-Microbe Interactions, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Toulouse UniversityCastanet Tolosan, France
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy, and Sustainable Development, Casaccia Research CentreRome, Italy
| | - Antonio J. Monforte
- Instituto de Biología Molecular y Celular de Plantas, Agencia Estatal Consejo Superior de Investigaciones Científicas, Universidad Politécnica de ValenciaValencia, Spain
| | - Ana M. Fortes
- Faculdade de Ciências de Lisboa, Instituto de Biossistemas e Ciências Integrativas (BioISI), Universidade de LisboaLisboa, Portugal
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas, Agencia Estatal Consejo Superior de Investigaciones Científicas, Universidad Politécnica de ValenciaValencia, Spain
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Price EJ, Bhattacharjee R, Lopez-Montes A, Fraser PD. Metabolite profiling of yam ( Dioscorea spp.) accessions for use in crop improvement programmes. Metabolomics 2017; 13:144. [PMID: 29104519 PMCID: PMC5641283 DOI: 10.1007/s11306-017-1279-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/22/2017] [Indexed: 01/30/2023]
Abstract
INTRODUCTION Ninety-seven percent of yam (Dioscorea spp.) production takes place in low income food deficit countries (LIFDCs) and the crop provides 200 calories a day to approximately 300 million people. Therefore, yams are vital for food security. Yams have high-yield potential and high market value potential yet current breeding of yam is hindered by a lack of genomic information and genetic resources. New tools are needed to modernise breeding strategies and unlock the potential of yam to improve livelihood in LIFDCs. OBJECTIVES Metabolomic screening has been undertaken on a diverse panel of Dioscorea accessions to assess the utility of the approach for advancing breeding strategies in this understudied crop. METHODS Polar and lipophilic extracts from tubers of accessions from the global yam breeding program have been comprehensively profiled via gas chromatography-mass spectrometry. RESULTS A visual pathway representation of the measured yam tuber metabolome has been delivered as a resource for biochemical evaluation of yam germplasm. Over 200 compounds were routinely measured in tubers, providing a major advance for the chemo-typing of this crop. Core biochemical redundancy concealed trends that were only elucidated following detailed mining of global metabolomics data. Combined analysis on leaf and tuber material identified a subset of metabolites which allow accurate species classification and highlighted the potential of predicting tuber composition from leaf profiles. Metabolic variation was accession-specific and often localised to compound classes, which will aid trait-targeting for metabolite markers. CONCLUSIONS Metabolomics provides a standalone platform with potential to deliver near-future crop gains for yam. The approach compliments the genetic advancements currently underway and integration with other '-omics' studies will deliver a significant advancement to yam breeding strategies.
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Affiliation(s)
- Elliott J. Price
- Royal Holloway University of London, Egham, Surrey, TW20 0EX UK
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW20 3AB UK
| | | | - Antonio Lopez-Montes
- International Institute of Tropical Agriculture, Oyo Road, PMB 5320 Ibadan, Nigeria
| | - Paul D. Fraser
- Royal Holloway University of London, Egham, Surrey, TW20 0EX UK
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Maria John KM, Natarajan S, Luthria DL. Metabolite changes in nine different soybean varieties grown under field and greenhouse conditions. Food Chem 2016; 211:347-55. [PMID: 27283642 DOI: 10.1016/j.foodchem.2016.05.055] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 03/30/2016] [Accepted: 05/10/2016] [Indexed: 02/08/2023]
Abstract
Global food security remains a worldwide concern due to changing climate, increasing population, and reduced agriculture acreages. Greenhouse cultivation increases productivity by extending growing seasons, reducing pest infestations and providing protection against short term drastic weather fluctuations like frost, heat, rain, and wind. In the present study, we examined and compared the metabolic responses of nine soybean varieties grown under field and greenhouse conditions. Extracts were assayed by GC-FID, GC-MS, and LC-MS for the identification of 10 primary (amino acids, organic acids, and sugars) and 10 secondary (isoflavones, fatty acid methyl esters) metabolites. Sugar molecules (glucose, sucrose, and pinitol) and isoflavone aglycons were increased but the isoflavones glucoside content decreased in the greenhouse cultivated soybeans. The amino acids and organic acids varied between the varieties. The results show that clustering (PCA and PLS-DA) patterns of soybean metabolites were significantly influenced by the genetic variation and growing conditions.
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Affiliation(s)
- K M Maria John
- Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, United States
| | - Savithiry Natarajan
- Soybean Genomics and Improvement Laboratory, Plant Sciences Institute, ARS, USDA, Beltsville, MD 20705, United States
| | - Devanand L Luthria
- Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, United States.
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37
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Ralley L, Schuch W, Fraser PD, Bramley PM. Genetic modification of tomato with the tobacco lycopene β-cyclase gene produces high β-carotene and lycopene fruit. Z NATURFORSCH C 2016; 71:295-301. [PMID: 27487494 DOI: 10.1515/znc-2016-0102] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/06/2016] [Indexed: 12/16/2023]
Abstract
Transgenic Solanum lycopersicum plants expressing an additional copy of the lycopene β-cyclase gene (LCYB) from Nicotiana tabacum, under the control of the Arabidopsis polyubiquitin promoter (UBQ3), have been generated. Expression of LCYB was increased some 10-fold in ripening fruit compared to vegetative tissues. The ripe fruit showed an orange pigmentation, due to increased levels (up to 5-fold) of β-carotene, with negligible changes to other carotenoids, including lycopene. Phenotypic changes in carotenoids were found in vegetative tissues, but levels of biosynthetically related isoprenoids such as tocopherols, ubiquinone and plastoquinone were barely altered. Transformants showed tolerance to the bleaching herbicide β-cyclase inhibitor, 2-(4-chlorophenylthio) triethylamine. The phenotype was inherited for at least three generations.
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Wen W, Brotman Y, Willmitzer L, Yan J, Fernie AR. Broadening Our Portfolio in the Genetic Improvement of Maize Chemical Composition. Trends Genet 2016; 32:459-469. [DOI: 10.1016/j.tig.2016.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/03/2016] [Accepted: 05/09/2016] [Indexed: 12/14/2022]
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Calafiore R, Ruggieri V, Raiola A, Rigano MM, Sacco A, Hassan MI, Frusciante L, Barone A. Exploiting Genomics Resources to Identify Candidate Genes Underlying Antioxidants Content in Tomato Fruit. FRONTIERS IN PLANT SCIENCE 2016; 7:397. [PMID: 27092148 PMCID: PMC4824784 DOI: 10.3389/fpls.2016.00397] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/14/2016] [Indexed: 05/18/2023]
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40
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Liu Z, Alseekh S, Brotman Y, Zheng Y, Fei Z, Tieman DM, Giovannoni JJ, Fernie AR, Klee HJ. Identification of a Solanum pennellii Chromosome 4 Fruit Flavor and Nutritional Quality-Associated Metabolite QTL. FRONTIERS IN PLANT SCIENCE 2016; 7:1671. [PMID: 27881988 PMCID: PMC5101573 DOI: 10.3389/fpls.2016.01671] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/24/2016] [Indexed: 05/20/2023]
Abstract
A major resource for tomato quality improvement and gene discovery is the collection of introgression lines (ILs) of cultivated Solanum lycopersicum that contain different, defined chromosomal segments derived from the wild tomato relative, S. pennellii. Among these lines, IL4-4, in which the bottom of S. lycopersicum (cv. M82) chromosome 4 is replaced by the corresponding S. pennellii segment, is altered in many primary and secondary metabolites, including many related to fruit flavor and nutritional quality. Here, we provide a comprehensive profile of IL4-4 ripe fruit metabolites, the transcriptome and fine mapping of sub-ILs. Remarkably, out of 327 quantified metabolites, 185 were significantly changed in IL4-4 fruit, compared to the control. These altered metabolites include volatile organic compounds, primary and secondary metabolites. Partial least squares enhanced discriminant analysis of the metabolite levels among sub-ILs indicated that a genome region encompassing 20 putative open reading frames is responsible for most of the metabolic changes in IL4-4 fruit. This work provides comprehensive insights into IL4-4 fruit biochemistry, identifying a small region of the genome that has major effects on a large and diverse set of metabolites.
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Affiliation(s)
- Zhongyuan Liu
- Horticultural Sciences Department, Genetics Institute, University of Florida, GainesvilleFL, USA
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant PhysiologyPotsdam-Golm, Germany
| | - Yariv Brotman
- Max Planck Institute of Molecular Plant PhysiologyPotsdam-Golm, Germany
- Department of Life Sciences, Ben-Gurion University of the NegevBeersheba, Israel
| | - Yi Zheng
- US Department of Agriculture–Agricultural Research Service Robert W. Holley Center for Agriculture and Health, Cornell University, IthacaNY, USA
- Robert W. Holley Center for Agriculture and Health, Cornell University and US Department of Agriculture–Agricultural Research Service, IthacaNY, USA
| | - Zhangjun Fei
- US Department of Agriculture–Agricultural Research Service Robert W. Holley Center for Agriculture and Health, Cornell University, IthacaNY, USA
- Robert W. Holley Center for Agriculture and Health, Cornell University and US Department of Agriculture–Agricultural Research Service, IthacaNY, USA
| | - Denise M. Tieman
- Horticultural Sciences Department, Genetics Institute, University of Florida, GainesvilleFL, USA
| | - James J. Giovannoni
- US Department of Agriculture–Agricultural Research Service Robert W. Holley Center for Agriculture and Health, Cornell University, IthacaNY, USA
- Robert W. Holley Center for Agriculture and Health, Cornell University and US Department of Agriculture–Agricultural Research Service, IthacaNY, USA
| | | | - Harry J. Klee
- Horticultural Sciences Department, Genetics Institute, University of Florida, GainesvilleFL, USA
- *Correspondence: Harry J. Klee,
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Identification of Genetic Differentiation between Waxy and Common Maize by SNP Genotyping. PLoS One 2015; 10:e0142585. [PMID: 26566240 PMCID: PMC4643885 DOI: 10.1371/journal.pone.0142585] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 10/23/2015] [Indexed: 11/18/2022] Open
Abstract
Waxy maize (Zea mays L. var. ceratina) is an important vegetable and economic crop that is thought to have originated from cultivated flint maize and most recently underwent divergence from common maize. In this study, a total of 110 waxy and 110 common maize inbred lines were genotyped with 3072 SNPs to evaluate the genetic diversity, population structure, and linkage disequilibrium decay as well as identify putative loci that are under positive selection. The results revealed abundant genetic diversity in the studied panel and that genetic diversity was much higher in common than in waxy maize germplasms. Principal coordinate analysis and neighbor-joining cluster analysis consistently classified the 220 accessions into two major groups and a mixed group with mixed ancestry. Subpopulation structure in both waxy and common maize sets were associated with the germplasm origin and corresponding heterotic groups. The LD decay distance (1500–2000 kb) in waxy maize was lower than that in common maize. Fourteen candidate loci were identified as under positive selection between waxy and common maize at the 99% confidence level. The information from this study can assist waxy maize breeders by enhancing parental line selection and breeding program design.
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Discovering metabolic indices for early detection of squash (Cucurbita maxima) storage quality using GC-MS-based metabolite profiling. Food Chem 2015; 196:1150-5. [PMID: 26593601 DOI: 10.1016/j.foodchem.2015.10.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 09/18/2015] [Accepted: 10/04/2015] [Indexed: 11/21/2022]
Abstract
Squash (Cucubita maxima) cultivars with good storage qualities are needed for breeding to improve poor crop supply during winter in Japan. We measured changes in squash constituents during different storage periods to identify compounds that were suitable to be used as indices of storage quality. Principal components analysis of compounds at 1-5 months after harvest showed that PC1 scores were lower for cultivars with a higher rather than lower SQ (storage quality) ranks. Partial least-squares regression analysis was performed using the peak areas of all compounds identified from the 15 cultivars at 1 month after harvest as explanation variables and SQ as the target variable. Variable influence on projection scores and rank correlation coefficients were higher for arabinose and xylose, which showed less temporal change during the storage period; hence, they were considered to be suitable indicators for storage evaluation. These data will be useful for future studies aiming to improve storage quality of squash.
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Alseekh S, Tohge T, Wendenberg R, Scossa F, Omranian N, Li J, Kleessen S, Giavalisco P, Pleban T, Mueller-Roeber B, Zamir D, Nikoloski Z, Fernie AR. Identification and mode of inheritance of quantitative trait loci for secondary metabolite abundance in tomato. THE PLANT CELL 2015; 27:485-512. [PMID: 25770107 PMCID: PMC4558650 DOI: 10.1105/tpc.114.132266] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 01/27/2015] [Accepted: 02/16/2015] [Indexed: 05/18/2023]
Abstract
A large-scale metabolic quantitative trait loci (mQTL) analysis was performed on the well-characterized Solanum pennellii introgression lines to investigate the genomic regions associated with secondary metabolism in tomato fruit pericarp. In total, 679 mQTLs were detected across the 76 introgression lines. Heritability analyses revealed that mQTLs of secondary metabolism were less affected by environment than mQTLs of primary metabolism. Network analysis allowed us to assess the interconnectivity of primary and secondary metabolism as well as to compare and contrast their respective associations with morphological traits. Additionally, we applied a recently established real-time quantitative PCR platform to gain insight into transcriptional control mechanisms of a subset of the mQTLs, including those for hydroxycinnamates, acyl-sugar, naringenin chalcone, and a range of glycoalkaloids. Intriguingly, many of these compounds displayed a dominant-negative mode of inheritance, which is contrary to the conventional wisdom that secondary metabolite contents decreased on domestication. We additionally performed an exemplary evaluation of two candidate genes for glycolalkaloid mQTLs via the use of virus-induced gene silencing. The combined data of this study were compared with previous results on primary metabolism obtained from the same material and to other studies of natural variance of secondary metabolism.
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Affiliation(s)
- Saleh Alseekh
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Takayuki Tohge
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Regina Wendenberg
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Federico Scossa
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Frutticoltura, 00134 Rome, Italy
| | - Nooshin Omranian
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany Institute of Biochemistry and Biology, University of Potsdam, D-14476 Potsdam-Golm, Germany
| | - Jie Li
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Sabrina Kleessen
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Patrick Giavalisco
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Tzili Pleban
- Institute of Plant Sciences and Genetics and Otto Warburg Centre for Biotechnology, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Bernd Mueller-Roeber
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany Institute of Biochemistry and Biology, University of Potsdam, D-14476 Potsdam-Golm, Germany
| | - Dani Zamir
- Institute of Plant Sciences and Genetics and Otto Warburg Centre for Biotechnology, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Zoran Nikoloski
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
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Toubiana D, Batushansky A, Tzfadia O, Scossa F, Khan A, Barak S, Zamir D, Fernie AR, Nikoloski Z, Fait A. Combined correlation-based network and mQTL analyses efficiently identified loci for branched-chain amino acid, serine to threonine, and proline metabolism in tomato seeds. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:121-33. [PMID: 25359542 DOI: 10.1111/tpj.12717] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 10/22/2014] [Indexed: 05/20/2023]
Abstract
Correlation-based network analysis (CNA) of the metabolic profiles of seeds of a tomato introgression line mapping population revealed a clique of proteinogenic amino acids: Gly, Ile, Pro, Ser, Thr, and Val. Correlations between profiles of these amino acids exhibited a statistically significant average correlation coefficient of 0.84 as compared with an average correlation coefficient of 0.39 over the 16 119 other metabolite cliques containing six metabolites. In silico removal of cliques was used to quantify their importance in determining seminal network properties, highlighting the strong effects of the amino acid clique. Quantitative trait locus analysis revealed co-localization for the six amino acids on chromosome 2, 4 and 10. Sequence analysis identified a unique set of 10 genes on chromosome 2 only, which were associated with amino acid metabolism and specifically the metabolism of Ser-Gly and their conversion into branched-chain amino acids. Metabolite profiling of a set of sublines, with introgressions on chromosome 2, identified a significant change in the abundance of the six amino acids in comparison with M82. Expression analysis of candidate genes affecting Ser metabolism matched the observation from the metabolite data, suggesting a coordinated behavior of the level of these amino acids at the genetic level. Analysis of transcription factor binding sites in the promoter regions of the identified genes suggested combinatorial response to light and the circadian clock.
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Affiliation(s)
- David Toubiana
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990, Midreshet Ben-Gurion, Israel
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Malcom JW, Hernandez KM, Likos R, Wayne T, Leibold MA, Juenger TE. Extensive cross-environment fitness variation lies along few axes of genetic variation in the model alga, Chlamydomonas reinhardtii. THE NEW PHYTOLOGIST 2015; 205:841-851. [PMID: 25264298 DOI: 10.1111/nph.13063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Accepted: 08/11/2014] [Indexed: 06/03/2023]
Abstract
Variation is essential to ecological and evolutionary dynamics, but genetic variation of quantitative traits may be concentrated in a limited number of dimensions, constraining ecoevolutionary dynamics. We describe high-dimension variation in natural accessions of the model alga, Chlamydomonas reinhardtii, and test the hypothesis that extensive fitness variation across 30 environments is constrained to a small number of axes. We used high-throughput phenotyping to investigate morphological, fitness, and genotype × environment (G × E) variation in 18 natural C. reinhardtii accessions in 30 environments. The organismal phenotypes of cell cycle, cell size, and phototactic behavior exhibited substantial genetic variation between lines, and we found up to 74-fold fitness variation across accessions and environments. Approximately 47% of the extensive G × E variation is accounted for by the first two principal components (PCs) of the G-matrix corresponding to covariation in metals response, nitrogen availability, or salt and nutrient response. The natural variation of C. reinhardtii accessions supports the hypothesis that, despite abundant genetic variation across single environments, the species' adaptive response should be constrained along few major axes of selection. These results highlight the utility of natural accessions for integrating ecoevolutionary and genetic research.
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Affiliation(s)
- Jacob W Malcom
- Department of Integrative Biology, The University of Texas at Austin, 1 University Station #C0930, Austin, TX, 78712, USA
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Rapson S, Wu M, Okada S, Das A, Shrestha P, Zhou XR, Wood C, Green A, Singh S, Liu Q. A case study on the genetic origin of the high oleic acid trait through FAD2-1 DNA sequence variation in safflower (Carthamus tinctorius L.). FRONTIERS IN PLANT SCIENCE 2015; 6:691. [PMID: 26442008 PMCID: PMC4563165 DOI: 10.3389/fpls.2015.00691] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/21/2015] [Indexed: 05/15/2023]
Abstract
The safflower (Carthamus tinctorius L.) is considered a strongly domesticated species with a long history of cultivation. The hybridization of safflower with its wild relatives has played an important role in the evolution of cultivars and is of particular interest with regards to their production of high quality edible oils. Original safflower varieties were all rich in linoleic acid, while varieties rich in oleic acid have risen to prominence in recent decades. The high oleic acid trait is controlled by a partially recessive allele ol at a single locus OL. The ol allele was found to be a defective microsomal oleate desaturase FAD2-1. Here we present DNA sequence data and Southern blot analysis suggesting that there has been an ancient hybridization and introgression of the FAD2-1 gene into C. tinctorius from its wild relative C. palaestinus. It is from this gene that FAD2-1Δ was derived more recently. Identification and characterization of the genetic origin and diversity of FAD2-1 could aid safflower breeders in reducing population size and generations required for the development of new high oleic acid varieties by using perfect molecular marker-assisted selection.
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Affiliation(s)
- Sara Rapson
- Commonwealth Scientific and Industrial Research Organization AgricultureCanberra, ACT, Australia
| | - Man Wu
- Commonwealth Scientific and Industrial Research Organization AgricultureCanberra, ACT, Australia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural SciencesAnyang, China
| | - Shoko Okada
- Commonwealth Scientific and Industrial Research Organization Land and WaterCanberra, ACT, Australia
| | - Alpana Das
- Commonwealth Scientific and Industrial Research Organization AgricultureCanberra, ACT, Australia
- Indian Council of Agricultural Research, Central Plantation Crops Research InstituteRC, Assam, India
| | - Pushkar Shrestha
- Commonwealth Scientific and Industrial Research Organization AgricultureCanberra, ACT, Australia
| | - Xue-Rong Zhou
- Commonwealth Scientific and Industrial Research Organization AgricultureCanberra, ACT, Australia
| | - Craig Wood
- Commonwealth Scientific and Industrial Research Organization AgricultureCanberra, ACT, Australia
| | - Allan Green
- Commonwealth Scientific and Industrial Research Organization Food and NutritionCanberra, ACT, Australia
| | - Surinder Singh
- Commonwealth Scientific and Industrial Research Organization AgricultureCanberra, ACT, Australia
| | - Qing Liu
- Commonwealth Scientific and Industrial Research Organization AgricultureCanberra, ACT, Australia
- *Correspondence: Qing Liu, Commonwealth Scientific and Industrial Research Organization Agriculture, PO Box 1600, Canberra, ACT 2601, Australia
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Natural occurring epialleles determine vitamin E accumulation in tomato fruits. Nat Commun 2014; 5:3027. [PMID: 24967512 DOI: 10.1038/ncomms5027] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 05/02/2014] [Indexed: 01/29/2023] Open
Abstract
Vitamin E (VTE) content is a low heritability nutritional trait for which the genetic determinants are poorly understood. Here, we focus on a previously detected major tomato VTE quantitative trait loci (QTL; mQTL(9-2-6)) and identify the causal gene as one encoding a 2-methyl-6-phytylquinol methyltransferase (namely VTE3(1)) that catalyses one of the final steps in the biosynthesis of γ- and α-tocopherols, which are the main forms of VTE. By reverse genetic approaches, expression analyses, siRNA profiling and DNA methylation assays, we demonstrate that mQTL(9-2-6) is an expression QTL associated with differential methylation of a SINE retrotransposon located in the promoter region of VTE3(1). Promoter DNA methylation can be spontaneously reverted leading to different epialleles affecting VTE3(1) expression and VTE content in fruits. These findings indicate therefore that naturally occurring epialleles are responsible for regulation of a nutritionally important metabolic QTL and provide direct evidence of a role for epigenetics in the determination of agronomic traits.
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Bogdanova VS, Kosterin OE, Yadrikhinskiy AK. Wild peas vary in their cross-compatibility with cultivated pea (Pisum sativum subsp. sativum L.) depending on alleles of a nuclear-cytoplasmic incompatibility locus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1163-72. [PMID: 24619163 DOI: 10.1007/s00122-014-2288-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 02/12/2014] [Indexed: 05/10/2023]
Abstract
KEY MESSAGE Divergent wild and endemic peas differ in hybrid sterility in reciprocal crosses with cultivated pea depending on alleles of a nuclear 'speciation gene' involved in nuclear-cytoplasmic compatibility. BACKGROUND In hybrids between cultivated and wild peas, nuclear-cytoplasmic conflict frequently occurs. One of the nuclear genes involved, Scs1, was earlier mapped on Linkage Group III. RESULTS In reciprocal crosses of seven divergent pea accessions with cultivated P. sativum, some alleles of Scs1 manifested incompatibility with an alien cytoplasm as a decrease in pollen fertility to about 50 % in the heterozygotes and lack of some genotypic classes among F2 segregants. Earlier, we defined monophyletic evolutionary lineages A, B, C and D of pea according to allelic state of three markers, from nuclear, plastid and mitochondrial genomes. All tested representatives of wild peas from the lineages A and C exhibited incompatibility due to Scs1 deleterious effects in crosses with testerlines of P. sativum subsp. sativum (the common cultivated pea) at least in one direction. A wild pea from the lineage B and a cultivated pea from the lineage D were compatible with the testerline in both directions. The tested accession of cultivated P. abyssinicum (lineage A) was partially compatible in both directions. The Scs1 alleles of some pea accessions even originating from the same geographic area were remarkably different in their compatibility with cultivated Pisum sativum cytoplasm. CONCLUSION Variability of a gene involved in reproductive isolation is of important evolutionary role and nominate Scs1 as a speciation gene.
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Affiliation(s)
- V S Bogdanova
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Acad. Lavrentyev ave. 10, Novosibirsk, 630090, Russia
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Li Y, Fan C, Xing Y, Yun P, Luo L, Yan B, Peng B, Xie W, Wang G, Li X, Xiao J, Xu C, He Y. Chalk5 encodes a vacuolar H+-translocating pyrophosphatase influencing grain chalkiness in rice. Nat Genet 2014; 46:398-404. [DOI: 10.1038/ng.2923] [Citation(s) in RCA: 212] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 02/20/2014] [Indexed: 01/07/2023]
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De B, Nag G. Metabolic diversity in the grains of Indian varieties of rice. C R Biol 2014; 337:283-93. [PMID: 24702898 DOI: 10.1016/j.crvi.2014.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/23/2014] [Accepted: 01/24/2014] [Indexed: 12/20/2022]
Abstract
The aim of the present work was to analyze metabolic diversity in 26 different indica varieties of rice grains. Seventy-six metabolites could be identified in the methanol extracts of each of the rice varieties analyzed by gas chromatography-mass spectrometry. These metabolites included 9 sugars/sugar alcohols, 17 amino acids/derivatives, 18 fatty acids, 5 free phenolic acids and 19 other organic acids, 3 phytosterols, 5 other constituents. Cluster analyses to extract information for similarity and differences in metabolites unveiled diversity in metabolite profile. Two hierarchical clusters were generated based on the metabolite contents of the rice varieties. The first cluster (cluster I) consisted of one variety only. The second cluster again segregated into four clusters (clusters II, III, IV and V). Very distinct differences were visible amongst the clusters with respect to their sugars/sugar alcohols, organic acid, amino acid and fatty acid, phenol, and sterol profiles. Metabolites determine nutritional quality, taste, aroma. This and future efforts on the metabolomic information would help biochemists and nutritionists to better understand the nutritional quality of such grains at varietal level and correlating metabolites and long term human health related issues.
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Affiliation(s)
- Bratati De
- Phytochemistry and Pharmacognosy research Laboratory, Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, India.
| | - Gargi Nag
- Phytochemistry and Pharmacognosy research Laboratory, Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, India
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