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Thakur NR, Gorthy S, Vemula A, Odeny DA, Ruperao P, Sargar PR, Mehtre SP, Kalpande HV, Habyarimana E. Genome-wide association study and expression of candidate genes for Fe and Zn concentration in sorghum grains. Sci Rep 2024; 14:12729. [PMID: 38830906 PMCID: PMC11148041 DOI: 10.1038/s41598-024-63308-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/27/2024] [Indexed: 06/05/2024] Open
Abstract
Sorghum germplasm showed grain Fe and Zn genetic variability, but a few varieties were biofortified with these minerals. This work contributes to narrowing this gap. Fe and Zn concentrations along with 55,068 high-quality GBS SNP data from 140 sorghum accessions were used in this study. Both micronutrients exhibited good variability with respective ranges of 22.09-52.55 ppm and 17.92-43.16 ppm. Significant marker-trait associations were identified on chromosomes 1, 3, and 5. Two major effect SNPs (S01_72265728 and S05_58213541) explained 35% and 32% of Fe and Zn phenotypic variance, respectively. The SNP S01_72265728 was identified in the cytochrome P450 gene and showed a positive effect on Fe accumulation in the kernel, while S05_58213541 was intergenic near Sobic.005G134800 (zinc-binding ribosomal protein) and showed negative effect on Zn. Tissue-specific in silico expression analysis resulted in higher levels of Sobic.003G350800 gene product in several tissues such as leaf, root, flower, panicle, and stem. Sobic.005G188300 and Sobic.001G463800 were expressed moderately at grain maturity and anthesis in leaf, root, panicle, and seed tissues. The candidate genes expressed in leaves, stems, and grains will be targeted to improve grain and stover quality. The haplotypes identified will be useful in forward genetics breeding.
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Affiliation(s)
- Niranjan Ravindra Thakur
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
- Vasantrao Naik Marathwada Agriculture University, Parbhani, Maharashtra, India
| | - Sunita Gorthy
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - AnilKumar Vemula
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Pradeep Ruperao
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Pramod Ramchandra Sargar
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
- Vasantrao Naik Marathwada Agriculture University, Parbhani, Maharashtra, India
| | | | - Hirakant V Kalpande
- Vasantrao Naik Marathwada Agriculture University, Parbhani, Maharashtra, India
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India.
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Ferreira MV, Naranjo E, Denis N, Cobine P, De La Fuente L, Siri MI. Calcium modulation of bacterial wilt disease on potato. Appl Environ Microbiol 2024; 90:e0024224. [PMID: 38690890 PMCID: PMC11107177 DOI: 10.1128/aem.00242-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 03/22/2024] [Indexed: 05/03/2024] Open
Abstract
Ralstonia solanacearum species complex (RSSC) is a phytopathogenic bacterial group that causes bacterial wilt in several crops, being potato (Solanum tuberosum) one of the most important hosts. The relationship between the potato plant ionome (mineral and trace elements composition) and the resistance levels to this pathogen has not been addressed until now. Mineral content of xylem sap, roots, stems and leaves of potato genotypes with different levels of resistance to bacterial wilt was assessed in this work, revealing a positive correlation between divalent calcium (Ca) cation concentrations and genotype resistance. The aim of this study was to investigate the effect of Ca on bacterial wilt resistance, and on the growth and virulence of RSSC. Ca supplementation significantly decreased the growth rate of Ralstonia pseudosolanacearum GMI1000 in minimal medium and affected several virulence traits such as biofilm formation and twitching motility. We also incorporate for the first time the use of microfluidic chambers to follow the pathogen growth and biofilm formation in conditions mimicking the plant vascular system. By using this approach, a reduction in biofilm formation was observed when both, rich and minimal media, were supplemented with Ca. Assessment of the effect of Ca amendments on bacterial wilt progress in potato genotypes revealed a significant delay in disease progress, or a complete absence of wilting symptoms in the case of partially resistant genotypes. This work contributes to the understanding of Ca effect on virulence of this important pathogen and provides new strategies for an integrated control of bacterial wilt on potato. IMPORTANCE Ralstonia solanacearum species complex (RSSC) includes a diverse group of bacterial strains that cause bacterial wilt. This disease is difficult to control due to pathogen aggressiveness, persistence, wide range of hosts, and wide geographic distribution in tropical, subtropical, and temperate regions. RSSC causes considerable losses depending on the pathogen strain, host, soil type, environmental conditions, and cultural practices. In potato, losses of $19 billion per year have been estimated for this pathogen worldwide. In this study, we report for the first time the mineral composition found in xylem sap and plant tissues of potato germplasm with different levels of resistance to bacterial wilt. This study underscores the crucial role of calcium (Ca) concentration in the xylem sap and stem in relation to the resistance of different genotypes. Our in vitro experiments provide evidence of Ca's inhibitory effect on the growth, biofilm formation, and twitching movement of the model RSSC strain R. pseudosolanacearum GMI1000. This study introduces a novel element, the Ca concentration, which should be included into the integrated disease control management strategies for bacterial wilt in potatoes.
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Affiliation(s)
- María Virginia Ferreira
- Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Eber Naranjo
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
| | - Nicol Denis
- Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Paul Cobine
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Leonardo De La Fuente
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
| | - María Inés Siri
- Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
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Ferrão LFV, Dhakal R, Dias R, Tieman D, Whitaker V, Gore MA, Messina C, Resende MFR. Machine learning applications to improve flavor and nutritional content of horticultural crops through breeding and genetics. Curr Opin Biotechnol 2023; 83:102968. [PMID: 37515935 DOI: 10.1016/j.copbio.2023.102968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/31/2023]
Abstract
Over the last decades, significant strides were made in understanding the biochemical factors influencing the nutritional content and flavor profile of fruits and vegetables. Product differentiation in the produce aisle is the natural consequence of increasing consumer power in the food industry. Cotton-candy grapes, specialty tomatoes, and pineapple-flavored white strawberries provide a few examples. Given the increased demand for flavorful varieties, and pressing need to reduce micronutrient malnutrition, we expect breeding to increase its prioritization toward these traits. Reaching this goal will, in part, necessitate knowledge of the genetic architecture controlling these traits, as well as the development of breeding methods that maximize their genetic gain. Can artificial intelligence (AI) help predict flavor preferences, and can such insights be leveraged by breeding programs? In this Perspective, we outline both the opportunities and challenges for the development of more flavorful and nutritious crops, and how AI can support these breeding initiatives.
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Affiliation(s)
- Luís Felipe V Ferrão
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Rakshya Dhakal
- Plant Breeding Graduate Program, University of Florida, Gainesville, FL, United States
| | - Raquel Dias
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, United States
| | - Denise Tieman
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Vance Whitaker
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States; Plant Breeding Graduate Program, University of Florida, Gainesville, FL, United States
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Carlos Messina
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States; Plant Breeding Graduate Program, University of Florida, Gainesville, FL, United States
| | - Márcio F R Resende
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States; Plant Breeding Graduate Program, University of Florida, Gainesville, FL, United States.
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Kudapa H, Barmukh R, Vemuri H, Gorthy S, Pinnamaneni R, Vetriventhan M, Srivastava RK, Joshi P, Habyarimana E, Gupta SK, Govindaraj M. Genetic and genomic interventions in crop biofortification: Examples in millets. FRONTIERS IN PLANT SCIENCE 2023; 14:1123655. [PMID: 36950360 PMCID: PMC10025513 DOI: 10.3389/fpls.2023.1123655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Micronutrient malnutrition is a serious threat to the developing world's human population, which largely relies on a cereal-based diet that lacks diversity and micronutrients. Besides major cereals, millets represent the key sources of energy, protein, vitamins, and minerals for people residing in the dryland tropics and drought-prone areas of South Asia and sub-Saharan Africa. Millets serve as multi-purpose crops with several salient traits including tolerance to abiotic stresses, adaptation to diverse agro-ecologies, higher productivity in nutrient-poor soils, and rich nutritional characteristics. Considering the potential of millets in empowering smallholder farmers, adapting to changing climate, and transforming agrifood systems, the year 2023 has been declared by the United Nations as the International Year of Millets. In this review, we highlight recent genetic and genomic innovations that can be explored to enhance grain micronutrient density in millets. We summarize the advances made in high-throughput phenotyping to accurately measure grain micronutrient content in cereals. We shed light on genetic diversity in millet germplasm collections existing globally that can be exploited for developing nutrient-dense and high-yielding varieties to address food and nutritional security. Furthermore, we describe the progress made in the fields of genomics, proteomics, metabolomics, and phenomics with an emphasis on enhancing the grain nutritional content for designing competitive biofortified varieties for the future. Considering the close genetic-relatedness within cereals, upcoming research should focus on identifying the genetic and genomic basis of nutritional traits in millets and introgressing them into major cereals through integrated omics approaches. Recent breakthroughs in the genome editing toolbox would be crucial for mainstreaming biofortification in millets.
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Affiliation(s)
- Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Rutwik Barmukh
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Hindu Vemuri
- International Maize and Wheat Improvement Center (CIMMYT), Patancheru, Telangana, India
| | - Sunita Gorthy
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | | | - Mani Vetriventhan
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Priyanka Joshi
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - S. K. Gupta
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Mahalingam Govindaraj
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
- HarvestPlus Program, Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
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5
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Harris ZN, Pratt JE, Bhakta N, Frawley E, Klein LL, Kwasniewski MT, Migicovsky Z, Miller AJ. Temporal and environmental factors interact with rootstock genotype to shape leaf elemental composition in grafted grapevines. PLANT DIRECT 2022; 6:e440. [PMID: 35999957 PMCID: PMC9389545 DOI: 10.1002/pld3.440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/28/2022] [Accepted: 08/01/2022] [Indexed: 05/19/2023]
Abstract
Plants take up elements through their roots and transport them to their shoot systems for use in numerous biochemical, physiological, and structural functions. Elemental composition of above-ground plant tissues, such as leaves, reflects both above- and below-ground activities of the plant, as well the local environment. Perennial, grafted plants, where the root system of one individual is fused to the shoot system of a genetically distinct individual, offer a powerful experimental system in which to study how genetically distinct root systems influence the elemental composition of a common shoot system. We measured elemental composition of over 7,000 leaves in the grapevine cultivar "Chambourcin" growing ungrafted and grafted to three rootstock genotypes. Leaves were collected over multiple years and phenological stages (across the season) and along a developmental time series. Temporal components of this study had the largest effect on leaf elemental composition, and rootstock genotype interacted with year, phenological stage, and leaf age to differentially modulate leaf elemental composition. Further, the local, above-ground environment affected leaf elemental composition, an effect influenced by rootstock genotype. This work highlights the dynamic nature by which root systems interact with shoot systems to respond to temporal and environmental variation.
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Affiliation(s)
- Zachary N. Harris
- Department of BiologySaint Louis UniversitySt. LouisMissouriUSA
- Donald Danforth Plant Science CenterSt. LouisMissouriUSA
| | - Julia E. Pratt
- Department of BiologySaint Louis UniversitySt. LouisMissouriUSA
- Donald Danforth Plant Science CenterSt. LouisMissouriUSA
| | - Niyati Bhakta
- Department of BiologySaint Louis UniversitySt. LouisMissouriUSA
- Donald Danforth Plant Science CenterSt. LouisMissouriUSA
| | - Emma Frawley
- Department of BiologySaint Louis UniversitySt. LouisMissouriUSA
- Donald Danforth Plant Science CenterSt. LouisMissouriUSA
| | - Laura L. Klein
- Department of BiologySaint Louis UniversitySt. LouisMissouriUSA
- Donald Danforth Plant Science CenterSt. LouisMissouriUSA
| | - Misha T. Kwasniewski
- Department of Food SciencePennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Faculty of AgricultureDalhousie UniversityTruroNova ScotiaCanada
| | - Allison J. Miller
- Department of BiologySaint Louis UniversitySt. LouisMissouriUSA
- Donald Danforth Plant Science CenterSt. LouisMissouriUSA
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6
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Wahinya FW, Yamazaki K, Jing Z, Takami T, Kamiya T, Kajiya-Kanegae H, Takanashi H, Iwata H, Tsutsumi N, Fujiwara T, Sakamoto W. Sorghum Ionomics Reveals the Functional SbHMA3a Allele that Limits Excess Cadmium Accumulation in Grains. PLANT & CELL PHYSIOLOGY 2022; 63:713-728. [PMID: 35312772 DOI: 10.1093/pcp/pcac035] [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: 02/04/2022] [Revised: 03/07/2022] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
Understanding uptake and redistribution of essential minerals or sequestering of toxic elements is important for optimized crop production. Although the mechanisms controlling mineral transport have been elucidated in rice and other species, little is understood in sorghum-an important C4 cereal crop. Here, we assessed the genetic factors that govern grain ionome profiles in sorghum using recombinant inbred lines (RILs) derived from a cross between BTx623 and NOG (Takakibi). Pairwise correlation and clustering analysis of 22 elements, measured in sorghum grains harvested under greenhouse conditions, indicated that the parental lines, as well as the RILs, show different ionomes. In particular, BTx623 accumulated significantly higher levels of cadmium (Cd) than NOG, because of differential root-to-shoot translocation factors between the two lines. Quantitative trait locus (QTL) analysis revealed a prominent QTL for grain Cd concentration on chromosome 2. Detailed analysis identified SbHMA3a, encoding a P1B-type ATPase heavy metal transporter, as responsible for low Cd accumulation in grains; the NOG allele encoded a functional HMA3 transporter (SbHMA3a-NOG) whose Cd-transporting activity was confirmed by heterologous expression in yeast. BTx623 possessed a truncated, loss-of-function SbHMA3a allele. The functionality of SbHMA3a in NOG was confirmed by Cd concentrations of F2 grains derived from the reciprocal cross, in which the NOG allele behaved in a dominant manner. We concluded that SbHMA3a-NOG is a Cd transporter that sequesters excess Cd in root tissues, as shown in other HMA3s. Our findings will facilitate the isolation of breeding cultivars with low Cd in grains or in exploiting high-Cd cultivars for phytoremediation.
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Affiliation(s)
- Fiona Wacera Wahinya
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046 Japan
| | - Kiyoshi Yamazaki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Zihuan Jing
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046 Japan
| | - Tsuneaki Takami
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046 Japan
| | - Takehiro Kamiya
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Hiromi Kajiya-Kanegae
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, 2-14-1 Nishi-shimbashi, Minato-ku, Tokyo, 105-0003 Japan
| | - Hideki Takanashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Hiroyoshi Iwata
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Nobuhiro Tsutsumi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Toru Fujiwara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046 Japan
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7
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Gladman N, Olson A, Wei S, Chougule K, Lu Z, Tello-Ruiz M, Meijs I, Van Buren P, Jiao Y, Wang B, Kumar V, Kumari S, Zhang L, Burke J, Chen J, Burow G, Hayes C, Emendack Y, Xin Z, Ware D. SorghumBase: a web-based portal for sorghum genetic information and community advancement. PLANTA 2022; 255:35. [PMID: 35015132 PMCID: PMC8752523 DOI: 10.1007/s00425-022-03821-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/27/2021] [Indexed: 05/05/2023]
Abstract
SorghumBase provides a community portal that integrates genetic, genomic, and breeding resources for sorghum germplasm improvement. Public research and development in agriculture rely on proper data and resource sharing within stakeholder communities. For plant breeders, agronomists, molecular biologists, geneticists, and bioinformaticians, centralizing desirable data into a user-friendly hub for crop systems is essential for successful collaborations and breakthroughs in germplasm development. Here, we present the SorghumBase web portal ( https://www.sorghumbase.org ), a resource for the sorghum research community. SorghumBase hosts a wide range of sorghum genomic information in a modular framework, built with open-source software, to provide a sustainable platform. This initial release of SorghumBase includes: (1) five sorghum reference genome assemblies in a pan-genome browser; (2) genetic variant information for natural diversity panels and ethyl methanesulfonate (EMS)-induced mutant populations; (3) search interface and integrated views of various data types; (4) links supporting interconnectivity with other repositories including genebank, QTL, and gene expression databases; and (5) a content management system to support access to community news and training materials. SorghumBase offers sorghum investigators improved data collation and access that will facilitate the growth of a robust research community to support genomics-assisted breeding.
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Affiliation(s)
- Nicholas Gladman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Zhenyuan Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | | | - Ivar Meijs
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Peter Van Buren
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Yinping Jiao
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, 79409, USA
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Vivek Kumar
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - John Burke
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX, 79415, USA
| | - Junping Chen
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX, 79415, USA
| | - Gloria Burow
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX, 79415, USA
| | - Chad Hayes
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX, 79415, USA
| | - Yves Emendack
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX, 79415, USA
| | - Zhanguo Xin
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX, 79415, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
- U.S. Department of Agriculture-Agricultural Research Service, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY, 14853, USA.
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8
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Sushree Shyamli P, Rana S, Suranjika S, Muthamilarasan M, Parida A, Prasad M. Genetic determinants of micronutrient traits in graminaceous crops to combat hidden hunger. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3147-3165. [PMID: 34091694 DOI: 10.1007/s00122-021-03878-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/29/2021] [Indexed: 06/12/2023]
Abstract
KEY MESSAGE Improving the nutritional content of graminaceous crops is imperative to ensure nutritional security, wherein omics approaches play pivotal roles in dissecting this complex trait and contributing to trait improvement. Micronutrients regulate the metabolic processes to ensure the normal functioning of the biological system in all living organisms. Micronutrient deficiency, thereby, can be detrimental that can result in serious health issues. Grains of graminaceous crops serve as an important source of micronutrients to the human population; however, the rise in hidden hunger and malnutrition indicates an insufficiency in meeting the nutritional requirements. Improving the elemental composition and nutritional value of the graminaceous crops using conventional and biotechnological approaches is imperative to address this issue. Identifying the genetic determinants underlying the micronutrient biosynthesis and accumulation is the first step toward achieving this goal. Genetic and genomic dissection of this complex trait has been accomplished in major cereals, and several genes, alleles, and QTLs underlying grain micronutrient content were identified and characterized. However, no comprehensive study has been reported on minor cereals such as small millets, which are rich in micronutrients and other bioactive compounds. A comparative narrative on the reports available in major and minor Graminaceae species will illustrate the knowledge gained from studying the micronutrient traits in major cereals and provides a roadmap for dissecting this trait in other minor species, including millets. In this context, this review explains the progress made in studying micronutrient traits in major cereals and millets using omics approaches. Moreover, it provides insights into deploying integrated omics approaches and strategies for genetic improvement in micronutrient traits in graminaceous crops.
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Affiliation(s)
- P Sushree Shyamli
- Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
- Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, Haryana (NCR Delhi), 121001, India
| | - Sumi Rana
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Sandhya Suranjika
- Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India
| | - Mehanathan Muthamilarasan
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Ajay Parida
- Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India.
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Cobb JN, Chen C, Shi Y, Maron LG, Liu D, Rutzke M, Greenberg A, Craft E, Shaff J, Paul E, Akther K, Wang S, Kochian LV, Zhang D, Zhang M, McCouch SR. Genetic architecture of root and shoot ionomes in rice (Oryza sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2613-2637. [PMID: 34018019 PMCID: PMC8277617 DOI: 10.1007/s00122-021-03848-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/29/2021] [Indexed: 05/09/2023]
Abstract
KEY MESSAGE Association analysis for ionomic concentrations of 20 elements identified independent genetic factors underlying the root and shoot ionomes of rice, providing a platform for selecting and dissecting causal genetic variants. Understanding the genetic basis of mineral nutrient acquisition is key to fully describing how terrestrial organisms interact with the non-living environment. Rice (Oryza sativa L.) serves both as a model organism for genetic studies and as an important component of the global food system. Studies in rice ionomics have primarily focused on above ground tissues evaluated from field-grown plants. Here, we describe a comprehensive study of the genetic basis of the rice ionome in both roots and shoots of 6-week-old rice plants for 20 elements using a controlled hydroponics growth system. Building on the wealth of publicly available rice genomic resources, including a panel of 373 diverse rice lines, 4.8 M genome-wide single-nucleotide polymorphisms, single- and multi-marker analysis pipelines, an extensive tome of 321 candidate genes and legacy QTLs from across 15 years of rice genetics literature, we used genome-wide association analysis and biparental QTL analysis to identify 114 genomic regions associated with ionomic variation. The genetic basis for root and shoot ionomes was highly distinct; 78 loci were associated with roots and 36 loci with shoots, with no overlapping genomic regions for the same element across tissues. We further describe the distribution of phenotypic variation across haplotypes and identify candidate genes within highly significant regions associated with sulfur, manganese, cadmium, and molybdenum. Our analysis provides critical insight into the genetic basis of natural phenotypic variation for both root and shoot ionomes in rice and provides a comprehensive resource for dissecting and testing causal genetic variants.
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Affiliation(s)
- Joshua N Cobb
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
- RiceTec Inc, Alvin, TX, 77511, USA
| | - Chen Chen
- Department of Statistics, Purdue University, West Lafayette, IN, 47907-2054, USA
- Ausy Consulting, Esperantolaan 8, 3001, Heverlee, Belgium
| | - Yuxin Shi
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
| | - Lyza G Maron
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
| | - Danni Liu
- Department of Statistics, Purdue University, West Lafayette, IN, 47907-2054, USA
| | - Mike Rutzke
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
| | - Anthony Greenberg
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
- Bayesic Research, LLC, 452 Sheffield Rd, Ithaca, NY, 14850, USA
| | - Eric Craft
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
| | - Jon Shaff
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, 14853-1901, USA
| | - Edyth Paul
- GeneFlow, Inc, Centreville, VA, 20120, USA
| | - Kazi Akther
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
| | - Shaokui Wang
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
- Department of Plant Breeding, South China Agriculture University, Guangdong, 510642, China
| | - Leon V Kochian
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, 14853-1901, USA
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada
| | - Dabao Zhang
- Department of Statistics, Purdue University, West Lafayette, IN, 47907-2054, USA
| | - Min Zhang
- Department of Statistics, Purdue University, West Lafayette, IN, 47907-2054, USA.
| | - Susan R McCouch
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA.
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10
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Wu D, Tanaka R, Li X, Ramstein GP, Cu S, Hamilton JP, Buell CR, Stangoulis J, Rocheford T, Gore MA. High-resolution genome-wide association study pinpoints metal transporter and chelator genes involved in the genetic control of element levels in maize grain. G3-GENES GENOMES GENETICS 2021; 11:6156830. [PMID: 33677522 PMCID: PMC8759812 DOI: 10.1093/g3journal/jkab059] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/21/2021] [Indexed: 12/18/2022]
Abstract
Despite its importance to plant function and human health, the genetics underpinning element levels in maize grain remain largely unknown. Through a genome-wide association study in the maize Ames panel of nearly 2,000 inbred lines that was imputed with ∼7.7 million SNP markers, we investigated the genetic basis of natural variation for the concentration of 11 elements in grain. Novel associations were detected for the metal transporter genes rte2 (rotten ear2) and irt1 (iron-regulated transporter1) with boron and nickel, respectively. We also further resolved loci that were previously found to be associated with one or more of five elements (copper, iron, manganese, molybdenum, and/or zinc), with two metal chelator and five metal transporter candidate causal genes identified. The nas5 (nicotianamine synthase5) gene involved in the synthesis of nicotianamine, a metal chelator, was found associated with both zinc and iron and suggests a common genetic basis controlling the accumulation of these two metals in the grain. Furthermore, moderate predictive abilities were obtained for the 11 elemental grain phenotypes with two whole-genome prediction models: Bayesian Ridge Regression (0.33–0.51) and BayesB (0.33–0.53). Of the two models, BayesB, with its greater emphasis on large-effect loci, showed ∼4–10% higher predictive abilities for nickel, molybdenum, and copper. Altogether, our findings contribute to an improved genotype-phenotype map for grain element accumulation in maize.
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Affiliation(s)
- Di Wu
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Ryokei Tanaka
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Xiaowei Li
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | | | - Suong Cu
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - James Stangoulis
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Torbert Rocheford
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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11
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Ali S, Tyagi A, Bae H. Ionomic Approaches for Discovery of Novel Stress-Resilient Genes in Plants. Int J Mol Sci 2021; 22:7182. [PMID: 34281232 PMCID: PMC8267685 DOI: 10.3390/ijms22137182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 01/03/2023] Open
Abstract
Plants, being sessile, face an array of biotic and abiotic stresses in their lifespan that endanger their survival. Hence, optimized uptake of mineral nutrients creates potential new routes for enhancing plant health and stress resilience. Recently, minerals (both essential and non-essential) have been identified as key players in plant stress biology, owing to their multifaceted functions. However, a realistic understanding of the relationship between different ions and stresses is lacking. In this context, ionomics will provide new platforms for not only understanding the function of the plant ionome during stresses but also identifying the genes and regulatory pathways related to mineral accumulation, transportation, and involvement in different molecular mechanisms under normal or stress conditions. This article provides a general overview of ionomics and the integration of high-throughput ionomic approaches with other "omics" tools. Integrated omics analysis is highly suitable for identification of the genes for various traits that confer biotic and abiotic stress tolerance. Moreover, ionomics advances being used to identify loci using qualitative trait loci and genome-wide association analysis of element uptake and transport within plant tissues, as well as genetic variation within species, are discussed. Furthermore, recent developments in ionomics for the discovery of stress-tolerant genes in plants have also been addressed; these can be used to produce more robust crops with a high nutritional value for sustainable agriculture.
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Affiliation(s)
- Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea;
| | - Anshika Tyagi
- National Institute for Plant Biotechnology, New Delhi 110012, India;
| | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea;
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12
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Hao H, Li Z, Leng C, Lu C, Luo H, Liu Y, Wu X, Liu Z, Shang L, Jing HC. Sorghum breeding in the genomic era: opportunities and challenges. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1899-1924. [PMID: 33655424 PMCID: PMC7924314 DOI: 10.1007/s00122-021-03789-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/05/2021] [Indexed: 05/04/2023]
Abstract
The importance and potential of the multi-purpose crop sorghum in global food security have not yet been fully exploited, and the integration of the state-of-art genomics and high-throughput technologies into breeding practice is required. Sorghum, a historically vital staple food source and currently the fifth most important major cereal, is emerging as a crop with diverse end-uses as food, feed, fuel and forage and a model for functional genetics and genomics of tropical grasses. Rapid development in high-throughput experimental and data processing technologies has significantly speeded up sorghum genomic researches in the past few years. The genomes of three sorghum lines are available, thousands of genetic stocks accessible and various genetic populations, including NAM, MAGIC, and mutagenised populations released. Functional and comparative genomics have elucidated key genetic loci and genes controlling agronomical and adaptive traits. However, the knowledge gained has far away from being translated into real breeding practices. We argue that the way forward is to take a genome-based approach for tailored designing of sorghum as a multi-functional crop combining excellent agricultural traits for various end uses. In this review, we update the new concepts and innovation systems in crop breeding and summarise recent advances in sorghum genomic researches, especially the genome-wide dissection of variations in genes and alleles for agronomically important traits. Future directions and opportunities for sorghum breeding are highlighted to stimulate discussion amongst sorghum academic and industrial communities.
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Affiliation(s)
- Huaiqing Hao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zhigang Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Chuanyuan Leng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Cheng Lu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Luo
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuanming Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyuan Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhiquan Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Li Shang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- Engineering Laboratory for Grass-based Livestock Husbandry, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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13
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Mural RV, Grzybowski M, Miao C, Damke A, Sapkota S, Boyles RE, Salas Fernandez MG, Schnable PS, Sigmon B, Kresovich S, Schnable JC. Meta-Analysis Identifies Pleiotropic Loci Controlling Phenotypic Trade-offs in Sorghum. Genetics 2021; 218:6294935. [PMID: 34100945 PMCID: PMC9335936 DOI: 10.1093/genetics/iyab087] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/07/2021] [Indexed: 01/03/2023] Open
Abstract
Community association populations are composed of phenotypically and genetically diverse accessions. Once these populations are genotyped, the resulting marker data can be reused by different groups investigating the genetic basis of different traits. Because the same genotypes are observed and scored for a wide range of traits in different environments, these populations represent a unique resource to investigate pleiotropy. Here we assembled a set of 234 separate trait datasets for the Sorghum Association Panel, a group of 406 sorghum genotypes widely employed by the sorghum genetics community. Comparison of genome wide association studies conducted with two independently generated marker sets for this population demonstrate that existing genetic marker sets do not saturate the genome and likely capture only 35-43% of potentially detectable loci controlling variation for traits scored in this population. While limited evidence for pleiotropy was apparent in cross-GWAS comparisons, a multivariate adaptive shrinkage approach recovered both known pleiotropic effects of existing loci and new pleiotropic effects, particularly significant impacts of known dwarfing genes on root architecture. In addition, we identified new loci with pleiotropic effects consistent with known trade-offs in sorghum development. These results demonstrate the potential for mining existing trait datasets from widely used community association populations to enable new discoveries from existing trait datasets as new, denser genetic marker datasets are generated for existing community association populations.
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Affiliation(s)
- Ravi V Mural
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Marcin Grzybowski
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Chenyong Miao
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Alyssa Damke
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Sirjan Sapkota
- Advanced Plant Technology Program, Clemson University, Clemson, SC 29634 USA.,Department of Plant and Environment Sciences, Clemson University, Clemson, SC 29634 USA
| | - Richard E Boyles
- Department of Plant and Environment Sciences, Clemson University, Clemson, SC 29634 USA.,Pee Dee Research and Education Center, Clemson University, Florence, SC 29532 USA
| | | | | | - Brandi Sigmon
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Stephen Kresovich
- Department of Plant and Environment Sciences, Clemson University, Clemson, SC 29634 USA.,Feed the Future Innovation Lab for Crop Improvement Cornell University, Ithaca, NY 14850 USA
| | - James C Schnable
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
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14
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Zhang L, MacQueen A, Bonnette J, Fritschi FB, Lowry DB, Juenger TE. QTL x environment interactions underlie ionome divergence in switchgrass. G3-GENES GENOMES GENETICS 2021; 11:6259145. [PMID: 33914881 PMCID: PMC8495926 DOI: 10.1093/g3journal/jkab144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/23/2021] [Indexed: 01/02/2023]
Abstract
Ionomics measures elemental concentrations in biological organisms and provides a snapshot of physiology under different conditions. In this study, we evaluate genetic variation of the ionome in outbred, perennial switchgrass in three environments across the species' native range, and explore patterns of genotype-by-environment interactions. We grew 725 clonally replicated genotypes of a large full sib family from a four-way linkage mapping population, created from deeply diverged upland and lowland switchgrass ecotypes, at three common gardens. Concentrations of 18 mineral elements were determined in whole post-anthesis tillers using ion coupled plasma mass spectrometry (ICP-MS). These measurements were used to identify quantitative trait loci (QTL) with and without QTL-by-environment interactions (QTLxE) using a multi-environment QTL mapping approach. We found that element concentrations varied significantly both within and between switchgrass ecotypes, and GxE was present at both the trait and QTL level. Concentrations of 14 of the 18 elements were under some genetic control, and 77 QTL were detected for these elements. 74% of QTL colocalized multiple elements, half of QTL exhibited significant QTLxE, and roughly equal numbers of QTL had significant differences in magnitude and sign of their effects across environments. The switchgrass ionome is under moderate genetic control and by loci with highly variable effects across environments.
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Affiliation(s)
- Li Zhang
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Alice MacQueen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Jason Bonnette
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Felix B Fritschi
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211
| | - David B Lowry
- Department of Plant Biology and DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
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15
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D’Oria A, Courbet G, Lornac A, Pluchon S, Arkoun M, Maillard A, Etienne P, Diquélou S, Ourry A. Specificity and Plasticity of the Functional Ionome of Brassica napus and Triticum aestivum Exposed to Micronutrient or Beneficial Nutrient Deprivation and Predictive Sensitivity of the Ionomic Signatures. FRONTIERS IN PLANT SCIENCE 2021; 12:641678. [PMID: 33643368 PMCID: PMC7902711 DOI: 10.3389/fpls.2021.641678] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/12/2021] [Indexed: 06/02/2023]
Abstract
The specific variation in the functional ionome was studied in Brassica napus and Triticum aestivum plants subjected to micronutrient or beneficial mineral nutrient deprivation. Effects of these deprivations were compared to those of macronutrient deprivation. In order to identify early events, plants were harvested after 22 days, i.e., before any significant reduction in growth relative to control plants. Root uptake, tissue concentrations and relative root nutrient contents were analyzed revealing numerous interactions with respect to the 20 elements quantified. The assessment of the functional ionome under individual mineral nutrient deficiency allows the identification of a large number of interactions between elements, although it is not totally exhaustive, and gives access to specific ionomic signatures that discriminate among deficiencies in N, P, S, K, Ca, Mn, Fe, Zn, Na, Si, and Se in both species, plus Mg, Cl, Cu, and Mo in wheat. Ionome modifications and components of ionomic signatures are discussed in relation to well-known mechanisms that may explain crosstalks between mineral nutrients, such as between Na and K, V, Se, Mo and S or Fe, Zn and Cu. More surprisingly, when deprived of beneficial nutrients such as Na, Si, Co, or Se, the plant ionome was strongly modified while these beneficial nutrients contributed greatly to the leaf ionomic signature of most mineral deficiencies.
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Affiliation(s)
- Aurélien D’Oria
- UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, Normandie Université, UNICAEN, INRAE, Caen, France
- Laboratoire de Nutrition Végétale, Centre Mondial de l’Innovation, Le Groupe Roullier, Saint-Malo, France
| | - Galatéa Courbet
- UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, Normandie Université, UNICAEN, INRAE, Caen, France
| | - Aurélia Lornac
- UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, Normandie Université, UNICAEN, INRAE, Caen, France
| | - Sylvain Pluchon
- Laboratoire de Nutrition Végétale, Centre Mondial de l’Innovation, Le Groupe Roullier, Saint-Malo, France
| | - Mustapha Arkoun
- Laboratoire de Nutrition Végétale, Centre Mondial de l’Innovation, Le Groupe Roullier, Saint-Malo, France
| | - Anne Maillard
- Laboratoire de Nutrition Végétale, Centre Mondial de l’Innovation, Le Groupe Roullier, Saint-Malo, France
| | - Philippe Etienne
- UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, Normandie Université, UNICAEN, INRAE, Caen, France
| | - Sylvain Diquélou
- UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, Normandie Université, UNICAEN, INRAE, Caen, France
| | - Alain Ourry
- UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, Normandie Université, UNICAEN, INRAE, Caen, France
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16
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Stich B, Benke A, Schmidt M, Urbany C, Shi R, von Wirén N. The maize shoot ionome: Its interaction partners, predictive power, and genetic determinants. PLANT, CELL & ENVIRONMENT 2020; 43:2095-2111. [PMID: 32529648 DOI: 10.1111/pce.13823] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 04/05/2020] [Accepted: 04/18/2020] [Indexed: 05/28/2023]
Abstract
An improved understanding of how to manipulate the accumulation and enrichment of mineral elements in aboveground plant tissues holds promise for future resource efficient and sustainable crop production. The objectives of this study were to (a) evaluate the influence of Fe regimes on mineral element concentrations and contents in the maize shoot as well as their correlations, (b) examine the predictive ability of physiological and morphological traits of individual genotypes of the IBM population from the concentration of mineral elements, and (c) identify genetic factors influencing the mineral element composition within and across Fe regimes. We evaluated the concentration and content of 12 mineral elements in shoots of the IBM population grown in sufficient and deficient Fe regimes and found for almost all mineral elements a significant (α = 0.05) genotypic variance. Across all mineral elements, the variance of genotype*Fe regime interactions was on average even more pronounced. High prediction abilities indicated that mineral elements are powerful predictors of morphological and physiological traits. Furthermore, our results suggest that ZmHMA2/3 and ZmMOT1 are major players in the natural genetic variation of Cd and Mo concentrations and contents of maize shoots, respectively.
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Affiliation(s)
- Benjamin Stich
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Andreas Benke
- Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Maria Schmidt
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, Germany
| | - Claude Urbany
- Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Rongli Shi
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Nicolaus von Wirén
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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17
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Li M, Shao M, Zeng D, Ju T, Kellogg EA, Topp CN. Comprehensive 3D phenotyping reveals continuous morphological variation across genetically diverse sorghum inflorescences. THE NEW PHYTOLOGIST 2020; 226:1873-1885. [PMID: 32162345 PMCID: PMC7317572 DOI: 10.1111/nph.16533] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/23/2020] [Indexed: 05/21/2023]
Abstract
●Inflorescence architecture in plants is often complex and challenging to quantify, particularly for inflorescences of cereal grasses. Methods for capturing inflorescence architecture and for analyzing the resulting data are limited to a few easily captured parameters that may miss the rich underlying diversity. ●Here, we apply X-ray computed tomography combined with detailed morphometrics, offering new imaging and computational tools to analyze three-dimensional inflorescence architecture. To show the power of this approach, we focus on the panicles of Sorghum bicolor, which vary extensively in numbers, lengths, and angles of primary branches, as well as the three-dimensional shape, size, and distribution of the seed. ●We imaged and comprehensively evaluated the panicle morphology of 55 sorghum accessions that represent the five botanical races in the most common classification system of the species, defined by genetic data. We used our data to determine the reliability of the morphological characters for assigning specimens to race and found that seed features were particularly informative. ●However, the extensive overlap between botanical races in multivariate trait space indicates that the phenotypic range of each group extends well beyond its overall genetic background, indicating unexpectedly weak correlation between morphology, genetic identity, and domestication history.
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Affiliation(s)
- Mao Li
- Donald Danforth Plant Science CenterSt LouisMO63132USA
| | - Mon‐Ray Shao
- Donald Danforth Plant Science CenterSt LouisMO63132USA
| | - Dan Zeng
- Department of Computer Science and EngineeringWashington UniversitySt LouisMO63130USA
| | - Tao Ju
- Department of Computer Science and EngineeringWashington UniversitySt LouisMO63130USA
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18
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Fatiukha A, Klymiuk V, Peleg Z, Saranga Y, Cakmak I, Krugman T, Korol AB, Fahima T. Variation in phosphorus and sulfur content shapes the genetic architecture and phenotypic associations within the wheat grain ionome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:555-572. [PMID: 31571297 DOI: 10.1111/tpj.14554] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 09/10/2019] [Accepted: 09/23/2019] [Indexed: 05/04/2023]
Abstract
Dissection of the genetic basis of wheat ionome is crucial for understanding the physiological and biochemical processes underlying mineral accumulation in seeds, as well as for efficient crop breeding. Most of the elements essential for plants are metals stored in seeds as chelate complexes with phytic acid or sulfur-containing compounds. We assume that the involvement of phosphorus and sulfur in metal chelation is the reason for strong phenotypic correlations within ionome. Adjustment of element concentrations for the effect of variation in phosphorus and sulfur seed content resulted in drastic change of phenotypic correlations between the elements. The genetic architecture of wheat grain ionome was characterized by quantitative trait loci (QTL) analysis using a cross between durum and wild emmer wheat. QTL analysis of the adjusted traits and two-trait analysis of the initial traits paired with either P or S considerably improved QTL detection power and accuracy, resulting in the identification of 105 QTLs and 617 QTL effects for 11 elements. Candidate gene search revealed some potential functional associations between QTLs and corresponding genes within their intervals. Thus, we have shown that accounting for variation in P and S is crucial for understanding of the physiological and genetic regulation of mineral composition of wheat grain ionome and can be implemented for other plants.
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Affiliation(s)
- Andrii Fatiukha
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Khoushy Ave, Mt. Carmel, Haifa, 3498838, Israel
| | - Valentyna Klymiuk
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Khoushy Ave, Mt. Carmel, Haifa, 3498838, Israel
| | - Zvi Peleg
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Yehoshua Saranga
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Ismail Cakmak
- Faculty of Engineering & Natural Sciences, Sabanci University, Tuzla İstanbul, 34956, Turkey
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
| | - Abraham B Korol
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Khoushy Ave, Mt. Carmel, Haifa, 3498838, Israel
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Khoushy Ave, Mt. Carmel, Haifa, 3498838, Israel
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19
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Kimani W, Zhang LM, Wu XY, Hao HQ, Jing HC. Genome-wide association study reveals that different pathways contribute to grain quality variation in sorghum (Sorghum bicolor). BMC Genomics 2020; 21:112. [PMID: 32005168 PMCID: PMC6995107 DOI: 10.1186/s12864-020-6538-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 01/27/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND In sorghum (Sorghum bicolor), one paramount breeding objective is to increase grain quality. The nutritional quality and end use value of sorghum grains are primarily influenced by the proportions of tannins, starch and proteins, but the genetic basis of these grain quality traits remains largely unknown. This study aimed to dissect the natural variation of sorghum grain quality traits and identify the underpinning genetic loci by genome-wide association study. RESULTS Levels of starch, tannins and 17 amino acids were quantified in 196 diverse sorghum inbred lines, and 44 traits based on known metabolic pathways and biochemical interactions amongst the 17 amino acids calculated. A Genome-wide association study (GWAS) with 3,512,517 SNPs from re-sequencing data identified 14, 15 and 711 significant SNPs which represented 14, 14, 492 genetic loci associated with levels of tannins, starch and amino acids in sorghum grains, respectively. Amongst these significant SNPs, two SNPs were associated with tannin content on chromosome 4 and colocalized with three previously identified loci for Tannin1, and orthologs of Zm1 and TT16 genes. One SNP associated with starch content colocalized with sucrose phosphate synthase gene. Furthermore, homologues of opaque1 and opaque2 genes associated with amino acid content were identified. Using the KEGG pathway database, six and three candidate genes of tannins and starch were mapped into 12 and 3 metabolism pathways, respectively. Thirty-four candidate genes were mapped into 16 biosynthetic and catabolic pathways of amino acids. We finally reconstructed the biosynthetic pathways for aspartate and branched-chain amino acids based on 15 candidate genes identified in this study. CONCLUSION Promising candidate genes associated with grain quality traits have been identified in the present study. Some of them colocalized with previously identified genetic regions, but novel candidate genes involved in various metabolic pathways which influence grain quality traits have been dissected. Our study acts as an entry point for further validation studies to elucidate the complex mechanisms controlling grain quality traits such as tannins, starch and amino acids in sorghum.
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Affiliation(s)
- Wilson Kimani
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Min Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China
| | - Xiao-Yuan Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China
| | - Huai-Qing Hao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China.
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Engineering Laboratory for Grass-based Livestock Husbandry, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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20
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Habyarimana E, Dall’Agata M, De Franceschi P, Baloch FS. Genome-wide association mapping of total antioxidant capacity, phenols, tannins, and flavonoids in a panel of Sorghum bicolor and S. bicolor × S. halepense populations using multi-locus models. PLoS One 2019; 14:e0225979. [PMID: 31805171 PMCID: PMC6894842 DOI: 10.1371/journal.pone.0225979] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 11/15/2019] [Indexed: 12/02/2022] Open
Abstract
Sorghum is widely used for producing food, feed, and biofuel, and it is increasingly grown to produce grains rich in health-promoting antioxidants. The conventional use of grain color as a proxy to indirectly select against or for antioxidants polyphenols in sorghum grain was hampered by the lack of consistency between grain color and the expected antioxidants concentration. Marker-assisted selection built upon significant loci identified through linkage disequilibrium studies showed interesting potential in several plant breeding and animal husbandry programs, and can be used in sorghum breeding for consumer-tailored antioxidant production. The purpose of this work was therefore to conduct genome-wide association study of sorghum grain antioxidants using single nucleotide polymorphisms in a novel diversity panel of Sorghum bicolor landraces and S. bicolor × S. halepense recombinant inbred lines. The recombinant inbred lines outperformed landraces for antioxidant production and contributed novel polymorphism. Antioxidant traits were highly correlated and showed very high broad-sense heritability. The genome-wide association analysis uncovered 96 associations 55 of which were major quantitative trait loci (QTLs) explaining 15 to 31% of the observed antioxidants variability. Eight major QTLs localized in novel chromosomal regions. Twenty-four pleiotropic major effect markers and two novel functional markers (Chr9_1550093, Chr10_50169631) were discovered. A novel pleiotropic major effect marker (Chr1_61095994) explained the highest proportion (R2 = 27–31%) of the variance observed in most traits evaluated in this work, and was in linkage disequilibrium with a hotspot of 19 putative glutathione S-transferase genes conjugating anthocyanins into vacuoles. On chromosome four, a hotspot region was observed involving major effect markers linked with putative MYB-bHLH-WD40 complex genes involved in the biosynthesis of the polyphenol class of flavonoids. The findings in this work are expected to help the scientific community particularly involved in marker assisted breeding for the development of sorghum cultivars with consumer-tailored antioxidants concentration.
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Affiliation(s)
- Ephrem Habyarimana
- CREA Research Center for Cereal and Industrial Crops, Bologna, Italy
- * E-mail:
| | | | | | - Faheem S. Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant Izzet Baysal University, Bolu, Turkey
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21
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Zhang H, Wang ML, Schaefer R, Dang P, Jiang T, Chen C. GWAS and Coexpression Network Reveal Ionomic Variation in Cultivated Peanut. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:12026-12036. [PMID: 31589432 DOI: 10.1021/acs.jafc.9b04939] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Peanut is an important legume providing products with nutrient dense including mineral nutrition. However, the genetic basis underlying the variations in the mineral composition in peanut is still unknown. Genome-wide association studies (GWAS) of the concentrations of 13 mineral elements combined with coexpression network were performed using a diverse panel of 120 genotypes mainly selected from the U.S. peanut mini core collection. A total of 36 significant quantitative trait loci (QTLs) associated with five elemental concentrations were identified with phenotypic variation explained (PVE) from 18.35% to 27.56%, in which 24 QTLs were for boron (B), 2 QTLs for copper (Cu), 6 QTLs for sodium (Na), 3 QTLs for sulfur (S), and 1 QTL for zinc (Zn). A total of 110 nonredundant candidate causal genes identified were significantly associated with elemental accumulation, which included one high-priority overlap (HPO) candidate gene arahy.KQD4NT, an important elemental/metal transporter gene located on LGB04 with position 5,413,913-5,417,353.
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Affiliation(s)
- Hui Zhang
- Department of Crop, Soil, and Environmental Sciences , Auburn University , Auburn , Alabama 36849 , United States
| | - Ming Li Wang
- USDA-ARS Plant Genetic Resources Conservation , Griffin , Georgia 30223 , United States
| | - Robert Schaefer
- Equine Genetics and Genomics Lab , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Phat Dang
- USDA-ARS National Peanut Research Laboratory , Dawson , Georgia 39842 , United States
| | - Tao Jiang
- Department of Crop, Soil, and Environmental Sciences , Auburn University , Auburn , Alabama 36849 , United States
| | - Charles Chen
- Department of Crop, Soil, and Environmental Sciences , Auburn University , Auburn , Alabama 36849 , United States
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22
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Fikas AA, Dilkes BP, Baxter I. Multivariate analysis reveals environmental and genetic determinants of element covariation in the maize grain ionome. PLANT DIRECT 2019; 3:e00139. [PMID: 31245778 PMCID: PMC6589523 DOI: 10.1002/pld3.139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/25/2019] [Accepted: 04/02/2019] [Indexed: 05/06/2023]
Abstract
The integrated responses of biological systems to genetic and environmental variation result in substantial covariance in multiple phenotypes. The resultant pleiotropy, environmental effects, and genotype-by-environmental interactions (GxE) are foundational to our understanding of biology and genetics. Yet, the treatment of correlated characters, and the identification of the genes encoding functions that generate this covariance, has lagged. As a test case for analyzing the genetic basis underlying multiple correlated traits, we analyzed maize kernel ionomes from Intermated B73 x Mo17 (IBM) recombinant inbred populations grown in 10 environments. Plants obtain elements from the soil through genetic and biochemical pathways responsive to physiological state and environment. Most perturbations affect multiple elements which leads the ionome, the full complement of mineral nutrients in an organism, to vary as an integrated network rather than a set of distinct single elements. We compared quantitative trait loci (QTL) determining single-element variation to QTL that predict variation in principal components (PCs) of multiple-element covariance. Single-element and multivariate approaches detected partially overlapping sets of loci. QTL influencing trait covariation were detected at loci that were not found by mapping single-element traits. Moreover, this approach permitted testing environmental components of trait covariance, and identified multi-element traits that were determined by both genetic and environmental factors as well as genotype-by-environment interactions. Growth environment had a profound effect on the elemental profiles and multi-element phenotypes were significantly correlated with specific environmental variables.
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Affiliation(s)
- Alexandra Asaro Fikas
- Donald Danforth Plant Science CenterSt. LouisMissouri
- Washington University in St. LouisSt. LouisMissouri
| | - Brian P. Dilkes
- Department of BiochemistryPurdue UniversityWest LafayetteIndiana
| | - Ivan Baxter
- Donald Danforth Plant Science CenterSt. LouisMissouri
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23
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Mace E, Innes D, Hunt C, Wang X, Tao Y, Baxter J, Hassall M, Hathorn A, Jordan D. The Sorghum QTL Atlas: a powerful tool for trait dissection, comparative genomics and crop improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:751-766. [PMID: 30343386 DOI: 10.1007/s00122-018-3212-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/11/2018] [Indexed: 05/20/2023]
Abstract
We describe the development and application of the Sorghum QTL Atlas, a high-resolution, open-access research platform to facilitate candidate gene identification across three cereal species, sorghum, maize and rice. The mechanisms governing the genetic control of many quantitative traits are only poorly understood and have yet to be fully exploited. Over the last two decades, over a thousand QTL and GWAS studies have been published in the major cereal crops including sorghum, maize and rice. A large body of information has been generated on the genetic basis of quantitative traits, their genomic location, allelic effects and epistatic interactions. However, such QTL information has not been widely applied by cereal improvement programs and genetic researchers worldwide. In part this is due to the heterogeneous nature of QTL studies which leads QTL reliability variation from study to study. Using approaches to adjust the QTL confidence interval, this platform provides access to the most updated sorghum QTL information than any database available, spanning 23 years of research since 1995. The QTL database provides information on the predicted gene models underlying the QTL CI, across all sorghum genome assembly gene sets and maize and rice genome assemblies and also provides information on the diversity of the underlying genes and information on signatures of selection in sorghum. The resulting high-resolution, open-access research platform facilitates candidate gene identification across 3 cereal species, sorghum, maize and rice. Using a number of trait examples, we demonstrate the power and resolution of the resource to facilitate comparative genomics approaches to provide a bridge between genomics and applied breeding.
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Affiliation(s)
- Emma Mace
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, 4370, Australia.
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia.
| | - David Innes
- Department of Agriculture and Fisheries, Ecosciences Precinct, Brisbane, QLD, 4102, Australia
| | - Colleen Hunt
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Xuemin Wang
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, 4370, Australia
| | - Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, 4370, Australia
| | - Jared Baxter
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Michael Hassall
- Department of Agriculture and Fisheries, Leslie Research Facility, Toowoomba, QLD, 4350, Australia
| | - Adrian Hathorn
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - David Jordan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, 4370, Australia
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24
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Boyles RE, Brenton ZW, Kresovich S. Genetic and genomic resources of sorghum to connect genotype with phenotype in contrasting environments. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:19-39. [PMID: 30260043 DOI: 10.1111/tpj.14113] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/30/2018] [Accepted: 09/03/2018] [Indexed: 05/10/2023]
Abstract
With the recent development of genomic resources and high-throughput phenotyping platforms, the 21st century is primed for major breakthroughs in the discovery, understanding and utilization of plant genetic variation. Significant advances in agriculture remain at the forefront to increase crop production and quality to satisfy the global food demand in a changing climate all while reducing the environmental impacts of the world's food production. Sorghum, a resilient C4 grain and grass important for food and energy production, is being extensively dissected genetically and phenomically to help connect the relationship between genetic and phenotypic variation. Unlike genetically modified crops such as corn or soybean, sorghum improvement has relied heavily on public research; thus, many of the genetic resources serve a dual purpose for both academic and commercial pursuits. Genetic and genomic resources not only provide the foundation to identify and understand the genes underlying variation, but also serve as novel sources of genetic and phenotypic diversity in plant breeding programs. To better disseminate the collective information of this community, we discuss: (i) the genomic resources of sorghum that are at the disposal of the research community; (ii) the suite of sorghum traits as potential targets for increasing productivity in contrasting environments; and (iii) the prospective approaches and technologies that will help to dissect the genotype-phenotype relationship as well as those that will apply foundational knowledge for sorghum improvement.
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Affiliation(s)
- Richard E Boyles
- Pee Dee Research and Education Center, Clemson University, 2200 Pocket Rd, Florence, SC, 29506, USA
- Advanced Plant Technology Program, Clemson University, 105 Collings St, Clemson, SC, 29634, USA
| | - Zachary W Brenton
- Advanced Plant Technology Program, Clemson University, 105 Collings St, Clemson, SC, 29634, USA
- Department of Plant and Environment Sciences, Clemson University, 171 Poole Agricultural Center, Clemson, SC, 29634, USA
| | - Stephen Kresovich
- Advanced Plant Technology Program, Clemson University, 105 Collings St, Clemson, SC, 29634, USA
- Department of Plant and Environment Sciences, Clemson University, 171 Poole Agricultural Center, Clemson, SC, 29634, USA
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25
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Chaparro JM, Holm DG, Broeckling CD, Prenni JE, Heuberger AL. Metabolomics and Ionomics of Potato Tuber Reveals an Influence of Cultivar and Market Class on Human Nutrients and Bioactive Compounds. Front Nutr 2018; 5:36. [PMID: 29876353 PMCID: PMC5974217 DOI: 10.3389/fnut.2018.00036] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/19/2018] [Indexed: 01/11/2023] Open
Abstract
Potato (Solanum tuberosum L.) is an important global food crop that contains phytochemicals with demonstrated effects on human health. Understanding sources of chemical variation of potato tuber can inform breeding for improved health attributes of the cooked food. Here, a comprehensive metabolomics (UPLC- and GC-MS) and ionomics (ICP-MS) analysis of raw and cooked potato tuber was performed on 60 unique potato genotypes that span 5 market classes including russet, red, yellow, chip, and specialty potatoes. The analyses detected 2,656 compounds that included known bioactives (43 compounds), nutrients (42), lipids (76), and 23 metals. Most nutrients and bioactives were partially degraded during cooking (44 out of 85; 52%), however genotypes with high quantities of bioactives remained highest in the cooked tuber. Chemical variation was influenced by genotype and market class. Specifically, ~53% of all detected compounds from cooked potato varied among market class and 40% varied by genotype. The most notable metabolite profiles were observed in yellow-flesh potato which had higher levels of carotenoids and specialty potatoes which had the higher levels of chlorogenic acid as compared to the other market classes. Variation in several molecules with known association to health was observed among market classes and included vitamins (e.g., pyridoxal, ~2-fold variation), bioactives (e.g., chlorogenic acid, ~40-fold variation), medicinals (e.g., kukoamines, ~6-fold variation), and minerals (e.g., calcium, iron, molybdenum, ~2-fold variation). Furthermore, more metabolite variation was observed within market class than among market class (e.g., α-tocopherol, ~1-fold variation among market class vs. ~3-fold variation within market class). Taken together, the analysis characterized significant metabolite and mineral variation in raw and cooked potato tuber, and support the potential to breed new cultivars for improved health traits.
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Affiliation(s)
- Jacqueline M. Chaparro
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, United States
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, United States
| | - David G. Holm
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, United States
| | - Corey D. Broeckling
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, United States
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, United States
| | - Jessica E. Prenni
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, United States
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, United States
| | - Adam L. Heuberger
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, United States
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
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26
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Pauli D, Ziegler G, Ren M, Jenks MA, Hunsaker DJ, Zhang M, Baxter I, Gore MA. Multivariate Analysis of the Cotton Seed Ionome Reveals a Shared Genetic Architecture. G3 (BETHESDA, MD.) 2018; 8:1147-1160. [PMID: 29437829 PMCID: PMC5873906 DOI: 10.1534/g3.117.300479] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 01/28/2018] [Indexed: 02/01/2023]
Abstract
To mitigate the effects of heat and drought stress, a better understanding of the genetic control of physiological responses to these environmental conditions is needed. To this end, we evaluated an upland cotton (Gossypium hirsutum L.) mapping population under water-limited and well-watered conditions in a hot, arid environment. The elemental concentrations (ionome) of seed samples from the population were profiled in addition to those of soil samples taken from throughout the field site to better model environmental variation. The elements profiled in seeds exhibited moderate to high heritabilities, as well as strong phenotypic and genotypic correlations between elements that were not altered by the imposed irrigation regimes. Quantitative trait loci (QTL) mapping results from a Bayesian classification method identified multiple genomic regions where QTL for individual elements colocalized, suggesting that genetic control of the ionome is highly interrelated. To more fully explore this genetic architecture, multivariate QTL mapping was implemented among groups of biochemically related elements. This analysis revealed both additional and pleiotropic QTL responsible for coordinated control of phenotypic variation for elemental accumulation. Machine learning algorithms that utilized only ionomic data predicted the irrigation regime under which genotypes were evaluated with very high accuracy. Taken together, these results demonstrate the extent to which the seed ionome is genetically interrelated and predictive of plant physiological responses to adverse environmental conditions.
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Affiliation(s)
- Duke Pauli
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Greg Ziegler
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Plant Genetics Research Unit, St. Louis, Missouri 63132
| | - Min Ren
- Department of Statistics, Purdue University, West Lafayette, Indiana 47907
| | - Matthew A Jenks
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia 26506, and
| | | | - Min Zhang
- Department of Statistics, Purdue University, West Lafayette, Indiana 47907
| | - Ivan Baxter
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Plant Genetics Research Unit, St. Louis, Missouri 63132
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853,
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27
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Ziegler G, Nelson R, Granada S, Krishnan HB, Gillman JD, Baxter I. Genomewide association study of ionomic traits on diverse soybean populations from germplasm collections. PLANT DIRECT 2018; 2:e00033. [PMID: 31245681 PMCID: PMC6508489 DOI: 10.1002/pld3.33] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/06/2017] [Accepted: 11/14/2017] [Indexed: 05/17/2023]
Abstract
The elemental content of a soybean seed is a determined by both genetic and environmental factors and is an important component of its nutritional value. The elemental content is chemically stable, making the samples stored in germplasm repositories an intriguing source of experimental material. To test the efficacy of using samples from germplasm banks for gene discovery, we analyzed the elemental profile of seeds from 1,653 lines in the USDA Soybean Germplasm Collection. We observed large differences in the elemental profiles based on where the lines were grown, which lead us to break up the genetic analysis into multiple small experiments. Despite these challenges, we were able to identify candidate single nucleotide polymorphisms (SNPs) controlling elemental accumulation as well as lines with extreme elemental accumulation phenotypes. Our results suggest that elemental analysis of germplasm samples can identify SNPs in linkage disequilibrium to genes, which can be leveraged to assist in crop improvement efforts.
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Affiliation(s)
- Greg Ziegler
- USDA‐ARS Plant Genetics Research UnitSt. LouisMOUSA
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Randall Nelson
- Soybean/Maize Germplasm, Pathology and Genetics Research Unit and Department of Crop SciencesUSDA‐ARSUniversity of IllinoisUrbanaILUSA
| | | | - Hari B. Krishnan
- USDA‐ARS Plant Genetics Research UnitColumbiaMOUSA
- Plant Science DivisionUniversity of MissouriColumbiaMOUSA
| | - Jason D. Gillman
- USDA‐ARS Plant Genetics Research UnitColumbiaMOUSA
- Plant Science DivisionUniversity of MissouriColumbiaMOUSA
| | - Ivan Baxter
- USDA‐ARS Plant Genetics Research UnitSt. LouisMOUSA
- Donald Danforth Plant Science CenterSt. LouisMOUSA
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28
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Veley KM, Berry JC, Fentress SJ, Schachtman DP, Baxter I, Bart R. High-throughput profiling and analysis of plant responses over time to abiotic stress. PLANT DIRECT 2017; 1:e00023. [PMID: 31245669 PMCID: PMC6508565 DOI: 10.1002/pld3.23] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 09/28/2017] [Indexed: 05/21/2023]
Abstract
Sorghum (Sorghum bicolor (L.) Moench) is a rapidly growing, high-biomass crop prized for abiotic stress tolerance. However, measuring genotype-by-environment (G x E) interactions remains a progress bottleneck. We subjected a panel of 30 genetically diverse sorghum genotypes to a spectrum of nitrogen deprivation and measured responses using high-throughput phenotyping technology followed by ionomic profiling. Responses were quantified using shape (16 measurable outputs), color (hue and intensity), and ionome (18 elements). We measured the speed at which specific genotypes respond to environmental conditions, in terms of both biomass and color changes, and identified individual genotypes that perform most favorably. With this analysis, we present a novel approach to quantifying color-based stress indicators over time. Additionally, ionomic profiling was conducted as an independent, low-cost, and high-throughput option for characterizing G x E, identifying the elements most affected by either genotype or treatment and suggesting signaling that occurs in response to the environment. This entire dataset and associated scripts are made available through an open-access, user-friendly, web-based interface. In summary, this work provides analysis tools for visualizing and quantifying plant abiotic stress responses over time. These methods can be deployed as a time-efficient method of dissecting the genetic mechanisms used by sorghum to respond to the environment to accelerate crop improvement.
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Affiliation(s)
- Kira M. Veley
- Donald Danforth Plant Science CenterSaint LouisMOUSA
| | | | | | - Daniel P. Schachtman
- Department of Agronomy and Horticulture and Center for Plant Science InnovationUniversity of Nebraska–LincolnLincolnNEUSA
| | - Ivan Baxter
- Donald Danforth Plant Science CenterSaint LouisMOUSA
- USDA‐ARSSaint LouisMOUSA
| | - Rebecca Bart
- Donald Danforth Plant Science CenterSaint LouisMOUSA
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29
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Bazakos C, Hanemian M, Trontin C, Jiménez-Gómez JM, Loudet O. New Strategies and Tools in Quantitative Genetics: How to Go from the Phenotype to the Genotype. ANNUAL REVIEW OF PLANT BIOLOGY 2017; 68:435-455. [PMID: 28226236 DOI: 10.1146/annurev-arplant-042916-040820] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Quantitative genetics has a long history in plants: It has been used to study specific biological processes, identify the factors important for trait evolution, and breed new crop varieties. These classical approaches to quantitative trait locus mapping have naturally improved with technology. In this review, we show how quantitative genetics has evolved recently in plants and how new developments in phenotyping, population generation, sequencing, gene manipulation, and statistics are rejuvenating both the classical linkage mapping approaches (for example, through nested association mapping) as well as the more recently developed genome-wide association studies. These strategies are complementary in most instances, and indeed, one is often used to confirm the results of the other. Despite significant advances, an emerging trend is that the outcome and efficiency of the different approaches depend greatly on the genetic architecture of the trait in the genetic material under study.
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Affiliation(s)
- Christos Bazakos
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78026 Versailles Cedex, France;
| | - Mathieu Hanemian
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78026 Versailles Cedex, France;
| | - Charlotte Trontin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78026 Versailles Cedex, France;
| | - José M Jiménez-Gómez
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78026 Versailles Cedex, France;
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78026 Versailles Cedex, France;
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30
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Burghardt LT, Young ND, Tiffin P. A Guide to Genome-Wide Association Mapping in Plants. ACTA ACUST UNITED AC 2017; 2:22-38. [PMID: 31725973 DOI: 10.1002/cppb.20041] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Genome-wide association studies (GWAS) have developed into a valuable approach for identifying the genetic basis of phenotypic variation. In this article, we provide an overview of the design, analysis, and interpretation of GWAS. First, we present results from simulations that explore key elements of experimental design as well as considerations for collecting the relevant genomic and phenotypic data. Next, we outline current statistical methods and tools used for GWA analyses and discuss the inclusion of covariates to account for population structure and the interpretation of results. Given that many false positive associations will occur in any GWA analysis, we highlight strategies for prioritizing GWA candidates for further statistical and empirical validation. While focused on plants, the material we cover is also applicable to other systems. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Liana T Burghardt
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota
| | - Nevin D Young
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota
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Chopra R, Burow G, Burke JJ, Gladman N, Xin Z. Genome-wide association analysis of seedling traits in diverse Sorghum germplasm under thermal stress. BMC PLANT BIOLOGY 2017; 17:12. [PMID: 28086798 PMCID: PMC5237230 DOI: 10.1186/s12870-016-0966-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 12/23/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Climate variability due to fluctuation in temperature is a worldwide concern that imperils crop production. The need to understand how the germplasm variation in major crops can be utilized to aid in discovering and developing breeding lines that can withstand and adapt to temperature fluctuations is more necessary than ever. Here, we analyzed the genetic variation associated with responses to thermal stresses in a sorghum association panel (SAP) representing major races and working groups to identify single nucleotide polymorphisms (SNPs) that are associated with resilience to temperature stress in a major cereal crop. RESULTS The SAP exhibited extensive variation for seedling traits under cold and heat stress. Genome-wide analyses identified 30 SNPs that were strongly associated with traits measured at seedling stage under cold stress and tagged genes that act as regulators of anthocyanin expression and soluble carbohydrate metabolism. Meanwhile, 12 SNPs were significantly associated with seedling traits under heat stress and these SNPs tagged genes that function in sugar metabolism, and ion transport pathways. Evaluation of co-expression networks for genes near the significantly associated SNPs indicated complex gene interactions for cold and heat stresses in sorghum. We focused and validated the expression of four genes in the network of Sb06g025040, a basic-helix-loop-helix (bHLH) transcription factor that was proposed to be involved in purple color pigmentation of leaf, and observed that genes in this network were upregulated during cold stress in a moderately tolerant line as compared to the more sensitive line. CONCLUSION This study facilitated the tagging of genome regions associated with variation in seedling traits of sorghum under cold and heat stress. These findings show the potential of genotype information for development of temperature resilient sorghum cultivars and further characterization of genes and their networks responsible for adaptation to thermal stresses. Knowledge on the gene networks from this research can be extended to the other cereal crops to better understand the genetic basis of resilience to temperature fluctuations during plant developmental stages.
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Affiliation(s)
- Ratan Chopra
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA.
| | - Gloria Burow
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA.
| | - John J Burke
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA
| | - Nicholas Gladman
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA
| | - Zhanguo Xin
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA
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Manickavelu A, Hattori T, Yamaoka S, Yoshimura K, Kondou Y, Onogi A, Matsui M, Iwata H, Ban T. Genetic Nature of Elemental Contents in Wheat Grains and Its Genomic Prediction: Toward the Effective Use of Wheat Landraces from Afghanistan. PLoS One 2017; 12:e0169416. [PMID: 28072876 PMCID: PMC5224831 DOI: 10.1371/journal.pone.0169416] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/16/2016] [Indexed: 11/19/2022] Open
Abstract
Profiling elemental contents in wheat grains and clarifying the underlying genetic systems are important for the breeding of biofortified crops. Our objective was to evaluate the genetic potential of 269 Afghan wheat landraces for increasing elemental contents in wheat cultivars. The contents of three major (Mg, K, and P) and three minor (Mn, Fe, and Zn) elements in wheat grains were measured by energy dispersive X-ray fluorescence spectrometry. Large variations in elemental contents were observed among landraces. Marker-based heritability estimates were low to moderate, suggesting that the elemental contents are complex quantitative traits. Genetic correlations between two locations (Japan and Afghanistan) and among the six elements were estimated using a multi-response Bayesian linear mixed model. Low-to-moderate genetic correlations were observed among major elements and among minor elements respectively, but not between major and minor elements. A single-response genome-wide association study detected only one significant marker, which was associated with Zn, suggesting it will be difficult to increase the elemental contents of wheat by conventional marker-assisted selection. Genomic predictions for major elemental contents were moderately or highly accurate, whereas those for minor elements were mostly low or moderate. Our results indicate genomic selection may be useful for the genetic improvement of elemental contents in wheat.
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Affiliation(s)
- Alagu Manickavelu
- Plant Genetic Resources Division, Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
- Department of Genomic Science, Central University of Kerala, Riverside Transit Campus, Kerala, India
| | - Tomohiro Hattori
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shuhei Yamaoka
- Plant Genetic Resources Division, Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Kazusa Yoshimura
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Youichi Kondou
- College of Science and Engineering, Kanto Gakuin University, Yokohama, Kanagawa, Japan
| | - Akio Onogi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Minami Matsui
- Centre for Sustainable Resource Sciences, Yokohama, Kanagawa, Japan
| | - Hiroyoshi Iwata
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- * E-mail:
| | - Tomohiro Ban
- Plant Genetic Resources Division, Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
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Genetic architecture of kernel composition in global sorghum germplasm. BMC Genomics 2017; 18:15. [PMID: 28056770 PMCID: PMC5217548 DOI: 10.1186/s12864-016-3403-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/09/2016] [Indexed: 12/30/2022] Open
Abstract
Background Sorghum [Sorghum bicolor (L.) Moench] is an important cereal crop for dryland areas in the United States and for small-holder farmers in Africa. Natural variation of sorghum grain composition (protein, fat, and starch) between accessions can be used for crop improvement, but the genetic controls are still unresolved. The goals of this study were to quantify natural variation of sorghum grain composition and to identify single-nucleotide polymorphisms (SNPs) associated with variation in grain composition concentrations. Results In this study, we quantified protein, fat, and starch in a global sorghum diversity panel using near-infrared spectroscopy (NIRS). Protein content ranged from 8.1 to 18.8%, fat content ranged from 1.0 to 4.3%, and starch content ranged from 61.7 to 71.1%. Durra and bicolor-durra sorghum from Ethiopia and India had the highest protein and fat and the lowest starch content, while kafir sorghum from USA, India, and South Africa had the lowest protein and the highest starch content. Genome-wide association studies (GWAS) identified quantitative trait loci (QTL) for sorghum protein, fat, and starch. Previously published RNAseq data was used to identify candidate genes within a GWAS QTL region. A putative alpha-amylase 3 gene, which has previously been shown to be associated with grain composition traits, was identified as a strong candidate for protein and fat variation. Conclusions We identified promising sources of genetic material for manipulation of grain composition traits, and several loci and candidate genes that may control sorghum grain composition. This survey of grain composition in sorghum germplasm and identification of protein, fat, and starch QTL contributes to our understanding of the genetic basis of natural variation in sorghum grain nutritional traits. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3403-x) contains supplementary material, which is available to authorized users.
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Bokor B, Ondoš S, Vaculík M, Bokorová S, Weidinger M, Lichtscheidl I, Turňa J, Lux A. Expression of Genes for Si Uptake, Accumulation, and Correlation of Si with Other Elements in Ionome of Maize Kernel. FRONTIERS IN PLANT SCIENCE 2017; 8:1063. [PMID: 28674553 PMCID: PMC5474966 DOI: 10.3389/fpls.2017.01063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 06/02/2017] [Indexed: 05/09/2023]
Abstract
The mineral composition of cells, tissues, and organs is decisive for the functioning of the organisms, and is at the same time an indicator for understanding of physiological processes. We measured the composition of the ionome in the different tissues of maize kernels by element microanalysis, with special emphasis on silicon (Si). We therefore also measured the expression levels of the Si transporter genes ZmLsi1, ZmLsi2 and ZmLsi6, responsible for Si uptake and accumulation. Two weeks after pollination ZmLsi1 and ZmLsi6 genes were expressed, and expression continued until the final developmental stage of the kernels, while ZmLsi2 was not expressed. These results suggest that exclusively ZmLsi1 and ZmLsi6 are responsible for Si transport in various stages of kernel development. Expression level of ZmLsi genes was consistent with Si accumulation within kernel tissues. Silicon was mainly accumulated in pericarp and embryo proper and the lowest Si content was detected in soft endosperm and the scutellum. Correlation linkages between the distribution of Si and some other elements (macroelements Mg, P, S, N, P, and Ca and microelements Cl, Zn, and Fe) were found. The relation of Si with Mg was detected in all kernel tissues. The Si linkage with other elements was rather specific and found only in certain kernel tissues of maize. These relations may have effect on nutrient uptake and accumulation.
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Affiliation(s)
- Boris Bokor
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in BratislavaBratislava, Slovakia
- Comenius University Science ParkBratislava, Slovakia
- *Correspondence: Boris Bokor,
| | - Slavomír Ondoš
- Department of Human Geography and Demography, Faculty of Natural Sciences, Comenius University in BratislavaBratislava, Slovakia
| | - Marek Vaculík
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in BratislavaBratislava, Slovakia
- Institute of Botany, Plant Science and Biodiversity Centre of Slovak Academy of SciencesBratislava, Slovakia
| | - Silvia Bokorová
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in BratislavaBratislava, Slovakia
| | - Marieluise Weidinger
- Core Facility Cell Imaging and Ultrastructure Research, University of ViennaVienna, Austria
| | - Irene Lichtscheidl
- Core Facility Cell Imaging and Ultrastructure Research, University of ViennaVienna, Austria
| | - Ján Turňa
- Comenius University Science ParkBratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in BratislavaBratislava, Slovakia
| | - Alexander Lux
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in BratislavaBratislava, Slovakia
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The Interaction of Genotype and Environment Determines Variation in the Maize Kernel Ionome. G3-GENES GENOMES GENETICS 2016; 6:4175-4183. [PMID: 27770027 PMCID: PMC5144985 DOI: 10.1534/g3.116.034827] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Plants obtain soil-resident elements that support growth and metabolism from the water-flow facilitated by transpiration and active transport processes. The availability of elements in the environment interacts with the genetic capacity of organisms to modulate element uptake through plastic adaptive responses, such as homeostasis. These interactions should cause the elemental contents of plants to vary such that the effects of genetic polymorphisms will be dramatically dependent on the environment in which the plant is grown. To investigate genotype by environment interactions underlying elemental accumulation, we analyzed levels of elements in maize kernels of the Intermated B73 × Mo17 (IBM) recombinant inbred population grown in 10 different environments, spanning a total of six locations and five different years. In analyses conducted separately for each environment, we identified a total of 79 quantitative trait loci (QTL) controlling seed elemental accumulation. While a set of these QTL was found in multiple environments, the majority were specific to a single environment, suggesting the presence of genetic by environment interactions. To specifically identify and quantify QTL by environment interactions (QEIs), we implemented two methods: linear modeling with environmental covariates, and QTL analysis on trait differences between growouts. With these approaches, we found several instances of QEI, indicating that elemental profiles are highly heritable, interrelated, and responsive to the environment.
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Watanabe T, Maejima E, Yoshimura T, Urayama M, Yamauchi A, Owadano M, Okada R, Osaki M, Kanayama Y, Shinano T. The Ionomic Study of Vegetable Crops. PLoS One 2016; 11:e0160273. [PMID: 27478901 PMCID: PMC4968822 DOI: 10.1371/journal.pone.0160273] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 07/15/2016] [Indexed: 02/03/2023] Open
Abstract
Soil contains various essential and nonessential elements, all of which can be absorbed by plants. Plant ionomics is the study of the accumulation of these elements (the ionome) in plants. The ionomic profile of a plant is affected by various factors, including species, variety, organ, and environment. In this study, we cultivated various vegetable crop species and cultivars under the same field conditions and analyzed the level of accumulation of each element in the edible and nonedible parts using ionomic techniques. The concentration of each element in the edible parts differed between species, which could be partly explained by differences in the types of edible organs (root, leaf, seed, and fruit). For example, the calcium concentration was lower in seeds and fruit than in other organs because of the higher dependency of calcium accumulation on xylem transfer. The concentration of several essential microelements and nonessential elements in the edible parts also varied greatly between cultivars of the same species, knowledge of which will help in the breeding of vegetables that are biofortified or contain lower concentrations of toxic elements. Comparison of the ionomes of the fruit and leaves of tomato (Solanum lycopersicum) and eggplant (S. melongena) indicated that cadmium and boron had higher levels of accumulation in eggplant fruit, likely because of their effective transport in the phloem. We also found that homologous elements that have been reported to share the same uptake/transport system often showed significant correlation only in a few families and that the slopes of these relationships differed between families. Therefore, these differences in the characteristics of mineral accumulation are likely to affect the ionomic profiles of different families.
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Affiliation(s)
- Toshihiro Watanabe
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, 0608589, Japan
- * E-mail:
| | - Eriko Maejima
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, 0608589, Japan
| | - Tomoko Yoshimura
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, 0608589, Japan
| | - Masaru Urayama
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, 0608589, Japan
| | - Aiko Yamauchi
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, 0608589, Japan
| | - Masako Owadano
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, 0608589, Japan
| | - Ryosuke Okada
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, 0608589, Japan
| | - Mitsuru Osaki
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kitaku, Sapporo, 0608589, Japan
| | - Yoshinori Kanayama
- Graduate School of Agricultural Science, Tohoku University, Sendai, 9818555, Japan
| | - Takuro Shinano
- Agricultural Radiation Research Center, NARO Tohoku Agricultural Research Center, 50 Aza Harajyukuminami, Arai, Fukushima, 9602156, Japan
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