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Ye W, Di Caprio L, Bruno P, Jaccard C, Bustos-Segura C, Arce CCM, Benrey B. Cultivar-Specific Defense Responses in Wild and Cultivated Squash Induced by Belowground and Aboveground Herbivory. J Chem Ecol 2024:10.1007/s10886-024-01523-9. [PMID: 38914799 DOI: 10.1007/s10886-024-01523-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 06/08/2024] [Accepted: 06/14/2024] [Indexed: 06/26/2024]
Abstract
Plant domestication often alters plant traits, including chemical and physical defenses against herbivores. In squash, domestication leads to reduced levels of cucurbitacins and leaf trichomes, influencing interactions with insects. However, the impact of domestication on inducible defenses in squash remains poorly understood. Here, we investigated the chemical and physical defensive traits of wild and domesticated squash (Cucurbita argyrosperma), and compared their responses to belowground and aboveground infestation by the root-feeding larvae and the leaf-chewing adults of the banded cucumber beetle Diabrotica balteata (Coleoptera: Chrysomelidae). Wild populations contained cucurbitacins in roots and cotyledons but not in leaves, whereas domesticated varieties lacked cucurbitacins in all tissues. Belowground infestation by D. balteata larvae did not increase cucurbitacin levels in the roots but triggered the expression of cucurbitacin biosynthetic genes, irrespective of domestication status, although the response varied among different varieties. Conversely, whereas wild squash had more leaf trichomes than domesticated varieties, the induction of leaf trichomes in response to herbivory was greater in domesticated plants. Leaf herbivory varied among varieties but there was a trend of higher leaf damage on wild squash than domesticated varieties. Overall, squash plants responded to both belowground and aboveground herbivory by activating chemical defense-associated gene expression in roots and upregulating their physical defense in leaves, respectively. While domestication suppressed both chemical and physical defenses, our findings suggest that it may enhance inducible defense mechanisms by increasing trichome induction in response to herbivory.
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Affiliation(s)
- Wenfeng Ye
- Laboratory of Fundamental and Applied Research in Chemical Ecology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Leandro Di Caprio
- Laboratory of Evolutionary Entomology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Pamela Bruno
- Laboratory of Fundamental and Applied Research in Chemical Ecology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Plant Production Systems, Route Des Eterpys 18, 1964, Agroscope, Conthey, Switzerland
| | - Charlyne Jaccard
- Laboratory of Evolutionary Entomology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Carlos Bustos-Segura
- Laboratory of Evolutionary Entomology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Sensory Ecology, Institute of Ecology and Environmental Sciences of Paris, INRAE, Versailles, France
| | - Carla C M Arce
- Laboratory of Fundamental and Applied Research in Chemical Ecology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Betty Benrey
- Laboratory of Evolutionary Entomology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
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Pence MG, Koch M, DeMond J, Rudgers G. Applying knowledge and experience from potato ( Solanum tuberosum) to update genetic stability data requirements in the risk assessment for vegetatively propagated biotech crops. Front Bioeng Biotechnol 2024; 12:1376634. [PMID: 38638325 PMCID: PMC11024249 DOI: 10.3389/fbioe.2024.1376634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/20/2024] [Indexed: 04/20/2024] Open
Abstract
Regulatory agencies require data on genetic stability as part of the safety assessment for biotech crops, even though the genetic stability of a plant is not necessarily an environmental, human or animal health safety concern. While sexual reproduction has the potential to introduce genomic variation in conventionally bred and biotech crops, vegetative propagation is genetically stable. In vegetatively propagated crops, meiosis does not occur thus limiting the number of homologous recombination events that could lead to chromosomal rearrangements in progeny plants. Genetic stability data is often, but should not be, an automatic requirement for the safety assessment of vegetatively propagated biotech crops. Genetic stability data from biotech potato events has demonstrated that vegetative propagation of potato tubers does not affect the stability of introduced DNA sequences or lead to loss of trait efficacy. The knowledge and experience gained from over 30 years of assessing the safety of biotech crops can be used by regulatory authorities to eliminate data requirements that do not address environmental, food or feed safety concerns. As a first step, regulators should consider removing requirements for genetic stability as part of the safety review for vegetatively propagated biotech crops.
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Affiliation(s)
- Matthew G. Pence
- Simplot Plant Sciences, J. R. Simplot Company, Boise, ID, United States
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van den Burg S, Deolu-Ajayi AO, Nauta R, Cervi WR, van der Werf A, Poelman M, Wilbers GJ, Snethlage J, van Alphen M, van der Meer IM. Knowledge gaps on how to adapt crop production under changing saline circumstances in the Netherlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:170118. [PMID: 38232830 DOI: 10.1016/j.scitotenv.2024.170118] [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: 08/31/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
Salinization, the increase and accumulation of salts in water and soil, impacts productivity of arable crops and is exacerbated by climate change. The Netherlands, like several other deltas and semi-arid regions, faces increasing salinization that negatively impacts agriculture and freshwater availability. Although a lot of salinity expertise exist in the Netherlands, several knowledge gaps on the impact of salinization in the Netherlands, as well as steps to facilitate closing this knowledge gaps to improve saline agriculture in the Netherlands, still exist. This review/opinion article moves beyond existing papers on salinization in bringing together various adaptation measures by thoroughly reviewing the measures through a triple P (People, Planet, Profit) lens. Five main salinity adaptation measures of the crop-soil-water continuum are 1) breeding and selection of salt tolerant varieties, 2) increased cultivation of halophytes, 3) soil management interventions, 4) use of biostimulants, and 5) irrigation techniques. These adaptation measures are described, discussed and analysed for their compliance to the sustainable development elements People, Planet and Profit. All five adaptation measures have potential positive impact on livelihood, contribute to food security and generate revenue but on the other hand, these measures may contribute to unwarranted changes of the ecosystem. The paper ends with a concluding chapter in which the bottlenecks and knowledge gaps that need resolving are identified based on the critical, including triple P, assessment of the discussed adaptation measures. Three key knowledge gaps on breeding, agronomy, environmental sciences and socioeconomics are identified with several approaches that lead to insights elucidated. Thereby informing on future research and action plans to optimize implementation of salinity adaptation measures in the Netherlands.
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Affiliation(s)
- Sander van den Burg
- Wageningen Economic Research, Wageningen University and Research, P. O. Box 29703, 2502 LS The Hague, the Netherlands
| | - Ayodeji O Deolu-Ajayi
- Wageningen Plant Research, Agrosystems Research, Wageningen University and Research, P. O. Box 16, 6700 AA Wageningen, the Netherlands.
| | - Reinier Nauta
- Wageningen Marine Research, Wageningen University and Research, P. O. Box 77, 4400 AB Yerseke, the Netherlands
| | - Walter Rossi Cervi
- Wageningen Economic Research, Wageningen University and Research, P. O. Box 29703, 2502 LS The Hague, the Netherlands
| | - Adrie van der Werf
- Wageningen Plant Research, Agrosystems Research, Wageningen University and Research, P. O. Box 16, 6700 AA Wageningen, the Netherlands
| | - Marnix Poelman
- Wageningen Marine Research, Wageningen University and Research, P. O. Box 77, 4400 AB Yerseke, the Netherlands
| | - Gert-Jan Wilbers
- Wageningen Environmental Research, Wageningen University and Research, P. O. Box 47, 6708 PB Wageningen, the Netherlands
| | - Judit Snethlage
- Wageningen Environmental Research, Wageningen University and Research, P. O. Box 47, 6708 PB Wageningen, the Netherlands
| | - Monica van Alphen
- Wageningen Economic Research, Wageningen University and Research, P. O. Box 29703, 2502 LS The Hague, the Netherlands
| | - Ingrid M van der Meer
- Wageningen Plant Research, Bioscience, Wageningen University and Research, P. O. Box 16, 6700 AA Wageningen, the Netherlands
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Luo X, Yang Y, Lin X, Xiao J. Deciphering spike architecture formation towards yield improvement in wheat. J Genet Genomics 2023; 50:835-845. [PMID: 36907353 DOI: 10.1016/j.jgg.2023.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/12/2023]
Abstract
Wheat is the most widely grown crop globally, providing 20% of the daily consumed calories and protein content around the world. With the growing global population and frequent occurrence of extreme weather caused by climate change, ensuring adequate wheat production is essential for food security. The architecture of the inflorescence plays a crucial role in determining the grain number and size, which is a key trait for improving yield. Recent advances in wheat genomics and gene cloning techniques have improved our understanding of wheat spike development and its applications in breeding practices. Here, we summarize the genetic regulation network governing wheat spike formation, the strategies used for identifying and studying the key factors affecting spike architecture, and the progress made in breeding applications. Additionally, we highlight future directions that will aid in the regulatory mechanistic study of wheat spike determination and targeted breeding for grain yield improvement.
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Affiliation(s)
- Xumei Luo
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiman Yang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xuelei Lin
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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5
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Bedford JA, Carine M, Chapman MA. Detection of locally adapted genomic regions in wild rice (Oryza rufipogon) using environmental association analysis. G3 (BETHESDA, MD.) 2023; 13:jkad194. [PMID: 37619981 PMCID: PMC10542315 DOI: 10.1093/g3journal/jkad194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023]
Abstract
Oryza rufipogon is the wild progenitor of cultivated rice Oryza sativa and exhibits high levels of genetic diversity across its distribution, making it a useful resource for the identification of abiotic stress-tolerant varieties and genes that could limit future climate-changed-induced yield losses. To investigate local adaptation in O. rufipogon, we analyzed single nucleotide polymorphism (SNP) data from a panel of 286 samples located across a diverse range of climates. Environmental association analysis (EAA), a genome-wide association study (GWAS)-based method, was used and revealed 15 regions of the genome significantly associated with various climate factors. Genes within these environmentally associated regions have putative functions in abiotic stress response, phytohormone signaling, and the control of flowering time. This provides an insight into potential local adaptation in O. rufipogon and reveals possible locally adaptive genes that may provide opportunities for breeding novel rice varieties with climate change-resilient phenotypes.
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Affiliation(s)
- James A Bedford
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
- Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Mark Carine
- Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
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Jaccard C, Ye W, Bustos-Segura C, Glauser G, Kaplan I, Benrey B. Consequences of squash (Cucurbita argyrosperma) domestication for plant defence and herbivore interactions. PLANTA 2023; 257:106. [PMID: 37127808 PMCID: PMC10151309 DOI: 10.1007/s00425-023-04139-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/19/2023] [Indexed: 05/03/2023]
Abstract
MAIN CONCLUSION Cucurbita argyrosperma domestication affected plant defence by downregulating the cucurbitacin synthesis-associated genes. However, tissue-specific suppression of defences made the cultivars less attractive to co-evolved herbivores Diabrotica balteata and Acalymma spp. Plant domestication reduces the levels of defensive compounds, increasing susceptibility to insects. In squash, the reduction of cucurbitacins has independently occurred several times during domestication. The mechanisms underlying these changes and their consequences for insect herbivores remain unknown. We investigated how Cucurbita argyrosperma domestication has affected plant chemical defence and the interactions with two herbivores, the generalist Diabrotica balteata and the specialist Acalymma spp. Cucurbitacin levels and associated genes in roots and cotyledons in three wild and four domesticated varieties were analysed. Domesticated varieties contained virtually no cucurbitacins in roots and very low amounts in cotyledons. Contrastingly, cucurbitacin synthesis-associated genes were highly expressed in the roots of wild populations. Larvae of both insects strongly preferred to feed on the roots of wild squash, negatively affecting the generalist's performance but not that of the specialist. Our findings illustrate that domestication results in tissue-specific suppression of chemical defence, making cultivars less attractive to co-evolved herbivores. In the case of squash, this may be driven by the unique role of cucurbitacins in stimulating feeding in chrysomelid beetles.
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Affiliation(s)
- Charlyne Jaccard
- Laboratory of Evolutionary Entomology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - Wenfeng Ye
- Laboratory for Fundamental and Applied Research in Chemical Ecology (FARCE), Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - Carlos Bustos-Segura
- Laboratory of Evolutionary Entomology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - Gaetan Glauser
- Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, Avenue de Bellevaux 51, 2000, Neuchâtel, Switzerland
| | - Ian Kaplan
- Department of Entomology, Purdue University, West Lafayette, IN, 47907, USA
| | - Betty Benrey
- Laboratory of Evolutionary Entomology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland.
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Arguello-Blanco MN, Sneller CH. The effect of cycles of genomic selection on the wheat (T. aestivum) genome. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:70. [PMID: 36952091 DOI: 10.1007/s00122-023-04279-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/07/2022] [Indexed: 06/18/2023]
Abstract
We documented changes in the wheat genome attributed to genomic selection including loss of diversity, and changes in population structure and linkage disequilibrium patterns. We conclude that training and prediction populations need to co-evolve instead of the use of a static training population. Genomic selection (GS) is widely used in plant breeding to shorten breeding cycles. Our objective was to assess the impact of rapid cycling GS on the wheat genome. We used 3927 markers to genotype a training population (YTP) and individuals from five cycles (YC1-YC5) of GS for grain yield. We assessed changes of allele frequency, genetic distance, population structure, and linkage disequilibrium (LD). We found 27.3% of all markers had a significant allele frequency change by YC5, 18% experienced a significant change attributed to selection, and 9.3% had a significant change due to either drift or selection. A total of 725 of 3927 markers were fixed by YC5 with selection fixing 7.3% of the 725 markers. The genetic distance between cycles increased over time. The Fst value of 0.224 between YTP and YC5 indicates their relationship was low. The number LD blocks decreased over time and the correlation between LD matrices also decreased over time. Overall, we found a reduction in genetic diversity, increased genetic differentiation of cycles from the training population, and restructuring of the LD patterns over cycles. The accuracy of GS depends on the genomic similarity of the training population and the prediction populations. Our results show that the similarity can decline rapidly over cycles of GS and compromise the predictive ability of the YTP-based model. Our results support implementing a GS scheme where the training and prediction populations co-evolve instead of the use of a static training population.
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Affiliation(s)
- M N Arguello-Blanco
- Department of Horticulture and Crop Science, The Ohio State University, 1680 Madison Av, Wooster, OH, 446591, USA
| | - Clay H Sneller
- Department of Horticulture and Crop Science, The Ohio State University, 1680 Madison Av, Wooster, OH, 446591, USA.
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Mapping Genetic Variation in Arabidopsis in Response to Plant Growth-Promoting Bacterium Azoarcus olearius DQS-4T. Microorganisms 2023; 11:microorganisms11020331. [PMID: 36838296 PMCID: PMC9961961 DOI: 10.3390/microorganisms11020331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 02/03/2023] Open
Abstract
Plant growth-promoting bacteria (PGPB) can enhance plant health by facilitating nutrient uptake, nitrogen fixation, protection from pathogens, stress tolerance and/or boosting plant productivity. The genetic determinants that drive the plant-bacteria association remain understudied. To identify genetic loci highly correlated with traits responsive to PGPB, we performed a genome-wide association study (GWAS) using an Arabidopsis thaliana population treated with Azoarcus olearius DQS-4T. Phenotypically, the 305 Arabidopsis accessions tested responded differently to bacterial treatment by improving, inhibiting, or not affecting root system or shoot traits. GWA mapping analysis identified several predicted loci associated with primary root length or root fresh weight. Two statistical analyses were performed to narrow down potential gene candidates followed by haplotype block analysis, resulting in the identification of 11 loci associated with the responsiveness of Arabidopsis root fresh weight to bacterial inoculation. Our results showed considerable variation in the ability of plants to respond to inoculation by A. olearius DQS-4T while revealing considerable complexity regarding statistically associated loci with the growth traits measured. This investigation is a promising starting point for sustainable breeding strategies for future cropping practices that may employ beneficial microbes and/or modifications of the root microbiome.
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Yan P, Xie Z, Feng K, Qiu X, Zhang L, Zhang H. Genetic diversity analysis and fingerprint construction of Korean pine ( Pinus koraiensis) clonal seed orchard. FRONTIERS IN PLANT SCIENCE 2023; 13:1079571. [PMID: 36726668 PMCID: PMC9886227 DOI: 10.3389/fpls.2022.1079571] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/29/2022] [Indexed: 06/18/2023]
Abstract
Korean pine is a native tree species in Northeast China. In order to meet the needs of germplasm resource evaluation and molecular marker-assisted breeding of Korean pine, we collected Korean pine clones from 7 populations in Northeast China, analyzed the genetic diversity and genetic structure by SSR molecular marker technology and clustered them to revealed the inter- and intrapopulation differentiation characteristics of each clone. The fingerprint profiles of 161 Korean pine clones were also constructed. 77 alleles were detected for 11 markers, and 18 genotypes were identified on average for each marker. The PIC of the different markers ranged from 0.155-0.855, and the combination of PI and PIsibs for the 11 markers was 3.1 × 10-8 and 1.14 × 10-3, respectively. MANOVA showed that genetic variation existed mainly within populations, accounting for 98% of the total variation. The level of genetic differentiation among populations was low, with an average Nm between populations of 11.036. Genetic diversity is lower in the Lushuihe population and higher in the Tieli population. The 161 Korean pine clones were divided into 4 or 7 populations, and the 7 populations were not clearly distinguished from each other, with only the Lushuihe population showing partial differentiation. There is no significant correlation between the genetic distance of Korean pine populations and the geographical distance of their superior tree sources. This result can provide recommendations for future Korean pine breeding programs. The combination of 11 markers could completely distinguish 161 clones and establish the fingerprint. Genetic diversity of Korean pine clones from the 7 populations was abundant, and the genetic distances of individuals and populations were evenly dispersed. The fingerprint map can be used for the identification of Korean pine clones.
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Affiliation(s)
- Pingyu Yan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zixiong Xie
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Kele Feng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xinyu Qiu
- Heilongjiang Academy of Forestry, Harbin, China
| | - Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Hanguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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Capo-chichi LJA, Elakhdar A, Kubo T, Nyachiro J, Juskiw P, Capettini F, Slaski JJ, Ramirez GH, Beattie AD. Genetic diversity and population structure assessment of Western Canadian barley cooperative trials. FRONTIERS IN PLANT SCIENCE 2023; 13:1006719. [PMID: 36699829 PMCID: PMC9868428 DOI: 10.3389/fpls.2022.1006719] [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: 07/29/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Studying the population structure and genetic diversity of historical datasets is a proposed use for association analysis. This is particularly important when the dataset contains traits that are time-consuming or costly to measure. A set of 96 elite barley genotypes, developed from eight breeding programs of the Western Canadian Cooperative Trials were used in the current study. Genetic diversity, allelic variation, and linkage disequilibrium (LD) were investigated using 5063 high-quality SNP markers via the Illumina 9K Barley Infinium iSelect SNP assay. The distribution of SNPs markers across the barley genome ranged from 449 markers on chromosome 1H to 1111 markers on chromosome 5H. The average polymorphism information content (PIC) per locus was 0.275 and ranged from 0.094 to 0.375. Bayesian clustering in STRUCTURE and principal coordinate analysis revealed that the populations are differentiated primarily due to the different breeding program origins and ear-row type into five subpopulations. Analysis of molecular variance based on PhiPT values suggested that high values of genetic diversity were observed within populations and accounted for 90% of the total variance. Subpopulation 5 exhibited the most diversity with the highest values of the diversity indices, which represent the breeding program gene pool of AFC, AAFRD, AU, and BARI. With increasing genetic distance, the LD values, expressed as r2, declined to below the critical r2 = 0.18 after 3.91 cM, and the same pattern was observed on each chromosome. Our results identified an important pattern of genetic diversity among the Canadian barley panel that was proposed to be representative of target breeding programs and may have important implications for association mapping in the future. This highlight, that efforts to identify novel variability underlying this diversity may present practical breeding opportunities to develop new barley genotypes.
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Affiliation(s)
- Ludovic J. A. Capo-chichi
- Department of Renewable Resources, Faculty of Agriculture, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Ammar Elakhdar
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Field Crops Research Institute, Agricultural Research Center, Giza, Egypt
| | - Takahiko Kubo
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Joseph Nyachiro
- Field Crop Development Centre, Alberta Agriculture and Forestry, Lacombe, AB, Canada
| | - Patricia Juskiw
- Field Crop Development Centre, Alberta Agriculture and Forestry, Lacombe, AB, Canada
| | - Flavio Capettini
- Field Crop Development Centre, Alberta Agriculture and Forestry, Lacombe, AB, Canada
| | - Jan J. Slaski
- Ecosystems and Plant Sciences, InnoTech Alberta Inc., Vegreville, AB, Canada
| | - Guillermo Hernandez Ramirez
- Department of Renewable Resources, Faculty of Agriculture, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Aaron D. Beattie
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada
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Chen J, Cao J, Bian Y, Zhang H, Li X, Wu Z, Guo G, Lv G. Identification of Genetic Variations and Candidate Genes Responsible for Stalk Sugar Content and Agronomic Traits in Fresh Corn via GWAS across Multiple Environments. Int J Mol Sci 2022; 23:ijms232113490. [PMID: 36362278 PMCID: PMC9655584 DOI: 10.3390/ijms232113490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/10/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
The stem and leaves of fresh corn plants can be used as green silage or can be converted to biofuels, and the stalk sugar content and yield directly determine the application value of fresh corn. To identify the genetic variations and candidate genes responsible for the related traits in fresh corn, the genome-wide scan and genome-wide association analysis (GWAS) were performed. A total of 32 selective regions containing 172 genes were detected between sweet and waxy corns. Using the stalk sugar content and seven other agronomic traits measured in four seasons over two years, the GWAS identified ninety-two significant single nucleotide polymorphisms (SNPs). Most importantly, seven SNPs associated with the stalk sugar content were detected across multiple environments, which could explain 13.68–17.82% of the phenotypic variation. Accessions differing in genotype for certain significant SNPs showed significant variation in the stalk sugar content and other agronomic traits, and the expression levels of six important candidate genes were significantly different between two materials with different stalk sugar content. The genetic variations and candidate genes provide valuable resources for future studies of the molecular mechanism of the stalk sugar content and establish the foundation for molecular marker-assisted breeding of fresh corn.
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Affiliation(s)
- Jianjian Chen
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Hangzhou 310004, China
| | - Jinming Cao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Yunlong Bian
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Hui Zhang
- Zhejiang Agricultural Technology Extension Center, Hangzhou 310004, China
| | - Xiangnan Li
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Hangzhou 310004, China
| | - Zhenxing Wu
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Hangzhou 310004, China
| | - Guojin Guo
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Hangzhou 310004, China
| | - Guihua Lv
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Hangzhou 310004, China
- Correspondence: ; Tel.: +86-013454997051
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Zhu T, van Zanten M, De Smet I. Wandering between hot and cold: temperature dose-dependent responses. TRENDS IN PLANT SCIENCE 2022; 27:1124-1133. [PMID: 35810070 DOI: 10.1016/j.tplants.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Plants in most natural habitats are exposed to a continuously changing environment, including fluctuating temperatures. Temperature variations can trigger acclimation or tolerance responses, depending on the severity of the signal. To guarantee food security under a changing climate, we need to fully understand how temperature response and tolerance are triggered and regulated. Here, we put forward the concept that responsiveness to temperature should be viewed in the context of dose-dependency. We discuss physiological, developmental, and molecular examples, predominantly from the model plant Arabidopsis thaliana, illustrating monophasic signaling responses across the physiological temperature gradient.
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Affiliation(s)
- Tingting Zhu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Martijn van Zanten
- Plant Stress Resilience, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium.
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Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons. Proc Natl Acad Sci U S A 2022; 119:e2208496119. [PMID: 36122204 PMCID: PMC9522333 DOI: 10.1073/pnas.2208496119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Wild relatives of domesticated plants provide a rich resource for crop improvement and a valuable comparative perspective for understanding genomic, physiological, and agricultural traits. Here, we provide high-quality reference genomes of one early domesticated form of the economically most important cotton species, Gossypium hirsutum, and two other wild species, to clarify evolutionary relationships and understand the genomic changes that characterize these species and their close relatives. We document abundant gene resources involved in adaptation to environmental challenges, highlighting the potential for introgression of favorable genes into domesticated cotton and for increasing resilience to climate variability. Our study complements other recent genomic analyses in the cotton genus and provides a valuable foundation for breeding improved cotton varieties. Allotetraploid cotton (Gossypium) species represents a model system for the study of plant polyploidy, molecular evolution, and domestication. Here, chromosome-scale genome sequences were obtained and assembled for two recently described wild species of tetraploid cotton, Gossypium ekmanianum [(AD)6, Ge] and Gossypium stephensii [(AD)7, Gs], and one early form of domesticated Gossypium hirsutum, race punctatum [(AD)1, Ghp]. Based on phylogenomic analysis, we provide a dated whole-genome level perspective for the evolution of the tetraploid Gossypium clade and resolved the evolutionary relationships of Gs, Ge, and domesticated G. hirsutum. We describe genomic structural variation that arose during Gossypium evolution and describe its correlates—including phenotypic differentiation, genetic isolation, and genetic convergence—that contributed to cotton biodiversity and cotton domestication. Presence/absence variation is prominent in causing cotton genomic structural variations. A presence/absence variation-derived gene encoding a phosphopeptide-binding protein is implicated in increasing fiber length during cotton domestication. The relatively unimproved Ghp offers the potential for gene discovery related to adaptation to environmental challenges. Expanded gene families enoyl-CoA δ isomerase 3 and RAP2-7 may have contributed to abiotic stress tolerance, possibly by targeting plant hormone-associated biochemical pathways. Our results generate a genomic context for a better understanding of cotton evolution and for agriculture.
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Fuentes-Cardenas IS, Cuba-Puma R, Marcilla-Truyenque S, Begazo-Gutiérrez H, Zolla G, Fuentealba C, Shetty K, Ranilla LG. Diversity of the Peruvian Andean maize ( Zea mays L.) race Cabanita: Polyphenols, carotenoids, in vitro antioxidant capacity, and physical characteristics. Front Nutr 2022; 9:983208. [PMID: 36225880 PMCID: PMC9549777 DOI: 10.3389/fnut.2022.983208] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/29/2022] [Indexed: 12/03/2022] Open
Abstract
The high diversity of the Peruvian Andean maize (Zea mays L.) represents a biological and genetic heritage relevant for food security, but few studies are targeted toward its characterization and consequent valorization and preservation. The objective of this study was to evaluate the potential of the Peruvian Andean maize race Cabanita with respect to its bioactive profiles (free and bound phenolic and carotenoid composition), physical characteristics, and in vitro antioxidant properties. Maize landraces with variable kernel pigmentation were collected from two provinces (Caylloma and Castilla) within the Arequipa region (among ten Andean sites) and the phytochemical profile was evaluated by Ultra High-Performance Liquid Chromatography with diode array detector (UHPLC-DAD). All maize samples were important sources of phenolic compounds mainly soluble p-coumaric and ferulic acid derivatives whereas anthocyanins were only detected in maize with partially red pigmented kernels. Major phenolic compounds in the bound phenolic fractions were ferulic acid and its derivatives along with p-coumaric acid. Carotenoid compounds including xanthophylls such as lutein, lutein isomers, and zeaxanthin were only detected in orange and white-yellow pigmented maize and are reported for the first time in Peruvian landraces. The multivariate analysis using Principal Components Analysis (PCA) revealed low variability of all data which may indicate a level of similarity among maize samples based on evaluated variables. However, maize grown in Caylloma province showed more homogeneous physical characteristics and higher yield, whereas higher phenolic contents and antioxidant capacity were observed in maize from Castilla. Samples CAY (yellow-pigmented kernel, Castilla) and COM (orange-pigmented kernel, Caylloma) had the highest total phenolic (246.7 mg/100 g dried weight basis, DW) and carotenoid (1.95 μg/g DW) contents among all samples. The variable Andean environmental conditions along with differences in farming practices may play a role and should be confirmed with further studies. Current results provide the metabolomic basis for future research using integrated omics platforms targeted toward the complete characterization of the ethnic-relevant maize race Cabanita.
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Affiliation(s)
| | - Rody Cuba-Puma
- Laboratory of Research in Food Science, Universidad Catolica de Santa Maria, Arequipa, Perú
| | | | - Huber Begazo-Gutiérrez
- Estación Experimental Agraria Arequipa, Instituto Nacional de Innovación Agraria (INIA), Arequipa, Perú
| | - Gastón Zolla
- Laboratorio de Fisiologia Molecular de Plantas, PIPS de Cereales y Granos Nativos, Facultad de Agronomia, Universidad Nacional Agraria La Molina, Lima, Perú
| | - Claudia Fuentealba
- Escuela de Alimentos, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Kalidas Shetty
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Lena Gálvez Ranilla
- Laboratory of Research in Food Science, Universidad Catolica de Santa Maria, Arequipa, Perú
- Escuela Profesional de Ingeniería de Industria Alimentaria, Facultad de Ciencias e Ingenierías Biológicas y Químicas, Universidad Catolica de Santa Maria, Arequipa, Perú
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15
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Source Identification and Genome-Wide Association Analysis of Crown Rot Resistance in Wheat. PLANTS 2022; 11:plants11151912. [PMID: 35893616 PMCID: PMC9329777 DOI: 10.3390/plants11151912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 11/28/2022]
Abstract
Crown rot (CR) is a soil-borne disease of wheat in arid and semiarid areas of the world. The incidence rate and severity of CR are increasing with each passing year, which seriously threatens the safety of world wheat production. Here, 522 wheat varieties/lines representing genetic diversity were used to identify and evaluate the resistance source to CR disease. Six varieties, including Zimai 12, Xinong 509, Mazhamai, Sifangmai, and Dawson, were classified as resistant ® to CR. Seventy-nine varieties were classified as moderately resistant (MR) to CR, accounting for 15.13% of the tested varieties. The wheat 660 K SNP array was used to identify resistance loci by genome-wide association analysis (GWAS). A total of 33 SNPs, located on chromosomes 1A, 1B, 1D, 4A, and 4D, were significantly correlated with seedling resistance to CR in two years. Among them, one SNP on chromosome 1A and nine SNPs on chromosome 1B showed most significant resistance to disease, phenotypic variance explained (PVE) by these SNPs were more than 8.45%. Except that significant locus AX-110436287 and AX109621209 on chromosome 1B and AX-94692276 on 1D are close to the already reported QTL, other SNPs are newly discovered resistance loci. These results could lay a strong theoretical foundation for the genetic improvement and breeding for CR resistance in wheat.
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Shi X, Zhou Z, Li W, Qin M, Yang P, Hou J, Huang F, Lei Z, Wu Z, Wang J. Genome-wide association study reveals the genetic architecture for calcium accumulation in grains of hexaploid wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2022; 22:229. [PMID: 35508960 PMCID: PMC9066855 DOI: 10.1186/s12870-022-03602-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/15/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND Hexaploid wheat (Triticum aestivum L.) is a leading cereal crop worldwide. Understanding the mechanism of calcium (Ca) accumulation in wheat is important to reduce the risk of human micronutrient deficiencies. However, the mechanisms of Ca accumulation in wheat grain are only partly understood. RESULTS Here, a genome-wide association study (GWAS) was performed to dissect the genetic basis of Ca accumulation in wheat grain using an association population consisting of 207 varieties, with phenotypic data from three locations. In total, 11 non-redundant genetic loci associated with Ca concentration were identified and they explained, on average, 9.61-26.93% of the phenotypic variation. Cultivars containing more superior alleles had increased grain Ca concentrations. Notably, four non-redundant loci were mutually verified by different statistical models in at least two environments, indicating their stability across different environments. Four putative candidate genes linked to Ca accumulation were revealed from the stable genetic loci. Among them, two genes, associated with the stable genetic loci on chromosomes 4A (AX-108912427) and 3B (AX-110922471), encode the subunits of V-type Proton ATPase (TraesCS4A02G428900 and TraesCS3B02G241000), which annotated as the typical generators of a proton gradient that might be involved in Ca homeostasis in wheat grain. CONCLUSION To identify genetic loci associated with Ca accumulation, we conducted GWAS on Ca concentrations and detected 11 genetic loci; whereas four genetic loci were stable across different environments. A genetic loci hot spot exists at the end of chromosome 4A and associated with the putative candidate gene TraesCS4A02G428900. The candidate gene TraesCS4A02G428900 encodes V-type proton ATPase subunit e and highly expressed in wheat grains, and it possibly involved in Ca accumulation. This study increases our understanding of the genetic architecture of Ca accumulation in wheat grains, which is potentially helpful for wheat Ca biofortification pyramid breeding.
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Affiliation(s)
- Xia Shi
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Zhengfu Zhou
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Wenxu Li
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Maomao Qin
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Pan Yang
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Jinna Hou
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Fangfang Huang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhensheng Lei
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
- The Shennong Laboratory, Zhengzhou, 450002, Henan, China.
- College of Chemistry and Environment Engineering, Pingdingshan University, Pingdingshan, 467000, China.
| | - Zhengqing Wu
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
| | - Jiansheng Wang
- College of Chemistry and Environment Engineering, Pingdingshan University, Pingdingshan, 467000, China.
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17
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Meng Q, Manghwar H, Hu W. Study on Supergenus Rubus L.: Edible, Medicinal, and Phylogenetic Characterization. PLANTS (BASEL, SWITZERLAND) 2022; 11:1211. [PMID: 35567211 PMCID: PMC9102695 DOI: 10.3390/plants11091211] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Rubus L. is one of the most diverse genera belonging to Rosaceae; it consists of more than 700 species with a worldwide distribution. It thus provides an ideal natural "supergenus" for studying the importance of its edible, medicinal, and phylogenetic characteristics for application in our daily lives and fundamental scientific studies. The Rubus genus includes many economically important species, such as blackberry (R. fruticosus L.), red raspberry (R. ideaus L.), black raspberry (R. occidentalis L.), and raspberry (R. chingii Hu), which are widely utilized in the fresh fruit market and the medicinal industry. Although Rubus species have existed in human civilization for hundreds of years, their utilization as fruit and in medicine is still largely inadequate, and many questions on their complex phylogenetic relationships need to be answered. In this review, we briefly summarize the history and progress of studies on Rubus, including its domestication as a source of fresh fruit, its medicinal uses in pharmacology, and its systematic position in the phylogenetic tree. Recent available evidence indicates that (1) thousands of Rubus cultivars were bred via time- and labor-consuming methods from only a few wild species, and new breeding strategies and germplasms were thus limited; (2) many kinds of species in Rubus have been used as medicinal herbs, though only a few species (R. ideaus L., R. chingii Hu, and R. occidentalis L.) have been well studied; (3) the phylogeny of Rubus is very complex, with the main reason for this possibly being the existence of multiple reproductive strategies (apomixis, hybridization, and polyploidization). Our review addresses the utilization of Rubus, summarizing major relevant achievements and proposing core prospects for future application, and thus could serve as a useful roadmap for future elite cultivar breeding and scientific studies.
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Affiliation(s)
- Qinglin Meng
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (Q.M.); (H.M.)
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (Q.M.); (H.M.)
| | - Weiming Hu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (Q.M.); (H.M.)
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18
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Jambuthenne DT, Riaz A, Athiyannan N, Alahmad S, Ng WL, Ziems L, Afanasenko O, Periyannan SK, Aitken E, Platz G, Godwin I, Voss-Fels KP, Dinglasan E, Hickey LT. Mining the Vavilov wheat diversity panel for new sources of adult plant resistance to stripe rust. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1355-1373. [PMID: 35113190 PMCID: PMC9033734 DOI: 10.1007/s00122-022-04037-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Multi-year evaluation of the Vavilov wheat diversity panel identified new sources of adult plant resistance to stripe rust. Genome-wide association studies revealed the key genomic regions influencing resistance, including seven novel loci. Wheat stripe rust (YR) caused by Puccinia striiformis f. sp. tritici (Pst) poses a significant threat to global food security. Resistance genes commonly found in many wheat varieties have been rendered ineffective due to the rapid evolution of the pathogen. To identify novel sources of adult plant resistance (APR), 292 accessions from the N.I. Vavilov Institute of Plant Genetic Resources, Saint Petersburg, Russia, were screened for known APR genes (i.e. Yr18, Yr29, Yr46, Yr33, Yr39 and Yr59) using linked polymerase chain reaction (PCR) molecular markers. Accessions were evaluated against Pst (pathotype 134 E16 A + Yr17 + Yr27) at seedling and adult plant stages across multiple years (2014, 2015 and 2016) in Australia. Phenotypic analyses identified 132 lines that potentially carry novel sources of APR to YR. Genome-wide association studies (GWAS) identified 68 significant marker-trait associations (P < 0.001) for YR resistance, representing 47 independent quantitative trait loci (QTL) regions. Fourteen genomic regions overlapped with previously reported Yr genes, including Yr29, Yr56, Yr5, Yr43, Yr57, Yr30, Yr46, Yr47, Yr35, Yr36, Yrxy1, Yr59, Yr52 and YrYL. In total, seven QTL (positioned on chromosomes 1D, 2A, 3A, 3D, 5D, 7B and 7D) did not collocate with previously reported genes or QTL, indicating the presence of promising novel resistance factors. Overall, the Vavilov diversity panel provides a rich source of new alleles which could be used to broaden the genetic bases of YR resistance in modern wheat varieties.
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Affiliation(s)
- Dilani T Jambuthenne
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Adnan Riaz
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Naveenkumar Athiyannan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food,, Canberra, ACT, Australia
| | - Samir Alahmad
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Wei Ling Ng
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Laura Ziems
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Olga Afanasenko
- Department of Plant Resistance To Diseases, All Russian Research Institute for Plant Protection, St Petersburg, Russia, 196608
| | - Sambasivam K Periyannan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food,, Canberra, ACT, Australia
| | - Elizabeth Aitken
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Greg Platz
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, Australia
| | - Ian Godwin
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Kai P Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Eric Dinglasan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia.
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia.
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Genetic Architecture of Grain Yield-Related Traits in Sorghum and Maize. Int J Mol Sci 2022; 23:ijms23052405. [PMID: 35269548 PMCID: PMC8909957 DOI: 10.3390/ijms23052405] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/06/2022] [Accepted: 02/18/2022] [Indexed: 02/08/2023] Open
Abstract
Grain size, grain number per panicle, and grain weight are crucial determinants of yield-related traits in cereals. Understanding the genetic basis of grain yield-related traits has been the main research object and nodal in crop science. Sorghum and maize, as very close C4 crops with high photosynthetic rates, stress tolerance and large biomass characteristics, are extensively used to produce food, feed, and biofuels worldwide. In this review, we comprehensively summarize a large number of quantitative trait loci (QTLs) associated with grain yield in sorghum and maize. We placed great emphasis on discussing 22 fine-mapped QTLs and 30 functionally characterized genes, which greatly hinders our deep understanding at the molecular mechanism level. This review provides a general overview of the comprehensive findings on grain yield QTLs and discusses the emerging trend in molecular marker-assisted breeding with these QTLs.
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Bashir SS, Hussain A, Hussain SJ, Wani OA, Zahid Nabi S, Dar NA, Baloch FS, Mansoor S. Plant drought stress tolerance: understanding its physiological, biochemical and molecular mechanisms. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2021.2020161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Sheikh Shanawaz Bashir
- Department of Botany, School of Chemical and Life Science, Jamia Hamdard University, New Delhi, India
| | - Anjuman Hussain
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Sofi Javed Hussain
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Owais Ali Wani
- Department of Soil Science, FoA, Wadura, Sopore, Sher-e-Kashmir University of Agricultural Sciences & Technology Shalimar Kashmir, Srinagar, Jammu and Kashmir, India
| | - Sheikh Zahid Nabi
- Division of Biochemistry, Faculty of Basic Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, India
| | - Niyaz A. Dar
- ARSSSS Pampore, Sher-e-Kashmir University of Agricultural Sciences and Technology, Shalimar Kashmir, Srinagar, Jammu and Kashmir, India
| | - Faheem Shehzad Baloch
- Department of Plant Protection, Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Sheikh Mansoor
- Division of Biochemistry, Faculty of Basic Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, India
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21
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Saradadevi GP, Das D, Mangrauthia SK, Mohapatra S, Chikkaputtaiah C, Roorkiwal M, Solanki M, Sundaram RM, Chirravuri NN, Sakhare AS, Kota S, Varshney RK, Mohannath G. Genetic, Epigenetic, Genomic and Microbial Approaches to Enhance Salt Tolerance of Plants: A Comprehensive Review. BIOLOGY 2021; 10:biology10121255. [PMID: 34943170 PMCID: PMC8698797 DOI: 10.3390/biology10121255] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 12/17/2022]
Abstract
Simple Summary Globally, soil salinity, which refers to salt-affected soils, is increasing due to various environmental factors and human activities. Soil salinity poses one of the most serious challenges in the field of agriculture as it significantly reduces the growth and yield of crop plants, both quantitatively and qualitatively. Over the last few decades, several studies have been carried out to understand plant biology in response to soil salinity stress with a major emphasis on genetic and other hereditary components. Based on the outcome of these studies, several approaches are being followed to enhance plants’ ability to tolerate salt stress while still maintaining reasonable levels of crop yields. In this manuscript, we comprehensively list and discuss various biological approaches being followed and, based on the recent advances in the field of molecular biology, we propose some new approaches to improve salinity tolerance of crop plants. The global scientific community can make use of this information for the betterment of crop plants. This review also highlights the importance of maintaining global soil health to prevent several crop plant losses. Abstract Globally, soil salinity has been on the rise owing to various factors that are both human and environmental. The abiotic stress caused by soil salinity has become one of the most damaging abiotic stresses faced by crop plants, resulting in significant yield losses. Salt stress induces physiological and morphological modifications in plants as a result of significant changes in gene expression patterns and signal transduction cascades. In this comprehensive review, with a major focus on recent advances in the field of plant molecular biology, we discuss several approaches to enhance salinity tolerance in plants comprising various classical and advanced genetic and genetic engineering approaches, genomics and genome editing technologies, and plant growth-promoting rhizobacteria (PGPR)-based approaches. Furthermore, based on recent advances in the field of epigenetics, we propose novel approaches to create and exploit heritable genome-wide epigenetic variation in crop plants to enhance salinity tolerance. Specifically, we describe the concepts and the underlying principles of epigenetic recombinant inbred lines (epiRILs) and other epigenetic variants and methods to generate them. The proposed epigenetic approaches also have the potential to create additional genetic variation by modulating meiotic crossover frequency.
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Affiliation(s)
- Gargi Prasad Saradadevi
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad 500078, India; (G.P.S.); (S.M.)
| | - Debajit Das
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, India; (D.D.); (C.C.)
| | - Satendra K. Mangrauthia
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Sridev Mohapatra
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad 500078, India; (G.P.S.); (S.M.)
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, India; (D.D.); (C.C.)
| | - Manish Roorkiwal
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India;
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
| | - Manish Solanki
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Raman Meenakshi Sundaram
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Neeraja N. Chirravuri
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Akshay S. Sakhare
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Suneetha Kota
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
- Correspondence: (S.K.); (R.K.V.); (G.M.); Tel.: +91-40-245-91268 (S.K.); +91-84-556-83305 (R.K.V.); +91-40-66303697 (G.M.)
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India;
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
- Correspondence: (S.K.); (R.K.V.); (G.M.); Tel.: +91-40-245-91268 (S.K.); +91-84-556-83305 (R.K.V.); +91-40-66303697 (G.M.)
| | - Gireesha Mohannath
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad 500078, India; (G.P.S.); (S.M.)
- Correspondence: (S.K.); (R.K.V.); (G.M.); Tel.: +91-40-245-91268 (S.K.); +91-84-556-83305 (R.K.V.); +91-40-66303697 (G.M.)
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Zhang Q, Zhang D, Yu K, Ji J, Liu N, Zhang Y, Xu M, Zhang YJ, Ma X, Liu S, Sun WH, Yu X, Hu W, Lan SR, Liu ZJ, Liu W. Frequent germplasm exchanges drive the high genetic diversity of Chinese-cultivated common apricot germplasm. HORTICULTURE RESEARCH 2021; 8:215. [PMID: 34593777 PMCID: PMC8484454 DOI: 10.1038/s41438-021-00650-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/08/2021] [Accepted: 06/25/2021] [Indexed: 05/22/2023]
Abstract
The genetic diversity of germplasm is critical for exploring genetic and phenotypic resources and has important implications for crop-breeding sustainability and improvement. However, little is known about the factors that shape and maintain genetic diversity. Here, we assembled a high-quality chromosome-level reference of the Chinese common apricot 'Yinxiangbai', and we resequenced 180 apricot accessions that cover four major ecogeographical groups in China and other accessions from occidental countries. We concluded that Chinese-cultivated common apricot germplasms possessed much higher genetic diversity than those cultivated in Western countries. We also detected seven migration events among different apricot groups, where 27% of the genome was identified as being introgressed. Remarkably, we demonstrated that these introgressed regions drove the current high level of germplasm diversity in Chinese-cultivated common apricots by introducing different genes related to distinct phenotypes from different cultivated groups. Our results highlight the consideration that introgressed regions may provide an important reservoir of genetic resources that can be used to sustain modern breeding programs.
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Affiliation(s)
- Qiuping Zhang
- Liaoning Institute of Pomology, Yingkou, 115009, China
| | - Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Kang Yu
- BGI Institute of Applied Agriculture, BGI-Agro, Shenzhen, 518210, China
| | - Jingjing Ji
- BGI Institute of Applied Agriculture, BGI-Agro, Shenzhen, 518210, China
| | - Ning Liu
- Liaoning Institute of Pomology, Yingkou, 115009, China
| | - Yuping Zhang
- Liaoning Institute of Pomology, Yingkou, 115009, China
| | - Ming Xu
- Liaoning Institute of Pomology, Yingkou, 115009, China
| | - Yu-Jun Zhang
- Liaoning Institute of Pomology, Yingkou, 115009, China
| | - Xiaoxue Ma
- Liaoning Institute of Pomology, Yingkou, 115009, China
| | - Shuo Liu
- Liaoning Institute of Pomology, Yingkou, 115009, China
| | - Wei-Hong Sun
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xia Yu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenqi Hu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Si-Ren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Institute of Vegetable and Flowers, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005, China.
| | - Weisheng Liu
- Liaoning Institute of Pomology, Yingkou, 115009, China.
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23
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Maity A, Lamichaney A, Joshi DC, Bajwa A, Subramanian N, Walsh M, Bagavathiannan M. Seed Shattering: A Trait of Evolutionary Importance in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:657773. [PMID: 34220883 PMCID: PMC8248667 DOI: 10.3389/fpls.2021.657773] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/21/2021] [Indexed: 05/26/2023]
Abstract
Seed shattering refers to the natural shedding of seeds when they ripe, a phenomenon typically observed in wild and weedy plant species. The timing and extent of this phenomenon varies considerably among plant species. Seed shattering is primarily a genetically controlled trait; however, it is significantly influenced by environmental conditions, management practices and their interactions, especially in agro-ecosystems. This trait is undesirable in domesticated crops where consistent efforts have been made to minimize it through conventional and molecular breeding approaches. However, this evolutionary trait serves as an important fitness and survival mechanism for most weeds that utilize it to ensure efficient dispersal of their seeds, paving the way for persistent soil seedbank development and sustained future populations. Weeds have continuously evolved variations in seed shattering as an adaptation under changing management regimes. High seed retention is common in many cropping weeds where weed maturity coincides with crop harvest, facilitating seed dispersal through harvesting operations, though some weeds have notoriously high seed shattering before crop harvest. However, high seed retention in some of the most problematic agricultural weed species such as annual ryegrass (Lolium rigidum), wild radish (Raphanus raphanistrum), and weedy amaranths (Amaranthus spp.) provides an opportunity to implement innovative weed management approaches such as harvest weed seed control, which aims at capturing and destroying weed seeds retained at crop harvest. The integration of such management options with other practices is important to avoid the rapid evolution of high seed shattering in target weed species. Advances in genetics and molecular biology have shown promise for reducing seed shattering in important crops, which could be exploited for manipulating seed shattering in weed species. Future research should focus on developing a better understanding of various seed shattering mechanisms in plants in relation to changing climatic and management regimes.
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Affiliation(s)
- Aniruddha Maity
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Seed Technology Division, ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Amrit Lamichaney
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Dinesh Chandra Joshi
- Division of Crop Improvement, ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, India
| | - Ali Bajwa
- Weed Research Unit, New South Wales Department of Primary Industries, Wagga Wagga, NSW, Australia
| | - Nithya Subramanian
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Michael Walsh
- Sydney Institute of Agriculture, The University of Sydney, Sydney, NSW, Australia
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24
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Yu C, Miao R, Khanna M. Maladaptation of U.S. corn and soybeans to a changing climate. Sci Rep 2021; 11:12351. [PMID: 34117293 PMCID: PMC8196191 DOI: 10.1038/s41598-021-91192-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/20/2021] [Indexed: 11/08/2022] Open
Abstract
We quantify long-run adaptation of U.S. corn and soybean yields to changes in temperature and precipitation over 1951-2017. Results show that although the two crops became more heat- and drought-tolerant, their productivity under normal temperature and precipitation conditions decreased. Over 1951-2017, heat- and drought-tolerance increased corn and soybean yields by 33% and 20%, whereas maladaptation to normal conditions reduced yields by 41% and 87%, respectively, with large spatial variations in effects. Changes in climate are projected to reduce average corn and soybean yields by 39-68% and 86-92%, respectively, by 2050 relative to 2013-2017 depending on the warming scenario. After incorporating estimated effects of climate-neutral technological advances, the net change in yield ranges from (-)13 to 62% for corn and (-)57 to (-)26% for soybeans in 2050 relative to 2013-2017. Our analysis uncovers the inherent trade-offs and limitations of existing approaches to crop adaptation.
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Affiliation(s)
- Chengzheng Yu
- Department of Agricultural and Consumer Economics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ruiqing Miao
- Department of Agricultural Economics and Rural Sociology, Auburn University, Auburn, AL, USA
| | - Madhu Khanna
- Department of Agricultural and Consumer Economics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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25
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Özbek Ö, Zencirci N. Characterization of Genetic Diversity in Cultivated Einkorn Wheat (Triticum monococcum L. ssp. monococcum) Landrace Populations from Turkey as Revealed by ISSR. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421060089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Xiao Y, Jiang S, Cheng Q, Wang X, Yan J, Zhang R, Qiao F, Ma C, Luo J, Li W, Liu H, Yang W, Song W, Meng Y, Warburton ML, Zhao J, Wang X, Yan J. The genetic mechanism of heterosis utilization in maize improvement. Genome Biol 2021; 22:148. [PMID: 33971930 PMCID: PMC8108465 DOI: 10.1186/s13059-021-02370-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In maize hybrid breeding, complementary pools of parental lines with reshuffled genetic variants are established for superior hybrid performance. To comprehensively decipher the genetics of heterosis, we present a new design of multiple linked F1 populations with 42,840 F1 maize hybrids, generated by crossing a synthetic population of 1428 maternal lines with 30 elite testers from diverse genetic backgrounds and phenotyped for agronomic traits. RESULTS We show that, although yield heterosis is correlated with the widespread, minor-effect epistatic QTLs, it may be resulted from a few major-effect additive and dominant QTLs in early developmental stages. Floral transition is probably one critical stage for heterosis formation, in which epistatic QTLs are activated by paternal contributions of alleles that counteract the recessive, deleterious maternal alleles. These deleterious alleles, while rare, epistatically repress other favorable QTLs. We demonstrate this with one example, showing that Brachytic2 represses the Ubiquitin3 locus in the maternal lines; in hybrids, the paternal allele alleviates this repression, which in turn recovers the height of the plant and enhances the weight of the ear. Finally, we propose a molecular design breeding by manipulating key genes underlying the transition from vegetative-to-reproductive growth. CONCLUSION The new population design is used to dissect the genetic basis of heterosis which accelerates maize molecular design breeding by diminishing deleterious epistatic interactions.
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Affiliation(s)
- Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuqin Jiang
- National Maize Improvement Center, Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qian Cheng
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Shaanxi, China
| | - Xiaqing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agricultural & Forestry Sciences, Beijing, 100097, China
| | - Jun Yan
- National Maize Improvement Center, Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Ruyang Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agricultural & Forestry Sciences, Beijing, 100097, China
| | - Feng Qiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuang Ma
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Shaanxi, China
| | - Jingyun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haijun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenyu Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenhao Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yijiang Meng
- College of Life Science, Hebei Agricultural University, Baoding, 071001, China
| | - Marilyn L Warburton
- United States Department of Agriculture-Agricultural Research Service, Corn Host Plant Resistance Research Unit, Box 9555, MS, 39762, Mississippi State, USA
| | - Jiuran Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agricultural & Forestry Sciences, Beijing, 100097, China.
| | - Xiangfeng Wang
- National Maize Improvement Center, Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
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Chen Z, Yu L, Liu W, Zhang J, Wang N, Chen X. Research progress of fruit color development in apple (Malus domestica Borkh.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 162:267-279. [PMID: 33711720 DOI: 10.1016/j.plaphy.2021.02.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
Apple (Malus domestica Borkh.) is one of the most widely produced and economically important fruits in temperate regions. Fruit color development in apple is a major focus for both breeders and researchers as consumers associate brightly colored red apples with ripeness and a good flavor. In recent years, great progress has been made in the research of apple fruit color development, but its development mechanism has not been systematic dissected from the aspects of genetics, transcription or environmental factors. Here, we summarize research on the coloration of apple fruit, including the development of important genomic databases to identify important genomic regions and genes, genetic and transcriptional factors that regulate pigment accumulation, environmental factors that affect anthocyanin synthesis, and the current breeding progress of red-skinned and red-fleshed apples. We describe key transcription factors, such as MYB, bHLH, and WD40, which are involved in the regulation of anthocyanin synthesis and fruit color development in apple. We also discuss the regulation of apple color by external environmental factors such as light, temperature, and water. The aim of this review is to provide insights into the molecular mechanisms underlying anthocyanin biosynthesis in apple. This information will provide significant guidance for the breeding of high-quality red-skinned and red-fleshed apple varieties.
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Affiliation(s)
- Zijing Chen
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China; Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai'an, Shandong, 271000, China
| | - Lei Yu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China; Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai'an, Shandong, 271000, China
| | - Wenjun Liu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China; Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai'an, Shandong, 271000, China
| | - Jing Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China; Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai'an, Shandong, 271000, China
| | - Nan Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China; Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai'an, Shandong, 271000, China.
| | - Xuesen Chen
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China; Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Tai'an, Shandong, 271000, China.
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28
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Chen Z, Gallavotti A. Improving architectural traits of maize inflorescences. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:21. [PMID: 37309422 PMCID: PMC10236070 DOI: 10.1007/s11032-021-01212-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/02/2021] [Indexed: 06/13/2023]
Abstract
The domestication and improvement of maize resulted in radical changes in shoot architecture relative to its wild progenitor teosinte. In particular, critical modifications involved a reduction of branching and an increase in inflorescence size to meet the needs for human consumption and modern agricultural practices. Maize is a major contributor to global agricultural production by providing large and inexpensive quantities of food, animal feed, and ethanol. Maize is also a classic system for studying the genetic regulation of inflorescence formation and its enlarged female inflorescences directly influence seed production and yield. Studies on the molecular and genetic networks regulating meristem proliferation and maintenance, including receptor-ligand interactions, transcription factor regulation, and hormonal control, provide important insights into maize inflorescence development and reveal potential avenues for the targeted modification of specific architectural traits. In this review, we summarize recent findings on the molecular mechanisms controlling inflorescence formation and discuss how this knowledge can be applied to improve maize productivity in the face of present and future environmental challenges.
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Affiliation(s)
- Zongliang Chen
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854-8020 USA
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854-8020 USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901 USA
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29
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Bruggeman SA, Horvath DP, Fennell AY, Gonzalez-Hernandez JL, Clay SA. Teosinte (Zea mays ssp parviglumis) growth and transcriptomic response to weed stress identifies similarities and differences between varieties and with modern maize varieties. PLoS One 2020; 15:e0237715. [PMID: 32822374 PMCID: PMC7444550 DOI: 10.1371/journal.pone.0237715] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 07/31/2020] [Indexed: 12/22/2022] Open
Abstract
Transcriptomic responses of plants to weed presence gives insight on the physiological and molecular mechanisms involved in the stress response. This study evaluated transcriptomic and morphological responses of two teosinte (Zea mays ssp parviglumis) (an ancestor of domesticated maize) lines (Ames 21812 and Ames 21789) to weed presence and absence during two growing seasons. Responses were compared after 6 weeks of growth in Aurora, South Dakota, USA. Plant heights between treatments were similar in Ames 21812, whereas branch number decreased when weeds were present. Ames 21789 was 45% shorter in weedy vs weed-free plots, but branch numbers were similar between treatments. Season-long biomass was reduced in response to weed stress in both lines. Common down-regulated subnetworks in weed-stressed plants were related to light, photosynthesis, and carbon cycles. Several unique response networks (e.g. aging, response to chitin) and gene sets were present in each line. Comparing transcriptomic responses of maize (determined in an adjacent study) and teosinte lines indicated three common gene ontologies up-regulated when weed-stressed: jasmonic acid response/signaling, UDP-glucosyl and glucuronyltransferases, and quercetin glucosyltransferase (3-O and 7-O). Overall, morphologic and transcriptomic differences suggest a greater varietal (rather than a conserved) response to weed stress, and implies multiple responses are possible. These findings offer insights into opportunities to define and manipulate gene expression of several different pathways of modern maize varieties to improve performance under weedy conditions.
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Affiliation(s)
- S. A. Bruggeman
- Biology Department, St. Augustana University, Sioux Falls, SD, United States of America
| | - D. P. Horvath
- USDA-ARS-ETSARC, Sunflower and Plant Biology Research Unit, Fargo, ND, United States of America
| | - A. Y. Fennell
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States of America
| | - J. L. Gonzalez-Hernandez
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States of America
| | - S. A. Clay
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States of America
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Gálvez Ranilla L. The Application of Metabolomics for the Study of Cereal Corn ( Zea mays L.). Metabolites 2020; 10:E300. [PMID: 32717792 PMCID: PMC7463750 DOI: 10.3390/metabo10080300] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/11/2022] Open
Abstract
Corn (Zea mays L.) is an important cereal crop indigenous to the Americas, where its genetic biodiversity is still preserved, especially among native populations from Mesoamerica and South America. The use of metabolomics in corn has mainly focused on understanding the potential differences of corn metabolomes under different biotic and abiotic stresses or to evaluate the influence of genetic and environmental factors. The increase of diet-linked non-communicable diseases has increased the interest to optimize the content of bioactive secondary metabolites in current corn breeding programs to produce novel functional foods. This review provides perspectives on the role of metabolomics in the characterization of health-relevant metabolites in corn biodiversity and emphasizes the integration of metabolomics in breeding strategies targeting the enrichment of phenolic bioactive metabolites such as anthocyanins in corn kernels.
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Affiliation(s)
- Lena Gálvez Ranilla
- Laboratory of Research in Food Science, Universidad Catolica de Santa Maria, Urb. San Jose s/n, 04013 Arequipa, Peru
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31
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Tosi M, Mitter EK, Gaiero J, Dunfield K. It takes three to tango: the importance of microbes, host plant, and soil management to elucidate manipulation strategies for the plant microbiome. Can J Microbiol 2020; 66:413-433. [DOI: 10.1139/cjm-2020-0085] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The world’s population is expected to grow to almost 10 billion by 2050, placing unprecedented demands on agriculture and natural resources. The risk in food security is also aggravated by climate change and land degradation, which compromise agricultural productivity. In recent years, our understanding of the role of microbial communities on ecosystem functioning, including plant-associated microbes, has advanced considerably. Yet, translating this knowledge into practical agricultural technologies is challenged by the intrinsic complexity of agroecosystems. Here, we review current strategies for plant microbiome manipulation, classifying them into three main pillars: (i) introducing and engineering microbiomes, (ii) breeding and engineering the host plant, and (iii) selecting agricultural practices that enhance resident soil and plant-associated microbial communities. In each of these areas, we analyze current trends in research, as well as research priorities and future perspectives.
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Affiliation(s)
- Micaela Tosi
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | | | - Jonathan Gaiero
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Kari Dunfield
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada
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32
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Seasonal Changes in the Metabolic Profiles and Biological Activity in Leaves of Diospyros digyna and D. rekoi "Zapote" Trees. PLANTS 2019; 8:plants8110449. [PMID: 31731430 PMCID: PMC6918230 DOI: 10.3390/plants8110449] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 10/14/2019] [Accepted: 10/19/2019] [Indexed: 01/15/2023]
Abstract
Leaves of semi-domesticated Diospyros digyna and wild D. rekoi trees, sampled seasonally in Mexico in 2014, were analyzed. Metabolic fingerprints revealed higher metabolite diversity in D. rekoi leaves. The TLC bands characteristic of glycosylated flavonoids, predominant in this species, matched the detection of quercetin and quercetin 3-O-glucuronides by liquid chromatography (UPLC-MS) of spring leaf extracts (LEs). Further gas chromatography (GC-MS) analysis revealed abundant fatty acids, organic acids, and secondary metabolites including trigonelline, p-coumaric, and ferulic and nicotinic acids. Phenolic-like compounds prevailed in D. digyna LEs, while unidentified triterpenoids and dihydroxylated coumarins were detected by UPLC-MS and GC-MS. A paucity of leaf metabolites in leaves of this species, compared to D. rekoi, was evident. Higher antioxidant capacity (AOC) was detected in D. digyna LEs. The AOC was season-independent in D. digyna but not in D. rekoi. The AOC in both species was concentrated in distinct TLC single bands, although seasonal variation in band intensity was observed among trees sampled. The AOC in D. digyna LEs could be ascribed to the coumarin esculetin. The LEs moderately inhibited phytopathogenic bacteria but not fungi. Leaf chemistry differences in these Mesoamerican Diospyros species substantiated previous variability reported in tree physiology and fruit physical chemistry, postulated to result from domestication and seasonality.
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Can H, Kal U, Ozyigit II, Paksoy M, Turkmen O. Construction, characteristics and high throughput molecular screening methodologies in some special breeding populations: a horticultural perspective. J Genet 2019. [DOI: 10.1007/s12041-019-1129-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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34
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Pérez-Jaramillo JE, de Hollander M, Ramírez CA, Mendes R, Raaijmakers JM, Carrión VJ. Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia. MICROBIOME 2019; 7:114. [PMID: 31412927 PMCID: PMC6694607 DOI: 10.1186/s40168-019-0727-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 07/30/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood. RESULTS Here, we investigated if the transition from a native to an agricultural soil affected rhizobacterial community assembly of wild and modern common bean (Phaseolus vulgaris) and if this led to a depletion of rhizobacterial diversity. The impact of the bean genotype on rhizobacterial assembly was more prominent in the agricultural soil than in the native soil. Although only 113 operational taxonomic units (OTUs) out of a total of 15,925 were shared by all eight bean accessions grown in native and agricultural soils, this core microbiome represented a large fraction (25.9%) of all sequence reads. More OTUs were exclusively found in the rhizosphere of common bean in the agricultural soil as compared to the native soil and in the rhizosphere of modern bean accessions as compared to wild accessions. Co-occurrence analyses further showed a reduction in complexity of the interactions in the bean rhizosphere microbiome in the agricultural soil as compared to the native soil. CONCLUSIONS Collectively, these results suggest that habitat expansion of common bean from its native soil environment to an agricultural context had an unexpected overall positive effect on rhizobacterial diversity and led to a stronger bean genotype-dependent effect on rhizosphere microbiome assembly.
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Affiliation(s)
- Juan E. Pérez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE The Netherlands
- Institute of Biology, University of Antioquia, Calle 67 #53-108, Medellín, Colombia
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
| | - Camilo A. Ramírez
- Institute of Biology, University of Antioquia, Calle 67 #53-108, Medellín, Colombia
| | - Rodrigo Mendes
- Embrapa Meio Ambiente, Rodovia SP 340 - km 127.5, Jaguariúna, 13820-000 Brazil
| | - Jos M. Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE The Netherlands
| | - Víctor J. Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE The Netherlands
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Barchi L, Acquadro A, Alonso D, Aprea G, Bassolino L, Demurtas O, Ferrante P, Gramazio P, Mini P, Portis E, Scaglione D, Toppino L, Vilanova S, Díez MJ, Rotino GL, Lanteri S, Prohens J, Giuliano G. Single Primer Enrichment Technology (SPET) for High-Throughput Genotyping in Tomato and Eggplant Germplasm. FRONTIERS IN PLANT SCIENCE 2019; 10:1005. [PMID: 31440267 PMCID: PMC6693525 DOI: 10.3389/fpls.2019.01005] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/18/2019] [Indexed: 05/20/2023]
Abstract
Single primer enrichment technology (SPET) is a new, robust, and customizable solution for targeted genotyping. Unlike genotyping by sequencing (GBS), and like DNA chips, SPET is a targeted genotyping technology, relying on the sequencing of a region flanking a primer. Its reliance on single primers, rather than on primer pairs, greatly simplifies panel design, and allows higher levels of multiplexing than PCR-based genotyping. Thanks to the sequencing of the regions surrounding the target SNP, SPET allows the discovery of thousands of closely linked, novel SNPs. In order to assess the potential of SPET for high-throughput genotyping in plants, a panel comprising 5k target SNPs, designed both on coding regions and introns/UTRs, was developed for tomato and eggplant. Genotyping of two panels composed of 400 tomato and 422 eggplant accessions, comprising both domesticated material and wild relatives, generated a total of 12,002 and 30,731 high confidence SNPs, respectively, which comprised both target and novel SNPs in an approximate ratio of 1:1.6, and 1:5.5 in tomato and eggplant, respectively. The vast majority of the markers was transferrable to related species that diverged up to 3.4 million years ago (Solanum pennellii for tomato and S. macrocarpon for eggplant). Maximum Likelihood phylogenetic trees and PCA outputs obtained from the whole dataset highlighted genetic relationships among accessions and species which were congruent with what was previously reported in literature. Better discrimination among domesticated accessions was achieved by using the target SNPs, while better discrimination among wild species was achieved using the whole SNP dataset. Our results reveal that SPET genotyping is a robust, high-throughput technology for genetic fingerprinting, with a high degree of cross-transferability between crops and their cultivated and wild relatives, and allows identification of duplicates and mislabeled accessions in genebanks.
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Affiliation(s)
| | | | - David Alonso
- COMAV, Universitat Politècnica de Valencia, Valencia, Spain
| | - Giuseppe Aprea
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Laura Bassolino
- CREA-GB, Research Centre for Genomics and Bioinformatics, Montanaso Lombardo, Italy
| | - Olivia Demurtas
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Paola Ferrante
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | | | - Paola Mini
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | | | | | - Laura Toppino
- CREA-GB, Research Centre for Genomics and Bioinformatics, Montanaso Lombardo, Italy
| | | | | | | | | | - Jaime Prohens
- COMAV, Universitat Politècnica de Valencia, Valencia, Spain
| | - Giovanni Giuliano
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
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Lewandowska S, Michalak I, Niemczyk K, Detyna J, Bujak H, Arik P. Influence of the Static Magnetic Field and Algal Extract on the Germination of Soybean Seeds. OPEN CHEM 2019. [DOI: 10.1515/chem-2019-0039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractThis study examines the effect of a separate static magnetic field (SMF) and algal extract and their synergistic effect on soybean seeds germination. To our knowledge, this is the first time these kinds of factors were used for the biostimulation of soybean seeds germination. Soybean – Glycine max (L.) Merrill variety ‘Merlin’ was used in the present study. The exposure of seeds to the magnetic field was applied for 3, 6 and 12 min. The algal extract, produced from a freshwater green macroalga – Cladophora glomerata using an ultrasonic homogenizer, was used directly to the paper substrate at a dose of 10%. The highest germination ability of soybean seeds was observed in a group, where the magnetic field (12 min.) was used together with 10% of algal extract. However, it was very low – only 21%, which may have resulted from the seed dormancy. Future experiments on soybean seeds are required to confirm the stimulation effect of the magnetic field (various induction values) and algal extract on seeds germination.
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Affiliation(s)
- Sylwia Lewandowska
- Department of Genetics, Plant Breeding and Seed Production, Wrocław University of Environmental and Life Sciences, Pl. Grunwaldzki 24A, 50-363Wrocław, Poland
| | - Izabela Michalak
- Department of Advanced Material Technologies, Faculty of Chemistry, Wrocław University of Science and Technology, Smoluchowskiego 25, 50-372Wrocław, Poland
| | - Katarzyna Niemczyk
- Department of Mechanics, Materials Science and Engineering, Faculty of Mechanical Engineering, Wrocław University of Science and Technology, Smoluchowskiego 25, 50-370Wrocław, Poland
| | - Jerzy Detyna
- Department of Mechanics, Materials Science and Engineering, Faculty of Mechanical Engineering, Wrocław University of Science and Technology, Smoluchowskiego 25, 50-370Wrocław, Poland
| | - Henryk Bujak
- Department of Genetics, Plant Breeding and Seed Production, Wrocław University of Environmental and Life Sciences, Pl. Grunwaldzki 24A, 50-363Wrocław, Poland
| | - Pelin Arik
- Department of Advanced Material Technologies, Faculty of Chemistry, Wrocław University of Science and Technology, Smoluchowskiego 25, 50-372Wrocław, Poland
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37
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Hernández-Terán A, Wegier A, Benítez M, Lira R, Sosa Fuentes TG, Escalante AE. In vitro performance in cotton plants with different genetic backgrounds: the case of Gossypium hirsutum in Mexico, and its implications for germplasm conservation. PeerJ 2019; 7:e7017. [PMID: 31218120 PMCID: PMC6563797 DOI: 10.7717/peerj.7017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/24/2019] [Indexed: 11/20/2022] Open
Abstract
One of the best ex situ conservation strategies for wild germplasm is in vitro conservation of genetic banks. The success of in vitro conservation relies heavily on the micropropagation or performance of the species of interest. In the context of global change, crop production challenges and climate change, we face a reality of intensified crop production strategies, including genetic engineering, which can negatively impact biodiversity conservation. However, the possible consequences of transgene presence for the in vitro performance of populations and its implications for biodiversity conservation are poorly documented. In this study we analyzed experimental evidence of the potential effects of transgene presence on the in vitro performance of Gossypium hirsutum L. populations, representing the Mexican genetic diversity of the species, and reflect on the implications of such presence for ex situ genetic conservation of the natural variation of the species. We followed an experimental in vitro performance approach, in which we included individuals from different wild cotton populations as well as individuals from domesticated populations, in order to differentiate the effects of domestication traits dragged into the wild germplasm pool via gene flow from the effects of transgene presence. We evaluated the in vitro performance of five traits related to plant establishment (N = 300): propagation rate, leaf production rate, height increase rate, microbial growth and root development. Then we conducted statistical tests (PERMANOVA, Wilcoxon post-hoc tests, and NMDS multivariate analyses) to evaluate the differences in the in vitro performance of the studied populations. Although direct causality of the transgenes to observed phenotypes requires strict control of genotypes, the overall results suggest detrimental consequences for the in vitro culture performance of wild cotton populations in the presence of transgenes. This provides experimental, statistically sound evidence to support the implementation of transgene screening of plants to reduce time and economic costs in in vitro establishment, thus contributing to the overarching goal of germplasm conservation for future adaptation.
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Affiliation(s)
- Alejandra Hernández-Terán
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ana Wegier
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rafael Lira
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Reyes, Mexico
| | | | - Ana E Escalante
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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38
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Fernie AR, Yan J. De Novo Domestication: An Alternative Route toward New Crops for the Future. MOLECULAR PLANT 2019; 12:615-631. [PMID: 30999078 DOI: 10.1016/j.molp.2019.03.016] [Citation(s) in RCA: 171] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 05/19/2023]
Abstract
Current global agricultural production must feed over 7 billion people. However, productivity varies greatly across the globe and is under threat from both increased competitions for land and climate change and associated environmental deterioration. Moreover, the increase in human population size and dietary changes are putting an ever greater burden on agriculture. The majority of this burden is met by the cultivation of a very small number of species, largely in locations that differ from their origin of domestication. Recent technological advances have raised the possibility of de novo domestication of wild plants as a viable solution for designing ideal crops while maintaining food security and a more sustainable low-input agriculture. Here we discuss how the discovery of multiple key domestication genes alongside the development of technologies for accurate manipulation of several target genes simultaneously renders de novo domestication a route toward crops for the future.
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Affiliation(s)
- Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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39
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Yundaeng C, Somta P, Amkul K, Kongjaimun A, Kaga A, Tomooka N. Construction of genetic linkage map and genome dissection of domestication-related traits of moth bean (Vigna aconitifolia), a legume crop of arid areas. Mol Genet Genomics 2019; 294:621-635. [PMID: 30739203 DOI: 10.1007/s00438-019-01536-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 01/31/2019] [Indexed: 10/27/2022]
Abstract
The moth bean (Vigna aconitifolia), possibly the most primitive crop of the genus Vigna, is a highly drought- and heat-resistant legume grown in arid areas. Moth bean domestication involved phenotypic changes, including reduction of seed dormancy and pod shattering, increased organ size, and earlier flowering and maturity. However, the genetics of the domestication process in moth bean is not known. In this study, we constructed a genetic linkage map for moth bean and used the map to identify quantitative trait loci (QTL) for domestication-related traits of an F2 population of 188 individuals produced from a cross of wild moth bean (TN67) and cultivated moth bean (ICPMO056). The genetic linkage map comprised 11 linkage groups (LG) of 172 simple sequence repeat markers and spanned a total length of 1016.8 centiMorgan (cM), with an average marker distance of 7.34 cM. A comparative genome analysis showed high genome synteny between moth bean and mungbean (Vigna radiata), adzuki bean (Vigna angularis), rice bean (Vigna umbellata), and yardlong bean (Vigna unguiculata). In total, 50 QTLs and 3 genes associated with 20 domestication-related traits were identified. Most of the QTLs belonged to five LGs (1, 2, 4, 7, and 10). Key traits related to domestication such as seed dormancy and pod shattering were controlled by large-effect QTLs (PVE > 20%) with one or two minor QTLs, whereas all other traits were controlled by one-seven minor QTLs, apart from seed weight, which was controlled by one major and seven minor QTLs. These results suggest that a small number of mutations with large phenotypic effects have contributed to the domestication of the moth bean. Comparative analysis of QTLs with related Vigna crops revealed that there are several domestication-related large-effect QTLs that had not been used in moth bean domestication. This study provides a basic genetic map and identified genome regions associated with domestication-related traits, which will be useful for the genetic improvement of the moth bean and related Vigna species.
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Affiliation(s)
- Chutintorn Yundaeng
- Department of Agronomy, Faculty of Agriculture at Kampaheng Saen, Kasetsart University, Kamphaeng Saen Campus, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kampaheng Saen, Kasetsart University, Kamphaeng Saen Campus, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand. .,Center for Agricultural Biotechnology (AG-BIO/PEDRO-CHE), Kasetsart University, Kamphaeng Saen Campus, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand. .,Center of Advanced Studies for Agriculture and Food (CASAF), Kasetsart University Institute for Advanced Studies, Kasetsart University (NRU-KU), Bangkok, 10900, Thailand.
| | - Kitiya Amkul
- Department of Agronomy, Faculty of Agriculture at Kampaheng Saen, Kasetsart University, Kamphaeng Saen Campus, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand.,Center of Advanced Studies for Agriculture and Food (CASAF), Kasetsart University Institute for Advanced Studies, Kasetsart University (NRU-KU), Bangkok, 10900, Thailand
| | - Alisa Kongjaimun
- Faculty of Animal Sciences and Agricultural Technology, Silpakorn University, Cha-Am, Phetchaburi, 76120, Thailand
| | - Akito Kaga
- Soybean and Field Crop Applied Genomics Research Unit, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Norihiko Tomooka
- Genetic Resources Center, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
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40
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Raza A, Razzaq A, Mehmood SS, Zou X, Zhang X, Lv Y, Xu J. Impact of Climate Change on Crops Adaptation and Strategies to Tackle Its Outcome: A Review. PLANTS (BASEL, SWITZERLAND) 2019; 8:E34. [PMID: 30704089 PMCID: PMC6409995 DOI: 10.3390/plants8020034] [Citation(s) in RCA: 379] [Impact Index Per Article: 75.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/16/2019] [Accepted: 01/28/2019] [Indexed: 11/17/2022]
Abstract
Agriculture and climate change are internally correlated with each other in various aspects, as climate change is the main cause of biotic and abiotic stresses, which have adverse effects on the agriculture of a region. The land and its agriculture are being affected by climate changes in different ways, e.g., variations in annual rainfall, average temperature, heat waves, modifications in weeds, pests or microbes, global change of atmospheric CO₂ or ozone level, and fluctuations in sea level. The threat of varying global climate has greatly driven the attention of scientists, as these variations are imparting negative impact on global crop production and compromising food security worldwide. According to some predicted reports, agriculture is considered the most endangered activity adversely affected by climate changes. To date, food security and ecosystem resilience are the most concerning subjects worldwide. Climate-smart agriculture is the only way to lower the negative impact of climate variations on crop adaptation, before it might affect global crop production drastically. In this review paper, we summarize the causes of climate change, stresses produced due to climate change, impacts on crops, modern breeding technologies, and biotechnological strategies to cope with climate change, in order to develop climate resilient crops. Revolutions in genetic engineering techniques can also aid in overcoming food security issues against extreme environmental conditions, by producing transgenic plants.
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Affiliation(s)
- Ali Raza
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
| | - Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan.
| | - Sundas Saher Mehmood
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
| | - Xiling Zou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
| | - Xuekun Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
| | - Yan Lv
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
| | - Jinsong Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
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41
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Ng DWK, Abeysinghe JK, Kamali M. Regulating the Regulators: The Control of Transcription Factors in Plant Defense Signaling. Int J Mol Sci 2018; 19:E3737. [PMID: 30477211 PMCID: PMC6321093 DOI: 10.3390/ijms19123737] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 01/12/2023] Open
Abstract
Being sessile, plants rely on intricate signaling pathways to mount an efficient defense against external threats while maintaining the cost balance for growth. Transcription factors (TFs) form a repertoire of master regulators in controlling various processes of plant development and responses against external stimuli. There are about 58 families of TFs in plants and among them, six major TF families (AP2/ERF (APETALA2/ethylene responsive factor), bHLH (basic helix-loop-helix), MYB (myeloblastosis related), NAC (no apical meristem (NAM), Arabidopsis transcription activation factor (ATAF1/2), and cup-shaped cotyledon (CUC2)), WRKY, and bZIP (basic leucine zipper)) are found to be involved in biotic and abiotic stress responses. As master regulators of plant defense, the expression and activities of these TFs are subjected to various transcriptional and post-transcriptional controls, as well as post-translational modifications. Many excellent reviews have discussed the importance of these TFs families in mediating their downstream target signaling pathways in plant defense. In this review, we summarize the molecular regulatory mechanisms determining the expression and activities of these master regulators themselves, providing insights for studying their variation and regulation in crop wild relatives (CWR). With the advance of genome sequencing and the growing collection of re-sequencing data of CWR, now is the time to re-examine and discover CWR for the lost or alternative alleles of TFs. Such approach will facilitate molecular breeding and genetic improvement of domesticated crops, especially in stress tolerance and defense responses, with the aim to address the growing concern of climate change and its impact on agriculture crop production.
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Affiliation(s)
- Danny W-K Ng
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Jayami K Abeysinghe
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China.
| | - Maedeh Kamali
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China.
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Abdelrahman M, Al-Sadi AM, Pour-Aboughadareh A, Burritt DJ, Tran LSP. Genome editing using CRISPR/Cas9-targeted mutagenesis: An opportunity for yield improvements of crop plants grown under environmental stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 131:31-36. [PMID: 29628199 DOI: 10.1016/j.plaphy.2018.03.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 03/07/2018] [Accepted: 03/11/2018] [Indexed: 05/10/2023]
Abstract
Developing more crops able to sustainably produce high yields when grown under biotic/abiotic stresses is an important goal, if crop production and food security are to be guaranteed in the face of ever-increasing human population and unpredictable global climatic conditions. However, conventional crop improvement, through random mutagenesis or genetic recombination, is time-consuming and cannot keep pace with increasing food demands. Targeted genome editing (GE) technologies, especially clustered regularly interspaced short palindromic repeats (CRISPR)/(CRISPR)-associated protein 9 (Cas9), have great potential to aid in the breeding of crops that are able to produce high yields under conditions of biotic/abiotic stress. This is due to their high efficiency, accuracy and low risk of off-target effects, compared with conventional random mutagenesis methods. The use of CRISPR/Cas9 system has grown very rapidly in recent years with numerous examples of targeted mutagenesis in crop plants, including gene knockouts, modifications, and the activation and repression of target genes. The potential of the GE approach for crop improvement has been clearly demonstrated. However, the regulation and social acceptance of GE crops still remain a challenge. In this review, we evaluate the recent applications of the CRISPR/Cas9-mediated GE, as a means to produce crop plants with greater resilience to the stressors they encounter when grown under increasing stressful environmental conditions.
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Affiliation(s)
- Mostafa Abdelrahman
- Graduate School of Life Sciences, Tohoku University, Sendai 9808577, Japan; Department of Botany, Faculty of Science, Aswan University, Aswan 81528, Egypt
| | - Abdullah M Al-Sadi
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, P.O. Box 8, Al Khoud 123, Oman
| | - Alireza Pour-Aboughadareh
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Tehran, Karaj, Iran
| | - David J Burritt
- Department of Botany, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Lam-Son Phan Tran
- Plant Stress Research Group & Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam; Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.
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43
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Abdelrahman M, Jogaiah S, Burritt DJ, Tran LSP. Legume genetic resources and transcriptome dynamics under abiotic stress conditions. PLANT, CELL & ENVIRONMENT 2018; 41:1972-1983. [PMID: 29314055 DOI: 10.1111/pce.13123] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/08/2017] [Accepted: 12/08/2017] [Indexed: 05/04/2023]
Abstract
Grain legumes are an important source of nutrition and income for billions of consumers and farmers around the world. However, the low productivity of new legume varieties, due to the limited genetic diversity available for legume breeding programmes and poor policymaker support, combined with an increasingly unpredictable global climate is resulting in a large gap between current yields and the increasing demand for legumes as food. Hence, there is a need for novel approaches to develop new high-yielding legume cultivars that are able to cope with a range of environmental stressors. Next-generation technologies are providing the tools that could enable the more rapid and cost-effective genomic and transcriptomic studies for most major crops, allowing the identification of key functional and regulatory genes involved in abiotic stress resistance. In this review, we provide an overview of the recent achievements regarding abiotic stress resistance in a wide range of legume crops and highlight the transcriptomic and miRNA approaches that have been used. In addition, we critically evaluate the availability and importance of legume genetic resources with desirable abiotic stress resistance traits.
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Affiliation(s)
- Mostafa Abdelrahman
- Laboratory of Genomic Reproductive Biology, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
- Botany Department, Faculty of Science, Aswan University, Aswan, 81528, Egypt
| | - Sudisha Jogaiah
- Plant Healthcare and Diagnostic Center, Department of Studies in Biotechnology and Microbiology, Karnatak University, Dharwad, 580 003, India
| | - David J Burritt
- Department of Botany, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Lam-Son Phan Tran
- Plant Stress Research Group & Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
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44
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Pandian S, Satish L, Rameshkumar R, Muthuramalingam P, Rency AS, Rathinapriya P, Ramesh M. Analysis of population structure and genetic diversity in an exotic germplasm collection of Eleusine coracana (L.) Gaertn. using genic-SSR markers. Gene 2018; 653:80-90. [DOI: 10.1016/j.gene.2018.02.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/22/2018] [Accepted: 02/07/2018] [Indexed: 11/30/2022]
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Gaillard MDP, Glauser G, Robert CAM, Turlings TCJ. Fine-tuning the 'plant domestication-reduced defense' hypothesis: specialist vs generalist herbivores. THE NEW PHYTOLOGIST 2018; 217:355-366. [PMID: 28877341 DOI: 10.1111/nph.14757] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 07/14/2017] [Indexed: 05/19/2023]
Abstract
Domesticated plants are assumed to have weakened chemical defenses. We argue, however, that artificial selection will have maintained defense traits against specialized herbivores that have coexisted with the crops throughout their domestication. We assessed the performance of eight species of insect herbivores from three feeding guilds on six European maize lines and six populations of their wild ancestor, teosinte. A metabolomics approach was used in an attempt to identify compounds responsible for observed differences in insect performance. Insects consistently performed better on maize than on teosinte. As hypothesized, this difference was greater for generalist herbivores that are normally not found on teosinte. We also found clear differences in defense metabolites among the different genotypes, but none that consistently correlated with differences in performance. Concentrations of benzoxazinoids, the main chemical defense in maize, tended to be higher in leaves of teosinte, but the reverse was true for the roots. It appears that chemical defenses that target specialized insects are still present at higher concentrations in cultivated maize than compounds that are more effective against generalists. These weakened broad-spectrum defenses in crops may explain the successes of novel pests.
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Affiliation(s)
- Mickaël D P Gaillard
- Laboratory for Fundamental and Applied Research in Chemical Ecology (FARCE), University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - Gaétan Glauser
- Neuchâtel Platform of Analytical Chemistry (NPAC), University of Neuchâtel, Avenue de Bellevaux 51, 2000, Neuchâtel, Switzerland
| | - Christelle A M Robert
- Laboratory for Fundamental and Applied Research in Chemical Ecology (FARCE), University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
- Institute of Plant Sciences, Section Biotic Interactions, University of Bern, Altenbergrain 21, 3013, Bern, Switzerland
| | - Ted C J Turlings
- Laboratory for Fundamental and Applied Research in Chemical Ecology (FARCE), University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
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NGS-Based Genotyping, High-Throughput Phenotyping and Genome-Wide Association Studies Laid the Foundations for Next-Generation Breeding in Horticultural Crops. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9030038] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Demographic trends and changes to climate require a more efficient use of plant genetic resources in breeding programs. Indeed, the release of high-yielding varieties has resulted in crop genetic erosion and loss of diversity. This has produced an increased susceptibility to severe stresses and a reduction of several food quality parameters. Next generation sequencing (NGS) technologies are being increasingly used to explore “gene space” and to provide high-resolution profiling of nucleotide variation within germplasm collections. On the other hand, advances in high-throughput phenotyping are bridging the genotype-to-phenotype gap in crop selection. The combination of allelic and phenotypic data points via genome-wide association studies is facilitating the discovery of genetic loci that are associated with key agronomic traits. In this review, we provide a brief overview on the latest NGS-based and phenotyping technologies and on their role to unlocking the genetic potential of vegetable crops; then, we discuss the paradigm shift that is underway in horticultural crop breeding.
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McClure T, Cocuron JC, Osmark V, McHale LK, Alonso AP. Impact of Environment on the Biomass Composition of Soybean (Glycine max) seeds. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:6753-6761. [PMID: 28723152 DOI: 10.1021/acs.jafc.7b01457] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Factors including genetics, fertilization, and climatic conditions, can alter the biomass composition of soybean seeds, consequently impacting their market value and usage. This study specifically determined the content of protein and oil, as well as the composition of proteinogenic amino acids and fatty acids in seeds from 10 diverse soybean cultivars grown in four different sites. The results highlighted that different environments produce a different composition for the 10 cultivars under investigation. Specifically, the levels of oleic and linoleic acids, important contributors to oil stability, were negatively correlated. Although the protein and oil contents were higher in some locations, their "quality" was lower in terms of composition of essential amino acids and oleic acid, respectively. Finally, proteinogenic histidine and glutamate were the main contributors to the separation between Central and Northern growing sites. Taken together, these results can guide future breeding and engineering efforts aiming to develop specialized soybean lines.
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Affiliation(s)
- Tamara McClure
- The Ohio State University , Department of Molecular Genetics, Columbus, Ohio 43210, United States
- The Ohio State University , Center for Applied Plant Sciences, Columbus, Ohio 43210, United States
| | - Jean-Christophe Cocuron
- The Ohio State University , Department of Molecular Genetics, Columbus, Ohio 43210, United States
- The Ohio State University , Center for Applied Plant Sciences, Columbus, Ohio 43210, United States
| | | | - Leah K McHale
- The Ohio State University , Center for Applied Plant Sciences, Columbus, Ohio 43210, United States
- The Ohio State University , Department of Horticulture and Crop Science, Columbus, Ohio 43210, United States
- The Ohio State University , Center for Soybean Research, Columbus, Ohio 43210, United States
| | - Ana Paula Alonso
- The Ohio State University , Department of Molecular Genetics, Columbus, Ohio 43210, United States
- The Ohio State University , Center for Applied Plant Sciences, Columbus, Ohio 43210, United States
- The Ohio State University , Center for Soybean Research, Columbus, Ohio 43210, United States
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48
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Acquadro A, Barchi L, Gramazio P, Portis E, Vilanova S, Comino C, Plazas M, Prohens J, Lanteri S. Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes. PLoS One 2017; 12:e0180774. [PMID: 28686642 PMCID: PMC5501601 DOI: 10.1371/journal.pone.0180774] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/21/2017] [Indexed: 11/18/2022] Open
Abstract
Brinjal (Solanum melongena), scarlet (S. aethiopicum) and gboma (S. macrocarpon) eggplants are three Old World domesticates. The genomic DNA of a collection of accessions belonging to the three cultivated species, along with a representation of various wild relatives, was characterized for the presence of single nucleotide polymorphisms (SNPs) using a genotype-by-sequencing approach. A total of 210 million useful reads were produced and were successfully aligned to the reference eggplant genome sequence. Out of the 75,399 polymorphic sites identified among the 76 entries in study, 12,859 were associated with coding sequence. A genetic relationships analysis, supported by the output of the FastSTRUCTURE software, identified four major sub-groups as present in the germplasm panel. The first of these clustered S. aethiopicum with its wild ancestor S. anguivi; the second, S. melongena, its wild progenitor S. insanum, and its relatives S. incanum, S. lichtensteinii and S. linneanum; the third, S. macrocarpon and its wild ancestor S. dasyphyllum; and the fourth, the New World species S. sisymbriifolium, S. torvum and S. elaeagnifolium. By applying a hierarchical FastSTRUCTURE analysis on partitioned data, it was also possible to resolve the ambiguous membership of the accessions of S. campylacanthum, S. violaceum, S. lidii, S. vespertilio and S. tomentsum, as well as to genetically differentiate the three species of New World Origin. A principal coordinates analysis performed both on the entire germplasm panel and also separately on the entries belonging to sub-groups revealed a clear separation among species, although not between each of the domesticates and their respective wild ancestors. There was no clear differentiation between either distinct cultivar groups or different geographical provenance. Adopting various approaches to analyze SNP variation provided support for interpretation of results. The genotyping-by-sequencing approach showed to be highly efficient for both quantifying genetic diversity and establishing genetic relationships among and within cultivated eggplants and their wild relatives. The relevance of these results to the evolution of eggplants, as well as to their genetic improvement, is discussed.
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Affiliation(s)
- Alberto Acquadro
- University of Turin—DISAFA—Plant Genetics and Breeding, University of Turin, Largo Braccini 2, Grugliasco, Torino, Italy
| | - Lorenzo Barchi
- University of Turin—DISAFA—Plant Genetics and Breeding, University of Turin, Largo Braccini 2, Grugliasco, Torino, Italy
| | - Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, Valencia, Spain
| | - Ezio Portis
- University of Turin—DISAFA—Plant Genetics and Breeding, University of Turin, Largo Braccini 2, Grugliasco, Torino, Italy
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, Valencia, Spain
| | - Cinzia Comino
- University of Turin—DISAFA—Plant Genetics and Breeding, University of Turin, Largo Braccini 2, Grugliasco, Torino, Italy
| | - Mariola Plazas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Camino de Vera 14, Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, Valencia, Spain
| | - Sergio Lanteri
- University of Turin—DISAFA—Plant Genetics and Breeding, University of Turin, Largo Braccini 2, Grugliasco, Torino, Italy
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Sathyanarayana N, Pittala RK, Tripathi PK, Chopra R, Singh HR, Belamkar V, Bhardwaj PK, Doyle JJ, Egan AN. Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers. BMC Genomics 2017; 18:409. [PMID: 28545396 PMCID: PMC5445377 DOI: 10.1186/s12864-017-3780-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 05/10/2017] [Indexed: 12/14/2022] Open
Abstract
Background The medicinal legume Mucuna pruriens (L.) DC. has attracted attention worldwide as a source of the anti-Parkinson’s drug L-Dopa. It is also a popular green manure cover crop that offers many agronomic benefits including high protein content, nitrogen fixation and soil nutrients. The plant currently lacks genomic resources and there is limited knowledge on gene expression, metabolic pathways, and genetics of secondary metabolite production. Here, we present transcriptomic resources for M. pruriens, including a de novo transcriptome assembly and annotation, as well as differential transcript expression analyses between root, leaf, and pod tissues. We also develop microsatellite markers and analyze genetic diversity and population structure within a set of Indian germplasm accessions. Results One-hundred ninety-one million two hundred thirty-three thousand two hundred forty-two bp cleaned reads were assembled into 67,561 transcripts with mean length of 626 bp and N50 of 987 bp. Assembled sequences were annotated using BLASTX against public databases with over 80% of transcripts annotated. We identified 7,493 simple sequence repeat (SSR) motifs, including 787 polymorphic repeats between the parents of a mapping population. 134 SSRs from expressed sequenced tags (ESTs) were screened against 23 M. pruriens accessions from India, with 52 EST-SSRs retained after quality control. Population structure analysis using a Bayesian framework implemented in fastSTRUCTURE showed nearly similar groupings as with distance-based (neighbor-joining) and principal component analyses, with most of the accessions clustering per geographical origins. Pair-wise comparison of transcript expression in leaves, roots and pods identified 4,387 differentially expressed transcripts with the highest number occurring between roots and leaves. Differentially expressed transcripts were enriched with transcription factors and transcripts annotated as belonging to secondary metabolite pathways. Conclusions The M. pruriens transcriptomic resources generated in this study provide foundational resources for gene discovery and development of molecular markers. Polymorphic SSRs identified can be used for genetic diversity, marker-trait analyses, and development of functional markers for crop improvement. The results of differential expression studies can be used to investigate genes involved in L-Dopa synthesis and other key metabolic pathways in M. pruriens. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3780-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- N Sathyanarayana
- Department of Botany, Sikkim University, 6th Mile, Tadong-737102, Gangtok, Sikkim, India.
| | - Ranjith Kumar Pittala
- Department of Botany, Sikkim University, 6th Mile, Tadong-737102, Gangtok, Sikkim, India
| | - Pankaj Kumar Tripathi
- Department of Botany, Sikkim University, 6th Mile, Tadong-737102, Gangtok, Sikkim, India
| | - Ratan Chopra
- United States Department of Agriculture, Agriculture Research Service, 3810 4th St., Lubbock, TX, 79415, USA
| | - Heikham Russiachand Singh
- Department of Plant Science, McGill University, Raymond Building, 21111 Lakeshore Road, Ste. Anne de Bellevue, Quebec, H9X 3V9, Canada
| | - Vikas Belamkar
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Pardeep Kumar Bhardwaj
- Institute of Bioresources and Sustainable Development, ikkim Centre, Tadong-737102, Gangtok, Sikkim, India
| | - Jeff J Doyle
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 412 Mann Library, Ithaca, NY, 14853, USA
| | - Ashley N Egan
- Department of Botany, Smithsonian Institution, National Museum of Natural History, US National Herbarium, 10th and Constitution Ave NW, Washington, DC, 20013, USA.
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50
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Karn A, Gillman JD, Flint-Garcia SA. Genetic Analysis of Teosinte Alleles for Kernel Composition Traits in Maize. G3 (BETHESDA, MD.) 2017; 7:1157-1164. [PMID: 28188181 PMCID: PMC5386864 DOI: 10.1534/g3.117.039529] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 02/03/2017] [Indexed: 11/18/2022]
Abstract
Teosinte (Zea mays ssp. parviglumis) is the wild ancestor of modern maize (Zea mays ssp. mays). Teosinte contains greater genetic diversity compared with maize inbreds and landraces, but its use is limited by insufficient genetic resources to evaluate its value. A population of teosinte near isogenic lines (NILs) was previously developed to broaden the resources for genetic diversity of maize, and to discover novel alleles for agronomic and domestication traits. The 961 teosinte NILs were developed by backcrossing 10 geographically diverse parviglumis accessions into the B73 (reference genome inbred) background. The NILs were grown in two replications in 2009 and 2010 in Columbia, MO and Aurora, NY, respectively, and near infrared reflectance spectroscopy and nuclear magnetic resonance calibrations were developed and used to rapidly predict total kernel starch, protein, and oil content on a dry matter basis in bulk whole grains of teosinte NILs. Our joint-linkage quantitative trait locus (QTL) mapping analysis identified two starch, three protein, and six oil QTL, which collectively explained 18, 23, and 45% of the total variation, respectively. A range of strong additive allelic effects for kernel starch, protein, and oil content were identified relative to the B73 allele. Our results support our hypothesis that teosinte harbors stronger alleles for kernel composition traits than maize, and that teosinte can be exploited for the improvement of kernel composition traits in modern maize germplasm.
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Affiliation(s)
- Avinash Karn
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211
| | - Jason D Gillman
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211
- United States Department of Agriculture-Agricultural Research Service, Columbia, Missouri 65211
| | - Sherry A Flint-Garcia
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211
- United States Department of Agriculture-Agricultural Research Service, Columbia, Missouri 65211
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