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Milla R, Westgeest AJ, Maestre-Villanueva J, Núñez-Castillo S, Gómez-Fernández A, Vasseur F, Violle C, Balarynová J, Smykal P. Evolutionary pathways to lower biomass allocation to the seed coat in crops: insights from allometric scaling. THE NEW PHYTOLOGIST 2024; 243:466-476. [PMID: 38757753 DOI: 10.1111/nph.19821] [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: 02/05/2024] [Accepted: 04/26/2024] [Indexed: 05/18/2024]
Abstract
Crops generally have seeds larger than their wild progenitors´ and with reduced dormancy. In wild plants, seed mass and allocation to the seed coat (a proxy for physical dormancy) scale allometrically so that larger seeds tend to allocate less to the coats. Larger seeds and lightweight coats might thus have evolved as correlated traits in crops. We tested whether 34 crops and 22 of their wild progenitors fit the allometry described in the literature, which would indicate co-selection of both traits during crop evolution. Deviations from the allometry would suggest that other evolutionary processes contribute to explain the emergence of larger, lightweight-coated seeds in crops. Crops fitted the scaling slope but deviated from its intercept in a consistent way: Seed coats of crops were lighter than expected by their seed size. The wild progenitors of crops displayed the same trend, indicating that deviations cannot be solely attributed to artificial selection during or after domestication. The evolution of seeds with small coats in crops likely resulted from a combination of various pressures, including the selection of wild progenitors with coats smaller than other wild plants, further decreases during early evolution under cultivation, and indirect selection due to the seed coat-seed size allometry.
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Affiliation(s)
- Rubén Milla
- ECOEVO Group, Departamento de Biología, Geología, Física y Química Inorgánica, Instituto de Investigación en Cambio Global (IICG-URJC), Universidad Rey Juan Carlos, Tulipán s/n, Móstoles, 28933, Spain
| | | | - Jorge Maestre-Villanueva
- ECOEVO Group, Departamento de Biología, Geología, Física y Química Inorgánica, Instituto de Investigación en Cambio Global (IICG-URJC), Universidad Rey Juan Carlos, Tulipán s/n, Móstoles, 28933, Spain
| | - Sergio Núñez-Castillo
- ECOEVO Group, Departamento de Biología, Geología, Física y Química Inorgánica, Instituto de Investigación en Cambio Global (IICG-URJC), Universidad Rey Juan Carlos, Tulipán s/n, Móstoles, 28933, Spain
| | - Alicia Gómez-Fernández
- ECOEVO Group, Departamento de Biología, Geología, Física y Química Inorgánica, Instituto de Investigación en Cambio Global (IICG-URJC), Universidad Rey Juan Carlos, Tulipán s/n, Móstoles, 28933, Spain
| | - François Vasseur
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, 34090, France
| | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, 34090, France
| | - Jana Balarynová
- Department of Botany, Faculty of Science, Palacky University, Olomouc, CZ-783 71, Czech Republic
| | - Petr Smykal
- Department of Botany, Faculty of Science, Palacky University, Olomouc, CZ-783 71, Czech Republic
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Klčová B, Balarynová J, Trněný O, Krejčí P, Cechová MZ, Leonova T, Gorbach D, Frolova N, Kysil E, Orlova A, Ihling С, Frolov A, Bednář P, Smýkal P. Domestication has altered gene expression and secondary metabolites in pea seed coat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2269-2295. [PMID: 38578789 DOI: 10.1111/tpj.16734] [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: 11/24/2023] [Accepted: 03/09/2024] [Indexed: 04/07/2024]
Abstract
The mature seed in legumes consists of an embryo and seed coat. In contrast to knowledge about the embryo, we know relatively little about the seed coat. We analyzed the gene expression during seed development using a panel of cultivated and wild pea genotypes. Gene co-expression analysis identified gene modules related to seed development, dormancy, and domestication. Oxidoreductase genes were found to be important components of developmental and domestication processes. Proteomic and metabolomic analysis revealed that domestication favored proteins involved in photosynthesis and protein metabolism at the expense of seed defense. Seed coats of wild peas were rich in cell wall-bound metabolites and the protective compounds predominated in their seed coats. Altogether, we have shown that domestication altered pea seed development and modified (mostly reduced) the transcripts along with the protein and metabolite composition of the seed coat, especially the content of the compounds involved in defense. We investigated dynamic profiles of selected identified phenolic and flavonoid metabolites across seed development. These compounds usually deteriorated the palatability and processing of the seeds. Our findings further provide resources to study secondary metabolism and strategies for improving the quality of legume seeds which comprise an important part of the human protein diet.
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Affiliation(s)
- Barbora Klčová
- Department of Botany, Faculty of Sciences, Palacky University, Šlechtitelů 27, Olomouc, 773 71, Czech Republic
| | - Jana Balarynová
- Department of Botany, Faculty of Sciences, Palacky University, Šlechtitelů 27, Olomouc, 773 71, Czech Republic
| | - Oldřich Trněný
- Agricultural Research Ltd., Zemědělská 1, Troubsko, 664 41, Czech Republic
| | - Petra Krejčí
- Department of Analytical Chemistry, Faculty of Sciences, Palacky University, 17. listopadu 1192/12, Olomouc, 771 46, Czech Republic
| | - Monika Zajacová Cechová
- Department of Analytical Chemistry, Faculty of Sciences, Palacky University, 17. listopadu 1192/12, Olomouc, 771 46, Czech Republic
| | - Tatiana Leonova
- Department of Bioorganic Chemistry, Leibniz-Institut für Pflanzenbiochemie, Weinberg 3, Halle (Saale), 06120, Germany
| | - Daria Gorbach
- Department of Bioorganic Chemistry, Leibniz-Institut für Pflanzenbiochemie, Weinberg 3, Halle (Saale), 06120, Germany
| | - Nadezhda Frolova
- Laboratory of Analytical Biochemistry, Timiryazev Institute of Plant Physiology, Botanicheskaja 36, Moscow, 127276, Russia
| | - Elana Kysil
- Department of Bioorganic Chemistry, Leibniz-Institut für Pflanzenbiochemie, Weinberg 3, Halle (Saale), 06120, Germany
| | - Anastasia Orlova
- Laboratory of Analytical Biochemistry, Timiryazev Institute of Plant Physiology, Botanicheskaja 36, Moscow, 127276, Russia
| | - Сhristian Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle (Saale), 06120, Germany
| | - Andrej Frolov
- Laboratory of Analytical Biochemistry, Timiryazev Institute of Plant Physiology, Botanicheskaja 36, Moscow, 127276, Russia
| | - Petr Bednář
- Department of Analytical Chemistry, Faculty of Sciences, Palacky University, 17. listopadu 1192/12, Olomouc, 771 46, Czech Republic
| | - Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacky University, Šlechtitelů 27, Olomouc, 773 71, Czech Republic
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Cao Z, Socquet-Juglard D, Daba K, Vandenberg A, Bett KE. Understanding genome structure facilitates the use of wild lentil germplasm for breeding: A case study with shattering loci. THE PLANT GENOME 2024; 17:e20455. [PMID: 38747009 DOI: 10.1002/tpg2.20455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 07/02/2024]
Abstract
Plant breeders are generally reluctant to cross elite crop cultivars with their wild relatives to introgress novel desirable traits due to associated negative traits such as pod shattering. This results in a genetic bottleneck that could be reduced through better understanding of the genomic locations of the gene(s) controlling this trait. We integrated information on parental genomes, pod shattering data from multiple environments, and high-density genetic linkage maps to identify pod shattering quantitative trait loci (QTLs) in three lentil interspecific recombinant inbred line populations. The broad-sense heritability on a multi-environment basis varied from 0.46 (in LR-70, Lens culinaris × Lens odemensis) to 0.77 (in LR-68, Lens orientalis × L. culinaris). Genetic linkage maps of the interspecific populations revealed reciprocal translocations of chromosomal segments that differed among the populations, and which were associated with reduced recombination. LR-68 had a 2-5 translocation, LR-70 had 1-5, 2-6, and 2-7 translocations, and LR-86 had a 2-7 translocation in one parent relative to the other. Segregation distortion was also observed for clusters of single nucleotide polymorphisms on multiple chromosomes per population, further affecting introgression. Two major QTL, on chromosomes 4 and 7, were repeatedly detected in the three populations and contain several candidate genes. These findings will be of significant value for lentil breeders to strategically access novel superior alleles while minimizing the genetic impact of pod shattering from wild parents.
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Affiliation(s)
- Zhe Cao
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Didier Socquet-Juglard
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ketema Daba
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Albert Vandenberg
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Kirstin E Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Wen Z, Lu X, Wen J, Wang Z, Chai M. Physical Seed Dormancy in Legumes: Molecular Advances and Perspectives. PLANTS (BASEL, SWITZERLAND) 2024; 13:1473. [PMID: 38891282 PMCID: PMC11174410 DOI: 10.3390/plants13111473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024]
Abstract
Physical dormancy of seeds is a form of dormancy due to the presence of an impermeable seed coat layer, and it represents a feature for plants to adapt to environmental changes over an extended period of phylogenetic evolution. However, in agricultural practice, physical dormancy is problematic. because it prevents timely and uniform seed germination. Therefore, physical dormancy is an important agronomical trait to target in breeding and domestication, especially for many leguminous crops. Compared to the well-characterized physiological dormancy, research progress on physical dormancy at the molecular level has been limited until recent years, due to the lack of suitable research materials. This review focuses on the structure of seed coat, factors affecting physical dormancy, genes controlling physical dormancy, and plants suitable for studying physical dormancy at the molecular level. Our goal is to provide a plethora of information for further molecular research on physical dormancy.
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Affiliation(s)
- Zhaozhu Wen
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Xuran Lu
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Jiangqi Wen
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA
| | - Zengyu Wang
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Maofeng Chai
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
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Williams OR, Vander Schoor JK, Butler JB, Hecht VFG, Weller JL. Physical seed dormancy in pea is genetically separable from seed coat thickness and roughness. FRONTIERS IN PLANT SCIENCE 2024; 15:1359226. [PMID: 38476691 PMCID: PMC10927720 DOI: 10.3389/fpls.2024.1359226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/09/2024] [Indexed: 03/14/2024]
Abstract
Introduction The seeds of wild pea (Pisum) exhibit marked physical dormancy due to impermeability of the seed coat to water, and the loss of this dormancy is thought to have been critical for domestication. Wild pea seed coats are also notably thick and rough, traits that have also reduced during domestication and are anecdotally linked to increased permeability. However, how these traits specifically interact with permeability is unclear. Methods To investigate this, we examined the genetic control of differences in seed coat characteristics between wild P. sativum ssp. humile and a non-dormant domesticated P. s. sativum accession in a recombinant inbred population. QTL effects were confirmed and their locations refined in segregating F4/5 populations. Results In this population we found a moderate correlation between testa thickness and permeability, and identified loci that affect them independently, suggesting no close functional association. However, the major loci affecting both testa thickness and permeability collocated closely with Mendel's pigmentation locus A, suggesting flavonoid compounds under its control might contribute significantly to both traits. We also show that seed coat roughness is oligogenic in this population, with the major locus independent of both testa thickness and permeability, suggesting selection for smooth seed was unlikely to be due to effects on either of these traits. Discussion Results indicate loss of seed coat dormancy during domestication was not primarily driven by reduced testa thickness or smooth seededness. The close association between major permeability and thickness QTL and Mendel's 'A' warrant further study, particularly regarding the role of flavonoids.
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Affiliation(s)
- Owen R. Williams
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Jacqueline K. Vander Schoor
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Jakob B. Butler
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Tasmania, Hobart, TAS, Australia
| | | | - James L. Weller
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Tasmania, Hobart, TAS, Australia
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Yong B, Zhu W, Wei S, Li B, Wang Y, Xu N, Lu J, Chen Q, He C. Parallel selection of loss-of-function alleles of Pdh1 orthologous genes in warm-season legumes for pod indehiscence and plasticity is related to precipitation. THE NEW PHYTOLOGIST 2023; 240:863-879. [PMID: 37501344 DOI: 10.1111/nph.19150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/04/2023] [Indexed: 07/29/2023]
Abstract
Pod dehiscence facilitates seed dispersal in wild legumes but results in yield loss in cultivated legumes. The evolutionary genetics of the legume pod dehiscence trait remain largely elusive. We characterized the pod dehiscence of chromosome segment substitution lines of Glycine max crossed with Glycine soja and found that the gene underlying the predominant quantitative trait locus (QTL) of soybean pod-shattering trait was Pod dehiscence 1 (Pdh1). A few rare loss-of-function (LoF) Pdh1 alleles were identified in G. soja, while only an allele featuring a premature stop codon was selected for pod indehiscence in cultivated soybean and spread to low-precipitation regions with increased frequency. Moreover, correlated interactions among Pdh1's haplotype, gene expression, and environmental changes for the developmental plasticity of the pod dehiscence trait were revealed in G. max. We found that orthologous Pdh1 genes specifically originated in warm-season legumes and their LoF alleles were then parallel-selected during the domestication of legume crops. Our results provide insights into the convergent evolution of pod dehiscence in warm-season legumes, facilitate an understanding of the intricate interactions between genetic robustness and environmental adaptation for developmental plasticity, and guide the breeding of new legume varieties with pod indehiscence.
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Affiliation(s)
- Bin Yong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
| | - Weiwei Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
| | - Siming Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
| | - Bingbing Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
| | - Yan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Nan Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
| | - Jiangjie Lu
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 311121, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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Sedláková V, Zeljković SĆ, Štefelová N, Smýkal P, Hanáček P. Phenylpropanoid Content of Chickpea Seed Coats in Relation to Seed Dormancy. PLANTS (BASEL, SWITZERLAND) 2023; 12:2687. [PMID: 37514301 PMCID: PMC10384132 DOI: 10.3390/plants12142687] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/07/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
The physical dormancy of seeds is likely to be mediated by the chemical composition and the thickness of the seed coat. Here, we investigate the link between the content of phenylpropanoids (i.e., phenolics and flavonoids) present in the chickpea seed coat and dormancy. The relationship between selected phenolic and flavonoid metabolites of chickpea seed coats and dormancy level was assessed using wild and cultivated chickpea parental genotypes and a derived population of recombinant inbred lines (RILs). The selected phenolic and flavonoid metabolites were analyzed via the LC-MS/MS method. Significant differences in the concentration of certain phenolic acids were found among cultivated (Cicer arietinum, ICC4958) and wild chickpea (Cicer reticulatum, PI489777) parental genotypes. These differences were observed in the contents of gallic, caffeic, vanillic, syringic, p-coumaric, salicylic, and sinapic acids, as well as salicylic acid-2-O-β-d-glucoside and coniferaldehyde. Additionally, significant differences were observed in the flavonoids myricetin, quercetin, luteolin, naringenin, kaempferol, isoorientin, orientin, and isovitexin. When comparing non-dormant and dormant RILs, significant differences were observed in gallic, 3-hydroxybenzoic, syringic, and sinapic acids, as well as the flavonoids quercitrin, quercetin, naringenin, kaempferol, and morin. Phenolic acids were generally more highly concentrated in the wild parental genotype and dormant RILs. We compared the phenylpropanoid content of chickpea seed coats with related legumes, such as pea, lentil, and faba bean. This information could be useful in chickpea breeding programs to reduce dormancy.
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Affiliation(s)
- Veronika Sedláková
- Department of Plant Biology, Mendel University in Brno, 613 00 Brno, Czech Republic
| | - Sanja Ćavar Zeljković
- Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, 783 71 Olomouc, Czech Republic
- Czech Advanced Technology and Research Institute, Palacký University, 783 71 Olomouc, Czech Republic
| | - Nikola Štefelová
- Czech Advanced Technology and Research Institute, Palacký University, 783 71 Olomouc, Czech Republic
| | - Petr Smýkal
- Department of Botany, Faculty of Science, Palacký University, 783 71 Olomouc, Czech Republic
| | - Pavel Hanáček
- Department of Plant Biology, Mendel University in Brno, 613 00 Brno, Czech Republic
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Balarynová J, Klčová B, Tarkowská D, Turečková V, Trněný O, Špundová M, Ochatt S, Smýkal P. Domestication has altered the ABA and gibberellin profiles in developing pea seeds. PLANTA 2023; 258:25. [PMID: 37351659 PMCID: PMC10290032 DOI: 10.1007/s00425-023-04184-2] [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: 04/04/2023] [Accepted: 06/12/2023] [Indexed: 06/24/2023]
Abstract
MAIN CONCLUSION We showed that wild pea seeds contained a more diverse combination of bioactive GAs and had higher ABA content than domesticated peas. Although the role of abscisic acid (ABA) and gibberellins (GAs) interplay has been extensively studied in Arabidopsis and cereals models, comparatively little is known about the effect of domestication on the level of phytohormones in legume seeds. In legumes, as in other crops, seed dormancy has been largely or entirely removed during domestication. In this study, we have measured the endogenous levels of ABA and GAs comparatively between wild and domesticated pea seeds during their development. We have shown that wild seeds contained more ABA than domesticated ones, which could be important for preparing the seeds for the period of dormancy. ABA was catabolised particularly by an 8´-hydroxylation pathway, and dihydrophaseic acid was the main catabolite in seed coats as well as embryos. Besides, the seed coats of wild and pigmented cultivated genotypes were characterised by a broader spectrum of bioactive GAs compared to non-pigmented domesticated seeds. GAs in both seed coat and embryo were synthesized mainly by a 13-hydroxylation pathway, with GA29 being the most abundant in the seed coat and GA20 in the embryos. Measuring seed water content and water loss indicated domesticated pea seeds´ desiccation was slower than that of wild pea seeds. Altogether, we showed that pea domestication led to a change in bioactive GA composition and a lower ABA content during seed development.
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Affiliation(s)
- Jana Balarynová
- Department of Botany, Faculty of Science, Palacky University, 783 71, Olomouc, Czech Republic
| | - Barbora Klčová
- Department of Botany, Faculty of Science, Palacky University, 783 71, Olomouc, Czech Republic
| | - Danuše Tarkowská
- Laboratory of Growth Regulators, Palacky University and Institute of Experimental Botany, Czech Academy of Sciences, 783 71, Olomouc, Czech Republic
| | - Veronika Turečková
- Laboratory of Growth Regulators, Palacky University and Institute of Experimental Botany, Czech Academy of Sciences, 783 71, Olomouc, Czech Republic
| | - Oldřich Trněný
- Agriculture Research Ltd., 664 41, Troubsko, Czech Republic
| | - Martina Špundová
- Department of Biophysics, Faculty of Science, Palacky University, 783 71, Olomouc, Czech Republic
| | - Sergio Ochatt
- Agroécologie, InstitutAgro Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Petr Smýkal
- Department of Botany, Faculty of Science, Palacky University, 783 71, Olomouc, Czech Republic.
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Ali S, Kucek LK, Riday H, Krom N, Krogman S, Cooper K, Jacobs L, Mehta P, Trammell M, Bhamidimarri S, Butler T, Saha MC, Monteros MJ. Transcript profiling of hairy vetch (Vicia villosa Roth) identified interesting genes for seed dormancy. THE PLANT GENOME 2023; 16:e20330. [PMID: 37125613 DOI: 10.1002/tpg2.20330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Hairy vetch, a diploid annual legume species, has a robust growth habit, high biomass yield, and winter hardy characteristics. Seed hardness is a major constraint for growing hairy vetch commercially. Hard seeded cultivars are valuable as forages, whereas soft seeded and shatter resistant cultivars have advantages for their use as a cover crop. Transcript analysis of hairy vetch was performed to understand the genetic mechanisms associated with important hairy vetch traits. RNA was extracted from leaves, flowers, immature pods, seed coats, and cotyledons of contrasting soft and hard seeded "AU Merit" plants. A range of 31.22-79.18 Gb RNA sequence data per tissue sample were generated with estimated coverage of 1040-2639×. RNA sequence assembly and mapping of the contigs against the Medicago truncatula (V4.0) genome identified 76,422 gene transcripts. A total of 24,254 transcripts were constitutively expressed in hairy vetch tissues. Key genes, such as KNOX4 (a class II KNOTTED-like homeobox KNOXII gene), qHs1 (endo-1,4-β-glucanase), GmHs1-1 (calcineurin-like metallophosphoesterase), chitinase, shatterproof 1 and 2 (SHP1, SHP2), shatter resistant 1-5 (SHAT1-5)(NAC transcription factor), PDH1 (prephenate dehydrogenase 1), and pectin methylesterases with a potential role in seed hardness and pod shattering, were further explored based on genes involved in seed hardness from other species to query the hairy vetch transcriptome data. Identification of interesting candidate genes in hairy vetch can facilitate the development of improved cultivars with desirable seed characteristics for use as a forage and as a cover crop.
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Affiliation(s)
- Shahjahan Ali
- USDA-ARS, US Dairy Forage Research Center, Madison, Wisconsin, USA
| | | | | | - Nick Krom
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | - Sarah Krogman
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | | | - Lynne Jacobs
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | - Perdeep Mehta
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | - Michael Trammell
- Oklahoma State University Cooperative Extension, Shawnee, Oklahoma, USA
| | | | - Twain Butler
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | - Malay C Saha
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
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10
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Transcriptomic insights into the effects of abscisic acid on the germination of Magnolia sieboldii K. Koch seed. Gene 2023; 853:147066. [PMID: 36455787 DOI: 10.1016/j.gene.2022.147066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/07/2022] [Accepted: 11/18/2022] [Indexed: 11/30/2022]
Abstract
Magnolia sieboldii K. Koch is a deciduous tree species. However, the wild resource of M. sieboldii has been declining due to excessive utilization and seed dormancy. In our previous research, M. sieboldii seeds have morphophysiological dormancy and low germination rates under natural conditions. The aim of the present study was to identify the genes involved in dormancy maintenance. In this study, the germination percentage of M. sieboldii seeds negatively correlated with the content of endogenous abscisic acid (ABA). The hydration of seeds for germination showed three distinct phases. Five key time points were identified: 0 h imbibition (dry seed, GZ), 0 day after imbibition (DAI), 16 DAI, 40 DAI, and 56 DAI. The comprehensive transcript profiles of M. sieboldii seeds treated with ABA and water at the five key germinating stages were obtained. A total of 9641 differentially expressed genes (DEGs) were identified, and 208 and 197 common DEGs were found throughout the ABA and water treatments, respectively. Compared with that in the GZ, 518, 696, 2133, and 1535 DEGs were identified in the SH group at 0, 16, 40 and 56 DAI, respectively. 666, 1725, 1560 and 1415 DEGs were identified in the ABA group at 0, 16, 40, and 56 DAI, respectively. Among the identified DEGs, 12 722 were annotated with GO terms, the top three enriched GO terms were different among the DEGs at 56 DAI in the ABA vs. SH treatments. KEGG pathway enrichment analysis for DEGs indicated that oxidative phosphorylation, protein processing in endoplasmic reticulum, starch and sucrose metabolism play an important role in seed response to ABA. 1926 TFs are obtained and classified into 72 families from the M. sieboldii transcriptome. Results of differential gene expression analysis together with qRT-PCR indicated that phase II is crucial for rapid and successful seed germination. This study is the first to present the global expression patterns of ABA-regulated transcripts in M. sieboldii seeds at different germinating phases.
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11
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Bohra A, Tiwari A, Kaur P, Ganie SA, Raza A, Roorkiwal M, Mir RR, Fernie AR, Smýkal P, Varshney RK. The Key to the Future Lies in the Past: Insights from Grain Legume Domestication and Improvement Should Inform Future Breeding Strategies. PLANT & CELL PHYSIOLOGY 2022; 63:1554-1572. [PMID: 35713290 PMCID: PMC9680861 DOI: 10.1093/pcp/pcac086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/09/2022] [Accepted: 06/15/2022] [Indexed: 05/11/2023]
Abstract
Crop domestication is a co-evolutionary process that has rendered plants and animals significantly dependent on human interventions for survival and propagation. Grain legumes have played an important role in the development of Neolithic agriculture some 12,000 years ago. Despite being early companions of cereals in the origin and evolution of agriculture, the understanding of grain legume domestication has lagged behind that of cereals. Adapting plants for human use has resulted in distinct morpho-physiological changes between the wild ancestors and domesticates, and this distinction has been the focus of several studies aimed at understanding the domestication process and the genetic diversity bottlenecks created. Growing evidence from research on archeological remains, combined with genetic analysis and the geographical distribution of wild forms, has improved the resolution of the process of domestication, diversification and crop improvement. In this review, we summarize the significance of legume wild relatives as reservoirs of novel genetic variation for crop breeding programs. We describe key legume features, which evolved in response to anthropogenic activities. Here, we highlight how whole genome sequencing and incorporation of omics-level data have expanded our capacity to monitor the genetic changes accompanying these processes. Finally, we present our perspective on alternative routes centered on de novo domestication and re-domestication to impart significant agronomic advances of novel crops over existing commodities. A finely resolved domestication history of grain legumes will uncover future breeding targets to develop modern cultivars enriched with alleles that improve yield, quality and stress tolerance.
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Affiliation(s)
- Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Abha Tiwari
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kalyanpur, Kanpur 208024, India
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Showkat Ahmad Ganie
- Department of Biotechnology, Visva-Bharati, Santiniketan, Santiniketan Road, Bolpur 731235, India
| | - Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China
| | - Manish Roorkiwal
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), UAE University, Sheik Khalifa Bin Zayed Street, Al Ain, Abu Dhabi 15551, UAE
| | - Reyazul Rouf Mir
- Division of Genetics & Plant Breeding, Faculty of Agriculture, SKUAST, Shalimar, Srinagar 190025, India
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacky University, Křížkovského 511/8, Olomouc 78371, Czech Republic
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12
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Fondevilla S, Krezdorn N, Rubiales D, Rotter B, Winter P. Bulked segregant transcriptome analysis in pea identifies key expression markers for resistance to Peyronellaea pinodes. Sci Rep 2022; 12:18159. [PMID: 36307494 PMCID: PMC9616913 DOI: 10.1038/s41598-022-22621-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/17/2022] [Indexed: 12/31/2022] Open
Abstract
Peyronellaea pinodes is a devastating pathogen of pea crop. Quantitative trait loci (QTL) associated with resistance have been identified, as well as genes differentially expressed between resistant and susceptible pea lines. The key question is which of these many genes located into these QTLs, or differentially expressed, are the key genes that distinguish resistant from susceptible plants and could be used as markers. To identify these key genes, in the present study we applied MACE (Massive Analysis of cDNA Ends) -Seq to a whole Recombinant Inbred Line population segregating for resistance to this disease and their parental lines and identified those genes which expression was more correlated with the level of resistance. We also compared gene expression profiles between the most resistant and the most susceptible families of the RIL population. A total of 6780 transcripts were differentially expressed between the parental lines after inoculation. Of them, 803 showed the same expression pattern in the bulks formed by the most resistant and most susceptible RIL families. These genes, showing a consistent expression pattern, could be used as expression markers to distinguish resistant from susceptible plants. The analysis of these genes also discovered the crucial mechanisms acting against P. pinodes.
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Affiliation(s)
- Sara Fondevilla
- Institute for Sustainable Agriculture, CSIC, 14004, Córdoba, Spain.
| | | | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, 14004, Córdoba, Spain
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Yang T, Liu R, Luo Y, Hu S, Wang D, Wang C, Pandey MK, Ge S, Xu Q, Li N, Li G, Huang Y, Saxena RK, Ji Y, Li M, Yan X, He Y, Liu Y, Wang X, Xiang C, Varshney RK, Ding H, Gao S, Zong X. Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics. Nat Genet 2022; 54:1553-1563. [PMID: 36138232 PMCID: PMC9534762 DOI: 10.1038/s41588-022-01172-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/26/2022] [Indexed: 12/21/2022]
Abstract
Complete and accurate reference genomes and annotations provide fundamental resources for functional genomics and crop breeding. Here we report a de novo assembly and annotation of a pea cultivar ZW6 with contig N50 of 8.98 Mb, which features a 243-fold increase in contig length and evident improvements in the continuity and quality of sequence in complex repeat regions compared with the existing one. Genome diversity of 118 cultivated and wild pea demonstrated that Pisum abyssinicum is a separate species different from P. fulvum and P. sativum within Pisum. Quantitative trait locus analyses uncovered two known Mendel's genes related to stem length (Le/le) and seed shape (R/r) as well as some candidate genes for pod form studied by Mendel. A pan-genome of 116 pea accessions was constructed, and pan-genes preferred in P. abyssinicum and P. fulvum showed distinct functional enrichment, indicating the potential value of them as pea breeding resources in the future.
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Affiliation(s)
- Tao Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rong Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingfeng Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dong Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Chenyu Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Manish K Pandey
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Quanle Xu
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Nana Li
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Science, Shandong Normal University, Jinan, China
| | - Guan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuning Huang
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rachit K Saxena
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Yishan Ji
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mengwei Li
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Yan
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuhua He
- Institute of Grain Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yujiao Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- Qinghai Academy of Agricultural and Forestry Sciences, Xining, China
| | - Xuejun Wang
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China
| | - Chao Xiang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- Murdoch's Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
| | - Hanfeng Ding
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China.
- College of Life Science, Shandong Normal University, Jinan, China.
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Xuxiao Zong
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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14
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Balarynová J, Klčová B, Sekaninová J, Kobrlová L, Cechová MZ, Krejčí P, Leonova T, Gorbach D, Ihling C, Smržová L, Trněný O, Frolov A, Bednář P, Smýkal P. The loss of polyphenol oxidase function is associated with hilum pigmentation and has been selected during pea domestication. THE NEW PHYTOLOGIST 2022; 235:1807-1821. [PMID: 35585778 DOI: 10.1111/nph.18256] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Seed coats serve as protective tissue to the enclosed embryo. As well as mechanical there are also chemical defence functions. During domestication, the property of the seed coat was altered including the removal of the seed dormancy. We used a range of genetic, transcriptomic, proteomic and metabolomic approaches to determine the function of the pea seed polyphenol oxidase (PPO) gene. Sequencing analysis revealed one nucleotide insertion or deletion in the PPO gene, with the functional PPO allele found in all wild pea samples, while most cultivated peas have one of the three nonfunctional ppo alleles. PPO functionality cosegregates with hilum pigmentation. PPO gene and protein expression, as well as enzymatic activity, was downregulated in the seed coats of cultivated peas. The functionality of the PPO gene relates to the oxidation and polymerisation of gallocatechin in the seed coat. Additionally, imaging mass spectrometry supports the hypothesis that hilum pigmentation is conditioned by the presence of both phenolic precursors and sufficient PPO activity. Taken together these results indicate that the nonfunctional polyphenol oxidase gene has been selected during pea domestication, possibly due to better seed palatability or seed coat visual appearance.
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Affiliation(s)
- Jana Balarynová
- Department of Botany, Faculty of Sciences, Palacky University, Olomouc, 783 71, Czech Republic
| | - Barbora Klčová
- Department of Botany, Faculty of Sciences, Palacky University, Olomouc, 783 71, Czech Republic
| | - Jana Sekaninová
- Department of Biochemistry, Faculty of Sciences, Palacky University, Olomouc, 783 71, Czech Republic
| | - Lucie Kobrlová
- Department of Botany, Faculty of Sciences, Palacky University, Olomouc, 783 71, Czech Republic
| | - Monika Zajacová Cechová
- Department of Analytical Chemistry, Faculty of Sciences, Palacky University, Olomouc, 771 46, Czech Republic
| | - Petra Krejčí
- Department of Analytical Chemistry, Faculty of Sciences, Palacky University, Olomouc, 771 46, Czech Republic
| | - Tatiana Leonova
- Department of Bioorganic Chemistry, Leibniz-Institut für Pflanzenbiochemie, Halle (Saale), 06120, Germany
- Department of Biochemistry, St Petersburg State University, St Petersburg, 199004, Russia
| | - Daria Gorbach
- Department of Biochemistry, St Petersburg State University, St Petersburg, 199004, Russia
| | - Christian Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University, Halle-Wittenberg, 06120, Germany
| | - Lucie Smržová
- Department of Botany, Faculty of Sciences, Palacky University, Olomouc, 783 71, Czech Republic
| | - Oldřich Trněný
- Agricultural Research Ltd, Troubsko, 664 41, Czech Republic
| | - Andrej Frolov
- Department of Bioorganic Chemistry, Leibniz-Institut für Pflanzenbiochemie, Halle (Saale), 06120, Germany
- Department of Biochemistry, St Petersburg State University, St Petersburg, 199004, Russia
| | - Petr Bednář
- Department of Analytical Chemistry, Faculty of Sciences, Palacky University, Olomouc, 771 46, Czech Republic
| | - Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacky University, Olomouc, 783 71, Czech Republic
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15
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Afridi M, Ahmad K, Malik SS, Rehman N, Yasin M, Khan SM, Hussain A, Khan MR. Genome-wide identification, phylogeny, and expression profiling analysis of shattering genes in rapeseed and mustard plants. J Genet Eng Biotechnol 2022; 20:124. [PMID: 35980545 PMCID: PMC9388710 DOI: 10.1186/s43141-022-00408-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 08/05/2022] [Indexed: 11/22/2022]
Abstract
Background Non-synchronized pods shattering in the Brassicaceae family bring upon huge yield losses around the world. The shattering process was validated to be controlled by eight genes in Arabidopsis, including SHP1, SHP2, FUL, IND, ALC, NAC, RPL, and PG. We performed genome-wide identification, characterization, and expression analysis of shattering genes in B.napus and B. juncea to gain understanding into this gene family and to explain their expression patterns in fresh and mature siliques. Results A comprehensive genome investigation of B.napus and B.juncea revealed 32 shattering genes, which were identified and categorized using protein motif structure, exon-intron organization, and phylogeny. The phylogenetic study revealed that these shattering genes contain little duplications, determined with a distinct chromosome number. Motifs of 32 shattering proteins were observed where motifs1 and 2 were found to be more conserved. A single motif was observed for other genes like Br-nS7, Br-nS9, Br-nS10, Br-jS21, Br-jS23, Br-jS24, Br-jS25, and Br-jS26. Synteny analysis was performed that validated a conserved pattern of blocks among these cultivars. RT-PCR based expressions profiles showed higher expression of shattering genes in B. juncea as compared to B.napus. SHP1, SHP2, and FUL gene were expressed more in mature silique. ALC gene was upregulated in fresh silique of B. napus but downregulation of ALC were observed in fresh silique of B. juncea. Conclusion This study authenticates the presence of shattering genes in the local cultivars of Brassica. It has been validated that the expression of shattering genes were more in B. juncea as compared to B.napus. The outcomes of this study contribute to the screening of more candidate genes for further investigation.
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Affiliation(s)
- Mahideen Afridi
- National Centre for Bioinformatics, Quaid-I-Azam University, Islamabad, 45320, Pakistan.
| | - Khurshid Ahmad
- Department of Biological Sciences, International Islamic University, Islamabad, 44000, Pakistan
| | - Shahana Seher Malik
- Department of Biology, College of Science, United Arab Emirates University, 15551, Al Ain, United Arab Emirates
| | - Nazia Rehman
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Center, Park Road, Islamabad, 44000, Pakistan
| | - Muhammad Yasin
- National Centre for Bioinformatics, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Shujaul Mulk Khan
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Adil Hussain
- Food and Biotechnology Research Centre (FBRC), Pakistan Council of Scientific and Industrial Research (PCSIR) Laboratories Complex, Ferozepur Road, Lahore, Punjab, 56400, Pakistan
| | - Muhammad Ramzan Khan
- National Centre for Bioinformatics, Quaid-I-Azam University, Islamabad, 45320, Pakistan.,National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Center, Park Road, Islamabad, 44000, Pakistan
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16
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The Seed Coat’s Impact on Crop Performance in Pea (Pisum sativum L.). PLANTS 2022; 11:plants11152056. [PMID: 35956534 PMCID: PMC9370168 DOI: 10.3390/plants11152056] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 11/17/2022]
Abstract
Seed development in angiosperms produces three genetically and developmentally distinct sub-compartments: the embryo, endosperm, and seed coat. The maternally derived seed coat protects the embryo and interacts closely with the external environment especially during germination and seedling establishment. Seed coat is a key contributor to seed composition and an important determinant of nutritional value for humans and livestock. In this review, we examined pea crop productivity through the lens of the seed coat, its contribution to several valued nutritional traits of the pea crop, and its potential as a breeding target. Key discoveries made in advancing the knowledge base for sensing and transmission of external signals, the architecture and chemistry of the pea seed coat, and relevant insights from other important legumes were discussed. Furthermore, for selected seed coat traits, known mechanisms of genetic regulation and efforts to modulate these mechanisms to facilitate composition and productivity improvements in pea were discussed, alongside opportunities to support the continued development and improvement of this underutilized crop. This review describes the most important features of seed coat development in legumes and highlights the key roles played by the seed coat in pea seed development, with a focus on advances made in the genetic and molecular characterization of pea and other legumes and the potential of this key seed tissue for targeted improvement and crop optimization.
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17
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Krejčí P, Cechová MZ, Nádvorníková J, Barták P, Kobrlová L, Balarynová J, Smýkal P, Bednář P. Combination of electronically driven micromanipulation with laser desorption ionization mass spectrometry – The unique tool for analysis of seed coat layers and revealing the mystery of seed dormancy. Talanta 2022; 242:123303. [DOI: 10.1016/j.talanta.2022.123303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/18/2022] [Accepted: 02/09/2022] [Indexed: 10/19/2022]
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18
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De-la-Cruz IM, Batsleer F, Bonte D, Diller C, Hytönen T, Muola A, Osorio S, Posé D, Vandegehuchte ML, Stenberg JA. Evolutionary Ecology of Plant-Arthropod Interactions in Light of the "Omics" Sciences: A Broad Guide. FRONTIERS IN PLANT SCIENCE 2022; 13:808427. [PMID: 35548276 PMCID: PMC9084618 DOI: 10.3389/fpls.2022.808427] [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: 11/03/2021] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Aboveground plant-arthropod interactions are typically complex, involving herbivores, predators, pollinators, and various other guilds that can strongly affect plant fitness, directly or indirectly, and individually, synergistically, or antagonistically. However, little is known about how ongoing natural selection by these interacting guilds shapes the evolution of plants, i.e., how they affect the differential survival and reproduction of genotypes due to differences in phenotypes in an environment. Recent technological advances, including next-generation sequencing, metabolomics, and gene-editing technologies along with traditional experimental approaches (e.g., quantitative genetics experiments), have enabled far more comprehensive exploration of the genes and traits involved in complex ecological interactions. Connecting different levels of biological organization (genes to communities) will enhance the understanding of evolutionary interactions in complex communities, but this requires a multidisciplinary approach. Here, we review traditional and modern methods and concepts, then highlight future avenues for studying the evolution of plant-arthropod interactions (e.g., plant-herbivore-pollinator interactions). Besides promoting a fundamental understanding of plant-associated arthropod communities' genetic background and evolution, such knowledge can also help address many current global environmental challenges.
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Affiliation(s)
- Ivan M. De-la-Cruz
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Femke Batsleer
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Dries Bonte
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Carolina Diller
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Timo Hytönen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- NIAB EMR, West Malling, United Kingdom
| | - Anne Muola
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
- Biodiversity Unit, University of Turku, Finland
| | - Sonia Osorio
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, Málaga, Spain
| | - David Posé
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, Málaga, Spain
| | - Martijn L. Vandegehuchte
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Johan A. Stenberg
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
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19
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Hellwig T, Abbo S, Ophir R. Phylogeny and disparate selection signatures suggest two genetically independent domestication events in pea (Pisum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:419-439. [PMID: 35061306 PMCID: PMC9303476 DOI: 10.1111/tpj.15678] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 01/15/2022] [Indexed: 05/25/2023]
Abstract
Domestication is considered a model of adaptation that can be used to draw conclusions about the modus operandi of selection in natural systems. Investigating domestication may give insights into how plants react to different intensities of human manipulation, which has direct implication for the continuing efforts of crop improvement. Therefore, scientists of various disciplines study domestication-related questions to understand the biological and cultural bases of the domestication process. We employed restriction site-associated DNA sequencing (RAD-seq) of 494 Pisum sativum (pea) samples from all wild and domesticated groups to analyze the genetic structure of the collection. Patterns of ancient admixture were investigated by analysis of admixture graphs. We used two complementary approaches, one diversity based and one based on differentiation, to detect the selection signatures putatively associated with domestication. An analysis of the subpopulation structure of wild P. sativum revealed five distinct groups with a notable geographic pattern. Pisum abyssinicum clustered unequivocally within the P. sativum complex, without any indication of hybrid origin. We detected 32 genomic regions putatively subjected to selection: 29 in P. sativum ssp. sativum and three in P. abyssinicum. The two domesticated groups did not share regions under selection and did not display similar haplotype patterns within those regions. Wild P. sativum is structured into well-diverged subgroups. Although Pisum sativum ssp. humile is not supported as a taxonomic entity, the so-called 'southern humile' is a genuine wild group. Introgression did not shape the variation observed within the sampled germplasm. The two domesticated pea groups display distinct genetic bases of domestication, suggesting two genetically independent domestication events.
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Affiliation(s)
- Timo Hellwig
- The Levi Eshkol School of AgricultureThe Hebrew University of JerusalemJerusalem, RehovotIsrael
- Volcani Center, Agricultural Research OrganizationRishon LeZionIsrael
- Institute of Plant Genetics, Heinrich‐Heine‐UniversityDüsseldorfGermany
| | - Shahal Abbo
- The Levi Eshkol School of AgricultureThe Hebrew University of JerusalemJerusalem, RehovotIsrael
| | - Ron Ophir
- Volcani Center, Agricultural Research OrganizationRishon LeZionIsrael
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Myxospermy Evolution in Brassicaceae: A Highly Complex and Diverse Trait with Arabidopsis as an Uncommon Model. Cells 2021; 10:cells10092470. [PMID: 34572119 PMCID: PMC8469493 DOI: 10.3390/cells10092470] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 01/13/2023] Open
Abstract
The ability to extrude mucilage upon seed imbibition (myxospermy) occurs in several Angiosperm taxonomic groups, but its ancestral nature or evolutionary convergence origin remains misunderstood. We investigated seed mucilage evolution in the Brassicaceae family with comparison to the knowledge accumulated in Arabidopsis thaliana. The myxospermy occurrence was evaluated in 27 Brassicaceae species. Phenotyping included mucilage secretory cell morphology and topochemistry to highlight subtle myxospermy traits. In parallel, computational biology was driven on the one hundred genes constituting the so-called A. thaliana mucilage secretory cell toolbox to confront their sequence conservation to the observed phenotypes. Mucilage secretory cells show high morphology diversity; the three studied Arabidopsis species had a specific extrusion modality compared to the other studied Brassicaceae species. Orthologous genes from the A. thaliana mucilage secretory cell toolbox were mostly found in all studied species without correlation with the occurrence of myxospermy or even more sub-cellular traits. Seed mucilage may be an ancestral feature of the Brassicaceae family. It consists of highly diverse subtle traits, probably underlined by several genes not yet characterized in A. thaliana or by species-specific genes. Therefore, A. thaliana is probably not a sufficient reference for future myxospermy evo-devo studies.
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21
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Zablatzká L, Balarynová J, Klčová B, Kopecký P, Smýkal P. Anatomy and Histochemistry of Seed Coat Development of Wild ( Pisum sativum subsp. elatius (M. Bieb.) Asch. et Graebn. and Domesticated Pea ( Pisum sativum subsp. sativum L.). Int J Mol Sci 2021; 22:4602. [PMID: 33925728 PMCID: PMC8125792 DOI: 10.3390/ijms22094602] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/26/2021] [Accepted: 04/26/2021] [Indexed: 11/16/2022] Open
Abstract
In angiosperms, the mature seed consists of embryo, endosperm, and a maternal plant-derived seed coat (SC). The SC plays a role in seed filling, protects the embryo, mediates dormancy and germination, and facilitates the dispersal of seeds. SC properties have been modified during the domestication process, resulting in the removal of dormancy, mediated by SC impermeability. This study compares the SC anatomy and histochemistry of two wild (JI64 and JI1794) and two domesticated (cv. Cameor and JI92) pea genotypes. Histochemical staining of five developmental stages: 13, 21, 27, 30 days after anthesis (DAA), and mature dry seeds revealed clear differences between both pea types. SC thickness is established early in the development (13 DAA) and is primarily governed by macrosclereid cells. Polyanionic staining by Ruthenium Red indicated non homogeneity of the SC, with a strong signal in the hilum, the micropyle, and the upper parts of the macrosclereids. High peroxidase activity was detected in both wild and cultivated genotypes and increased over the development peaking prior to desiccation. The detailed knowledge of SC anatomy is important for any molecular or biochemical studies, including gene expression and proteomic analysis, especially when comparing different genotypes and treatments. Analysis is useful for other crop-to-wild-progenitor comparisons of economically important legume crops.
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Affiliation(s)
- Lenka Zablatzká
- Department of Botany, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic; (L.Z.); (J.B.); (B.K.); (P.K.)
| | - Jana Balarynová
- Department of Botany, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic; (L.Z.); (J.B.); (B.K.); (P.K.)
| | - Barbora Klčová
- Department of Botany, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic; (L.Z.); (J.B.); (B.K.); (P.K.)
| | - Pavel Kopecký
- Department of Botany, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic; (L.Z.); (J.B.); (B.K.); (P.K.)
- Genetic Resources for Vegetables and Specialty Crops, Crop Research Institute, Šlechtitelů 29, 783 71 Olomouc, Czech Republic
| | - Petr Smýkal
- Department of Botany, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic; (L.Z.); (J.B.); (B.K.); (P.K.)
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Parker TA, Lo S, Gepts P. Pod shattering in grain legumes: emerging genetic and environment-related patterns. THE PLANT CELL 2021; 33:179-199. [PMID: 33793864 PMCID: PMC8136915 DOI: 10.1093/plcell/koaa025] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/26/2020] [Indexed: 05/25/2023]
Abstract
A reduction in pod shattering is one of the main components of grain legume domestication. Despite this, many domesticated legumes suffer serious yield losses due to shattering, particularly under arid conditions. Mutations related to pod shattering modify the twisting force of pod walls or the structural strength of the dehiscence zone in pod sutures. At a molecular level, a growing body of evidence indicates that these changes are controlled by a relatively small number of key genes that have been selected in parallel across grain legume species, supporting partial molecular convergence. Legume homologs of Arabidopsis thaliana silique shattering genes play only minor roles in legume pod shattering. Most domesticated grain legume species contain multiple shattering-resistance genes, with mutants of each gene typically showing only partial shattering resistance. Hence, crosses between varieties with different genes lead to transgressive segregation of shattering alleles, producing plants with either enhanced shattering resistance or atavistic susceptibility to the trait. The frequency of these resistance pod-shattering alleles is often positively correlated with environmental aridity. The continued development of pod-shattering-related functional information will be vital for breeding crops that are suited to the increasingly arid conditions expected in the coming decades.
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Affiliation(s)
- Travis A Parker
- Department of Plant Sciences/MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA 95616-8780
| | - Sassoum Lo
- Department of Plant Sciences/MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA 95616-8780
| | - Paul Gepts
- Department of Plant Sciences/MS1, Section of Crop & Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA 95616-8780
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23
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Soltani A, Walter KA, Wiersma AT, Santiago JP, Quiqley M, Chitwood D, Porch TG, Miklas P, McClean PE, Osorno JM, Lowry DB. The genetics and physiology of seed dormancy, a crucial trait in common bean domestication. BMC PLANT BIOLOGY 2021; 21:58. [PMID: 33482732 PMCID: PMC7821524 DOI: 10.1186/s12870-021-02837-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/11/2021] [Indexed: 05/21/2023]
Abstract
BACKGROUND Physical seed dormancy is an important trait in legume domestication. Although seed dormancy is beneficial in wild ecosystems, it is generally considered to be an undesirable trait in crops due to reduction in yield and / or quality. The physiological mechanism and underlying genetic factor(s) of seed dormancy is largely unknown in several legume species. Here we employed an integrative approach to understand the mechanisms controlling physical seed dormancy in common bean (Phaseolus vulgaris L.). RESULTS Using an innovative CT scan imaging system, we were able to track water movements inside the seed coat. We found that water uptake initiates from the bean seed lens. Using a scanning electron microscopy (SEM) we further identified several micro-cracks on the lens surface of non-dormant bean genotypes. Bulked segregant analysis (BSA) was conducted on a bi-parental RIL (recombinant inbred line) population, segregating for seed dormancy. This analysis revealed that the seed water uptake is associated with a single major QTL on Pv03. The QTL region was fine-mapped to a 118 Kb interval possessing 11 genes. Coding sequence analysis of candidate genes revealed a 5-bp insertion in an ortholog of pectin acetylesterase 8 that causes a frame shift, loss-of-function mutation in non-dormant genotype. Gene expression analysis of the candidate genes in the seed coat of contrasting genotypes indicated 21-fold lower expression of pectin acetylesterase 8 in non-dormant genotype. An analysis of mutational polymorphism was conducted among wild and domesticated beans. Although all the wild beans possessed the functional allele of pectin acetylesterase 8, the majority (77%) of domesticated beans had the non-functional allele suggesting that this variant was under strong selection pressure through domestication. CONCLUSIONS In this study, we identified the physiological mechanism of physical seed dormancy and have identified a candidate allele causing variation in this trait. Our findings suggest that a 5-bp insertion in an ortholog of pectin acetylesterase 8 is likely a major causative mutation underlying the loss of seed dormancy during domestication. Although the results of current study provide strong evidences for the role of pectin acetylesterase 8 in seed dormancy, further confirmations seem necessary by employing transgenic approaches.
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Affiliation(s)
- Ali Soltani
- Plant Resilience Institute, Michigan State University, East Lansing, MI, USA.
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
| | - Katelynn A Walter
- Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Andrew T Wiersma
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - James P Santiago
- Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Michelle Quiqley
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Daniel Chitwood
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Timothy G Porch
- USDA-ARS, Tropical Agriculture Research Station, Mayaguez, PR, USA
| | - Phillip Miklas
- USDA-ARS, Grain Legume Genetics Physiology Research Unit, Prosser, WA, USA
| | - Phillip E McClean
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Juan M Osorno
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - David B Lowry
- Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
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24
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Liber M, Duarte I, Maia AT, Oliveira HR. The History of Lentil ( Lens culinaris subsp. culinaris) Domestication and Spread as Revealed by Genotyping-by-Sequencing of Wild and Landrace Accessions. FRONTIERS IN PLANT SCIENCE 2021; 12:628439. [PMID: 33841458 PMCID: PMC8030269 DOI: 10.3389/fpls.2021.628439] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/15/2021] [Indexed: 05/06/2023]
Abstract
Protein-rich legumes accompanied carbohydrate-rich cereals since the beginning of agriculture and yet their domestication history is not as well understood. Lentil (Lens culinaris Medik. subsp. culinaris) was first cultivated in Southwest Asia (SWA) 8000-10,000 years ago but archeological evidence is unclear as to how many times it may have been independently domesticated, in which SWA region(s) this may have happened, and whether wild species within the Lens genus have contributed to the cultivated gene pool. In this study, we combined genotyping-by-sequencing (GBS) of 190 accessions from wild (67) and domesticated (123) lentils from the Old World with archeological information to explore the evolutionary history, domestication, and diffusion of lentils to different environments. GBS led to the discovery of 87,647 single-nucleotide polymorphisms (SNPs), which allowed us to infer the phylogeny of genus Lens. We confirmed previous studies proposing four groups within it. The only gene flow detected was between cultivated varieties and their progenitor (L. culinaris subsp. orientalis) albeit at very low levels. Nevertheless, a few putative hybrids or naturalized cultivars were identified. Within cultivated lentil, we found three geographic groups. Phylogenetics, population structure, and archeological data coincide in a scenario of protracted domestication of lentils, with two domesticated gene pools emerging in SWA. Admixed varieties are found throughout their range, suggesting a relaxed selection process. A small number of alleles involved in domestication and adaptation to climatic variables were identified. Both novel mutation and selection on standing variation are presumed to have played a role in adaptation of lentils to different environments. The results presented have implications for understanding the process of plant domestication (past), the distribution of genetic diversity in germplasm collections (present), and targeting genes in breeding programs (future).
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Affiliation(s)
- Marta Liber
- Interdisciplinary Center for Archaeology and Evolution of Human Behavior (ICArEHB), Universidade do Algarve, Faro, Portugal
- Department of Biomedical Sciences and Medicine (DCBM), Universidade do Algarve, Faro, Portugal
- Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, Portugal
| | - Isabel Duarte
- Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, Portugal
- Algarve Biomedical Center (ABC), Universidade do Algarve, Faro, Portugal
| | - Ana Teresa Maia
- Department of Biomedical Sciences and Medicine (DCBM), Universidade do Algarve, Faro, Portugal
- Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, Portugal
- Algarve Biomedical Center (ABC), Universidade do Algarve, Faro, Portugal
| | - Hugo R. Oliveira
- Interdisciplinary Center for Archaeology and Evolution of Human Behavior (ICArEHB), Universidade do Algarve, Faro, Portugal
- *Correspondence: Hugo R. Oliveira,
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First approach to pod dehiscence in faba bean: genetic and histological analyses. Sci Rep 2020; 10:17678. [PMID: 33077797 PMCID: PMC7572390 DOI: 10.1038/s41598-020-74750-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/11/2020] [Indexed: 02/08/2023] Open
Abstract
Pod dehiscence causes important yield losses in cultivated crops and therefore has been a key trait strongly selected against in crop domestication. In spite of the growing knowledge on the genetic basis of dehiscence in different crops, no information is available so far for faba bean. Here we conduct the first comprehensive study for faba bean pod dehiscence by combining, linkage mapping, comparative genomics, QTL analysis and histological examination of mature pods. Mapping of dehiscence-related genes revealed conservation of syntenic blocks among different legumes. Three QTLs were identified in faba bean chromosomes II, IV and VI, although none of them was stable across years. Histological analysis supports the convergent phenotypic evolution previously reported in cereals and related legume species but revealed a more complex pattern in faba bean. Contrary to common bean and soybean, the faba bean dehiscence zone appears to show functional equivalence to that described in crucifers. The lignified wall fiber layer, which is absent in the paucijuga primitive line Vf27, or less lignified and vacuolated in other dehiscent lines, appears to act as the major force triggering pod dehiscence in this species. While our findings, provide new insight into the mechanisms underlying faba bean dehiscence, full understanding of the molecular bases will require further studies combining precise phenotyping with genomic analysis.
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26
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Barrera-Redondo J, Piñero D, Eguiarte LE. Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners. Front Genet 2020; 11:742. [PMID: 32760427 PMCID: PMC7373799 DOI: 10.3389/fgene.2020.00742] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/22/2020] [Indexed: 01/07/2023] Open
Abstract
In the last decade, genomics and the related fields of transcriptomics and epigenomics have revolutionized the study of the domestication process in plants and animals, leading to new discoveries and new unresolved questions. Given that some domesticated taxa have been more studied than others, the extent of genomic data can range from vast to nonexistent, depending on the domesticated taxon of interest. This review is meant as a rough guide for students and academics that want to start a domestication research project using modern genomic tools, as well as for researchers already conducting domestication studies that are interested in following a genomic approach and looking for alternate strategies (cheaper or more efficient) and future directions. We summarize the theoretical and technical background needed to carry out domestication genomics, starting from the acquisition of a reference genome and genome assembly, to the sampling design for population genomics, paleogenomics, transcriptomics, epigenomics and experimental validation of domestication-related genes. We also describe some examples of the aforementioned approaches and the relevant discoveries they made to understand the domestication of the studied taxa.
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Affiliation(s)
| | | | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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27
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Renzi JP, Duchoslav M, Brus J, Hradilová I, Pechanec V, Václavek T, Machalová J, Hron K, Verdier J, Smýkal P. Physical Dormancy Release in Medicago truncatula Seeds Is Related to Environmental Variations. PLANTS (BASEL, SWITZERLAND) 2020; 9:E503. [PMID: 32295289 PMCID: PMC7238229 DOI: 10.3390/plants9040503] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/13/2020] [Accepted: 04/13/2020] [Indexed: 12/26/2022]
Abstract
Seed dormancy and timing of its release is an important developmental transition determining the survival of individuals, populations, and species in variable environments. Medicago truncatula was used as a model to study physical seed dormancy at the ecological and genetics level. The effect of alternating temperatures, as one of the causes releasing physical seed dormancy, was tested in 178 M. truncatula accessions over three years. Several coefficients of dormancy release were related to environmental variables. Dormancy varied greatly (4-100%) across accessions as well as year of experiment. We observed overall higher physical dormancy release under more alternating temperatures (35/15 °C) in comparison with less alternating ones (25/15 °C). Accessions from more arid climates released dormancy under higher experimental temperature alternations more than accessions originating from less arid environments. The plasticity of physical dormancy can probably distribute the germination through the year and act as a bet-hedging strategy in arid environments. On the other hand, a slight increase in physical dormancy was observed in accessions from environments with higher among-season temperature variation. Genome-wide association analysis identified 136 candidate genes related to secondary metabolite synthesis, hormone regulation, and modification of the cell wall. The activity of these genes might mediate seed coat permeability and, ultimately, imbibition and germination.
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Affiliation(s)
- Juan Pablo Renzi
- Instituto Nacional de Tecnología Agropecuaria, Hilario Ascasubi 8142, Argentina;
| | - Martin Duchoslav
- Department of Botany, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic; (M.D.); (I.H.)
| | - Jan Brus
- Department of Geoinformatics, Palacký University, 17. listopadu 50, 771 46 Olomouc, Czech Republic; (J.B.); (V.P.)
| | - Iveta Hradilová
- Department of Botany, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic; (M.D.); (I.H.)
| | - Vilém Pechanec
- Department of Geoinformatics, Palacký University, 17. listopadu 50, 771 46 Olomouc, Czech Republic; (J.B.); (V.P.)
| | - Tadeáš Václavek
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University, 17. listopadu 12, 771 46 Olomouc, Czech Republic; (T.V.); (J.M.); (K.H.)
| | - Jitka Machalová
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University, 17. listopadu 12, 771 46 Olomouc, Czech Republic; (T.V.); (J.M.); (K.H.)
| | - Karel Hron
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University, 17. listopadu 12, 771 46 Olomouc, Czech Republic; (T.V.); (J.M.); (K.H.)
| | - Jerome Verdier
- UMR 1345 Institut de Recherche en Horticulture et Semences, Agrocampus Ouest, INRA, Université d’Angers, SFR 4207 QUASAV, 49070 Beaucouzé, France;
| | - Petr Smýkal
- Department of Botany, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic; (M.D.); (I.H.)
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28
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Hu X, Yang L, Zhang Z. Non-destructive identification of single hard seed via multispectral imaging analysis in six legume species. PLANT METHODS 2020; 16:116. [PMID: 32863853 PMCID: PMC7448449 DOI: 10.1186/s13007-020-00659-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 08/18/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Physical dormancy (hard seed) occurs in most species of Leguminosae family and has great consequences not only for ecological adaptation but also for agricultural practice of these species. A rapid, nondestructive and on-site screening method to detect hard seed within species is fundamental important for maintaining seed vigor and germplasm storage as well as understanding seed adaptation to various environment. In this study, the potential of multispectral imaging with object-wise multivariate image analysis was evaluated as a way to identify hard and soft seeds in Acacia seyal, Galega orientulis, Glycyrrhiza glabra, Medicago sativa, Melilotus officinalis, and Thermopsis lanceolata. Principal component analysis (PCA), linear discrimination analysis (LDA), and support vector machines (SVM) methods were applied to classify hard and soft seeds according to their morphological features and spectral traits. RESULTS The performance of discrimination model via multispectral imaging analysis was varied with species. For M. officinalis, M. sativa, and G. orientulis, an excellent classification could be achieved in an independent validation data set. LDA model had the best calibration and validation abilities with the accuracy up to 90% for M. sativa. SVM got excellent seed discrimination results with classification accuracy of 91.67% and 87.5% for M. officinalis and G. orientulis, respectively. However, both LDA and SVM model failed to discriminate hard and soft seeds in A. seyal, G. glabra, and T. lanceolate. CONCLUSIONS Multispectral imaging together with multivariate analysis could be a promising technique to identify single hard seed in some legume species with high efficiency. More legume species with physical dormancy need to be studied in future research to extend the use of multispectral imaging techniques.
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Affiliation(s)
- Xiaowen Hu
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000 China
| | - Lingjie Yang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000 China
| | - Zuxin Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000 China
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29
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Yang P, Li Z, Wu C, Luo Y, Li J, Wang P, Gao X, Gao J, Feng B. Identification of Differentially Expressed Genes Involved in the Molecular Mechanism of Pericarp Elongation and Differences in Sucrose and Starch Accumulation between Vegetable and Grain Pea ( Pisum sativum L.). Int J Mol Sci 2019; 20:E6135. [PMID: 31817460 PMCID: PMC6941006 DOI: 10.3390/ijms20246135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 12/03/2019] [Accepted: 12/03/2019] [Indexed: 11/16/2022] Open
Abstract
Pea (Pisum sativum L.), as a major source of plant protein, is becoming one of the major cultivated crop species worldwide. In pea, the pericarp is an important determinant of the morphological characteristics and seed yield. To investigate the molecular mechanism of pericarp elongation as well as sucrose and starch accumulation in the pods of different pea cultivars, we performed transcriptomic analysis of the pericarp of two types of pea cultivar (vegetable pea and grain pea) using RNA-seq. A total of 239.44 Gb of clean sequence data were generated, and were aligned to the reference genome of Pisum sativum L. In the two samples, 1935 differentially expressed genes (DEGs) were identified. Among these DEGs, three antioxidant enzyme superoxide dismutase (SOD) were detected to have higher expression levels in the grain pea pericarps at the pod-elongating stages. Otherwise, five peroxidase (POD)-encoding genes were detected to have lower expression levels in the vegetative pericarps at the development stage of pea pod growth. Furthermore, genes related to starch and sucrose metabolism in the pea pod, such as SUS, INV, FBA, TPI, ADPase, SBE, SSS, and GBSS, were found to be differentially expressed. The RNA-seq data were validated through real-time quantitative RT-PCR of 13 randomly selected genes. Our findings provide the gene expression profile of, as well as differential expression information on, the two pea cultivars, which will lay the foundation for further studies on pod development and nutrition accumulation in the pea and provide valuable information for pea cultivar improvement.
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Affiliation(s)
- Pu Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (P.Y.); (Z.L.); (C.W.); (Y.L.); (J.L.); (P.W.); (X.G.); (J.G.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China
| | - Zhonghao Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (P.Y.); (Z.L.); (C.W.); (Y.L.); (J.L.); (P.W.); (X.G.); (J.G.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China
| | - Caoyang Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (P.Y.); (Z.L.); (C.W.); (Y.L.); (J.L.); (P.W.); (X.G.); (J.G.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China
| | - Yan Luo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (P.Y.); (Z.L.); (C.W.); (Y.L.); (J.L.); (P.W.); (X.G.); (J.G.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China
| | - Jing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (P.Y.); (Z.L.); (C.W.); (Y.L.); (J.L.); (P.W.); (X.G.); (J.G.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China
| | - Pengke Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (P.Y.); (Z.L.); (C.W.); (Y.L.); (J.L.); (P.W.); (X.G.); (J.G.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China
| | - Xiaoli Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (P.Y.); (Z.L.); (C.W.); (Y.L.); (J.L.); (P.W.); (X.G.); (J.G.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China
| | - Jinfeng Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (P.Y.); (Z.L.); (C.W.); (Y.L.); (J.L.); (P.W.); (X.G.); (J.G.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China
| | - Baili Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (P.Y.); (Z.L.); (C.W.); (Y.L.); (J.L.); (P.W.); (X.G.); (J.G.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China
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Shtark OY, Puzanskiy RK, Avdeeva GS, Yurkov AP, Smolikova GN, Yemelyanov VV, Kliukova MS, Shavarda AL, Kirpichnikova AA, Zhernakov AI, Afonin AM, Tikhonovich IA, Zhukov VA, Shishova MF. Metabolic alterations in pea leaves during arbuscular mycorrhiza development. PeerJ 2019; 7:e7495. [PMID: 31497392 PMCID: PMC6709666 DOI: 10.7717/peerj.7495] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 07/16/2019] [Indexed: 12/20/2022] Open
Abstract
Arbuscular mycorrhiza (AM) is known to be a mutually beneficial plant-fungal symbiosis; however, the effect of mycorrhization is heavily dependent on multiple biotic and abiotic factors. Therefore, for the proper employment of such plant-fungal symbiotic systems in agriculture, a detailed understanding of the molecular basis of the plant developmental response to mycorrhization is needed. The aim of this work was to uncover the physiological and metabolic alterations in pea (Pisum sativum L.) leaves associated with mycorrhization at key plant developmental stages. Plants of pea cv. Finale were grown in constant environmental conditions under phosphate deficiency. The plants were analyzed at six distinct time points, which corresponded to certain developmental stages of the pea: I: 7 days post inoculation (DPI) when the second leaf is fully unfolded with one pair of leaflets and a simple tendril; II: 21 DPI at first leaf with two pairs of leaflets and a complex tendril; III: 32 DPI when the floral bud is enclosed; IV: 42 DPI at the first open flower; V: 56 DPI when the pod is filled with green seeds; and VI: 90-110 DPI at the dry harvest stage. Inoculation with Rhizophagus irregularis had no effect on the fresh or dry shoot weight, the leaf photochemical activity, accumulation of chlorophyll a, b or carotenoids. However, at stage III (corresponding to the most active phase of mycorrhiza development), the number of internodes between cotyledons and the youngest completely developed leaf was lower in the inoculated plants than in those without inoculation. Moreover, inoculation extended the vegetation period of the host plants, and resulted in increase of the average dry weight per seed at stage VI. The leaf metabolome, as analyzed with GC-MS, included about three hundred distinct metabolites and showed a strong correlation with plant age, and, to a lesser extent, was influenced by mycorrhization. Metabolic shifts influenced the levels of sugars, amino acids and other intermediates of nitrogen and phosphorus metabolism. The use of unsupervised dimension reduction methods showed that (i) at stage II, the metabolite spectra of inoculated plants were similar to those of the control, and (ii) at stages IV and V, the leaf metabolic profiles of inoculated plants shifted towards the profiles of the control plants at earlier developmental stages. At stage IV the inoculated plants exhibited a higher level of metabolism of nitrogen, organic acids, and lipophilic compounds in comparison to control plants. Thus, mycorrhization led to the retardation of plant development, which was also associated with higher seed biomass accumulation in plants with an extended vegetation period. The symbiotic crosstalk between host plant and AM fungi leads to alterations in several biochemical pathways the details of which need to be elucidated in further studies.
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Affiliation(s)
- Oksana Y. Shtark
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Roman K. Puzanskiy
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
- Laboratory of Dynamics of Arctic Vegetation, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Galina S. Avdeeva
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Andrey P. Yurkov
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | | | | | - Marina S. Kliukova
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Alexey L. Shavarda
- Center for Molecular and Cell Technologies, St. Petersburg State University, St. Petersburg, Russia
| | | | - Aleksandr I. Zhernakov
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
| | - Alexey M. Afonin
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
| | - Igor A. Tikhonovich
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Vladimir A. Zhukov
- Department of Biotechnology, All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, Russia
| | - Maria F. Shishova
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
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Janská A, Pecková E, Sczepaniak B, Smýkal P, Soukup A. The role of the testa during the establishment of physical dormancy in the pea seed. ANNALS OF BOTANY 2019; 123:815-829. [PMID: 30534972 PMCID: PMC6526324 DOI: 10.1093/aob/mcy213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 11/08/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND A water-impermeable testa acts as a barrier to a seed's imbibition, thereby imposing dormancy. The physical and functional properties of the macrosclereids are thought to be critical determinants of dormancy; however, the mechanisms underlying the maintenance of and release from dormancy in pea are not well understood. METHODS Seeds of six pea accessions of contrasting dormancy type were tested for their ability to imbibe and the permeability of their testa was evaluated. Release from dormancy was monitored following temperature oscillation, lipid removal and drying. Histochemical and microscopic approaches were used to characterize the structure of the testa. KEY RESULTS The strophiole was identified as representing the major site for the entry of water into non-dormant seeds, while water entry into dormant seeds was distributed rather than localized. The major barrier for water uptake in dormant seeds was the upper section of the macrosclereids, referred to as the 'light line'. Dormancy could be released by thermocycling, dehydration or chloroform treatment. Assays based on either periodic acid or ruthenium red were used to visualize penetration through the testa. Lipids were detected within a subcuticular waxy layer in both dormant and non-dormant seeds. The waxy layer and the light line both formed at the same time as the establishment of secondary cell walls at the tip of the macrosclereids. CONCLUSIONS The light line was identified as the major barrier to water penetration in dormant seeds. Its outer border abuts a waxy subcuticular layer, which is consistent with the suggestion that the light line represents the interface between two distinct environments - the waxy subcuticular layer and the cellulose-rich secondary cell wall. The mechanistic basis of dormancy break includes changes in the testa's lipid layer, along with the mechanical disruption induced by oscillation in temperature and by a decreased moisture content of the embryo.
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Affiliation(s)
- Anna Janská
- Department of Experimental Plant Biology, Charles University, Prague, Czech Republic
| | - Eva Pecková
- Department of Experimental Plant Biology, Charles University, Prague, Czech Republic
| | - Bogna Sczepaniak
- Department of Experimental Plant Biology, Charles University, Prague, Czech Republic
| | - Petr Smýkal
- Department of Botany, Palacký University in Olomouc, Olomouc, Czech Republic
| | - Aleš Soukup
- Department of Experimental Plant Biology, Charles University, Prague, Czech Republic
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Nováková E, Zablatzká L, Brus J, Nesrstová V, Hanáček P, Kalendar R, Cvrčková F, Majeský Ľ, Smýkal P. Allelic Diversity of Acetyl Coenzyme A Carboxylase accD/ bccp Genes Implicated in Nuclear-Cytoplasmic Conflict in the Wild and Domesticated Pea ( Pisum sp.). Int J Mol Sci 2019; 20:E1773. [PMID: 30974846 PMCID: PMC6480052 DOI: 10.3390/ijms20071773] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/04/2019] [Accepted: 04/08/2019] [Indexed: 01/09/2023] Open
Abstract
Reproductive isolation is an important component of species differentiation. The plastid accD gene coding for the acetyl-CoA carboxylase subunit and the nuclear bccp gene coding for the biotin carboxyl carrier protein were identified as candidate genes governing nuclear-cytoplasmic incompatibility in peas. We examined the allelic diversity in a set of 195 geographically diverse samples of both cultivated (Pisum sativum, P. abyssinicum) and wild (P. fulvum and P. elatius) peas. Based on deduced protein sequences, we identified 34 accD and 31 bccp alleles that are partially geographically and genetically structured. The accD is highly variable due to insertions of tandem repeats. P. fulvum and P. abyssinicum have unique alleles and combinations of both genes. On the other hand, partial overlap was observed between P. sativum and P. elatius. Mapping of protein sequence polymorphisms to 3D structures revealed that most of the repeat and indel polymorphisms map to sequence regions that could not be modeled, consistent with this part of the protein being less constrained by requirements for precise folding than the enzymatically active domains. The results of this study are important not only from an evolutionary point of view but are also relevant for pea breeding when using more distant wild relatives.
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Affiliation(s)
- Eliška Nováková
- Department of Botany, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
| | - Lenka Zablatzká
- Department of Botany, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
| | - Jan Brus
- Department of Geoinformatics, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
| | - Viktorie Nesrstová
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University, 78371 Olomouc, Czech Republic.
| | - Pavel Hanáček
- Department of Plant Biology, Faculty of Agronomy, Mendel University, 61300 Brno, Czech Republic.
| | - Ruslan Kalendar
- National Center for Biotechnology, Astana 010000, Kazakhstan.
- Department of Agricultural Sciences, Viikki Plant Science Centre and Helsinki Sustainability Centre, University of Helsinki, FI-00014 Helsinki, Finland.
| | - Fatima Cvrčková
- Department of Experimental Plant Biology, Faculty of Sciences, Charles University, 12844 Prague, Czech Republic.
| | - Ľuboš Majeský
- Department of Botany, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
| | - Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
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Neu E, Domes HS, Menz I, Kaufmann H, Linde M, Debener T. Interaction of roses with a biotrophic and a hemibiotrophic leaf pathogen leads to differences in defense transcriptome activation. PLANT MOLECULAR BIOLOGY 2019; 99:299-316. [PMID: 30706286 DOI: 10.1007/s11103-018-00818-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 12/22/2018] [Indexed: 05/09/2023]
Abstract
Transcriptomic analysis resulted in the upregulation of the genes related to common defense mechanisms for black spot and the downregulation of the genes related to photosynthesis and cell wall modification for powdery mildew. Plant pathogenic fungi successfully colonize their hosts by manipulating the host defense mechanisms, which is accompanied by major transcriptome changes in the host. To characterize compatible plant pathogen interactions at early stages of infection by the obligate biotrophic fungus Podosphaera pannosa, which causes powdery mildew, and the hemibiotrophic fungus Diplocarpon rosae, which causes black spot, we analyzed changes in the leaf transcriptome after the inoculation of detached rose leaves with each pathogen. In addition, we analyzed differences in the transcriptomic changes inflicted by both pathogens as a first step to characterize specific infection strategies. Transcriptomic changes were analyzed using next-generation sequencing based on the massive analysis of cDNA ends approach, which was validated using high-throughput qPCR. We identified a large number of differentially regulated genes. A common set of the differentially regulated genes comprised of pathogenesis-related (PR) genes, such as of PR10 homologs, chitinases and defense-related transcription factors, such as various WRKY genes, indicating a conserved but insufficient PTI [pathogen associated molecular pattern (PAMP) triggered immunity] reaction. Surprisingly, most of the differentially regulated genes were specific to the interactions with either P. pannosa or D. rosae. Specific regulation in response to D. rosae was detected for genes from the phenylpropanoid and flavonoid pathways and for individual PR genes, such as paralogs of PR1 and PR5, and other factors of the salicylic acid signaling pathway. Differently, inoculation with P. pannosa leads in addition to the general pathogen response to a downregulation of genes related to photosynthesis and cell wall modification.
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Affiliation(s)
- Enzo Neu
- Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany
- KWS SAAT SE, 37574, Einbeck, Germany
| | - Helena Sophia Domes
- Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany
| | - Ina Menz
- Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany
| | - Helgard Kaufmann
- Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany
| | - Marcus Linde
- Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany
| | - Thomas Debener
- Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany.
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Cechová M, Hradilová I, Smýkal P, Barták P, Bednář P. Utilization of atmospheric solids analysis probe mass spectrometry for analysis of fatty acids on seed surface. Anal Bioanal Chem 2019; 411:1169-1180. [PMID: 30617396 DOI: 10.1007/s00216-018-1551-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/06/2018] [Accepted: 12/10/2018] [Indexed: 10/27/2022]
Abstract
Atmospheric solids analysis probe mass spectrometry (ASAP-MS) was used for the first time for direct surface analysis of plant material. It can be readily used for surface analysis of whole and intact pea seeds and their seed coats, and for the study of the profile of fatty acids on the outer surface. Furthermore, ASAP-MS in combination with multivariate statistics allowed classification of pea genotypes with respect to physical dormancy and investigation of related biological markers. Hexacosanoic and octacosanoic acids were suggested to be important markers likely influencing water transport through the seed coat into the embryo (with the highest significance for dormant L100 genotype). ASAP-MS provided higher selectivity and better signal of fatty acids compared to (MA)LDI-MS (laser desorption ionization mass spectrometry either matrix free or matrix assisted) providing on the other hand spatial distribution information and results obtained by both methods are mutually supportive. The developed ASAP-MS method and obtained results can be widely utilized in biological, food, and agricultural research. Graphical abstract ᅟ.
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Affiliation(s)
- Monika Cechová
- Regional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacký University, 17. Listopadu 12, 771 46, Olomouc, Czech Republic
| | - Iveta Hradilová
- Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71, Olomouc, Czech Republic
| | - Petr Smýkal
- Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71, Olomouc, Czech Republic
| | - Petr Barták
- Regional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacký University, 17. Listopadu 12, 771 46, Olomouc, Czech Republic
| | - Petr Bednář
- Regional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacký University, 17. Listopadu 12, 771 46, Olomouc, Czech Republic.
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Rau D, Murgia ML, Rodriguez M, Bitocchi E, Bellucci E, Fois D, Albani D, Nanni L, Gioia T, Santo D, Marcolungo L, Delledonne M, Attene G, Papa R. Genomic dissection of pod shattering in common bean: mutations at non-orthologous loci at the basis of convergent phenotypic evolution under domestication of leguminous species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:693-714. [PMID: 30422331 DOI: 10.1111/tpj.14155] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/14/2018] [Accepted: 10/30/2018] [Indexed: 05/05/2023]
Abstract
The complete or partial loss of shattering ability occurred independently during the domestication of several crops. Therefore, the study of this trait can provide an understanding of the link between phenotypic and molecular convergent evolution. The genetic dissection of 'pod shattering' in Phaseolus vulgaris is achieved here using a population of introgression lines and next-generation sequencing techniques. The 'occurrence' of the indehiscent phenotype (indehiscent versus dehiscent) depends on a major locus on chromosome 5. Furthermore, at least two additional genes are associated with the 'level' of shattering (number of shattering pods per plant: low versus high) and the 'mode' of shattering (non-twisting versus twisting pods), with all of these loci contributing to the phenotype by epistatic interactions. Comparative mapping indicates that the major gene identified on common bean chromosome 5 corresponds to one of the four quantitative trait loci for pod shattering in Vigna unguiculata. None of the loci identified comprised genes that are homologs of the known shattering genes in Glycine max. Therefore, although convergent domestication can be determined by mutations at orthologous loci, this was only partially true for P. vulgaris and V. unguiculata, which are two phylogenetically closely related crop species, and this was not the case for the more distant P. vulgaris and G. max. Conversely, comparative mapping suggests that the convergent evolution of the indehiscent phenotype arose through mutations in different genes from the same underlying gene networks that are involved in secondary cell-wall biosynthesis and lignin deposition patterning at the pod level.
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Affiliation(s)
- Domenico Rau
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. De Nicola, 07100, Sassari, Italy
| | - Maria L Murgia
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. De Nicola, 07100, Sassari, Italy
| | - Monica Rodriguez
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. De Nicola, 07100, Sassari, Italy
| | - Elena Bitocchi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Elisa Bellucci
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Davide Fois
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. De Nicola, 07100, Sassari, Italy
| | - Diego Albani
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. De Nicola, 07100, Sassari, Italy
| | - Laura Nanni
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Tania Gioia
- Scuola di Scienze Agrarie, Forestali, Alimentari e Ambientali, Università degli Studi della Basilicata, viale dell'Ateneo Lucano 10, 85100, Potenza, Italy
| | - Debora Santo
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Luca Marcolungo
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Cà Vignal 1, Strada Le Grazie 15, 37134, Verona, Italy
| | - Massimo Delledonne
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Cà Vignal 1, Strada Le Grazie 15, 37134, Verona, Italy
| | - Giovanna Attene
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. De Nicola, 07100, Sassari, Italy
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
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Hradilová I, Duchoslav M, Brus J, Pechanec V, Hýbl M, Kopecký P, Smržová L, Štefelová N, Vaclávek T, Bariotakis M, Machalová J, Hron K, Pirintsos S, Smýkal P. Variation in wild pea ( Pisum sativum subsp. elatius) seed dormancy and its relationship to the environment and seed coat traits. PeerJ 2019; 7:e6263. [PMID: 30656074 PMCID: PMC6336014 DOI: 10.7717/peerj.6263] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/11/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Seed germination is one of the earliest key events in the plant life cycle. The timing of transition from seed to seedling is an important developmental stage determining the survival of individuals that influences the status of populations and species. Because of wide geographical distribution and occurrence in diverse habitats, wild pea (Pisum sativum subsp. elatius) offers an excellent model to study physical type of seed dormancy in an ecological context. This study addresses the gap in knowledge of association between the seed dormancy, seed properties and environmental factors, experimentally testing oscillating temperature as dormancy release clue. METHODS Seeds of 97 pea accessions were subjected to two germination treatments (oscillating temperatures of 25/15 °C and 35/15 °C) over 28 days. Germination pattern was described using B-spline coefficients that aggregate both final germination and germination speed. Relationships between germination pattern and environmental conditions at the site of origin (soil and bioclimatic variables extracted from WorldClim 2.0 and SoilGrids databases) were studied using principal component analysis, redundancy analysis and ecological niche modelling. Seeds were analyzed for the seed coat thickness, seed morphology, weight and content of proanthocyanidins (PA). RESULTS Seed total germination ranged from 0% to 100%. Cluster analysis of germination patterns of seeds under two temperature treatments differentiated the accessions into three groups: (1) non-dormant (28 accessions, mean germination of 92%), (2) dormant at both treatments (29 acc., 15%) and (3) responsive to increasing temperature range (41 acc., with germination change from 15 to 80%). Seed coat thickness differed between groups with dormant and responsive accessions having thicker testa (median 138 and 140 µm) than non-dormant ones (median 84 mm). The total PA content showed to be higher in the seed coat of dormant (mean 2.18 mg g-1) than those of non-dormant (mean 1.77 mg g-1) and responsive accessions (mean 1.87 mg g-1). Each soil and bioclimatic variable and also germination responsivity (representing synthetic variable characterizing germination pattern of seeds) was spatially clustered. However, only one environmental variable (BIO7, i.e., annual temperature range) was significantly related to germination responsivity. Non-dormant and responsive accessions covered almost whole range of BIO7 while dormant accessions are found in the environment with higher annual temperature, smaller temperature variation, seasonality and milder winter. Ecological niche modelling showed a more localized potential distribution of dormant group. Seed dormancy in the wild pea might be part of a bet-hedging mechanism for areas of the Mediterranean basin with more unpredictable water availability in an otherwise seasonal environment. This study provides the framework for analysis of environmental aspects of physical seed dormancy.
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Affiliation(s)
- Iveta Hradilová
- Department of Botany, Palacký University Olomouc, Olomouc, Czech Republic
| | - Martin Duchoslav
- Department of Botany, Palacký University Olomouc, Olomouc, Czech Republic
| | - Jan Brus
- Department of Geoinformatics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Vilém Pechanec
- Department of Geoinformatics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Miroslav Hýbl
- The Centre of the Region Haná for Biotechnological and Agricultural Research, Crop Research Institute, Prague, Olomouc, Czech Republic
| | - Pavel Kopecký
- The Centre of the Region Haná for Biotechnological and Agricultural Research, Crop Research Institute, Prague, Olomouc, Czech Republic
| | - Lucie Smržová
- Department of Botany, Palacký University Olomouc, Olomouc, Czech Republic
| | - Nikola Štefelová
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Tadeáš Vaclávek
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Michael Bariotakis
- Department of Biology and Botanical Garden, University of Crete, Heraklion, Greece
| | - Jitka Machalová
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Karel Hron
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Stergios Pirintsos
- Department of Biology and Botanical Garden, University of Crete, Heraklion, Greece
| | - Petr Smýkal
- Department of Botany, Palacký University Olomouc, Olomouc, Czech Republic
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37
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Hradilová I, Duchoslav M, Brus J, Pechanec V, Hýbl M, Kopecký P, Smržová L, Štefelová N, Vaclávek T, Bariotakis M, Machalová J, Hron K, Pirintsos S, Smýkal P. Variation in wild pea ( Pisum sativum subsp. elatius) seed dormancy and its relationship to the environment and seed coat traits. PeerJ 2019; 7:e6263. [PMID: 30656074 DOI: 10.7717/peerj6263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/11/2018] [Indexed: 05/19/2023] Open
Abstract
BACKGROUND Seed germination is one of the earliest key events in the plant life cycle. The timing of transition from seed to seedling is an important developmental stage determining the survival of individuals that influences the status of populations and species. Because of wide geographical distribution and occurrence in diverse habitats, wild pea (Pisum sativum subsp. elatius) offers an excellent model to study physical type of seed dormancy in an ecological context. This study addresses the gap in knowledge of association between the seed dormancy, seed properties and environmental factors, experimentally testing oscillating temperature as dormancy release clue. METHODS Seeds of 97 pea accessions were subjected to two germination treatments (oscillating temperatures of 25/15 °C and 35/15 °C) over 28 days. Germination pattern was described using B-spline coefficients that aggregate both final germination and germination speed. Relationships between germination pattern and environmental conditions at the site of origin (soil and bioclimatic variables extracted from WorldClim 2.0 and SoilGrids databases) were studied using principal component analysis, redundancy analysis and ecological niche modelling. Seeds were analyzed for the seed coat thickness, seed morphology, weight and content of proanthocyanidins (PA). RESULTS Seed total germination ranged from 0% to 100%. Cluster analysis of germination patterns of seeds under two temperature treatments differentiated the accessions into three groups: (1) non-dormant (28 accessions, mean germination of 92%), (2) dormant at both treatments (29 acc., 15%) and (3) responsive to increasing temperature range (41 acc., with germination change from 15 to 80%). Seed coat thickness differed between groups with dormant and responsive accessions having thicker testa (median 138 and 140 µm) than non-dormant ones (median 84 mm). The total PA content showed to be higher in the seed coat of dormant (mean 2.18 mg g-1) than those of non-dormant (mean 1.77 mg g-1) and responsive accessions (mean 1.87 mg g-1). Each soil and bioclimatic variable and also germination responsivity (representing synthetic variable characterizing germination pattern of seeds) was spatially clustered. However, only one environmental variable (BIO7, i.e., annual temperature range) was significantly related to germination responsivity. Non-dormant and responsive accessions covered almost whole range of BIO7 while dormant accessions are found in the environment with higher annual temperature, smaller temperature variation, seasonality and milder winter. Ecological niche modelling showed a more localized potential distribution of dormant group. Seed dormancy in the wild pea might be part of a bet-hedging mechanism for areas of the Mediterranean basin with more unpredictable water availability in an otherwise seasonal environment. This study provides the framework for analysis of environmental aspects of physical seed dormancy.
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Affiliation(s)
- Iveta Hradilová
- Department of Botany, Palacký University Olomouc, Olomouc, Czech Republic
| | - Martin Duchoslav
- Department of Botany, Palacký University Olomouc, Olomouc, Czech Republic
| | - Jan Brus
- Department of Geoinformatics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Vilém Pechanec
- Department of Geoinformatics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Miroslav Hýbl
- The Centre of the Region Haná for Biotechnological and Agricultural Research, Crop Research Institute, Prague, Olomouc, Czech Republic
| | - Pavel Kopecký
- The Centre of the Region Haná for Biotechnological and Agricultural Research, Crop Research Institute, Prague, Olomouc, Czech Republic
| | - Lucie Smržová
- Department of Botany, Palacký University Olomouc, Olomouc, Czech Republic
| | - Nikola Štefelová
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Tadeáš Vaclávek
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Michael Bariotakis
- Department of Biology and Botanical Garden, University of Crete, Heraklion, Greece
| | - Jitka Machalová
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Karel Hron
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Stergios Pirintsos
- Department of Biology and Botanical Garden, University of Crete, Heraklion, Greece
| | - Petr Smýkal
- Department of Botany, Palacký University Olomouc, Olomouc, Czech Republic
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Trněný O, Brus J, Hradilová I, Rathore A, Das RR, Kopecký P, Coyne CJ, Reeves P, Richards C, Smýkal P. Molecular Evidence for Two Domestication Events in the Pea Crop. Genes (Basel) 2018; 9:genes9110535. [PMID: 30404223 PMCID: PMC6265838 DOI: 10.3390/genes9110535] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 10/25/2018] [Accepted: 10/29/2018] [Indexed: 12/02/2022] Open
Abstract
Pea, one of the founder crops from the Near East, has two wild species: Pisum sativum subsp. elatius, with a wide distribution centered in the Mediterranean, and P. fulvum, which is restricted to Syria, Lebanon, Israel, Palestine and Jordan. Using genome wide analysis of 11,343 polymorphic single nucleotide polymorphisms (SNPs) on a set of wild P. elatius (134) and P. fulvum (20) and 74 domesticated accessions (64 P. sativum landraces and 10 P. abyssinicum), we demonstrated that domesticated P. sativum and the Ethiopian pea (P. abyssinicum) were derived from different P. elatius genepools. Therefore, pea has at least two domestication events. The analysis does not support a hybrid origin of P. abyssinicum, which was likely introduced into Ethiopia and Yemen followed by eco-geographic adaptation. Both P. sativum and P. abyssinicum share traits that are typical of domestication, such as non-dormant seeds. Non-dormant seeds were also found in several wild P. elatius accessions which could be the result of crop to wild introgression or natural variation that may have been present during pea domestication. A sub-group of P. elatius overlaps with P. sativum landraces. This may be a consequence of bidirectional gene-flow or may suggest that this group of P. elatius is the closest extant wild relative of P. sativum.
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Affiliation(s)
- Oldřich Trněný
- Agricultural Research Ltd., 66441 Troubsko, Czech Republic.
| | - Jan Brus
- Department of Geoinformatics, Palacký University, 783 71 Olomouc, Czech Republic.
| | - Iveta Hradilová
- Department of Botany, Palacký University, 783 71 Olomouc, Czech Republic.
| | - Abhishek Rathore
- The International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana 502324, India.
| | - Roma R Das
- The International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana 502324, India.
| | - Pavel Kopecký
- Crop Research Institute, The Centre of the Region Haná for biotechnological and Agricultural Research, 783 71 Olomouc, Czech Republic.
| | - Clarice J Coyne
- United States Department of Agriculture, Washington State University, Pullman, WA 99164-6402, USA.
| | - Patrick Reeves
- United States Department of Agriculture, National Laboratory for Genetic Resources Preservation, Fort Collins, CO 80521, USA.
| | - Christopher Richards
- United States Department of Agriculture, National Laboratory for Genetic Resources Preservation, Fort Collins, CO 80521, USA.
| | - Petr Smýkal
- Department of Botany, Palacký University, 783 71 Olomouc, Czech Republic.
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Pod Shattering: A Homologous Series of Variation Underlying Domestication and an Avenue for Crop Improvement. AGRONOMY-BASEL 2018. [DOI: 10.3390/agronomy8080137] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In wild habitats, fruit dehiscence is a critical strategy for seed dispersal; however, in cultivated crops it is one of the major sources of yield loss. Therefore, indehiscence of fruits, pods, etc., was likely to be one of the first traits strongly selected in crop domestication. Even with the historical selection against dehiscence in early domesticates, it is a trait still targeted in many breeding programs, particularly in minor or underutilized crops. Here, we review dehiscence in pulse (grain legume) crops, which are of growing importance as a source of protein in human and livestock diets, and which have received less attention than cereal crops and the model plant Arabidopsis thaliana. We specifically focus on the (i) history of indehiscence in domestication across legumes, (ii) structures and the mechanisms involved in shattering, (iii) the molecular pathways underlying this important trait, (iv) an overview of the extent of crop losses due to shattering, and the effects of environmental factors on shattering, and, (v) efforts to reduce shattering in crops. While our focus is mainly pulse crops, we also included comparisons to crucifers and cereals because there is extensive research on shattering in these taxa.
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Ramakrishna G, Kaur P, Nigam D, Chaduvula PK, Yadav S, Talukdar A, Singh NK, Gaikwad K. Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits. BMC PLANT BIOLOGY 2018; 18:141. [PMID: 29986650 PMCID: PMC6038289 DOI: 10.1186/s12870-018-1341-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 06/05/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Water permeability governed by seed coat is a major facet of seed crops, especially soybean, whose seeds lack physiological dormancy and experience rapid deterioration in seed viability under prolonged storage. Moreover, the physiological and chemical characteristics of soybean seeds are known to vary with seed coat color. Thus, to underpin the genes controlling water permeability in soybean seeds, we carried out an in-depth characterization of the associated genomic variation. RESULTS In the present study, we have analyzed genomic variation between cultivated soybean and its wild progenitor with implications on seed permeability, a trait related to seed storability. Whole genome resequencing of G.max and G. soja, identified SNPs and InDels which were further characterized on the basis of their genomic location and impact on gene expression. Chromosomal density distribution of the variation was assessed across the genome and genes carrying SNPs and InDels were characterized into different metabolic pathways. Seed hardiness is a complex trait that is affected by the allelic constitution of a genetic locus as well as by a tricky web of plant hormone interactions. Seven genes that hold a probable role in the determination of seed permeability were selected and their expression differences at different stages of water imbibition were analyzed. Variant interaction network derived 205 downstream interacting partners of 7 genes confirmed their role in seed related traits. Interestingly, genes encoding for Type I- Inositol polyphosphate 5 phosphatase1 and E3 Ubiquitin ligase could differentiate parental genotypes, revealed protein conformational deformations and were found to segregate among RILs in coherence with their permeability scores. The 2 identified genes, thus showed a preliminary association with the desirable permeability characteristics. CONCLUSION In the light of above outcomes, 2 genes were identified that revealed preliminary, but a relevant association with soybean seed permeability trait and hence could serve as a primary material for understanding the molecular pathways controlling seed permeability traits in soybean.
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Affiliation(s)
- G. Ramakrishna
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Parampreet Kaur
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Deepti Nigam
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Pavan K. Chaduvula
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Sangita Yadav
- ICAR- IARI, Division of Seed Science and Technology, Pusa Campus, New Delhi, 110012 India
| | - Akshay Talukdar
- ICAR- IARI, Division of Genetics, Pusa Campus, New Delhi, India
| | - Nagendra Kumar Singh
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Kishor Gaikwad
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
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Hao X, Yang T, Liu R, Hu J, Yao Y, Burlyaeva M, Wang Y, Ren G, Zhang H, Wang D, Chang J, Zong X. An RNA Sequencing Transcriptome Analysis of Grasspea ( Lathyrus sativus L.) and Development of SSR and KASP Markers. FRONTIERS IN PLANT SCIENCE 2017; 8:1873. [PMID: 29163598 PMCID: PMC5671653 DOI: 10.3389/fpls.2017.01873] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/13/2017] [Indexed: 05/28/2023]
Abstract
Grasspea (Lathyrus sativus L., 2n = 14) has great agronomic potential because of its ability to survive under extreme conditions, such as drought and flood. However, this legume is less investigated because of its sparse genomic resources and very slow breeding process. In this study, 570 million quality-filtered and trimmed cDNA sequence reads with total length of over 82 billion bp were obtained using the Illumina NextSeqTM 500 platform. Approximately two million contigs and 142,053 transcripts were assembled from our RNA-Seq data, which resulted in 27,431 unigenes with an average length of 1,250 bp and maximum length of 48,515 bp. The unigenes were of high-quality. For example, the stay-green (SGR) gene of grasspea was aligned with the SGR gene of pea with high similarity. Among these unigenes, 3,204 EST-SSR primers were designed, 284 of which were randomly chosen for validation. Of these validated unigenes, 87 (30.6%) EST-SSR primers produced polymorphic amplicons among 43 grasspea accessions selected from different geographical locations. Meanwhile, 146,406 SNPs were screened and 50 SNP loci were randomly chosen for the kompetitive allele-specific PCR (KASP) validation. Over 80% (42) SNP loci were successfully transformed to KASP markers. Comparison of the dendrograms according to the SSR and KASP markers showed that the different marker systems are partially consistent with the dendrogram constructed in our study.
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Affiliation(s)
- Xiaopeng Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Institute of Crop Germplasm Resources, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Tao Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rong Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinguo Hu
- USDA-ARS Western Regional Plant Introduction Station, Pullman, WA, United States
| | - Yang Yao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Marina Burlyaeva
- Department of Leguminous Crops Genetic Resources, N.I.Vavilov All-Russian Institute of Plant Genetic Resources, St. Petersburg, Russia
| | - Yan Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Institute of Crop Germplasm Resources, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Guixing Ren
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongyan Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dong Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianwu Chang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Institute of Crop Germplasm Resources, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Xuxiao Zong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Cechová M, Válková M, Hradilová I, Janská A, Soukup A, Smýkal P, Bednář P. Towards Better Understanding of Pea Seed Dormancy Using Laser Desorption/Ionization Mass Spectrometry. Int J Mol Sci 2017; 18:E2196. [PMID: 29065445 PMCID: PMC5666877 DOI: 10.3390/ijms18102196] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/11/2017] [Accepted: 10/16/2017] [Indexed: 02/07/2023] Open
Abstract
Seed coats of six pea genotypes contrasting in dormancy were studied by laser desorption/ionization mass spectrometry (LDI-MS). Multivariate statistical analysis discriminated dormant and non-dormant seeds in mature dry state. Separation between dormant and non-dormant types was observed despite important markers of particular dormant genotypes differ from each other. Normalized signals of long-chain hydroxylated fatty acids (HLFA) in dormant JI64 genotype seed coats were significantly higher than in other genotypes. These compounds seem to be important markers likely influencing JI64 seed imbibition and germination. HLFA importance was supported by study of recombinant inbred lines (JI64xJI92) contrasting in dormancy but similar in other seed properties. Furthemore HLFA distribution in seed coat was studied by mass spectrometry imaging. HLFA contents in strophiole and hilum are significantly lower compared to other parts indicating their role in water uptake. Results from LDI-MS experiments are useful in understanding (physical) dormancy (first phases of germination) mechanism and properties related to food processing technologies (e.g., seed treatment by cooking).
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Affiliation(s)
- Monika Cechová
- Regional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacký University, 17. Listopadu 12, 771 46 Olomouc, Czech Republic.
| | - Markéta Válková
- Regional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacký University, 17. Listopadu 12, 771 46 Olomouc, Czech Republic.
| | - Iveta Hradilová
- Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic.
| | - Anna Janská
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic.
| | - Aleš Soukup
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic.
| | - Petr Smýkal
- Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic.
| | - Petr Bednář
- Regional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacký University, 17. Listopadu 12, 771 46 Olomouc, Czech Republic.
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Das A, Kim DW, Khadka P, Rakwal R, Rohila JS. Unraveling Key Metabolomic Alterations in Wheat Embryos Derived from Freshly Harvested and Water-Imbibed Seeds of Two Wheat Cultivars with Contrasting Dormancy Status. FRONTIERS IN PLANT SCIENCE 2017; 8:1203. [PMID: 28747920 PMCID: PMC5506182 DOI: 10.3389/fpls.2017.01203] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/26/2017] [Indexed: 05/20/2023]
Abstract
Untimely rains in wheat fields during harvest season can cause pre-harvest sprouting (PHS), which deteriorates the yield and quality of wheat crop. Metabolic homeostasis of the embryo plays a role in seed dormancy, determining the status of the maturing grains either as dormant (PHS-tolerant) or non-dormant (PHS-susceptible). Very little is known for direct measurements of global metabolites in embryonic tissues of dormant and non-dormant wheat seeds. In this study, physiologically matured and freshly harvested wheat seeds of PHS-tolerant (cv. Sukang, dormant) and PHS-susceptible (cv. Baegjoong, non-dormant) cultivars were water-imbibed, and the isolated embryos were subjected to high-throughput, global non-targeted metabolomic profiling. A careful comparison of identified metabolites between Sukang and Baegjoong embryos at 0 and 48 h after imbibition revealed that several key metabolic pathways [such as: lipids, fatty acids, oxalate, hormones, the raffinose family of oligosaccharides (RFOs), and amino acids] and phytochemicals were differentially regulated between dormant and non-dormant varieties. Most of the membrane lipids were highly reduced in Baegjoong compared to Sukang, which indicates that the cell membrane instability in response to imbibition could also be a key factor in non-dormant wheat varieties for their untimely germination. This study revealed that several key marker metabolites (e.g., RFOs: glucose, fructose, maltose, and verbascose), were highly expressed in Baegjoong after imbibition. Furthermore, the data showed that the key secondary metabolites and phytochemicals (vitexin, chrysoeriol, ferulate, salidroside and gentisic acid), with known antioxidant properties, were comparatively low at basal levels in PHS-susceptible, non-dormant cultivar, Baegjoong. In conclusion, the results of this investigation revealed that after imbibition the metabolic homeostasis of dormant wheat is significantly less affected compared to non-dormant wheat. The inferences from this study combined with proteomic and transcriptomic studies will advance the molecular understanding of the pathways and enzyme regulations during PHS.
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Affiliation(s)
- Aayudh Das
- Department of Plant Biology, University of Vermont, BurlingtonVT, United States
- Department of Biology and Microbiology, South Dakota State University, BrookingsSD, United States
| | - Dea-Wook Kim
- National Institute of Crop Science, Rural Development AdministrationWanju-gun, South Korea
| | - Pramod Khadka
- Department of Biology and Microbiology, South Dakota State University, BrookingsSD, United States
| | - Randeep Rakwal
- Faculty of Health and Sport Sciences, University of TsukubaTsukuba, Japan
| | - Jai S. Rohila
- Department of Biology and Microbiology, South Dakota State University, BrookingsSD, United States
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