1
|
Brilhante M, Catarino S, Darbyshire I, Bandeira S, Moldão M, Duarte MC, Romeiras MM. Diversity patterns and conservation of the Vigna spp. in Mozambique: A comprehensive study. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.1057785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Mozambique supports a high diversity of native legume species, including many Crop Wild Relatives (CWRs). Among them, the still understudied genus Vigna is a particularly notable and promising donor of favorable traits for crop improvement. This study aims to provide an updated overview of Vigna CWRs diversity in Mozambique, defining a conservation strategy for priority target taxa and areas. A checklist of Vigna taxa was prepared and using five criteria (taxonomic group, ethnobotanical value, global and regional distributions, and ex situ conservation status), the prioritization of each taxon was determined. The distribution of Vigna native to Mozambique was studied and diversity hotspots were detected; gaps in in situ conservation were analyzed by overlaying species distribution with Mozambique’s Protected Areas Network. Maps predicting the differences between future conditions and baseline values were performed to investigate expected changes in temperature and precipitation in Vigna’s occurrence areas. There are 21 Vigna native taxa occurring in Mozambique, with the Chimanimani Mountains and Mount Gorongosa, as diversity hotspots for the genus. Following the IUCN Red List criteria, 13 taxa are of Least Concern, while the remaining eight are currently Not Evaluated. According to their priority level for further conservation actions, 24% of the taxa are of high priority, 67% of medium priority, and 9% of low priority. The important hotspot of Chimanimani Mountains is among the areas most affected by the predicted future increase in temperature and reduction of rainfall. The obtained distribution and species richness maps, represent a relevant first tool to evaluate and improve the effectiveness of Protected Areas and IPAs of Mozambique for the conservation of Vigna CWRs. The in situ gap analysis showed that 52% of the Vigna taxa are unprotected; this could be overcome by establishing reserves in Vigna diversity centers, considering the different types of habitats to which the different taxa are adapted, and by increasing in situ protection for the high priority ones. The ex situ conservation of Vigna is very limited and storing seed collections of these CWRs, is an essential component in global food security, as some taxa seem suitable as donors of genetic material to increase resistance to pests and diseases, or to drought and salinity. Overall, we provide recommendations for future research, collecting, and management, to conserve Vigna CWR in Mozambique, providing new data for their sustainable use in crop enhancement, as well as proposing measures for future conservation programs.
Collapse
|
2
|
Wolfgang A, Temme N, Tilcher R, Berg G. Understanding the sugar beet holobiont for sustainable agriculture. Front Microbiol 2023; 14:1151052. [PMID: 37138624 PMCID: PMC10149816 DOI: 10.3389/fmicb.2023.1151052] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/31/2023] [Indexed: 05/05/2023] Open
Abstract
The importance of crop-associated microbiomes for the health and field performance of plants has been demonstrated in the last decades. Sugar beet is the most important source of sucrose in temperate climates, and-as a root crop-yield heavily depends on genetics as well as on the soil and rhizosphere microbiomes. Bacteria, fungi, and archaea are found in all organs and life stages of the plant, and research on sugar beet microbiomes contributed to our understanding of the plant microbiome in general, especially of microbiome-based control strategies against phytopathogens. Attempts to make sugar beet cultivation more sustainable are increasing, raising the interest in biocontrol of plant pathogens and pests, biofertilization and -stimulation as well as microbiome-assisted breeding. This review first summarizes already achieved results on sugar beet-associated microbiomes and their unique traits, correlating to their physical, chemical, and biological peculiarities. Temporal and spatial microbiome dynamics during sugar beet ontogenesis are discussed, emphasizing the rhizosphere formation and highlighting knowledge gaps. Secondly, potential or already tested biocontrol agents and application strategies are discussed, providing an overview of how microbiome-based sugar beet farming could be performed in the future. Thus, this review is intended as a reference and baseline for further sugar beet-microbiome research, aiming to promote investigations in rhizosphere modulation-based biocontrol options.
Collapse
Affiliation(s)
- Adrian Wolfgang
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Nora Temme
- KWS SAAT SE & Co. KGaA, Einbeck, Germany
| | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Microbiome Biotechnology Department, Leibniz-Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- *Correspondence: Gabriele Berg
| |
Collapse
|
3
|
Yolcu S, Alavilli H, Ganesh P, Asif M, Kumar M, Song K. An Insight into the Abiotic Stress Responses of Cultivated Beets ( Beta vulgaris L.). PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010012. [PMID: 35009016 PMCID: PMC8747243 DOI: 10.3390/plants11010012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/12/2021] [Accepted: 12/14/2021] [Indexed: 05/03/2023]
Abstract
Cultivated beets (sugar beets, fodder beets, leaf beets, and garden beets) belonging to the species Beta vulgaris L. are important sources for many products such as sugar, bioethanol, animal feed, human nutrition, pulp residue, pectin extract, and molasses. Beta maritima L. (sea beet or wild beet) is a halophytic wild ancestor of all cultivated beets. With a requirement of less water and having shorter growth period than sugarcane, cultivated beets are preferentially spreading from temperate regions to subtropical countries. The beet cultivars display tolerance to several abiotic stresses such as salt, drought, cold, heat, and heavy metals. However, many environmental factors adversely influence growth, yield, and quality of beets. Hence, selection of stress-tolerant beet varieties and knowledge on the response mechanisms of beet cultivars to different abiotic stress factors are most required. The present review discusses morpho-physiological, biochemical, and molecular responses of cultivated beets (B. vulgaris L.) to different abiotic stresses including alkaline, cold, heat, heavy metals, and UV radiation. Additionally, we describe the beet genes reported for their involvement in response to these stress conditions.
Collapse
Affiliation(s)
- Seher Yolcu
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey;
- Correspondence: (S.Y.); (H.A.); (K.S.)
| | - Hemasundar Alavilli
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Korea
- Correspondence: (S.Y.); (H.A.); (K.S.)
| | - Pushpalatha Ganesh
- Department of Plant Biotechnology, M. S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Odisha 761211, India;
| | - Muhammad Asif
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey;
| | - Manu Kumar
- Department of Life Science, College of Life Science and Biotechnology, Dongguk University, Seoul 10326, Korea;
| | - Kihwan Song
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Korea
- Correspondence: (S.Y.); (H.A.); (K.S.)
| |
Collapse
|
4
|
Manel S, Andrello M, Henry K, Verdelet D, Darracq A, Guerin PE, Desprez B, Devaux P. Predicting genotype environmental range from genome-environment associations. Mol Ecol 2018; 27:2823-2833. [DOI: 10.1111/mec.14723] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/12/2018] [Accepted: 05/02/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Stéphanie Manel
- EPHE; PSL Research University; CNRS, UM, SupAgro, IND, INRA; UMR 5175 CEFE; Montpellier France
| | - Marco Andrello
- EPHE; PSL Research University; CNRS, UM, SupAgro, IND, INRA; UMR 5175 CEFE; Montpellier France
| | | | | | | | - Pierre-Edouard Guerin
- EPHE; PSL Research University; CNRS, UM, SupAgro, IND, INRA; UMR 5175 CEFE; Montpellier France
| | | | | |
Collapse
|
5
|
Monteiro F, Frese L, Castro S, Duarte MC, Paulo OS, Loureiro J, Romeiras MM. Genetic and Genomic Tools to Asssist Sugar Beet Improvement: The Value of the Crop Wild Relatives. FRONTIERS IN PLANT SCIENCE 2018; 9:74. [PMID: 29467772 PMCID: PMC5808244 DOI: 10.3389/fpls.2018.00074] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 01/15/2018] [Indexed: 05/21/2023]
Abstract
Sugar beet (Beta vulgaris L. ssp. vulgaris) is one of the most important European crops for both food and sugar production. Crop improvement has been developed to enhance productivity, sugar content or other breeder's desirable traits. The introgression of traits from Crop Wild Relatives (CWR) has been done essentially for lessening biotic stresses constraints, namely using Beta and Patellifolia species which exhibit disease resistance characteristics. Several studies have addressed crop-to-wild gene flow, yet, for breeding programs genetic variability associated with agronomically important traits remains unexplored regarding abiotic factors. To accomplish such association from phenotype-to-genotype, screening for wild relatives occurring in habitats where selective pressures are in play (i.e., populations in salt marshes for salinity tolerance; populations subjected to pathogen attacks and likely evolved resistance to pathogens) are the most appropriate streamline to identify causal genetic information. By selecting sugar beet CWR species based on genomic tools, rather than random variations, is a promising but still seldom explored route toward the development of improved crops. In this perspective, a viable streamline for sugar beet improvement is proposed through the use of different genomic tools by recurring to sugar beet CWRs and focusing on agronomic traits associated with abiotic stress tolerance. Overall, identification of genomic and epigenomic landscapes associated to adaptive ecotypes, along with the cytogenetic and habitat characterization of sugar beet CWR, will enable to identify potential hotspots for agrobiodiversity of sugar beet crop improvement toward abiotic stress tolerance.
Collapse
Affiliation(s)
- Filipa Monteiro
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa, Lisboa, Portugal
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Lothar Frese
- Institute for Breeding Research on Agricultural Crops, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Quedlinburg, Germany
| | - Sílvia Castro
- Department of Life Sciences, Centre for Functional Ecology, Universidade de Coimbra, Coimbra, Portugal
| | - Maria C. Duarte
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa, Lisboa, Portugal
| | - Octávio S. Paulo
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa, Lisboa, Portugal
| | - João Loureiro
- Department of Life Sciences, Centre for Functional Ecology, Universidade de Coimbra, Coimbra, Portugal
| | - Maria M. Romeiras
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa, Lisboa, Portugal
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| |
Collapse
|
6
|
Andrello M, Henry K, Devaux P, Verdelet D, Desprez B, Manel S. Insights into the genetic relationships among plants of Beta section Beta using SNP markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1857-1866. [PMID: 28589246 DOI: 10.1007/s00122-017-2929-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/30/2017] [Indexed: 05/23/2023]
Abstract
Using a much higher number of SNP markers and larger sample sizes than all the previous studies, we characterized the genetic relationships among wild and cultivated plants of section Beta. We analyzed the genetic variation of Beta section Beta, which includes wild taxa (Beta macrocarpa, B. patula, B. vulgaris subsp. adanensis and B. vulgaris subsp. maritima) and cultivars (fodder beet, sugar beet, garden beet, leaf beet, and swiss chards), using 9724 single nucleotide polymorphism markers. The analyses conducted at the individual level without a priori groups confirmed the strong differentiation of B. macrocarpa and B. vulgaris subsp. adanensis from the other taxa. B. vulgaris subsp. maritima showed a complex genetic structure partly following a geographical pattern, which confounded the differences between this taxon and the cultivated varieties. Cultivated varieties were structured into three main groups: garden beets, fodder and sugar beets, and leaf beets and swiss chards. The genetic structure described here will be helpful to correctly estimate linkage disequilibrium and to test for statistical associations between genetic markers and environmental variables.
Collapse
Affiliation(s)
- Marco Andrello
- EPHE, PSL Research University, CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, Biogéographie et Ecologie des Vertébrés, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Karine Henry
- Florimond Desprez, 59242, Cappelle En Pévèle, France
| | - Pierre Devaux
- Florimond Desprez, 59242, Cappelle En Pévèle, France
| | | | - Bruno Desprez
- Florimond Desprez, 59242, Cappelle En Pévèle, France
| | - Stéphanie Manel
- EPHE, PSL Research University, CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, Biogéographie et Ecologie des Vertébrés, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| |
Collapse
|
7
|
Nachtigall M, Bülow L, Schubert J, Frese L. Development of SSR markers for the genus Patellifolia (Chenopodiaceae). APPLICATIONS IN PLANT SCIENCES 2016; 4:apps1600040. [PMID: 27610279 PMCID: PMC5001861 DOI: 10.3732/apps.1600040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 05/23/2016] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY Microsatellite primers were developed to promote studies on the patterns of genetic diversity within Patellifolia patellaris (Chenopodiaceae) and the relationship between the three species of the genus Patellifolia. METHODS AND RESULTS The genomic sequence from P. procumbens was screened for simple sequence repeats (SSRs), and 3648 SSRs were identified. A subset of 53 SSR markers was validated, of which 25 proved to be polymorphic in the three species except for the P. webbiana-specific marker JKIPat16. The number of alleles ranged from 85 in P. patellaris, 187 in P. procumbens, and 202 in P. webbiana. CONCLUSIONS The set of 25 new markers will facilitate studies of the relationships between the three Patellifolia species and of the spatial and temporal distribution of genetic diversity within the species.
Collapse
Affiliation(s)
- Marion Nachtigall
- Institute for Breeding Research on Agricultural Crops, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Lorenz Bülow
- Institute for Breeding Research on Agricultural Crops, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Jörg Schubert
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Lothar Frese
- Institute for Breeding Research on Agricultural Crops, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| |
Collapse
|
8
|
Romeiras MM, Vieira A, Silva DN, Moura M, Santos-Guerra A, Batista D, Duarte MC, Paulo OS. Evolutionary and Biogeographic Insights on the Macaronesian Beta-Patellifolia Species (Amaranthaceae) from a Time-Scaled Molecular Phylogeny. PLoS One 2016; 11:e0152456. [PMID: 27031338 PMCID: PMC4816301 DOI: 10.1371/journal.pone.0152456] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 03/15/2016] [Indexed: 01/29/2023] Open
Abstract
The Western Mediterranean Region and Macaronesian Islands are one of the top biodiversity hotspots of Europe, containing a significant native genetic diversity of global value among the Crop Wild Relatives (CWR). Sugar beet is the primary crop of the genus Beta (subfamily Betoideae, Amaranthaceae) and despite the great economic importance of this genus, and of the close relative Patellifolia species, a reconstruction of their evolutionary history is still lacking. We analyzed nrDNA (ITS) and cpDNA gene (matK, trnH-psbA, trnL intron, rbcL) sequences to: (i) investigate the phylogenetic relationships within the Betoideae subfamily, and (ii) elucidate the historical biogeography of wild beet species in the Western Mediterranean Region, including the Macaronesian Islands. The results support the Betoideae as a monophyletic group (excluding the Acroglochin genus) and provide a detailed inference of relationships within this subfamily, revealing: (i) a deep genetic differentiation between Beta and Patellifolia species, which may have occurred in Late Oligocene; and (ii) the occurrence of a West-East genetic divergence within Beta, indicating that the Mediterranean species probably differentiated by the end of the Miocene. This was interpreted as a signature of species radiation induced by dramatic habitat changes during the Messinian Salinity Crisis (MSC, 5.96-5.33 Mya). Moreover, colonization events during the Pleistocene also played a role in shaping the current diversity patterns among and within the Macaronesian Islands. The origin and number of these events could not be revealed due to insufficient phylogenetic resolution, suggesting that the diversification was quite recent in these archipelagos, and unravelling potential complex biogeographic patterns with hybridization and gene flow playing an important role. Finally, three evolutionary lineages were identified corresponding to major gene pools of sugar beet wild relatives, which provide useful information for establishing in situ and ex situ conservation priorities in the hotspot area of the Macaronesian Islands.
Collapse
Affiliation(s)
- Maria M. Romeiras
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- * E-mail:
| | - Ana Vieira
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
| | - Diogo N. Silva
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
| | - Monica Moura
- Research Network in Biodiversity and Evolutionary Biology, Associate Laboratory (CIBIO/InBIO), Universidade do Porto, Vairão, Portugal
- Universidade dos Açores, Dep. Biologia, Ponta Delgada, Portugal
| | | | - Dora Batista
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
| | - Maria Cristina Duarte
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Octávio S. Paulo
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| |
Collapse
|
9
|
Andrello M, Henry K, Devaux P, Desprez B, Manel S. Taxonomic, spatial and adaptive genetic variation of Beta section Beta. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:257-271. [PMID: 26526552 DOI: 10.1007/s00122-015-2625-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 10/17/2015] [Indexed: 06/05/2023]
Abstract
KEY MESSAGE The genetic variation of Beta section Beta is structured into four taxonomic and spatial clusters. There are significant associations between molecular markers and environmental variables. ABSTRACT We investigated the genetic diversity of Beta section Beta, which includes the wild and cultivated relatives of the sugar beet. The taxa included in the study were: Beta vulgaris subsp. maritima, B. vulgaris subsp. adanensis, B. macrocarpa, B. patula and B. vulgaris subsp. vulgaris (garden beet, leaf beet and swiss chards). We collected 1264 accessions originating from the entire distribution area of these taxa and genotyped them for 4436 DArT markers (DArTs). We showed that the genetic variation of these accessions is structured into four taxonomic and spatial clusters: (1) samples of Beta macrocarpa, (2) samples of Beta vulgaris subsp. adanensis, (3) Mediterranean and Asian samples and (4) Atlantic and Northern European samples. These last two clusters were mainly composed of samples of Beta vulgaris subsp. maritima. We investigated in deeper detail the genetic structure of B. vulgaris subsp. maritima, which constituted the majority (80%) of the wild samples. This subspecies exhibited a clinal genetic variation from South-East to North-West. We detected some markers significantly associated to environmental variables in B. vulgaris subsp. maritima. These associations are interpreted as results of natural selection. The variable most often involved in the associations was annual mean temperature. Therefore, these markers can be useful for the development of frost-tolerant winter beets and drought-tolerant rain-fed beets.
Collapse
Affiliation(s)
- Marco Andrello
- Laboratoire Biogeographie et écologie des vertébrés, CEFE UMR 5175, CNRS - Universite de Montpellier - Universite Paul-Valery Montpellier - EPHE, 34293, Montpellier Cedex 5, France.
| | - Karine Henry
- Florimond Desprez, 59242, Cappelle En Pévèle, France
| | - Pierre Devaux
- Florimond Desprez, 59242, Cappelle En Pévèle, France
| | - Bruno Desprez
- Florimond Desprez, 59242, Cappelle En Pévèle, France
| | - Stéphanie Manel
- Laboratoire Biogeographie et écologie des vertébrés, CEFE UMR 5175, CNRS - Universite de Montpellier - Universite Paul-Valery Montpellier - EPHE, 34293, Montpellier Cedex 5, France
| |
Collapse
|
10
|
Ribeiro IC, Pinheiro C, Ribeiro CM, Veloso MM, Simoes-Costa MC, Evaristo I, Paulo OS, Ricardo CP. Genetic Diversity and Physiological Performance of Portuguese Wild Beet (Beta vulgaris spp. maritima) from Three Contrasting Habitats. FRONTIERS IN PLANT SCIENCE 2016; 7:1293. [PMID: 27630646 PMCID: PMC5006101 DOI: 10.3389/fpls.2016.01293] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/12/2016] [Indexed: 05/20/2023]
Abstract
The establishment of stress resilient sugar beets (Beta vulgaris spp. vulgaris) is an important breeding goal since this cash crop is susceptible to drought and salinity. The genetic diversity in cultivated sugar beets is low and the beet wild relatives are useful genetic resources for tolerance traits. Three wild beet populations (Beta vulgaris spp. maritima) from contrasting environments, Vaiamonte (VMT, dry inland hill), Comporta (CMP, marsh) and Oeiras (OEI, coastland), and one commercial sugar beet (Isella variety, SB), are compared. At the genetic level, the use of six microsatellite allowed to detect a total of seventy six alleles. It was observed that CMP population has the highest value concerning the effective number of alleles and of expected heterozygosity. By contrast, sugar beet has the lowest values for all the parameters considered. Loci analysis with STRUCTURE allows defining three genetic clusters, the sea beet (OEI and CMP), the inland ruderal beet (VMT) and the sugar beet (SB). A screening test for progressive drought and salinity effects demonstrated that: all populations were able to recover from severe stress; drought impact was higher than that from salinity; the impact on biomass (total, shoot, root) was population specific. The distinct strategies were also visible at physiological level. We evaluated the physiological responses of the populations under drought and salt stress, namely at initial stress stages, late stress stages, and early stress recovery. Multivariate analysis showed that the physiological performance can be used to discriminate between genotypes, with a strong contribution of leaf temperature and leaf osmotic adjustment. However, the separation achieved and the groups formed are dependent on the stress type, stress intensity and duration. Each of the wild beet populations evaluated is very rich in genetic terms (allelic richness) and exhibited physiological plasticity, i.e., the capacity to physiologically adjust to changing environments. These characteristics emphasize the importance of the wild beet ecotypes for beet improvement programs. Two striking ecotypes are VMT, which is the best to cope with drought and salinity, and CMP which has the highest root to shoot ratio. These genotypes can supply breeding programs with distinct goals.
Collapse
Affiliation(s)
- Isa C. Ribeiro
- Instituto de Tecnologia Química e Biológica, Universidade NOVA de LisboaOeiras, Portugal
| | - Carla Pinheiro
- Instituto de Tecnologia Química e Biológica, Universidade NOVA de LisboaOeiras, Portugal
- Faculdade de Ciências e Tecnologia, Universidade NOVA de LisboaCaparica, Portugal
- *Correspondence: Carla Pinheiro,
| | - Carla M. Ribeiro
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de LisboaLisboa, Portugal
| | - Maria M. Veloso
- INIAV, Unidade de Investigação de Biotecnologia e Recursos GenéticosOeiras, Portugal
- Instituto Superior de Agronomia, Linking Landscape, Environment, Agriculture and Food, Universidade de LisboaLisboa, Portugal
| | - Maria C. Simoes-Costa
- Instituto Superior de Agronomia, Linking Landscape, Environment, Agriculture and Food, Universidade de LisboaLisboa, Portugal
| | - Isabel Evaristo
- INIAV, Unidade de Investigação de Sistemas Agrários e Florestais e Sanidade VegetalOeiras, Portugal
| | - Octávio S. Paulo
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de LisboaLisboa, Portugal
| | - Cândido P. Ricardo
- Instituto de Tecnologia Química e Biológica, Universidade NOVA de LisboaOeiras, Portugal
| |
Collapse
|
11
|
Iquebal MA, Jaiswal S, Angadi UB, Sablok G, Arora V, Kumar S, Rai A, Kumar D. SBMDb: first whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav111. [PMID: 26647370 PMCID: PMC4672366 DOI: 10.1093/database/bav111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 10/24/2015] [Indexed: 11/14/2022]
Abstract
DNA marker plays important role as valuable tools to increase crop productivity by finding plausible answers to genetic variations and linking the Quantitative Trait Loci (QTL) of beneficial trait. Prior approaches in development of Short Tandem Repeats (STR) markers were time consuming and inefficient. Recent methods invoking the development of STR markers using whole genomic or transcriptomics data has gained wide importance with immense potential in developing breeding and cultivator improvement approaches. Availability of whole genome sequences and in silico approaches has revolutionized bulk marker discovery. We report world's first sugarbeet whole genome marker discovery having 145 K markers along with 5 K functional domain markers unified in common platform using MySQL, Apache and PHP in SBMDb. Embedded markers and corresponding location information can be selected for desired chromosome, location/interval and primers can be generated using Primer3 core, integrated at backend. Our analyses revealed abundance of 'mono' repeat (76.82%) over 'di' repeats (13.68%). Highest density (671.05 markers/Mb) was found in chromosome 1 and lowest density (341.27 markers/Mb) in chromosome 6. Current investigation of sugarbeet genome marker density has direct implications in increasing mapping marker density. This will enable present linkage map having marker distance of ∼2 cM, i.e. from 200 to 2.6 Kb, thus facilitating QTL/gene mapping. We also report e-PCR-based detection of 2027 polymorphic markers in panel of five genotypes. These markers can be used for DUS test of variety identification and MAS/GAS in variety improvement program. The present database presents wide source of potential markers for developing and implementing new approaches for molecular breeding required to accelerate industrious use of this crop, especially for sugar, health care products, medicines and color dye. Identified markers will also help in improvement of bioenergy trait of bioethanol and biogas production along with reaping advantage of crop efficiency in terms of low water and carbon footprint especially in era of climate change. Database URL: http://webapp.cabgrid.res.in/sbmdb/.
Collapse
Affiliation(s)
- Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India
| | - U B Angadi
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India
| | - Gaurav Sablok
- Biotechnology Unit, Department of Botany, Jai Narain Vyas University, Jodhpur 342003, India, Plant Functional Biology and Climate Change Cluster (C3), University of Technology, Sydney, PO Box 123 Broadway New South Wales 2007, Australia
| | - Vasu Arora
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India
| | - Sunil Kumar
- National Bureau of Agriculturally Important Microorganisms, Kusmaur, Mau NathBhanjan, Uttar Pradesh 275101, India and Institute of Life Sciences, Nalco Square, Bhubaneswar 751023, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India,
| |
Collapse
|
12
|
Fan H, Zhang Y, Sun H, Liu J, Wang Y, Wang X, Li D, Yu J, Han C. Transcriptome Analysis of Beta macrocarpa and Identification of Differentially Expressed Transcripts in Response to Beet Necrotic Yellow Vein Virus Infection. PLoS One 2015; 10:e0132277. [PMID: 26196682 PMCID: PMC4719419 DOI: 10.1371/journal.pone.0132277] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 06/11/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Rhizomania is one of the most devastating diseases of sugar beet. It is caused by Beet necrotic yellow vein virus (BNYVV) transmitted by the obligate root-infecting parasite Polymyxa betae. Beta macrocarpa, a wild beet species widely used as a systemic host in the laboratory, can be rub-inoculated with BNYVV to avoid variation associated with the presence of the vector P. betae. To better understand disease and resistance between beets and BNYVV, we characterized the transcriptome of B. macrocarpa and analyzed global gene expression of B. macrocarpa in response to BNYVV infection using the Illumina sequencing platform. RESULTS The overall de novo assembly of cDNA sequence data generated 75,917 unigenes, with an average length of 1054 bp. Based on a BLASTX search (E-value ≤ 10-5) against the non-redundant (NR, NCBI) protein, Swiss-Prot, the Gene Ontology (GO), Clusters of Orthologous Groups of proteins (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, there were 39,372 unigenes annotated. In addition, 4,834 simple sequence repeats (SSRs) were also predicted, which could serve as a foundation for various applications in beet breeding. Furthermore, comparative analysis of the two transcriptomes revealed that 261 genes were differentially expressed in infected compared to control plants, including 128 up- and 133 down-regulated genes. GO analysis showed that the changes in the differently expressed genes were mainly enrichment in response to biotic stimulus and primary metabolic process. CONCLUSION Our results not only provide a rich genomic resource for beets, but also benefit research into the molecular mechanisms of beet- BNYV Vinteraction.
Collapse
Affiliation(s)
- Huiyan Fan
- State Key Laboratory for Agrobiotechnology and Department of Plant
Pathology, China Agricultural University, Beijing, 100193,
China
- College of Pharmacy, Zhejiang Chinese Medicine University, Hangzhou,
310053, Zhejiang, China
| | - Yongliang Zhang
- State Key Laboratory for Agrobiotechnology and Department of Plant
Pathology, China Agricultural University, Beijing, 100193,
China
| | - Haiwen Sun
- State Key Laboratory for Agrobiotechnology and Department of Plant
Pathology, China Agricultural University, Beijing, 100193,
China
| | - Junying Liu
- State Key Laboratory for Agrobiotechnology and Department of Plant
Pathology, China Agricultural University, Beijing, 100193,
China
| | - Ying Wang
- State Key Laboratory for Agrobiotechnology and Department of Plant
Pathology, China Agricultural University, Beijing, 100193,
China
| | - Xianbing Wang
- State Key Laboratory for Agrobiotechnology and Department of Plant
Pathology, China Agricultural University, Beijing, 100193,
China
| | - Dawei Li
- State Key Laboratory for Agrobiotechnology and Department of Plant
Pathology, China Agricultural University, Beijing, 100193,
China
| | - Jialin Yu
- State Key Laboratory for Agrobiotechnology and Department of Plant
Pathology, China Agricultural University, Beijing, 100193,
China
| | - Chenggui Han
- State Key Laboratory for Agrobiotechnology and Department of Plant
Pathology, China Agricultural University, Beijing, 100193,
China
| |
Collapse
|