51
|
Calleja-Cabrera J, Boter M, Oñate-Sánchez L, Pernas M. Root Growth Adaptation to Climate Change in Crops. FRONTIERS IN PLANT SCIENCE 2020; 11:544. [PMID: 32457782 PMCID: PMC7227386 DOI: 10.3389/fpls.2020.00544] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/09/2020] [Indexed: 05/05/2023]
Abstract
Climate change is threatening crop productivity worldwide and new solutions to adapt crops to these environmental changes are urgently needed. Elevated temperatures driven by climate change affect developmental and physiological plant processes that, ultimately, impact on crop yield and quality. Plant roots are responsible for water and nutrients uptake, but changes in soil temperatures alters this process limiting crop growth. With the predicted variable climatic forecast, the development of an efficient root system better adapted to changing soil and environmental conditions is crucial for enhancing crop productivity. Root traits associated with improved adaptation to rising temperatures are increasingly being analyzed to obtain more suitable crop varieties. In this review, we will summarize the current knowledge about the effect of increasing temperatures on root growth and their impact on crop yield. First, we will describe the main alterations in root architecture that different crops undergo in response to warmer soils. Then, we will outline the main coordinated physiological and metabolic changes taking place in roots and aerial parts that modulate the global response of the plant to increased temperatures. We will discuss on some of the main regulatory mechanisms controlling root adaptation to warmer soils, including the activation of heat and oxidative pathways to prevent damage of root cells and disruption of root growth; the interplay between hormonal regulatory pathways and the global changes on gene expression and protein homeostasis. We will also consider that in the field, increasing temperatures are usually associated with other abiotic and biotic stresses such as drought, salinity, nutrient deficiencies, and pathogen infections. We will present recent advances on how the root system is able to integrate and respond to complex and different stimuli in order to adapt to an increasingly changing environment. Finally, we will discuss the new prospects and challenges in this field as well as the more promising pathways for future research.
Collapse
Affiliation(s)
| | | | | | - M. Pernas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| |
Collapse
|
52
|
Agriculture and the Disruption of Plant–Microbial Symbiosis. Trends Ecol Evol 2020; 35:426-439. [DOI: 10.1016/j.tree.2020.01.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 01/13/2020] [Accepted: 01/21/2020] [Indexed: 12/29/2022]
|
53
|
Zhou Y, Coventry DR, Gupta VVSR, Fuentes D, Merchant A, Kaiser BN, Li J, Wei Y, Liu H, Wang Y, Gan S, Denton MD. The preceding root system drives the composition and function of the rhizosphere microbiome. Genome Biol 2020; 21:89. [PMID: 32252812 PMCID: PMC7137527 DOI: 10.1186/s13059-020-01999-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 03/12/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The soil environment is responsible for sustaining most terrestrial plant life, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere, and how it responds to agricultural management such as crop rotations and soil tillage, is vital for improving global food production. RESULTS This study establishes an in-depth soil microbial gene catalogue based on the living-decaying rhizosphere niches in a cropping soil. The detritusphere microbiome regulates the composition and function of the rhizosphere microbiome to a greater extent than plant type: rhizosphere microbiomes of wheat and chickpea were homogenous (65-87% similarity) in the presence of decaying root (DR) systems but were heterogeneous (3-24% similarity) where DR was disrupted by tillage. When the microbiomes of the rhizosphere and the detritusphere interact in the presence of DR, there is significant degradation of plant root exudates by the rhizosphere microbiome, and genes associated with membrane transporters, carbohydrate and amino acid metabolism are enriched. CONCLUSIONS The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the detritusphere microbiome in determining the metagenome of developing root systems. Modifications in root microbial function through soil management can ultimately govern plant health, productivity and food security.
Collapse
Affiliation(s)
- Yi Zhou
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064 Australia
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, The University of Adelaide, Glen Osmond, SA 5064 Australia
| | - David R. Coventry
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064 Australia
| | | | - David Fuentes
- School of Life and Environmental Sciences, University of Sydney, Brownlow Hill, NSW 2570 Australia
| | - Andrew Merchant
- School of Life and Environmental Sciences, University of Sydney, Brownlow Hill, NSW 2570 Australia
| | - Brent N. Kaiser
- School of Life and Environmental Sciences, University of Sydney, Brownlow Hill, NSW 2570 Australia
| | - Jishun Li
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, The University of Adelaide, Glen Osmond, SA 5064 Australia
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong, 250013 China
| | - Yanli Wei
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, The University of Adelaide, Glen Osmond, SA 5064 Australia
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong, 250013 China
| | - Huan Liu
- BGI-Shenzhen, Shenzhen, 518083 Guangdong China
| | - Yayu Wang
- BGI-Shenzhen, Shenzhen, 518083 Guangdong China
| | - Shuheng Gan
- BGI-Shenzhen, Shenzhen, 518083 Guangdong China
| | - Matthew D. Denton
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064 Australia
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, The University of Adelaide, Glen Osmond, SA 5064 Australia
| |
Collapse
|
54
|
Stathi E, Kougioumoutzis K, Abraham EM, Trigas P, Ganopoulos I, Avramidou EV, Tani E. Population genetic variability and distribution of the endangered Greek endemic Cicer graecum under climate change scenarios. AOB PLANTS 2020; 12:plaa007. [PMID: 32257090 PMCID: PMC7102496 DOI: 10.1093/aobpla/plaa007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/10/2020] [Indexed: 06/11/2023]
Abstract
The Mediterranean hot spot includes numerous endemic and socio-economically important plant species seriously threatened by climate change and habitat loss. In this study, the genetic diversity of five populations of Cicer graecum, an endangered endemic species from northern Peloponnisos, Greece and a wild relative of the cultivated Cicer arietinum, was investigated using inter-simple sequence repeats (ISSRs) and amplified fragment length polymorphism (AFLP) markers in order to determine levels and structure of genetic variability. Nei's gene diversity by ISSR and AFLP markers indicated medium to high genetic diversity at the population level. Moreover, AMOVA results suggest that most of the variation exists within (93 % for AFLPs and 65 % for ISSRs), rather than among populations. Furthermore, Principal Component Analysis based on ISSRs positively correlated the genetic differentiation among the populations to the geographic distances, suggesting that the gene flow among distant populations is limited. The ecological adaptation of C. graecum populations was also investigated by correlation of their genetic diversity with certain environmental variables. Aridity arose as the dominant factor positively affecting the genetic diversity of C. graecum populations. We modelled the realized climatic niche of C. graecum in an ensemble forecasting scheme under three different global circulation models and two climate change scenarios. In all cases, a severe range contraction for C. graecum is projected, highlighting the high extinction risk that is probably going to face during the coming decades. These results could be a valuable tool towards the implementation of an integrated in situ and ex situ conservation scheme approach for activating management programmes for this endemic and threatened species.
Collapse
Affiliation(s)
- Efthalia Stathi
- Department of Crop Science, Laboratory of Plant Breeding and Biometry, Agricultural University of Athens, Iera Odos, Athens, Greece
| | - Konstantinos Kougioumoutzis
- Department of Crop Science, Laboratory of Systematic Botany, Agricultural University of Athens, Iera Odos, Athens, Greece
| | - Eleni M Abraham
- Laboratory of Range Science, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Panayiotis Trigas
- Department of Crop Science, Laboratory of Systematic Botany, Agricultural University of Athens, Iera Odos, Athens, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, HAO-DEMETER, Thermi, Thessaloniki, Greece
| | - Evangelia V Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Athens, HAO “DEMETER”, Terma Alkmanos, Ilisia, Athens, Greece
| | - Eleni Tani
- Department of Crop Science, Laboratory of Plant Breeding and Biometry, Agricultural University of Athens, Iera Odos, Athens, Greece
| |
Collapse
|
55
|
Sokolkova AB, Chang PL, Carrasquila-Garcia N, Noujdina NV, Cook DR, Nuzhdin SV, Samsonova MG. The Signatures of Ecological Adaptation in the Genomes of Chickpea Landraces. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920020244] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
56
|
Pradeep K, Bell RW, Vance W. Variation of Cicer Germplasm to Manganese Toxicity Tolerance. FRONTIERS IN PLANT SCIENCE 2020; 11:588065. [PMID: 33329649 PMCID: PMC7733998 DOI: 10.3389/fpls.2020.588065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/29/2020] [Indexed: 05/21/2023]
Abstract
After aluminum, manganese toxicity is the most limiting factor for crops grown in acidic soils worldwide. But overall, research on Mn toxicity is still limited. The poor acid tolerance of chickpea may be related to Mn toxicity, but there has been no previous screening of chickpea germplasm (nor in its wild Cicer relatives, Cicer reticulatum and Cicer echinospermum) for tolerance to Mn toxicity. A screening technique was developed for tolerance to Mn toxicity using three released cultivars of chickpea (Cicer arietinum L), Ambar, PBA HatTrick, and PBA Striker; one accession each of C. reticulatum and C. echinospermum; and lupin (Lupinus angustifolius) as a Mn-tolerant check, with eight Mn concentrations of 2, 25, 50, 100, 150, 200, 250, and 500 μM Mn as MnSO4 in a low-ionic-strength nutrient solution. The plants were harvested at 14 and 28 days after Mn treatments. The nutrient uptake in shoots (young, old leaves, and the rest of the shoot) and roots was investigated. The best discrimination between tolerant and intolerant Cicer genotypes based on relative shoot dry weight, root dry weight, total root length, and scoring of toxicity symptoms was achieved at 150 μM Mn after 14 days of growth in Mn solution. Among the chickpea cultivars, the greater relative plant growth (both shoot and root) of Ambar and PBA Striker at 100-200 μM Mn contrasted with that of PBA HatTrick, while the C. echinospermum accession was more tolerant to Mn toxicity than C. reticulatum. Manganese tolerance in both domestic cultivars and wild accessions was associated with internal tolerance to excess Mn following greater uptake of Mn and translocation of Mn from roots to shoots.
Collapse
|
57
|
Ozkuru E, Ates D, Nemli S, Erdogmus S, Karaca N, Yilmaz H, Yagmur B, Kartal C, Tosun M, Ozdestan O, Otles S, Kahriman A, Tanyolac B. Association mapping of loci linked to copper, phosphorus, and potassium concentrations in the seeds of C. arietinum and C. reticulatum. Genomics 2019; 111:1873-1881. [DOI: 10.1016/j.ygeno.2018.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/26/2018] [Accepted: 12/17/2018] [Indexed: 12/22/2022]
|
58
|
Ramoneda J, Le Roux J, Frossard E, Bester C, Oettlé N, Frey B, Gamper HA. Insights from invasion ecology: Can consideration of eco-evolutionary experience promote benefits from root mutualisms in plant production? AOB PLANTS 2019; 11:plz060. [PMID: 31777649 PMCID: PMC6863469 DOI: 10.1093/aobpla/plz060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 09/13/2019] [Indexed: 06/10/2023]
Abstract
Mutualistic plant-microbial functioning relies on co-adapted symbiotic partners as well as conducive environmental conditions. Choosing particular plant genotypes for domestication and subsequent cultivar selection can narrow the gene pools of crop plants to a degree that they are no longer able to benefit from microbial mutualists. Elevated mineral nutrient levels in cultivated soils also reduce the dependence of crops on nutritional support by mutualists such as mycorrhizal fungi and rhizobia. Thus, current ways of crop production are predestined to compromise the propagation and function of microbial symbionts, limiting their long-term benefits for plant yield stability. The influence of mutualists on non-native plant establishment and spread, i.e. biological invasions, provides an unexplored analogue to contemporary crop production that accounts for mutualistic services from symbionts like rhizobia and mycorrhizae. The historical exposure of organisms to biotic interactions over evolutionary timescales, or so-called eco-evolutionary experience (EEE), has been used to explain the success of such invasions. In this paper, we stress that consideration of the EEE concept can shed light on how to overcome the loss of microbial mutualist functions following crop domestication and breeding. We propose specific experimental approaches to utilize the wild ancestors of crops to determine whether crop domestication compromised the benefits derived from root microbial symbioses or not. This can predict the potential for success of mutualistic symbiosis manipulation in modern crops and the maintenance of effective microbial mutualisms over the long term.
Collapse
Affiliation(s)
- Josep Ramoneda
- Group of Plant Nutrition, Department of Environmental Systems Science, ETH Zurich, Lindau, Switzerland
| | - Johannes Le Roux
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Emmanuel Frossard
- Group of Plant Nutrition, Department of Environmental Systems Science, ETH Zurich, Lindau, Switzerland
| | - Cecilia Bester
- South African Agricultural Research Council (ARC-Infruitec), Nieuwoudtville Northern Cape, Stellenbosch Central, Stellenbosch, South Africa
| | - Noel Oettlé
- Environmental Monitoring Group (EMG), Nieuwoudtville Northern Cape, South Africa
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | | |
Collapse
|
59
|
Sivasakthi K, Marques E, Kalungwana N, Carrasquilla-Garcia N, Chang PL, Bergmann EM, Bueno E, Cordeiro M, Sani SGA, Udupa SM, Rather IA, Rouf Mir R, Vadez V, Vandemark GJ, Gaur PM, Cook DR, Boesch C, von Wettberg EJ, Kholova J, Penmetsa RV. Functional Dissection of the Chickpea ( Cicer arietinum L.) Stay-Green Phenotype Associated with Molecular Variation at an Ortholog of Mendel's I Gene for Cotyledon Color: Implications for Crop Production and Carotenoid Biofortification. Int J Mol Sci 2019; 20:E5562. [PMID: 31703441 PMCID: PMC6888616 DOI: 10.3390/ijms20225562] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 10/31/2019] [Accepted: 11/01/2019] [Indexed: 11/16/2022] Open
Abstract
"Stay-green" crop phenotypes have been shown to impact drought tolerance and nutritional content of several crops. We aimed to genetically describe and functionally dissect the particular stay-green phenomenon found in chickpeas with a green cotyledon color of mature dry seed and investigate its potential use for improvement of chickpea environmental adaptations and nutritional value. We examined 40 stay-green accessions and a set of 29 BC2F4-5 stay-green introgression lines using a stay-green donor parent ICC 16340 and two Indian elite cultivars (KAK2, JGK1) as recurrent parents. Genetic studies of segregating populations indicated that the green cotyledon trait is controlled by a single recessive gene that is invariantly associated with the delayed degreening (extended chlorophyll retention). We found that the chickpea ortholog of Mendel's I locus of garden pea, encoding a SGR protein as very likely to underlie the persistently green cotyledon color phenotype of chickpea. Further sequence characterization of this chickpea ortholog CaStGR1 (CaStGR1, for carietinum stay-green gene 1) revealed the presence of five different molecular variants (alleles), each of which is likely a loss-of-function of the chickpea protein (CaStGR1) involved in chlorophyll catabolism. We tested the wild type and green cotyledon lines for components of adaptations to dry environments and traits linked to agronomic performance in different experimental systems and different levels of water availability. We found that the plant processes linked to disrupted CaStGR1 gene did not functionality affect transpiration efficiency or water usage. Photosynthetic pigments in grains, including provitaminogenic carotenoids important for human nutrition, were 2-3-fold higher in the stay-green type. Agronomic performance did not appear to be correlated with the presence/absence of the stay-green allele. We conclude that allelic variation in chickpea CaStGR1 does not compromise traits linked to environmental adaptation and agronomic performance, and is a promising genetic technology for biofortification of provitaminogenic carotenoids in chickpea.
Collapse
Affiliation(s)
- Kaliamoorthy Sivasakthi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, India; (K.S.); (V.V.); (P.M.G.)
| | - Edward Marques
- Department of Plant and Soil Science, University of Vermont, and Gund Institute for the Environment, Burlington, VT 05405, USA; (E.M.); (E.B.)
| | - Ng’andwe Kalungwana
- School of Food Science and Nutrition, University of Leeds, Leeds, LS2 9JT, UK; (N.K.); (C.B.)
| | - Noelia Carrasquilla-Garcia
- Department of Plant Pathology, University of California, Davis, CA 95616, USA; (N.C.-G.); (P.L.C.); (E.M.B.); (M.C.); (D.R.C.)
| | - Peter L. Chang
- Department of Plant Pathology, University of California, Davis, CA 95616, USA; (N.C.-G.); (P.L.C.); (E.M.B.); (M.C.); (D.R.C.)
| | - Emily M. Bergmann
- Department of Plant Pathology, University of California, Davis, CA 95616, USA; (N.C.-G.); (P.L.C.); (E.M.B.); (M.C.); (D.R.C.)
| | - Erika Bueno
- Department of Plant and Soil Science, University of Vermont, and Gund Institute for the Environment, Burlington, VT 05405, USA; (E.M.); (E.B.)
| | - Matilde Cordeiro
- Department of Plant Pathology, University of California, Davis, CA 95616, USA; (N.C.-G.); (P.L.C.); (E.M.B.); (M.C.); (D.R.C.)
| | - Syed Gul A.S. Sani
- Department of Plant Pathology, University of California, Davis, CA 95616, USA; (N.C.-G.); (P.L.C.); (E.M.B.); (M.C.); (D.R.C.)
| | - Sripada M. Udupa
- International Center for Agricultural Research in the Dry Areas (ICARDA), P.O.Box 6299, Rue Hafiane Cherkaoui, 10112 Rabat, Morocco;
| | - Irshad A. Rather
- Division of Genetics & Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences & Technology (SKUAST), Sopore 193 201, India; (I.A.R.); (R.R.M.)
| | - Reyazul Rouf Mir
- Division of Genetics & Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences & Technology (SKUAST), Sopore 193 201, India; (I.A.R.); (R.R.M.)
| | - Vincent Vadez
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, India; (K.S.); (V.V.); (P.M.G.)
| | - George J. Vandemark
- Grain Legume Genetics and Physiology Research, USDA-ARS, and, Washington State University, Pullman, WA 99164, USA;
| | - Pooran M. Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, India; (K.S.); (V.V.); (P.M.G.)
| | - Douglas R. Cook
- Department of Plant Pathology, University of California, Davis, CA 95616, USA; (N.C.-G.); (P.L.C.); (E.M.B.); (M.C.); (D.R.C.)
| | - Christine Boesch
- School of Food Science and Nutrition, University of Leeds, Leeds, LS2 9JT, UK; (N.K.); (C.B.)
| | - Eric J.B. von Wettberg
- Department of Plant and Soil Science, University of Vermont, and Gund Institute for the Environment, Burlington, VT 05405, USA; (E.M.); (E.B.)
| | - Jana Kholova
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, India; (K.S.); (V.V.); (P.M.G.)
| | - R. Varma Penmetsa
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| |
Collapse
|
60
|
Karaca N, Ates D, Nemli S, Ozkuru E, Yilmaz H, Yagmur B, Kartal C, Tosun M, Ocak OO, Otles S, Kahriman A, Tanyolac MB. Association mapping of magnesium and manganese concentrations in the seeds of C. arietinum and C. reticulatum. Genomics 2019; 112:1633-1642. [PMID: 31669504 DOI: 10.1016/j.ygeno.2019.09.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 09/05/2019] [Accepted: 09/16/2019] [Indexed: 12/30/2022]
Abstract
Chickpea (Cicer arietinum L.) is one of the oldest and most important pulse crops grown and consumed all over the world, especially in developing countries. Magnesium (Mg) and manganese (Mn) are essential plant nutrients in terms of human health and many health problems arise in their deficiencies. The objectives of this study were to characterize genetic variability in the seed Mg and Mn concentrations and identify single nucleotide polymorphism (SNP) markers associated with these traits in 107 Cicer reticulatum and 73C. arietinum genotypes, using a genome wide association study. The genotypes were grown in four environments, characterized for Mg and Mn concentrations, and genotyped with 121,841 SNP markers. The population showed three-fold and two-fold variation for the Mg and Mn concentrations, respectively. The population structure was identified using STRUCTURE software, which divided 180 genotypes into two (K = 2) groups. Principal component analysis and neighbor joining tree analysis confirmed the results of STRUCTURE. A total of 4 and 16 consistent SNPs were detected for the Mg and Mn concentrations, respectively. The identified markers can be utilized in breeding of chickpea to increase Mg and Mn levels in order to improve human and livestock nutrition.
Collapse
Affiliation(s)
- Nur Karaca
- Ege University, Department of Bioengineering, 35040, Bornova, Izmir, Turkey
| | - Duygu Ates
- Ege University, Department of Bioengineering, 35040, Bornova, Izmir, Turkey
| | - Seda Nemli
- Ege University, Department of Bioengineering, 35040, Bornova, Izmir, Turkey
| | - Esin Ozkuru
- Ege University, Department of Bioengineering, 35040, Bornova, Izmir, Turkey
| | - Hasan Yilmaz
- Ege University, Department of Bioengineering, 35040, Bornova, Izmir, Turkey
| | - Bulent Yagmur
- Ege University, Department of Soil Sciences, 35040, Bornova, Izmir, Turkey
| | - Canan Kartal
- Ege University, Department of Food Engineering, 35040, Bornova, Izmir, Turkey
| | - Muzaffer Tosun
- Ege University, Department of Field Crops, 35040, Bornova, Izmir, Turkey
| | - Ozgul Ozdestan Ocak
- Ege University, Department of Food Engineering, 35040, Bornova, Izmir, Turkey
| | - Semih Otles
- Ege University, Department of Food Engineering, 35040, Bornova, Izmir, Turkey
| | - Abdullah Kahriman
- Harran University, Department of Field Crops, 64000 Sanli Urfa, Turkey
| | | |
Collapse
|
61
|
Michaels HJ, Cartwright CA, Wakeley Tomlinson EF. Relationships Among Population Size, Environmental Factors, and Reproduction in Lupinus perennis (Fabaceae). AMERICAN MIDLAND NATURALIST 2019. [DOI: 10.1674/0003-0031-182.2.160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Helen J. Michaels
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio 43403
| | - Carrie A. Cartwright
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio 43403
| | | |
Collapse
|
62
|
Shin MG, Bulyntsev SV, Chang PL, Korbu LB, Carrasquila-Garcia N, Vishnyakova MA, Samsonova MG, Cook DR, Nuzhdin SV. Multi-trait analysis of domestication genes in Cicer arietinum - Cicer reticulatum hybrids with a multidimensional approach: Modeling wide crosses for crop improvement. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 285:122-131. [PMID: 31203876 DOI: 10.1016/j.plantsci.2019.04.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/17/2019] [Accepted: 04/20/2019] [Indexed: 06/09/2023]
Abstract
Domestication and subsequent breeding have eroded genetic diversity in the modern chickpea crop by ˜100-fold. Corresponding reductions to trait variation create the need, and an opportunity, to identify and harness the genetic capacity of wild species for crop improvement. Here we analyze trait segregation in a series of wild x cultivated hybrid populations to delineate the genetic underpinnings of domestication traits. Two species of wild chickpea, C. reticulatum and C. echinospermum, were crossed with the elite, early flowering C. arietinum cultivar ICCV96029. KASP genotyping of F2 parents with an FT-linked molecular marker enabled selection of 284 F3 families with reduced phenological variation: 255 F3 families of C. arietinum x reticulatum (AR) derived from 17 diverse wild parents and 29 F3 families of C. arietinum x echinospermum (AE) from 3 wild parents. The combined 284 lineages were genotyped using a genotyping-by-sequencing strategy and phenotyped for agronomic traits. 50 QTLs in 11 traits were detected from AR and 35 QTLs in 10 traits from the combined data. Using hierarchical clustering to assign traits to six correlated groups and mixed model based multi-trait mapping, four pleiotropic loci were identified. Bayesian analysis further identified four inter-trait relationships controlling the duration of vegetative growth and seed maturation, for which the underlying pleiotropic genes were mapped. A random forest approach was used to explore the most extreme trait differences between AR and AE progenies, identifying traits most characteristic of wild species origin. Knowledge of the genomic basis of traits that segregate in wild-cultivated hybrid populations will facilitate chickpea improvement by linking genetic and phenotypic variation in a quantitative genetic framework.
Collapse
Affiliation(s)
- Min-Gyoung Shin
- University of Southern California, Program Quantitative and Computational Biology, Dornsife College of Letters Arts & Science, Los Angeles, CA 90089, USA.
| | - Sergey V Bulyntsev
- Federal Research Center The NI Vavilov All Russian Institute of Plant Genetic Resources, St Petersburg, Russia.
| | - Peter L Chang
- University of Southern California, Program Molecular & Computational Biology, Dornsife College of Letters Arts & Science, Los Angeles, CA 90089, USA; University of California Davis, Department of Plant Pathology, Davis, CA 95616, USA.
| | - Lijalem Balcha Korbu
- University of California Davis, Department of Plant Pathology, Davis, CA 95616, USA; Ethiopian Institute of Agricultural Research, Debre Zeit, Ethiopia.
| | | | - Margarita A Vishnyakova
- Federal Research Center The NI Vavilov All Russian Institute of Plant Genetic Resources, St Petersburg, Russia.
| | - Maria G Samsonova
- Peter the Great St Petersburg Polytechnich University, Department of Applied Mathematics, St Petersburg, Russia.
| | - Douglas R Cook
- University of California Davis, Department of Plant Pathology, Davis, CA 95616, USA.
| | - Sergey V Nuzhdin
- University of Southern California, Program Molecular & Computational Biology, Dornsife College of Letters Arts & Science, Los Angeles, CA 90089, USA; Peter the Great St Petersburg Polytechnich University, Department of Applied Mathematics, St Petersburg, Russia.
| |
Collapse
|
63
|
Amalraj A, Taylor J, Sutton T. A hydroponics based high throughput screening system for Phytophthora root rot resistance in chickpea ( Cicer arietinum L.). PLANT METHODS 2019; 15:82. [PMID: 31372178 PMCID: PMC6659211 DOI: 10.1186/s13007-019-0463-3] [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: 01/29/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Phytophthora root rot (PRR) caused by P. medicaginis is a major soil borne disease in chickpea growing regions of Australia. Sources of resistance have been identified in both cultivated and wild Cicer species. However, the molecular basis underlying PRR resistance is not known. Current phenotyping methods rely on mycelium slurry or oospore inoculum. Sensitive and reliable methods are desirable to study variation for PRR resistance in chickpea and allow for a controlled inoculation process to better capture early defence responses following PRR infection. RESULTS In this study, a procedure for P. medicaginis zoospore production was standardized and used as the inoculum to develop a hydroponics based in planta infection method to screen chickpea genotypes with established levels of PRR resistance. The efficiency of the system was both qualitatively validated based on observation of characteristic PRR symptom development, and quantitatively validated based on the amount of pathogen DNA in roots. This system was scaled up to screen two biparental mapping populations previously developed for PRR studies. For each of the screenings, plant survival time was measured after inoculation and used to derive Kaplan-Meier estimates of plant survival (KME-survival). KME-survival and canker length were then selected as phenotypic traits associated with PRR resistance. Genetic analysis of these traits was conducted which identified quantitative trait loci (QTL). Additionally, these hydroponic traits and a set of previously published plant survival traits obtained from multiple PRR field experiments were combined in a model-based correlation analysis. The results suggest that the underlying genetic basis for plant survival during PRR infection within hydroponics and field disease environments is linked. The QTL QRBprrkms03 and QRBprrck03 on chromosome 4 identified for the traits KME-survival and canker length, respectively, correspond to the same region reported for PRR resistance in a field disease experiment. CONCLUSION A hydroponics based screening system will facilitate reliable and rapid screening in both small- and large-scale experiments to study PRR disease in chickpea. It can be applied in chickpea breeding programs to screen for PRR resistance and classify the virulence of new and existing P. medicaginis isolates.
Collapse
Affiliation(s)
- Amritha Amalraj
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA 5064 Australia
| | - Julian Taylor
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA 5064 Australia
| | - Tim Sutton
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA 5064 Australia
- South Australian Research and Development Institute, GPO Box 397, Adelaide, SA 5001 Australia
| |
Collapse
|
64
|
Zwart RS, Thudi M, Channale S, Manchikatla PK, Varshney RK, Thompson JP. Resistance to Plant-Parasitic Nematodes in Chickpea: Current Status and Future Perspectives. FRONTIERS IN PLANT SCIENCE 2019; 10:966. [PMID: 31428112 PMCID: PMC6689962 DOI: 10.3389/fpls.2019.00966] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/10/2019] [Indexed: 06/10/2023]
Abstract
Plant-parasitic nematodes constrain chickpea (Cicer arietinum) production, with annual yield losses estimated to be 14% of total global production. Nematode species causing significant economic damage in chickpea include root-knot nematodes (Meloidogyne artiella, M. incognita, and M. javanica), cyst nematode (Heterodera ciceri), and root-lesion nematode (Pratylenchus thornei). Reduced functionality of roots from nematode infestation leads to water stress and nutrient deficiency, which in turn lead to poor plant growth and reduced yield. Integration of resistant crops with appropriate agronomic practices is recognized as the safest and most practical, economic and effective control strategy for plant-parasitic nematodes. However, breeding for resistance to plant-parasitic nematodes has numerous challenges that originate from the narrow genetic diversity of the C. arietinum cultigen. While levels of resistance to M. artiella, H. ciceri, and P. thornei have been identified in wild Cicer species that are superior to resistance levels in the C. arietinum cultigen, barriers to interspecific hybridization restrict the use of these crop wild relatives, as sources of nematode resistance. Wild Cicer species of the primary genepool, C. reticulatum and C. echinospermum, are the only species that have been used to introgress resistance genes into the C. arietinum cultigen. The availability of genomic resources, including genome sequence and re-sequence information, the chickpea reference set and mini-core collections, and new wild Cicer collections, provide unprecedented opportunities for chickpea improvement. This review surveys progress in the identification of novel genetic sources of nematode resistance in international germplasm collections and recommends genome-assisted breeding strategies to accelerate introgression of nematode resistance into elite chickpea cultivars.
Collapse
Affiliation(s)
- Rebecca S. Zwart
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Mahendar Thudi
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Sonal Channale
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Praveen K. Manchikatla
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - John P. Thompson
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
| |
Collapse
|
65
|
Greenlon A, Chang PL, Damtew ZM, Muleta A, Carrasquilla-Garcia N, Kim D, Nguyen HP, Suryawanshi V, Krieg CP, Yadav SK, Patel JS, Mukherjee A, Udupa S, Benjelloun I, Thami-Alami I, Yasin M, Patil B, Singh S, Sarma BK, von Wettberg EJB, Kahraman A, Bukun B, Assefa F, Tesfaye K, Fikre A, Cook DR. Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria. Proc Natl Acad Sci U S A 2019; 116:15200-15209. [PMID: 31285337 PMCID: PMC6660780 DOI: 10.1073/pnas.1900056116] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Although microorganisms are known to dominate Earth's biospheres and drive biogeochemical cycling, little is known about the geographic distributions of microbial populations or the environmental factors that pattern those distributions. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of the nitrogen-fixing bacterial symbionts of the crop chickpea, generating 1,027 draft whole-genome sequences at the level of bacterial populations, including 14 high-quality PacBio genomes from a phylogenetically representative subset. We find that diverse Mesorhizobium taxa perform symbiosis with chickpea and have largely overlapping global distributions. However, sampled locations cluster based on the phylogenetic diversity of Mesorhizobium populations, and diversity clusters correspond to edaphic and environmental factors, primarily soil type and latitude. Despite long-standing evolutionary divergence and geographic isolation, the diverse taxa observed to nodulate chickpea share a set of integrative conjugative elements (ICEs) that encode the major functions of the symbiosis. This symbiosis ICE takes 2 forms in the bacterial chromosome-tripartite and monopartite-with tripartite ICEs confined to a broadly distributed superspecies clade. The pairwise evolutionary relatedness of these elements is controlled as much by geographic distance as by the evolutionary relatedness of the background genome. In contrast, diversity in the broader gene content of Mesorhizobium genomes follows a tight linear relationship with core genome phylogenetic distance, with little detectable effect of geography. These results illustrate how geography and demography can operate differentially on the evolution of bacterial genomes and offer useful insights for the development of improved technologies for sustainable agriculture.
Collapse
Affiliation(s)
- Alex Greenlon
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Peter L Chang
- Department of Plant Pathology, University of California, Davis, CA 95616
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Zehara Mohammed Damtew
- College of Natural Sciences, Addis Ababa University, Addis Ababa, 32853 Ethiopia
- Debre Zeit Agricultural Research Center, Ethiopian Institute for Agricultural Research, Bishoftu, Ethiopia
| | - Atsede Muleta
- College of Natural Sciences, Addis Ababa University, Addis Ababa, 32853 Ethiopia
| | | | - Donghyun Kim
- International Crop Research Institute for the Semi-Arid Tropics, Hyderabad 502324, India
| | - Hien P Nguyen
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 183-8509 Tokyo, Japan
| | - Vasantika Suryawanshi
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Christopher P Krieg
- Department of Biological Sciences, Florida International University, Miami, FL 33199
| | - Sudheer Kumar Yadav
- Department of Mycology and Plant Pathology, Banaras Hindu University, Varanasi 221005, India
| | - Jai Singh Patel
- Department of Mycology and Plant Pathology, Banaras Hindu University, Varanasi 221005, India
| | - Arpan Mukherjee
- Department of Mycology and Plant Pathology, Banaras Hindu University, Varanasi 221005, India
| | - Sripada Udupa
- Biodiversity and Integrated Gene Management Program, International Center for Agricultural Research in the Dry Areas, 10112 Rabat, Morocco
| | - Imane Benjelloun
- Institute National de la Recherche Agronomique, 10100 Rabat, Morocco
| | - Imane Thami-Alami
- Institute National de la Recherche Agronomique, 10100 Rabat, Morocco
| | | | - Bhuvaneshwara Patil
- Department of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad 580001, India
| | - Sarvjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana 141027, India
| | - Birinchi Kumar Sarma
- Department of Mycology and Plant Pathology, Banaras Hindu University, Varanasi 221005, India
| | - Eric J B von Wettberg
- Department of Biological Sciences, Florida International University, Miami, FL 33199
- Department of Plant and Soil Science, University of Vermont, Burlington, VT 05405
| | - Abdullah Kahraman
- Department of Field Crops, Faculty of Agriculture, Harran University, 63100 Sanliurfa, Turkey
| | - Bekir Bukun
- Department of Plant Protection, Dicle University, 21280 Diyarbakir, Turkey
| | - Fassil Assefa
- College of Natural Sciences, Addis Ababa University, Addis Ababa, 32853 Ethiopia
| | - Kassahun Tesfaye
- College of Natural Sciences, Addis Ababa University, Addis Ababa, 32853 Ethiopia
| | - Asnake Fikre
- Debre Zeit Agricultural Research Center, Ethiopian Institute for Agricultural Research, Bishoftu, Ethiopia
| | - Douglas R Cook
- Department of Plant Pathology, University of California, Davis, CA 95616;
| |
Collapse
|
66
|
Ortega R, Hecht VFG, Freeman JS, Rubio J, Carrasquilla-Garcia N, Mir RR, Penmetsa RV, Cook DR, Millan T, Weller JL. Altered Expression of an FT Cluster Underlies a Major Locus Controlling Domestication-Related Changes to Chickpea Phenology and Growth Habit. FRONTIERS IN PLANT SCIENCE 2019; 10:824. [PMID: 31333691 PMCID: PMC6616154 DOI: 10.3389/fpls.2019.00824] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 06/07/2019] [Indexed: 05/20/2023]
Abstract
Flowering time is a key trait in breeding and crop evolution, due to its importance for adaptation to different environments and for yield. In the particular case of chickpea, selection for early phenology was essential for the successful transition of this species from a winter to a summer crop. Here, we used genetic and expression analyses in two different inbred populations to examine the genetic control of domestication-related differences in flowering time and growth habit between domesticated chickpea and its wild progenitor Cicer reticulatum. A single major quantitative trait locus for flowering time under short-day conditions [Days To Flower (DTF)3A] was mapped to a 59-gene interval on chromosome three containing a cluster of three FT genes, which collectively showed upregulated expression in domesticated relative to wild parent lines. An equally strong association with growth habit suggests a pleiotropic effect of the region on both traits. These results indicate the likely molecular explanation for the characteristic early flowering of domesticated chickpea, and the previously described growth habit locus Hg. More generally, they point to de-repression of this specific gene cluster as a conserved mechanism for achieving adaptive early phenology in temperate legumes.
Collapse
Affiliation(s)
- Raul Ortega
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | | | - Jules S. Freeman
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- Scion, Rotorua, New Zealand
| | - Josefa Rubio
- E. Genomica y Biotecnologia, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), Córdoba, Spain
| | | | - Reyazul Rouf Mir
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - R. Varma Penmetsa
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Douglas R. Cook
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Teresa Millan
- Department of Genetics ETSIAM, University of Córdoba, Córdoba, Spain
| | - James L. Weller
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| |
Collapse
|
67
|
Reen RA, Mumford MH, Thompson JP. Novel Sources of Resistance to Root-Lesion Nematode ( Pratylenchus thornei) in a New Collection of Wild Cicer Species ( C. reticulatum and C. echinospermum) to Improve Resistance in Cultivated Chickpea ( C. arietinum). PHYTOPATHOLOGY 2019; 109:1270-1279. [PMID: 30895867 DOI: 10.1094/phyto-02-19-0047-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Pratylenchus thornei, a nematode species that feeds and reproduces in chickpea (Cicer arietinum) roots, is widespread throughout the Mediterranean basin and Indian subcontinent. In Australia, it can cause yield losses up to approximately 25% of intolerant chickpea cultivars. Potential for improvement has been hindered by the narrow genetic diversity of cultivated chickpea and a limited world collection of original wild Cicer spp. in the primary gene pool, consisting of 18 C. reticulatum and 10 C. echinospermum accessions. Recently, collections of C. reticulatum and C. echinospermum from Turkey have substantially increased the number of accessions. This study evaluated 133 C. reticulatum and 41 C. echinospermum accessions from the new collection for resistance to P. thornei under controlled conditions in repeated glasshouse pot experiments. The aim of the study was to identify accessions with resistance superior to that currently available in Australian germplasm. Both wild Cicer spp. were found, on average, to be more resistant to P. thornei (P < 0.001) than C. arietinum. Combined analyses across experiments to determine genetic rankings showed that 13 (7%) wild accessions were significantly more resistant than the most resistant C. echinospermum reference ILWC 246, while another 40 (23%) accessions were significantly more resistant than the least susceptible Australian chickpea cultivar PBA Seamer. Mean P. thornei population densities differed significantly between collection sites in Turkey and within each of the genetic population groups. The sites Kayatepe and Baristepe1, and genetic population groups Ret_A and Ret_F associated with sites Oyali and Baristepe1, produced the lowest P. thornei population densities. This is the first report assessing the resistance to P. thornei of this new collection which offers novel sources of P. thornei resistance and untapped genetic diversity valuable for international chickpea breeding programs to exploit.
Collapse
Affiliation(s)
- Roslyn A Reen
- 1 Centre for Crop Health, University of Southern Queensland, Toowoomba, 4350, QLD, Australia
| | - Michael H Mumford
- 2 Department of Agriculture and Fisheries, Leslie Research Facility, Toowoomba, 4350, QLD Australia
| | - John P Thompson
- 1 Centre for Crop Health, University of Southern Queensland, Toowoomba, 4350, QLD, Australia
| |
Collapse
|
68
|
Warschefsky EJ, von Wettberg EJB. Population genomic analysis of mango (Mangifera indica) suggests a complex history of domestication. THE NEW PHYTOLOGIST 2019; 222:2023-2037. [PMID: 30730057 DOI: 10.1111/nph.15731] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 01/21/2019] [Indexed: 05/22/2023]
Abstract
Humans have domesticated diverse species from across the plant kingdom, yet much of our foundational knowledge of domestication has come from studies investigating relatively few of the most important annual food crops. Here, we examine the impacts of domestication on genetic diversity in a tropical perennial fruit species, mango (Mangifera indica). We used restriction site associated DNA sequencing to generate genomic single nucleotide polymorphism (SNP) data from 106 mango cultivars from seven geographical regions along with 52 samples of closely related species and unidentified cultivars to identify centers of mango genetic diversity and examine how post-domestication dispersal shaped the geographical distribution of diversity. We identify two gene pools of cultivated mango, representing Indian and Southeast Asian germplasm. We found no significant genetic bottleneck associated with the introduction of mango into new regions of the world. By contrast, we show that mango populations in introduced regions have elevated levels of diversity. Our results suggest that mango has a more complex history of domestication than previously supposed, perhaps including multiple domestication events, hybridization and regional selection. Our work has direct implications for mango breeding and genebank management, and also builds on recent efforts to understand how woody perennial crops respond to domestication.
Collapse
Affiliation(s)
- Emily J Warschefsky
- Biological Sciences, Florida International University, 11200 SW 8th St., Miami, FL, 33199, USA
| | - Eric J B von Wettberg
- Biological Sciences, Florida International University, 11200 SW 8th St., Miami, FL, 33199, USA
- Plant and Soil Science, The University of Vermont, 63 Carrigan Drive, Burlington, VT, USA
| |
Collapse
|
69
|
Zhang H, Yasmin F, Song BH. Neglected treasures in the wild - legume wild relatives in food security and human health. CURRENT OPINION IN PLANT BIOLOGY 2019; 49:17-26. [PMID: 31085425 PMCID: PMC6817337 DOI: 10.1016/j.pbi.2019.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 05/08/2023]
Abstract
The legume family (Fabaceae) is the third-largest flowering family with over 18 000 species worldwide that are rich in proteins, oils, and nutrients. However, the production potential of legume-derived food cannot meet increasing global demand. Wild legumes represent a large group of wild species adaptive to diverse habitats and harbor rich genetic diversity for the improvement of the agronomic, nutritional, and medicinal values of the domesticated legumes. Accumulating evidence suggests that the genetic variation retained in these under-exploited leguminous wild relatives can be used to improve crop yield, nutrient contents, and resistance/tolerance to environmental stresses via the integration of omics, genetics, and genome-editing technologies.
Collapse
Affiliation(s)
- Hengyou Zhang
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Farida Yasmin
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Bao-Hua Song
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| |
Collapse
|
70
|
Varshney RK, Thudi M, Roorkiwal M, He W, Upadhyaya HD, Yang W, Bajaj P, Cubry P, Rathore A, Jian J, Doddamani D, Khan AW, Garg V, Chitikineni A, Xu D, Gaur PM, Singh NP, Chaturvedi SK, Nadigatla GVPR, Krishnamurthy L, Dixit GP, Fikre A, Kimurto PK, Sreeman SM, Bharadwaj C, Tripathi S, Wang J, Lee SH, Edwards D, Polavarapu KKB, Penmetsa RV, Crossa J, Nguyen HT, Siddique KHM, Colmer TD, Sutton T, von Wettberg E, Vigouroux Y, Xu X, Liu X. Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits. Nat Genet 2019; 51:857-864. [DOI: 10.1038/s41588-019-0401-3] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 03/21/2019] [Indexed: 11/09/2022]
|
71
|
Fawcett S, Sistla S, Dacosta‐Calheiros M, Kahraman A, Reznicek AA, Rosenberg R, von Wettberg EJB. Tracking microhabitat temperature variation with iButton data loggers. APPLICATIONS IN PLANT SCIENCES 2019; 7:e01237. [PMID: 31024781 PMCID: PMC6476170 DOI: 10.1002/aps3.1237] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/07/2019] [Indexed: 05/11/2023]
Abstract
PREMISE OF THE STUDY Fine-scale variation in temperature and soil moisture contribute to microhabitats across the landscape, affecting plant phenology, distribution, and fitness. The recent availability of compact and inexpensive temperature and humidity data loggers such as iButtons has facilitated research on microclimates. METHODS AND RESULTS Here, we highlight the use of iButtons in three distinct settings: comparisons of empirical data to modeled climate data for rare rock ferns in the genus Asplenium in eastern North America; generation of fine-scale data to predict flowering time and vernalization responsiveness of crop wild relatives of chickpea from southeastern Anatolia; and measurements of extreme thermal variation of solar array installations in Vermont. DISCUSSION We highlight a range of challenges with iButtons, including serious limitations of the Hygrochron function that affect their utility for measuring soil moisture, and methods for protecting them from the elements and from human interference. Finally, we provide MATLAB code to facilitate the processing of raw iButton data.
Collapse
Affiliation(s)
- Susan Fawcett
- Pringle Herbarium, Department of Plant BiologyUniversity of Vermont63 Carrigan DriveBurlingtonVermont05401USA
| | - Seeta Sistla
- Biological and Life SciencesHampshire College893 West StreetAmherstMassachusetts01002USA
| | - Manny Dacosta‐Calheiros
- Biological SciencesFlorida International University11200 SW 8th Street (CP‐304)MiamiFlorida33199USA
| | - Abdullah Kahraman
- Department of Field CropsHarran UniversityOsmanbey YerleşkesiŞanlıurfa‐Mardin Karayolu Üzeri 18 Km63300ŞanlıurfaTurkey
| | - Anton A. Reznicek
- University of Michigan Herbarium3600 Varsity DriveAnn ArborMichigan48108USA
| | - Rachel Rosenberg
- Biological and Life SciencesHampshire College893 West StreetAmherstMassachusetts01002USA
| | - Eric J. B. von Wettberg
- Biological SciencesFlorida International University11200 SW 8th Street (CP‐304)MiamiFlorida33199USA
- Department of Plant and Soil ScienceUniversity of Vermont63 Carrigan DriveBurlingtonVermont05401USA
| |
Collapse
|
72
|
Amalraj A, Taylor J, Bithell S, Li Y, Moore K, Hobson K, Sutton T. Mapping resistance to Phytophthora root rot identifies independent loci from cultivated (Cicer arietinum L.) and wild (Cicer echinospermum P.H. Davis) chickpea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1017-1033. [PMID: 30535647 DOI: 10.1007/s00122-018-3256-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 11/30/2018] [Indexed: 05/05/2023]
Abstract
Major QTL for Phytophthora root rot resistance have been identified in three mapping populations with independent sources of resistance contributed by C. echinospermum and C. arietinum. Phytophthora root rot (PRR) caused by the oomycete Phytophthora medicaginis is a major soil-borne disease of chickpea in Australia. With no economic in-crop control of PRR, a genetic approach to improve resistance is the most practical management option. Moderate field resistance has been incorporated in the cultivated C. arietinum variety, Yorker, and a higher level of resistance has been identified in a derivative of wild chickpea (C. echinospermum, interspecific breeding line 04067-81-2-1-1). These genotypes and two other released varieties were used to develop one intra-specific and two interspecific F6-derived recombinant inbred line mapping populations for genetic analysis of resistance. The Yorker × Genesis114 (YG), Rupali × 04067-81-2-1-1 (RB) and Yorker × 04067-81-2-1-1 (YB) populations were genotyped using genotyping-by-sequencing and phenotyped for PRR under three field environments with a mixture of 10 P. medicaginis isolates. Whole-genome QTL analysis identified major QTL QRBprrsi01, QYBprrsi01, QRBprrsi03 and QYBprrsi02 for PRR resistance on chromosomes 3 and 6, in RB and YB populations, respectively, with the resistance source derived from the wild Cicer species. QTL QYGprrsi02 and QYGprrsi03 were also identified on chromosomes 5 and 6 in YG population from C. arietinum. Aligning QTL regions to the corresponding chickpea reference genome suggested that the resistance source from C. arietinum and C. echinospermum may be different. The findings from this study provide tools for marker-assisted selection in chickpea breeding and information to assist the development of populations suitable for fine-mapping of resistance loci to determine the molecular basis for PRR resistance in chickpea.
Collapse
Affiliation(s)
- Amritha Amalraj
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia
| | - Julian Taylor
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia
| | - Sean Bithell
- NSW Department of Primary Industries, 4 Marsden Park Rd, Tamworth, NSW, 2340, Australia
| | - Yongle Li
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia
| | - Kevin Moore
- NSW Department of Primary Industries, 4 Marsden Park Rd, Tamworth, NSW, 2340, Australia
| | - Kristy Hobson
- NSW Department of Primary Industries, 4 Marsden Park Rd, Tamworth, NSW, 2340, Australia
| | - Tim Sutton
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia.
- South Australian Research and Development Institute, GPO Box 397, Adelaide, SA, 5001, Australia.
| |
Collapse
|
73
|
Kozlov K, Singh A, Berger J, Bishop-von Wettberg E, Kahraman A, Aydogan A, Cook D, Nuzhdin S, Samsonova M. Non-linear regression models for time to flowering in wild chickpea combine genetic and climatic factors. BMC PLANT BIOLOGY 2019; 19:94. [PMID: 30890147 PMCID: PMC6423741 DOI: 10.1186/s12870-019-1685-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
BACKGROUND Accurate prediction of crop flowering time is required for reaching maximal farm efficiency. Several models developed to accomplish this goal are based on deep knowledge of plant phenology, requiring large investment for every individual crop or new variety. Mathematical modeling can be used to make better use of more shallow data and to extract information from it with higher efficiency. Cultivars of chickpea, Cicer arietanum, are currently being improved by introgressing wild C. reticulatum biodiversity with very different flowering time requirements. More understanding is required for how flowering time will depend on environmental conditions in these cultivars developed by introgression of wild alleles. RESULTS We built a novel model for flowering time of wild chickpeas collected at 21 different sites in Turkey and grown in 4 distinct environmental conditions over several different years and seasons. We propose a general approach, in which the analytic forms of dependence of flowering time on climatic parameters, their regression coefficients, and a set of predictors are inferred automatically by stochastic minimization of the deviation of the model output from data. By using a combination of Grammatical Evolution and Differential Evolution Entirely Parallel method, we have identified a model that reflects the influence of effects of day length, temperature, humidity and precipitation and has a coefficient of determination of R2=0.97. CONCLUSIONS We used our model to test two important hypotheses. We propose that chickpea phenology may be strongly predicted by accession geographic origin, as well as local environmental conditions at the site of growth. Indeed, the site of origin-by-growth environment interaction accounts for about 14.7% of variation in time period from sowing to flowering. Secondly, as the adaptation to specific environments is blueprinted in genomes, the effects of genes on flowering time may be conditioned on environmental factors. Genotype-by-environment interaction accounts for about 17.2% of overall variation in flowering time. We also identified several genomic markers associated with different reactions to climatic factor changes. Our methodology is general and can be further applied to extend existing crop models, especially when phenological information is limited.
Collapse
Affiliation(s)
- Konstantin Kozlov
- Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya, St. Petersburg, 195251 Russia
| | - Anupam Singh
- Program Molecular and Computation Biology, University of California, University Park, Los-Angeles, 24105 CA USA
| | - Jens Berger
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, Underwood Ave, Perth, 6014 WA Australia
| | - Eric Bishop-von Wettberg
- Department of Plant and Soil Science, University of Vermont, 63 Carrigan Drive, Burlington, 05405 VT USA
| | - Abdullah Kahraman
- Department of Field Crops, Faculty of Agriculture, Harran University, Osmanbey Campus, Sanliurfa, 63100 Turkey
| | - Abdulkadir Aydogan
- Central Research Institute for Field Crops (CRIFC), P.O. Box 226, Ankara, 06042 Turkey
| | - Douglas Cook
- Deptartment of Plant Pathology, University of California, One Shields Ave, Davis, 95616-8680 CA USA
| | - Sergey Nuzhdin
- Program Molecular and Computation Biology, University of California, University Park, Los-Angeles, 24105 CA USA
| | - Maria Samsonova
- Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya, St. Petersburg, 195251 Russia
| |
Collapse
|
74
|
Varshney RK, Pandey MK, Bohra A, Singh VK, Thudi M, Saxena RK. Toward the sequence-based breeding in legumes in the post-genome sequencing era. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:797-816. [PMID: 30560464 PMCID: PMC6439141 DOI: 10.1007/s00122-018-3252-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/27/2018] [Indexed: 05/19/2023]
Abstract
Efficiency of breeding programs of legume crops such as chickpea, pigeonpea and groundnut has been considerably improved over the past decade through deployment of modern genomic tools and technologies. For instance, next-generation sequencing technologies have facilitated availability of genome sequence assemblies, re-sequencing of several hundred lines, development of HapMaps, high-density genetic maps, a range of marker genotyping platforms and identification of markers associated with a number of agronomic traits in these legume crops. Although marker-assisted backcrossing and marker-assisted selection approaches have been used to develop superior lines in several cases, it is the need of the hour for continuous population improvement after every breeding cycle to accelerate genetic gain in the breeding programs. In this context, we propose a sequence-based breeding approach which includes use of independent or combination of parental selection, enhancing genetic diversity of breeding programs, forward breeding for early generation selection, and genomic selection using sequencing/genotyping technologies. Also, adoption of speed breeding technology by generating 4-6 generations per year will be contributing to accelerate genetic gain. While we see a huge potential of the sequence-based breeding to revolutionize crop improvement programs in these legumes, we anticipate several challenges especially associated with high-quality and precise phenotyping at affordable costs, data analysis and management related to improving breeding operation efficiency. Finally, integration of improved seed systems and better agronomic packages with the development of improved varieties by using sequence-based breeding will ensure higher genetic gains in farmers' fields.
Collapse
Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
| | - Vikas K Singh
- International Rice Research Institute (IRRI), IRRI South Asia Hub, ICRISAT, Hyderabad, 502324, India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| |
Collapse
|
75
|
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.
Collapse
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
| |
Collapse
|
76
|
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.
Collapse
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
| |
Collapse
|
77
|
Burgarella C, Barnaud A, Kane NA, Jankowski F, Scarcelli N, Billot C, Vigouroux Y, Berthouly-Salazar C. Adaptive Introgression: An Untapped Evolutionary Mechanism for Crop Adaptation. FRONTIERS IN PLANT SCIENCE 2019; 10:4. [PMID: 30774638 PMCID: PMC6367218 DOI: 10.3389/fpls.2019.00004] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 01/04/2019] [Indexed: 05/18/2023]
Abstract
Global environmental changes strongly impact wild and domesticated species biology and their associated ecosystem services. For crops, global warming has led to significant changes in terms of phenology and/or yield. To respond to the agricultural challenges of this century, there is a strong need for harnessing the genetic variability of crops and adapting them to new conditions. Gene flow, from either the same species or a different species, may be an immediate primary source to widen genetic diversity and adaptions to various environments. When the incorporation of a foreign variant leads to an increase of the fitness of the recipient pool, it is referred to as "adaptive introgression". Crop species are excellent case studies of this phenomenon since their genetic variability has been considerably reduced over space and time but most of them continue exchanging genetic material with their wild relatives. In this paper, we review studies of adaptive introgression, presenting methodological approaches and challenges to detecting it. We pay particular attention to the potential of this evolutionary mechanism for the adaptation of crops. Furthermore, we discuss the importance of farmers' knowledge and practices in shaping wild-to-crop gene flow. Finally, we argue that screening the wild introgression already existing in the cultivated gene pool may be an effective strategy for uncovering wild diversity relevant for crop adaptation to current environmental changes and for informing new breeding directions.
Collapse
Affiliation(s)
- Concetta Burgarella
- Institut de Recherche pour le Développement, UMR DIADE, Montpellier, France
- DIADE, Université de Montpellier, Montpellier, France
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Institut National de la Recherche Agronomique, Montpellier SupAgro, Montpellier, France
- *Correspondence: Concetta Burgarella, Cécile Berthouly-Salazar,
| | - Adeline Barnaud
- Institut de Recherche pour le Développement, UMR DIADE, Montpellier, France
- DIADE, Université de Montpellier, Montpellier, France
| | - Ndjido Ardo Kane
- Laboratoire National de Recherches sur les Productions Végétales, Institut Sénégalais de Recherches Agricoles, Dakar, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux, Dakar, Senegal
| | - Frédérique Jankowski
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UPR GREEN, Montpellier, France
- GREEN, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Université de Montpellier, Montpellier, France
- Bureau d’Analyses Macro-Economiques, Institut Sénégalais de Recherches Agricoles, Dakar, Senegal
| | - Nora Scarcelli
- Institut de Recherche pour le Développement, UMR DIADE, Montpellier, France
- DIADE, Université de Montpellier, Montpellier, France
| | - Claire Billot
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Institut National de la Recherche Agronomique, Montpellier SupAgro, Montpellier, France
| | - Yves Vigouroux
- Institut de Recherche pour le Développement, UMR DIADE, Montpellier, France
- DIADE, Université de Montpellier, Montpellier, France
| | - Cécile Berthouly-Salazar
- Institut de Recherche pour le Développement, UMR DIADE, Montpellier, France
- DIADE, Université de Montpellier, Montpellier, France
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux, Dakar, Senegal
- *Correspondence: Concetta Burgarella, Cécile Berthouly-Salazar,
| |
Collapse
|
78
|
Zaidem ML, Groen SC, Purugganan MD. Evolutionary and ecological functional genomics, from lab to the wild. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:40-55. [PMID: 30444573 DOI: 10.1111/tpj.14167] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/10/2018] [Accepted: 11/13/2018] [Indexed: 05/12/2023]
Abstract
Plant phenotypes are the result of both genetic and environmental forces that act to modulate trait expression. Over the last few years, numerous approaches in functional genomics and systems biology have led to a greater understanding of plant phenotypic variation and plant responses to the environment. These approaches, and the questions that they can address, have been loosely termed evolutionary and ecological functional genomics (EEFG), and have been providing key insights on how plants adapt and evolve. In particular, by bringing these studies from the laboratory to the field, EEFG studies allow us to gain greater knowledge of how plants function in their natural contexts.
Collapse
Affiliation(s)
- Maricris L Zaidem
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
| | - Simon C Groen
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
| | - Michael D Purugganan
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
- Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| |
Collapse
|
79
|
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.
Collapse
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.
| |
Collapse
|
80
|
Chen YH, Ruiz-Arocho J, von Wettberg EJ. Crop domestication: anthropogenic effects on insect-plant interactions in agroecosystems. CURRENT OPINION IN INSECT SCIENCE 2018; 29:56-63. [PMID: 30551826 DOI: 10.1016/j.cois.2018.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/13/2018] [Accepted: 06/20/2018] [Indexed: 05/14/2023]
Abstract
Although crop domestication is considered a model system for understanding evolution, the eco-evolutionary effects of domesticated crops on higher trophic levels have rarely been discussed. Changes in size, shape, quality, or timing of plant traits during domestication can influence entire arthropod communities. The plant traits specific to crop plants can be rare in nature. In the face of such novelty, it is important to understand how species and trophic levels vary in their responses. Although the evidence is still limited, crop domestication can influence the ecology, genetics, and evolution of plants, insect herbivores, natural enemies, and pollinators. We call for more study on how eco-evolutionary processes operate under domestication to provide new insight on the sustainability of species interactions within agroecosystems.
Collapse
Affiliation(s)
- Yolanda H Chen
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, USA.
| | - Jorge Ruiz-Arocho
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, USA
| | - Eric Jb von Wettberg
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, USA
| |
Collapse
|
81
|
Shunmugam ASK, Kannan U, Jiang Y, Daba KA, Gorim LY. Physiology Based Approaches for Breeding of Next-Generation Food Legumes. PLANTS (BASEL, SWITZERLAND) 2018; 7:E72. [PMID: 30205575 PMCID: PMC6161296 DOI: 10.3390/plants7030072] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/31/2018] [Accepted: 09/07/2018] [Indexed: 01/05/2023]
Abstract
Plant breeders and agricultural scientists of the 21st century are challenged to increase the yield potentials of crops to feed the growing world population. Climate change, the resultant stresses and increasing nutrient deficiencies are factors that are to be considered in designing modern plant breeding pipelines. Underutilized food legumes have the potential to address these issues and ensure food security in developing nations of the world. Food legumes in the past have drawn limited research funding and technological attention when compared to cereal crops. Physiological breeding strategies that were proven to be successful in cereals are to be adapted to legume crop improvement to realize their potential. The gap between breeders and physiologists should be narrowed by collaborative approaches to understand complex traits in legumes. This review discusses the potential of physiology based approaches in food legume breeding and how they impact yield gains and abiotic stress tolerance in these crops. The influence of roots and root system architectures in food legumes' breeding is also discussed. Molecular breeding to map the relevant physiological traits and the potentials of gene editing those traits are detailed. It is imperative to unlock the potentials of these underutilized crops to attain sustainable environmental and nutritional food security.
Collapse
Affiliation(s)
- Arun S K Shunmugam
- Department of Plant Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N5A8, Canada.
| | - Udhaya Kannan
- Department of Plant Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N5A8, Canada.
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Center, 107 Science Place, Saskatoon, SK S7N0X2, Canada.
| | - Yunfei Jiang
- Department of Plant Agriculture, University of Guelph, 50 Stone Road E., Guelph, ON N1G2W1, Canada.
| | - Ketema A Daba
- Department of Plant Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N5A8, Canada.
| | - Linda Y Gorim
- Department of Plant Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N5A8, Canada.
| |
Collapse
|
82
|
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.
Collapse
|
83
|
Abstract
Humans have domesticated hundreds of plant and animal species as sources of food, fiber, forage, and tools over the past 12,000 years, with manifold effects on both human society and the genetic structure of the domesticated species. The outcomes of crop domestication were shaped by selection driven by human preferences, cultivation practices, and agricultural environments, as well as other population genetic processes flowing from the ensuing reduction in effective population size. It is obvious that any selection imposes a reduction of diversity, favoring preferred genotypes, such as nonshattering seeds or increased palatability. Furthermore, agricultural practices greatly reduced effective population sizes of crops, allowing genetic drift to alter genotype frequencies. Current advances in molecular technologies, particularly of genome sequencing, provide evidence of human selection acting on numerous loci during and after crop domestication. Population-level molecular analyses also enable us to clarify the demographic histories of the domestication process itself, which, together with expanded archaeological studies, can illuminate the origins of crops. Domesticated plant species are found in 160 taxonomic families. Approximately 2500 species have undergone some degree of domestication, and 250 species are considered to be fully domesticated. The evolutionary trajectory from wild to crop species is a complex process. Archaeological records suggest that there was a period of predomestication cultivation while humans first began the deliberate planting of wild stands that had favorable traits. Later, crops likely diversified as they were grown in new areas, sometimes beyond the climatic niche of their wild relatives. However, the speed and level of human intentionality during domestication remains a topic of active discussion. These processes led to the so-called domestication syndrome, that is, a group of traits that can arise through human preferences for ease of harvest and growth advantages under human propagation. These traits included reduced dispersal ability of seeds and fruits, changes to plant structure, and changes to plant defensive characteristics and palatability. Domestication implies the action of selective sweeps on standing genetic variation, as well as new genetic variation introduced via mutation or introgression. Furthermore, genetic bottlenecks during domestication or during founding events as crops moved away from their centers of origin may have further altered gene pools. To date, a few hundred genes and loci have been identified by classical genetic and association mapping as targets of domestication and postdomestication divergence. However, only a few of these have been characterized, and for even fewer is the role of the wild-type allele in natural populations understood. After domestication, only favorable haplotypes are retained around selected genes, which creates a genetic valley with extremely low genetic diversity. These “selective sweeps” can allow mildly deleterious alleles to come to fixation and may create a genetic load in the cultivated gene pool. Although the population-wide genomic consequences of domestication offer several predictions for levels of the genetic diversity in crops, our understanding of how this diversity corresponds to nutritional aspects of crops is not well understood. Many studies have found that modern cultivars have lower levels of key micronutrients and vitamins. We suspect that selection for palatability and increased yield at domestication and during postdomestication divergence exacerbated the low nutrient levels of many crops, although relatively little work has examined this question. Lack of diversity in modern germplasm may further limit our capacity to breed for higher nutrient levels, although little effort has gone into this beyond a handful of staple crops. This is an area where an understanding of domestication across many crop taxa may provide the necessary insight for breeding more nutritious crops in a rapidly changing world.
Collapse
|
84
|
Green H, Broun P, Cook D, Cooper K, Drewnowski A, Pollard D, Sweeney G, Roulin A. Healthy and sustainable diets for future generations. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2018; 98:3219-3224. [PMID: 29427307 PMCID: PMC6033153 DOI: 10.1002/jsfa.8953] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/15/2018] [Accepted: 02/04/2018] [Indexed: 05/27/2023]
Abstract
Global food systems will face unprecedented challenges in the coming years. They will need to meet the nutritional needs of a growing population and feed an expanding demand for proteins. This is against a backdrop of increasing environmental challenges (water resources, climate change, soil health) and the need to improve farming livelihoods. Collaborative efforts by a variety of stakeholders are needed to ensure that future generations have access to healthy and sustainable diets. Food will play an increasingly important role in the global discourse on health. These topics were explored during Nestlé's second international conference on 'Planting Seeds for the Future of Food: The Agriculture, Nutrition and Sustainability Nexus', which took place in July 2017. This article discusses some of the key issues from the perspective of three major stakeholder groups, namely farming/agriculture, the food industry and consumers. © 2018 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Collapse
Affiliation(s)
- Hilary Green
- Nutrition, Health and Wellness UnitNestlé Research CentreLausanneSwitzerland
| | - Pierre Broun
- Nestlé Research and Development CentreToursFrance
| | - Douglas Cook
- Department of Plant PathologyUniversity of CaliforniaDavisUSA
| | - Karen Cooper
- Nutrition, Health and Wellness UnitNestlé Research CentreLausanneSwitzerland
| | - Adam Drewnowski
- Center for Public Health NutritionUniversity of WashingtonSeattleUSA
| | - Duncan Pollard
- Stakeholders Engagement in Sustainability, Operations, Nestec SAVeveySwitzerland
| | - Gary Sweeney
- Nutrition, Health and Wellness UnitNestlé Research CentreLausanneSwitzerland
| | - Anne Roulin
- Nutrition, Health and Wellness UnitNestlé Research CentreLausanneSwitzerland
| |
Collapse
|