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Jaiswal SK, Dakora FD. Seed-Coat Pigmentation Plays a Crucial Role in Partner Selection and N 2 Fixation in Legume-Root-Microbe Associations in African Soils. PLANTS (BASEL, SWITZERLAND) 2024; 13:1464. [PMID: 38891273 PMCID: PMC11175086 DOI: 10.3390/plants13111464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024]
Abstract
Legume-rhizobia symbiosis is the most important plant-microbe interaction in sustainable agriculture due to its ability to provide much needed N in cropping systems. This interaction is mediated by the mutual recognition of signaling molecules from the two partners, namely legumes and rhizobia. In legumes, these molecules are in the form of flavonoids and anthocyanins, which are responsible for the pigmentation of plant organs, such as seeds, flowers, fruits, and even leaves. Seed-coat pigmentation in legumes is a dominant factor influencing gene expression relating to N2 fixation and may be responsible for the different N2-fixing abilities observed among legume genotypes under field conditions in African soils. Common bean, cowpea, Kersting's groundnut, and Bambara groundnut landraces with black seed-coat color are reported to release higher concentrations of nod-gene-inducing flavonoids and anthocyanins compared with the Red and Cream landraces. Black seed-coat pigmentation is considered a biomarker for enhanced nodulation and N2 fixation in legumes. Cowpea, Bambara groundnut, and Kersting's bean with differing seed-coat colors are known to attract different soil rhizobia based on PCR-RFLP analysis of bacterial DNA. Even when seeds of the same legume with diverse seed-coat colors were planted together in one hole, the nodulating bradyrhizobia clustered differently in the PCR-RFLP dendrogram. Kersting's groundnut, Bambara groundnut, and cowpea with differing seed-coat colors were selectively nodulated by different bradyrhizobial species. The 16S rRNA amplicon sequencing also found significant selective influences of seed-coat pigmentation on microbial community structure in the rhizosphere of five Kersting's groundnut landraces. Seed-coat color therefore plays a dominant role in the selection of the bacterial partner in the legume-rhizobia symbiosis.
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Affiliation(s)
- Sanjay K. Jaiswal
- Department of Chemistry, Tshwane University of Technology, Arcadia Campus, Pretoria 0183, South Africa
| | - Felix D. Dakora
- Department of Chemistry, Tshwane University of Technology, Arcadia Campus, Pretoria 0183, South Africa
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2
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Krieg CP, Smith DD, Adams MA, Berger J, Layegh Nikravesh N, von Wettberg EJ. Greater ecophysiological stress tolerance in the core environment than in extreme environments of wild chickpea (Cicer reticulatum). Sci Rep 2024; 14:5744. [PMID: 38459248 PMCID: PMC10923935 DOI: 10.1038/s41598-024-56457-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/05/2024] [Indexed: 03/10/2024] Open
Abstract
Global climate change and land use change underlie a need to develop new crop breeding strategies, and crop wild relatives (CWR) have become an important potential source of new genetic material to improve breeding efforts. Many recent approaches assume adaptive trait variation increases towards the relative environmental extremes of a species range, potentially missing valuable trait variation in more moderate or typical climates. Here, we leveraged distinct genotypes of wild chickpea (Cicer reticulatum) that differ in their relative climates from moderate to more extreme and perform targeted assessments of drought and heat tolerance. We found significance variation in ecophysiological function and stress tolerance between genotypes but contrary to expectations and current paradigms, it was individuals from more moderate climates that exhibited greater capacity for stress tolerance than individuals from warmer and drier climates. These results indicate that wild germplasm collection efforts to identify adaptive variation should include the full range of environmental conditions and habitats instead of only environmental extremes, and that doing so may significantly enhance the success of breeding programs broadly.
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Affiliation(s)
| | | | - Mark A Adams
- Swinburne University of Technology, Hawthorn, VIC, Australia
| | - Jens Berger
- CSIRO, Agriculture and Food, Perth, WA, Australia
| | | | - Eric J von Wettberg
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, USA
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3
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Guerra-García A, Trněný O, Brus J, Renzi JP, Kumar S, Bariotakis M, Coyne CJ, Chitikineni A, Bett KE, Varshney R, Pirintsos S, Berger J, von Wettberg EJB, Smýkal P. Genetic structure and ecological niche space of lentil's closest wild relative, Lens orientalis (Boiss.) Schmalh. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:232-244. [PMID: 38230798 DOI: 10.1111/plb.13615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/27/2023] [Indexed: 01/18/2024]
Abstract
Crops arose from wild ancestors and to understand their domestication it is essential to compare the cultivated species with their crop wild relatives. These represent an important source of further crop improvement, in particular in relation to climate change. Although there are about 58,000 Lens accessions held in genebanks, only 1% are wild. We examined the geographic distribution and genetic diversity of the lentil's immediate progenitor L. orientalis. We used Genotyping by Sequencing (GBS) to identify and characterize differentiation among accessions held at germplasm collections. We then determined whether genetically distinct clusters of accessions had been collected from climatically distinct locations. Of the 195 genotyped accessions, 124 were genuine L. orientalis with four identified genetic groups. Although an environmental distance matrix was significantly correlated with geographic distance in a Mantel test, the four identified genetic clusters were not found to occupy significantly different environmental space. Maxent modelling gave a distinct predicted distribution pattern centred in the Fertile Crescent, with intermediate probabilities of occurrence in parts of Turkey, Greece, Cyprus, Morocco, and the south of the Iberian Peninsula with NW Africa. Future projections did not show any dramatic alterations in the distribution according to the climate change scenarios tested. We have found considerable diversity in L. orientalis, some of which track climatic variability. The results of the study showed the genetic diversity of wild lentil and indicate the importance of ongoing collections and in situ conservation for our future capacity to harness the genetic variation of the lentil progenitor.
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Affiliation(s)
- A Guerra-García
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - O Trněný
- Agriculture Research Ltd, Troubsko, Czech Republic
| | - J Brus
- Department of Geoinformatics, Palacký University, Olomouc, Czech Republic
| | - J P Renzi
- Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
| | - S Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - M Bariotakis
- Department of Biology, University of Crete, Heraklion, Greece
- Botanical Garden, Rethymnon, Greece
| | - C J Coyne
- Western Regional Plant Introduction Station, USDA-ARS, Pullman, WA, USA
| | - A Chitikineni
- International Crop Research Institute for the semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - K E Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - R Varshney
- International Crop Research Institute for the semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
- Murdoch University, Murdoch, WA, Australia
| | - S Pirintsos
- Department of Biology, University of Crete, Heraklion, Greece
| | - J Berger
- CSIRO Plant Industry, Wembley, WA, Australia
| | - E J B von Wettberg
- Department of Plant and Soil Sciences, Gund Institute for the Environment, University of Vermont, Burlington, VT, USA
| | - P Smýkal
- Department of Botany, Palacký University, Olomouc, Czech Republic
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4
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Wu T, Shen P, Dai J, Ma Y, Feng Y. A Pathway to Assess Genetic Variation of Wheat Germplasm by Multidimensional Traits with Digital Images. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0119. [PMID: 38026469 PMCID: PMC10665127 DOI: 10.34133/plantphenomics.0119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 11/04/2023] [Indexed: 12/01/2023]
Abstract
In this paper, a new pathway was proposed to assess the germplasm genetic variation by multidimensional traits of wheat seeds generated from digital images. A machine vision platform was first established to reconstruct wheat germplasm 3D model from omnidirectional image sequences of wheat seeds. Then, multidimensional traits were conducted from the wheat germplasm 3D model, including seed length, width, thickness, surface area, volume, maximum projection area, roundness, and 2 new defined traits called cardioid-derived area and the index of adjustment (J index). To assess genetic variation of wheat germplasm, phenotypic coefficients of variation (PCVs), analysis of variance (ANOVA), clustering, and the defined genetic variation factor (GVF) were calculated using the extracted morphological traits of 15 wheat accessions comprising 13 offspring and 2 parents. The measurement accuracy of 3D reconstruction model is demonstrated by the correlation coefficient (R) and root mean square errors (RMSEs). Results of PCVs among all the traits show importance of multidimensional traits, as seed volume (22.4%), cardioid-derived area (16.97%), and maximum projection area (14.67%). ANOVA shows a highly significance difference among all accessions. The results of GVF innovatively reflect the connection between genotypic variance and phenotypic traits from parents to offspring. Our results confirmed that extracting multidimensional traits from digital images is a promising high-throughput and cost-efficient pathway that can be included as a valuable approach in genetic variation assessment, and it can provide useful information for genetic improvement, preservation, and evaluation of wheat germplasm.
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Affiliation(s)
- Tingting Wu
- College of Mechanical and Electronic Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Agricultural Internet of Things, Ministry of Agriculture and Rural Affairs, Yangling, Shaanxi 712100, China
| | - Peng Shen
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jianlong Dai
- College of Mechanical and Electronic Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuntao Ma
- College of Land Science and Technology,
China Agricultural University, Beijing 100091, China
| | - Yi Feng
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
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Vrobel O, Tarkowski P. Can plant hormonomics be built on simple analysis? A review. PLANT METHODS 2023; 19:107. [PMID: 37833752 PMCID: PMC10576392 DOI: 10.1186/s13007-023-01090-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/08/2023] [Indexed: 10/15/2023]
Abstract
The field of plant hormonomics focuses on the qualitative and quantitative analysis of the hormone complement in plant samples, akin to other omics sciences. Plant hormones, alongside primary and secondary metabolites, govern vital processes throughout a plant's lifecycle. While active hormones have received significant attention, studying all related compounds provides valuable insights into internal processes. Conventional single-class plant hormone analysis employs thorough sample purification, short analysis and triple quadrupole tandem mass spectrometry. Conversely, comprehensive hormonomics analysis necessitates minimal purification, robust and efficient separation and better-performing mass spectrometry instruments. This review summarizes the current status of plant hormone analysis methods, focusing on sample preparation, advances in chromatographic separation and mass spectrometric detection, including a discussion on internal standard selection and the potential of derivatization. Moreover, current approaches for assessing the spatiotemporal distribution are evaluated. The review touches on the legitimacy of the term plant hormonomics by exploring the current status of methods and outlining possible future trends.
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Affiliation(s)
- Ondřej Vrobel
- Department of Biochemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
- Czech Advanced Technology and Research Institute, Palacky University, Olomouc, Czech Republic
- Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Olomouc, Czech Republic
| | - Petr Tarkowski
- Czech Advanced Technology and Research Institute, Palacky University, Olomouc, Czech Republic.
- Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Olomouc, Czech Republic.
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Lin YP, Chen HW, Yeh PM, Anand SS, Lin J, Li J, Noble T, Nair R, Schafleitner R, Samsononova M, Bishop-von-Wettberg E, Nuzhdin S, Ting CT, Lawn RJ, Lee CR. Demographic history and distinct selection signatures of two domestication genes in mungbean. PLANT PHYSIOLOGY 2023; 193:1197-1212. [PMID: 37335936 DOI: 10.1093/plphys/kiad356] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/10/2023] [Accepted: 06/03/2023] [Indexed: 06/21/2023]
Abstract
Domestication is the long and complex process underlying the evolution of crops, in which artificial directional selection transformed wild progenitors into the desired form, affecting genomic variation and leaving traces of selection at targeted loci. However, whether genes controlling important domestication traits follow the same evolutionary pattern expected under the standard selective sweep model remains unclear. With whole-genome resequencing of mungbean (Vigna radiata), we investigated this issue by resolving its global demographic history and targeted dissection of the molecular footprints of genes underlying 2 key traits representing different stages of domestication. Mungbean originated in Asia, and the Southeast Asian wild population migrated to Australia about 50 thousand generations ago. Later in Asia, the cultivated form diverged from the wild progenitor. We identified the gene associated with the pod shattering resistance trait, VrMYB26a, with lower expression across cultivars and reduced polymorphism in the promoter region, reflecting a hard selective sweep. On the other hand, the stem determinacy trait was associated with VrDet1. We found that 2 ancient haplotypes of this gene have lower gene expression and exhibited intermediate frequencies in cultivars, consistent with selection favoring independent haplotypes in a soft selective sweep. In mungbean, contrasting signatures of selection were identified from the detailed dissection of 2 important domestication traits. The results suggest complex genetic architecture underlying the seemingly simple process of directional artificial selection and highlight the limitations of genome-scan methods relying on hard selective sweeps.
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Affiliation(s)
- Ya-Ping Lin
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan
- World Vegetable Center, Tainan 74199, Taiwan
| | - Hung-Wei Chen
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Pei-Min Yeh
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Shashi S Anand
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Jiunn Lin
- Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Juan Li
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
- Swiss Institute for Bioinformatics, 1015 Lausanne, Switzerland
| | - Thomas Noble
- Australian Department of Agriculture and Fisheries, Warwick, Queensland 4370, Australia
| | - Ramakrishnan Nair
- World Vegetable Center South and Central Asia, ICRISAT Campus, Patancheru, Hyderabad, Telangana 502324, India
| | | | - Maria Samsononova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 19525 St. Petersburg, Russia
| | - Eric Bishop-von-Wettberg
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 19525 St. Petersburg, Russia
- Department of Plant and Soil Science and Gund Institute for the Environment, University of Vermont, Burlington, VT 05405, USA
| | - Sergey Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Chau-Ti Ting
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Robert J Lawn
- College of Science & Engineering, James Cook University, Townsville, Queensland 4814, Australia
| | - Cheng-Ruei Lee
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan
- Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan
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7
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Rouichi S, Idrissi O, Sohail Q, Marrou H, Sinclair TR, Hejjaoui K, Amri M, Ghanem ME. Limited-transpiration trait in response to high vapor pressure deficit from wild to cultivated species: study of the Lens genus. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4875-4887. [PMID: 37422910 DOI: 10.1093/jxb/erad264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Lentil (Lens culinaris Medik.) is commonly grown in drought-prone areas where terminal heat and drought are frequent. The limited-transpiration (TRlim) trait under high vapor pressure deficit (VPD) could be a way to conserve water and increase yield under water deficit conditions. The TRlim trait was examined in cultivated and wild lentil species together with its evolution throughout the breeding pipeline. Sixty-one accessions representing the six wild lentil species (L. orientalis, L. tomentosus, L. odemensis, L. lamottei, L. ervoides, and L. nigricans) and 13 interspecific advanced lines were evaluated in their transpiration response to high VPD. A large variation in transpiration rate (TR) response to increased VPD was recorded among wild lentil accessions, with 43 accessions exhibiting a breakpoint (BP) in their TR response to increasing VPD, with values ranging from 0.92 kPa to 3.38 kPa under greenhouse conditions. Ten genotypes for the interspecific advanced lines displayed a BP with an average of 1.95 kPa, much lower than previously reported for cultivated lentil. Results from field experiments suggest that the TRlim trait (BP=0.97 kPa) positively affected yield and yield-related parameters during the years with late-season water stress. The selection of TRlim genotypes for high VPD environments could improve lentil productivity in drought-prone areas.
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Affiliation(s)
- Salma Rouichi
- College of Sustainable Agriculture and Environmental Science, AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Omar Idrissi
- Laboratory of Food Legumes Breeding, Regional Center of Agricultural Research of Settat, National Institute of Agricultural Research, Avenue Ennasr, BP 415 Rabat Principale, Rabat 10090, Morocco
| | - Quahir Sohail
- College of Sustainable Agriculture and Environmental Science, AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Hélène Marrou
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Thomas R Sinclair
- Crop and Soil Sciences Department, North Carolina State University, Raleigh, NC, USA
| | - Kamal Hejjaoui
- College of Sustainable Agriculture and Environmental Science, AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Moez Amri
- College of Sustainable Agriculture and Environmental Science, AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Michel Edmond Ghanem
- College of Sustainable Agriculture and Environmental Science, AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
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Şahin ES, Talapov T, Ateş D, Can C, Tanyolaç MB. Genome wide association study of genes controlling resistance to Didymella rabiei Pathotype IV through genotyping by sequencing in chickpeas (Cicer arietinum). Genomics 2023; 115:110699. [PMID: 37597791 DOI: 10.1016/j.ygeno.2023.110699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 08/08/2023] [Accepted: 08/15/2023] [Indexed: 08/21/2023]
Abstract
Ascochyta blight (AB) is a major disease in chickpeas (Cicer arietinum L.) that can cause a yield loss of up to 100%. Chickpea germplasm collections at the center of origin offer great potential to discover novel sources of resistance to pests and diseases. Herein, 189 Cicer arietinum samples were genotyped via genotyping by sequencing. This chickpea collection was phenotyped for resistance to an aggressive Turkish Didymella rabiei Pathotype IV isolate. Genome-wide association studies based on different models revealed 19 single nucleotide polymorphism (SNP) associations on chromosomes 1, 2, 3, 4, 7, and 8. Although eight of these SNPs have been previously reported, to the best of our knowledge, the remaining ten were associated with AB resistance for the first time. The regions identified in this study can be addressed in future studies to reveal the genetic mechanism underlying AB resistance and can also be utilized in chickpea breeding programs to improve AB resistance in new chickpea varieties.
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Affiliation(s)
- Erdem Sefa Şahin
- Republic of Turkey, Ministry of Agriculture and Forestry, Aegean Agricultural Research Institute, Izmir, Turkey; Department of Bioengineering, Molecular Genetic Laboratory, Ege University, Izmir, Turkey
| | - Talap Talapov
- Department of Biology, Gaziantep University, Gaziantep, Turkey
| | - Duygu Ateş
- Department of Bioengineering, Molecular Genetic Laboratory, Ege University, Izmir, Turkey
| | - Canan Can
- Department of Biology, Gaziantep University, Gaziantep, Turkey
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9
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Lakmes A, Jhar A, Brennan AC, Kahriman A. Inheritance of Early and Late Ascochyta Blight Resistance in Wide Crosses of Chickpea. Genes (Basel) 2023; 14:genes14020316. [PMID: 36833243 PMCID: PMC9957483 DOI: 10.3390/genes14020316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/11/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
Chickpea (Cicer arietinum) is a globally important food legume but its yield is negatively impacted by the fungal pathogen Ascochyta blight (Ascochyta rabiei) causing necrotic lesions leading to plant death. Past studies have found that Ascochyta resistance is polygenic. It is important to find new resistance genes from the wider genepool of chickpeas. This study reports the inheritance of Ascochyta blight resistance of two wide crosses between the cultivar Gokce and wild chickpea accessions of C. reticulatum and C. echinospermum under field conditions in Southern Turkey. Following inoculation, infection damage was scored weekly for six weeks. The families were genotyped for 60 SNPs mapped to the reference genome for quantitative locus (QTL) mapping of resistance. Family lines showed broad resistance score distributions. A late responding QTL on chromosome 7 was identified in the C. reticulatum family and three early responding QTLs on chromosomes 2, 3, and 6 in the C. echinospermum family. Wild alleles mostly showed reduced disease severity, while heterozygous genotypes were most diseased. Interrogation of 200k bp genomic regions of the reference CDC Frontier genome surrounding QTLs identified nine gene candidates involved in disease resistance and cell wall remodeling. This study identifies new candidate chickpea Ascochyta blight resistance QTLs of breeding potential.
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Affiliation(s)
- Abdulkarim Lakmes
- Department of Field Crops, Harran University, Sanliurfa 63100, Turkey
| | - Abdullah Jhar
- Department of Field Crops, Harran University, Sanliurfa 63100, Turkey
| | - Adrian C. Brennan
- Biosciences Department, Durham University, Durham DH1 3LE, UK
- Correspondence:
| | - Abdullah Kahriman
- Department of Field Crops, Harran University, Sanliurfa 63100, Turkey
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10
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Gutierrez A, Grillo MA. Effects of Domestication on Plant-Microbiome Interactions. PLANT & CELL PHYSIOLOGY 2022; 63:1654-1666. [PMID: 35876043 DOI: 10.1093/pcp/pcac108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 07/15/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Through the process of domestication, selection is targeted on a limited number of plant traits that are typically associated with yield. As an unintended consequence, domesticated plants often perform poorly compared to their wild progenitors for a multitude of traits that were not under selection during domestication, including abiotic and biotic stress tolerance. Over the past decade, advances in sequencing technology have allowed for the rigorous characterization of host-associated microbial communities, termed the microbiome. It is now clear that nearly every conceivable plant interaction with the environment is mediated by interactions with the microbiome. For this reason, plant-microbiome interactions are an area of great promise for plant breeding and crop improvement. Here, we review the literature to assess the potential impact that domestication has had on plant-microbiome interactions and the current understanding of the genetic basis of microbiome variation to inform plant breeding efforts. Overall, we find limited evidence that domestication impacts the diversity of microbiomes, but domestication is often associated with shifts in the abundance and composition of microbial communities, including taxa of known functional significance. Moreover, genome-wide association studies and mutant analysis have not revealed a consistent set of core candidate genes or genetic pathways that confer variation in microbiomes across systems. However, such studies do implicate a consistent role for plant immunity, root traits, root and leaf exudates and cell wall integrity as key traits that control microbiome colonization and assembly. Therefore, selection on these key traits may pose the most immediate promise for enhancing plant-microbiome interactions through breeding.
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Affiliation(s)
- Andres Gutierrez
- Department of Biology, Loyola University Chicago, 1032 W. Sheridan Rd, Chicago, IL 60660, USA
| | - Michael A Grillo
- Department of Biology, Loyola University Chicago, 1032 W. Sheridan Rd, Chicago, IL 60660, USA
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11
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Bohra A, Tiwari A, Kaur P, Ganie SA, Raza A, Roorkiwal M, Mir RR, Fernie AR, Smýkal P, Varshney RK. The Key to the Future Lies in the Past: Insights from Grain Legume Domestication and Improvement Should Inform Future Breeding Strategies. PLANT & CELL PHYSIOLOGY 2022; 63:1554-1572. [PMID: 35713290 PMCID: PMC9680861 DOI: 10.1093/pcp/pcac086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/09/2022] [Accepted: 06/15/2022] [Indexed: 05/11/2023]
Abstract
Crop domestication is a co-evolutionary process that has rendered plants and animals significantly dependent on human interventions for survival and propagation. Grain legumes have played an important role in the development of Neolithic agriculture some 12,000 years ago. Despite being early companions of cereals in the origin and evolution of agriculture, the understanding of grain legume domestication has lagged behind that of cereals. Adapting plants for human use has resulted in distinct morpho-physiological changes between the wild ancestors and domesticates, and this distinction has been the focus of several studies aimed at understanding the domestication process and the genetic diversity bottlenecks created. Growing evidence from research on archeological remains, combined with genetic analysis and the geographical distribution of wild forms, has improved the resolution of the process of domestication, diversification and crop improvement. In this review, we summarize the significance of legume wild relatives as reservoirs of novel genetic variation for crop breeding programs. We describe key legume features, which evolved in response to anthropogenic activities. Here, we highlight how whole genome sequencing and incorporation of omics-level data have expanded our capacity to monitor the genetic changes accompanying these processes. Finally, we present our perspective on alternative routes centered on de novo domestication and re-domestication to impart significant agronomic advances of novel crops over existing commodities. A finely resolved domestication history of grain legumes will uncover future breeding targets to develop modern cultivars enriched with alleles that improve yield, quality and stress tolerance.
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Affiliation(s)
- Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Abha Tiwari
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kalyanpur, Kanpur 208024, India
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Showkat Ahmad Ganie
- Department of Biotechnology, Visva-Bharati, Santiniketan, Santiniketan Road, Bolpur 731235, India
| | - Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China
| | - Manish Roorkiwal
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), UAE University, Sheik Khalifa Bin Zayed Street, Al Ain, Abu Dhabi 15551, UAE
| | - Reyazul Rouf Mir
- Division of Genetics & Plant Breeding, Faculty of Agriculture, SKUAST, Shalimar, Srinagar 190025, India
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacky University, Křížkovského 511/8, Olomouc 78371, Czech Republic
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12
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Mondaca P, Valenzuela P, Quiroz W, Valdenegro M, Abades S, Celis-Diez JL. Environmental conditions and plant physiology modulate Cu phytotoxicity in field-contaminated soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 246:114179. [PMID: 36244170 DOI: 10.1016/j.ecoenv.2022.114179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 09/30/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
Foliar Cu concentration has been widely used as a biomarker of plant growth in phytotoxicity bioassays. This relation has helped find plant processes altered by Cu in dose-response experiments (a bivariate approach). However, when plants are grown in field conditions, their responses can vary in function of multiple variables, such as the environment, plant physiology, and other elements in plant (plant ionome). These sources of variability are commonly unreported, which could limit bioassays' utility. Thus, the present study aimed to assess and integrate the mentioned sources of variability on Cu phytotoxicity. Lettuce was used as plant model. Lettuces were grown in growth chambers with contrasting light and air humidity conditions and on two different field-contaminated soils (sandy and loamy soils). Results showed that environmental conditions significantly affected foliar Cu and plant growth, but this effect differed in the two studied soils. Foliar Cu was not a good biomarker of plant growth. In contrast, integrating the potential phytotoxicity effect with the plant's nutritional status allowed a better understanding of plant growth. We remarked on using a structural equation modeling approach (SEM) to integrate plant physiology and plant ionome as moderators of plant growth. Results showed that plant growth was primarily related to plant nutritional status rather than Cu phytotoxicity. Also, the foliar Cu concentration would affect plant nutritional status due to photosynthesis-related plant processes and cation balance. Finally, this research invites to state and include sources of variability when assessing phytotoxicity. This way, it is possible to advance toward understanding complex linked processes occurring in field conditions.
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Affiliation(s)
- Pedro Mondaca
- Escuela de Agronomía, Pontificia Universidad Católica de Valparaíso, Chile
| | - Patricio Valenzuela
- Departamento de Sistemas y Recursos Naturales, Universidad Politécnica de Madrid, Madrid, Spain
| | - Waldo Quiroz
- Instituto de Química, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Monika Valdenegro
- Escuela de Agronomía, Pontificia Universidad Católica de Valparaíso, Chile
| | - Sebastián Abades
- GEMA Center for Genomics, Ecology & Environment, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Juan L Celis-Diez
- Escuela de Agronomía, Pontificia Universidad Católica de Valparaíso, Chile; Instituto de Ecología y Biodiversidad, Chile.
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13
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Fan M, Li X, Zhang Y, Wu S, Song Z, Yin H, Liu W, Fan Z, Li J. Floral organ transcriptome in Camellia sasanqua provided insight into stamen petaloid. BMC PLANT BIOLOGY 2022; 22:474. [PMID: 36199021 PMCID: PMC9535933 DOI: 10.1186/s12870-022-03860-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The cultivated Camellia sasanqua forms a divergent double flower pattern, and the stamen petaloid is a vital factor in the phenomenon. However, the regulation mechanism remains largely unclear. RESULTS Here, a comprehensive comparative transcriptome analysis of the wild-type, "semi-double", "peony double", and "rose double" was performed. The cluster analysis of global gene expression level showed petal and stamen difficulty separable in double flower. The crucial pathway and genes related to double flower patterns regulation were identified by pairwise comparisons and weighted gene coexpression network (WGCNA). Divergent genes expression, such as AUX1 and AHP, are involved in plant hormone signaling and photosynthesis, and secondary metabolites play an important role. Notably, the diversity of a petal-specific model exhibits a similar molecular signature to the stamen, containing extensin protein and PSBO1, supporting the stamen petaloid point. Moreover, the expansion of class A gene activity influenced the double flower formation, showing that the key function of gene expression was probably demolished. CONCLUSIONS Overall, this work confirmed the ABCE model and provided new insights for elucidating the molecular signature of double formation.
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Affiliation(s)
- Menglong Fan
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xinlei Li
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China.
| | - Ying Zhang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Si Wu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Zhixin Song
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Hengfu Yin
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Weixin Liu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Zhengqi Fan
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Jiyuan Li
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
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14
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Rutherford S, Wilson TC, Yap JYS, Lee E, Errington G, Rossetto M. Evolutionary processes in an undescribed eucalypt: implications for the translocation of a critically endangered species. ANNALS OF BOTANY 2022; 130:491-508. [PMID: 35802354 PMCID: PMC9510949 DOI: 10.1093/aob/mcac091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS Knowledge of the evolutionary processes responsible for the distribution of threatened and highly localized species is important for their conservation. Population genomics can provide insights into evolutionary processes to inform management practices, including the translocation of threatened plant species. In this study, we focus on a critically endangered eucalypt, Eucalyptus sp. Cattai, which is restricted to a 40-km2 area of Sydney, Australia, and is threatened by increased urbanization. Eucalyptus sp. Cattai has yet to be formally described in part due to its suspected hybrid origin. Here, we examined evolutionary processes and species boundaries in E. sp. Cattai to determine whether translocation was warranted. METHODS We used genome-wide scans to investigate the evolutionary relationships of E. sp. Cattai with related species, and to assess levels of genetic health and admixture. Morphological trait and genomic data were obtained from seedlings of E. sp. Cattai propagated in a common garden to assess their genetic provenance and hybrid status. KEY RESULTS All analyses revealed that E. sp. Cattai was strongly supported as a distinct species. Genetic diversity varied across populations, and clonality was unexpectedly high. Interspecific hybridization was detected, and was more prevalent in seedlings compared to in situ adult plants, indicating that post-zygotic barriers may restrict the establishment of hybrids. CONCLUSIONS Multiple evolutionary processes (e.g. hybridization and clonality) can operate within one rare and restricted species. Insights regarding evolutionary processes from our study were used to assist with the translocation of genetically 'pure' and healthy ex situ seedlings to nearby suitable habitat. Our findings demonstrate that it is vital to provide an understanding of evolutionary relationships and processes with an examination of population genomics in the design and implementation of an effective translocation strategy.
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Affiliation(s)
| | - Trevor C Wilson
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Sydney, Australia
| | - Jia-Yee Samantha Yap
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Sydney, Australia
| | - Enhua Lee
- Biodiversity and Conservation Division, New South Wales Department of Planning and Environment, Sydney, Australia
| | - Graeme Errington
- Australian PlantBank, Australian Institute of Botanical Science, Australian Botanic Garden, Mount Annan, New South Wales, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Sydney, Australia
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15
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Kalve S, Gali KK, Tar’an B. Genome-wide association analysis of stress tolerance indices in an interspecific population of chickpea. FRONTIERS IN PLANT SCIENCE 2022; 13:933277. [PMID: 36061786 PMCID: PMC9437449 DOI: 10.3389/fpls.2022.933277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Chickpea is a cool season crop that is highly vulnerable to abiotic stresses such as heat and drought. High temperature during early flowering and pod development stages significantly reduces the crop yield. The wild relatives of chickpeas can be potential donors for the introgression of heat and drought tolerance into cultivated chickpeas for crop improvement. Initially, 600 interspecific lines were derived from crosses between two elite cultivars, CDC Leader (kabuli chickpea) and CDC Consul (desi chickpea), and 20 accessions of Cicer reticulatum. The F5 interspecific lines were tested for agronomic and seed quality traits including reaction to ascochyta blight disease under field conditions at two locations in 2018. A subset of 195 lines were selected based on resistance to ascochyta blight and acceptable seed quality. These lines were evaluated for their performance under suboptimal conditions at Lucky Lake (2019 and 2020) and Moose Jaw (2019), Saskatchewan, Canada, and Yuma, Arizona, United States (2019-2020). The lines were grown and evaluated at two seeding dates, normal (SD1) and late (SD2) seeding dates, at each location and year. The same lines were genotyped using Cicer60K Axiom® SNP chip. The population structure was determined based on 35,431 informative SNPs using fastStructure, and the interspecific lines were clustered at a k-value of 15. Significant marker-trait associations were identified for seed yield from SD1 and SD2 seeding dates, and stress tolerance indices (ATI, K1STI, MP, SSPI, and TOL) using phenotypic values both from individual locations and combined analyses based on BLUP values. SNP marker Ca2_34600347 was significantly associated with yield from both the seeding dates. This and other SNP markers identified in this study may be useful for marker-assisted introgression of abiotic stress tolerance in chickpea.
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16
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Jia Y, Pradeep K, Vance WH, Zhang X, Weir B, Wei H, Deng Z, Zhang Y, Xu X, Zhao C, Berger JD, Bell RW, Li C. Identification of two chickpea multidrug and toxic compound extrusion transporter genes transcriptionally upregulated upon aluminum treatment in root tips. FRONTIERS IN PLANT SCIENCE 2022; 13:909045. [PMID: 35991422 PMCID: PMC9389367 DOI: 10.3389/fpls.2022.909045] [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: 03/31/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Aluminum (Al) toxicity poses a significant challenge for the yield improvement of chickpea, which is an economically important legume crop with high nutritional value in human diets. The genetic basis of Al-tolerance in chickpea remains unclear. Here, we assessed the Al-tolerance of 8 wild Cicer and one cultivated chickpea (PBA Pistol) accessions by measuring the root elongation in solution culture under control (0 μM Al3+) and Al treatments (15, 30 μM Al3+). Compared to PBA Pistol, the wild Cicer accessions displayed both tolerant and sensitive phenotypes, supporting wild Cicer as a potential genetic pool for Al-tolerance improvement. To identify potential genes related to Al-tolerance in chickpea, genome-wide screening of multidrug and toxic compound extrusion (MATE) encoding genes was performed. Fifty-six MATE genes were identified in total, which can be divided into 4 major phylogenetic groups. Four chickpea MATE genes (CaMATE1-4) were clustered with the previously characterized citrate transporters MtMATE66 and MtMATE69 in Medicago truncatula. Transcriptome data showed that CaMATE1-4 have diverse expression profiles, with CaMATE2 being root-specific. qRT-PCR analyses confirmed that CaMATE2 and CaMATE4 were highly expressed in root tips and were up-regulated upon Al treatment in all chickpea lines. Further measurement of carboxylic acids showed that malonic acid, instead of malate or citrate, is the major extruded acid by Cicer spp. root. Protein structural modeling analyses revealed that CaMATE2 has a divergent substrate-binding cavity from Arabidopsis AtFRD3, which may explain the different acid-secretion profile for chickpea. Pangenome survey showed that CaMATE1-4 have much higher genetic diversity in wild Cicer than that in cultivated chickpea. This first identification of CaMATE2 and CaMATE4 responsive to Al3+ treatment in Cicer paves the way for future functional characterization of MATE genes in Cicer spp., and to facilitate future design of gene-specific markers for Al-tolerant line selection in chickpea breeding programs.
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Affiliation(s)
- Yong Jia
- Western Crop Genetic Alliance, Murdoch University, Perth, WA, Australia
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Department of Primary Industry and Regional Development, Government of Western Australia, Perth, WA, Australia
| | - Karthika Pradeep
- Centre for Sustainable Farming Systems, Future Foods Institute, Murdoch University, Perth, WA, Australia
| | - Wendy H. Vance
- Centre for Sustainable Farming Systems, Future Foods Institute, Murdoch University, Perth, WA, Australia
| | - Xia Zhang
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Brayden Weir
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Hongru Wei
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Zhiwei Deng
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Yujuan Zhang
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Xuexin Xu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Changxing Zhao
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | | | - Richard William Bell
- Centre for Sustainable Farming Systems, Future Foods Institute, Murdoch University, Perth, WA, Australia
| | - Chengdao Li
- Western Crop Genetic Alliance, Murdoch University, Perth, WA, Australia
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Department of Primary Industry and Regional Development, Government of Western Australia, Perth, WA, Australia
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17
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Renzi JP, Coyne CJ, Berger J, von Wettberg E, Nelson M, Ureta S, Hernández F, Smýkal P, Brus J. How Could the Use of Crop Wild Relatives in Breeding Increase the Adaptation of Crops to Marginal Environments? FRONTIERS IN PLANT SCIENCE 2022; 13:886162. [PMID: 35783966 PMCID: PMC9243378 DOI: 10.3389/fpls.2022.886162] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/11/2022] [Indexed: 06/01/2023]
Abstract
Alongside the use of fertilizer and chemical control of weeds, pests, and diseases modern breeding has been very successful in generating cultivars that have increased agricultural production several fold in favorable environments. These typically homogeneous cultivars (either homozygous inbreds or hybrids derived from inbred parents) are bred under optimal field conditions and perform well when there is sufficient water and nutrients. However, such optimal conditions are rare globally; indeed, a large proportion of arable land could be considered marginal for agricultural production. Marginal agricultural land typically has poor fertility and/or shallow soil depth, is subject to soil erosion, and often occurs in semi-arid or saline environments. Moreover, these marginal environments are expected to expand with ongoing climate change and progressive degradation of soil and water resources globally. Crop wild relatives (CWRs), most often used in breeding as sources of biotic resistance, often also possess traits adapting them to marginal environments. Wild progenitors have been selected over the course of their evolutionary history to maintain their fitness under a diverse range of stresses. Conversely, modern breeding for broad adaptation has reduced genetic diversity and increased genetic vulnerability to biotic and abiotic challenges. There is potential to exploit genetic heterogeneity, as opposed to genetic uniformity, in breeding for the utilization of marginal lands. This review discusses the adaptive traits that could improve the performance of cultivars in marginal environments and breeding strategies to deploy them.
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Affiliation(s)
- Juan Pablo Renzi
- Instituto Nacional de Tecnología Agropecuaria, Hilario Ascasubi, Argentina
- CERZOS, Departamento de Agronomía, Universidad Nacional del Sur (CONICET), Bahía Blanca, Argentina
| | | | - Jens Berger
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Wembley, WA, Australia
| | - Eric von Wettberg
- Department of Plant and Soil Science, Gund Institute for Environment, University of Vermont, Burlington, VT, United States
- Department of Applied Mathematics, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Matthew Nelson
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Wembley, WA, Australia
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Soledad Ureta
- CERZOS, Departamento de Agronomía, Universidad Nacional del Sur (CONICET), Bahía Blanca, Argentina
| | - Fernando Hernández
- CERZOS, Departamento de Agronomía, Universidad Nacional del Sur (CONICET), Bahía Blanca, Argentina
| | - Petr Smýkal
- Department of Botany, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Jan Brus
- Department of Geoinformatics, Faculty of Sciences, Palacký University, Olomouc, Czechia
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18
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Phylogenetic Analysis and Flower Color Evolution of the Subfamily Linoideae (Linaceae). PLANTS 2022; 11:plants11121579. [PMID: 35736730 PMCID: PMC9231132 DOI: 10.3390/plants11121579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022]
Abstract
The taxonomy of the subfamily Linoideae at the intergeneric and section levels has been questioned throughout the years, and the evolution of floral characters remains poorly understood. In particular, the evolution of flower color is still uncertain, despite its ecological importance and being one of the most variable and striking traits in Angiospermae. We evaluated the phylogenetic relationships of the genera and sections and used the phylogeny to reconstruct the ancestral state of flower color. The results suggest reevaluating the taxonomic status of segregated genera and re-incorporating them into Linum. Four of the five sections currently accepted were recovered as monophyletic (Cathartolinum, Dasylinum, Linum, and Syllinum). We propose accepting the section Stellerolinon and reevaluating Linopsis, whose representatives were recovered in three separate clades. The ancestral flower color for Linoideae was yellow-white. The flower colors purple and yellow-white were recovered at the deepest nodes of the two main clades. Pink, blue, and red colors were the most recent to evolve. These results appear to be related to diversification events, biogeographical history, and ecological aspects of the subfamily. Our reconstruction constitutes the first plausible scenario that explores the evolution of flower color, leading to new testable hypotheses for future research on the flax group.
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19
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Lu R, Chen Y, Zhang X, Feng Y, Comes HP, Li Z, Zheng Z, Yuan Y, Wang L, Huang Z, Guo Y, Sun G, Olsen KM, Chen J, Qiu Y. Genome sequencing and transcriptome analyses provide insights into the origin and domestication of water caltrop (Trapa spp., Lythraceae). PLANT BIOTECHNOLOGY JOURNAL 2022; 20:761-776. [PMID: 34861095 PMCID: PMC8989495 DOI: 10.1111/pbi.13758] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Humans have domesticated diverse species from across the plant kingdom; however, our current understanding of plant domestication is largely founded on major cereal crops. Here, we examine the evolutionary processes and genetic basis underlying the domestication of water caltrop (Trapa spp., Lythraceae), a traditional, yet presently underutilized non-cereal crop that sustained early Chinese agriculturalists. We generated a chromosome-level genome assembly of tetraploid T. natans, and then divided the allotetraploid genome into two subgenomes. Based on resequencing data from 57 accessions, representing cultivated diploid T. natans, wild T. natans (2x and 4x) and diploid T. incisa, we showed that water caltrop was likely first domesticated in the Yangtze River Valley as early as 6300 yr BP, and experienced a second improvement c. 800 years ago. We also provided strong support for an allotetraploid origin of T. natans within the past 230 000-310 000 years. By integrating selective sweep and transcriptome profiling analyses, we identified a number of genes potentially selected and/or differentially expressed during domestication, some of which likely contributed not only to larger fruit sizes but also to a more vigorous root system, facilitating nutrient uptake, environmental stress response and underwater photosynthesis. Our results shed light on the evolutionary and domestication history of water caltrop, one of the earliest domesticated crops in China. This study has implications for genomic-assisted breeding of this presently underutilized aquatic plant, and improves our general understanding of plant domestication.
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Affiliation(s)
- Rui‐Sen Lu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life SciencesZhejiang UniversityHangzhouZhejiangChina
- Institute of BotanyJiangsu Province and Chinese Academy of SciencesNanjingChina
| | - Yang Chen
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life SciencesZhejiang UniversityHangzhouZhejiangChina
| | - Xin‐Yi Zhang
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life SciencesZhejiang UniversityHangzhouZhejiangChina
| | - Yu Feng
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life SciencesZhejiang UniversityHangzhouZhejiangChina
| | | | - Zheng Li
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonAZUSA
| | - Zhai‐Sheng Zheng
- Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery)JinhuaZhejiangChina
| | - Ye Yuan
- Jiaxing Academy of Agricultural SciencesJiaxingChina
| | - Ling‐Yun Wang
- Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery)JinhuaZhejiangChina
| | - Zi‐Jian Huang
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life SciencesZhejiang UniversityHangzhouZhejiangChina
| | - Yi Guo
- Department of Archaeology, Cultural Heritage and MuseologyZhejiang UniversityHangzhouChina
| | - Guo‐Ping Sun
- Zhejiang Provincial Research Institute of Cultural Relics and ArchaeologyHangzhouChina
| | - Kenneth M. Olsen
- Department of BiologyWashington University in St LouisSt LouisMOUSA
| | - Jun Chen
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life SciencesZhejiang UniversityHangzhouZhejiangChina
| | - Ying‐Xiong Qiu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life SciencesZhejiang UniversityHangzhouZhejiangChina
- Wuhan Botanical GardenChinese Academy of SciencesWuhanHubeiChina
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20
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Bohra A, Bansal KC, Graner A. The 3366 chickpea genomes for research and breeding. TRENDS IN PLANT SCIENCE 2022; 27:217-219. [PMID: 34865982 DOI: 10.1016/j.tplants.2021.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Genome sequences provide an unprecedented resource to rapidly develop modern crops. A recent paper by Varshney et al. provides genome variation maps of 3366 chickpea accessions. Here, we highlight how this breakthrough research can fundamentally change breeding practices of chickpea and potentially other crops.
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Affiliation(s)
- Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India.
| | - Kailash C Bansal
- National Academy of Agricultural Sciences (NAAS), NASC Complex, Pusa, New Delhi, India
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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21
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Fan M, Zhang Y, Li X, Wu S, Yang M, Yin H, Liu W, Fan Z, Li J. Multi-Approach Analysis Reveals Pathways of Cold Tolerance Divergence in Camellia japonica. FRONTIERS IN PLANT SCIENCE 2022; 13:811791. [PMID: 35283896 PMCID: PMC8914472 DOI: 10.3389/fpls.2022.811791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Understanding the molecular mechanism of the cold response is critical to improve horticultural plant cold tolerance. Here, we documented the physiological, transcriptome, proteome, and hormonal dynamics to cold stress in temperate genotype (Tg) and subtropical genotype (Sg) populations of Camellia japonica. Tg C. japonica suffered minimal osmotic and oxidative damage compared to Sg C. japonica under the same cold treatment. Transcriptional and translational differences increased under the cold treatment, indicating that Tg C. japonica was affected by the environment and displayed both conserved and divergent mechanisms. About 60% of the genes responding to cold had similar dynamics in the two populations, but 1,896 transcripts and 455 proteins differentially accumulated in response to the cold between Tg and Sg C. japonica. Co-expression analysis showed that the ribosomal protein and genes related to photosynthesis were upregulated in Tg C. japonica, and tryptophan, phenylpropanoid, and flavonoid metabolism were regulated differently between the two populations under cold stress. The divergence of these genes reflected a difference in cold responsiveness. In addition, the decrease in the abscisic acid (ABA)/gibberellic acid (GA) ratio regulated by biosynthetic signal transduction pathway enhanced cold resistance in Tg C. japonica, suggesting that hormones may regulate the difference in cold responsiveness. These results provide a new understanding of the molecular mechanism of cold stress and will improve cold tolerance in horticultural plants.
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Affiliation(s)
| | | | - XinLei Li
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
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22
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Fitak RR. OptM: estimating the optimal number of migration edges on population trees using Treemix. Biol Methods Protoc 2021; 6:bpab017. [PMID: 34595352 PMCID: PMC8476930 DOI: 10.1093/biomethods/bpab017] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 11/25/2022] Open
Abstract
The software Treemix has become extensively used to estimate the number of migration events, or edges (m), on population trees from genome-wide allele frequency data. However, the appropriate number of edges to include remains unclear. Here, I show that an optimal value of m can be inferred from the second-order rate of change in likelihood (Δm) across incremental values of m. Repurposed from its original use to estimate the number of population clusters in the software Structure (ΔK), I show using simulated populations that Δm performs equally as well as current recommendations for Treemix. A demonstration of an empirical dataset from domestic dogs indicates that this method may be preferable in large, complex population histories and can prioritize migration events for subsequent investigation. The method has been implemented in a freely available R package called “OptM” and as a web application (https://rfitak.shinyapps.io/OptM/) to interface directly with the output files of Treemix.
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Affiliation(s)
- Robert R Fitak
- Department of Biology, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816, USA
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23
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Razzaq A, Wani SH, Saleem F, Yu M, Zhou M, Shabala S. Rewilding crops for climate resilience: economic analysis and de novo domestication strategies. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6123-6139. [PMID: 34114599 DOI: 10.1093/jxb/erab276] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/09/2021] [Indexed: 05/08/2023]
Abstract
To match predicted population growth, annual food production should be doubled by 2050. This is not achievable by current agronomical and breeding practices, due to the impact of climate changes and associated abiotic stresses on agricultural production systems. Here, we analyze the impact of global climate trends on crop productivity and show that the overall loss in crop production from climate-driven abiotic stresses may exceed US$170 billion year-1 and represents a major threat to global food security. We also show that abiotic stress tolerance had been present in wild progenitors of modern crops but was lost during their domestication. We argue for a major shift in our paradigm of crop breeding, focusing on climate resilience, and call for a broader use of wild relatives as a major tool in this process. We argue that, while molecular tools are currently in place to harness the potential of climate-resilient genes present in wild relatives, the complex polygenic nature of tolerance traits remains a major bottleneck in this process. Future research efforts should be focused not only on finding appropriate wild relatives but also on development of efficient cell-based high-throughput phenotyping platforms allowing assessment of the in planta operation of key genes.
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Affiliation(s)
- Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisald 38040,Pakistan
| | - Shabir Hussain Wani
- Mountain Research Center for Field Crops, Khudwani, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, J&K,India
| | - Fozia Saleem
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisald 38040,Pakistan
| | - Min Yu
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000,China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tas 7001,Australia
| | - Sergey Shabala
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000,China
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tas 7001,Australia
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24
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Shin MG, Nuzhdin SV. Interspecific Sample Prioritization Can Improve QTL Detection With Tree-Based Predictive Models. Front Genet 2021; 12:684882. [PMID: 34552613 PMCID: PMC8450460 DOI: 10.3389/fgene.2021.684882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/09/2021] [Indexed: 11/16/2022] Open
Abstract
Due to increasing demand for new advanced crops, considerable efforts have been made to explore the improvement of stress and disease resistance cultivar traits through the study of wild crops. When both wild and interspecific hybrid materials are available, a common approach has been to study two types of materials separately and simply compare the quantitative trait locus (QTL) regions. However, combining the two types of materials can potentially create a more efficient method of finding predictive QTLs. In this simulation study, we focused on scenarios involving causal marker expression suppressed by trans-regulatory mechanisms, where the otherwise easily lost associated signals benefit the most from combining the two types of data. A probabilistic sampling approach was used to prioritize consistent genotypic phenotypic patterns across both types of data sets. We chose random forest and gradient boosting to apply the prioritization scheme and found that both facilitated the investigation of predictive causal markers in most of the biological scenarios simulated.
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Affiliation(s)
- Min-Gyoung Shin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Sergey V Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
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25
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Varshney RK, Barmukh R, Roorkiwal M, Qi Y, Kholova J, Tuberosa R, Reynolds MP, Tardieu F, Siddique KHM. Breeding custom-designed crops for improved drought adaptation. ADVANCED GENETICS (HOBOKEN, N.J.) 2021; 2:e202100017. [PMID: 36620433 PMCID: PMC9744523 DOI: 10.1002/ggn2.202100017] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 01/11/2023]
Abstract
The current pace of crop improvement is inadequate to feed the burgeoning human population by 2050. Higher, more stable, and sustainable crop production is required against a backdrop of drought stress, which causes significant losses in crop yields. Tailoring crops for drought adaptation may hold the key to address these challenges and provide resilient production systems for future harvests. Understanding the genetic and molecular landscape of the functionality of alleles associated with adaptive traits will make designer crop breeding the prospective approach for crop improvement. Here, we highlight the potential of genomics technologies combined with crop physiology for high-throughput identification of the genetic architecture of key drought-adaptive traits and explore innovative genomic breeding strategies for designing future crops.
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Affiliation(s)
- Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia,State Agricultural Biotechnology Centre, Centre for Crop and Food InnovationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Rutwik Barmukh
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Manish Roorkiwal
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Yiping Qi
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA,Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMarylandUSA
| | - Jana Kholova
- Crop Physiology and ModellingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Roberto Tuberosa
- Department of Agricultural and Food SciencesUniversity of BolognaBolognaItaly
| | | | - Francois Tardieu
- Université de Montpellier, INRAE, Laboratoire d'Ecophysiologie des Plantes sous Stress, EnvironnementauxMontpellierFrance
| | - Kadambot H. M. Siddique
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
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26
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Yuan HY, Caron CT, Ramsay L, Fratini R, de la Vega MP, Vandenberg A, Weller JL, Bett KE. Genetic and gene expression analysis of flowering time regulation by light quality in lentil. ANNALS OF BOTANY 2021; 128:481-496. [PMID: 34185828 PMCID: PMC8414921 DOI: 10.1093/aob/mcab083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/28/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Flowering time is important due to its roles in plant adaptation to different environments and subsequent formation of crop yield. Changes in light quality affect a range of developmental processes including flowering time, but little is known about light quality-induced flowering time control in lentil. This study aims to investigate the genetic basis for differences in flowering response to light quality in lentil. METHODS We explored variation in flowering time caused by changes in red/far-red-related light quality environments of a lentil interspecific recombinant inbred line (RIL) population developed from a cross between Lens culinaris cv. Lupa and L. orientalis accession BGE 016880. A genetic linkage map was constructed and then used for identifying quantitative trait loci (QTLs) associated with flowering time regulation under different light quality environments. Differential gene expression analysis through transcriptomic study and RT-qPCR were used to identify potential candidate genes. KEY RESULTS QTL mapping located 13 QTLs controlling flower time under different light quality environments, with phenotypic variance explained ranging from 1.7 to 62.9 %. Transcriptomic profiling and gene expression analysis for both parents of this interspecific RIL population identified flowering-related genes showing environment-specific differential expression (flowering DEGs). One of these, a member of the florigen gene family FTa1 (LcFTa1), was located close to three major QTLs. Furthermore, gene expression results suggested that two other florigen genes (LcFTb1 and LcFTb2), MADS-box transcription factors such as LcAGL6/13d, LcSVPb, LcSOC1b and LcFULb, as well as bHLH transcription factor LcPIF6 and Gibberellin 20 oxidase LcGA20oxC,G may also be involved in the light quality response. CONCLUSIONS Our results show that a major component of flowering time sensitivity to light quality is tightly linked to LcFTa1 and associated with changes in its expression. This work provides a foundation for crop improvement of lentil with better adaptation to variable light environments.
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Affiliation(s)
- Hai Ying Yuan
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Carolyn T Caron
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Larissa Ramsay
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Richard Fratini
- Area de Genética, Departamento de Biología Molecular, Universidad de León, León, Spain
| | | | - Albert Vandenberg
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - James L Weller
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Kirstin E Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
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27
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Hellwig T, Abbo S, Sherman A, Ophir R. Prospects for the natural distribution of crop wild-relatives with limited adaptability: The case of the wild pea Pisum fulvum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 310:110957. [PMID: 34315583 DOI: 10.1016/j.plantsci.2021.110957] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/12/2021] [Accepted: 05/22/2021] [Indexed: 06/13/2023]
Abstract
Plant breeders and conservationist depend on knowledge about the genetic variation of their species of interest. Pisum fulvum, a wild relative of domesticated pea, has attracted attention as a genetic resource for crop improvement, yet little information about its diversity in the wild has been published hitherto. We sampled 15 populations of P. fulvum from Israeli natural habitats and conducted genotyping by sequencing to analyse their genetic diversity and adaptive state. We also attempted to evaluate the species past demography and the prospects of its future reaction to environmental changes. The results suggest that genetic diversity of P. fulvum is low to medium and is distributed between well diverged populations. Surprisingly, with 56 % in the total population the selfing rate was found to be significantly lower than expected from a species that is commonly assumed to be a predominant selfer. We found a strong genetic bottleneck during the last glacial period and only limited patterns of isolation by distance and environment, which explained 13 %-18 % of the genetic variation. Despite the weak signatures of genome-wide IBE, 1,354 markers were significantly correlated with environmental factors, 1,233 of which were located within known genes with a nonsynonymous to synonymous ratio of 0.382. Species distribution modelling depicted an ongoing fragmentation and decreased habitable area over the next 80 years under two different socio-economic pathways. Our results suggest that complex interactions of substantial drift and selection shaped the genome of P. fulvum. Climate changeis likely to cause further erosion of genetic diversity in P. fulvum. Systematic ex-situ conservation may be advisable to safeguard genetic variability for future utilization of this species.
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Affiliation(s)
- Timo Hellwig
- R.H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, POB 12, Rehovot, 761001, Israel; Institute of Plant Sciences, Agricultural Research Organization - Volcani Center, P.O.B 15159, Rishon LeZion, 7505101, Israel
| | - Shahal Abbo
- R.H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, POB 12, Rehovot, 761001, Israel
| | - Amir Sherman
- Institute of Plant Sciences, Agricultural Research Organization - Volcani Center, P.O.B 15159, Rishon LeZion, 7505101, Israel
| | - Ron Ophir
- Institute of Plant Sciences, Agricultural Research Organization - Volcani Center, P.O.B 15159, Rishon LeZion, 7505101, Israel.
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28
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Mwape VW, Khentry Y, Newman TE, Denton-Giles M, Derbyshire MC, Chen K, Berger J, Kamphuis LG. Identification of Sources of Sclerotinia sclerotiorum Resistance in a Collection of Wild Cicer Germplasm. PLANT DISEASE 2021; 105:2314-2324. [PMID: 33851865 DOI: 10.1094/pdis-02-21-0367-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Sclerotinia sclerotiorum is an important fungal pathogen of chickpea (Cicer arietinum L.), and it can cause yield losses up to 100%. The wild progenitors are much more diverse than domesticated chickpea, and this study describes how this relates to S. sclerotiorum resistance. Initially, the pathogenicity of nine Australian S. sclerotiorum isolates was examined on three Cicer lines to develop a robust phenotyping assay, and significant differences in isolate aggressiveness were identified with six isolates being classed as highly aggressive and three as moderately aggressive. We identified two S. sclerotiorum isolates, CU8.20 and CU10.12, to be highly aggressive and moderately aggressive, respectively. A subsequent phenotyping assay was conducted using the two isolates to evaluate 86 wild Cicer accessions (Cicer reticulatum and Cicer echinospermum) and two C. arietinum varieties for resistance to S. sclerotiorum. A subset of 12 genotypes was further evaluated, and subsequently, two wild Cicer accessions with consistently high levels of resistance to S. sclerotiorum were examined using the initially characterized nine isolates. Wild Cicer accessions Karab_084 and Deste_063 demonstrated consistent partial resistance to S. sclerotiorum. There were significant differences in responses to S. sclerotiorum across wild Cicer collection sites. The Cermik, Karabahce, and Destek sites' responses to the aggressive isolate CU8.20 ranged from resistant to susceptible, highlighting an interaction between isolate genotype and chickpea collection site for sclerotinia stem rot resistance. This is the first evidence of partial stem resistance identified in wild Cicer germplasm, which can be adopted in chickpea breeding programs to enhance S. sclerotiorum resistance in future chickpea varieties.
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Affiliation(s)
- Virginia W Mwape
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Floreat, WA 6104, Australia
| | - Yuphin Khentry
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
| | - Toby E Newman
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
| | - Matthew Denton-Giles
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
| | - Mark C Derbyshire
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
| | - Kefei Chen
- Statistics for the Australian Grains Industry-West, Curtin University, Bentley, WA 6102, Australia
| | - Jens Berger
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Floreat, WA 6104, Australia
| | - Lars G Kamphuis
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Floreat, WA 6104, Australia
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29
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Kholová J, Urban MO, Cock J, Arcos J, Arnaud E, Aytekin D, Azevedo V, Barnes AP, Ceccarelli S, Chavarriaga P, Cobb JN, Connor D, Cooper M, Craufurd P, Debouck D, Fungo R, Grando S, Hammer GL, Jara CE, Messina C, Mosquera G, Nchanji E, Ng EH, Prager S, Sankaran S, Selvaraj M, Tardieu F, Thornton P, Valdes-Gutierrez SP, van Etten J, Wenzl P, Xu Y. In pursuit of a better world: crop improvement and the CGIAR. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5158-5179. [PMID: 34021317 PMCID: PMC8272562 DOI: 10.1093/jxb/erab226] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/20/2021] [Indexed: 05/10/2023]
Abstract
The CGIAR crop improvement (CI) programs, unlike commercial CI programs, which are mainly geared to profit though meeting farmers' needs, are charged with meeting multiple objectives with target populations that include both farmers and the community at large. We compiled the opinions from >30 experts in the private and public sector on key strategies, methodologies, and activities that could the help CGIAR meet the challenges of providing farmers with improved varieties while simultaneously meeting the goals of: (i) nutrition, health, and food security; (ii) poverty reduction, livelihoods, and jobs; (iii) gender equality, youth, and inclusion; (iv) climate adaptation and mitigation; and (v) environmental health and biodiversity. We review the crop improvement processes starting with crop choice, moving through to breeding objectives, production of potential new varieties, selection, and finally adoption by farmers. The importance of multidisciplinary teams working towards common objectives is stressed as a key factor to success. The role of the distinct disciplines, actors, and their interactions throughout the process from crop choice through to adoption by farmers is discussed and illustrated.
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Affiliation(s)
- Jana Kholová
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad-502324, India
| | - Milan Oldřich Urban
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - James Cock
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Jairo Arcos
- HarvestPlus, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Elizabeth Arnaud
- Bioversity International, Parc scientifique Agropolis II, 1990 Boulevard de la Lironde, 34397 Montpellier, France
| | | | - Vania Azevedo
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad-502324, India
| | | | | | - Paul Chavarriaga
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | | | - David Connor
- Department of Agriculture and Food, The University of Melbourne, Australia
| | - Mark Cooper
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Peter Craufurd
- CIMMYT, 1st floor, National Plant Breeding and Genetics Centre, NARC Research Station, Khumaltor, Lalitpur, PO Box 5186, Kathmandu, Nepal
| | - Daniel Debouck
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Robert Fungo
- International Center for Tropical Agriculture, PO Box 6247, Kampala, Uganda
- School of Food Technology, Nutrition & Bio-Engineering, Makerere University, PO Box, 7062, Kampala, Uganda
| | - Stefania Grando
- Independent Consultant, Corso Mazzini 256, 63100 Ascoli Piceno, Italy
| | - Graeme L Hammer
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Carlos E Jara
- Independent Consultant, Hacienda Real, Torre 2, CP 760033, Cali, Colombia
| | - Charlie Messina
- Corteva Agriscience, 7200 62nd Avenue, Johnston, IA 50131, USA
| | - Gloria Mosquera
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Eileen Nchanji
- International Center for Tropical Agriculture, African hub, Box 823-00621, Nairobi, Kenya
| | - Eng Hwa Ng
- International Maize and Wheat Improvement Center (CIMMYT); México-Veracruz, El Batán Km. 45, 56237, Mexico
| | - Steven Prager
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Sindhujan Sankaran
- Department of Biological Systems Engineering, Washington State University, 1935 E. Grimes Way, PO Box 646120, Pullman, WA 99164, USA
| | - Michael Selvaraj
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - François Tardieu
- INRA Centre de Montpellier, Montpellier, Languedoc-Roussillon, France
| | - Philip Thornton
- CGIAR Research Program on Climate Change, Agriculture 37 and Food Security (CCAFS), International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Sandra P Valdes-Gutierrez
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Jacob van Etten
- Bioversity International, Parc scientifique Agropolis II, 1990 Boulevard de la Lironde, 34397 Montpellier, France
| | - Peter Wenzl
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Yunbi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- International Maize and Wheat Improvement Center (CIMMYT), El Batan Texcoco 56130, Mexico
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30
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Kholová J, Urban MO, Cock J, Arcos J, Arnaud E, Aytekin D, Azevedo V, Barnes AP, Ceccarelli S, Chavarriaga P, Cobb JN, Connor D, Cooper M, Craufurd P, Debouck D, Fungo R, Grando S, Hammer GL, Jara CE, Messina C, Mosquera G, Nchanji E, Ng EH, Prager S, Sankaran S, Selvaraj M, Tardieu F, Thornton P, Valdes-Gutierrez SP, van Etten J, Wenzl P, Xu Y. In pursuit of a better world: crop improvement and the CGIAR. JOURNAL OF EXPERIMENTAL BOTANY 2021. [PMID: 34021317 DOI: 10.5281/zenodo.4638248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The CGIAR crop improvement (CI) programs, unlike commercial CI programs, which are mainly geared to profit though meeting farmers' needs, are charged with meeting multiple objectives with target populations that include both farmers and the community at large. We compiled the opinions from >30 experts in the private and public sector on key strategies, methodologies, and activities that could the help CGIAR meet the challenges of providing farmers with improved varieties while simultaneously meeting the goals of: (i) nutrition, health, and food security; (ii) poverty reduction, livelihoods, and jobs; (iii) gender equality, youth, and inclusion; (iv) climate adaptation and mitigation; and (v) environmental health and biodiversity. We review the crop improvement processes starting with crop choice, moving through to breeding objectives, production of potential new varieties, selection, and finally adoption by farmers. The importance of multidisciplinary teams working towards common objectives is stressed as a key factor to success. The role of the distinct disciplines, actors, and their interactions throughout the process from crop choice through to adoption by farmers is discussed and illustrated.
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Affiliation(s)
- Jana Kholová
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad-502324, India
| | - Milan Oldřich Urban
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - James Cock
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Jairo Arcos
- HarvestPlus, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Elizabeth Arnaud
- Bioversity International, Parc scientifique Agropolis II, 1990 Boulevard de la Lironde, 34397 Montpellier, France
| | | | - Vania Azevedo
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad-502324, India
| | | | | | - Paul Chavarriaga
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | | | - David Connor
- Department of Agriculture and Food, The University of Melbourne, Australia
| | - Mark Cooper
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Peter Craufurd
- CIMMYT, 1st floor, National Plant Breeding and Genetics Centre, NARC Research Station, Khumaltor, Lalitpur, PO Box 5186, Kathmandu, Nepal
| | - Daniel Debouck
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Robert Fungo
- International Center for Tropical Agriculture, PO Box 6247, Kampala, Uganda
- School of Food Technology, Nutrition & Bio-Engineering, Makerere University, PO Box, 7062, Kampala, Uganda
| | - Stefania Grando
- Independent Consultant, Corso Mazzini 256, 63100 Ascoli Piceno, Italy
| | - Graeme L Hammer
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Carlos E Jara
- Independent Consultant, Hacienda Real, Torre 2, CP 760033, Cali, Colombia
| | - Charlie Messina
- Corteva Agriscience, 7200 62nd Avenue, Johnston, IA 50131, USA
| | - Gloria Mosquera
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Eileen Nchanji
- International Center for Tropical Agriculture, African hub, Box 823-00621, Nairobi, Kenya
| | - Eng Hwa Ng
- International Maize and Wheat Improvement Center (CIMMYT); México-Veracruz, El Batán Km. 45, 56237, Mexico
| | - Steven Prager
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Sindhujan Sankaran
- Department of Biological Systems Engineering, Washington State University, 1935 E. Grimes Way, PO Box 646120, Pullman, WA 99164, USA
| | - Michael Selvaraj
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - François Tardieu
- INRA Centre de Montpellier, Montpellier, Languedoc-Roussillon, France
| | - Philip Thornton
- CGIAR Research Program on Climate Change, Agriculture 37 and Food Security (CCAFS), International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Sandra P Valdes-Gutierrez
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Jacob van Etten
- Bioversity International, Parc scientifique Agropolis II, 1990 Boulevard de la Lironde, 34397 Montpellier, France
| | - Peter Wenzl
- International Center for Tropical Agriculture, Km 17 Recta Cali-Palmira, CP 763537, A.A. 12 6713, Cali, Colombia
| | - Yunbi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- International Maize and Wheat Improvement Center (CIMMYT), El Batan Texcoco 56130, Mexico
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31
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Toker C, Berger J, Eker T, Sari D, Sari H, Gokturk RS, Kahraman A, Aydin B, von Wettberg EJ. Cicer turcicum: A New Cicer Species and Its Potential to Improve Chickpea. FRONTIERS IN PLANT SCIENCE 2021; 12:662891. [PMID: 33936152 PMCID: PMC8082243 DOI: 10.3389/fpls.2021.662891] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
Genetic resources of the genus Cicer L. are not only limited when compared to other important food legumes and major cereal crops but also, they include several endemic species with endangered status based on the criteria of the International Union for Conservation of Nature. The chief threats to endemic and endangered Cicer species are over-grazing and habitat change in their natural environments driven by climate changes. During a collection mission in east and south-east Anatolia (Turkey), a new Cicer species was discovered, proposed here as C. turcicum Toker, Berger & Gokturk. Here, we describe the morphological characteristics, images, and ecology of the species, and present preliminary evidence of its potential utility for chickpea improvement. C. turcicum is an annual species, endemic to southeast Anatolia and to date has only been located in a single population distant from any other known annual Cicer species. It belongs to section Cicer M. Pop. of the subgenus Pseudononis M. Pop. of the genus Cicer L. (Fabaceae) and on the basis of internal transcribed spacer (ITS) sequence similarity appears to be a sister species of C. reticulatum Ladiz. and C. echinospermum P.H. Davis, both of which are inter-fertile with domestic chickpea (C. arietinum L.). With the addition of C. turcicum, the genus Cicer now comprises 10 annual and 36 perennial species. As a preliminary evaluation of its potential for chickpea improvement two accessions of C. turcicum were field screened for reproductive heat tolerance and seeds were tested for bruchid resistance alongside a representative group of wild and domestic annual Cicer species. C. turcicum expressed the highest heat tolerance and similar bruchid resistance as C. judaicum Boiss. and C. pinnatifidum Juab. & Spach, neither of which are in the primary genepool of domestic chickpea. Given that C. arietinum and C. reticulatum returned the lowest and the second lowest tolerance and resistance scores, C. turcicum may hold much potential for chickpea improvement if its close relatedness supports interspecific hybridization with the cultigen. Crossing experiments are currently underway to explore this question.
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Affiliation(s)
- Cengiz Toker
- Department of Field Crops, Akdeniz University, Antalya, Turkey
| | - Jens Berger
- CSIRO Agriculture and Food, Wembley, WA, Australia
| | - Tuba Eker
- Department of Field Crops, Akdeniz University, Antalya, Turkey
| | - Duygu Sari
- Department of Field Crops, Akdeniz University, Antalya, Turkey
| | - Hatice Sari
- Department of Field Crops, Akdeniz University, Antalya, Turkey
| | | | | | - Bilal Aydin
- Department of Field Crops, Harran University, Şanlıurfa, Turkey
| | - Eric J. von Wettberg
- Department of Plant and Soil Science and Gund Institute for Environment, University of Vermont, Burlington, VT, United States
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32
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Landis JB, Miller CM, Broz AK, Bennett AA, Carrasquilla-Garcia N, Cook DR, Last RL, Bedinger PA, Moghe GD. Migration through a Major Andean Ecogeographic Disruption as a Driver of Genetic and Phenotypic Diversity in a Wild Tomato Species. Mol Biol Evol 2021; 38:3202-3219. [PMID: 33822137 PMCID: PMC8321546 DOI: 10.1093/molbev/msab092] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Evolutionary dynamics at the population level play a central role in creating the diversity of life on our planet. In this study, we sought to understand the origins of such population-level variation in mating systems and defensive acylsugar chemistry in Solanum habrochaites—a wild tomato species found in diverse Andean habitats in Ecuador and Peru. Using Restriction-site-Associated-DNA-Sequencing (RAD-seq) of 50 S. habrochaites accessions, we identified eight population clusters generated via isolation and hybridization dynamics of 4–6 ancestral populations. Detailed characterization of mating systems of these clusters revealed emergence of multiple self-compatible (SC) groups from progenitor self-incompatible populations in the northern part of the species range. Emergence of these SC groups was also associated with fixation of deleterious alleles inactivating acylsugar acetylation. The Amotape-Huancabamba Zone—a geographical landmark in the Andes with high endemism and isolated microhabitats—was identified as a major driver of differentiation in the northern species range, whereas large geographical distances contributed to population structure and evolution of a novel SC group in the central and southern parts of the range, where the species was also inferred to have originated. Findings presented here highlight the role of the diverse ecogeography of Peru and Ecuador in generating population differentiation, and enhance our understanding of the microevolutionary processes that create biological diversity.
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Affiliation(s)
- Jacob B Landis
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA.,Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | | - Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Alexandra A Bennett
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | | - Douglas R Cook
- Department of Plant Pathology, University of California, Davis, Davis, CA, USA
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | | | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
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33
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Kushwah A, Bhatia D, Rani U, Yadav IS, Singh I, Bharadwaj C, Singh S. Molecular mapping of quantitative trait loci for ascochyta blight and botrytis grey mould resistance in an inter-specific cross in chickpea ( Cicer arietinum L.) using genotyping by sequencing. BREEDING SCIENCE 2021; 71:229-239. [PMID: 34377071 PMCID: PMC8329888 DOI: 10.1270/jsbbs.20085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/23/2020] [Indexed: 06/13/2023]
Abstract
Ascochyta blight (AB) and botrytis grey mould (BGM) are the most devastating fungal diseases of chickpea worldwide. The wild relative of chickpea, C. reticulatum acc. ILWC 292 was found resistant to BGM whereas, GPF2 (Cicer arietinum L.) is resistant to AB. A total of 187 F8 Recombinant Inbred Lines (RILs) developed from an inter-specific cross of GPF2 × C. reticulatum acc. ILWC 292 were used to identify quantitative trait loci (QTLs) responsible for resistance to AB and BGM. RILs along with parents were evaluated under artificial epiphytotic field/laboratory conditions for two years. Highly significant differences (P < 0.001) were observed for reaction to both pathogens in both years. Parents and RILs were genotyped-by-sequencing to identify genome wide single nucleotide polymorphism (SNPs). A total of 1365 filtered and parental polymorphic SNPs were used for linkage map construction, of which, 673 SNPs were arranged on eight linkage groups. Composite interval mapping revealed three QTLs for AB and four QTLs for BGM resistance. Out of which, two QTLs for AB and three QTLs for BGM were consistent in both years. These QTLs can be targeted for further fine mapping for deployment of resistance to AB and BGM in elite chickpea cultivars using marker-assisted-selection.
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Affiliation(s)
- Ashutosh Kushwah
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India, 141004
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India, 141004
| | - Upasana Rani
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India, 141004
| | - Inderjit Singh Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India, 141004
| | - Inderjit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India, 141004
| | - C Bharadwaj
- ICAR-Indian Agricultural Research Institute, New Delhi, India, 110012
| | - Sarvjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India, 141004
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34
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Ithnin M, Vu WT, Shin MG, Suryawanshi V, Sherbina K, Zolkafli SH, Serdari NM, Amiruddin MD, Abdullah N, Mustaffa S, Marjuni M, Nookiah R, Kushairi A, Marjoram P, Nuzhdin SV, Chang PL, Singh R. Genomic diversity and genome-wide association analysis related to yield and fatty acid composition of wild American oil palm. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 304:110731. [PMID: 33568284 DOI: 10.1016/j.plantsci.2020.110731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 05/15/2023]
Abstract
Existing Elaeis guineensis cultivars lack sufficient genetic diversity due to extensive breeding. Harnessing variation in wild crop relatives is necessary to expand the breadth of agronomically valuable traits. Using RAD sequencing, we examine the natural diversity of wild American oil palm populations (Elaeis oleifera), a sister species of the cultivated Elaeis guineensis oil palm. We genotyped 192 wild E. oleifera palms collected from seven Latin American countries along with four cultivated E. guineensis palms. Honduras, Costa Rica, Panama and Colombia palms are panmictic and genetically similar. Genomic patterns of diversity suggest that these populations likely originated from the Amazon Basin. Despite evidence of a genetic bottleneck and high inbreeding observed in these populations, there is considerable genetic and phenotypic variation for agronomically valuable traits. Genome-wide association revealed several candidate genes associated with fatty acid composition along with vegetative and yield-related traits. These observations provide valuable insight into the geographic distribution of diversity, phenotypic variation and its genetic architecture that will guide choices of wild genotypes for crop improvement.
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Affiliation(s)
- Maizura Ithnin
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Wendy T Vu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Min-Gyoung Shin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Vasantika Suryawanshi
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Katrina Sherbina
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Siti Hazirah Zolkafli
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Norhalida Mohamed Serdari
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Mohd Din Amiruddin
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Norziha Abdullah
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Suzana Mustaffa
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Marhalil Marjuni
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Rajanaidu Nookiah
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Ahmad Kushairi
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Paul Marjoram
- Department of Preventative Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Sergey V Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter L Chang
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
| | - Rajinder Singh
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia.
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35
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Newman TE, Jacques S, Grime C, Kamphuis FL, Lee RC, Berger J, Kamphuis LG. Identification of Novel Sources of Resistance to Ascochyta Blight in a Collection of Wild Cicer Accessions. PHYTOPATHOLOGY 2021; 111:369-379. [PMID: 32787627 DOI: 10.1094/phyto-04-20-0137-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Chickpea production is constrained worldwide by the necrotrophic fungal pathogen Ascochyta rabiei, the causal agent of Ascochyta blight (AB). To reduce the impact of this disease, novel sources of resistance are required in chickpea cultivars. Here, we screened a new collection of wild Cicer accessions for AB resistance and identified accessions resistant to multiple, highly pathogenic isolates. In addition to this, analyses demonstrated that some collection sites of C. echinospermum harbor predominantly resistant accessions, knowledge that can inform future collection missions. Furthermore, a genome-wide association study identified regions of the C. reticulatum genome associated with AB resistance and investigation of these regions identified candidate resistance genes. Taken together, these results can be utilized to enhance the resistance of chickpea cultivars to this globally yield-limiting disease.
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Affiliation(s)
- Toby E Newman
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Silke Jacques
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Christy Grime
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Fiona L Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Robert C Lee
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Jens Berger
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Floreat, Western Australia, Australia
| | - Lars G Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
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36
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Sokolkova AB, Bulyntsev SV, Chang PL, Carrasquila-Garcia N, Cook DR, von Wettberg E, Vishnyakova MA, Nuzhdin SV, Samsonova MG. A Genomic Analysis of Historic Chickpea Landraces. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921010061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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37
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Vance W, Pradeep K, Strachan SR, Diffey S, Bell RW. Novel Sources of Tolerance to Aluminium Toxicity in Wild Cicer ( Cicer reticulatum and Cicer echinospermum) Collections. FRONTIERS IN PLANT SCIENCE 2021; 12:678211. [PMID: 34249045 PMCID: PMC8269930 DOI: 10.3389/fpls.2021.678211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/25/2021] [Indexed: 05/05/2023]
Abstract
In acid soils, the toxic form of aluminium, Al3+, significantly inhibits root growth and elongation, leading to less water and nutrient uptake. Previous research had shown differential Al toxicity tolerance among cultivated Cicer arietinum L. (chickpea); however, the potential for developing tolerant cultivars is limited by the narrow genetic diversity of cultivated chickpeas. Recent collections from Turkey of wild Cicer species, Cicer reticulatum, and Cicer echinospermum, have increased the available gene pool significantly, but there has been no large-scale screening of wild Cicer for acid tolerance or Al3+ toxicity tolerance. This study evaluated 167 wild Cicer and 17 Australian chickpea cultivars in a series of screenings under controlled growth conditions. The pH of 4.2 and Al concentrations of 15 and 60 μM Al were selected for large-scale screening based on dose response experiments in a low ionic strength nutrient solution. The change in root length showed better discrimination between tolerant and sensitive lines when compared with shoot and root dry weights and was used as a selection criterion. In a large-scale screening, 13 wild Cicer reticulatum accessions had a higher root tolerance index (≥50%), and eight had higher relative change in root length (≥40%) compared with PBA Monarch, which showed greater tolerance among the Australian domestic cultivars screened. In general, C. reticulatum species were found to be more tolerant than C. echinospermum, while genetic population groups Ret_5, Ret_6, and Ret_7 from Diyarbakir and Mardin Province were more tolerant than other groups. Among C. echinospermum, Ech_6 from the Siv-Diyar collection site of the Urfa Province showed better tolerance than other groups. In this first detailed screening of aluminium toxicity tolerance in the new wild Cicer collections, we identified accessions that were more tolerant than current domestic cultivars, providing promising germplasm for breeding programs to expand chickpea adaptation to acid soils.
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Affiliation(s)
- Wendy Vance
- Centre for Sustainable Farming Systems, Future Food Institute, Murdoch University, Perth, WA, Australia
- *Correspondence: Wendy Vance
| | - Karthika Pradeep
- Centre for Sustainable Farming Systems, Future Food Institute, Murdoch University, Perth, WA, Australia
| | - Scott R. Strachan
- Centre for Sustainable Farming Systems, Future Food Institute, Murdoch University, Perth, WA, Australia
| | | | - Richard W. Bell
- Centre for Sustainable Farming Systems, Future Food Institute, Murdoch University, Perth, WA, Australia
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38
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Berger J, Pushpavalli R, Ludwig C, Parsons S, Basdemir F, Whisson K. Wild and Domestic Differences in Plant Development and Responses to Water Deficit in Cicer. Front Genet 2020; 11:607819. [PMID: 33343641 PMCID: PMC7746823 DOI: 10.3389/fgene.2020.607819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/10/2020] [Indexed: 11/25/2022] Open
Abstract
There is growing interest in widening the genetic diversity of domestic crops using wild relatives to break linkage drag and/or introduce new adaptive traits, particularly in narrow crops such as chickpea. To this end, it is important to understand wild and domestic adaptive differences to develop greater insight into how wild traits can be exploited for crop improvement. Here, we study wild and domestic Cicer development and water-use over the lifecycle, measuring responses to reproductive water deficit, a key Mediterranean selection pressure, using mini-lysimeters (33 L round pots) in common gardens under contrasting water regimes. Wild and domestic Cicer were consistently separated by later phenology, greater water extraction and lower water use efficiency (WUE) and harvest index in the former, and much greater yield-responsiveness in the latter. Throughout the lifecycle, there was greater vegetative investment in wild, and greater reproductive investment in domestic Cicer, reflected in root and harvest indices, rates of leaf area, and pod growth. Domestic WUE was consistently greater than wild, suggesting differences in water-use regulation and partitioning. Large wild-domestic differences revealed in this study are indicative of evolution under contrasting selection pressures. Cicer domestication has selected for early phenology, greater early vigor, and reproductive efficiency, attributes well-suited to a time-delimited production system, where the crop is protected from grazing, disease, and competition, circumstances that do not pertain in the wild. Wild Cicer attributes are more competitive: higher peak rates of leaf area growth, greater ad libitum water-use, and extraction under terminal drought associated with greater vegetative dry matter allocation, leading to a lower reproductive capacity and efficiency than in domestic chickpea. These traits strengthen competitive capacity throughout the growing season and are likely to facilitate recovery from grazing, two significant selection pressures faced by wild, rather than domesticated Cicer. While increased water extraction may be useful for improving chickpea drought tolerance, this trait must be evaluated independently of the other associated wild traits. To this end, the wild-domestic populations have been developed.
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Affiliation(s)
- Jens Berger
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Agriculture and Food, Wembley, WA, Australia
| | - Raju Pushpavalli
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Agriculture and Food, Wembley, WA, Australia
| | - Christiane Ludwig
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Agriculture and Food, Wembley, WA, Australia
| | - Sylvia Parsons
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Agriculture and Food, Wembley, WA, Australia
| | - Fatma Basdemir
- Ceylanpinar Agriculture Vocational School, University of Harran, Sanliurfa, Turkey
| | - Kelly Whisson
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Agriculture and Food, Wembley, WA, Australia
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39
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Marques E, Krieg CP, Dacosta-Calheiros E, Bueno E, Sessa E, Penmetsa RV, von Wettberg E. The Impact of Domestication on Aboveground and Belowground Trait Responses to Nitrogen Fertilization in Wild and Cultivated Genotypes of Chickpea ( Cicer sp.). Front Genet 2020; 11:576338. [PMID: 33343625 PMCID: PMC7738563 DOI: 10.3389/fgene.2020.576338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/06/2020] [Indexed: 02/02/2023] Open
Abstract
Despite the importance of crop responses to low fertility conditions, few studies have examined the extent to which domestication may have limited crop responses to low-fertility environments in aboveground and belowground traits. Moreover, studies that have addressed this topic have used a limited number of wild accessions, therefore overlooking the genotypic and phenotypic diversity of wild relatives. To examine how domestication has affected the response of aboveground and belowground agronomic traits, we measured root and leaf functional traits in an extensive set of wild and domesticated chickpea accessions grown in low and high nitrogen soil environments. Unlike previous studies, the wild accessions used in this study broadly capture the genetic and phenotypic diversity of domesticated chickpea’s (Cicer arietinum) closest compatible wild relative (C. reticulatum). Our results suggest that the domestication of chickpea led to greater capacities for plasticity in morphological and biomass related traits but may have lowered the capacity to modify physiological traits related to gas exchange. Wild chickpea displayed greater phenotypic plasticity for physiological traits including stomatal conductance, canopy level photosynthesis, leaf level photosynthesis, and leaf C/N ratio. In contrast to domesticated chickpea, wild chickpea displayed phenotypes consistent with water loss prevention, by exhibiting lower specific leaf area, stomatal conductance and maintaining efficient water-use. In addition to these general patterns, our results indicate that the domestication dampened the variation in response type to higher nitrogen environments for belowground and aboveground traits, which suggests reduced genetic diversity in current crop germplasm collections.
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Affiliation(s)
- Edward Marques
- Department of Plant and Soil Science and Gund Institute for the Environment, University of Vermont, Burlington, VT, United States.,Department of Biological Sciences, Florida International University, Miami, FL, United States
| | - Christopher P Krieg
- Department of Biology, University of Florida, Gainesville, FL, United States
| | | | - Erika Bueno
- Department of Biological Sciences, Florida International University, Miami, FL, United States
| | - Emily Sessa
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - R Varma Penmetsa
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Eric von Wettberg
- Department of Plant and Soil Science and Gund Institute for the Environment, University of Vermont, Burlington, VT, United States.,Department of Biological Sciences, Florida International University, Miami, FL, United States
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40
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Moenga SM, Gai Y, Carrasquilla-Garcia N, Perilla-Henao LM, Cook DR. Gene co-expression analysis reveals transcriptome divergence between wild and cultivated chickpea under drought stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1195-1214. [PMID: 32920943 DOI: 10.1111/tpj.14988] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
Ancestral adaptations in crop wild relatives can provide a genetic reservoir for crop improvement. Here we document physiological changes to mild and severe drought stress, and the associated transcriptome dynamics in both wild and cultivated chickpea. Over 60% of transcriptional changes were related to metabolism, indicating that metabolic plasticity is a core and conserved drought response. In addition, changes in RNA processing and protein turnover were predominant in the data, suggestive of broad restructuring of the chickpea proteome in response to drought. While 12% of the drought-responsive transcripts have similar dynamics in cultivated and wild accessions, numerous transcripts had expression patterns unique to particular genotypes, or that distinguished wild from cultivated genotypes and whose divergence may be a consequence of domestication. These and other comparisons provide a transcriptional correlate of previously described species' genetic diversity, with wild accessions well differentiated from each other and from cultivars, and cultivars essentially indistinguishable at the broad transcriptome level. We identified metabolic pathways such as phenylpropanoid metabolism, and biological processes such as stomatal development, which are differentially regulated across genotypes with potential consequences on drought tolerance. These data indicate that wild Cicer reticulatum may provide both conserved and divergent mechanisms as a resource in breeding for drought tolerance in cultivated chickpea.
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Affiliation(s)
- Susan M Moenga
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
| | - Yunpeng Gai
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Noelia Carrasquilla-Garcia
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
| | - Laura M Perilla-Henao
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
| | - Douglas R Cook
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
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41
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Wilkey AP, Brown AV, Cannon SB, Cannon EKS. GCViT: a method for interactive, genome-wide visualization of resequencing and SNP array data. BMC Genomics 2020; 21:822. [PMID: 33228531 PMCID: PMC7686774 DOI: 10.1186/s12864-020-07217-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/09/2020] [Indexed: 01/07/2023] Open
Abstract
Background Large genotyping datasets have become commonplace due to efficient, cheap methods for SNP identification. Typical genotyping datasets may have thousands to millions of data points per accession, across tens to thousands of accessions. There is a need for tools to help rapidly explore such datasets, to assess characteristics such as overall differences between accessions and regional anomalies across the genome. Results We present GCViT (Genotype Comparison Visualization Tool), for visualizing and exploring large genotyping datasets. GCViT can be used to identify introgressions, conserved or divergent genomic regions, pedigrees, and other features for more detailed exploration. The program can be used online or as a local instance for whole genome visualization of resequencing or SNP array data. The program performs comparisons of variants among user-selected accessions to identify allele differences and similarities between accessions and a user-selected reference, providing visualizations through histogram, heatmap, or haplotype views. The resulting analyses and images can be exported in various formats. Conclusions GCViT provides methods for interactively visualizing SNP data on a whole genome scale, and can produce publication-ready figures. It can be used in online or local installations. GCViT enables users to confirm or identify genomics regions of interest associated with particular traits. GCViT is freely available at https://github.com/LegumeFederation/gcvit. The 1.0 version described here is available at 10.5281/zenodo.4008713.
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Affiliation(s)
- Andrew P Wilkey
- ORISE Fellow, USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
| | - Anne V Brown
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
| | - Steven B Cannon
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
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Karaca N, Ates D, Nemli S, Ozkuru E, Yilmaz H, Yagmur B, Kartal C, Tosun M, Ozdestan O, Otles S, Kahriman A, Chang P, Tanyolac MB. Identification of SNP Markers Associated with Iron and Zinc Concentrations in Cicer Seeds. Curr Genomics 2020; 21:212-223. [PMID: 33071615 PMCID: PMC7521033 DOI: 10.2174/1389202921666200413150951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 03/18/2020] [Accepted: 03/27/2020] [Indexed: 12/30/2022] Open
Abstract
Background Cicer reticulatum L. is the wild progenitor of chickpea Cicer arietinum L., the fourth most important pulse crop in the world. Iron (Fe) and zinc (Zn) are vital micronutrients that play crucial roles in sustaining life by acting as co-factors for various proteins. Aims and Objectives
In order to improve micronutrient-dense chickpea lines, this study aimed to investigate variability and detect DNA markers associated with Fe and Zn concentrations in the seeds of 73 cultivated (C. arietinum L.) and 107 C. reticulatum genotypes. Methods
A set of 180 accessions was genotyped using 20,868 single nucleotide polymorphism (SNP) markers obtained from genotyping by sequencing analysis. Results
The results revealed substantial variation in the seed Fe and Zn concentration of the surveyed population. Using STRUCTURE software, the population structure was divided into two groups according to the principal component analysis and neighbor-joining tree analysis. A total of 23 and 16 associated SNP markers related to Fe and Zn concentrations, respectively were identified in TASSEL software by the mixed linear model method. Significant SNP markers found in more than two environments were accepted as more reliable than those that only existed in a single environment. Conclusion
The identified markers can be used in marker-assisted selection in chickpea breeding programs for the improvement of seed Fe and Zn concentrations in the chickpea.
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Affiliation(s)
- Nur Karaca
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Duygu Ates
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Seda Nemli
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Esin Ozkuru
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Hasan Yilmaz
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Bulent Yagmur
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Canan Kartal
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Muzaffer Tosun
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Ozgul Ozdestan
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Semih Otles
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Abdullah Kahriman
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Peter Chang
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Muhammed Bahattin Tanyolac
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
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Sokolkova A, Burlyaeva M, Valiannikova T, Vishnyakova M, Schafleitner R, Lee CR, Ting CT, Nair RM, Nuzhdin S, Samsonova M, von Wettberg E. Genome-wide association study in accessions of the mini-core collection of mungbean (Vigna radiata) from the World Vegetable Gene Bank (Taiwan). BMC PLANT BIOLOGY 2020; 20:363. [PMID: 33050907 PMCID: PMC7556912 DOI: 10.1186/s12870-020-02579-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/26/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Mungbean (Vigna radiata (L.) R. Wilczek, or green gram) is important tropical and sub-tropical legume and a rich source of dietary protein and micronutrients. In this study we employ GWAS to examine the genetic basis of variation in several important traits in mungbean, using the mini-core collection established by the World Vegetable Center, which includes 296 accessions that represent the major market classes. This collection has been grown in a common field plot in southern European part of Russia in 2018. RESULTS We used 5041 SNPs in 293 accessions that passed strict filtering for genetic diversity, linkage disequilibrium, population structure and GWAS analysis. Polymorphisms were distributed among all chromosomes, but with variable density. Linkage disequilibrium decayed in approximately 105 kb. Four distinct subgroups were identified within 293 accessions with 70% of accessions attributed to one of the four populations. By performing GWAS on the mini-core collection we have found several loci significantly associated with two important agronomical traits. Four SNPs associated with possibility of maturation in Kuban territory of Southern Russia in 2018 were identified within a region of strong linkage which contains genes encoding zinc finger A20 and an AN1 domain stress-associated protein. CONCLUSIONS The core collection of mungbean established by the World Vegetable Center is a valuable resource for mungbean breeding. The collection has been grown in southern European part of Russia in 2018 under incidental stresses caused by abnormally hot weather and different photoperiod. We have found several loci significantly associated with color of hypocotyl and possibility of maturation under these stressful conditions. SNPs associated with possibility of maturation localize to a region on chromosome 2 with strong linkage, in which genes encoding zinc finger A20 and AN1 domain stress associated protein (SAP) are located. Phenotyping of WorldVeg collection for maturation traits in temperate climatic locations is important as phenology remains a critical breeding target for mungbean. As demand rises for mungbean, production in temperate regions with shorter growing seasons becomes crucial to keep up with needs. Uncovering SNPs for phenology traits will speed breeding efforts.
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Affiliation(s)
- Alena Sokolkova
- Peter the Great St. Petersburg Polytechnic University, Department of Applied Mathematics, St. Petersburg, Russia
| | - Marina Burlyaeva
- Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - Tatjana Valiannikova
- Kuban Branch of Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), Krasnodar region, Russia
| | - Margarita Vishnyakova
- Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | | | | | | | - Ramakrishnan Madhavan Nair
- World Vegetable Center, South and Central Asia, ICRISAT Campus, Patancheru, Hyderabad, Telangana, 502324, India
| | - Sergey Nuzhdin
- Peter the Great St. Petersburg Polytechnic University, Department of Applied Mathematics, St. Petersburg, Russia
- University of Southern California, Los Angeles, CA, 90089, USA
| | - Maria Samsonova
- Peter the Great St. Petersburg Polytechnic University, Department of Applied Mathematics, St. Petersburg, Russia.
| | - Eric von Wettberg
- Peter the Great St. Petersburg Polytechnic University, Department of Applied Mathematics, St. Petersburg, Russia.
- University of Vermont, Burlington, VT, 05405, USA.
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Mittell EA, Cobbold CA, Ijaz UZ, Kilbride EA, Moore KA, Mable BK. Feral populations of Brassica oleracea along Atlantic coasts in western Europe. Ecol Evol 2020; 10:11810-11825. [PMID: 33145003 PMCID: PMC7593181 DOI: 10.1002/ece3.6821] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 01/16/2023] Open
Abstract
There has been growing emphasis on the role that crop wild relatives might play in supporting highly selected agriculturally valuable species in the face of climate change. In species that were domesticated many thousands of years ago, distinguishing wild populations from escaped feral forms can be challenging, but reintroducing variation from either source could supplement current cultivated forms. For economically important cabbages (Brassicaceae: Brassica oleracea), "wild" populations occur throughout Europe but little is known about their genetic variation or potential as resources for breeding more resilient crop varieties. The main aim of this study was to characterize the population structure of geographically isolated wild cabbage populations along the coasts of the UK and Spain, including the Atlantic range edges. Double-digest restriction-site-associated DNA sequencing was used to sample individual cabbage genomes, assess the similarity of plants from 20 populations, and explore environment-genotype associations across varying climatic conditions. Interestingly, there were no indications of isolation by distance; several geographically close populations were genetically more distinct from each other than to distant populations. Furthermore, several distant populations shared genetic ancestry, which could indicate that they were established by escapees of similar source cultivars. However, there were signals of local adaptation to different environments, including a possible relationship between genetic diversity and soil pH. Overall, these results highlight wild cabbages in the Atlantic region as an important genetic resource worthy of further research into their relationship with existing crop varieties.
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Affiliation(s)
- Elizabeth A. Mittell
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
- School of BiologyUniversity of St AndrewsSt AndrewsUK
| | - Christina A. Cobbold
- School of Mathematics and StatisticsUniversity of GlasgowGlasgowUK
- The Boyd Orr Centre for Population and Ecosystem HealthUniversity of GlasgowGlasgowUK
| | | | - Elizabeth A. Kilbride
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
| | | | - Barbara K. Mable
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
- The Boyd Orr Centre for Population and Ecosystem HealthUniversity of GlasgowGlasgowUK
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Martínez-Romero E, Aguirre-Noyola JL, Taco-Taype N, Martínez-Romero J, Zuñiga-Dávila D. Plant microbiota modified by plant domestication. Syst Appl Microbiol 2020; 43:126106. [PMID: 32847781 DOI: 10.1016/j.syapm.2020.126106] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 12/19/2022]
Abstract
Human life became largely dependent on agricultural products after distinct crop-domestication events occurred around 10,000 years ago in different geographical sites. Domestication selected suitable plants for human agricultural practices with unexpected consequences on plant microbiota, which has notable effects on plant growth and health. Among other traits, domestication has changed root architecture, exudation, or defense responses that could have modified plant microbiota. Here we present the comparison of reported data on the microbiota from widely consumed cereals and legumes and their ancestors showing that different bacteria were found in domesticated and wild plant microbiomes in some cases. Considering the large variability in plant microbiota, adequate sampling efforts and function-based approaches are needed to further support differences between the microbiota from wild and domesticated plants. The study of wild plant microbiomes could provide a valuable resource of unexploited beneficial bacteria for crops.
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Affiliation(s)
| | | | - Nataly Taco-Taype
- Laboratorio de Ecología Microbiana, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
| | | | - Doris Zuñiga-Dávila
- Laboratorio de Ecología Microbiana, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
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Liu J, Yu X, Qin Q, Dinkins RD, Zhu H. The Impacts of Domestication and Breeding on Nitrogen Fixation Symbiosis in Legumes. Front Genet 2020; 11:00973. [PMID: 33014021 PMCID: PMC7461779 DOI: 10.3389/fgene.2020.00973] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/31/2020] [Indexed: 01/12/2023] Open
Abstract
Legumes are the second most important family of crop plants. One defining feature of legumes is their unique ability to establish a nitrogen-fixing root nodule symbiosis with soil bacteria known as rhizobia. Since domestication from their wild relatives, crop legumes have been under intensive breeding to improve yield and other agronomic traits but with little attention paid to the belowground symbiosis traits. Theoretical models predict that domestication and breeding processes, coupled with high−input agricultural practices, might have reduced the capacity of crop legumes to achieve their full potential of nitrogen fixation symbiosis. Testing this prediction requires characterizing symbiosis traits in wild and breeding populations under both natural and cultivated environments using genetic, genomic, and ecological approaches. However, very few experimental studies have been dedicated to this area of research. Here, we review how legumes regulate their interactions with soil rhizobia and how domestication, breeding and agricultural practices might have affected nodulation capacity, nitrogen fixation efficiency, and the composition and function of rhizobial community. We also provide a perspective on how to improve legume-rhizobial symbiosis in sustainable agricultural systems.
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Affiliation(s)
- Jinge Liu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Xiaocheng Yu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Qiulin Qin
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Randy D Dinkins
- Forage-Animal Production Research Unit, United States Department of Agriculture-Agricultural Research Service, Lexington, KY, United States
| | - Hongyan Zhu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
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Zhang F, Batley J. Exploring the application of wild species for crop improvement in a changing climate. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:218-222. [PMID: 32029361 DOI: 10.1016/j.pbi.2019.12.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/27/2019] [Accepted: 12/27/2019] [Indexed: 06/10/2023]
Abstract
Modern agriculture is currently facing challenges from a burgeoning population and changing climate, which requires improved crops with adaptation to climate and elite yield and quality traits. While there is a breeding bottleneck caused by intensive selection, gene banks containing conserved wild relatives and landraces can be used as breeding resources. However, with limited genetic information available on these wild relatives, the application has been hindered. With the development of both genomics and bioinformatics techniques, it is now easier to identify the genetic variation in wild species, which can be utilized for the introgression of elite traits. These wild species can therefore play an important role in food security and breeding sustainability.
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Affiliation(s)
- Fangning Zhang
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley 6009, Australia.
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Genomic Analysis of Vavilov's Historic Chickpea Landraces Reveals Footprints of Environmental and Human Selection. Int J Mol Sci 2020; 21:ijms21113952. [PMID: 32486400 PMCID: PMC7313079 DOI: 10.3390/ijms21113952] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 12/17/2022] Open
Abstract
A defining challenge of the 21st century is meeting the nutritional demands of the growing human population, under a scenario of limited land and water resources and under the specter of climate change. The Vavilov seed bank contains numerous landraces collected nearly a hundred years ago, and thus may contain ‘genetic gems’ with the potential to enhance modern breeding efforts. Here, we analyze 407 landraces, sampled from major historic centers of chickpea cultivation and secondary diversification. Genome-Wide Association Studies (GWAS) conducted on both phenotypic traits and bioclimatic variables at landraces sampling sites as extended phenotypes resulted in 84 GWAS hits associated to various regions. The novel haploblock-based test identified haploblocks enriched for single nucleotide polymorphisms (SNPs) associated with phenotypes and bioclimatic variables. Subsequent bi-clustering of traits sharing enriched haploblocks underscored both non-random distribution of SNPs among several haploblocks and their association with multiple traits. We hypothesize that these clusters of pleiotropic SNPs represent co-adapted genetic complexes to a range of environmental conditions that chickpea experienced during domestication and subsequent geographic radiation. Linking genetic variation to phenotypic data and a wealth of historic information preserved in historic seed banks are the keys for genome-based and environment-informed breeding intensification.
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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: 49] [Impact Index Per Article: 12.3] [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.
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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
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50
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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]
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