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Thakro V, Varshney N, Malik N, Daware A, Srivastava R, Mohanty JK, Basu U, Narnoliya L, Jha UC, Tripathi S, Tyagi AK, Parida SK. Functional allele of a MATE gene selected during domestication modulates seed color in chickpea. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:53-71. [PMID: 37738381 DOI: 10.1111/tpj.16469] [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: 05/17/2023] [Revised: 08/14/2023] [Accepted: 08/29/2023] [Indexed: 09/24/2023]
Abstract
Seed color is one of the key target traits of domestication and artificial selection in chickpeas due to its implications on consumer preference and market value. The complex seed color trait has been well dissected in several crop species; however, the genetic mechanism underlying seed color variation in chickpea remains poorly understood. Here, we employed an integrated genomics strategy involving QTL mapping, high-density mapping, map-based cloning, association analysis, and molecular haplotyping in an inter-specific RIL mapping population, association panel, wild accessions, and introgression lines (ILs) of Cicer gene pool. This delineated a MATE gene, CaMATE23, encoding a Transparent Testa (TT) and its natural allele (8-bp insertion) and haplotype underlying a major QTL governing seed color on chickpea chromosome 4. Signatures of selective sweep and a strong purifying selection reflected that CaMATE23, especially its 8-bp insertion natural allelic variant, underwent selection during chickpea domestication. Functional investigations revealed that the 8-bp insertion containing the third cis-regulatory RY-motif element in the CaMATE23 promoter is critical for enhanced binding of CaFUSCA3 transcription factor, a key regulator of seed development and flavonoid biosynthesis, thereby affecting CaMATE23 expression and proanthocyanidin (PA) accumulation in the seed coat to impart varied seed color in chickpea. Consequently, overexpression of CaMATE23 in Arabidopsis tt12 mutant partially restored the seed color phenotype to brown pigmentation, ascertaining its functional role in PA accumulation in the seed coat. These findings shed new light on the seed color regulation and evolutionary history, and highlight the transcriptional regulation of CaMATE23 by CaFUSCA3 in modulating seed color in chickpea. The functionally relevant InDel variation, natural allele, and haplotype from CaMATE23 are vital for translational genomic research, including marker-assisted breeding, for developing chickpea cultivars with desirable seed color that appeal to consumers and meet global market demand.
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Affiliation(s)
- Virevol Thakro
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Nidhi Varshney
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Naveen Malik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, 303002, India
| | - Anurag Daware
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rishi Srivastava
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jitendra K Mohanty
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Udita Basu
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Laxmi Narnoliya
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
| | - Shailesh Tripathi
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
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Saxena S, Pal G, Pandey A. Functional characterization of 2-oxoglutarate-dependent dioxygenase gene family in chickpea. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111836. [PMID: 37619866 DOI: 10.1016/j.plantsci.2023.111836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/07/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023]
Abstract
Chickpea is an important leguminous crop plant with two cultivated types, desi and kabuli. It is nutritionally enriched in flavonoid content in addition to minerals and vitamins imparting huge health benefits to human beings. Our study elucidates the functionality of 2-oxoglutarate dependent dioxygenase (2-ODD) gene family members i.e., flavanone-3-hydroxylase (F3H), flavonol synthase (FLS) and anthocyanidin synthase (ANS) in chickpea using heterologous bacterial system and in-planta studies in Arabidopsis. This provides information about the biosynthesis of two very significant sub-classes of flavonoids- flavonols and anthocyanins. Here, we show that all the three homologs of F3H in chickpea can utilize not just naringenin but also eriodictyol as their substrate. Moreover, we show that FLS in chickpea exhibits bifunctionality having both FLS and F3H activity. Also, our study indicates the richness of desi chickpea over kabuli type through gene expression and metabolite content analyses. Overall, our study establishes the functionality of 2-ODD gene family involved in the early and late steps of flavonoid biosynthesis pathway in chickpea. It paves way for better genetic manipulation of the pathway for direct or indirect synthesis of three major subclasses of flavonoids (flavonol, anthocyanin and proanthocyanin) to develop nutritious, environmentally stable and healthy chickpea (Cicer arietinum) crop.
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Affiliation(s)
- Samiksha Saxena
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Gaurav Pal
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Ashutosh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
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Lauterberg M, Tschiersch H, Papa R, Bitocchi E, Neumann K. Engaging Precision Phenotyping to Scrutinize Vegetative Drought Tolerance and Recovery in Chickpea Plant Genetic Resources. PLANTS (BASEL, SWITZERLAND) 2023; 12:2866. [PMID: 37571019 PMCID: PMC10421427 DOI: 10.3390/plants12152866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/24/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023]
Abstract
Precise and high-throughput phenotyping (HTP) of vegetative drought tolerance in chickpea plant genetic resources (PGR) would enable improved screening for genotypes with low relative loss of biomass formation and reliable physiological performance. It could also provide a basis to further decipher the quantitative trait drought tolerance and recovery and gain a better understanding of the underlying mechanisms. In the context of climate change and novel nutritional trends, legumes and chickpea in particular are becoming increasingly important because of their high protein content and adaptation to low-input conditions. The PGR of legumes represent a valuable source of genetic diversity that can be used for breeding. However, the limited use of germplasm is partly due to a lack of available characterization data. The development of HTP systems offers a perspective for the analysis of dynamic plant traits such as abiotic stress tolerance and can support the identification of suitable genetic resources with a potential breeding value. Sixty chickpea accessions were evaluated on an HTP system under contrasting water regimes to precisely evaluate growth, physiological traits, and recovery under optimal conditions in comparison to drought stress at the vegetative stage. In addition to traits such as Estimated Biovolume (EB), Plant Height (PH), and several color-related traits over more than forty days, photosynthesis was examined by chlorophyll fluorescence measurements on relevant days prior to, during, and after drought stress. With high data quality, a wide phenotypic diversity for adaptation, tolerance, and recovery to drought was recorded in the chickpea PGR panel. In addition to a loss of EB between 72% and 82% after 21 days of drought, photosynthetic capacity decreased by 16-28%. Color-related traits can be used as indicators of different drought stress stages, as they show the progression of stress.
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Affiliation(s)
- Madita Lauterberg
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany; (M.L.)
| | - Henning Tschiersch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany; (M.L.)
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany; (M.L.)
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Sedláková V, Zeljković SĆ, Štefelová N, Smýkal P, Hanáček P. Phenylpropanoid Content of Chickpea Seed Coats in Relation to Seed Dormancy. PLANTS (BASEL, SWITZERLAND) 2023; 12:2687. [PMID: 37514301 PMCID: PMC10384132 DOI: 10.3390/plants12142687] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/07/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
The physical dormancy of seeds is likely to be mediated by the chemical composition and the thickness of the seed coat. Here, we investigate the link between the content of phenylpropanoids (i.e., phenolics and flavonoids) present in the chickpea seed coat and dormancy. The relationship between selected phenolic and flavonoid metabolites of chickpea seed coats and dormancy level was assessed using wild and cultivated chickpea parental genotypes and a derived population of recombinant inbred lines (RILs). The selected phenolic and flavonoid metabolites were analyzed via the LC-MS/MS method. Significant differences in the concentration of certain phenolic acids were found among cultivated (Cicer arietinum, ICC4958) and wild chickpea (Cicer reticulatum, PI489777) parental genotypes. These differences were observed in the contents of gallic, caffeic, vanillic, syringic, p-coumaric, salicylic, and sinapic acids, as well as salicylic acid-2-O-β-d-glucoside and coniferaldehyde. Additionally, significant differences were observed in the flavonoids myricetin, quercetin, luteolin, naringenin, kaempferol, isoorientin, orientin, and isovitexin. When comparing non-dormant and dormant RILs, significant differences were observed in gallic, 3-hydroxybenzoic, syringic, and sinapic acids, as well as the flavonoids quercitrin, quercetin, naringenin, kaempferol, and morin. Phenolic acids were generally more highly concentrated in the wild parental genotype and dormant RILs. We compared the phenylpropanoid content of chickpea seed coats with related legumes, such as pea, lentil, and faba bean. This information could be useful in chickpea breeding programs to reduce dormancy.
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Affiliation(s)
- Veronika Sedláková
- Department of Plant Biology, Mendel University in Brno, 613 00 Brno, Czech Republic
| | - Sanja Ćavar Zeljković
- Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, 783 71 Olomouc, Czech Republic
- Czech Advanced Technology and Research Institute, Palacký University, 783 71 Olomouc, Czech Republic
| | - Nikola Štefelová
- Czech Advanced Technology and Research Institute, Palacký University, 783 71 Olomouc, Czech Republic
| | - Petr Smýkal
- Department of Botany, Faculty of Science, Palacký University, 783 71 Olomouc, Czech Republic
| | - Pavel Hanáček
- Department of Plant Biology, Mendel University in Brno, 613 00 Brno, Czech Republic
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Basu U, Parida SK. The developmental dynamics in cool season legumes with focus on chickpea. PLANT MOLECULAR BIOLOGY 2023; 111:473-491. [PMID: 37016106 DOI: 10.1007/s11103-023-01340-w] [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: 10/21/2022] [Accepted: 02/09/2023] [Indexed: 06/19/2023]
Abstract
Chickpea is one of the most widely consumed grain legume world-wide. Advances in next-generation sequencing and genomics tools have led to genetic dissection and identification of potential candidate genes regulating agronomic traits in chickpea. However, the developmental particularities and its potential in reforming the yield and nutritional value remain largely unexplored. Studies in crops such as rice, maize, tomato and pea have highlighted the contribution of key regulator of developmental events in yield related traits. A comprehensive knowledge on the development aspects of a crop can pave way for new vistas to explore. Pea and Medicago are the close relatives of genus Cicer and the basic developmental events in these legumes are similar. However, there are some distinct developmental features in chickpea which hold potential for future crop improvement endeavours. The global chickpea germplasm encompasses wide range of diversities in terms of morphology at both vegetative and reproductive stages. There is an immediate need for understanding the genetic and molecular basis of this diversity and utilizing them for the yield contributing trait improvement. The review discusses some of the key developmental events which have potential in yield enhancement and the lessons which can be learnt from model legumes in this regard.
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Affiliation(s)
- Udita Basu
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, P.O. Box: 10531, New Delhi, 110067, India
| | - Swarup K Parida
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, P.O. Box: 10531, New Delhi, 110067, India.
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Pal L, Dwivedi V, Gupta SK, Saxena S, Pandey A, Chattopadhyay D. Biochemical analysis of anthocyanin and proanthocyanidin and their regulation in determining chickpea flower and seed coat colour. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:130-148. [PMID: 36205079 DOI: 10.1093/jxb/erac392] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 10/06/2022] [Indexed: 05/20/2023]
Abstract
Flower and seed coat colour are important agronomic traits in chickpea (Cicer arietinum L.). Cultivated chickpeas are of two types namely, desi (dark seeded, purple flowered) and kabuli (light seeded, white flowered). There has been limited information about the molecular mechanism underlying colour variation of flower and seed coats in desi and kabuli chickpea. We profiled the anthocyanin and proanthocyanidin (PA) contents in chickpea flowers and seed coats. Tissue-specific silencing of two genes encoding a basic helix-loop-helix (CabHLH) protein and a tonoplast-localized multidrug and toxic compound extrusion (CaMATE1) transporter in a desi genotype resulted in the reduction in expression of anthocyanin and PA biosynthetic genes and anthocyanin and PA contents in the flower and seed coat, and produced flowers and seeds with kabuli characteristics. Transcriptional regulation of a subset of anthocyanin and PA biosynthetic genes by a natural CabHLH variant and transport assay of a natural CaMATE1 variant explained the association of these alleles with the kabuli phenotype. We carried out a detailed molecular characterization of these genes, and provided evidence that kabuli chickpea flower and seed colour phenotypes can be derived by manipulation of single genes in a desi chickpea background.
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Affiliation(s)
- Lalita Pal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vikas Dwivedi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Santosh Kumar Gupta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Samiksha Saxena
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ashutosh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Debasis Chattopadhyay
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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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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Rajput R, Tyagi S, Naik J, Pucker B, Stracke R, Pandey A. The R2R3-MYB gene family in Cicer arietinum: genome-wide identification and expression analysis leads to functional characterization of proanthocyanidin biosynthesis regulators in the seed coat. PLANTA 2022; 256:67. [PMID: 36038740 DOI: 10.1007/s00425-022-03979-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
We identified 119 typical CaMYB encoding genes and reveal the major components of the proanthocyanidin regulatory network. CaPARs emerged as promising targets for genetic engineering toward improved agronomic traits in C. arietinum. Chickpea (Cicer arietinum) is among the eight oldest crops and has two main types, i.e., desi and kabuli, whose most obvious difference is the color of their seeds. We show that this color difference is due to differences in proanthocyanidin content of seed coats. Using a targeted approach, we performed in silico analysis, metabolite profiling, molecular, genetic, and biochemical studies to decipher the transcriptional regulatory network involved in proanthocyanidin biosynthesis in the seed coat of C. arietinum. Based on the annotated C. arietinum reference genome sequence, we identified 119 typical CaMYB encoding genes, grouped in 32 distinct clades. Two CaR2R3-MYB transcription factors, named CaPAR1 and CaPAR2, clustering with known proanthocyanidin regulators (PARs) were identified and further analyzed. The expression of CaPAR genes correlated well with the expression of the key structural proanthocyanidin biosynthesis genes CaANR and CaLAR and with proanthocyanidin levels. Protein-protein interaction studies suggest the in vivo interaction of CaPAR1 and CaPAR2 with the bHLH-type transcription factor CaTT8. Co-transfection analyses using Arabidopsis thaliana protoplasts showed that the CaPAR proteins form a MBW complex with CaTT8 and CaTTG1, able to activate the promoters of CaANR and CaLAR in planta. Finally, transgenic expression of CaPARs in the proanthocyanidin-deficient A. thaliana mutant tt2-1 leads to complementation of the transparent testa phenotype. Taken together, our results reveal main components of the proanthocyanidin regulatory network in C. arietinum and suggest that CaPARs are relevant targets of genetic engineering toward improved agronomic traits.
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Affiliation(s)
- Ruchika Rajput
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shivi Tyagi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jogindra Naik
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Boas Pucker
- Chair of Genetics and Genomics of Plants, Bielefeld University, 33615, Bielefeld, Germany
- Institute of Plant Biology and Braunschweig Integrated Centre of Systems Biology (BRICS), TU Brunswick, Brunswick, Germany
| | - Ralf Stracke
- Chair of Genetics and Genomics of Plants, Bielefeld University, 33615, Bielefeld, Germany
| | - Ashutosh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Mohanty JK, Jha UC, Dixit GP, Parida SK. Harnessing the hidden allelic diversity of wild Cicer to accelerate genomics-assisted chickpea crop improvement. Mol Biol Rep 2022; 49:5697-5715. [PMID: 35708861 DOI: 10.1007/s11033-022-07613-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/17/2022] [Indexed: 10/18/2022]
Abstract
Chickpea, commonly called Bengal gram or Garbanzo bean, faces a productivity crisis around the globe due to numerous biotic and abiotic stresses. The eroded genetic base of the cultivated Cicer gene pool is becoming a significant bottleneck in developing stress-resilient chickpea cultivars. In this scenario, the crop wild relatives (CWR) of chickpea, with the useful genomic wealth of their wild adaptation, give a ray of hope to improve the genetic background of the cultivated Cicer gene pool. To extrapolate these unearthed genomic diversities of wild, we require a thorough understanding of the pre-historic domestication episodes that are changing their shape with the expansion of the available scientific evidence. Keeping aforesaid in view, the current review article provides a glimpsed overview on several efforts done so far to reveal the mysterious origin and evolution of the Cicer gene pool, along with the constraints in their utilization for chickpea crop improvement. It encapsulates various stress-resilient CWR of chickpea and their use in several pre-breeding programs to develop numerous breeding populations for crop genetic enhancement. Further, this review will recapitulate the significant contributions of structural, functional and comparative genomics, pan-genomics and diverse genomics-assisted breeding strategy in dissecting the untapped trait-specific allelic/gene diversity and domestication pattern behind the CWR of chickpea, along with their potential and promises. We expect the newly explored genetic variations may be used in the breeding programs for re-wilding the cultigens' genomic background to open a new avenue for genetic gain and crop improvement capacity of chickpea.
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Affiliation(s)
- Jitendra Kumar Mohanty
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Uday Chand Jha
- ICAR-Indian Institute of Pulse Research (IIPR), Kanpur, 208024, India
| | - G P Dixit
- ICAR-Indian Institute of Pulse Research (IIPR), Kanpur, 208024, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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10
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Hellwig T, Abbo S, Ophir R. Phylogeny and disparate selection signatures suggest two genetically independent domestication events in pea (Pisum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:419-439. [PMID: 35061306 PMCID: PMC9303476 DOI: 10.1111/tpj.15678] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 01/15/2022] [Indexed: 05/25/2023]
Abstract
Domestication is considered a model of adaptation that can be used to draw conclusions about the modus operandi of selection in natural systems. Investigating domestication may give insights into how plants react to different intensities of human manipulation, which has direct implication for the continuing efforts of crop improvement. Therefore, scientists of various disciplines study domestication-related questions to understand the biological and cultural bases of the domestication process. We employed restriction site-associated DNA sequencing (RAD-seq) of 494 Pisum sativum (pea) samples from all wild and domesticated groups to analyze the genetic structure of the collection. Patterns of ancient admixture were investigated by analysis of admixture graphs. We used two complementary approaches, one diversity based and one based on differentiation, to detect the selection signatures putatively associated with domestication. An analysis of the subpopulation structure of wild P. sativum revealed five distinct groups with a notable geographic pattern. Pisum abyssinicum clustered unequivocally within the P. sativum complex, without any indication of hybrid origin. We detected 32 genomic regions putatively subjected to selection: 29 in P. sativum ssp. sativum and three in P. abyssinicum. The two domesticated groups did not share regions under selection and did not display similar haplotype patterns within those regions. Wild P. sativum is structured into well-diverged subgroups. Although Pisum sativum ssp. humile is not supported as a taxonomic entity, the so-called 'southern humile' is a genuine wild group. Introgression did not shape the variation observed within the sampled germplasm. The two domesticated pea groups display distinct genetic bases of domestication, suggesting two genetically independent domestication events.
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Affiliation(s)
- Timo Hellwig
- The Levi Eshkol School of AgricultureThe Hebrew University of JerusalemJerusalem, RehovotIsrael
- Volcani Center, Agricultural Research OrganizationRishon LeZionIsrael
- Institute of Plant Genetics, Heinrich‐Heine‐UniversityDüsseldorfGermany
| | - Shahal Abbo
- The Levi Eshkol School of AgricultureThe Hebrew University of JerusalemJerusalem, RehovotIsrael
| | - Ron Ophir
- Volcani Center, Agricultural Research OrganizationRishon LeZionIsrael
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Rocchetti L, Gioia T, Logozzo G, Brezeanu C, Pereira LG, la Rosa LD, Marzario S, Pieri A, Fernie AR, Alseekh S, Susek K, Cook DR, Varshney RK, Agrawal SK, Hamwieh A, Bitocchi E, Papa R. Towards the Development, Maintenance and Standardized Phenotypic Characterization of Single-Seed-Descent Genetic Resources for Chickpea. Curr Protoc 2022; 2:e371. [PMID: 35179832 DOI: 10.1002/cpz1.371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Here we present the approach used to develop the INCREASE "Intelligent Chickpea" Collections, from analysis of the information on the life history and population structure of chickpea germplasm, the availability of genomic and genetic resources, the identification of key phenotypic traits and methodologies to characterize chickpea. We present two phenotypic protocols within H2O20 Project INCREASE to characterize, develop, and maintain chickpea single-seed-descent (SSD) line collections. Such protocols and related genetic resource data from the project will be available for the legume community to apply the standardized approaches to develop Chickpea Intelligent Collections further or for multiplication/seed-increase purposes. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Characterization of chickpea seeds for seed-trait descriptors Basic Protocol 2: Characterization of chickpea lines for plant-trait descriptors specific for primary seed increase.
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Affiliation(s)
- Lorenzo Rocchetti
- Department of Agricultural, Food, and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Tania Gioia
- School of Agriculture, Forestry, Food, and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Giuseppina Logozzo
- School of Agriculture, Forestry, Food, and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Creola Brezeanu
- Staţiunea de Cercetare Dezvoltare Pentru Legumicultură, Bacău, Romania
| | - Luis Guasch Pereira
- Spanish Plant Genetic Resources National Center, National Institute for Agricultural and Food Research and Technology (CRF-INIA-CSIC), Alcalá de Henares, Madrid, Spain
| | - Lucía De la Rosa
- Spanish Plant Genetic Resources National Center, National Institute for Agricultural and Food Research and Technology (CRF-INIA-CSIC), Alcalá de Henares, Madrid, Spain
| | - Stefania Marzario
- School of Agriculture, Forestry, Food, and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Alice Pieri
- Department of Agricultural, Food, and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Center for Plant Systems Biology, Plovdiv, Bulgaria
| | - Karolina Susek
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Douglas R Cook
- Department of Plant Pathology, University of California Davis, Davis, California
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India
| | - Shiv Kumar Agrawal
- Genetic Resources Section, International Center for Agricultural Research in Dry Areas (ICARDA), Agdal Rabat, Morocco
| | - Aladdin Hamwieh
- Genetic Resources Section, International Center for Agricultural Research in Dry Areas (ICARDA), Agdal Rabat, Morocco
| | - Elena Bitocchi
- Department of Agricultural, Food, and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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12
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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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13
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Rajkumar MS, Garg R, Jain M. Genome resequencing reveals DNA polymorphisms associated with seed size/weight determination in chickpea. Genomics 2021; 113:1458-1468. [PMID: 33744344 DOI: 10.1016/j.ygeno.2021.03.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/23/2021] [Accepted: 03/14/2021] [Indexed: 12/14/2022]
Abstract
Crop productivity in legumes is determined by number and size/weight of seeds. To understand the genetic basis of seed size/weight in chickpea, we performed genome resequencing of 13 small- and 5 large-seeded genotypes using Illumina platform. Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) differentiating small- and large-seeded genotypes were identified. A total of 17,902 SNPs and 2594 InDels located in promoter and/or coding regions that may contribute to seed size/weight were detected. Of these, 266 SNPs showed significant association with seed size/weight trait. Twenty-three genes including those involved in cell growth/division, encoding transcription factors and located within QTLs associated with seed size/weight harbored SNPs within transcription factor binding motif(s) and/or coding region. The non-synonymous SNPs were found to affect the mutational sensitivity and stability of the encoded proteins. Overall, we provided a high-quality SNP map for large-scale genotyping applications and identified candidate genes that determine seed size/weight in chickpea.
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Affiliation(s)
- Mohan Singh Rajkumar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh 201314, India
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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14
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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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15
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Ku YS, Contador CA, Ng MS, Yu J, Chung G, Lam HM. The Effects of Domestication on Secondary Metabolite Composition in Legumes. Front Genet 2020; 11:581357. [PMID: 33193705 PMCID: PMC7530298 DOI: 10.3389/fgene.2020.581357] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/31/2020] [Indexed: 12/13/2022] Open
Abstract
Legumes are rich in secondary metabolites, such as polyphenols, alkaloids, and saponins, which are important defense compounds to protect the plant against herbivores and pathogens, and act as signaling molecules between the plant and its biotic environment. Legume-sourced secondary metabolites are well known for their potential benefits to human health as pharmaceuticals and nutraceuticals. During domestication, the color, smell, and taste of crop plants have been the focus of artificial selection by breeders. Since these agronomic traits are regulated by secondary metabolites, the basis behind the genomic evolution was the selection of the secondary metabolite composition. In this review, we will discuss the classification, occurrence, and health benefits of secondary metabolites in legumes. The differences in their profiles between wild legumes and their cultivated counterparts will be investigated to trace the possible effects of domestication on secondary metabolite compositions, and the advantages and drawbacks of such modifications. The changes in secondary metabolite contents will also be discussed at the genetic level to examine the genes responsible for determining the secondary metabolite composition that might have been lost due to domestication. Understanding these genes would enable breeding programs and metabolic engineering to produce legume varieties with favorable secondary metabolite profiles for facilitating adaptations to a changing climate, promoting beneficial interactions with biotic factors, and enhancing health-beneficial secondary metabolite contents for human consumption.
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Affiliation(s)
- Yee-Shan Ku
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Carolina A. Contador
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Ming-Sin Ng
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Jeongjun Yu
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
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16
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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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17
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Paauw M, Koes R, Quattrocchio FM. Alteration of flavonoid pigmentation patterns during domestication of food crops. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3719-3735. [PMID: 30949670 DOI: 10.1093/jxb/erz141] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 03/15/2019] [Indexed: 05/20/2023]
Abstract
Flavonoids are plant pigments that provide health benefits for human and animal consumers. Understanding why domesticated crops have altered pigmentation patterns and unraveling the molecular/genetic mechanisms that underlie this will facilitate the breeding of new (healthier) varieties. We present an overview of changes in flavonoid pigmentation patterns that have occurred during crop domestication and, where possible, link them to the molecular changes that brought about the new phenotypes. We consider species that lost flavonoid pigmentation in the edible part of the plant at some point during domestication (like cereals). We also consider the converse situation, for example eggplant (aubergine), which instead gained strong anthocyanin accumulation in the skin of the fruit during domestication, and some varieties of citrus and apple that acquired anthocyanins in the fruit flesh. Interestingly, the genes responsible for such changes are sometimes closely linked to, or have pleiotropic effects on, important domestication genes, suggesting accidental and perhaps inevitable changes of anthocyanin patterning during domestication. In other cases, flavonoid pigmentation patterns in domesticated crops are the result of cultural preferences, with examples being found in varieties of citrus, barley, wheat, and maize. Finally, and more recently, in some species, anthocyanins seem to have been the direct target of selection in a second wave of domestication that followed the introduction of industrial food processing.
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Affiliation(s)
- Misha Paauw
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park, XH, Amsterdam, Netherlands
| | - Ronald Koes
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park, XH, Amsterdam, Netherlands
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18
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Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria. Proc Natl Acad Sci U S A 2019; 116:15200-15209. [PMID: 31285337 DOI: 10.1073/pnas.1900056116] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Although microorganisms are known to dominate Earth's biospheres and drive biogeochemical cycling, little is known about the geographic distributions of microbial populations or the environmental factors that pattern those distributions. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of the nitrogen-fixing bacterial symbionts of the crop chickpea, generating 1,027 draft whole-genome sequences at the level of bacterial populations, including 14 high-quality PacBio genomes from a phylogenetically representative subset. We find that diverse Mesorhizobium taxa perform symbiosis with chickpea and have largely overlapping global distributions. However, sampled locations cluster based on the phylogenetic diversity of Mesorhizobium populations, and diversity clusters correspond to edaphic and environmental factors, primarily soil type and latitude. Despite long-standing evolutionary divergence and geographic isolation, the diverse taxa observed to nodulate chickpea share a set of integrative conjugative elements (ICEs) that encode the major functions of the symbiosis. This symbiosis ICE takes 2 forms in the bacterial chromosome-tripartite and monopartite-with tripartite ICEs confined to a broadly distributed superspecies clade. The pairwise evolutionary relatedness of these elements is controlled as much by geographic distance as by the evolutionary relatedness of the background genome. In contrast, diversity in the broader gene content of Mesorhizobium genomes follows a tight linear relationship with core genome phylogenetic distance, with little detectable effect of geography. These results illustrate how geography and demography can operate differentially on the evolution of bacterial genomes and offer useful insights for the development of improved technologies for sustainable agriculture.
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19
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Narnoliya L, Basu U, Bajaj D, Malik N, Thakro V, Daware A, Sharma A, Tripathi S, Hegde VS, Upadhyaya HD, Singh AK, Tyagi AK, Parida SK. Transcriptional signatures modulating shoot apical meristem morphometric and plant architectural traits enhance yield and productivity in chickpea. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:864-883. [PMID: 30758092 DOI: 10.1111/tpj.14284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 01/31/2019] [Accepted: 02/07/2019] [Indexed: 06/09/2023]
Abstract
Plant height (PH) and plant width (PW), two of the major plant architectural traits determining the yield and productivity of a crop, are defined by diverse morphometric characteristics of the shoot apical meristem (SAM). The identification of potential molecular tags from a single gene that simultaneously modulates these plant/SAM architectural traits is therefore prerequisite to achieve enhanced yield and productivity in crop plants, including chickpea. Large-scale multienvironment phenotyping of the association panel and mapping population have ascertained the efficacy of three vital SAM morphometric trait parameters, SAM width, SAM height and SAM area, as key indicators to unravel the genetic basis of the wide PW and PH trait variations observed in desi chickpea. This study integrated a genome-wide association study (GWAS); quantitative trait locus (QTL)/fine-mapping and map-based cloning with molecular haplotyping; transcript profiling; and protein-DNA interaction assays for the dissection of plant architectural traits in chickpea. These exertions delineated natural alleles and superior haplotypes from a CabHLH121 transcription factor (TF) gene within the major QTL governing PW, PH and SAM morphometric traits. A genome-wide protein-DNA interaction assay assured the direct binding of a known stem cell master regulator, CaWUS, to the WOX-homeodomain TF binding sites of a CabHLH121 gene and its constituted haplotypes. The differential expression of CaWUS and transcriptional regulation of its target CabHLH121 gene/haplotypes were apparent, suggesting their collective role in altering SAM morphometric characteristics and plant architectural traits in the contrasting near isogenic lines (NILs). The NILs introgressed with a superior haplotype of a CabHLH121 exhibited optimal PW and desirable PH as well as enhanced yield and productivity without compromising any component of agronomic performance. These molecular signatures of the CabHLH121 TF gene have the potential to regulate both PW and PH traits through the modulation of proliferation, differentiation and maintenance of the meristematic stem cell population in the SAM; therefore, these signatures will be useful in the translational genomic study of chickpea genetic enhancement. The restructured cultivars with desirable PH (semidwarf) and PW will ensure maximal planting density in a specified cultivable field area, thereby enhancing the overall yield and productivity of chickpea. This can essentially facilitate the achievement of better remunerative outputs by farmers with rational land use, therefore ensuring global food security in the present scenario of an increasing population density and shrinking per capita land area.
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Affiliation(s)
- Laxmi Narnoliya
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Udita Basu
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Deepak Bajaj
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Naveen Malik
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Virevol Thakro
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anurag Daware
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Akash Sharma
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Venkatraman S Hegde
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the SemiArid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Ashok K Singh
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Akhilesh K Tyagi
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Swarup K Parida
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
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20
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Varshney RK, Thudi M, Roorkiwal M, He W, Upadhyaya HD, Yang W, Bajaj P, Cubry P, Rathore A, Jian J, Doddamani D, Khan AW, Garg V, Chitikineni A, Xu D, Gaur PM, Singh NP, Chaturvedi SK, Nadigatla GVPR, Krishnamurthy L, Dixit GP, Fikre A, Kimurto PK, Sreeman SM, Bharadwaj C, Tripathi S, Wang J, Lee SH, Edwards D, Polavarapu KKB, Penmetsa RV, Crossa J, Nguyen HT, Siddique KHM, Colmer TD, Sutton T, von Wettberg E, Vigouroux Y, Xu X, Liu X. Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits. Nat Genet 2019; 51:857-864. [DOI: 10.1038/s41588-019-0401-3] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 03/21/2019] [Indexed: 11/09/2022]
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21
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Basu U, Bajaj D, Sharma A, Malik N, Daware A, Narnoliya L, Thakro V, Upadhyaya HD, Kumar R, Tripathi S, Bharadwaj C, Tyagi AK, Parida SK. Genetic dissection of photosynthetic efficiency traits for enhancing seed yield in chickpea. PLANT, CELL & ENVIRONMENT 2019; 42:158-173. [PMID: 29676051 DOI: 10.1111/pce.13319] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 04/03/2018] [Indexed: 06/08/2023]
Abstract
Understanding the genetic basis of photosynthetic efficiency (PE) contributing to enhanced seed yield per plant (SYP) is vital for genomics-assisted crop improvement of chickpea. The current study employed an integrated genomic strategy involving photosynthesis pathway gene-based association mapping, genome-wide association study, quantitative trait loci (QTL) mapping, and expression profiling. This identified 16 potential single nucleotide polymorphism loci linked to major QTLs underlying 16 candidate genes significantly associated with PE and SYP traits in chickpea. The allelic variants were tightly linked to positively interacting QTLs regulating both enhanced PE and SYP traits as exemplified by a chlorophyll A-B binding protein-coding gene. The leaf tissue-specific pronounced up-regulated expression of 16 associated genes in germplasm accessions and homozygous individuals of mapping population was evident. Such combinatorial genomic strategy coupled with gene haplotype-specific association and in silico protein-protein interaction study delineated natural alleles and superior haplotypes from a chlorophyll A-B binding (CAB) protein-coding gene and its interacting gene, Timing of CAB Expression 1 (TOC1), which appear to be most promising candidates in modulating chickpea PE and SYP traits. These functionally pertinent molecular signatures identified have efficacy to drive marker-assisted selection for developing PE-enriched cultivars with high seed yield in chickpea.
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Affiliation(s)
- Udita Basu
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Akash Sharma
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Naveen Malik
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anurag Daware
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Laxmi Narnoliya
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Virevol Thakro
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Rajendra Kumar
- U.P. Council of Agricultural Research, Gomati Nagar, Lucknow, 226010, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Chellapilla Bharadwaj
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
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22
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Chen YH, Ruiz-Arocho J, von Wettberg EJ. Crop domestication: anthropogenic effects on insect-plant interactions in agroecosystems. CURRENT OPINION IN INSECT SCIENCE 2018; 29:56-63. [PMID: 30551826 DOI: 10.1016/j.cois.2018.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/13/2018] [Accepted: 06/20/2018] [Indexed: 05/14/2023]
Abstract
Although crop domestication is considered a model system for understanding evolution, the eco-evolutionary effects of domesticated crops on higher trophic levels have rarely been discussed. Changes in size, shape, quality, or timing of plant traits during domestication can influence entire arthropod communities. The plant traits specific to crop plants can be rare in nature. In the face of such novelty, it is important to understand how species and trophic levels vary in their responses. Although the evidence is still limited, crop domestication can influence the ecology, genetics, and evolution of plants, insect herbivores, natural enemies, and pollinators. We call for more study on how eco-evolutionary processes operate under domestication to provide new insight on the sustainability of species interactions within agroecosystems.
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Affiliation(s)
- Yolanda H Chen
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, USA.
| | - Jorge Ruiz-Arocho
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, USA
| | - Eric Jb von Wettberg
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, USA
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23
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McClean PE, Bett KE, Stonehouse R, Lee R, Pflieger S, Moghaddam SM, Geffroy V, Miklas P, Mamidi S. White seed color in common bean (Phaseolus vulgaris) results from convergent evolution in the P (pigment) gene. THE NEW PHYTOLOGIST 2018; 219:1112-1123. [PMID: 29897103 DOI: 10.1111/nph.15259] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/20/2018] [Indexed: 05/10/2023]
Abstract
The presence of seed color in common bean (Phaseolus vulgaris) requires the dominant-acting P (pigment) gene, and white seed is a recessive phenotype in all domesticated races of the species. P was classically associated with seed size, thus describing it as the first genetic marker for a quantitative trait. The molecular structure of P was characterized to understand the selection of white seeds during bean diversification and the relationship of P to seed weight. P was identified by homology searches, a genome-wide association study (GWAS) and gene remodeling, and confirmed by gene silencing. Allelic variation was assessed by a combination of resequencing and marker development, and the relationship between P and seed weight was assessed by a GWAS study. P is a member of clade B of subclass IIIf of plant basic helix-loop-helix (bHLH) proteins. Ten race-specific P alleles conditioned the white seed phenotype, and each causative mutation affected at least one bHLH domain required for color expression. GWAS analysis confirmed the classic association of P with seed weight. In common bean, white seeds are the result of convergent evolution and, among plant species, orthologous convergence on a single transcription factor gene was observed.
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Affiliation(s)
- Phillip E McClean
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, 58108, USA
| | - Kirstin E Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Robert Stonehouse
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Rian Lee
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Stephanie Pflieger
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, Orsay, 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, Orsay, 91405, France
| | | | - Valerie Geffroy
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, Orsay, 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, Orsay, 91405, France
| | - Phil Miklas
- USDA-ARS, Grain Legumes Genetics and Physiology Research Unit, Prosser, WA, 99350, USA
| | - Sujan Mamidi
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
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24
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Jha UC. Current advances in chickpea genomics: applications and future perspectives. PLANT CELL REPORTS 2018; 37:947-965. [PMID: 29860584 DOI: 10.1007/s00299-018-2305-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/23/2018] [Indexed: 05/27/2023]
Abstract
Chickpea genomics promises to illuminate our understanding of genome organization, structural variations, evolutionary and domestication-related insights and fundamental biology of legume crops. Unprecedented advancements of next generation sequencing (NGS) technologies have enabled in decoding of multiple chickpea genome sequences and generating huge genomic resources in chickpea both at functional and structural level. This review is aimed to update the current progress of chickpea genomics ranging from high density linkage map development, genome-wide association studies (GWAS), functional genomics resources for various traits, emerging role of abiotic stress responsive coding and non-coding RNAs after the completion of draft chickpea genome sequences. Additionally, the current efforts of whole genome re-sequencing (WGRS) approach of global chickpea germplasm to capture the global genetic diversity existing in the historically released varieties across the world and increasing the resolution of the previously identified candidate gene(s) of breeding importance have been discussed. Thus, the outcomes of these genomics resources will assist in genomics-assisted selection and facilitate breeding of climate-resilient chickpea cultivars for sustainable agriculture.
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Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
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25
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Sani SGAS, Chang PL, Zubair A, Carrasquilla-Garcia N, Cordeiro M, Penmetsa RV, Munis MFH, Nuzhdin SV, Cook DR, von Wettberg EJ. Genetic Diversity, Population Structure, and Genetic Correlation with Climatic Variation in Chickpea ( Cicer arietinum) Landraces from Pakistan. THE PLANT GENOME 2018; 11:170067. [PMID: 29505627 DOI: 10.3835/plantgenome2017.08.0067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Chickpea ( L.) production in arid regions, such as those predominant in Pakistan, faces immense challenges of drought and heat stress. Addressing these challenges is made more difficult by the lack of genetic and phenotypic characterization of available cultivated varieties and breeding materials. Genotyping-by-sequencing offers a rapid and cost-effective means to identify genome-wide nucleotide variation in crop germplasm. When combined with extended crop phenotypes deduced from climatic variation at sites of collection, the data can predict which portions of genetic variation might have roles in climate resilience. Here we use 8113 single nucleotide polymorphism markers to determine genetic variation and compare population structure within a previously uncharacterized collection of 77 landraces and 5 elite cultivars, currently grown in situ on farms throughout the chickpea growing regions of Pakistan. The compiled landraces span a striking aridity gradient into the Thal Desert of the Punjab. Despite low levels of variation across the collection and limited genetic structure, we found some differentiation between accessions from arid, semiarid, irrigated, and coastal areas. In a subset of 232 markers, we found evidence of differentiation along gradients of elevation and isothermality. Our results highlight the utility of exploring large germplasm collections for nucleotide variation associated with environmental extremes, and the use of such data to nominate germplasm accessions with the potential to improve crop drought tolerance and other environmental traits.
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26
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von Wettberg EJB, Chang PL, Başdemir F, Carrasquila-Garcia N, Korbu LB, Moenga SM, Bedada G, Greenlon A, Moriuchi KS, Singh V, Cordeiro MA, Noujdina NV, Dinegde KN, Shah Sani SGA, Getahun T, Vance L, Bergmann E, Lindsay D, Mamo BE, Warschefsky EJ, Dacosta-Calheiros E, Marques E, Yilmaz MA, Cakmak A, Rose J, Migneault A, Krieg CP, Saylak S, Temel H, Friesen ML, Siler E, Akhmetov Z, Ozcelik H, Kholova J, Can C, Gaur P, Yildirim M, Sharma H, Vadez V, Tesfaye K, Woldemedhin AF, Tar'an B, Aydogan A, Bukun B, Penmetsa RV, Berger J, Kahraman A, Nuzhdin SV, Cook DR. Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation. Nat Commun 2018; 9:649. [PMID: 29440741 PMCID: PMC5811434 DOI: 10.1038/s41467-018-02867-z] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/04/2018] [Indexed: 12/30/2022] Open
Abstract
Domesticated species are impacted in unintended ways during domestication and breeding. Changes in the nature and intensity of selection impart genetic drift, reduce diversity, and increase the frequency of deleterious alleles. Such outcomes constrain our ability to expand the cultivation of crops into environments that differ from those under which domestication occurred. We address this need in chickpea, an important pulse legume, by harnessing the diversity of wild crop relatives. We document an extreme domestication-related genetic bottleneck and decipher the genetic history of wild populations. We provide evidence of ancestral adaptations for seed coat color crypsis, estimate the impact of environment on genetic structure and trait values, and demonstrate variation between wild and cultivated accessions for agronomic properties. A resource of genotyped, association mapping progeny functionally links the wild and cultivated gene pools and is an essential resource chickpea for improvement, while our methods inform collection of other wild crop progenitor species.
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Affiliation(s)
- Eric J B von Wettberg
- Department of Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, FL, 33199, USA.
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, 05405, USA.
| | - Peter L Chang
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Fatma Başdemir
- Faculty of Agriculture, Dicle University, Diyarbakir, 21280, Turkey
| | | | - Lijalem Balcha Korbu
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, 32853, Ethiopia
- Ethiopian Institute of Agricultural Research, Addis Ababa, P.O. Box 2003, Ethiopia
| | - Susan M Moenga
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
| | - Gashaw Bedada
- Hawassa University, Hawassa, 005, Ethiopia
- Oromia Agricultural Research Institute (OARI), Addis Ababa, P.O. Box 81265, Ethiopia
| | - Alex Greenlon
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
| | - Ken S Moriuchi
- Department of Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, FL, 33199, USA
| | - Vasantika Singh
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Matilde A Cordeiro
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Nina V Noujdina
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Applied Mathematics, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Kassaye Negash Dinegde
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, 32853, Ethiopia
- Ethiopian Institute of Agricultural Research, Addis Ababa, P.O. Box 2003, Ethiopia
| | - Syed Gul Abbas Shah Sani
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
- Department of Plant Sciences, Quaid-i-Azam University Islamabad, Islamabad, 45320, Pakistan
| | - Tsegaye Getahun
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, 32853, Ethiopia
| | - Lisa Vance
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
| | - Emily Bergmann
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
| | - Donna Lindsay
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N5A8, Canada
| | - Bullo Erena Mamo
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
| | - Emily J Warschefsky
- Department of Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, FL, 33199, USA
| | - Emmanuel Dacosta-Calheiros
- Department of Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, FL, 33199, USA
| | - Edward Marques
- Department of Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, FL, 33199, USA
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, 05405, USA
| | | | - Ahmet Cakmak
- Department of Field Crops, Faculty of Agriculture, Harran University, Sanliurfa, 63100, Turkey
| | - Janna Rose
- Department of Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, FL, 33199, USA
| | - Andrew Migneault
- Department of Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, FL, 33199, USA
| | - Christopher P Krieg
- Department of Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, FL, 33199, USA
- Department of Botany, University of Florida, Gainesville, FL, 33181, USA
| | - Sevgi Saylak
- Faculty of Agriculture, Dicle University, Diyarbakir, 21280, Turkey
| | - Hamdi Temel
- Faculty of Agriculture, Dicle University, Diyarbakir, 21280, Turkey
| | - Maren L Friesen
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48823, USA
| | - Eleanor Siler
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48823, USA
| | - Zhaslan Akhmetov
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
| | - Huseyin Ozcelik
- Black Sea Agricultural Research Institute, Samsun, P.O. Box 39, Turkey
| | - Jana Kholova
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502324, Telangana, India
| | - Canan Can
- Department of Biology, Gaziantep University, Gaziantep, 27310, Turkey
| | - Pooran Gaur
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502324, Telangana, India
| | - Mehmet Yildirim
- Faculty of Agriculture, Dicle University, Diyarbakir, 21280, Turkey
| | - Hari Sharma
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502324, Telangana, India
| | - Vincent Vadez
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502324, Telangana, India
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, 32853, Ethiopia
| | | | - Bunyamin Tar'an
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N5A8, Canada
| | - Abdulkadir Aydogan
- Central Research Institute for Field Crops (CRIFC), Ankara, 06042, Turkey
| | - Bekir Bukun
- Faculty of Agriculture, Dicle University, Diyarbakir, 21280, Turkey
| | - R Varma Penmetsa
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
| | - Jens Berger
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, Perth, 6014, WA, Australia
| | - Abdullah Kahraman
- Department of Field Crops, Faculty of Agriculture, Harran University, Sanliurfa, 63100, Turkey
| | - Sergey V Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Applied Mathematics, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Douglas R Cook
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA.
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27
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Plekhanova E, Vishnyakova MA, Bulyntsev S, Chang PL, Carrasquilla-Garcia N, Negash K, Wettberg EV, Noujdina N, Cook DR, Samsonova MG, Nuzhdin SV. Genomic and phenotypic analysis of Vavilov's historic landraces reveals the impact of environment and genomic islands of agronomic traits. Sci Rep 2017; 7:4816. [PMID: 28684880 PMCID: PMC5500531 DOI: 10.1038/s41598-017-05087-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 05/24/2017] [Indexed: 12/30/2022] Open
Abstract
The Vavilov Institute of Plant Genetic Resources (VIR), in St. Petersburg, Russia, houses a unique genebank, with historical collections of landraces. When they were collected, the geographical distribution and genetic diversity of most crops closely reflected their historical patterns of cultivation established over the preceding millennia. We employed a combination of genomics, computational biology and phenotyping to characterize VIR's 147 chickpea accessions from Turkey and Ethiopia, representing chickpea's center of origin and a major location of secondary diversity. Genotyping by sequencing identified 14,059 segregating polymorphisms and genome-wide association studies revealed 28 GWAS hits in potential candidate genes likely to affect traits of agricultural importance. The proportion of polymorphisms shared among accessions is a strong predictor of phenotypic resemblance, and of environmental similarity between historical sampling sites. We found that 20 out of 28 polymorphisms, associated with multiple traits, including days to maturity, plant phenology, and yield-related traits such as pod number, localized to chromosome 4. We hypothesize that selection and introgression via inadvertent hybridization between more and less advanced morphotypes might have resulted in agricultural improvement genes being aggregated to genomic 'agro islands', and in genotype-to-phenotype relationships resembling widespread pleiotropy.
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Affiliation(s)
- Elena Plekhanova
- Department of Applied Mathematics, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia
| | - Margarita A Vishnyakova
- Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - Sergey Bulyntsev
- Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - Peter L Chang
- Department of Plant Pathology, University of California, Davis, CA, USA.,Program Molecular and Computation Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, USA
| | | | - Kassaye Negash
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Eric von Wettberg
- Department of Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, FL, USA
| | - Nina Noujdina
- School of Architecture, University of Southern California, Los Angeles, CA, USA
| | - Douglas R Cook
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Maria G Samsonova
- Department of Applied Mathematics, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia
| | - Sergey V Nuzhdin
- Department of Applied Mathematics, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia. .,Program Molecular and Computation Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, USA.
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28
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Kates HR, Soltis PS, Soltis DE. Evolutionary and domestication history of Cucurbita (pumpkin and squash) species inferred from 44 nuclear loci. Mol Phylogenet Evol 2017; 111:98-109. [PMID: 28288944 DOI: 10.1016/j.ympev.2017.03.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 02/28/2017] [Accepted: 03/01/2017] [Indexed: 11/28/2022]
Abstract
Phylogenetics can facilitate the study of plant domestication by resolving sister relationships between crops and their wild relatives, thereby identifying the ancestors of cultivated plants. Previous phylogenetic studies of the six Cucurbita crop lineages (pumpkins and squashes) and their wild relatives suggest histories of deep coalescence that complicate uncovering the genetic origins of the six crop taxa. We investigated the evolution of wild and domesticated Cucurbita using the most comprehensive and robust molecular-based phylogeny for Cucurbita to date based on 44 loci derived from introns of single-copy nuclear genes. We discovered novel relationships among Cucurbita species and recovered the first Cucurbita tree with well-supported resolution within species. Cucurbita comprises a clade of mesophytic annual species that includes all six crop taxa and a grade of xerophytic perennial species that represent the ancestral xerophytic habit of the genus. Based on phylogenetic resolution within-species we hypothesize that the magnitude of domestication bottlenecks varies among Cucurbita crop lineages. Our phylogeny clarifies how wild Cucurbita species are related to the domesticated taxa. We find close relationships between two wild species and crop lineages not previously identified. Expanded geographic sampling of key wild species is needed for improved understanding of the evolution of domesticated Cucurbita.
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Affiliation(s)
- Heather R Kates
- Univ Florida, Genet Inst, Gainesville, FL 32611, USA; Univ Florida, Florida Museum Nat Hist, Gainesville, FL 32611, USA.
| | - Pamela S Soltis
- Univ Florida, Genet Inst, Gainesville, FL 32611, USA; Univ Florida, Florida Museum Nat Hist, Gainesville, FL 32611, USA
| | - Douglas E Soltis
- Univ Florida, Genet Inst, Gainesville, FL 32611, USA; Univ Florida, Florida Museum Nat Hist, Gainesville, FL 32611, USA; Univ Florida, Dept Biol, Gainesville, FL 32611, USA
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29
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De Giovanni C, Pavan S, Taranto F, Di Rienzo V, Miazzi MM, Marcotrigiano AR, Mangini G, Montemurro C, Ricciardi L, Lotti C. Genetic variation of a global germplasm collection of chickpea ( Cicer arietinum L.) including Italian accessions at risk of genetic erosion. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:197-205. [PMID: 28250595 PMCID: PMC5313401 DOI: 10.1007/s12298-016-0397-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/18/2016] [Accepted: 11/18/2016] [Indexed: 05/17/2023]
Abstract
Chickpea (Cicer arietinum L.) is one of the most important legumes worldwide. We addressed this study to the genetic characterization of a germplasm collection from main chickpea growing countries. Several Italian traditional landraces at risk of genetic erosion were included in the analysis. Twenty-two simple sequence repeat (SSR) markers, widely used to explore genetic variation in plants, were selected and yielded 218 different alleles. Structure analysis and hierarchical clustering indicated that a model with three distinct subpopulations best fits the data. The composition of two subpopulations, named K1 and K2, broadly reflects the commercial classification of chickpea in the two types desi and kabuli, respectively. The third subpopulation (K3) is composed by both desi and kabuli genotypes. Italian accessions group both in K2 and K3. Interestingly, this study highlights genetic distance between desi genotypes cultivated in Asia and Ethiopia, which respectively represent the chickpea primary and the secondary centres of diversity. Moreover, European desi are closer to the Ethiopian gene pool. Overall, this study will be of importance for chickpea conservation genetics and breeding, which is limited by the poor characterization of germplasm collection.
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Affiliation(s)
- C. De Giovanni
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
| | - S. Pavan
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
| | - F. Taranto
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
| | - V. Di Rienzo
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
| | - M. M. Miazzi
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
| | - A. R. Marcotrigiano
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
| | - G. Mangini
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
| | - C. Montemurro
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
| | - L. Ricciardi
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
| | - C. Lotti
- Department of Agriculture, Food and Environmental Science, University of Foggia, Via Napoli 25, 71100 Foggia, Italy
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