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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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2
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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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3
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George AF, Luo X, Neidleman J, Hoh R, Vohra P, Thomas R, Shin MG, Lee MJ, Blish CA, Deeks S, Greene WC, Lee SA, Roan NR. Deep Phenotypic Analysis of Blood and Lymphoid T and NK Cells From HIV+ Controllers and ART-Suppressed Individuals. Front Immunol 2022; 13:803417. [PMID: 35154118 PMCID: PMC8829545 DOI: 10.3389/fimmu.2022.803417] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/04/2022] [Indexed: 12/03/2022] Open
Abstract
T and natural killer (NK) cells are effector cells with key roles in anti-HIV immunity, including in lymphoid tissues, the major site of HIV persistence. However, little is known about the features of these effector cells from people living with HIV (PLWH), particularly from those who initiated antiretroviral therapy (ART) during acute infection. Our study design was to use 42-parameter CyTOF to conduct deep phenotyping of paired blood- and lymph node (LN)-derived T and NK cells from three groups of HIV+ aviremic individuals: elite controllers (N = 5), and ART-suppressed individuals who had started therapy during chronic (N = 6) vs. acute infection (N = 8), the latter of which is associated with better outcomes. We found that acute-treated individuals are enriched for specific subsets of T and NK cells, including blood-derived CD56-CD16+ NK cells previously associated with HIV control, and LN-derived CD4+ T follicular helper cells with heightened expansion potential. An in-depth comparison of the features of the cells from blood vs. LNs of individuals from our cohort revealed that T cells from blood were more activated than those from LNs. By contrast, LNs were enriched for follicle-homing CXCR5+ CD8+ T cells, which expressed increased levels of inhibitory receptors and markers of survival and proliferation as compared to their CXCR5- counterparts. In addition, a subset of memory-like CD56brightTCF1+ NK cells was enriched in LNs relative to blood. These results together suggest unique T and NK cell features in acute-treated individuals, and highlight the importance of examining effector cells not only in blood but also the lymphoid tissue compartment, where the reservoir mostly persists, and where these cells take on distinct phenotypic features.
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Affiliation(s)
- Ashley F. George
- Gladstone Institute of Virology, San Francisco, CA, United States,Department of Urology, University of California San Francisco, San Francisco, CA, United States
| | - Xiaoyu Luo
- Gladstone Institute of Virology, San Francisco, CA, United States
| | - Jason Neidleman
- Gladstone Institute of Virology, San Francisco, CA, United States,Department of Urology, University of California San Francisco, San Francisco, CA, United States
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases and Global Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Poonam Vohra
- Department of Pathology, University of California San Francisco, San Francisco, CA, United States
| | - Reuben Thomas
- Gladstone Institutes, San Francisco, CA, United States
| | | | - Madeline J. Lee
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States,Program in Immunology, Stanford School of Medicine, Stanford, CA, United States
| | - Catherine A. Blish
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States,Program in Immunology, Stanford School of Medicine, Stanford, CA, United States
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases and Global Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Warner C. Greene
- Gladstone Institute of Virology, San Francisco, CA, United States,Departments of Medicine, and Microbiology & Immunology, University of California San Francisco, San Francisco, CA, United States
| | - Sulggi A. Lee
- Zuckerberg San Francisco General Hospital and the University of California San Francisco, San Francisco, CA, United States,*Correspondence: Sulggi A. Lee, ; Nadia R. Roan,
| | - Nadia R. Roan
- Gladstone Institute of Virology, San Francisco, CA, United States,Department of Urology, University of California San Francisco, San Francisco, CA, United States,*Correspondence: Sulggi A. Lee, ; Nadia R. Roan,
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DeWeese KJ, Osborne MG. Understanding the metabolome and metagenome as extended phenotypes: The next frontier in macroalgae domestication and improvement. JOURNAL OF THE WORLD AQUACULTURE SOCIETY 2021; 52:1009-1030. [PMID: 34732977 PMCID: PMC8562568 DOI: 10.1111/jwas.12782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 02/25/2021] [Indexed: 06/01/2023]
Abstract
"Omics" techniques (including genomics, transcriptomics, metabolomics, proteomics, and metagenomics) have been employed with huge success in the improvement of agricultural crops. As marine aquaculture of macroalgae expands globally, biologists are working to domesticate species of macroalgae by applying these techniques tested in agriculture to wild macroalgae species. Metabolomics has revealed metabolites and pathways that influence agriculturally relevant traits in crops, allowing for informed crop crossing schemes and genomic improvement strategies that would be pivotal to inform selection on macroalgae for domestication. Advances in metagenomics have improved understanding of host-symbiont interactions and the potential for microbial organisms to improve crop outcomes. There is much room in the field of macroalgal biology for further research toward improvement of macroalgae cultivars in aquaculture using metabolomic and metagenomic analyses. To this end, this review discusses the application and necessary expansion of the omics tool kit for macroalgae domestication as we move to enhance seaweed farming worldwide.
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Affiliation(s)
- Kelly J DeWeese
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, California, Los Angeles
| | - Melisa G Osborne
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, California, Los Angeles
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Shin MG, Nuzhdin SV. Interspecific Sample Prioritization Can Improve QTL Detection With Tree-Based Predictive Models. Front Genet 2021; 12:684882. [PMID: 34552613 PMCID: PMC8450460 DOI: 10.3389/fgene.2021.684882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/09/2021] [Indexed: 11/16/2022] Open
Abstract
Due to increasing demand for new advanced crops, considerable efforts have been made to explore the improvement of stress and disease resistance cultivar traits through the study of wild crops. When both wild and interspecific hybrid materials are available, a common approach has been to study two types of materials separately and simply compare the quantitative trait locus (QTL) regions. However, combining the two types of materials can potentially create a more efficient method of finding predictive QTLs. In this simulation study, we focused on scenarios involving causal marker expression suppressed by trans-regulatory mechanisms, where the otherwise easily lost associated signals benefit the most from combining the two types of data. A probabilistic sampling approach was used to prioritize consistent genotypic phenotypic patterns across both types of data sets. We chose random forest and gradient boosting to apply the prioritization scheme and found that both facilitated the investigation of predictive causal markers in most of the biological scenarios simulated.
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Affiliation(s)
- Min-Gyoung Shin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Sergey V Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
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Ithnin M, Vu WT, Shin MG, Suryawanshi V, Sherbina K, Zolkafli SH, Serdari NM, Amiruddin MD, Abdullah N, Mustaffa S, Marjuni M, Nookiah R, Kushairi A, Marjoram P, Nuzhdin SV, Chang PL, Singh R. Genomic diversity and genome-wide association analysis related to yield and fatty acid composition of wild American oil palm. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 304:110731. [PMID: 33568284 DOI: 10.1016/j.plantsci.2020.110731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 05/15/2023]
Abstract
Existing Elaeis guineensis cultivars lack sufficient genetic diversity due to extensive breeding. Harnessing variation in wild crop relatives is necessary to expand the breadth of agronomically valuable traits. Using RAD sequencing, we examine the natural diversity of wild American oil palm populations (Elaeis oleifera), a sister species of the cultivated Elaeis guineensis oil palm. We genotyped 192 wild E. oleifera palms collected from seven Latin American countries along with four cultivated E. guineensis palms. Honduras, Costa Rica, Panama and Colombia palms are panmictic and genetically similar. Genomic patterns of diversity suggest that these populations likely originated from the Amazon Basin. Despite evidence of a genetic bottleneck and high inbreeding observed in these populations, there is considerable genetic and phenotypic variation for agronomically valuable traits. Genome-wide association revealed several candidate genes associated with fatty acid composition along with vegetative and yield-related traits. These observations provide valuable insight into the geographic distribution of diversity, phenotypic variation and its genetic architecture that will guide choices of wild genotypes for crop improvement.
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Affiliation(s)
- Maizura Ithnin
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Wendy T Vu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Min-Gyoung Shin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Vasantika Suryawanshi
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Katrina Sherbina
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Siti Hazirah Zolkafli
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Norhalida Mohamed Serdari
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Mohd Din Amiruddin
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Norziha Abdullah
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Suzana Mustaffa
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Marhalil Marjuni
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Rajanaidu Nookiah
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Ahmad Kushairi
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Paul Marjoram
- Department of Preventative Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Sergey V Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter L Chang
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
| | - Rajinder Singh
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia.
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