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Khan AW, Garg V, Sun S, Gupta S, Dudchenko O, Roorkiwal M, Chitikineni A, Bayer PE, Shi C, Upadhyaya HD, Bohra A, Bharadwaj C, Mir RR, Baruch K, Yang B, Coyne CJ, Bansal KC, Nguyen HT, Ronen G, Aiden EL, Veneklaas E, Siddique KHM, Liu X, Edwards D, Varshney RK. Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea. Nat Genet 2024; 56:1225-1234. [PMID: 38783120 DOI: 10.1038/s41588-024-01760-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 04/18/2024] [Indexed: 05/25/2024]
Abstract
Chickpea (Cicer arietinum L.)-an important legume crop cultivated in arid and semiarid regions-has limited genetic diversity. Efforts are being undertaken to broaden its diversity by utilizing its wild relatives, which remain largely unexplored. Here, we present the Cicer super-pangenome based on the de novo genome assemblies of eight annual Cicer wild species. We identified 24,827 gene families, including 14,748 core, 2,958 softcore, 6,212 dispensable and 909 species-specific gene families. The dispensable genome was enriched for genes related to key agronomic traits. Structural variations between cultivated and wild genomes were used to construct a graph-based genome, revealing variations in genes affecting traits such as flowering time, vernalization and disease resistance. These variations will facilitate the transfer of valuable traits from wild Cicer species into elite chickpea varieties through marker-assisted selection or gene-editing. This study offers valuable insights into the genetic diversity and potential avenues for crop improvement in chickpea.
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Affiliation(s)
- Aamir W Khan
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, USA
| | - Vanika Garg
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | | | - Saurabh Gupta
- Curtin Health Innovation Research Institute (CHIRI), Curtin Medical School, Curtin University, Perth, Western Australia, Australia
| | - Olga Dudchenko
- Department of Molecular and Human Genetics, Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Philipp E Bayer
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
| | | | - Hari D Upadhyaya
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, USA
| | - Abhishek Bohra
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | | | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir,Wadura Campus, Kashmir, India
| | | | | | - Clarice J Coyne
- USDA-ARS Plant Germplasm Introduction and Testing, Washington State University, Pullman, WA, USA
| | - Kailash C Bansal
- National Academy of Agricultural Sciences (NAAS), NASC Complex, New Delhi, India
| | - Henry T Nguyen
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, USA
| | - Gil Ronen
- NRGene Ltd, Park HaMada, Ness Ziona, Israel
| | - Erez Lieberman Aiden
- Department of Molecular and Human Genetics, Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Erik Veneklaas
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Kadambot H M Siddique
- UWA Institute of Agriculture, and School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Xin Liu
- BGI Research, Qingdao, China.
- BGI Research, Shenzhen, China.
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia.
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
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Daware A, Mohanty JK, Narnoliya L, Singh A, Rathore D, Thakro V, Francis A, Singh NP, Francis P, Tripathi S, Chattopadhyay D, Parida SK. Uncovering DNA methylation landscapes to decipher evolutionary footprints of phenotypic diversity in chickpea. DNA Res 2024; 31:dsae013. [PMID: 38702947 PMCID: PMC11149376 DOI: 10.1093/dnares/dsae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 05/02/2024] [Indexed: 05/06/2024] Open
Abstract
Genetic diversity and environmental factors are long believed to be the dominant contributors to phenotypic diversity in crop plants. However, it has been recently established that, besides genetic variation, epigenetic variation, especially variation in DNA methylation, plays a significant role in determining phenotypic diversity in crop plants. Therefore, assessing DNA methylation diversity in crop plants becomes vital, especially in the case of crops like chickpea, which has a narrow genetic base. Thus, in the present study, we employed whole-genome bisulfite sequencing to assess DNA methylation diversity in wild and cultivated (desi and kabuli) chickpea. This revealed extensive DNA methylation diversity in both wild and cultivated chickpea. Interestingly, the methylation diversity was found to be significantly higher than genetic diversity, suggesting its potential role in providing vital phenotypic diversity for the evolution and domestication of the Cicer gene pool. The phylogeny based on DNA methylation variation also indicates a potential complementary role of DNA methylation variation in addition to DNA sequence variation in shaping chickpea evolution. Besides, the study also identified diverse epi-alleles of many previously known genes of agronomic importance. The Cicer MethVarMap database developed in this study enables researchers to readily visualize methylation variation within the genes and genomic regions of their interest (http://223.31.159.7/cicer/public/). Therefore, epigenetic variation like DNA methylation variation can potentially explain the paradox of high phenotypic diversity despite the narrow genetic base in chickpea and can potentially be employed for crop improvement.
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Affiliation(s)
- Anurag Daware
- 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
| | - Laxmi Narnoliya
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Akansha Singh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Deepanshi Rathore
- 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
| | - Aleena Francis
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Nagendra Pratap Singh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Philip Francis
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shailesh Tripathi
- Indian Institute of Pulses Research (IIPR), Uttar Pradesh, Kanpur 208024, India
| | - Debasis Chattopadhyay
- 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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3
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Mehmetoğlu E, Kaymaz Y, Ateş D, Kahraman A, Tanyolaç MB. The complete chloroplast genome of Cicer reticulatum and comparative analysis against relative Cicer species. Sci Rep 2023; 13:17871. [PMID: 37857674 PMCID: PMC10587350 DOI: 10.1038/s41598-023-44599-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023] Open
Abstract
The chloroplast (cp) genome is an adequate genomic resource to investigate evolutionary relationships among plant species and it carries marker genes available for species identification. The Cicer reticulatum is one of perennial species as the progenitor of cultivated chickpeas. Although a large part of the land plants has a quadruple chloroplast genome organization, the cp genome of C. reticulatum consists of one LSC (Large Single Copy Region), one SSC (Small Single Copy Region), and one IR (Inverted Repeat) region, which indicates that it has an untypical and unique structure. This type of chloroplast genome belongs to the IR-lacking clade. Chloroplast DNA (cpDNA) was extracted from fresh leaves using a high salt-based protocol and sequencing was performed using DNA Nanoball Sequencing technology. The comparative analysis employed between the species to examine genomic differences and gene homology. The study also included codon usage frequency analysis, hotspot divergence analysis, and phylogenetic analysis using various bioinformatics tools. The cp genome of C. reticulatum was found 125,794 bp in length, with an overall GC content of 33.9%. With a total of 79 protein-coding genes, 34 tRNA genes, and 4 rRNA genes. Comparative genomic analysis revealed 99.93% similarity between C. reticulatum and C. arietinum. Phylogenetic analysis further indicated that the closest evolutionary relative to C. arietinum was C. reticulatum, whereas the previously sequenced wild Cicer species displayed slight distinctions across their entire coding regions. Several genomic regions, such as clpP and ycf1, were found to exhibit high nucleotide diversity, suggesting their potential utility as markers for investigating the evolutionary relationships within the Cicer genus. The first complete cp genome sequence of C. reticulatum will provide novel insights for future genetic research on Cicer crops.
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Affiliation(s)
- Ezgi Mehmetoğlu
- Faculty of Engineering, Department of Bioengineering, Ege University, 35100, Bornova, Izmir, Turkey
| | - Yasin Kaymaz
- Faculty of Engineering, Department of Bioengineering, Ege University, 35100, Bornova, Izmir, Turkey
| | - Duygu Ateş
- Faculty of Engineering, Department of Bioengineering, Ege University, 35100, Bornova, Izmir, Turkey
| | - Abdullah Kahraman
- Faculty of Agriculture, Department of Field Crops, Harran University, S. Urfa, 64000, Şanlıurfa, Turkey
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Sari D, Sari H, Ikten C, Toker C. Genome-wide discovery of di-nucleotide SSR markers based on whole genome re-sequencing data of Cicer arietinum L. and Cicer reticulatum Ladiz. Sci Rep 2023; 13:10351. [PMID: 37365279 DOI: 10.1038/s41598-023-37268-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 06/19/2023] [Indexed: 06/28/2023] Open
Abstract
Simple sequence repeats (SSRs) are valuable genetic markers due to their co-dominant inheritance, multi-allelic and reproducible nature. They have been largely used for exploiting genetic architecture of plant germplasms, phylogenetic analysis, and mapping studies. Among the SSRs, di-nucleotide repeats are the most frequent of the simple repeats distributed throughout the plant genomes. In present study, we aimed to discover and develop di-nucleotide SSR markers by using the whole genome re-sequencing (WGRS) data from Cicer arietinum L. and C. reticulatum Ladiz. A total of 35,329 InDels were obtained in C. arietinum, whereas 44,331 InDels in C. reticulatum. 3387 InDels with 2 bp length were detected in C. arietinum, there were 4704 in C. reticulatum. Among 8091 InDels, 58 di-nucleotide regions that were polymorphic between two species were selected and used for validation. We tested primers for evaluation of genetic diversity in 30 chickpea genotypes including C. arietinum, C. reticulatum, C. echinospermum P.H. Davis, C. anatolicum Alef., C. canariense A. Santos & G.P. Lewis, C. microphyllum Benth., C. multijugum Maesen, C. oxyodon Boiss. & Hohen. and C. songaricum Steph ex DC. A total of 244 alleles were obtained for 58 SSR markers giving an average of 2.36 alleles per locus. The observed heterozygosity was 0.08 while the expected heterozygosity was 0.345. Polymorphism information content was found to be 0.73 across all loci. Phylogenetic tree and principal coordinate analysis clearly divided the accessions into four groups. The SSR markers were also evaluated in 30 genotypes of a RIL population obtained from an interspecific cross between C. arietinum and C. reticulatum. Chi-square (χ2) test revealed an expected 1:1 segregation ratio in the population. These results demonstrated the success of SSR identification and marker development for chickpea with the use of WGRS data. The newly developed 58 SSR markers are expected to be useful for chickpea breeders.
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Affiliation(s)
- Duygu Sari
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, 07070, Antalya, Turkey.
| | - Hatice Sari
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, 07070, Antalya, Turkey
| | - Cengiz Ikten
- Department of Plant Protection, Faculty of Agriculture, Akdeniz University, 07070, Antalya, Turkey
| | - Cengiz Toker
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, 07070, Antalya, Turkey
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5
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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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Gayacharan, Parida SK, Mondal N, Yadav R, Vishwakarma H, Rana JC. Mining legume germplasm for genetic gains: An Indian perspective. Front Genet 2023; 14:996828. [PMID: 36816034 PMCID: PMC9933516 DOI: 10.3389/fgene.2023.996828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 01/05/2023] [Indexed: 01/24/2023] Open
Abstract
Legumes play a significant role in food and nutritional security and contribute to environmental sustainability. Although legumes are highly beneficial crops, it has not yet been possible to enhance their yield and production to a satisfactory level. Amid a rising population and low yield levels, per capita average legume consumption in India has fallen by 71% over the last 50 years, and this has led to protein-related malnutrition in a large segment of the Indian population, especially women and children. Several factors have hindered attempts to achieve yield enhancement in grain legumes, including biotic and abiotic pressures, a lack of good ideotypes, less amenability to mechanization, poorer responsiveness to fertilizer input, and a poor genetic base. Therefore, there is a need to mine the approximately 0.4 million ex situ collections of legumes that are being conserved in gene banks globally for identification of ideal donors for various traits. The Indian National Gene Bank conserves over 63,000 accessions of legumes belonging to 61 species. Recent initiatives have been undertaken in consortia mode with the aim of unlocking the genetic potential of ex situ collections and conducting large-scale germplasm characterization and evaluation analyses. We assume that large-scale phenotyping integrated with omics-based science will aid the identification of target traits and their use to enhance genetic gains. Additionally, in cases where the genetic base of major legumes is narrow, wild relatives have been evaluated, and these are being exploited through pre-breeding. Thus far, >200 accessions of various legumes have been registered as unique donors for various traits of interest.
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Affiliation(s)
- Gayacharan
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Swarup K. Parida
- DBT-National Institute of Plant Genome Research, New Delhi, India
| | - Nupur Mondal
- Shivaji College, University of Delhi, New Delhi, India
| | - Rashmi Yadav
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | - Jai C. Rana
- Alliance of Bioversity International and CIAT, India Office, National Agricultural Science Complex, New Delhi, India
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7
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Mokhtar MM, Fouad AS, Abd-Elhalim HM, El Allali A. CicerSpTEdb2.0: An Upgrade of Cicer Species Transposable Elements Database. Methods Mol Biol 2023; 2703:71-82. [PMID: 37646938 DOI: 10.1007/978-1-0716-3389-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
To meet the critical demand of LTR-RTs data-driven research, we updated the CicerSpTEdb database to version 2.0, which includes more accurate intact LTR-RT elements with annotation of internal domains. We also added the ability to BLAST against TEs of Cicer species. As a result, 3701 intact LTR-RTs were detected in the studied genomes, including 2840 Copia and 861 Gypsy elements. Of the 3701 intact LTR-RTs, 588 were in C. arietinum, including 475 Copia and 113 Gypsy. While 1373 were detected in C. reticulatum, including 1041 Copia and 332 Gypsy. Furthermore, 1740 were found in C. echinospermum, including 1324 Copia and 416 Gypsy. Based on LTR-RT clades, the analysis classified the 3701 identified intact LTR-RTs in the studied genomes as Ale (850), SIRE (740), unknown (455), Ikeros (323), Reina (290), Tork (290), Ivana (282), Tekay (197), Athila (128), TAR (99), CRM (31), and Ogre (16) elements. The newly updated CicerSpTEdb2.0 will be a valuable resource for TEs of Cicer species and their comparative genomics.Database URL: http://cicersptedb.easyomics.org/index.php.
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Affiliation(s)
- Morad M Mokhtar
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Ahmed S Fouad
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Haytham M Abd-Elhalim
- Agricultural Genetic Engineering Research Institute, Agricultural Research Center, Giza, Egypt
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco.
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8
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Zhang H, Mascher M, Abbo S, Jayakodi M. Advancing Grain Legumes Domestication and Evolution Studies with Genomics. PLANT & CELL PHYSIOLOGY 2022; 63:1540-1553. [PMID: 35534441 PMCID: PMC9680859 DOI: 10.1093/pcp/pcac062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 06/14/2023]
Abstract
Grain legumes were domesticated in parallel with cereals in several regions of the world and formed the economic basis of early farming cultures. Since then, legumes have played a vital role in human and animal diets and in fostering agrobiodiversity. Increasing grain legume cultivation will be crucial to safeguard nutritional security and the resilience of agricultural ecosystems across the globe. A better understanding of the molecular underpinnings of domestication and crop evolution of grain legumes may be translated into practical approaches in modern breeding programs to stabilize yield, which is threatened by evolving pathogens and changing climates. During recent decades, domestication research in all crops has greatly benefited from the fast progress in genomic technologies. Yet still, many questions surrounding the domestication and diversification of legumes remain unanswered. In this review, we assess the potential of genomic approaches in grain legume research. We describe the centers of origin and the crucial domestication traits of grain legumes. In addition, we survey the effect of domestication on both above-ground and below-ground traits that have economic importance. Finally, we discuss open questions in grain legume domestication and diversification and outline how to bridge the gap between the preservation of historic crop diversity and their utilization in modern plant breeding.
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Affiliation(s)
- Hailin Zhang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, Seeland 06466, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, Seeland 06466, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, Leipzig 04103, Germany
| | - Shahal Abbo
- The Levi Eshkol School of Agriculture, The Hebrew University of Jerusalem, POB 12, Rehovot 7610001, Israel
| | - Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, Seeland 06466, Germany
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Singh G, Gudi S, Amandeep, Upadhyay P, Shekhawat PK, Nayak G, Goyal L, Kumar D, Kumar P, Kamboj A, Thada A, Shekhar S, Koli GK, DP M, Halladakeri P, Kaur R, Kumar S, Saini P, Singh I, Ayoubi H. Unlocking the hidden variation from wild repository for accelerating genetic gain in legumes. FRONTIERS IN PLANT SCIENCE 2022; 13:1035878. [PMID: 36438090 PMCID: PMC9682257 DOI: 10.3389/fpls.2022.1035878] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/17/2022] [Indexed: 11/02/2023]
Abstract
The fluctuating climates, rising human population, and deteriorating arable lands necessitate sustainable crops to fulfil global food requirements. In the countryside, legumes with intriguing but enigmatic nitrogen-fixing abilities and thriving in harsh climatic conditions promise future food security. However, breaking the yield plateau and achieving higher genetic gain are the unsolved problems of legume improvement. Present study gives emphasis on 15 important legume crops, i.e., chickpea, pigeonpea, soybean, groundnut, lentil, common bean, faba bean, cowpea, lupin, pea, green gram, back gram, horse gram, moth bean, rice bean, and some forage legumes. We have given an overview of the world and India's area, production, and productivity trends for all legume crops from 1961 to 2020. Our review article investigates the importance of gene pools and wild relatives in broadening the genetic base of legumes through pre-breeding and alien gene introgression. We have also discussed the importance of integrating genomics, phenomics, speed breeding, genetic engineering and genome editing tools in legume improvement programmes. Overall, legume breeding may undergo a paradigm shift once genomics and conventional breeding are integrated in the near future.
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Affiliation(s)
- Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Amandeep
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Priyanka Upadhyay
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Pooja Kanwar Shekhawat
- Division of Crop Improvement, Plant Breeding and Genetics, Indian Council of Agricultural Research (ICAR)-Central Soil Salinity Research Institute, Karnal, Haryana, India
- Department of Plant Breeding and Genetics, Sri Karan Narendra Agriculture University, Jobner, Rajasthan, India
| | - Gyanisha Nayak
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Lakshay Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Deepak Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Pradeep Kumar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Akashdeep Kamboj
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Antra Thada
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Shweta Shekhar
- Department of Plant Molecular Biology and Biotechnology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Ganesh Kumar Koli
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Meghana DP
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Priyanka Halladakeri
- Department of Genetics and Plant Breeding, Anand Agricultural University, Anand, Gujarat, India
| | - Rajvir Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Sumit Kumar
- Department of Agronomy, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Pawan Saini
- CSB-Central Sericultural Research & Training Institute (CSR&TI), Ministry of Textiles, Govt. of India, Jammu- Kashmir, Pampore, India
| | - Inderjit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Habiburahman Ayoubi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
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Singh RK, Singh C, Chandana BS, Mahto RK, Patial R, Gupta A, Gahlaut V, Hamwieh A, Upadhyaya HD, Kumar R. Exploring Chickpea Germplasm Diversity for Broadening the Genetic Base Utilizing Genomic Resourses. Front Genet 2022; 13:905771. [PMID: 36035111 PMCID: PMC9416867 DOI: 10.3389/fgene.2022.905771] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/24/2022] [Indexed: 12/01/2022] Open
Abstract
Legume crops provide significant nutrition to humans as a source of protein, omega-3 fatty acids as well as specific macro and micronutrients. Additionally, legumes improve the cropping environment by replenishing the soil nitrogen content. Chickpeas are the second most significant staple legume food crop worldwide behind dry bean which contains 17%–24% protein, 41%–51% carbohydrate, and other important essential minerals, vitamins, dietary fiber, folate, β-carotene, anti-oxidants, micronutrients (phosphorus, calcium, magnesium, iron, and zinc) as well as linoleic and oleic unsaturated fatty acids. Despite these advantages, legumes are far behind cereals in terms of genetic improvement mainly due to far less effort, the bottlenecks of the narrow genetic base, and several biotic and abiotic factors in the scenario of changing climatic conditions. Measures are now called for beyond conventional breeding practices to strategically broadening of narrow genetic base utilizing chickpea wild relatives and improvement of cultivars through advanced breeding approaches with a focus on high yield productivity, biotic and abiotic stresses including climate resilience, and enhanced nutritional values. Desirable donors having such multiple traits have been identified using core and mini core collections from the cultivated gene pool and wild relatives of Chickpea. Several methods have been developed to address cross-species fertilization obstacles and to aid in inter-specific hybridization and introgression of the target gene sequences from wild Cicer species. Additionally, recent advances in “Omics” sciences along with high-throughput and precise phenotyping tools have made it easier to identify genes that regulate traits of interest. Next-generation sequencing technologies, whole-genome sequencing, transcriptomics, and differential genes expression profiling along with a plethora of novel techniques like single nucleotide polymorphism exploiting high-density genotyping by sequencing assays, simple sequence repeat markers, diversity array technology platform, and whole-genome re-sequencing technique led to the identification and development of QTLs and high-density trait mapping of the global chickpea germplasm. These altogether have helped in broadening the narrow genetic base of chickpeas.
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Affiliation(s)
| | - Charul Singh
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - B S Chandana
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | - Rohit K Mahto
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | - Ranjana Patial
- Department of Agricultural Sciences, Chandigarh University, Mohali, India
| | - Astha Gupta
- School of Agricultural Sciences, Sharda University, Greater Noida, India
| | - Vijay Gahlaut
- Institute of Himalayan Bioresource Technology (CSIR), Pālampur, India
| | - Aladdin Hamwieh
- International Center for Agriculture Research in the Dry Areas (ICARDA), Giza, Egypt
| | - H D Upadhyaya
- Department of Entomology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
| | - Rajendra Kumar
- Indian Agricultural Research Institute (ICAR), New Delhi, India
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11
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Arriagada O, Cacciuttolo F, Cabeza RA, Carrasco B, Schwember AR. A Comprehensive Review on Chickpea ( Cicer arietinum L.) Breeding for Abiotic Stress Tolerance and Climate Change Resilience. Int J Mol Sci 2022; 23:ijms23126794. [PMID: 35743237 PMCID: PMC9223724 DOI: 10.3390/ijms23126794] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 02/05/2023] Open
Abstract
Chickpea is one of the most important pulse crops worldwide, being an excellent source of protein. It is grown under rain-fed conditions averaging yields of 1 t/ha, far from its potential of 6 t/ha under optimum conditions. The combined effects of heat, cold, drought, and salinity affect species productivity. In this regard, several physiological, biochemical, and molecular mechanisms are reviewed to confer tolerance to abiotic stress. A large collection of nearly 100,000 chickpea accessions is the basis of breeding programs, and important advances have been achieved through conventional breeding, such as germplasm introduction, gene/allele introgression, and mutagenesis. In parallel, advances in molecular biology and high-throughput sequencing have allowed the development of specific molecular markers for the genus Cicer, facilitating marker-assisted selection for yield components and abiotic tolerance. Further, transcriptomics, proteomics, and metabolomics have permitted the identification of specific genes, proteins, and metabolites associated with tolerance to abiotic stress of chickpea. Furthermore, some promising results have been obtained in studies with transgenic plants and with the use of gene editing to obtain drought-tolerant chickpea. Finally, we propose some future lines of research that may be useful to obtain chickpea genotypes tolerant to abiotic stress in a scenario of climate change.
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Affiliation(s)
- Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (O.A.); (F.C.)
| | - Felipe Cacciuttolo
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (O.A.); (F.C.)
| | - Ricardo A. Cabeza
- Departamento de Producción Agrícola, Facultad de Ciencias Agrarias, Universidad de Talca, Talca 3460000, Chile;
| | - Basilio Carrasco
- Centro de Estudios en Alimentos Procesados (CEAP), Av. Lircay s/n, Talca 3480094, Chile;
| | - Andrés R. Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (O.A.); (F.C.)
- Correspondence:
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12
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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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13
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Yadav S, Yadava YK, Kohli D, Meena S, Kalwan G, Bharadwaj C, Gaikwad K, Arora A, Jain PK. Genome-wide identification, in silico characterization and expression analysis of the RNA helicase gene family in chickpea (C. arietinum L.). Sci Rep 2022; 12:9778. [PMID: 35697711 PMCID: PMC9192698 DOI: 10.1038/s41598-022-13823-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/27/2022] [Indexed: 11/18/2022] Open
Abstract
The RNA helicases are an important class of enzymes which are known to influence almost every aspect of RNA metabolism. The majority of RNA helicases belong to the SF2 (superfamily 2) superfamily, members of which are further categorized into three separate subfamilies i.e., the DEAD, DEAH and DExD/H-box subfamilies. In chickpea, these RNA helicases have not been characterized until now. A genome-wide analysis across the chickpea genome led to the identification of a total of 150 RNA helicase genes which included 50 DEAD, 33 DEAH and 67 DExD/H-box genes. These were distributed across all the eight chromosomes, with highest number on chromosome 4 (26) and least on chromosome 8 (8). Gene duplication analysis resulted in identification of 15 paralogous gene pairs with Ka/Ks values < 1, indicating towards the genes being under purifying selection during the course of evolution. The promoter regions of the RNA helicase genes were enriched in cis-acting elements like the light and ABA-responsive elements. The drought responsiveness of the genes was analysed by studying the expression profiles of few of these genes, in two different genotypes, the cultivated variety ICC 8261 (kabuli, C. arietinum) and the wild accession ILWC 292 (C. reticulatum), through qRT-PCR. These genotypes were selected based on their drought responsiveness in a field experiment, where it was observed that the percentage (%) reduction in relative water content (RWC) and membrane stability index (MSI) for the drought stressed plants after withholding water for 24 days, over the control or well-watered plants, was least for both the genotypes. The genes CaDEAD50 and CaDExD/H66 were identified as drought-responsive RNA helicase genes in chickpea. The protein encoded by the CaDExD/H66 gene shares a high degree of homology with one of the CLSY (CLASSY) proteins of A. thaliana. We hypothesize that this gene could possibly be involved in regulation of DNA methylation levels in chickpea by regulating siRNA production, in conjunction with other proteins like the Argonaute, RNA dependent RNA polymerases and Dicer-like proteins.
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Affiliation(s)
- Sheel Yadav
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Yashwant K Yadava
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Deshika Kohli
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Shashi Meena
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Gopal Kalwan
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - C Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Ajay Arora
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - P K Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
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14
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Mokhtar MM, Alsamman AM, Abd-Elhalim HM, El Allali A. CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species. PLoS One 2021; 16:e0259540. [PMID: 34762703 PMCID: PMC8584679 DOI: 10.1371/journal.pone.0259540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/20/2021] [Indexed: 11/19/2022] Open
Abstract
Recently, Cicer species have experienced increased research interest due to their economic importance, especially in genetics, genomics, and crop improvement. The Cicer arietinum, Cicer reticulatum, and Cicer echinospermum genomes have been sequenced and provide valuable resources for trait improvement. Since the publication of the chickpea draft genome, progress has been made in genome assembly, functional annotation, and identification of polymorphic markers. However, work is still needed to identify transposable elements (TEs) and make them available for researchers. In this paper, we present CicerSpTEdb, a comprehensive TE database for Cicer species that aims to improve our understanding of the organization and structural variations of the chickpea genome. Using structure and homology-based methods, 3942 C. echinospermum, 3579 C. reticulatum, and 2240 C. arietinum TEs were identified. Comparisons between Cicer species indicate that C. echinospermum has the highest number of LTR-RT and hAT TEs. C. reticulatum has more Mutator, PIF Harbinger, Tc1 Mariner, and CACTA TEs, while C. arietinum has the highest number of Helitron. CicerSpTEdb enables users to search and visualize TEs by location and download their results. The database will provide a powerful resource that can assist in developing TE target markers for molecular breeding and answer related biological questions. Database URL: http://cicersptedb.easyomics.org/index.php.
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Affiliation(s)
- Morad M. Mokhtar
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- * E-mail: (AEA); (MMM)
| | | | - Haytham M. Abd-Elhalim
- Agricultural Genetic Engineering Research Institute, Agricultural Research Center, Giza, Egypt
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- * E-mail: (AEA); (MMM)
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15
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Carmona-Molero R, Jimenez-Lopez JC, Caballo C, Gil J, Millán T, Die JV. Aldehyde Dehydrogenase 3 Is an Expanded Gene Family with Potential Adaptive Roles in Chickpea. PLANTS 2021; 10:plants10112429. [PMID: 34834791 PMCID: PMC8619295 DOI: 10.3390/plants10112429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/26/2021] [Accepted: 11/04/2021] [Indexed: 11/23/2022]
Abstract
Legumes play an important role in ensuring food security, improving nutrition and enhancing ecosystem resilience. Chickpea is a globally important grain legume adapted to semi-arid regions under rain-fed conditions. A growing body of research shows that aldehyde dehydrogenases (ALDHs) represent a gene class with promising potential for plant adaptation improvement. Aldehyde dehydrogenases constitute a superfamily of proteins with important functions as ‘aldehyde scavengers’ by detoxifying aldehydes molecules, and thus play important roles in stress responses. We performed a comprehensive study of the ALDH superfamily in the chickpea genome and identified 27 unique ALDH loci. Most chickpea ALDHs originated from duplication events and the ALDH3 gene family was noticeably expanded. Based on the physical locations of genes and sequence similarities, our results suggest that segmental duplication is a major driving force in the expansion of the ALDH family. Supported by expression data, the findings of this study offer new potential target genes for improving stress tolerance in chickpea that will be useful for breeding programs.
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Affiliation(s)
- Rocío Carmona-Molero
- Department of Genetics ETSIAM, University of Córdoba, 14071 Córdoba, Spain; (R.C.-M.); (J.G.); (T.M.)
| | - Jose C. Jimenez-Lopez
- Department of Biochemistry, Cell and Molecular Biology of Plants, EEZ-CSIC, 18008 Granada, Spain;
- Institute of Agriculture and School of Agriculture and Environment, The University of Western Australia, Perth 6009, Australia
| | - Cristina Caballo
- Área de Genómica y Biotecnología, IFAPA, Alameda del Obispo, 14080 Córdoba, Spain;
| | - Juan Gil
- Department of Genetics ETSIAM, University of Córdoba, 14071 Córdoba, Spain; (R.C.-M.); (J.G.); (T.M.)
| | - Teresa Millán
- Department of Genetics ETSIAM, University of Córdoba, 14071 Córdoba, Spain; (R.C.-M.); (J.G.); (T.M.)
| | - Jose V. Die
- Department of Genetics ETSIAM, University of Córdoba, 14071 Córdoba, Spain; (R.C.-M.); (J.G.); (T.M.)
- Correspondence:
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16
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Thudi M, Palakurthi R, Schnable JC, Chitikineni A, Dreisigacker S, Mace E, Srivastava RK, Satyavathi CT, Odeny D, Tiwari VK, Lam HM, Hong YB, Singh VK, Li G, Xu Y, Chen X, Kaila S, Nguyen H, Sivasankar S, Jackson SA, Close TJ, Shubo W, Varshney RK. Genomic resources in plant breeding for sustainable agriculture. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153351. [PMID: 33412425 PMCID: PMC7903322 DOI: 10.1016/j.jplph.2020.153351] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 05/19/2023]
Abstract
Climate change during the last 40 years has had a serious impact on agriculture and threatens global food and nutritional security. From over half a million plant species, cereals and legumes are the most important for food and nutritional security. Although systematic plant breeding has a relatively short history, conventional breeding coupled with advances in technology and crop management strategies has increased crop yields by 56 % globally between 1965-85, referred to as the Green Revolution. Nevertheless, increased demand for food, feed, fiber, and fuel necessitates the need to break existing yield barriers in many crop plants. In the first decade of the 21st century we witnessed rapid discovery, transformative technological development and declining costs of genomics technologies. In the second decade, the field turned towards making sense of the vast amount of genomic information and subsequently moved towards accurately predicting gene-to-phenotype associations and tailoring plants for climate resilience and global food security. In this review we focus on genomic resources, genome and germplasm sequencing, sequencing-based trait mapping, and genomics-assisted breeding approaches aimed at developing biotic stress resistant, abiotic stress tolerant and high nutrition varieties in six major cereals (rice, maize, wheat, barley, sorghum and pearl millet), and six major legumes (soybean, groundnut, cowpea, common bean, chickpea and pigeonpea). We further provide a perspective and way forward to use genomic breeding approaches including marker-assisted selection, marker-assisted backcrossing, haplotype based breeding and genomic prediction approaches coupled with machine learning and artificial intelligence, to speed breeding approaches. The overall goal is to accelerate genetic gains and deliver climate resilient and high nutrition crop varieties for sustainable agriculture.
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Affiliation(s)
- Mahendar Thudi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India; University of Southern Queensland, Toowoomba, Australia
| | - Ramesh Palakurthi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Emma Mace
- Agri-Science Queensland, Department of Agriculture & Fisheries (DAF), Warwick, Australia
| | - Rakesh K Srivastava
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - C Tara Satyavathi
- Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Damaris Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | | | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Yan Bin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Vikas K Singh
- South Asia Hub, International Rice Research Institute (IRRI), Hyderabad, India
| | - Guowei Li
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yunbi Xu
- International Maize and Wheat Improvement Center (CYMMIT), Mexico DF, Mexico; Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Sanjay Kaila
- Department of Biotechnology, Ministry of Science and Technology, Government of India, India
| | - Henry Nguyen
- National Centre for Soybean Research, University of Missouri, Columbia, USA
| | - Sobhana Sivasankar
- Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | | | | | - Wan Shubo
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
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17
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A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature 2021; 599:622-627. [PMID: 34759320 PMCID: PMC8612933 DOI: 10.1038/s41586-021-04066-1] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 09/28/2021] [Indexed: 11/17/2022]
Abstract
Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1. So far, few chickpea (Cicer arietinum) germplasm accessions have been characterized at the genome sequence level2. Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic diversity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.
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Doležalová A, Sládeková L, Šimoníková D, Holušová K, Karafiátová M, Varshney RK, Doležel J, Hřibová E. Karyotype Differentiation in Cultivated Chickpea Revealed by Oligopainting Fluorescence in situ Hybridization. FRONTIERS IN PLANT SCIENCE 2021; 12:791303. [PMID: 35145533 PMCID: PMC8822127 DOI: 10.3389/fpls.2021.791303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/29/2021] [Indexed: 05/22/2023]
Abstract
Chickpea (Cicer arietinum L.) is one of the main sources of plant proteins in the Indian subcontinent and West Asia, where two different morphotypes, desi and kabuli, are grown. Despite the progress in genome mapping and sequencing, the knowledge of the chickpea genome at the chromosomal level, including the long-range molecular chromosome organization, is limited. Earlier cytogenetic studies in chickpea suffered from a limited number of cytogenetic landmarks and did not permit to identify individual chromosomes in the metaphase spreads or to anchor pseudomolecules to chromosomes in situ. In this study, we developed a system for fast molecular karyotyping for both morphotypes of cultivated chickpea. We demonstrate that even draft genome sequences are adequate to develop oligo-fluorescence in situ hybridization (FISH) barcodes for the identification of chromosomes and comparative analysis among closely related chickpea genotypes. Our results show the potential of oligo-FISH barcoding for the identification of structural changes in chromosomes, which accompanied genome diversification among chickpea cultivars. Moreover, oligo-FISH barcoding in chickpea pointed out some problematic, most probably wrongly assembled regions of the pseudomolecules of both kabuli and desi reference genomes. Thus, oligo-FISH appears as a powerful tool not only for comparative karyotyping but also for the validation of genome assemblies.
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Affiliation(s)
- Alžběta Doležalová
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Lucia Sládeková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Denisa Šimoníková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Kateřina Holušová
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Miroslava Karafiátová
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
| | - Jaroslav Doležel
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Eva Hřibová
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- *Correspondence: Eva Hřibová,
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Karaca N, Ates D, Nemli S, Ozkuru E, Yilmaz H, Yagmur B, Kartal C, Tosun M, Ozdestan O, Otles S, Kahriman A, Chang P, Tanyolac MB. Identification of SNP Markers Associated with Iron and Zinc Concentrations in Cicer Seeds. Curr Genomics 2020; 21:212-223. [PMID: 33071615 PMCID: PMC7521033 DOI: 10.2174/1389202921666200413150951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 03/18/2020] [Accepted: 03/27/2020] [Indexed: 12/30/2022] Open
Abstract
Background Cicer reticulatum L. is the wild progenitor of chickpea Cicer arietinum L., the fourth most important pulse crop in the world. Iron (Fe) and zinc (Zn) are vital micronutrients that play crucial roles in sustaining life by acting as co-factors for various proteins. Aims and Objectives
In order to improve micronutrient-dense chickpea lines, this study aimed to investigate variability and detect DNA markers associated with Fe and Zn concentrations in the seeds of 73 cultivated (C. arietinum L.) and 107 C. reticulatum genotypes. Methods
A set of 180 accessions was genotyped using 20,868 single nucleotide polymorphism (SNP) markers obtained from genotyping by sequencing analysis. Results
The results revealed substantial variation in the seed Fe and Zn concentration of the surveyed population. Using STRUCTURE software, the population structure was divided into two groups according to the principal component analysis and neighbor-joining tree analysis. A total of 23 and 16 associated SNP markers related to Fe and Zn concentrations, respectively were identified in TASSEL software by the mixed linear model method. Significant SNP markers found in more than two environments were accepted as more reliable than those that only existed in a single environment. Conclusion
The identified markers can be used in marker-assisted selection in chickpea breeding programs for the improvement of seed Fe and Zn concentrations in the chickpea.
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Affiliation(s)
- Nur Karaca
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Duygu Ates
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Seda Nemli
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Esin Ozkuru
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Hasan Yilmaz
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Bulent Yagmur
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Canan Kartal
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Muzaffer Tosun
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Ozgul Ozdestan
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Semih Otles
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Abdullah Kahriman
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Peter Chang
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Muhammed Bahattin Tanyolac
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
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20
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Abstract
Legumes (Fabaceae) are agronomically and economically one of the most important crops. Because legumes serve as a source of food, feed, and industrial materials, many studies in the field of legume genomics, including genome sequencing, have been conducted over the last decade. Here, we update the progress in genome sequencing of legume crops, including soybean (Glycine max [L.] Merr.), mung bean (V. radiata var. radiata), adzuki bean (V. angularis var. angularis), common bean (Phaseolus vulgaris L.), pigeon pea (Cajanus cajan), chickpea (Cicer arietinum), and peanut (Arachis hypogaea). Since the publication of the first reference genome sequence of each species, many accessions have been resequenced to study genetic diversity, speciation, and polyploidization in the legume lineage.
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Affiliation(s)
- Jungmin Ha
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Suk-Ha Lee
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea.
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21
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Qin S, Wei K, Cui Z, Liang Y, Li M, Gu L, Yang C, Zhou X, Li L, Xu W, Liu C, Miao J, Zhang Z. Comparative Genomics of Spatholobus suberectus and Insight Into Flavonoid Biosynthesis. FRONTIERS IN PLANT SCIENCE 2020; 11:528108. [PMID: 33013959 PMCID: PMC7500164 DOI: 10.3389/fpls.2020.528108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 08/19/2020] [Indexed: 05/09/2023]
Abstract
Spatholobus suberectus Dunn (S. suberectus), has been widely used in traditional medicines plant source of the Leguminosae family. Its vine stem of which plays an important role in the prevention and treatment of various diseases because it contains various flavonoids. Comparative genome analysis suggested well-conserved genomic components and genetic collinearity between the genome of S. suberectus and other genera of Leguminosae such as Glycine max. We discovered two whole genome duplications (WGD) events in S. suberectus and G. max lineage underwent a WGD after speciation from S. suberectus. The determination of expansion and contractions of orthologous gene families revealed 1,001 expanded gene families and 3,649 contracted gene families in the S. suberectus lineage. Comparing to the model plants, many novel flavonoid biosynthesis-related genes were predicted in the genome of S. suberectus, and the expression patterns of these genes in the roots are similar to those in the stems [such as the isoflavone synthase (IFS) genes]. The expansion of IFS from a single copy in the Leguminosae ancestor to four copies in S. suberectus, will accelerate the biosynthesis of flavonoids. MYB genes are widely involved in plant flavonoid biosynthesis and the most abundant member of the TF family in S. suberectus. Activated retrotransponson positive regulates the accumulation of flavonoid in S. suberectus by introducing the cis-elements of tissue-specific expressed MYBs. Our study not only provides significant insight into the evolution of specific flavonoid biosynthetic pathways in S. suberectus, but also would facilitate the development of tools for enhancing bioactive productivity by metabolic engineering in microbes or by molecular breeding for alleviating resource shortage of S. suberectus.
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Affiliation(s)
- Shuangshuang Qin
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Kunhua Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Zhanhu Cui
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ying Liang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Mingjie Li
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Li Gu
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chuyun Yang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaolei Zhou
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Linxuan Li
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Wei Xu
- Center for Research and Cooperation, Novogene Bioinformatics Institute, Beijing, China
| | - Can Liu
- Center for Research and Cooperation, Novogene Bioinformatics Institute, Beijing, China
- *Correspondence: Zhongyi Zhang, ; Can Liu, ; Jianhua Miao,
| | - Jianhua Miao
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- *Correspondence: Zhongyi Zhang, ; Can Liu, ; Jianhua Miao,
| | - Zhongyi Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Genetics, Breeding and Comprehensive Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Zhongyi Zhang, ; Can Liu, ; Jianhua Miao,
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22
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Farahani S, Maleki M, Mehrabi R, Kanouni H, Scheben A, Batley J, Talebi R. Whole Genome Diversity, Population Structure, and Linkage Disequilibrium Analysis of Chickpea ( Cicer arietinum L.) Genotypes Using Genome-Wide DArTseq-Based SNP Markers. Genes (Basel) 2019; 10:E676. [PMID: 31487948 PMCID: PMC6770975 DOI: 10.3390/genes10090676] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/26/2019] [Accepted: 08/20/2019] [Indexed: 01/09/2023] Open
Abstract
Characterization of genetic diversity, population structure, and linkage disequilibrium is a prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes, including advanced "Kabuli" breeding lines and Iranian landrace "Desi" chickpea genotypes, were genotyped using DArTseq-Based single nucleotide polymorphism (SNP) markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that was covered by SNPs varied from 16,236.36 kbp (LG8) to 67,923.99 kbp (LG5), while LG4 showed a higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6, and LG8 showed higher mean PIC value than average. Unweighted neighbor joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and discriminant analysis of principal component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r2 ≥ 0.8, while 2961 pairs of markers showed complete LD (r2 = 1), and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggest the presence of a high genetic diversity among the studied chickpea genotypes. This study also demonstrates the efficiency of DArTseq-based SNP genotyping for large-scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits, such as seed yield, abiotic, and biotic stresses, and therefore can be efficiently used in breeding programs to improve chickpea.
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Affiliation(s)
- Somayeh Farahani
- Department of Plant Protection, Varamin-Pishva Branch, Islamic Azad University, Varamin, P.O.Box: 33817-74895, Iran
| | - Mojdeh Maleki
- Department of Plant Protection, Varamin-Pishva Branch, Islamic Azad University, Varamin, P.O.Box: 33817-74895, Iran
| | - Rahim Mehrabi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan P.O. Box: 8415683111, Iran
| | - Homayoun Kanouni
- Kordestan Agricultural and Natural Resources and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Sanandaj, P.O.Box:714, Iran
| | - Armin Scheben
- School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Reza Talebi
- Department of Agronomy & Plant Breeding, College of Agriculture, Sanandaj Branch, Islamic Azad University, Sanandaj, P.O. Box:618, Iran.
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23
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Zwart RS, Thudi M, Channale S, Manchikatla PK, Varshney RK, Thompson JP. Resistance to Plant-Parasitic Nematodes in Chickpea: Current Status and Future Perspectives. FRONTIERS IN PLANT SCIENCE 2019; 10:966. [PMID: 31428112 PMCID: PMC6689962 DOI: 10.3389/fpls.2019.00966] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/10/2019] [Indexed: 06/10/2023]
Abstract
Plant-parasitic nematodes constrain chickpea (Cicer arietinum) production, with annual yield losses estimated to be 14% of total global production. Nematode species causing significant economic damage in chickpea include root-knot nematodes (Meloidogyne artiella, M. incognita, and M. javanica), cyst nematode (Heterodera ciceri), and root-lesion nematode (Pratylenchus thornei). Reduced functionality of roots from nematode infestation leads to water stress and nutrient deficiency, which in turn lead to poor plant growth and reduced yield. Integration of resistant crops with appropriate agronomic practices is recognized as the safest and most practical, economic and effective control strategy for plant-parasitic nematodes. However, breeding for resistance to plant-parasitic nematodes has numerous challenges that originate from the narrow genetic diversity of the C. arietinum cultigen. While levels of resistance to M. artiella, H. ciceri, and P. thornei have been identified in wild Cicer species that are superior to resistance levels in the C. arietinum cultigen, barriers to interspecific hybridization restrict the use of these crop wild relatives, as sources of nematode resistance. Wild Cicer species of the primary genepool, C. reticulatum and C. echinospermum, are the only species that have been used to introgress resistance genes into the C. arietinum cultigen. The availability of genomic resources, including genome sequence and re-sequence information, the chickpea reference set and mini-core collections, and new wild Cicer collections, provide unprecedented opportunities for chickpea improvement. This review surveys progress in the identification of novel genetic sources of nematode resistance in international germplasm collections and recommends genome-assisted breeding strategies to accelerate introgression of nematode resistance into elite chickpea cultivars.
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Affiliation(s)
- Rebecca S. Zwart
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Mahendar Thudi
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Sonal Channale
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Praveen K. Manchikatla
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - John P. Thompson
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
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24
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Qin S, Wu L, Wei K, Liang Y, Song Z, Zhou X, Wang S, Li M, Wu Q, Zhang K, Hui Y, Wang S, Miao J, Zhang Z. A draft genome for Spatholobus suberectus. Sci Data 2019; 6:113. [PMID: 31273216 PMCID: PMC6609623 DOI: 10.1038/s41597-019-0110-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 05/31/2019] [Indexed: 11/09/2022] Open
Abstract
Spatholobus suberectus Dunn (S. suberectus), which belongs to the Leguminosae, is an important medicinal plant in China. Owing to its long growth cycle and increased use in human medicine, wild resources of S. suberectus have decreased rapidly and may be on the verge of extinction. De novo assembly of the whole S. suberectus genome provides us a critical potential resource towards biosynthesis of the main bioactive components and seed development regulation mechanism of this plant. Utilizing several sequencing technologies such as Illumina HiSeq X Ten, single-molecule real-time sequencing, 10x Genomics, as well as new assembly techniques such as FALCON and chromatin interaction mapping (Hi-C), we assembled a chromosome-scale genome about 798 Mb in size. In total, 748 Mb (93.73%) of the contig sequences were anchored onto nine chromosomes with the longest scaffold being 103.57 Mb. Further annotation analyses predicted 31,634 protein-coding genes, of which 93.9% have been functionally annotated. All data generated in this study is available in public databases.
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Affiliation(s)
- Shuangshuang Qin
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Lingqing Wu
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Kunhua Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Ying Liang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Zhijun Song
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Xiaolei Zhou
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Shuo Wang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Mingjie Li
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qinghua Wu
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Kaijian Zhang
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Yuanyuan Hui
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Shuying Wang
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Jianhua Miao
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China.
| | - Zhongyi Zhang
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Genetics, Breeding and Comprehensive Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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25
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Basu U, Narnoliya L, Srivastava R, Sharma A, Bajaj D, Daware A, Thakro V, Malik N, Upadhyaya HD, Tripathi S, Hegde VS, Tyagi AK, Parida SK. CLAVATA signaling pathway genes modulating flowering time and flower number in chickpea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2017-2038. [PMID: 30929032 DOI: 10.1007/s00122-019-03335-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 03/20/2019] [Indexed: 05/26/2023]
Abstract
A combinatorial genomic strategy delineated functionally relevant natural allele of a CLAVATA gene and its marker (haplotype)-assisted introgression led to development of the early-flowering chickpea cultivars with high flower number and enhanced yield/productivity. Unraveling the genetic components involved in CLAVATA (CLV) signaling is crucial for modulating important shoot apical meristem (SAM) characteristics and ultimately regulating diverse SAM-regulated agromorphological traits in crop plants. A genome-wide scan identified 142 CLV1-, 28 CLV2- and 6 CLV3-like genes, and their comprehensive genomic constitution and phylogenetic relationships were deciphered in chickpea. The QTL/fine mapping and map-based cloning integrated with high-resolution association analysis identified SNP loci from CaCLV3_01 gene within a major CaqDTF1.1/CaqFN1.1 QTL associated with DTF (days to 50% flowering) and FN (flower number) traits in chickpea, which was further ascertained by quantitative expression profiling. Molecular haplotyping of CaCLV3_01 gene, expressed specifically in SAM, constituted two major haplotypes that differentiated the early-DTF and high-FN chickpea accessions from late-DTF and low-FN. Enhanced accumulation of transcripts of superior CaCLV3_01 gene haplotype and known flowering promoting genes was observed in the corresponding haplotype-introgressed early-DTF and high-FN near-isogenic lines (NILs) with narrow SAM width. The superior haplotype-introgressed NILs exhibited early-flowering, high-FN and enhanced seed yield/productivity without compromising agronomic performance. These delineated molecular signatures can regulate DTF and FN traits through SAM proliferation and differentiation and thereby will be useful for translational genomic study to develop early-flowering cultivars with enhanced yield/productivity.
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Affiliation(s)
- 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
| | - Rishi Srivastava
- 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
| | - Deepak Bajaj
- 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
| | - Virevol Thakro
- 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
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - V S Hegde
- 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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26
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Sharma A, Basu U, Malik N, Daware A, Thakro V, Narnoliya L, Bajaj D, Tripathi S, Hegde VS, Upadhyaya HD, Tyagi AK, Parida SK. Genome-wide cis-regulatory signatures for modulation of agronomic traits as exemplified by drought yield index (DYI) in chickpea. Funct Integr Genomics 2019; 19:973-992. [PMID: 31177403 DOI: 10.1007/s10142-019-00691-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 05/07/2019] [Accepted: 05/10/2019] [Indexed: 12/26/2022]
Abstract
Developing functional molecular tags from the cis-regulatory sequence components of genes is vital for their deployment in efficient genetic dissection of complex quantitative traits in crop plants including chickpea. The current study identified 431,194 conserved non-coding SNP (CNSNP) from the cis-regulatory element regions of genes which were annotated on a chickpea genome. These genome-wide CNSNP marker resources are made publicly accessible through a user-friendly web-database ( http://www.cnsnpcicarbase.com ). The CNSNP-based quantitative trait loci (QTL) and expression QTL (eQTL) mapping and genome-wide association study (GWAS) were further integrated with global gene expression landscapes, molecular haplotyping, and DNA-protein interaction study in the association panel and recombinant inbred lines (RIL) mapping population to decode complex genetic architecture of one of the vital seed yield trait under drought stress, drought yield index (DYI), in chickpea. This delineated two constituted natural haplotypes and alleles from a histone H3 protein-coding gene and its transcriptional regulator NAC transcription factor (TF) harboring the major QTLs and trans-acting eQTL governing DYI in chickpea. The effect of CNSNPs in TF-binding cis-element of a histone H3 gene in altering the binding affinity and transcriptional activity of NAC TF based on chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) assay was evident. The CNSNP-led promising molecular tags scanned will essentially have functional significance to decode transcriptional gene regulatory function and thus can drive translational genomic analysis in chickpea.
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Affiliation(s)
- Akash Sharma
- 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
| | - Naveen Malik
- 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
| | - Virevol Thakro
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Laxmi Narnoliya
- 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
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - V S Hegde
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, 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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de Camargo AC, Favero BT, Morzelle MC, Franchin M, Alvarez-Parrilla E, de la Rosa LA, Geraldi MV, Maróstica Júnior MR, Shahidi F, Schwember AR. Is Chickpea a Potential Substitute for Soybean? Phenolic Bioactives and Potential Health Benefits. Int J Mol Sci 2019; 20:E2644. [PMID: 31146372 PMCID: PMC6600242 DOI: 10.3390/ijms20112644] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/18/2019] [Accepted: 05/22/2019] [Indexed: 01/07/2023] Open
Abstract
Legume seeds are rich sources of protein, fiber, and minerals. In addition, their phenolic compounds as secondary metabolites render health benefits beyond basic nutrition. Lowering apolipoprotein B secretion from HepG2 cells and decreasing the level of low-density lipoprotein (LDL)-cholesterol oxidation are mechanisms related to the prevention of cardiovascular diseases (CVD). Likewise, low-level chronic inflammation and related disorders of the immune system are clinical predictors of cardiovascular pathology. Furthermore, DNA-damage signaling and repair are crucial pathways to the etiology of human cancers. Along CVD and cancer, the prevalence of obesity and diabetes is constantly increasing. Screening the ability of polyphenols in inactivating digestive enzymes is a good option in pre-clinical studies. In addition, in vivo studies support the role of polyphenols in the prevention and/or management of diabetes and obesity. Soybean, a well-recognized source of phenolic isoflavones, exerts health benefits by decreasing oxidative stress and inflammation related to the above-mentioned chronic ailments. Similar to soybeans, chickpeas are good sources of nutrients and phenolic compounds, especially isoflavones. This review summarizes the potential of chickpea as a substitute for soybean in terms of health beneficial outcomes. Therefore, this contribution may guide the industry in manufacturing functional foods and/or ingredients by using an undervalued feedstock.
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Affiliation(s)
- Adriano Costa de Camargo
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Casilla 306-22, Santiago, Chile.
| | - Bruno Trevenzoli Favero
- University of Copenhagen, Department of Plant and Environmental Sciences, 2630 Taastrup, Denmark.
| | - Maressa Caldeira Morzelle
- Department of Food and Nutrition, Faculty of Nutrition, Federal University of Mato Grosso, Fernando Correa Avenue, P.O. box 2367, Cuiabá, MT 78060-900, Brazil.
| | - Marcelo Franchin
- Department of Physiological Sciences, Piracicaba Dental School, University of Campinas, Piracicaba, SP 13414-903, Brazil.
| | - Emilio Alvarez-Parrilla
- Department of Chemical Biological Sciences, Universidad Autónoma de Ciudad Juárez, Anillo Envolvente del Pronaf y Estocolmo, s/n, Cd, Juárez, Chihuahua 32310, México.
| | - Laura A de la Rosa
- Department of Chemical Biological Sciences, Universidad Autónoma de Ciudad Juárez, Anillo Envolvente del Pronaf y Estocolmo, s/n, Cd, Juárez, Chihuahua 32310, México.
| | - Marina Vilar Geraldi
- Department of Food and Nutrition, University of Campinas-UNICAMP, Campinas, SP 13083-862, Brazil.
| | | | - Fereidoon Shahidi
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
| | - Andrés R Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Casilla 306-22, Santiago, Chile.
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Jain A, Roorkiwal M, Kale S, Garg V, Yadala R, Varshney RK. InDel markers: An extended marker resource for molecular breeding in chickpea. PLoS One 2019; 14:e0213999. [PMID: 30883592 PMCID: PMC6422259 DOI: 10.1371/journal.pone.0213999] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 03/05/2019] [Indexed: 12/03/2022] Open
Abstract
Chickpea is one of the most important food legumes that holds the key to meet rising global food and nutritional demand. In order to deploy molecular breeding approaches in crop improvement programs, user friendly and cost effective marker resources remain prerequisite. The advent of next generation sequencing (NGS) technology has resulted in the generation of several thousands of markers as part of several large scale genome sequencing and re-sequencing initiatives. Very recently, PCR based Insertion-deletions (InDels) are becoming a popular gel based genotyping solution because of their co-dominant, inexpensive, and highly polymorphic nature. With an objective to expand marker resources for genomics assisted breeding (GAB) in chickpea, whole genome re-sequencing data generated on five parental lines of one interspecific (ICC 4958 × PI 489777) and two intra-specific (ICC 283 × ICC 8261 and ICC 4958 × ICC 1882) mapping populations, were used for identification of InDels. A total of 231,658 InDels were identified using Dindel software with default parameters. Further, a total of 8,307 InDels with ≥20 bp size were selected for development of gel based markers, of which primers could be designed for 7,523 (90.56%) markers. On average, markers appeared at a frequency of 1,038 InDels/LG with a maximum number of markers on CaLG04 (1,952 InDels) and minimum on CaLG08 (360 InDels). In order to validate these InDels, a total of 423 primer pairs were randomly selected and tested on the selected parental lines. A high amplification rate of 80% was observed ranging from 46.06 to 58.01% polymorphism rate across parents on 3% agarose gel. This study clearly reflects the usefulness of available sequence data for the development of genome-wide InDels in chickpea that can further contribute and accelerate a wide range of genetic and molecular breeding activities in chickpea.
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Affiliation(s)
- Ankit Jain
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- * E-mail: (RKV); (MR)
| | - Sandip Kale
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Gatersleben, Germany
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Ramakrishna Yadala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- * E-mail: (RKV); (MR)
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Chen F, Song Y, Li X, Chen J, Mo L, Zhang X, Lin Z, Zhang L. Genome sequences of horticultural plants: past, present, and future. HORTICULTURE RESEARCH 2019; 6:112. [PMID: 31645966 PMCID: PMC6804536 DOI: 10.1038/s41438-019-0195-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/27/2019] [Accepted: 08/10/2019] [Indexed: 05/18/2023]
Abstract
Horticultural plants play various and critical roles for humans by providing fruits, vegetables, materials for beverages, and herbal medicines and by acting as ornamentals. They have also shaped human art, culture, and environments and thereby have influenced the lifestyles of humans. With the advent of sequencing technologies, there has been a dramatic increase in the number of sequenced genomes of horticultural plant species in the past decade. The genomes of horticultural plants are highly diverse and complex, often with a high degree of heterozygosity and a high ploidy due to their long and complex history of evolution and domestication. Here we summarize the advances in the genome sequencing of horticultural plants, the reconstruction of pan-genomes, and the development of horticultural genome databases. We also discuss past, present, and future studies related to genome sequencing, data storage, data quality, data sharing, and data visualization to provide practical guidance for genomic studies of horticultural plants. Finally, we propose a horticultural plant genome project as well as the roadmap and technical details toward three goals of the project.
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Affiliation(s)
- Fei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yunfeng Song
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiaojiang Li
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Junhao Chen
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300 China
| | - Lan Mo
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300 China
| | - Xingtan Zhang
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO 63103 USA
| | - Liangsheng Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology and Quality Science and Processing Technology in Special Starch, Key Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of Crops, College of Crop Science, Fuzhou, China
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Kumar M, Yusuf MA, Yadav P, Narayan S, Kumar M. Overexpression of Chickpea Defensin Gene Confers Tolerance to Water-Deficit Stress in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2019; 10:290. [PMID: 30915095 PMCID: PMC6423178 DOI: 10.3389/fpls.2019.00290] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 02/21/2019] [Indexed: 05/22/2023]
Abstract
Plant defensins are mainly known for their antifungal activity. However, limited information is available regarding their function in abiotic stresses. In this study, a defensin gene, Ca-AFP, from Cicer arietinum, commonly known as chickpea, was cloned and transformed in Arabidopsis thaliana for its functional characterization under simulated water-deficit conditions. Under simulated water-deficit conditions (mannitol and polyethylene glycol-6000 induced), the transgenic A. thaliana plants had higher accumulation of the Ca-AFP transcript compared to that under non-stress condition and showed higher germination rate, root length, and biomass than the wild-type (WT) plants. To get further insights into the role of Ca-AFP in conferring tolerance to water-deficit stress, we determined various physiological parameters and found significant reduction in the transpiration rate and stomatal conductance whereas the net photosynthesis and water use efficiency was increased in the transgenic plants compared to that in the WT plants under water deficit conditions. The transgenic plants showed enhanced superoxide dismutase, ascorbate peroxidase, and catalase activities, had higher proline, chlorophyll, and relative water content, and exhibited reduced ion leakage and malondialdehyde content under water-deficit conditions. Overall, our results indicate that overexpression of Ca-AFP could be an efficient approach for conferring tolerance to water-deficit stress in plants.
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Affiliation(s)
- Manoj Kumar
- Department of Biosciences, Integral University, Lucknow, India
- Department of Biotechnology, CSIR-National Botanical Research Institute, Lucknow, India
| | - Mohd Aslam Yusuf
- Department of Bioengineering, Integral University, Lucknow, India
| | - Pooja Yadav
- Department of Biotechnology, CSIR-National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shiv Narayan
- Plant Physiology Laboratory, CSIR-National Botanical Research Institute, Lucknow, India
| | - Manoj Kumar
- Department of Biotechnology, CSIR-National Botanical Research Institute, Lucknow, India
- *Correspondence: Manoj Kumar,
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Abstract
Chickpea is a highly nutritious grain legume crop, widely appreciated as a health food, especially in the Indian subcontinent. The major constraints on chickpea production are biotic (Helicoverpa, bruchid, aphid, ascochyta) and abiotic (drought, heat, salt, cold) stresses, which reduce the yield by up to 90%. Various strategies like conventional breeding, molecular breeding, and modern plant breeding have been used to overcome these problems. Conventionally, breeding programs aim at development of varieties that combine maximum number of traits through inter-specific hybridization, wide hybridization, and hybridization involving more than two parents. Breeding is difficult in this crop because of its self-pollinating nature and limited genetic variation. Recent advances in in vitro culture and gene technologies offer unique opportunities to realize the full potential of chickpea production. However, as of date, no transgenic chickpea variety has been approved for cultivation in the world. In this review, we provide an update on the development of genetically modified chickpea plants, including those resistant to Helicoverpa armigera, Callosobruchus maculatus, Aphis craccivora, as well as to drought and salt stress. The genes utilized for development of resistance against pod borer, bruchid, aphid, drought, and salt tolerance, namely, Bt, alpha amylase inhibitor, ASAL, P5CSF129A, and P5CS, respectively, are discussed.
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Danilevicz MF, Moharana KC, Venancio TM, Franco LO, Cardoso SRS, Cardoso M, Thiebaut F, Hemerly AS, Prosdocimi F, Ferreira PCG. Copaifera langsdorffii Novel Putative Long Non-Coding RNAs: Interspecies Conservation Analysis in Adaptive Response to Different Biomes. Noncoding RNA 2018; 4:ncrna4040027. [PMID: 30297664 PMCID: PMC6316758 DOI: 10.3390/ncrna4040027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/26/2018] [Accepted: 09/28/2018] [Indexed: 12/20/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in multiple regulatory pathways and its versatile form of action has disclosed a new layer in gene regulation. LncRNAs have their expression levels modulated during plant development, and in response to stresses with tissue-specific functions. In this study, we analyzed lncRNA from leaf samples collected from the legume Copaifera langsdorffii Desf. (copaíba) present in two divergent ecosystems: Cerrado (CER; Ecological Station of Botanical Garden in Brasília, Brazil) and Atlantic Rain Forest (ARF; Rio de Janeiro, Brazil). We identified 8020 novel lncRNAs, and they were compared to seven Fabaceae genomes and transcriptomes, to which 1747 and 2194 copaíba lncRNAs were mapped, respectively, to at least one species. The secondary structures of the lncRNAs that were conserved and differentially expressed between the populations were predicted using in silico methods. A few selected lncRNA were confirmed by RT-qPCR in the samples from both biomes; Additionally, the analysis of the lncRNA sequences predicted that some might act as microRNA (miRNA) targets or decoys. The emerging studies involving lncRNAs function and conservation have shown their involvement in several types of biotic and abiotic stresses. Thus, the conservation of lncRNAs among Fabaceae species considering their rapid turnover, suggests they are likely to have been under functional conservation pressure. Our results indicate the potential involvement of lncRNAs in the adaptation of C. langsdorffii in two different biomes.
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Affiliation(s)
- Monica F Danilevicz
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
| | - Kanhu C Moharana
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro 28013-602, Brazil.
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro 28013-602, Brazil.
| | - Luciana O Franco
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Diretoria de Pesquisa Científica, Rio de Janeiro 22460-030, Brazil.
| | - Sérgio R S Cardoso
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Diretoria de Pesquisa Científica, Rio de Janeiro 22460-030, Brazil.
| | - Mônica Cardoso
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Diretoria de Pesquisa Científica, Rio de Janeiro 22460-030, Brazil.
| | - Flávia Thiebaut
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
| | - Adriana S Hemerly
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
| | - Francisco Prosdocimi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
| | - Paulo C G Ferreira
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
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Basu U, Srivastava R, Bajaj D, Thakro V, Daware A, Malik N, Upadhyaya HD, Parida SK. Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea. Sci Rep 2018; 8:13240. [PMID: 30185866 PMCID: PMC6125345 DOI: 10.1038/s41598-018-29926-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 06/18/2018] [Indexed: 01/21/2023] Open
Abstract
We discovered 2150 desi and 2199 kabuli accessions-derived SNPs by cultivar-wise individual assembling of sequence-reads generated through genotyping-by-sequencing of 92 chickpea accessions. Subsequent large-scale validation and genotyping of these SNPs discovered 619 desi accessions-derived (DAD) SNPs, 531 kabuli accessions-derived (KAD) SNPs, 884 multiple accessions-derived (MAD) SNPs and 1083 two accessions (desi ICC 4958 and kabuli CDC Frontier)-derived (TAD) SNPs that were mapped on eight chromosomes. These informative SNPs were annotated in coding/non-coding regulatory sequence components of genes. The MAD-SNPs were efficient to detect high intra-specific polymorphic potential and wide natural allelic diversity level including high-resolution admixed-population genetic structure and precise phylogenetic relationship among 291 desi and kabuli accessions. This signifies their effectiveness in introgression breeding and varietal improvement studies targeting useful agronomic traits of chickpea. Six trait-associated genes with SNPs including quantitative trait nucleotides (QTNs) in combination explained 27.5% phenotypic variation for seed yield per plant (SYP). A pentatricopeptide repeat (PPR) gene with a synonymous-coding SNP/QTN significantly associated with SYP trait was found most-promising in chickpea. The essential information delineated can be of immense utility in genomics-assisted breeding applications to develop high-yielding chickpea cultivars.
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Affiliation(s)
- Udita Basu
- 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
| | - Deepak Bajaj
- 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
| | - Anurag Daware
- 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
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, Telangana, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Mehta CM, Pudake RN, Srivastava R, Palni U, Sharma AK. Development of PCR-based molecular marker for screening of disease-suppressive composts against Fusarium wilt of tomato ( Solanum lycopersicum L.). 3 Biotech 2018; 8:306. [PMID: 30002996 PMCID: PMC6035786 DOI: 10.1007/s13205-018-1331-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/02/2018] [Indexed: 10/28/2022] Open
Abstract
The present study was carried out to develop a PCR-based molecular marker suitable for screening of disease-suppressive composts against Fusarium wilt of tomato. An effective uncultured bacterial community was screened from our previous study on investigation of microbial communities in composts for their potential for biocontrol of Fusarium wilt. Based on available sequence information (Accession no. HQ388491) of selective community, PCR-based molecular markers were designed and tested for their specificity in different compost sample. To confirm specificity of designed marker, real-time reverse transcription-PCR (qRT-PCR) analysis was performed. Selective marker efficacy was further tested for different set of composts and results were cross-verified by conducting bioassay of same composts against Fusarium wilt in tomato crop. Results showed that out of two designed set of primers (i.e., PAC1F/PAC1R and PAC4F/PAC4R), primer set PAC4F/PAC4R resulted in successful amplification of 199 bp in highly disease-suppressive compost (i.e., CPP); however, no/below detection level amplification was observed in non-suppressive compost (JC). qRT-PCR analysis confirmed the specificity of selective marker by representing single peak in melting curve. A clear difference was observed in relative population of selective community in different set of composts. It was observed maximum in the most effective compost, i.e., CPP followed by other disease-suppressive composts. Cross-examination of results with bioassay confirmed that composts with presence of selective bacterial community having no/very less disease incidence of Fusarium. It is clearly evident from the study that such kind of molecular markers can be developed and used in future research focusing on compost-based disease suppression.
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Affiliation(s)
- C. M. Mehta
- Department of Biological Sciences, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, U. S. Nagar, Pantnagar, Uttarakhand 263145 India
- Department of Botany, DSB Campus, Kumaun University, Nainital, Uttarakhand 263002 India
- School of Agriculture, Lovely Professional University, Phagwara, Punjab 144411 India
| | - Ramesh N. Pudake
- Amity Institute of Nanotechnology, Amity University Uttar Pradesh, Noida, UP 201313 India
| | - Rashmi Srivastava
- Department of Biological Sciences, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, U. S. Nagar, Pantnagar, Uttarakhand 263145 India
| | - Uma Palni
- Department of Botany, DSB Campus, Kumaun University, Nainital, Uttarakhand 263002 India
| | - Anil K. Sharma
- Department of Biological Sciences, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, U. S. Nagar, Pantnagar, Uttarakhand 263145 India
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35
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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: 9] [Impact Index Per Article: 1.5] [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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Leonetti P, Accotto GP, Hanafy MS, Pantaleo V. Viruses and Phytoparasitic Nematodes of Cicer arietinum L.: Biotechnological Approaches in Interaction Studies and for Sustainable Control. FRONTIERS IN PLANT SCIENCE 2018; 9:319. [PMID: 29599788 PMCID: PMC5862823 DOI: 10.3389/fpls.2018.00319] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 02/27/2018] [Indexed: 05/31/2023]
Abstract
Cicer arietinum L. (chickpea) is the world's fourth most widely grown pulse. Chickpea seeds are a primary source of dietary protein for humans, and chickpea cultivation contributes to biological nitrogen fixation in the soil, given its symbiotic relationship with rhizobia. Therefore, chickpea cultivation plays a pivotal role in innovative sustainable models of agro-ecosystems inserted in crop rotation in arid and semi-arid environments for soil improvement and the reduction of chemical inputs. Indeed, the arid and semi-arid tropical zones of Africa and Asia have been primary areas of cultivation and diversification. Yet, nowadays, chickpea is gaining prominence in Canada, Australia, and South America where it constitutes a main ingredient in vegetarian and vegan diets. Viruses and plant parasitic nematodes (PPNs) have been considered to be of minor and local impact in primary areas of cultivation. However, the introduction of chickpea in new environments exposes the crop to these biotic stresses, compromising its yields. The adoption of high-throughput genomic technologies, including genome and transcriptome sequencing projects by the chickpea research community, has provided major insights into genome evolution as well as genomic architecture and domestication. This review summarizes the major viruses and PPNs that affect chickpea cultivation worldwide. We also present an overview of the current state of chickpea genomics. Accordingly, we explore the opportunities that genomics, post-genomics and novel editing biotechnologies are offering in order to understand chickpea diseases and stress tolerance and to design innovative control strategies.
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Affiliation(s)
- Paola Leonetti
- Institute for Sustainable Plant Protection, Research Unit of Bari, National Research Council, Bari, Italy
| | - Gian Paolo Accotto
- Institute for Sustainable Plant Protection, Research Unit of Turin, National Research Council, Turin, Italy
| | - Moemen S. Hanafy
- Department of Plant Biotechnology, National Research Centre, Cairo, Egypt
| | - Vitantonio Pantaleo
- Institute for Sustainable Plant Protection, Research Unit of Bari, National Research Council, Bari, Italy
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Li Y, Ruperao P, Batley J, Edwards D, Khan T, Colmer TD, Pang J, Siddique KHM, Sutton T. Investigating Drought Tolerance in Chickpea Using Genome-Wide Association Mapping and Genomic Selection Based on Whole-Genome Resequencing Data. FRONTIERS IN PLANT SCIENCE 2018; 9:190. [PMID: 29515606 PMCID: PMC5825913 DOI: 10.3389/fpls.2018.00190] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/01/2018] [Indexed: 05/06/2023]
Abstract
Drought tolerance is a complex trait that involves numerous genes. Identifying key causal genes or linked molecular markers can facilitate the fast development of drought tolerant varieties. Using a whole-genome resequencing approach, we sequenced 132 chickpea varieties and advanced breeding lines and found more than 144,000 single nucleotide polymorphisms (SNPs). We measured 13 yield and yield-related traits in three drought-prone environments of Western Australia. The genotypic effects were significant for all traits, and many traits showed highly significant correlations, ranging from 0.83 between grain yield and biomass to -0.67 between seed weight and seed emergence rate. To identify candidate genes, the SNP and trait data were incorporated into the SUPER genome-wide association study (GWAS) model, a modified version of the linear mixed model. We found that several SNPs from auxin-related genes, including auxin efflux carrier protein (PIN3), p-glycoprotein, and nodulin MtN21/EamA-like transporter, were significantly associated with yield and yield-related traits under drought-prone environments. We identified four genetic regions containing SNPs significantly associated with several different traits, which was an indication of pleiotropic effects. We also investigated the possibility of incorporating the GWAS results into a genomic selection (GS) model, which is another approach to deal with complex traits. Compared to using all SNPs, application of the GS model using subsets of SNPs significantly associated with the traits under investigation increased the prediction accuracies of three yield and yield-related traits by more than twofold. This has important implication for implementing GS in plant breeding programs.
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Affiliation(s)
- Yongle Li
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Pradeep Ruperao
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Tanveer Khan
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Timothy D. Colmer
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Jiayin Pang
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Tim Sutton
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
- South Australian Research and Development Institute, Adelaide, SA, Australia
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Genetic dissection of plant growth habit in chickpea. Funct Integr Genomics 2017; 17:711-723. [PMID: 28600722 DOI: 10.1007/s10142-017-0566-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/01/2017] [Accepted: 05/26/2017] [Indexed: 12/17/2022]
Abstract
A combinatorial genomics-assisted breeding strategy encompassing association analysis, genetic mapping and expression profiling is found most promising for quantitative dissection of complex traits in crop plants. The present study employed GWAS (genome-wide association study) using 24,405 SNPs (single nucleotide polymorphisms) obtained with genotyping-by-sequencing (GBS) of 92 sequenced desi and kabuli accessions of chickpea. This identified eight significant genomic loci associated with erect (E)/semi-erect (SE) vs. spreading (S)/semi-spreading (SS)/prostrate (P) plant growth habit (PGH) trait differentiation regardless of diverse desi and kabuli genetic backgrounds of chickpea. These associated SNPs in combination explained 23.8% phenotypic variation for PGH in chickpea. Five PGH-associated genes were validated successfully in E/SE and SS/S/P PGH-bearing parental accessions and homozygous individuals of three intra- and interspecific RIL (recombinant inbred line) mapping populations as well as 12 contrasting desi and kabuli chickpea germplasm accessions by selective genotyping through Sequenom MassARRAY. The shoot apical, inflorescence and floral meristems-specific expression, including upregulation (seven-fold) of five PGH-associated genes especially in germplasm accessions and homozygous RIL mapping individuals contrasting with E/SE PGH traits was apparent. Collectively, this integrated genomic strategy delineated diverse non-synonymous SNPs from five candidate genes with strong allelic effects on PGH trait variation in chickpea. Of these, two vernalization-responsive non-synonymous SNP alleles carrying SNF2 protein-coding gene and B3 transcription factor associated with PGH traits were found to be the most promising in chickpea. The SNP allelic variants associated with E/SE/SS/S PGH trait differentiation were exclusively present in all cultivated desi and kabuli chickpea accessions while wild species/accessions belonging to primary, secondary and tertiary gene pools mostly contained prostrate PGH-associated SNP alleles. This indicates strong adaptive natural/artificial selection pressure (Tajima's D 3.15 to 4.57) on PGH-associated target genomic loci during chickpea domestication. These vital leads thus have potential to decipher complex transcriptional regulatory gene function of PGH trait differentiation and for understanding the selective sweep-based PGH trait evolution and domestication pattern in cultivated and wild chickpea accessions adapted to diverse agroclimatic conditions. Collectively, the essential inputs generated will be of profound use in marker-assisted genetic enhancement to develop cultivars with desirable plant architecture of erect growth habit types in chickpea.
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Gupta S, Bhar A, Chatterjee M, Ghosh A, Das S. Transcriptomic dissection reveals wide spread differential expression in chickpea during early time points of Fusarium oxysporum f. sp. ciceri Race 1 attack. PLoS One 2017; 12:e0178164. [PMID: 28542579 PMCID: PMC5460890 DOI: 10.1371/journal.pone.0178164] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 05/09/2017] [Indexed: 12/19/2022] Open
Abstract
Plants' reaction to underground microorganisms is complex as sessile nature of plants compels them to prioritize their responses to diverse microorganisms both pathogenic and symbiotic. Roots of important crops are directly exposed to diverse microorganisms, but investigations involving root pathogens are significantly less. Thus, more studies involving root pathogens and their target crops are necessitated to enrich the understanding of underground interactions. Present study reported the molecular complexities in chickpea during Fusarium oxysporum f. sp. ciceri Race 1 (Foc1) infection. Transcriptomic dissections using RNA-seq showed significantly differential expression of molecular transcripts between infected and control plants of both susceptible and resistant genotypes. Radar plot analyses showed maximum expressional undulations after infection in both susceptible and resistant plants. Gene ontology and functional clustering showed large number of transcripts controlling basic metabolism of plants. Network analyses demonstrated defense components like peptidyl cis/trans isomerase, MAP kinase, beta 1,3 glucanase, serine threonine kinase, patatin like protein, lactolylglutathione lyase, coproporphyrinogen III oxidase, sulfotransferases; reactive oxygen species regulating components like respiratory burst oxidase, superoxide dismutases, cytochrome b5 reductase, glutathione reductase, thioredoxin reductase, ATPase; metabolism regulating components, myo inositol phosphate, carboxylate synthase; transport related gamma tonoplast intrinsic protein, and structural component, ubiquitins to serve as important nodals of defense signaling network. These nodal molecules probably served as hub controllers of defense signaling. Functional characterization of these hub molecules would not only help in developing better understanding of chickpea-Foc1 interaction but also place them as promising candidates for resistance management programs against vascular wilt of legumes.
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Affiliation(s)
- Sumanti Gupta
- Division of Plant Biology, Bose Institute, Centenary Campus, P 1/12, CIT Scheme, VII-M, Kankurgachi, Kolkata, West Bengal, India
| | - Anirban Bhar
- Division of Plant Biology, Bose Institute, Centenary Campus, P 1/12, CIT Scheme, VII-M, Kankurgachi, Kolkata, West Bengal, India
| | - Moniya Chatterjee
- Division of Plant Biology, Bose Institute, Centenary Campus, P 1/12, CIT Scheme, VII-M, Kankurgachi, Kolkata, West Bengal, India
| | - Amartya Ghosh
- Division of Plant Biology, Bose Institute, Centenary Campus, P 1/12, CIT Scheme, VII-M, Kankurgachi, Kolkata, West Bengal, India
| | - Sampa Das
- Division of Plant Biology, Bose Institute, Centenary Campus, P 1/12, CIT Scheme, VII-M, Kankurgachi, Kolkata, West Bengal, India
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Muñoz N, Liu A, Kan L, Li MW, Lam HM. Potential Uses of Wild Germplasms of Grain Legumes for Crop Improvement. Int J Mol Sci 2017; 18:E328. [PMID: 28165413 PMCID: PMC5343864 DOI: 10.3390/ijms18020328] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 01/26/2017] [Accepted: 01/26/2017] [Indexed: 01/14/2023] Open
Abstract
Challenged by population increase, climatic change, and soil deterioration, crop improvement is always a priority in securing food supplies. Although the production of grain legumes is in general lower than that of cereals, the nutritional value of grain legumes make them important components of food security. Nevertheless, limited by severe genetic bottlenecks during domestication and human selection, grain legumes, like other crops, have suffered from a loss of genetic diversity which is essential for providing genetic materials for crop improvement programs. Illustrated by whole-genome-sequencing, wild relatives of crops adapted to various environments were shown to maintain high genetic diversity. In this review, we focused on nine important grain legumes (soybean, peanut, pea, chickpea, common bean, lentil, cowpea, lupin, and pigeonpea) to discuss the potential uses of their wild relatives as genetic resources for crop breeding and improvement, and summarized the various genetic/genomic approaches adopted for these purposes.
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Affiliation(s)
- Nacira Muñoz
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
- Centro de Investigaciones Agropecuarias-INTA, Instituto de Fisiología y Recursos Genéticos Vegetales, Córdoba X5000, Argentina.
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba X5000, Argentina.
| | - Ailin Liu
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Leo Kan
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Man-Wah Li
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Hon-Ming Lam
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
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Roorkiwal M, Rathore A, Das RR, Singh MK, Jain A, Srinivasan S, Gaur PM, Chellapilla B, Tripathi S, Li Y, Hickey JM, Lorenz A, Sutton T, Crossa J, Jannink JL, Varshney RK. Genome-Enabled Prediction Models for Yield Related Traits in Chickpea. FRONTIERS IN PLANT SCIENCE 2016; 7:1666. [PMID: 27920780 PMCID: PMC5118446 DOI: 10.3389/fpls.2016.01666] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/24/2016] [Indexed: 05/20/2023]
Abstract
Genomic selection (GS) unlike marker-assisted backcrossing (MABC) predicts breeding values of lines using genome-wide marker profiling and allows selection of lines prior to field-phenotyping, thereby shortening the breeding cycle. A collection of 320 elite breeding lines was selected and phenotyped extensively for yield and yield related traits at two different locations (Delhi and Patancheru, India) during the crop seasons 2011-12 and 2012-13 under rainfed and irrigated conditions. In parallel, these lines were also genotyped using DArTseq platform to generate genotyping data for 3000 polymorphic markers. Phenotyping and genotyping data were used with six statistical GS models to estimate the prediction accuracies. GS models were tested for four yield related traits viz. seed yield, 100 seed weight, days to 50% flowering and days to maturity. Prediction accuracy for the models tested varied from 0.138 (seed yield) to 0.912 (100 seed weight), whereas performance of models did not show any significant difference for estimating prediction accuracy within traits. Kinship matrix calculated using genotyping data reaffirmed existence of two different groups within selected lines. There was not much effect of population structure on prediction accuracy. In brief, present study establishes the necessary resources for deployment of GS in chickpea breeding.
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Affiliation(s)
- Manish Roorkiwal
- Research Program-Grain Legumes, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Abhishek Rathore
- Research Program-Grain Legumes, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Roma R. Das
- Research Program-Grain Legumes, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Muneendra K. Singh
- Research Program-Grain Legumes, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Ankit Jain
- Research Program-Grain Legumes, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Samineni Srinivasan
- Research Program-Grain Legumes, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Pooran M. Gaur
- Research Program-Grain Legumes, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | | | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research InstituteDelhi, India
| | - Yongle Li
- Australian Centre for Plant Functional Genomics, University of AdelaideAdelaide, SA, Australia
| | - John M. Hickey
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of EdinburghEaster Bush, UK
| | - Aaron Lorenz
- Department of Agronomy and Horticulture, University of NebraskaLincoln, OR, USA
| | - Tim Sutton
- Australian Centre for Plant Functional Genomics, University of AdelaideAdelaide, SA, Australia
- Crop Improvement, South Australian Research and Development InstituteUrrbrae, SA, Australia
| | - Jose Crossa
- International Maize and Wheat Improvement CenterMexico, Mexico
| | - Jean-Luc Jannink
- School of Integrative Plant Science, Cornell UniversityIthaca, NY, USA
| | - Rajeev K. Varshney
- Research Program-Grain Legumes, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- School of Plant Biology and Institute of Agriculture, The University of Western AustraliaWestern Australia WA, Australia
- *Correspondence: Rajeev K. Varshney
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Varshney RK, Ribaut JM, Buckler ES, Tuberosa R, Rafalski JA, Langridge P. Can genomics boost productivity of orphan crops? Nat Biotechnol 2012; 30:1172-1176. [PMID: 23222781 DOI: 10.1007/978-3-319-66117-9_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Affiliation(s)
- Rajeev K Varshney
- Center of Excellence in Genomics (CEG), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
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