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Khassanova G, Oshergina I, Ten E, Jatayev S, Zhanbyrshina N, Gabdola A, Gupta NK, Schramm C, Pupulin A, Philp-Dutton L, Anderson P, Sweetman C, Jenkins CL, Soole KL, Shavrukov Y. Zinc finger knuckle genes are associated with tolerance to drought and dehydration in chickpea ( Cicer arietinum L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1354413. [PMID: 38766473 PMCID: PMC11099236 DOI: 10.3389/fpls.2024.1354413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/17/2024] [Indexed: 05/22/2024]
Abstract
Chickpea (Cicer arietinum L.) is a very important food legume and needs improved drought tolerance for higher seed production in dry environments. The aim of this study was to determine diversity and genetic polymorphism in zinc finger knuckle genes with CCHC domains and their functional analysis for practical improvement of chickpea breeding. Two CaZF-CCHC genes, Ca04468 and Ca07571, were identified as potentially important candidates associated with plant responses to drought and dehydration. To study these genes, various methods were used including Sanger sequencing, DArT (Diversity array technology) and molecular markers for plant genotyping, gene expression analysis using RT-qPCR, and associations with seed-related traits in chickpea plants grown in field trials. These genes were studied for genetic polymorphism among a set of chickpea accessions, and one SNP was selected for further study from four identified SNPs between the promoter regions of each of the two genes. Molecular markers were developed for the SNP and verified using the ASQ and CAPS methods. Genotyping of parents and selected breeding lines from two hybrid populations, and SNP positions on chromosomes with haplotype identification, were confirmed using DArT microarray analysis. Differential expression profiles were identified in the parents and the hybrid populations under gradual drought and rapid dehydration. The SNP-based genotypes were differentially associated with seed weight per plant but not with 100 seed weight. The two developed and verified SNP molecular markers for both genes, Ca04468 and Ca07571, respectively, could be used for marker-assisted selection in novel chickpea cultivars with improved tolerance to drought and dehydration.
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Affiliation(s)
- Gulmira Khassanova
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical Research University, Astana, Kazakhstan
- Department of Crop Breeding, A.I.Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Irina Oshergina
- Department of Crop Breeding, A.I.Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Evgeniy Ten
- Department of Crop Breeding, A.I.Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical Research University, Astana, Kazakhstan
| | - Nursaule Zhanbyrshina
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical Research University, Astana, Kazakhstan
| | - Ademi Gabdola
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical Research University, Astana, Kazakhstan
| | - Narendra K. Gupta
- Department of Plant Physiology, Sri Karan Narendra (SNK) Agricultural University, Jobster, Rajastan, India
| | - Carly Schramm
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Antonio Pupulin
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Lauren Philp-Dutton
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Peter Anderson
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Crystal Sweetman
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Colin L.D. Jenkins
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Kathleen L. Soole
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Yuri Shavrukov
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
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Rahman MW, Deokar AA, Lindsay D, Tar’an B. Novel Alleles from Cicer reticulatum L. for Genetic Improvement of Cultivated Chickpeas Identified through Genome Wide Association Analysis. Int J Mol Sci 2024; 25:648. [PMID: 38203819 PMCID: PMC10779240 DOI: 10.3390/ijms25010648] [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: 11/14/2023] [Revised: 12/24/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024] Open
Abstract
The availability of wild chickpea (Cicer reticulatum L.) accessions has the potential to be used for the improvement of important traits in cultivated chickpeas. The main objectives of this study were to evaluate the phenotypic and genetic variations of chickpea progeny derived from interspecific crosses between C. arietinum and C. reticulatum, and to establish the association between single nucleotide polymorphism (SNP) markers and a series of important agronomic traits in chickpea. A total of 486 lines derived from interspecific crosses between C. arietinum (CDC Leader) and 20 accessions of C. reticulatum were evaluated at different locations in Saskatchewan, Canada in 2017 and 2018. Significant variations were observed for seed weight per plant, number of seeds per plant, thousand seed weight, and plant biomass. Path coefficient analysis showed significant positive direct effects of the number of seeds per plant, thousand seed weight, and biomass on the total seed weight. Cluster analysis based on the agronomic traits generated six groups that allowed the identification of potential heterotic groups within the interspecific lines for yield improvement and resistance to ascochyta blight disease. Genotyping of the 381 interspecific lines using a modified genotyping by sequencing (tGBS) generated a total of 14,591 SNPs. Neighbour-joining cluster analysis using the SNP data grouped the lines into 20 clusters. The genome wide association analysis identified 51 SNPs that had significant associations with different traits. Several candidate genes associated with early flowering and yield components were identified. The candidate genes and the significant SNP markers associated with different traits have a potential to aid the trait introgression in the breeding program.
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Affiliation(s)
| | | | | | - Bunyamin Tar’an
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
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Susmitha P, Kumar P, Yadav P, Sahoo S, Kaur G, Pandey MK, Singh V, Tseng TM, Gangurde SS. Genome-wide association study as a powerful tool for dissecting competitive traits in legumes. FRONTIERS IN PLANT SCIENCE 2023; 14:1123631. [PMID: 37645459 PMCID: PMC10461012 DOI: 10.3389/fpls.2023.1123631] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/08/2023] [Indexed: 08/31/2023]
Abstract
Legumes are extremely valuable because of their high protein content and several other nutritional components. The major challenge lies in maintaining the quantity and quality of protein and other nutritional compounds in view of climate change conditions. The global need for plant-based proteins has increased the demand for seeds with a high protein content that includes essential amino acids. Genome-wide association studies (GWAS) have evolved as a standard approach in agricultural genetics for examining such intricate characters. Recent development in machine learning methods shows promising applications for dimensionality reduction, which is a major challenge in GWAS. With the advancement in biotechnology, sequencing, and bioinformatics tools, estimation of linkage disequilibrium (LD) based associations between a genome-wide collection of single-nucleotide polymorphisms (SNPs) and desired phenotypic traits has become accessible. The markers from GWAS could be utilized for genomic selection (GS) to predict superior lines by calculating genomic estimated breeding values (GEBVs). For prediction accuracy, an assortment of statistical models could be utilized, such as ridge regression best linear unbiased prediction (rrBLUP), genomic best linear unbiased predictor (gBLUP), Bayesian, and random forest (RF). Both naturally diverse germplasm panels and family-based breeding populations can be used for association mapping based on the nature of the breeding system (inbred or outbred) in the plant species. MAGIC, MCILs, RIAILs, NAM, and ROAM are being used for association mapping in several crops. Several modifications of NAM, such as doubled haploid NAM (DH-NAM), backcross NAM (BC-NAM), and advanced backcross NAM (AB-NAM), have also been used in crops like rice, wheat, maize, barley mustard, etc. for reliable marker-trait associations (MTAs), phenotyping accuracy is equally important as genotyping. Highthroughput genotyping, phenomics, and computational techniques have advanced during the past few years, making it possible to explore such enormous datasets. Each population has unique virtues and flaws at the genomics and phenomics levels, which will be covered in more detail in this review study. The current investigation includes utilizing elite breeding lines as association mapping population, optimizing the choice of GWAS selection, population size, and hurdles in phenotyping, and statistical methods which will analyze competitive traits in legume breeding.
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Affiliation(s)
- Pusarla Susmitha
- Regional Agricultural Research Station, Acharya N.G. Ranga Agricultural University, Andhra Pradesh, India
| | - Pawan Kumar
- Department of Genetics and Plant Breeding, College of Agriculture, Chaudhary Charan Singh (CCS) Haryana Agricultural University, Hisar, India
| | - Pankaj Yadav
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Rajasthan, India
| | - Smrutishree Sahoo
- Department of Genetics and Plant Breeding, School of Agriculture, Gandhi Institute of Engineering and Technology (GIET) University, Odisha, India
| | - Gurleen Kaur
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Manish K. Pandey
- Department of Genomics, Prebreeding and Bioinformatics, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Varsha Singh
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS, United States
| | - Te Ming Tseng
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS, United States
| | - Sunil S. Gangurde
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
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Mir AH, Bhat MA, Fayaz H, Wani AA, Dar SA, Maqbool S, Yasin M, Mir JI, Khan MA, Sofi PA, El-Sappah AH, Thudi M, Varshney RK, Mir RR. SSR markers in revealing extent of genetic diversity and phylogenetic relationships among chickpea core collection accessions for Western Himalayas. Mol Biol Rep 2022; 49:11469-11479. [PMID: 36006503 DOI: 10.1007/s11033-022-07858-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 08/11/2022] [Indexed: 10/15/2022]
Abstract
BACKGROUND The exploration of genetic diversity is the key source of germplasm conservation and potential to broaden its genetic base. The globally growing demand for chickpea suggests superior/climate-resilient varieties, which in turn necessitates the germplasm characterization to unravel underlying genetic variation. METHODOLOGY AND RESULTS A chickpea core collection comprising of diverse 192 accessions which include cultivated Cicer arietinum, and wild C. reticulatum, C. echinospermum, and C. microphyllum species were investigated to analyze their genetic diversity and relationship, by assaying 33 unlinked simple sequence repeat (SSR) markers. The results amplified a total of 323 alleles (Na), ranging from 2 to 8 with an average of 4.25 alleles per locus. Expected heterozygosity (He) differed from 0.46 to 0.86 with an average of 0.68. Polymorphic information content (PIC) ranged from 0.73 to 0.98 with an average of 0.89. Analysis of molecular variance (AMOVA) showed that most of the variation was among individuals (87%). Cluster analysis resulted in the formation of four distinct clusters. Cluster I represented all cultivated and clusters II, III, and IV comprised a heterogeneous group of cultivated and wild chickpea accessions. CONCLUSION We report considerable diversity and greater resolving power of SSR markers for assessing variability and interrelationship among the chickpea accessions. The chickpea core is expected to be an efficient resource for breeders for broadening the chickpea genetic base and could be useful for selective breeding of desirable traits and in the identification of target genes for genomics-assisted breeding.
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Affiliation(s)
- Asma Hamid Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir, Wadura Campus, Sopore, Kashmir, India
| | - Mohd Ashraf Bhat
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir, Wadura Campus, Sopore, Kashmir, India
| | - Humara Fayaz
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir, Wadura Campus, Sopore, Kashmir, India.,Department of Botany, Cytogenetics and Reproductive Biology Laboratory, University of Kashmir, Srinagar, Kashmir, India
| | - Aijaz A Wani
- Department of Botany, Cytogenetics and Reproductive Biology Laboratory, University of Kashmir, Srinagar, Kashmir, India
| | - Sher A Dar
- Dryland Agriculture Research Station (DARS), SKUAST-Kashmir, Budgam, Kashmir, India
| | - Showkat Maqbool
- Division of Animal Genetics and Breeding, SKUAST-Kashmir, FVSc & AH, Shuhama, Srinagar, Kashmir, India
| | - Mohammad Yasin
- Rafi Amhad Kidwai (RAK) College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya (RVSKV), Sehore, Madhya Pradesh, India
| | - Javid Iqbal Mir
- ICAR-Central Institute of Temperate Horticulture (CITH), Srinagar, Kashmir, India
| | - Mohd Anwar Khan
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir, Wadura Campus, Sopore, Kashmir, India
| | - Parvaze A Sofi
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir, Wadura Campus, Sopore, Kashmir, India
| | - Ahmed H El-Sappah
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Mahendar Thudi
- Center of Excellence in Genomics & Systems Biology (CEGSB), Iinternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India.,Department of Agricultural Biotechnology and Biotechnology, Rajendra Prasad Central Agricultural University, Pusa, Samasthipur, Bihar, India
| | - Rajeev Kumar Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB), Iinternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India.,State Agricultural Biotechnology Centre, Crop & Food Innovation Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir, Wadura Campus, Sopore, Kashmir, 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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Chandana BS, Mahto RK, Singh RK, Ford R, Vaghefi N, Gupta SK, Yadav HK, Manohar M, Kumar R. Epigenomics as Potential Tools for Enhancing Magnitude of Breeding Approaches for Developing Climate Resilient Chickpea. Front Genet 2022; 13:900253. [PMID: 35937986 PMCID: PMC9355295 DOI: 10.3389/fgene.2022.900253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/10/2022] [Indexed: 11/30/2022] Open
Abstract
Epigenomics has become a significant research interest at a time when rapid environmental changes are occurring. Epigenetic mechanisms mainly result from systems like DNA methylation, histone modification, and RNA interference. Epigenetic mechanisms are gaining importance in classical genetics, developmental biology, molecular biology, cancer biology, epidemiology, and evolution. Epigenetic mechanisms play important role in the action and interaction of plant genes during development, and also have an impact on classical plant breeding programs, inclusive of novel variation, single plant heritability, hybrid vigor, plant-environment interactions, stress tolerance, and performance stability. The epigenetics and epigenomics may be significant for crop adaptability and pliability to ambient alterations, directing to the creation of stout climate-resilient elegant crop cultivars. In this review, we have summarized recent progress made in understanding the epigenetic mechanisms in plant responses to biotic and abiotic stresses and have also tried to provide the ways for the efficient utilization of epigenomic mechanisms in developing climate-resilient crop cultivars, especially in chickpea, and other legume crops.
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Affiliation(s)
- B. S. Chandana
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | | | | | - Rebecca Ford
- Center for Planetary Health and Food Security, Griffith University, Brisbane, QLD, Australia
| | - Niloofar Vaghefi
- School of Agriculture and Food, University of Melbourne, Parkville, VIC, Australia
| | | | | | - Murli Manohar
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Rajendra Kumar
- Indian Agricultural Research Institute (ICAR), New Delhi, India
- *Correspondence: Rajendra Kumar,
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Hellwig T, Abbo S, Ophir R. Phylogeny and disparate selection signatures suggest two genetically independent domestication events in pea (Pisum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:419-439. [PMID: 35061306 PMCID: PMC9303476 DOI: 10.1111/tpj.15678] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 01/15/2022] [Indexed: 05/25/2023]
Abstract
Domestication is considered a model of adaptation that can be used to draw conclusions about the modus operandi of selection in natural systems. Investigating domestication may give insights into how plants react to different intensities of human manipulation, which has direct implication for the continuing efforts of crop improvement. Therefore, scientists of various disciplines study domestication-related questions to understand the biological and cultural bases of the domestication process. We employed restriction site-associated DNA sequencing (RAD-seq) of 494 Pisum sativum (pea) samples from all wild and domesticated groups to analyze the genetic structure of the collection. Patterns of ancient admixture were investigated by analysis of admixture graphs. We used two complementary approaches, one diversity based and one based on differentiation, to detect the selection signatures putatively associated with domestication. An analysis of the subpopulation structure of wild P. sativum revealed five distinct groups with a notable geographic pattern. Pisum abyssinicum clustered unequivocally within the P. sativum complex, without any indication of hybrid origin. We detected 32 genomic regions putatively subjected to selection: 29 in P. sativum ssp. sativum and three in P. abyssinicum. The two domesticated groups did not share regions under selection and did not display similar haplotype patterns within those regions. Wild P. sativum is structured into well-diverged subgroups. Although Pisum sativum ssp. humile is not supported as a taxonomic entity, the so-called 'southern humile' is a genuine wild group. Introgression did not shape the variation observed within the sampled germplasm. The two domesticated pea groups display distinct genetic bases of domestication, suggesting two genetically independent domestication events.
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Affiliation(s)
- Timo Hellwig
- The Levi Eshkol School of AgricultureThe Hebrew University of JerusalemJerusalem, RehovotIsrael
- Volcani Center, Agricultural Research OrganizationRishon LeZionIsrael
- Institute of Plant Genetics, Heinrich‐Heine‐UniversityDüsseldorfGermany
| | - Shahal Abbo
- The Levi Eshkol School of AgricultureThe Hebrew University of JerusalemJerusalem, RehovotIsrael
| | - Ron Ophir
- Volcani Center, Agricultural Research OrganizationRishon LeZionIsrael
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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: 1] [Impact Index Per Article: 0.3] [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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Genetic Structure of Wild Germplasm of Macadamia: Species Assignment, Diversity and Phylogeographic Relationships. PLANTS 2020; 9:plants9060714. [PMID: 32503327 PMCID: PMC7355489 DOI: 10.3390/plants9060714] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 05/29/2020] [Accepted: 05/30/2020] [Indexed: 11/25/2022]
Abstract
Macadamia is an Australian native rainforest tree that has been domesticated and traded internationally for its premium nuts. Common cultivars rely upon a limited gene pool that has exploited only two of the four species. Introducing a more diverse germplasm will broaden the genetic base for future crop improvement and better adaptation for changing environments. This study investigated the genetic structure of 302 accessions of wild germplasm using 2872 SNP and 8415 silicoDArT markers. Structure analysis and principal coordinate analysis (PCoA) assigned the 302 accessions into four distinct groups: (i) Macadamia integrifolia, (ii) M. tetraphylla, and (iii) M. jansenii and M. ternifolia, and (iv) admixtures or hybrids. Assignment of the four species matched well with previous characterisations, except for one M. integrifolia and four M. tetraphylla accessions. Using SNP markers, 94 previously unidentified accessions were assigned into the four distinct groups. Finally, 287 accessions were identified as pure examples of one of the four species and 15 as hybrids of M. integrifolia and M. tetraphylla. The admixed accessions showed the highest genetic diversity followed by M. integrifolia, while M. ternifolia and M. jansenii accessions were the least diverse. Mantel test analysis showed a significant correlation between genetic and geographic distance for M. integrifolia (r = 0.51, p = 0.05) and a positive but not significant correlation for M. tetraphylla (r = 0.45, p = 0.06). This study provides a population genetics overview of macadamia germplasm as a background for a conservation strategy and provides directions for future macadamia breeding.
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10
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Agre P, Asibe F, Darkwa K, Edemodu A, Bauchet G, Asiedu R, Adebola P, Asfaw A. Phenotypic and molecular assessment of genetic structure and diversity in a panel of winged yam (Dioscorea alata) clones and cultivars. Sci Rep 2019; 9:18221. [PMID: 31796820 PMCID: PMC6890776 DOI: 10.1038/s41598-019-54761-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 11/18/2019] [Indexed: 11/23/2022] Open
Abstract
A better understanding of the structure and extent of genetic variability in a breeding population of a crop is essential for translating genetic diversity to genetic gain. We assessed the nature and pattern of genetic variability and differentiation in a panel of 100 winged-yam (Dioscorea alata) accessions using 24 phenotypic traits and 6,918 single nucleotide polymorphism (SNP) markers. Multivariate analysis for phenotypic variability indicated that all phenotypic traits assessed were useful in discriminating the yam clones and cultivars. Cluster analysis based on phenotypic data distinguished two significant groups, while a corresponding analysis with SNP markers indicated three genetic groups. However, joint analysis for the phenotypic and genotypic data provided three clusters that could be useful for the identification of heterotic groups in the D. alata breeding program. Our analysis for phenotypic and molecular level diversity provided valuable information about overall diversity and variation in economically important traits useful for establishing crossing panels with contrasting traits of interest. The selection and hybridization of parental lines from the different heterotic groups identified would facilitate maximizing diversity and exploiting population heterosis in the D. alata breeding program.
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Affiliation(s)
- Paterne Agre
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria.
| | - Flora Asibe
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria.,Department of Crop Protection, Federal University of Agriculture, Abeokuta, Nigeria
| | - Kwabena Darkwa
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria.,Pan African University, Institute of Life and Earth Sciences, University of Ibadan, Ibadan, Nigeria
| | - Alex Edemodu
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | | | - Robert Asiedu
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Patrick Adebola
- International Institute of Tropical Agriculture (IITA), Abuja station, Nigeria
| | - Asrat Asfaw
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
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11
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Varshney RK, Thudi M, Roorkiwal M, He W, Upadhyaya HD, Yang W, Bajaj P, Cubry P, Rathore A, Jian J, Doddamani D, Khan AW, Garg V, Chitikineni A, Xu D, Gaur PM, Singh NP, Chaturvedi SK, Nadigatla GVPR, Krishnamurthy L, Dixit GP, Fikre A, Kimurto PK, Sreeman SM, Bharadwaj C, Tripathi S, Wang J, Lee SH, Edwards D, Polavarapu KKB, Penmetsa RV, Crossa J, Nguyen HT, Siddique KHM, Colmer TD, Sutton T, von Wettberg E, Vigouroux Y, Xu X, Liu X. Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits. Nat Genet 2019; 51:857-864. [DOI: 10.1038/s41588-019-0401-3] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 03/21/2019] [Indexed: 11/09/2022]
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12
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Das Bhowmik SS, Cheng AY, Long H, Tan GZH, Hoang TML, Karbaschi MR, Williams B, Higgins TJV, Mundree SG. Robust Genetic Transformation System to Obtain Non-chimeric Transgenic Chickpea. FRONTIERS IN PLANT SCIENCE 2019; 10:524. [PMID: 31105725 PMCID: PMC6498970 DOI: 10.3389/fpls.2019.00524] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 04/04/2019] [Indexed: 05/30/2023]
Abstract
Chickpea transformation is an important component for the genetic improvement of this crop, achieved through modern biotechnological approaches. However, recalcitrant tissue cultures and occasional chimerism, encountered during transformation, hinder the efficient generation of transgenic chickpeas. Two key parameters, namely micro-injury and light emitting diode (LED)-based lighting were used to increase transformation efficiency. Early PCR confirmation of positive in vitro transgenic shoots, together with efficient grafting and an extended acclimatization procedure contributed to the rapid generation of transgenic plants. High intensity LED light facilitate chickpea plants to complete their life cycle within 9 weeks thus enabling up to two generations of stable transgenic chickpea lines within 8 months. The method was validated with several genes from different sources, either as single or multi-gene cassettes. Stable transgenic chickpea lines containing GUS (uidA), stress tolerance (AtBAG4 and TlBAG), as well as Fe-biofortification (OsNAS2 and CaNAS2) genes have successfully been produced.
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Affiliation(s)
| | - Alam Yen Cheng
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Hao Long
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Grace Zi Hao Tan
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Thi My Linh Hoang
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Mohammad Reza Karbaschi
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Brett Williams
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Thomas Joseph V. Higgins
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Sagadevan G. Mundree
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
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13
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Das Bhowmik SS, Cheng AY, Long H, Tan GZH, Hoang TML, Karbaschi MR, Williams B, Higgins TJV, Mundree SG. Robust Genetic Transformation System to Obtain Non-chimeric Transgenic Chickpea. FRONTIERS IN PLANT SCIENCE 2019; 10:524. [PMID: 31105725 DOI: 10.3389/fpls.2019.00524/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 04/04/2019] [Indexed: 05/20/2023]
Abstract
Chickpea transformation is an important component for the genetic improvement of this crop, achieved through modern biotechnological approaches. However, recalcitrant tissue cultures and occasional chimerism, encountered during transformation, hinder the efficient generation of transgenic chickpeas. Two key parameters, namely micro-injury and light emitting diode (LED)-based lighting were used to increase transformation efficiency. Early PCR confirmation of positive in vitro transgenic shoots, together with efficient grafting and an extended acclimatization procedure contributed to the rapid generation of transgenic plants. High intensity LED light facilitate chickpea plants to complete their life cycle within 9 weeks thus enabling up to two generations of stable transgenic chickpea lines within 8 months. The method was validated with several genes from different sources, either as single or multi-gene cassettes. Stable transgenic chickpea lines containing GUS (uidA), stress tolerance (AtBAG4 and TlBAG), as well as Fe-biofortification (OsNAS2 and CaNAS2) genes have successfully been produced.
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Affiliation(s)
| | - Alam Yen Cheng
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Hao Long
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Grace Zi Hao Tan
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Thi My Linh Hoang
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Mohammad Reza Karbaschi
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Brett Williams
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Thomas Joseph V Higgins
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Sagadevan G Mundree
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
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14
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Omari S, Kamenir Y, Benichou JIC, Pariente S, Sela H, Perl-Treves R. Landraces of snake melon, an ancient Middle Eastern crop, reveal extensive morphological and DNA diversity for potential genetic improvement. BMC Genet 2018; 19:34. [PMID: 29792158 PMCID: PMC5966880 DOI: 10.1186/s12863-018-0619-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 04/30/2018] [Indexed: 12/05/2022] Open
Abstract
Background Snake melon (Cucumis melo var. flexuosus, “Faqqous”) is a traditional and ancient vegetable in the Mediterranean area. A collection of landraces from 42 grower fields in Israel and Palestinian territories was grown and characterized in a “Common Garden” rain-fed experiment, at the morphological-horticultural and molecular level using seq-DArT markers. Results The different landraces (“populations”) showed extensive variation in morphology and quantitative traits such as yield and femaleness, and clustered into four horticultural varieties. Yield was assessed by five harvests along the season, with middle harvests producing the highest yields. Yield correlated with early vigor, and with femaleness, but not with late vigor. At the molecular level, 2784 SNP were produced and > 90% were mapped to the melon genome. Populations were very polymorphic (46–72% of the markers biallelic in a 4 individuals sample), and observed heterozygosity was higher than the expected, suggesting gene flow among populations and extensive cross pollination among individuals in the field. Genetic distances between landraces were significantly correlated with the geographical distance between collecting sites, and with long term March precipitation average; variation in yield correlated with April temperature maxima. Conclusions The extensive variation suggests that selection of local snake melon could result in yield improvement. Correlations between traits and climatic variables could suggest local adaptation of landraces to the diverse environment in which they evolved. This study stresses the importance of preserving this germplasm, and its potential for breeding better snake melons as an heirloom crop in our region. Electronic supplementary material The online version of this article (10.1186/s12863-018-0619-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Samer Omari
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Yuri Kamenir
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Jennifer I C Benichou
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Sarah Pariente
- Department of Geography and Environment, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Hanan Sela
- Cereal Crop Improvement Institute, Faculty of Life Sciences, Tel-Aviv University, 6997801, Tel Aviv, Israel
| | - Rafael Perl-Treves
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel.
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15
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Sani SGAS, Chang PL, Zubair A, Carrasquilla-Garcia N, Cordeiro M, Penmetsa RV, Munis MFH, Nuzhdin SV, Cook DR, von Wettberg EJ. Genetic Diversity, Population Structure, and Genetic Correlation with Climatic Variation in Chickpea ( Cicer arietinum) Landraces from Pakistan. THE PLANT GENOME 2018; 11:170067. [PMID: 29505627 DOI: 10.3835/plantgenome2017.08.0067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Chickpea ( L.) production in arid regions, such as those predominant in Pakistan, faces immense challenges of drought and heat stress. Addressing these challenges is made more difficult by the lack of genetic and phenotypic characterization of available cultivated varieties and breeding materials. Genotyping-by-sequencing offers a rapid and cost-effective means to identify genome-wide nucleotide variation in crop germplasm. When combined with extended crop phenotypes deduced from climatic variation at sites of collection, the data can predict which portions of genetic variation might have roles in climate resilience. Here we use 8113 single nucleotide polymorphism markers to determine genetic variation and compare population structure within a previously uncharacterized collection of 77 landraces and 5 elite cultivars, currently grown in situ on farms throughout the chickpea growing regions of Pakistan. The compiled landraces span a striking aridity gradient into the Thal Desert of the Punjab. Despite low levels of variation across the collection and limited genetic structure, we found some differentiation between accessions from arid, semiarid, irrigated, and coastal areas. In a subset of 232 markers, we found evidence of differentiation along gradients of elevation and isothermality. Our results highlight the utility of exploring large germplasm collections for nucleotide variation associated with environmental extremes, and the use of such data to nominate germplasm accessions with the potential to improve crop drought tolerance and other environmental traits.
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16
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von Wettberg EJB, Chang PL, Başdemir F, Carrasquila-Garcia N, Korbu LB, Moenga SM, Bedada G, Greenlon A, Moriuchi KS, Singh V, Cordeiro MA, Noujdina NV, Dinegde KN, Shah Sani SGA, Getahun T, Vance L, Bergmann E, Lindsay D, Mamo BE, Warschefsky EJ, Dacosta-Calheiros E, Marques E, Yilmaz MA, Cakmak A, Rose J, Migneault A, Krieg CP, Saylak S, Temel H, Friesen ML, Siler E, Akhmetov Z, Ozcelik H, Kholova J, Can C, Gaur P, Yildirim M, Sharma H, Vadez V, Tesfaye K, Woldemedhin AF, Tar'an B, Aydogan A, Bukun B, Penmetsa RV, Berger J, Kahraman A, Nuzhdin SV, Cook DR. Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation. Nat Commun 2018; 9:649. [PMID: 29440741 PMCID: PMC5811434 DOI: 10.1038/s41467-018-02867-z] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/04/2018] [Indexed: 12/30/2022] Open
Abstract
Domesticated species are impacted in unintended ways during domestication and breeding. Changes in the nature and intensity of selection impart genetic drift, reduce diversity, and increase the frequency of deleterious alleles. Such outcomes constrain our ability to expand the cultivation of crops into environments that differ from those under which domestication occurred. We address this need in chickpea, an important pulse legume, by harnessing the diversity of wild crop relatives. We document an extreme domestication-related genetic bottleneck and decipher the genetic history of wild populations. We provide evidence of ancestral adaptations for seed coat color crypsis, estimate the impact of environment on genetic structure and trait values, and demonstrate variation between wild and cultivated accessions for agronomic properties. A resource of genotyped, association mapping progeny functionally links the wild and cultivated gene pools and is an essential resource chickpea for improvement, while our methods inform collection of other wild crop progenitor species.
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Affiliation(s)
- Eric J B von Wettberg
- Department of Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, FL, 33199, USA.
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, 05405, USA.
| | - Peter L Chang
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Fatma Başdemir
- Faculty of Agriculture, Dicle University, Diyarbakir, 21280, Turkey
| | | | - Lijalem Balcha Korbu
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, 32853, Ethiopia
- Ethiopian Institute of Agricultural Research, Addis Ababa, P.O. Box 2003, Ethiopia
| | - Susan M Moenga
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
| | - Gashaw Bedada
- Hawassa University, Hawassa, 005, Ethiopia
- Oromia Agricultural Research Institute (OARI), Addis Ababa, P.O. Box 81265, Ethiopia
| | - Alex Greenlon
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
| | - Ken S Moriuchi
- Department of Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, FL, 33199, USA
| | - Vasantika Singh
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Matilde A Cordeiro
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Nina V Noujdina
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Applied Mathematics, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Kassaye Negash Dinegde
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, 32853, Ethiopia
- Ethiopian Institute of Agricultural Research, Addis Ababa, P.O. Box 2003, Ethiopia
| | - Syed Gul Abbas Shah Sani
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
- Department of Plant Sciences, Quaid-i-Azam University Islamabad, Islamabad, 45320, Pakistan
| | - Tsegaye Getahun
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, 32853, Ethiopia
| | - Lisa Vance
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
| | - Emily Bergmann
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
| | - Donna Lindsay
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N5A8, Canada
| | - Bullo Erena Mamo
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
| | - Emily J Warschefsky
- Department of Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, FL, 33199, USA
| | - Emmanuel Dacosta-Calheiros
- Department of Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, FL, 33199, USA
| | - Edward Marques
- Department of Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, FL, 33199, USA
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, 05405, USA
| | | | - Ahmet Cakmak
- Department of Field Crops, Faculty of Agriculture, Harran University, Sanliurfa, 63100, Turkey
| | - Janna Rose
- Department of Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, FL, 33199, USA
| | - Andrew Migneault
- Department of Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, FL, 33199, USA
| | - Christopher P Krieg
- Department of Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, FL, 33199, USA
- Department of Botany, University of Florida, Gainesville, FL, 33181, USA
| | - Sevgi Saylak
- Faculty of Agriculture, Dicle University, Diyarbakir, 21280, Turkey
| | - Hamdi Temel
- Faculty of Agriculture, Dicle University, Diyarbakir, 21280, Turkey
| | - Maren L Friesen
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48823, USA
| | - Eleanor Siler
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48823, USA
| | - Zhaslan Akhmetov
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
| | - Huseyin Ozcelik
- Black Sea Agricultural Research Institute, Samsun, P.O. Box 39, Turkey
| | - Jana Kholova
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502324, Telangana, India
| | - Canan Can
- Department of Biology, Gaziantep University, Gaziantep, 27310, Turkey
| | - Pooran Gaur
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502324, Telangana, India
| | - Mehmet Yildirim
- Faculty of Agriculture, Dicle University, Diyarbakir, 21280, Turkey
| | - Hari Sharma
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502324, Telangana, India
| | - Vincent Vadez
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502324, Telangana, India
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, 32853, Ethiopia
| | | | - Bunyamin Tar'an
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N5A8, Canada
| | - Abdulkadir Aydogan
- Central Research Institute for Field Crops (CRIFC), Ankara, 06042, Turkey
| | - Bekir Bukun
- Faculty of Agriculture, Dicle University, Diyarbakir, 21280, Turkey
| | - R Varma Penmetsa
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA
| | - Jens Berger
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, Perth, 6014, WA, Australia
| | - Abdullah Kahraman
- Department of Field Crops, Faculty of Agriculture, Harran University, Sanliurfa, 63100, Turkey
| | - Sergey V Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Applied Mathematics, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Douglas R Cook
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA.
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17
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Sardos J, Perrier X, Doležel J, Hřibová E, Christelová P, Van den Houwe I, Kilian A, Roux N. DArT whole genome profiling provides insights on the evolution and taxonomy of edible Banana (Musa spp.). ANNALS OF BOTANY 2016; 118:1269-1278. [PMID: 27590334 PMCID: PMC5155597 DOI: 10.1093/aob/mcw170] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/20/2016] [Accepted: 06/17/2016] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Dessert and cooking bananas are vegetatively propagated crops of great importance for both the subsistence and the livelihood of people in developing countries. A wide diversity of diploid and triploid cultivars including AA, AB, AS, AT, AAA, AAB, ABB, AAS and AAT genomic constitutions exists. Within each of this genome groups, cultivars are classified into subgroups that are reported to correspond to varieties clonally derived from each other after a single sexual event. The number of those founding events at the basis of the diversity of bananas is a matter of debate. METHODS We analysed a large panel of 575 accessions, 94 wild relatives and 481 cultivated accessions belonging to the section Musa with a set of 498 DArT markers previously developed. KEY RESULTS DArT appeared successful and accurate to describe Musa diversity and help in the resolution of cultivated banana genome constitution and taxonomy, and highlighted discrepancies in the acknowledged classification of some accessions. This study also argues for at least two centres of domestication corresponding to South-East Asia and New Guinea, respectively. Banana domestication in New Guinea probably followed different schemes that those previously reported where hybridization underpins the emergence of edible banana. In addition, our results suggest that not all wild ancestors of bananas are known, especially in M. acuminata subspecies. We also estimate the extent of the two consecutive bottlenecks in edible bananas by evaluating the number of sexual founding events underlying our sets of edible diploids and triploids, respectively. CONCLUSIONS The attribution of clone identity to each sample of the sets allowed the detection of subgroups represented by several sets of clones. Although morphological characterization of some of the accessions is needed to correct potentially erroneous classifications, some of the subgroups seem polyclonal.
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Affiliation(s)
- J Sardos
- Bioversity International, Parc Scientifique Agropolis II, 1990 boulevard de la Lironde, 34397 Montpellier Cedex 5, France
| | - X Perrier
- CIRAD, UMR AGAP, 34398 Montpellier, France
| | - J Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - E Hřibová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - P Christelová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - I Van den Houwe
- Bioversity International, Willem De Croylaan 42, 3001 Leuven, Belgium
| | - A Kilian
- Diversity Arrays Technology Pty Ltd, Building 3, University of Canberra, Bruce, ACT 2617, Australia
| | - N Roux
- Bioversity International, Parc Scientifique Agropolis II, 1990 boulevard de la Lironde, 34397 Montpellier Cedex 5, France
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18
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Singh VK, Khan AW, Jaganathan D, Thudi M, Roorkiwal M, Takagi H, Garg V, Kumar V, Chitikineni A, Gaur PM, Sutton T, Terauchi R, Varshney RK. QTL-seq for rapid identification of candidate genes for 100-seed weight and root/total plant dry weight ratio under rainfed conditions in chickpea. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:2110-2119. [PMID: 27107184 PMCID: PMC5095801 DOI: 10.1111/pbi.12567] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/15/2016] [Accepted: 04/19/2016] [Indexed: 05/18/2023]
Abstract
Terminal drought is a major constraint to chickpea productivity. Two component traits responsible for reduction in yield under drought stress include reduction in seeds size and root length/root density. QTL-seq approach, therefore, was used to identify candidate genomic regions for 100-seed weight (100SDW) and total dry root weight to total plant dry weight ratio (RTR) under rainfed conditions. Genomewide SNP profiling of extreme phenotypic bulks from the ICC 4958 × ICC 1882 population identified two significant genomic regions, one on CaLG01 (1.08 Mb) and another on CaLG04 (2.7 Mb) linkage groups for 100SDW. Similarly, one significant genomic region on CaLG04 (1.10 Mb) was identified for RTR. Comprehensive analysis revealed four and five putative candidate genes associated with 100SDW and RTR, respectively. Subsequently, two genes (Ca_04364 and Ca_04607) for 100SDW and one gene (Ca_04586) for RTR were validated using CAPS/dCAPS markers. Identified candidate genomic regions and genes may be useful for molecular breeding for chickpea improvement.
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Affiliation(s)
- Vikas K Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Aamir W Khan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Deepa Jaganathan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Mahendar Thudi
- 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
| | - Hiroki Takagi
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Vinay Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pooran M Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Tim Sutton
- South Australian Research and Development Institute, Adelaide, Australia
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, Australia
| | | | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia.
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19
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Varma Penmetsa R, Carrasquilla-Garcia N, Bergmann EM, Vance L, Castro B, Kassa MT, Sarma BK, Datta S, Farmer AD, Baek JM, Coyne CJ, Varshney RK, von Wettberg EJB, Cook DR. Multiple post-domestication origins of kabuli chickpea through allelic variation in a diversification-associated transcription factor. THE NEW PHYTOLOGIST 2016; 211:1440-51. [PMID: 27193699 DOI: 10.1111/nph.14010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 03/24/2016] [Indexed: 05/28/2023]
Abstract
Chickpea (Cicer arietinum) is among the founder crops domesticated in the Fertile Crescent. One of two major forms of chickpea, the so-called kabuli type, has white flowers and light-colored seed coats, properties not known to exist in the wild progenitor. The origin of the kabuli form has been enigmatic. We genotyped a collection of wild and cultivated chickpea genotypes with 538 single nucleotide polymorphisms (SNPs) and examined patterns of molecular diversity relative to geographical sources and market types. In addition, we examined sequence and expression variation in candidate anthocyanin biosynthetic pathway genes. A reduction in genetic diversity and extensive genetic admixture distinguish cultivated chickpea from its wild progenitor species. Among germplasm, the kabuli form is polyphyletic. We identified a basic helix-loop-helix (bHLH) transcription factor at chickpea's B locus that conditions flower and seed colors, orthologous to Mendel's A gene of garden pea, whose loss of function is associated invariantly with the kabuli type of chickpea. From the polyphyletic distribution of the kabuli form in germplasm, an absence of nested variation within the bHLH gene and invariant association of loss of function of bHLH among the kabuli type, we conclude that the kabuli form arose multiple times during the phase of phenotypic diversification after initial domestication of cultivated chickpea.
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Affiliation(s)
- R Varma Penmetsa
- Department of Plant Pathology, University of California, One Shields Ave, Davis, CA, 95616, USA
| | | | - Emily M Bergmann
- Department of Plant Pathology, University of California, One Shields Ave, Davis, CA, 95616, USA
| | - Lisa Vance
- Department of Plant Pathology, University of California, One Shields Ave, Davis, CA, 95616, USA
| | - Brenna Castro
- Department of Plant Pathology, University of California, One Shields Ave, Davis, CA, 95616, USA
| | - Mulualem T Kassa
- Department of Plant Pathology, University of California, One Shields Ave, Davis, CA, 95616, USA
| | - Birinchi K Sarma
- Department of Plant Pathology, University of California, One Shields Ave, Davis, CA, 95616, USA
- Department of Mycology and Plant Pathology, Banaras Hindu University, Pandit Madan Mohan Malviya Road, Varanasi, Uttar Pradesh, 221005, India
| | - Subhojit Datta
- Department of Plant Pathology, University of California, One Shields Ave, Davis, CA, 95616, USA
- Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, 208024, India
| | - Andrew D Farmer
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA
| | - Jong-Min Baek
- Department of Plant Pathology, University of California, One Shields Ave, Davis, CA, 95616, USA
| | - Clarice J Coyne
- USDA-ARS, Western Regional Plant Introduction Station, Washington State University, 59 Johnson Hall, Pullman, WA, 99164-6402, USA
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Center of Excellence in Genomics, Patancheru, Andhra Pradesh, 502324, India
| | - Eric J B von Wettberg
- Department of Biological Sciences, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
- Kushlan Institute for Tropical Science, Fairchild Tropical Botanic Garden, 10901 Old Cutter Road, Coral Gables, FL, 33156, USA
| | - Douglas R Cook
- Department of Plant Pathology, University of California, One Shields Ave, Davis, CA, 95616, USA
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20
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van Oss R, Abbo S, Eshed R, Sherman A, Coyne CJ, Vandemark GJ, Zhang HB, Peleg Z. Genetic Relationship in Cicer Sp. Expose Evidence for Geneflow between the Cultigen and Its Wild Progenitor. PLoS One 2015; 10:e0139789. [PMID: 26447951 PMCID: PMC4597980 DOI: 10.1371/journal.pone.0139789] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/17/2015] [Indexed: 11/21/2022] Open
Abstract
There is a debate concerning mono- or poly-phyletic origins of the Near Eastern crops. In parallel, some authors claim that domestication was not possible within the natural range of the wild progenitors due to wild alleles flow into the nascent crops. Here we address both, the mono- or poly-phyletic origins and the domestications within or without the natural range of the progenitor, debates in order to understand the relationship between domesticated chickpea (Cicer arietinum L.) and its wild progenitor (C. reticulatum Ladizinsky) with special emphasis on its domestication centre in southeastern Turkey. A set of 103 chickpea cultivars and landraces from the major growing regions alongside wild accessions (C. reticulatum, C. echinospermum P.H Davis and C. bijugum K.H. Rech) sampled across the natural distribution range in eastern Turkey were genotyped with 194 SNPs markers. The genetic affinities between and within the studied taxa were assessed. The analysis suggests a mono-phyletic origin of the cultigen, with several wild accession as likely members of the wild stock of the cultigen. Clear separation between the wild and domesticated germplasm was apparent, with negligible level of admixture. A single C. reticulatum accession shows morphological and allelic signatures of admixture, a likely result of introgression. No evidence of geneflow from the wild into domesticated germplasm was found. The traditional farming systems of southeaster Turkey are characterized by occurrence of sympatric wild progenitor-domesticated forms of chickpea (and likewise cereals and other grain legumes). Therefore, both the authentic crop landraces and the wild populations native to the area are a unique genetic resource. Our results grant support to the notion of domestication within the natural distribution range of the wild progenitor, suggesting that the Neolithic domesticators were fully capable of selecting the desired phenotypes even when facing rare wild-domesticated introgression events.
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Affiliation(s)
- Ruth van Oss
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Levi Eshkol School of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shahal Abbo
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Levi Eshkol School of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ravit Eshed
- Genomic unit Plant Sciences Institute, Agricultural Research Organization (ARO)-Volcani Center, Bet Dagan, Israel
| | - Amir Sherman
- Genomic unit Plant Sciences Institute, Agricultural Research Organization (ARO)-Volcani Center, Bet Dagan, Israel
| | - Clarice J. Coyne
- USDA-ARS Western Regional Plant Introduction Station, Mail Stop 646402, Washington State University, Pullman, Washington, United States of America
| | - George J. Vandemark
- USDA-ARS Western Regional Plant Introduction Station, Mail Stop 646402, Washington State University, Pullman, Washington, United States of America
| | - Hong-Bin Zhang
- Department of Soil and Crop Sciences and Institute for Plant Genomics and Biotechnology, Texas A & M University, College Station, Texas, United States of America
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Levi Eshkol School of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
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21
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Parween S, Nawaz K, Roy R, Pole AK, Venkata Suresh B, Misra G, Jain M, Yadav G, Parida SK, Tyagi AK, Bhatia S, Chattopadhyay D. An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.). Sci Rep 2015; 5:12806. [PMID: 26259924 PMCID: PMC4531285 DOI: 10.1038/srep12806] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/06/2015] [Indexed: 11/09/2022] Open
Abstract
Chickpea (Cicer arietinum L.) is an important pulse legume crop. We previously reported a draft genome assembly of the desi chickpea cultivar ICC 4958. Here we report an advanced version of the ICC 4958 genome assembly (version 2.0) generated using additional sequence data and an improved genetic map. This resulted in 2.7-fold increase in the length of the pseudomolecules and substantial reduction of sequence gaps. The genome assembly covered more than 94% of the estimated gene space and predicted the presence of 30,257 protein-coding genes including 2230 and 133 genes encoding potential transcription factors (TF) and resistance gene homologs, respectively. Gene expression analysis identified several TF and chickpea-specific genes with tissue-specific expression and displayed functional diversification of the paralogous genes. Pairwise comparison of pseudomolecules in the desi (ICC 4958) and the earlier reported kabuli (CDC Frontier) chickpea assemblies showed an extensive local collinearity with incongruity in the placement of large sequence blocks along the linkage groups, apparently due to use of different genetic maps. Single nucleotide polymorphism (SNP)-based mining of intra-specific polymorphism identified more than four thousand SNPs differentiating a desi group and a kabuli group of chickpea genotypes.
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Affiliation(s)
- Sabiha Parween
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Kashif Nawaz
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Riti Roy
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Anil K. Pole
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - B. Venkata Suresh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Gopal Misra
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Mukesh Jain
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Gitanjali Yadav
- 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
| | - Akhilesh K. Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Debasis Chattopadhyay
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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22
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Gentzbittel L, Andersen SU, Ben C, Rickauer M, Stougaard J, Young ND. Naturally occurring diversity helps to reveal genes of adaptive importance in legumes. FRONTIERS IN PLANT SCIENCE 2015; 6:269. [PMID: 25954294 PMCID: PMC4404971 DOI: 10.3389/fpls.2015.00269] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 04/03/2015] [Indexed: 05/05/2023]
Abstract
Environmental changes challenge plants and drive adaptation to new conditions, suggesting that natural biodiversity may be a source of adaptive alleles acting through phenotypic plasticity and/or micro-evolution. Crosses between accessions differing for a given trait have been the most common way to disentangle genetic and environmental components. Interestingly, such man-made crosses may combine alleles that never meet in nature. Another way to discover adaptive alleles, inspired by evolution, is to survey large ecotype collections and to use association genetics to identify loci of interest. Both of these two genetic approaches are based on the use of biodiversity and may eventually help us in identifying the genes that plants use to respond to challenges such as short-term stresses or those due to global climate change. In legumes, two wild species, Medicago truncatula and Lotus japonicus, plus the cultivated soybean (Glycine max) have been adopted as models for genomic studies. In this review, we will discuss the resources, limitations and future plans for a systematic use of biodiversity resources in model legumes to pinpoint genes of adaptive importance in legumes, and their application in breeding.
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Affiliation(s)
- Laurent Gentzbittel
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Institut National Polytechnique de Toulouse, Ecole Nationale Supérieure Agronomique de Toulouse, Université Fédérale de ToulouseCastanet Tolosan, France
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Centre National de la Recherche ScientifiqueCastanet Tolosan, France
| | - Stig U. Andersen
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus UniversityAarhus, Denmark
| | - Cécile Ben
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Institut National Polytechnique de Toulouse, Ecole Nationale Supérieure Agronomique de Toulouse, Université Fédérale de ToulouseCastanet Tolosan, France
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Centre National de la Recherche ScientifiqueCastanet Tolosan, France
| | - Martina Rickauer
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Institut National Polytechnique de Toulouse, Ecole Nationale Supérieure Agronomique de Toulouse, Université Fédérale de ToulouseCastanet Tolosan, France
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Centre National de la Recherche ScientifiqueCastanet Tolosan, France
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus UniversityAarhus, Denmark
| | - Nevin D. Young
- Department of Plant Pathology, University of MinnesotaSt. Paul, MN, USA
- Department of Plant Biology, University of MinnesotaSt. Paul, MN, USA
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23
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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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