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Thirulogachandar V, Govind G, Hensel G, Kale SM, Kuhlmann M, Eschen-Lippold L, Rutten T, Koppolu R, Rajaraman J, Palakolanu SR, Seiler C, Sakuma S, Jayakodi M, Lee J, Kumlehn J, Komatsuda T, Schnurbusch T, Sreenivasulu N. HOMEOBOX2, the paralog of SIX-ROWED SPIKE1/HOMEOBOX1, is dispensable for barley spikelet development. J Exp Bot 2024; 75:2900-2916. [PMID: 38366171 DOI: 10.1093/jxb/erae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/14/2024] [Indexed: 02/18/2024]
Abstract
The HD-ZIP class I transcription factor Homeobox 1 (HvHOX1), also known as Vulgare Row-type Spike 1 (VRS1) or Six-rowed Spike 1, regulates lateral spikelet fertility in barley (Hordeum vulgare L.). It was shown that HvHOX1 has a high expression only in lateral spikelets, while its paralog HvHOX2 was found to be expressed in different plant organs. Yet, the mechanistic functions of HvHOX1 and HvHOX2 during spikelet development are still fragmentary. Here, we show that compared with HvHOX1, HvHOX2 is more highly conserved across different barley genotypes and Hordeum species, hinting at a possibly vital but still unclarified biological role. Using bimolecular fluorescence complementation, DNA-binding, and transactivation assays, we validate that HvHOX1 and HvHOX2 are bona fide transcriptional activators that may potentially heterodimerize. Accordingly, both genes exhibit similar spatiotemporal expression patterns during spike development and growth, albeit their mRNA levels differ quantitatively. We show that HvHOX1 delays the lateral spikelet meristem differentiation and affects fertility by aborting the reproductive organs. Interestingly, the ancestral relationship of the two genes inferred from their co-expressed gene networks suggested that HvHOX1 and HvHOX2 might play a similar role during barley spikelet development. However, CRISPR-derived mutants of HvHOX1 and HvHOX2 demonstrated the suppressive role of HvHOX1 on lateral spikelets, while the loss of HvHOX2 does not influence spikelet development. Collectively, our study shows that through the suppression of reproductive organs, lateral spikelet fertility is regulated by HvHOX1, whereas HvHOX2 is dispensable for spikelet development in barley.
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Affiliation(s)
- Venkatasubbu Thirulogachandar
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Hoher Weg 8, 06120 Halle (Saale), Germany
| | - Geetha Govind
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Götz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Sandip M Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Markus Kuhlmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Hoher Weg 8, 06120 Halle (Saale), Germany
| | | | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Ravi Koppolu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Jeyaraman Rajaraman
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Sudhakar Reddy Palakolanu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Christiane Seiler
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Shun Sakuma
- National Institute of Agrobiological Sciences (NIAS), Plant Genome Research Unit, Tsukuba 3058602, Japan
| | - Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Justin Lee
- Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, D-06120 Halle, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Takao Komatsuda
- National Institute of Agrobiological Sciences (NIAS), Plant Genome Research Unit, Tsukuba 3058602, Japan
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Nese Sreenivasulu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Hoher Weg 8, 06120 Halle (Saale), Germany
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Pandey MK, Gangurde SS, Shasidhar Y, Sharma V, Kale SM, Khan AW, Shah P, Joshi P, Bhat RS, Janila P, Bera SK, Varshney RK. Correction: High-throughput diagnostic markers for foliar fungal disease resistance and high oleic acid content in groundnut. BMC Plant Biol 2024; 24:336. [PMID: 38664611 PMCID: PMC11044379 DOI: 10.1186/s12870-024-05039-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2024]
Affiliation(s)
- Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
| | - Sunil S Gangurde
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Yaduru Shasidhar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sandip M Kale
- 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
| | - Priya Shah
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pushpesh Joshi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Pasupuleti Janila
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sandip K Bera
- ICAR-Directorate of Groundnut Research, Junagadh, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Murdoch University, Murdoch, Australia.
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3
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Pandey MK, Gangurde SS, Shasidhar Y, Sharma V, Kale SM, Khan AW, Shah P, Joshi P, Bhat RS, Janila P, Bera SK, Varshney RK. High-throughput diagnostic markers for foliar fungal disease resistance and high oleic acid content in groundnut. BMC Plant Biol 2024; 24:262. [PMID: 38594614 PMCID: PMC11005153 DOI: 10.1186/s12870-024-04987-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 04/03/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND Foliar diseases namely late leaf spot (LLS) and leaf rust (LR) reduce yield and deteriorate fodder quality in groundnut. Also the high oleic acid content has emerged as one of the most important traits for industries and consumers due to its increased shelf life and health benefits. RESULTS Genetic mapping combined with pooled sequencing approaches identified candidate resistance genes (LLSR1 and LLSR2 for LLS and LR1 for LR) for both foliar fungal diseases. The LLS-A02 locus housed LLSR1 gene for LLS resistance, while, LLS-A03 housed LLSR2 and LR1 genes for LLS and LR resistance, respectively. A total of 49 KASPs markers were developed from the genomic regions of important disease resistance genes, such as NBS-LRR, purple acid phosphatase, pentatricopeptide repeat-containing protein, and serine/threonine-protein phosphatase. Among the 49 KASP markers, 41 KASPs were validated successfully on a validation panel of contrasting germplasm and breeding lines. Of the 41 validated KASPs, 39 KASPs were designed for rust and LLS resistance, while two KASPs were developed using fatty acid desaturase (FAD) genes to control high oleic acid levels. These validated KASP markers have been extensively used by various groundnut breeding programs across the world which led to development of thousands of advanced breeding lines and few of them also released for commercial cultivation. CONCLUSION In this study, high-throughput and cost-effective KASP assays were developed, validated and successfully deployed to improve the resistance against foliar fungal diseases and oleic acid in groundnut. So far deployment of allele-specific and KASP diagnostic markers facilitated development and release of two rust- and LLS-resistant varieties and five high-oleic acid groundnut varieties in India. These validated markers provide opportunities for routine deployment in groundnut breeding programs.
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Affiliation(s)
- Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
| | - Sunil S Gangurde
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Yaduru Shasidhar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sandip M Kale
- 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
| | - Priya Shah
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pushpesh Joshi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Pasupuleti Janila
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sandip K Bera
- ICAR-Directorate of Groundnut Research, Junagadh, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Murdoch University, Murdoch, Australia.
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Schulthess AW, Kale SM, Zhao Y, Gogna A, Rembe M, Philipp N, Liu F, Beukert U, Serfling A, Himmelbach A, Oppermann M, Weise S, Boeven PHG, Schacht J, Longin CFH, Kollers S, Pfeiffer N, Korzun V, Fiebig A, Schüler D, Lange M, Scholz U, Stein N, Mascher M, Reif JC. Large-scale genotyping and phenotyping of a worldwide winter wheat genebank for its use in pre-breeding. Sci Data 2022; 9:784. [PMID: 36572688 PMCID: PMC9792552 DOI: 10.1038/s41597-022-01891-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/07/2022] [Indexed: 12/27/2022] Open
Abstract
Plant genetic resources (PGR) stored at genebanks are humanity's crop diversity savings for the future. Information on PGR contrasted with modern cultivars is key to select PGR parents for pre-breeding. Genotyping-by-sequencing was performed for 7,745 winter wheat PGR samples from the German Federal ex situ genebank at IPK Gatersleben and for 325 modern cultivars. Whole-genome shotgun sequencing was carried out for 446 diverse PGR samples and 322 modern cultivars and lines. In 19 field trials, 7,683 PGR and 232 elite cultivars were characterized for resistance to yellow rust - one of the major threats to wheat worldwide. Yield breeding values of 707 PGR were estimated using hybrid crosses with 36 cultivars - an approach that reduces the lack of agronomic adaptation of PGR and provides better estimates of their contribution to yield breeding. Cross-validations support the interoperability between genomic and phenotypic data. The here presented data are a stepping stone to unlock the functional variation of PGR for European pre-breeding and are the basis for future breeding and research activities.
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Affiliation(s)
- Albert W. Schulthess
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Sandip M. Kale
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany ,grid.418674.80000 0004 0533 4528Present Address: Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Yusheng Zhao
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Abhishek Gogna
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Maximilian Rembe
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Norman Philipp
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Fang Liu
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany ,grid.9227.e0000000119573309Present Address: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Ulrike Beukert
- grid.13946.390000 0001 1089 3517Julius Kühn Institute (Federal Research Centre for Cultivated Plants), Quedlinburg, Germany
| | - Albrecht Serfling
- grid.13946.390000 0001 1089 3517Julius Kühn Institute (Federal Research Centre for Cultivated Plants), Quedlinburg, Germany
| | - Axel Himmelbach
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Markus Oppermann
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Stephan Weise
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | | | | | - C. Friedrich H. Longin
- grid.9464.f0000 0001 2290 1502State Plant Breeding Institute, University of Hohenheim, Stuttgart, Germany
| | - Sonja Kollers
- grid.425691.dKWS SAAT SE & Co. KGaA, Einbeck, Germany
| | | | - Viktor Korzun
- grid.425691.dKWS SAAT SE & Co. KGaA, Einbeck, Germany
| | - Anne Fiebig
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Danuta Schüler
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Matthias Lange
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Uwe Scholz
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Nils Stein
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany ,grid.7450.60000 0001 2364 4210Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Martin Mascher
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany ,grid.421064.50000 0004 7470 3956German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Jochen C. Reif
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
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5
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Kale SM, Schulthess AW, Padmarasu S, Boeven PHG, Schacht J, Himmelbach A, Steuernagel B, Wulff BBH, Reif JC, Stein N, Mascher M. A catalogue of resistance gene homologs and a chromosome-scale reference sequence support resistance gene mapping in winter wheat. Plant Biotechnol J 2022; 20:1730-1742. [PMID: 35562859 PMCID: PMC9398310 DOI: 10.1111/pbi.13843] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/06/2022] [Accepted: 04/23/2022] [Indexed: 06/15/2023]
Abstract
A resistance gene atlas is an integral component of the breeder's arsenal in the fight against evolving pathogens. Thanks to high-throughput sequencing, catalogues of resistance genes can be assembled even in crop species with large and polyploid genomes. Here, we report on capture sequencing and assembly of resistance gene homologs in a diversity panel of 907 winter wheat genotypes comprising ex situ genebank accessions and current elite cultivars. In addition, we use accurate long-read sequencing and chromosome conformation capture sequencing to construct a chromosome-scale genome sequence assembly of cv. Attraktion, an elite variety representative of European winter wheat. We illustrate the value of our resource for breeders and geneticists by (i) comparing the resistance gene complements in plant genetic resources and elite varieties and (ii) conducting genome-wide associations scans (GWAS) for the fungal diseases yellow rust and leaf rust using reference-based and reference-free GWAS approaches. The gene content under GWAS peaks was scrutinized in the assembly of cv. Attraktion.
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Affiliation(s)
- Sandip M. Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Albert W. Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | | | | | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | | | - Brande B. H. Wulff
- John Innes CentreNorwich Research ParkNorwichUK
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Jochen C. Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
- Center for Integrated Breeding Research (CiBreed)Georg‐August‐University GöttingenGöttingenGermany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
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6
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Barmukh R, Roorkiwal M, Garg V, Khan AW, German L, Jaganathan D, Chitikineni A, Kholova J, Kudapa H, Sivasakthi K, Samineni S, Kale SM, Gaur PM, Sagurthi SR, Benitez‐Alfonso Y, Varshney RK. Genetic variation in CaTIFY4b contributes to drought adaptation in chickpea. Plant Biotechnol J 2022; 20:1701-1715. [PMID: 35534989 PMCID: PMC9398337 DOI: 10.1111/pbi.13840] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/28/2022] [Indexed: 05/26/2023]
Abstract
Chickpea production is vulnerable to drought stress. Identifying the genetic components underlying drought adaptation is crucial for enhancing chickpea productivity. Here, we present the fine mapping and characterization of 'QTL-hotspot', a genomic region controlling chickpea growth with positive consequences on crop production under drought. We report that a non-synonymous substitution in the transcription factor CaTIFY4b regulates seed weight and organ size in chickpea. Ectopic expression of CaTIFY4b in Medicago truncatula enhances root growth under water deficit. Our results suggest that allelic variation in 'QTL-hotspot' improves pre-anthesis water use, transpiration efficiency, root architecture and canopy development, enabling high-yield performance under terminal drought conditions. Gene expression analysis indicated that CaTIFY4b may regulate organ size under water deficit by modulating the expression of GRF-INTERACTING FACTOR1 (GIF1), a transcriptional co-activator of Growth-Regulating Factors. Taken together, our study offers new insights into the role of CaTIFY4b and on diverse physiological and molecular mechanisms underpinning chickpea growth and production under specific drought scenarios.
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Affiliation(s)
- Rutwik Barmukh
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- Department of GeneticsOsmania UniversityHyderabadIndia
| | - Manish Roorkiwal
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- Khalifa Center for Genetic Engineering and BiotechnologyUnited Arab Emirates UniversityAl‐AinUnited Arab Emirates
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
| | - Vanika Garg
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Aamir W. Khan
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Liam German
- Centre for Plant ScienceSchool of BiologyUniversity of LeedsLeedsUK
| | - Deepa Jaganathan
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Annapurna Chitikineni
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Jana Kholova
- Crop Physiology and ModellingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Himabindu Kudapa
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Kaliamoorthy Sivasakthi
- Crop Physiology and ModellingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Srinivasan Samineni
- Crop BreedingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Sandip M. Kale
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Pooran M. Gaur
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
- Crop BreedingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | | | | | - Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
- Murdoch’s Centre for Crop & Food InnovationState Agricultural Biotechnology CentreFood Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
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7
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Knudsen S, Wendt T, Dockter C, Thomsen HC, Rasmussen M, Egevang Jørgensen M, Lu Q, Voss C, Murozuka E, Østerberg JT, Harholt J, Braumann I, Cuesta-Seijo JA, Kale SM, Bodevin S, Tang Petersen L, Carciofi M, Pedas PR, Opstrup Husum J, Nielsen MTS, Nielsen K, Jensen MK, Møller LA, Gojkovic Z, Striebeck A, Lengeler K, Fennessy RT, Katz M, Garcia Sanchez R, Solodovnikova N, Förster J, Olsen O, Møller BL, Fincher GB, Skadhauge B. FIND-IT: Accelerated trait development for a green evolution. Sci Adv 2022; 8:eabq2266. [PMID: 36001660 PMCID: PMC9401622 DOI: 10.1126/sciadv.abq2266] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Improved agricultural and industrial production organisms are required to meet the future global food demands and minimize the effects of climate change. A new resource for crop and microbe improvement, designated FIND-IT (Fast Identification of Nucleotide variants by droplet DigITal PCR), provides ultrafast identification and isolation of predetermined, targeted genetic variants in a screening cycle of less than 10 days. Using large-scale sample pooling in combination with droplet digital PCR (ddPCR) greatly increases the size of low-mutation density and screenable variant libraries and the probability of identifying the variant of interest. The method is validated by screening variant libraries totaling 500,000 barley (Hordeum vulgare) individuals and isolating more than 125 targeted barley gene knockout lines and miRNA or promoter variants enabling functional gene analysis. FIND-IT variants are directly applicable to elite breeding pipelines and minimize time-consuming technical steps to accelerate the evolution of germplasm.
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Affiliation(s)
- Søren Knudsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Toni Wendt
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Christoph Dockter
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Magnus Rasmussen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Qiongxian Lu
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Cynthia Voss
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Emiko Murozuka
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Jesper Harholt
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Ilka Braumann
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Jose A. Cuesta-Seijo
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Sandip M. Kale
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Sabrina Bodevin
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Lise Tang Petersen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Pai Rosager Pedas
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Jeppe Opstrup Husum
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Kasper Nielsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Mikkel K. Jensen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Lillian Ambus Møller
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Zoran Gojkovic
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Alexander Striebeck
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Klaus Lengeler
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Ross T. Fennessy
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Michael Katz
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Rosa Garcia Sanchez
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Jochen Förster
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Ole Olsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Centre for Synthetic Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Geoffrey B. Fincher
- Australian Research Council Centre of Excellence in Plant Cell Walls School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Birgitte Skadhauge
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
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8
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Thiel J, Koppolu R, Trautewig C, Hertig C, Kale SM, Erbe S, Mascher M, Himmelbach A, Rutten T, Esteban E, Pasha A, Kumlehn J, Provart NJ, Vanderauwera S, Frohberg C, Schnurbusch T. Transcriptional landscapes of floral meristems in barley. Sci Adv 2021; 7:eabf0832. [PMID: 33910893 PMCID: PMC8081368 DOI: 10.1126/sciadv.abf0832] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/26/2021] [Indexed: 05/02/2023]
Abstract
Organ development in plants predominantly occurs postembryonically through combinatorial activity of meristems; therefore, meristem and organ fate are intimately connected. Inflorescence morphogenesis in grasses (Poaceae) is complex and relies on a specialized floral meristem, called spikelet meristem, that gives rise to all other floral organs and ultimately the grain. The fate of the spikelet determines reproductive success and contributes toward yield-related traits in cereal crops. Here, we examined the transcriptional landscapes of floral meristems in the temperate crop barley (Hordeum vulgare L.) using RNA-seq of laser capture microdissected tissues from immature, developing floral structures. Our unbiased, high-resolution approach revealed fundamental regulatory networks, previously unknown pathways, and key regulators of barley floral fate and will equally be indispensable for comparative transcriptional studies of grass meristems.
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Affiliation(s)
- J Thiel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany.
| | - R Koppolu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany.
| | - C Trautewig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - C Hertig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - S M Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - S Erbe
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - M Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - A Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - T Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - E Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - A Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - J Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - N J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - S Vanderauwera
- BASF Belgium Coordination Center CommV, Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Gent, Belgium
| | - C Frohberg
- BASF Belgium Coordination Center CommV, Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Gent, Belgium
| | - T Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany.
- Martin Luther University Halle-Wittenberg, Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, 06120 Halle, Germany
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9
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Sinha P, Singh VK, Saxena RK, Kale SM, Li Y, Garg V, Meifang T, Khan AW, Kim KD, Chitikineni A, Saxena KB, Sameer Kumar CV, Liu X, Xu X, Jackson S, Powell W, Nevo E, Searle IR, Lodha M, Varshney RK. Genome-wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea. Plant Biotechnol J 2020; 18:1697-1710. [PMID: 31925873 PMCID: PMC7336283 DOI: 10.1111/pbi.13333] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 12/26/2019] [Indexed: 05/20/2023]
Abstract
Hybrids are extensively used in agriculture to deliver an increase in yield, yet the molecular basis of heterosis is not well understood. Global DNA methylation analysis, transcriptome analysis and small RNA profiling were aimed to understand the epigenetic effect of the changes in gene expression level in the two hybrids and their parental lines. Increased DNA methylation was observed in both the hybrids as compared to their parents. This increased DNA methylation in hybrids showed that majority of the 24-nt siRNA clusters had higher expression in hybrids than the parents. Transcriptome analysis revealed that various phytohormones (auxin and salicylic acid) responsive hybrid-MPV DEGs were significantly altered in both the hybrids in comparison to MPV. DEGs associated with plant immunity and growth were overexpressed whereas DEGs associated with basal defence level were repressed. This antagonistic patterns of gene expression might contribute to the greater growth of the hybrids. It was also noticed that some common as well as unique changes in the regulatory pathways were associated with heterotic growth in both the hybrids. Approximately 70% and 67% of down-regulated hybrid-MPV DEGs were found to be differentially methylated in ICPH 2671 and ICPH 2740 hybrid, respectively. This reflected the association of epigenetic regulation in altered gene expressions. Our findings also revealed that miRNAs might play important roles in hybrid vigour in both the hybrids by regulating their target genes, especially in controlling plant growth and development, defence and stress response pathways. The above finding provides an insight into the molecular mechanism of pigeonpea heterosis.
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Affiliation(s)
- Pallavi Sinha
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - Vikas K. Singh
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
- International Rice Research Institute, South‐Asia HubPatancheruIndia
| | - Rachit K. Saxena
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - Sandip M. Kale
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
- The Leibniz Institute of Plant Genetics and Crop Plant ResearchGaterslebenGermany
| | | | - Vanika Garg
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | | | - Aamir W. Khan
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - Kyung Do Kim
- University of GeorgiaAthensUSA
- Myongji UniversityYonginRepublic of Korea
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - K. B. Saxena
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - C. V. Sameer Kumar
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | | | - Xun Xu
- BGI‐ShenzhenShenzhenChina
| | | | | | | | | | - Mukesh Lodha
- Centre for Cellular and Molecular Biology (CSIR)HyderabadIndia
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
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10
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Agarwal G, Clevenger J, Kale SM, Wang H, Pandey MK, Choudhary D, Yuan M, Wang X, Culbreath AK, Holbrook CC, Liu X, Varshney RK, Guo B. Publisher Correction: A recombination bin-map identified a major QTL for resistance to Tomato Spotted Wilt Virus in peanut (Arachis hypogaea). Sci Rep 2020; 10:2244. [PMID: 32024958 PMCID: PMC7002594 DOI: 10.1038/s41598-020-58891-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Gaurav Agarwal
- USDA-ARS, Crop Protection and Management Research Unit, Tifton, GA, USA.,University of Georgia, Department of Plant Pathology, Tifton, GA, USA.,International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics & Systems Biology, Hyderabad, India
| | - Josh Clevenger
- Mars Wrigley Confectionery, Center for Applied Genetic Technologies, Athens, GA, USA.,University of Georgia, Center for Applied Genetic Technologies, Athens, GA, USA
| | - Sandip M Kale
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics & Systems Biology, Hyderabad, India.,The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Hui Wang
- USDA-ARS, Crop Protection and Management Research Unit, Tifton, GA, USA.,University of Georgia, Department of Plant Pathology, Tifton, GA, USA
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics & Systems Biology, Hyderabad, India
| | - Divya Choudhary
- USDA-ARS, Crop Protection and Management Research Unit, Tifton, GA, USA.,University of Georgia, Department of Plant Pathology, Tifton, GA, USA
| | - Mei Yuan
- Shandong Academy of Agricultural Sciences, Peanut Research Institute, Qingdao, China
| | - Xingjun Wang
- Shandong Academy of Agricultural Sciences, Biotechnology Research Center, Jinan, China
| | | | | | - Xin Liu
- BGI-Shenzhen, Shenzhen, China
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics & Systems Biology, Hyderabad, India.
| | - Baozhu Guo
- USDA-ARS, Crop Protection and Management Research Unit, Tifton, GA, USA.
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11
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Garg V, Khan AW, Kudapa H, Kale SM, Chitikineni A, Qiwei S, Sharma M, Li C, Zhang B, Xin L, Kishor PK, Varshney RK. Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea. Plant Biotechnol J 2019; 17:914-931. [PMID: 30328278 PMCID: PMC6472043 DOI: 10.1111/pbi.13026] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/12/2018] [Accepted: 10/14/2018] [Indexed: 05/04/2023]
Abstract
Ascochyta blight (AB) is one of the major biotic stresses known to limit the chickpea production worldwide. To dissect the complex mechanisms of AB resistance in chickpea, three approaches, namely, transcriptome, small RNA and degradome sequencing were used. The transcriptome sequencing of 20 samples including two resistant genotypes, two susceptible genotypes and one introgression line under control and stress conditions at two time points (3rd and 7th day post inoculation) identified a total of 6767 differentially expressed genes (DEGs). These DEGs were mainly related to pathogenesis-related proteins, disease resistance genes like NBS-LRR, cell wall biosynthesis and various secondary metabolite synthesis genes. The small RNA sequencing of the samples resulted in the identification of 651 miRNAs which included 478 known and 173 novel miRNAs. A total of 297 miRNAs were differentially expressed between different genotypes, conditions and time points. Using degradome sequencing and in silico approaches, 2131 targets were predicted for 629 miRNAs. The combined analysis of both small RNA and transcriptome datasets identified 12 miRNA-mRNA interaction pairs that exhibited contrasting expression in resistant and susceptible genotypes and also, a subset of genes that might be post-transcriptionally silenced during AB infection. The comprehensive integrated analysis in the study provides better insights into the transcriptome dynamics and regulatory network components associated with AB stress in chickpea and, also offers candidate genes for chickpea improvement.
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Affiliation(s)
- Vanika Garg
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruTelanganaIndia
- Department of GeneticsOsmania UniversityHyderabadTelanganaIndia
| | - Aamir W. Khan
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruTelanganaIndia
| | - Himabindu Kudapa
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruTelanganaIndia
| | - Sandip M. Kale
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruTelanganaIndia
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruTelanganaIndia
| | | | - Mamta Sharma
- Integrated Crop ManagementICRISATPatancheruTelanganaIndia
| | | | - Baohong Zhang
- Department of BiologyEast Carolina UniversityGreenvilleNCUSA
| | | | | | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruTelanganaIndia
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12
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Roorkiwal M, Jain A, Kale SM, Doddamani D, Chitikineni A, Thudi M, Varshney RK. Development and evaluation of high-density Axiom ® CicerSNP Array for high-resolution genetic mapping and breeding applications in chickpea. Plant Biotechnol J 2018; 16:890-901. [PMID: 28913885 PMCID: PMC5866945 DOI: 10.1111/pbi.12836] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/06/2017] [Accepted: 09/10/2017] [Indexed: 05/04/2023]
Abstract
To accelerate genomics research and molecular breeding applications in chickpea, a high-throughput SNP genotyping platform 'Axiom® CicerSNP Array' has been designed, developed and validated. Screening of whole-genome resequencing data from 429 chickpea lines identified 4.9 million SNPs, from which a subset of 70 463 high-quality nonredundant SNPs was selected using different stringent filter criteria. This was further narrowed down to 61 174 SNPs based on p-convert score ≥0.3, of which 50 590 SNPs could be tiled on array. Among these tiled SNPs, a total of 11 245 SNPs (22.23%) were from the coding regions of 3673 different genes. The developed Axiom® CicerSNP Array was used for genotyping two recombinant inbred line populations, namely ICCRIL03 (ICC 4958 × ICC 1882) and ICCRIL04 (ICC 283 × ICC 8261). Genotyping data reflected high success and polymorphic rate, with 15 140 (29.93%; ICCRIL03) and 20 018 (39.57%; ICCRIL04) polymorphic SNPs. High-density genetic maps comprising 13 679 SNPs spanning 1033.67 cM and 7769 SNPs spanning 1076.35 cM were developed for ICCRIL03 and ICCRIL04 populations, respectively. QTL analysis using multilocation, multiseason phenotyping data on these RILs identified 70 (ICCRIL03) and 120 (ICCRIL04) main-effect QTLs on genetic map. Higher precision and potential of this array is expected to advance chickpea genetics and breeding applications.
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Affiliation(s)
- Manish Roorkiwal
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Ankit Jain
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Sandip M. Kale
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | | | - Annapurna Chitikineni
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Mahendar Thudi
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- School of Agriculture and Environment & Institute of AgricultureThe University of Western AustraliaCrawleyPerthAustralia
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13
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Sivasakthi K, Thudi M, Tharanya M, Kale SM, Kholová J, Halime MH, Jaganathan D, Baddam R, Thirunalasundari T, Gaur PM, Varshney RK, Vadez V. Plant vigour QTLs co-map with an earlier reported QTL hotspot for drought tolerance while water saving QTLs map in other regions of the chickpea genome. BMC Plant Biol 2018; 18:29. [PMID: 29409451 PMCID: PMC5801699 DOI: 10.1186/s12870-018-1245-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 01/21/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Terminal drought stress leads to substantial annual yield losses in chickpea (Cicer arietinum L.). Adaptation to water limitation is a matter of matching water supply to water demand by the crop. Therefore, harnessing the genetics of traits contributing to plant water use, i.e. transpiration rate and canopy development dynamics, is important to design crop ideotypes suited to a varying range of water limited environments. With an aim of identifying genomic regions for plant vigour (growth and canopy size) and canopy conductance traits, 232 recombinant inbred lines derived from a cross between ICC 4958 and ICC 1882, were phenotyped at vegetative stage under well-watered conditions using a high throughput phenotyping platform (LeasyScan). RESULTS Twenty one major quantitative trait loci (M-QTLs) were identified for plant vigour and canopy conductance traits using an ultra-high density bin map. Plant vigour traits had 13 M-QTLs on CaLG04, with favourable alleles from high vigour parent ICC 4958. Most of them co-mapped with a previously fine mapped major drought tolerance "QTL-hotspot" region on CaLG04. One M-QTL was found for canopy conductance on CaLG03 with the ultra-high density bin map. Comparative analysis of the QTLs found across different density genetic maps revealed that QTL size reduced considerably and % of phenotypic variation increased as marker density increased. CONCLUSION Earlier reported drought tolerance hotspot is a vigour locus. The fact that canopy conductance traits, i.e. the other important determinant of plant water use, mapped on CaLG03 provides an opportunity to manipulate these loci to tailor recombinants having low/high transpiration rate and plant vigour, fitted to specific drought stress scenarios in chickpea.
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Affiliation(s)
- Kaliamoorthy Sivasakthi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
- Bharathidasan University, Tiruchirappalli, Tamil Nadu India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | - Murugesan Tharanya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
- Bharathidasan University, Tiruchirappalli, Tamil Nadu India
| | - Sandip M. Kale
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | - Jana Kholová
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | - Mahamat Hissene Halime
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | - Deepa Jaganathan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | - Rekha Baddam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | | | - Pooran M. Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | - Vincent Vadez
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
- Institut de Recherche pour le Developpement (IRD), Université de Montpellier – UMR DIADE, 911 Avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France
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14
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Singh VK, Khan AW, Saxena RK, Sinha P, Kale SM, Parupalli S, Kumar V, Chitikineni A, Vechalapu S, Sameer Kumar CV, Sharma M, Ghanta A, Yamini KN, Muniswamy S, Varshney RK. Indel-seq: a fast-forward genetics approach for identification of trait-associated putative candidate genomic regions and its application in pigeonpea (Cajanus cajan). Plant Biotechnol J 2017; 15:906-914. [PMID: 28027425 PMCID: PMC5466435 DOI: 10.1111/pbi.12685] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 05/05/2023]
Abstract
Identification of candidate genomic regions associated with target traits using conventional mapping methods is challenging and time-consuming. In recent years, a number of single nucleotide polymorphism (SNP)-based mapping approaches have been developed and used for identification of candidate/putative genomic regions. However, in the majority of these studies, insertion-deletion (Indel) were largely ignored. For efficient use of Indels in mapping target traits, we propose Indel-seq approach, which is a combination of whole-genome resequencing (WGRS) and bulked segregant analysis (BSA) and relies on the Indel frequencies in extreme bulks. Deployment of Indel-seq approach for identification of candidate genomic regions associated with fusarium wilt (FW) and sterility mosaic disease (SMD) resistance in pigeonpea has identified 16 Indels affecting 26 putative candidate genes. Of these 26 affected putative candidate genes, 24 genes showed effect in the upstream/downstream of the genic region and two genes showed effect in the genes. Validation of these 16 candidate Indels in other FW- and SMD-resistant and FW- and SMD-susceptible genotypes revealed a significant association of five Indels (three for FW and two for SMD resistance). Comparative analysis of Indel-seq with other genetic mapping approaches highlighted the importance of the approach in identification of significant genomic regions associated with target traits. Therefore, the Indel-seq approach can be used for quick and precise identification of candidate genomic regions for any target traits in any crop species.
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Affiliation(s)
- Vikas K. Singh
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Aamir W. Khan
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Rachit K. Saxena
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Pallavi Sinha
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Sandip M. Kale
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Swathi Parupalli
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Vinay Kumar
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Suryanarayana Vechalapu
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | | | - Mamta Sharma
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Anuradha Ghanta
- Agricultural Research Station (ARS)‐TandurProfessor Jayashankar Telangana State Agricultural University (PJTSAU)HyderabadTelangana StateIndia
| | - Kalinati Narasimhan Yamini
- Agricultural Research Station (ARS)‐TandurProfessor Jayashankar Telangana State Agricultural University (PJTSAU)HyderabadTelangana StateIndia
| | - Sonnappa Muniswamy
- Agricultural Research Station (ARS)‐GulbargaUniversity of Agricultural Sciences (UAS)RaichurKarnatakaIndia
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
- School of Plant Biology and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
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15
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Saxena RK, Kale SM, Kumar V, Parupali S, Joshi S, Singh V, Garg V, Das RR, Sharma M, Yamini KN, Ghanta A, Rathore A, Sameerkumar CV, Saxena KB, Varshney RK. Genotyping-by-sequencing of three mapping populations for identification of candidate genomic regions for resistance to sterility mosaic disease in pigeonpea. Sci Rep 2017; 7:1813. [PMID: 28500330 PMCID: PMC5431754 DOI: 10.1038/s41598-017-01535-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 03/30/2017] [Indexed: 01/09/2023] Open
Abstract
Sterility mosaic disease (SMD) is one of the serious production constraints that may lead to complete yield loss in pigeonpea. Three mapping populations including two recombinant inbred lines and one F2, were used for phenotyping for SMD resistance at two locations in three different years. Genotyping-by-sequencing approach was used for simultaneous identification and genotyping of SNPs on above mentioned populations. In total, 212,464, 89,699 and 64,798 SNPs were identified in ICPL 20096 × ICPL 332 (PRIL_B), ICPL 20097 × ICP 8863 (PRIL_C) and ICP 8863 × ICPL 87119 (F2) respectively. By using high-quality SNPs, genetic maps were developed for PRIL_B (1,101 SNPs; 921.21 cM), PRIL_C (484 SNPs; 798.25 cM) and F2 (996 SNPs; 1,597.30 cM) populations. The average inter marker distance on these maps varied from 0.84 cM to 1.65 cM, which was lowest in all genetic mapping studies in pigeonpea. Composite interval mapping based QTL analysis identified a total of 10 QTLs including three major QTLs across the three populations. The phenotypic variance of the identified QTLs ranged from 3.6 to 34.3%. One candidate genomic region identified on CcLG11 seems to be promising QTL for molecular breeding in developing superior lines with enhanced resistance to SMD.
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Affiliation(s)
- Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Sandip M Kale
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Vinay Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Swathi Parupali
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Shourabh Joshi
- Institute of Biotechnology, Professor Jayshankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad, 500 030, India
| | - Vikas Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Roma R Das
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Mamta Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - K N Yamini
- Institute of Biotechnology, Professor Jayshankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad, 500 030, India
| | - Anuradha Ghanta
- Institute of Biotechnology, Professor Jayshankar Telangana State Agricultural University (PJTSAU), Rajendranagar, Hyderabad, 500 030, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - C V Sameerkumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - K B Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India.
- School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley, WA, 6009, Australia.
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16
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Pandey MK, Wang H, Khera P, Vishwakarma MK, Kale SM, Culbreath AK, Holbrook CC, Wang X, Varshney RK, Guo B. Genetic Dissection of Novel QTLs for Resistance to Leaf Spots and Tomato Spotted Wilt Virus in Peanut ( Arachis hypogaea L.). Front Plant Sci 2017; 8:25. [PMID: 28197153 PMCID: PMC5281592 DOI: 10.3389/fpls.2017.00025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/05/2017] [Indexed: 05/20/2023]
Abstract
Peanut is an important crop, economically and nutritiously, but high production cost is a serious challenge to peanut farmers as exemplified by chemical spray to control foliar diseases such as leaf spots and thrips, the vectors of tomato spotted wilt virus (TSWV). The objective of this research was to map the quantitative trait loci (QTLs) for resistance to leaf spots and TSWV in one recombinant inbred line (RIL) mapping population of "Tifrunner × GT-C20" for identification of linked markers for marker-assisted breeding. Here, we report the improved genetic linkage map with 418 marker loci with a marker density of 5.3 cM/loci and QTLs associated with multi-year (2010-2013) field phenotypes of foliar disease traits, including early leaf spot (ELS), late leaf spot (LLS), and TSWV. A total of 42 QTLs were identified with phenotypic variation explained (PVE) from 6.36 to 15.6%. There were nine QTLs for resistance to ELS, 22 QTLs for LLS, and 11 QTLs for TSWV, including six, five, and one major QTLs with PVE higher than 10% for resistance to each disease, respectively. Of the total 42 QTLs, 34 were mapped on the A sub-genome and eight mapped on the B sub-genome suggesting that the A sub-genome harbors more resistance genes than the B sub-genome. This genetic linkage map was also compared with two diploid peanut physical maps, and the overall co-linearity was 48.4% with an average co-linearity of 51.7% for the A sub-genome and 46.4% for the B sub-genome. The identified QTLs associated markers and potential candidate genes will be studied further for possible application in molecular breeding in peanut genetic improvement for disease resistance.
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Affiliation(s)
- Manish K. Pandey
- Crop Protection and Management Research Unit, United States Department of Agriculture, Agricultural Research ServiceTifton, GA, USA
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- Department of Plant Pathology, University of GeorgiaTifton, GA, USA
| | - Hui Wang
- Crop Protection and Management Research Unit, United States Department of Agriculture, Agricultural Research ServiceTifton, GA, USA
- Department of Plant Pathology, University of GeorgiaTifton, GA, USA
| | - Pawan Khera
- Crop Protection and Management Research Unit, United States Department of Agriculture, Agricultural Research ServiceTifton, GA, USA
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- Department of Plant Pathology, University of GeorgiaTifton, GA, USA
| | | | - Sandip M. Kale
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | | | - C. Corley Holbrook
- Crop Genetics and Breeding Research Unit, United States Department of Agriculture, Agricultural Research ServiceTifton, GA, USA
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural SciencesJinan, China
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Baozhu Guo
- Crop Protection and Management Research Unit, United States Department of Agriculture, Agricultural Research ServiceTifton, GA, USA
- Department of Plant Pathology, University of GeorgiaTifton, GA, USA
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17
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Pandey MK, Agarwal G, Kale SM, Clevenger J, Nayak SN, Sriswathi M, Chitikineni A, Chavarro C, Chen X, Upadhyaya HD, Vishwakarma MK, Leal-Bertioli S, Liang X, Bertioli DJ, Guo B, Jackson SA, Ozias-Akins P, Varshney RK. Development and Evaluation of a High Density Genotyping 'Axiom_Arachis' Array with 58 K SNPs for Accelerating Genetics and Breeding in Groundnut. Sci Rep 2017; 7:40577. [PMID: 28091575 PMCID: PMC5238394 DOI: 10.1038/srep40577] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 12/07/2016] [Indexed: 01/20/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) are the most abundant DNA sequence variation in the genomes which can be used to associate genotypic variation to the phenotype. Therefore, availability of a high-density SNP array with uniform genome coverage can advance genetic studies and breeding applications. Here we report the development of a high-density SNP array 'Axiom_Arachis' with 58 K SNPs and its utility in groundnut genetic diversity study. In this context, from a total of 163,782 SNPs derived from DNA resequencing and RNA-sequencing of 41 groundnut accessions and wild diploid ancestors, a total of 58,233 unique and informative SNPs were selected for developing the array. In addition to cultivated groundnuts (Arachis hypogaea), fair representation was kept for other diploids (A. duranensis, A. stenosperma, A. cardenasii, A. magna and A. batizocoi). Genotyping of the groundnut 'Reference Set' containing 300 genotypes identified 44,424 polymorphic SNPs and genetic diversity analysis provided in-depth insights into the genetic architecture of this material. The availability of the high-density SNP array 'Axiom_Arachis' with 58 K SNPs will accelerate the process of high resolution trait genetics and molecular breeding in cultivated groundnut.
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Affiliation(s)
- Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Gaurav Agarwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.,University of Georgia (UGA), Tifton, USA
| | - Sandip M Kale
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Spurthi N Nayak
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manda Sriswathi
- 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
| | - Carolina Chavarro
- Center for Applied Genetic Technologies, University of Georgia (UGA), Athens, USA
| | - Xiaoping Chen
- Crops Research Institute (CRI), Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, China
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish K Vishwakarma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Soraya Leal-Bertioli
- Center for Applied Genetic Technologies, University of Georgia (UGA), Athens, USA
| | - Xuanqiang Liang
- Crops Research Institute (CRI), Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, China
| | - David J Bertioli
- Center for Applied Genetic Technologies, University of Georgia (UGA), Athens, USA
| | - Baozhu Guo
- Crop Protection and Management Research Unit, USDA-ARS, Tifton, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia (UGA), Athens, USA
| | | | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.,The University of Western Australia, Crawley, Australia
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18
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Vishwakarma MK, Kale SM, Sriswathi M, Naresh T, Shasidhar Y, Garg V, Pandey MK, Varshney RK. Genome-Wide Discovery and Deployment of Insertions and Deletions Markers Provided Greater Insights on Species, Genomes, and Sections Relationships in the Genus Arachis. Front Plant Sci 2017; 8:2064. [PMID: 29312366 PMCID: PMC5742254 DOI: 10.3389/fpls.2017.02064] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 11/17/2017] [Indexed: 05/04/2023]
Abstract
Small insertions and deletions (InDels) are the second most prevalent and the most abundant structural variations in plant genomes. In order to deploy these genetic variations for genetic analysis in genus Arachis, we conducted comparative analysis of the draft genome assemblies of both the diploid progenitor species of cultivated tetraploid groundnut (Arachis hypogaea L.) i.e., Arachis duranensis (A subgenome) and Arachis ipaënsis (B subgenome) and identified 515,223 InDels. These InDels include 269,973 insertions identified in A. ipaënsis against A. duranensis while 245,250 deletions in A. duranensis against A. ipaënsis. The majority of the InDels were of single bp (43.7%) and 2-10 bp (39.9%) while the remaining were >10 bp (16.4%). Phylogenetic analysis using genotyping data for 86 (40.19%) polymorphic markers grouped 96 diverse Arachis accessions into eight clusters mostly by the affinity of their genome. This study also provided evidence for the existence of "K" genome, although distinct from both the "A" and "B" genomes, but more similar to "B" genome. The complete homology between A. monticola and A. hypogaea tetraploid taxa showed a very similar genome composition. The above analysis has provided greater insights into the phylogenetic relationship among accessions, genomes, sub species and sections. These InDel markers are very useful resource for groundnut research community for genetic analysis and breeding applications.
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Affiliation(s)
| | - Sandip M. Kale
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Manda Sriswathi
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Talari Naresh
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Yaduru Shasidhar
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
- *Correspondence: Manish K. Pandey
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
- The University of Western Australia, Crawley, WA, Australia
- Rajeev K. Varshney
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19
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Singh VK, Khan AW, Saxena RK, Kumar V, Kale SM, Sinha P, Chitikineni A, Pazhamala LT, Garg V, Sharma M, Sameer Kumar CV, Parupalli S, Vechalapu S, Patil S, Muniswamy S, Ghanta A, Yamini KN, Dharmaraj PS, Varshney RK. Next-generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea (Cajanus cajan). Plant Biotechnol J 2016; 14:1183-94. [PMID: 26397045 PMCID: PMC5054876 DOI: 10.1111/pbi.12470] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 07/29/2015] [Accepted: 08/06/2015] [Indexed: 05/20/2023]
Abstract
To map resistance genes for Fusarium wilt (FW) and sterility mosaic disease (SMD) in pigeonpea, sequencing-based bulked segregant analysis (Seq-BSA) was used. Resistant (R) and susceptible (S) bulks from the extreme recombinant inbred lines of ICPL 20096 × ICPL 332 were sequenced. Subsequently, SNP index was calculated between R- and S-bulks with the help of draft genome sequence and reference-guided assembly of ICPL 20096 (resistant parent). Seq-BSA has provided seven candidate SNPs for FW and SMD resistance in pigeonpea. In parallel, four additional genotypes were re-sequenced and their combined analysis with R- and S-bulks has provided a total of 8362 nonsynonymous (ns) SNPs. Of 8362 nsSNPs, 60 were found within the 2-Mb flanking regions of seven candidate SNPs identified through Seq-BSA. Haplotype analysis narrowed down to eight nsSNPs in seven genes. These eight nsSNPs were further validated by re-sequencing 11 genotypes that are resistant and susceptible to FW and SMD. This analysis revealed association of four candidate nsSNPs in four genes with FW resistance and four candidate nsSNPs in three genes with SMD resistance. Further, In silico protein analysis and expression profiling identified two most promising candidate genes namely C.cajan_01839 for SMD resistance and C.cajan_03203 for FW resistance. Identified candidate genomic regions/SNPs will be useful for genomics-assisted breeding in pigeonpea.
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Affiliation(s)
- Vikas K Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Aamir W Khan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Vinay Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Sandip M Kale
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Pallavi Sinha
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Lekha T Pazhamala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Mamta Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | | | - Swathi Parupalli
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Suryanarayana Vechalapu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Suyash Patil
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Sonnappa Muniswamy
- Agricultural Research Station (ARS)-Gulbarga, University of Agricultural Sciences (UAS), Raichur, Karnataka, India
| | - Anuradha Ghanta
- Institute of Biotechnology, Professor Jayshankar Telangana State Agricultural University (PJTSAU), Telangana, India
| | - Kalinati Narasimhan Yamini
- Institute of Biotechnology, Professor Jayshankar Telangana State Agricultural University (PJTSAU), Telangana, India
| | - Pallavi Subbanna Dharmaraj
- Agricultural Research Station (ARS)-Gulbarga, University of Agricultural Sciences (UAS), Raichur, Karnataka, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
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20
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Kale SM, Jaganathan D, Ruperao P, Chen C, Punna R, Kudapa H, Thudi M, Roorkiwal M, Katta MA, Doddamani D, Garg V, Kishor PBK, Gaur PM, Nguyen HT, Batley J, Edwards D, Sutton T, Varshney RK. Prioritization of candidate genes in "QTL-hotspot" region for drought tolerance in chickpea (Cicer arietinum L.). Sci Rep 2015; 5:15296. [PMID: 26478518 PMCID: PMC4609953 DOI: 10.1038/srep15296] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/22/2015] [Indexed: 01/20/2023] Open
Abstract
A combination of two approaches, namely QTL analysis and gene enrichment analysis were used to identify candidate genes in the “QTL-hotspot” region for drought tolerance present on the Ca4 pseudomolecule in chickpea. In the first approach, a high-density bin map was developed using 53,223 single nucleotide polymorphisms (SNPs) identified in the recombinant inbred line (RIL) population of ICC 4958 (drought tolerant) and ICC 1882 (drought sensitive) cross. QTL analysis using recombination bins as markers along with the phenotyping data for 17 drought tolerance related traits obtained over 1–5 seasons and 1–5 locations split the “QTL-hotspot” region into two subregions namely “QTL-hotspot_a” (15 genes) and “QTL-hotspot_b” (11 genes). In the second approach, gene enrichment analysis using significant marker trait associations based on SNPs from the Ca4 pseudomolecule with the above mentioned phenotyping data, and the candidate genes from the refined “QTL-hotspot” region showed enrichment for 23 genes. Twelve genes were found common in both approaches. Functional validation using quantitative real-time PCR (qRT-PCR) indicated four promising candidate genes having functional implications on the effect of “QTL-hotspot” for drought tolerance in chickpea.
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Affiliation(s)
- Sandip M Kale
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - Deepa Jaganathan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India.,Osmania University, Department of Genetics, Hyderabad, 500007, India
| | - Pradeep Ruperao
- The University of Western Australia, School of Plant Biology and the Institute of Agriculture, Crawley, 6009, Australia.,University of Queensland, School of Agriculture and Food Science, Queensland, 4072, Australia
| | - Charles Chen
- Oklahoma State University, Department of Biochemistry and Molecular Biology, Stillwater, 74074, USA
| | - Ramu Punna
- Cornell University, Biotechnology Building, Ithaca, 14853, USA
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - Mohan Avsk Katta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - Dadakhalandar Doddamani
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - P B Kavi Kishor
- Osmania University, Department of Genetics, Hyderabad, 500007, India
| | - Pooran M Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - Henry T Nguyen
- University of Missouri, National Center for Soybean Biotechnology and Division of Plant Sciences, Columbia, 65211, USA
| | - Jacqueline Batley
- The University of Western Australia, School of Plant Biology and the Institute of Agriculture, Crawley, 6009, Australia
| | - David Edwards
- The University of Western Australia, School of Plant Biology and the Institute of Agriculture, Crawley, 6009, Australia
| | - Tim Sutton
- South Australian Research and Development Institute, Adelaide, 5001, Australia.,University of Adelaide, Australia and School of Agriculture, Adelaide, 5064, Australia
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India.,The University of Western Australia, School of Plant Biology and the Institute of Agriculture, Crawley, 6009, Australia
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21
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Lomate PR, Mahajan NS, Kale SM, Gupta VS, Giri AP. Identification and expression profiling of Helicoverpa armigera microRNAs and their possible role in the regulation of digestive protease genes. Insect Biochem Mol Biol 2014; 54:129-137. [PMID: 25263090 DOI: 10.1016/j.ibmb.2014.09.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 09/18/2014] [Accepted: 09/19/2014] [Indexed: 06/03/2023]
Abstract
The present investigation is an effort to determine the possible roles of microRNAs (miRNAs) in the regulation of protease gene expression in Helicoverpa armigera upon exposure to plant protease inhibitors (PIs). Using Illumina platform, deep sequencing of 12 small RNA libraries was performed from H. armigera larvae fed on artificial diet (AD) or recombinant Capsicum annuum PI-7 (rCanPI-7) incorporated diet, at various time intervals (0.5, 2, 6, 12, 24, and 48 h). Sequencing data were analyzed with miRDeep2 software; a total of 186 unique miRNAs were identified from all the 12 libraries, out of which 96 were conserved while 90 were novel. These miRNAs showed all the conserved characteristics of insect miRNAs. Homology analysis revealed that most of the identified miRNAs were insect-specific, and more than 50 miRNAs were Lepidoptera-specific. Several candidate miRNAs (conserved and novel) were differentially expressed in rCanPI-7 fed larvae as compared to the larvae fed on AD. H. armigera miRNAs were found to have target sites in several protease genes as well as in protease regulation related genes such as serine PI and immune reactive PI. As expected, negative correlation in the relative abundance of miRNAs and their target mRNAs was evident from qualitative real time polymerase chain reaction analysis. The investigation revealed potential roles of miRNAs in H. armigera protease gene regulation.
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Affiliation(s)
- Purushottam R Lomate
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, MS, India
| | - Neha S Mahajan
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, MS, India
| | - Sandip M Kale
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, MS, India
| | - Vidya S Gupta
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, MS, India
| | - Ashok P Giri
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, MS, India.
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Barvkar VT, Pardeshi VC, Kale SM, Qiu S, Rollins M, Datla R, Gupta VS, Kadoo NY. Genome-wide identification and characterization of microRNA genes and their targets in flax (Linum usitatissimum): Characterization of flax miRNA genes. Planta 2013; 237:1149-61. [PMID: 23291876 DOI: 10.1007/s00425-012-1833-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Accepted: 12/18/2012] [Indexed: 05/11/2023]
Abstract
MicroRNAs (miRNAs) are small (20-24 nucleotide long) endogenous regulatory RNAs that play important roles in plant growth and development. They regulate gene expression at the post-transcriptional level by translational repression or target degradation and gene silencing. In this study, we identified 116 conserved miRNAs belonging to 23 families from the flax (Linum usitatissimum L.) genome using a computational approach. The precursor miRNAs varied in length; while most of the mature miRNAs were 21 nucleotide long, intergenic and showed conserved signatures of RNA polymerase II transcripts in their upstream regions. Promoter region analysis of the flax miRNA genes indicated prevalence of MYB transcription factor binding sites. Four miRNA gene clusters containing members of three phylogenetic groups were identified. Further, 142 target genes were predicted for these miRNAs and most of these represent transcriptional regulators. The miRNA encoding genes were expressed in diverse tissues as determined by digital expression analysis as well as real-time PCR. The expression of fourteen miRNAs and nine target genes was independently validated using the quantitative reverse transcription PCR (qRT-PCR). This study suggests that a large number of conserved plant miRNAs are also found in flax and these may play important roles in growth and development of flax.
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Affiliation(s)
- Vitthal T Barvkar
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, India
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Kale SM, Pardeshi VC, Barvkar VT, Gupta VS, Kadoo NY. Genome-wide identification and characterization of nucleotide binding site leucine-rich repeat genes in linseed reveal distinct patterns of gene structure. Genome 2012; 56:91-9. [PMID: 23517318 DOI: 10.1139/gen-2012-0135] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Plants employ different disease-resistance genes to detect pathogens and to induce defense responses. The largest class of these genes encodes proteins with nucleotide binding site (NBS) and leucine-rich repeat (LRR) domains. To identify the putative NBS-LRR encoding genes from linseed, we analyzed the recently published linseed genome sequence and identified 147 NBS-LRR genes. The NBS domain was used for phylogeny construction and these genes were classified into two well-known families, non-TIR (CNL) and TIR related (TNL), and formed eight clades in the neighbor-joining bootstrap tree. Eight different gene structures were observed among these genes. An unusual domain arrangement was observed in the TNL family members, predominantly in the TNL-5 clade members belonging to class D. About 12% of the genes observed were linseed specific. The study indicated that the linseed genes probably have an ancient origin with few progenitor genes. Quantitative expression analysis of five genes showed inducible expression. The in silico expression evidence was obtained for a few of these genes, and the expression was not correlated with the presence of any particular regulatory element or with unusual domain arrangement in those genes. This study will help in understanding the evolution of these genes, the development of disease resistant varieties, and the mechanism of disease resistance in linseed.
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Affiliation(s)
- Sandip M Kale
- Biochemical Sciences Division, National Chemical Laboratory, Pune 411008, India
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Barvkar VT, Pardeshi VC, Kale SM, Kadoo NY, Giri AP, Gupta VS. Proteome profiling of flax (Linum usitatissimum) seed: characterization of functional metabolic pathways operating during seed development. J Proteome Res 2012; 11:6264-76. [PMID: 23153172 DOI: 10.1021/pr300984r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Flax (Linum usitatissimum L.) seeds are an important source of food and feed due to the presence of various health promoting compounds, making it a nutritionally and economically important plant. An in-depth analysis of the proteome of developing flax seed is expected to provide significant information with respect to the regulation and accumulation of such storage compounds. Therefore, a proteomic analysis of seven seed developmental stages (4, 8, 12, 16, 22, 30, and 48 days after anthesis) in a flax variety, NL-97 was carried out using a combination of 1D-SDS-PAGE and LC-MSE methods. A total 1716 proteins were identified and their functional annotation revealed that a majority of them were involved in primary metabolism, protein destination, storage and energy. Three carbon assimilatory pathways appeared to operate in flax seeds. Reverse transcription quantitative PCR of selected 19 genes was carried out to understand their roles during seed development. Besides storage proteins, methionine synthase, RuBisCO and S-adenosylmethionine synthetase were highly expressed transcripts, highlighting their importance in flax seed development. Further, the identified proteins were mapped onto developmental seed specific expressed sequence tag (EST) libraries of flax to obtain transcriptional evidence and 81% of them had detectable expression at the mRNA level. This study provides new insights into the complex seed developmental processes operating in flax.
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Affiliation(s)
- Vitthal T Barvkar
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India
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Barvkar VT, Pardeshi VC, Kale SM, Kadoo NY, Gupta VS. Phylogenomic analysis of UDP glycosyltransferase 1 multigene family in Linum usitatissimum identified genes with varied expression patterns. BMC Genomics 2012; 13:175. [PMID: 22568875 PMCID: PMC3412749 DOI: 10.1186/1471-2164-13-175] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 05/08/2012] [Indexed: 10/28/2022] Open
Abstract
BACKGROUND The glycosylation process, catalyzed by ubiquitous glycosyltransferase (GT) family enzymes, is a prevalent modification of plant secondary metabolites that regulates various functions such as hormone homeostasis, detoxification of xenobiotics and biosynthesis and storage of secondary metabolites. Flax (Linum usitatissimum L.) is a commercially grown oilseed crop, important because of its essential fatty acids and health promoting lignans. Identification and characterization of UDP glycosyltransferase (UGT) genes from flax could provide valuable basic information about this important gene family and help to explain the seed specific glycosylated metabolite accumulation and other processes in plants. Plant genome sequencing projects are useful to discover complexity within this gene family and also pave way for the development of functional genomics approaches. RESULTS Taking advantage of the newly assembled draft genome sequence of flax, we identified 137 UDP glycosyltransferase (UGT) genes from flax using a conserved signature motif. Phylogenetic analysis of these protein sequences clustered them into 14 major groups (A-N). Expression patterns of these genes were investigated using publicly available expressed sequence tag (EST), microarray data and reverse transcription quantitative real time PCR (RT-qPCR). Seventy-three per cent of these genes (100 out of 137) showed expression evidence in 15 tissues examined and indicated varied expression profiles. The RT-qPCR results of 10 selected genes were also coherent with the digital expression analysis. Interestingly, five duplicated UGT genes were identified, which showed differential expression in various tissues. Of the seven intron loss/gain positions detected, two intron positions were conserved among most of the UGTs, although a clear relationship about the evolution of these genes could not be established. Comparison of the flax UGTs with orthologs from four other sequenced dicot genomes indicated that seven UGTs were flax diverged. CONCLUSIONS Flax has a large number of UGT genes including few flax diverged ones. Phylogenetic analysis and expression profiles of these genes identified tissue and condition specific repertoire of UGT genes from this crop. This study would facilitate precise selection of candidate genes and their further characterization of substrate specificities and in planta functions.
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Affiliation(s)
- Vitthal T Barvkar
- Plant Molecular Biology Group, Biochemical Sciences Division, National Chemical Laboratory, Pune, India
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Kale SM, Pakhmode VK. Bilateral Tessier no. 4 facial cleft with left eye anophthalmos: a case report. J Indian Soc Pedod Prev Dent 2000; 18:87-9. [PMID: 11324202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
Abstract
Craniofacial clefts are very rare and manifest in a variety of patterns. Tessier classified these clefts in 1973 and numbered them 0 to 14. Tessier No. 4 Facial cleft is a rare variant of craniofacial cleft. Not more than 50 cases are reported in world literature, amongst which only 5 cases are true bilateral in nature. However, combinations of two different variants are not very uncommon. A case of male Indian child aged 4 years with a true bilateral Tessier No. 4 Facial cleft is reported. He also had anophthalmos of the left eye. This is probably the first case in which true bilateral Tessier No. 4 Facial cleft with anophthalmos of one eye is noticed.
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Affiliation(s)
- S M Kale
- Dept. of Plastic & Maxillofacial Surgery, Govt. Medical College & Hospital, Nagpur
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Kale SM, Panchegaonkar MR. Treatment of sarcoptic mange in goats with oil of karanj. Indian Vet J 1969; 46:624-5. [PMID: 5387924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Kale SM. Transportation of sheep by rail and road. Indian Vet J 1966; 43:354-357. [PMID: 5939987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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Kale SM, Phadke AV, Jamkhedkar PP. Clinical trials with methyridine (promintic-I.C.I.) in sheep. Indian Vet J 1966; 43:357-61. [PMID: 5949472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Kale SM, Bhave VS, Jamkhedkar PP. Sporadic obstructive urolithiasis in rams. Indian Vet J 1966; 43:200-3. [PMID: 5948859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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