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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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Pazhamala LT, Chaturvedi P, Bajaj P, Srikanth S, Ghatak A, Chitikineni A, Bellaire A, Hingane A, Kumar CVS, Saxena KB, Weckwerth W, Saxena RK, Varshney RK. Multiomics approach unravels fertility transition in a pigeonpea line for a two-line hybrid system. Plant Genome 2020; 13:e20028. [PMID: 33016616 DOI: 10.1002/tpg2.20028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/05/2020] [Accepted: 04/18/2020] [Indexed: 05/17/2023]
Abstract
Pigeonpea [Cajanus cajan (L.) Millsp.] is a pulse crop cultivated in the semi-arid regions of Asia and Africa. It is a rich source of protein and capable of alleviating malnutrition, improving soil health and the livelihoods of small-holder farmers. Hybrid breeding has provided remarkable improvements for pigeonpea productivity, but owing to a tedious and costly seed production system, an alternative two-line hybrid technology is being explored. In this regard, an environment-sensitive male sterile line has been characterized as a thermosensitive male sterile line in pigeonpea precisely responding to day temperature. The male sterile and fertile anthers from five developmental stages were studied by integrating transcriptomics, proteomics and metabolomics supported by precise phenotyping and scanning electron microscopic study. Spatio-temporal analysis of anther transcriptome and proteome revealed 17 repressed DEGs/DEPs in sterile anthers that play a critical role in normal cell wall morphogenesis and tapetal cell development. The male fertility to sterility transition was mainly due to a perturbation in auxin homeostasis, leading to impaired cell wall modification and sugar transport. Limited nutrient utilization thus leads to microspore starvation in response to moderately elevated day temperature which could be restored with auxin-treatment in the male sterile line. Our findings outline a molecular mechanism that underpins fertility transition responses thereby providing a process-oriented two-line hybrid breeding framework for pigeonpea.
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Affiliation(s)
- Lekha T Pazhamala
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Palak Chaturvedi
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Prasad Bajaj
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Sandhya Srikanth
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Anke Bellaire
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, 1030, Austria
| | - Anupama Hingane
- Crop Improvement Theme, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - C V Sameer Kumar
- Crop Improvement Theme, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - K B Saxena
- Crop Improvement Theme, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Rachit K Saxena
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
- Institute of Agriculture, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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Bohra A, Saxena KB, Varshney RK, Saxena RK. Genomics-assisted breeding for pigeonpea improvement. Theor Appl Genet 2020; 133:1721-1737. [PMID: 32062675 DOI: 10.1007/s00122-020-03563-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 07/31/2019] [Accepted: 02/08/2020] [Indexed: 05/25/2023]
Abstract
The review outlines advances in pigeonpea genomics, breeding and seed delivery systems to achieve yield gains at farmers' field. Pigeonpea is a nutritious and stress-tolerant grain legume crop of tropical and subtropical regions. Decades of breeding efforts in pigeonpea have resulted in development of a number of high-yielding cultivars. Of late, the development of CMS-based hybrid technology has allowed the exploitation of heterosis for yield enhancement in this crop. Despite these positive developments, the actual on-farm yield of pigeonpea is still well below its potential productivity. Growing needs for high and sustainable pigeonpea yields motivate scientists to improve the breeding efficiency to deliver a steady stream of cultivars that will provide yield benefits under both ideal and stressed environments. To achieve this objective in the shortest possible time, it is imperative that various crop breeding activities are integrated with appropriate new genomics technologies. In this context, the last decade has seen a remarkable rise in the generation of important genomic resources such as genome-wide markers, high-throughput genotyping assays, saturated genome maps, marker/gene-trait associations, whole-genome sequence and germplasm resequencing data. In some cases, marker/gene-trait associations are being employed in pigeonpea breeding programs to improve the valuable yield and market-preferred traits. Embracing new breeding tools like genomic selection and speed breeding is likely to improve genetic gains. Breeding high-yielding pigeonpea cultivars with key adaptation traits also calls for a renewed focus on systematic selection and utilization of targeted genetic resources. Of equal importance is to overcome the difficulties being faced by seed industry to take the new cultivars to the doorstep of farmers.
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Affiliation(s)
- Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
| | - K B Saxena
- , 17, NMC Housing, Al Ain, Abu Dhabi, United Arab Emirates
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
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Saxena KB, Saxena RK, Hickey LT, Varshney RK. Can a speed breeding approach accelerate genetic gain in pigeonpea? Euphytica 2019; 215:202. [PMID: 0 DOI: 10.1007/s10681-019-2520-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/28/2019] [Indexed: 05/28/2023]
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Yadav P, Saxena KB, Hingane A, Kumar CVS, Kandalkar VS, Varshney RK, Saxena RK. An "Axiom Cajanus SNP Array" based high density genetic map and QTL mapping for high-selfing flower and seed quality traits in pigeonpea. BMC Genomics 2019; 20:235. [PMID: 30898108 PMCID: PMC6429735 DOI: 10.1186/s12864-019-5595-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/11/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pigeonpea has considerable extent of insect-aided natural out-crossing that impedes genetic purity of seeds. Pre-anthesis cleistogamy in pigeonpea promotes self-pollination which helps in maintaining genetic purity. The cleistogamous flowers are linked with shriveled seeds, an undesirable trait from variety adoption point of view, and breeding using genomics tools can help in overcoming this constraint. Therefore, in order to identify genomic regions governing these target traits, one recombinant inbred line (RIL) population was developed using contrasting parents (ICPL 99010 and ICP 5529) for flower shape and shriveled seeds. The RILs were phenotyped for two years and genotyped using the Axiom Cajanus SNP Array. RESULTS Out of the 56,512 unique sequence variations on the array, the mapping population showed 8634 single nucleotide polymorphism (SNPs) segregating across the genome. These data facilitated generation of a high density genetic map covering 6818 SNPs in 974 cM with an average inter-marker distance of 0.1 cM, which is the lowest amongst all pigeonpea genetic maps reported. Quantitative trait loci (QTL) analysis using this genetic map and phenotyping data identified 5 QTLs associated with cleistogamous flower, 3 QTLs for shriveled seed and 1 QTL for seed size. The phenotypic variance explained by these QTLs ranged from 9.1 to 50.6%. A consistent QTL "qCl3.2" was identified for cleistogamous flower on CcLG03 covering a span of 42 kb in the pigeonpea genome. Epistatic QTLs were also identified for cleistogamous flower and shriveled seed traits. CONCLUSION Identified QTLs and genomic interactions for cleistogamous flower, shriveled seed and seed size will help in incorporating the required floral architecture in pigeonpea varieties/lines. Besides, it will also be useful in understanding the molecular mechanisms, and map-based gene cloning for the target traits.
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Affiliation(s)
- Pooja Yadav
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India.,Department of Genetics and Plant Breeding, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya (RVSKVV), Gwalior, 474 002, India
| | - K B Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Anupama Hingane
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - C V Sameer Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - V S Kandalkar
- Department of Genetics and Plant Breeding, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya (RVSKVV), Gwalior, 474 002, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India.
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Saxena RK, Rathore A, Bohra A, Yadav P, Das RR, Khan AW, Singh VK, Chitikineni A, Singh IP, Kumar CVS, Saxena KB, Varshney RK. Development and Application of High-Density Axiom Cajanus SNP Array with 56K SNPs to Understand the Genome Architecture of Released Cultivars and Founder Genotypes. Plant Genome 2018; 11:180005. [PMID: 30512043 DOI: 10.3835/plantgenome2018.01.0005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
As one of the major outputs of next-generation sequencing (NGS), a large number of genome-wide single-nucleotide polymorphisms (SNPs) have been developed in pigeonpea [ (L.) Huth.]. However, SNPs require a genotyping platform or assay to be used in different evolutionary studies or in crop improvement programs. Therefore, we developed an Axiom SNP array with 56K SNPs uniformly distributed across the genome and assessed its utility in a genetic diversity study. From the whole-genome resequencing (WGRS) data on 104 pigeonpea lines, ∼2 million sequence variations (SNPs and insertion-deletions [InDels]) were identified, from which a subset of 56,512 unique and informative sequence variations were selected to develop the array. The Axiom SNP array developed was used for genotyping 103 pigeonpea lines encompassing 63 cultivars released between 1960 and 2014 and 40 breeding, germplasm, and founder lines. Genotyping data thus generated on 103 pigeonpea lines provided 51,201 polymorphic SNPs and InDels. Genetic diversity analysis provided in-depth insights into the genetic architecture and trends in temporal diversity in pigeonpea cultivars. Therefore, the continuous use of the high-density Axiom SNP array developed will accelerate high-resolution trait mapping, marker-assisted breeding, and genomic selection efforts in pigeonpea.
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Obala J, Saxena RK, Singh VK, Kumar CVS, Saxena KB, Tongoona P, Sibiya J, Varshney RK. Development of sequence-based markers for seed protein content in pigeonpea. Mol Genet Genomics 2018; 294:57-68. [PMID: 30173295 DOI: 10.1007/s00438-018-1484-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 08/22/2018] [Indexed: 12/30/2022]
Abstract
Pigeonpea is an important source of dietary protein to over a billion people globally, but genetic enhancement of seed protein content (SPC) in the crop has received limited attention for a long time. Use of genomics-assisted breeding would facilitate accelerating genetic gain for SPC. However, neither genetic markers nor genes associated with this important trait have been identified in this crop. Therefore, the present study exploited whole genome re-sequencing (WGRS) data of four pigeonpea genotypes (~ 12X coverage) to identify sequence-based markers and associated candidate genes for SPC. By combining a common variant filtering strategy on available WGRS data with knowledge of gene functions in relation to SPC, 108 sequence variants from 57 genes were identified. These genes were assigned to 19 GO molecular function categories with 56% belonging to only two categories. Furthermore, Sanger sequencing confirmed presence of 75.4% of the variants in 37 genes. Out of 30 sequence variants converted into CAPS/dCAPS markers, 17 showed high level of polymorphism between low and high SPC genotypes. Assay of 16 of the polymorphic CAPS/dCAPS markers on an F2 population of the cross ICP 5529 (high SPC) × ICP 11605 (low SPC), resulted in four of the CAPS/dCAPS markers significantly (P < 0.05) co-segregated with SPC. In summary, four markers derived from mutations in four genes will be useful for enhancing/regulating SPC in pigeonpea crop improvement programs.
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Affiliation(s)
- Jimmy Obala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
- University of KwaZulu-Natal, African Center for Crop Improvement, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Vikas K Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - C V Sameer Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - K B Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Pangirayi Tongoona
- University of KwaZulu-Natal, African Center for Crop Improvement, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Julia Sibiya
- University of KwaZulu-Natal, African Center for Crop Improvement, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
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Saxena RK, Patel K, Sameer Kumar CV, Tyagi K, Saxena KB, Varshney RK. Molecular mapping and inheritance of restoration of fertility (Rf) in A4 hybrid system in pigeonpea (Cajanus cajan (L.) Millsp.). Theor Appl Genet 2018; 131:1605-1614. [PMID: 29705915 PMCID: PMC6061154 DOI: 10.1007/s00122-018-3101-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/20/2018] [Indexed: 05/29/2023]
Abstract
We report molecular mapping and inheritance of restoration of fertility (Rf) in A4 hybrid system in pigeonpea. We have also developed PCR-based markers amenable to low-cost genotyping to identify fertility restorer lines. Commercial hybrids in pigeonpea are based on A4 cytoplasmic male sterility (CMS) system, and their fertility restoration is one of the key prerequisites for breeding. In this context, an effort has been made to understand the genetics and identify quantitative trait loci (QTL) associated with restoration of fertility (Rf). One F2 population was developed by crossing CMS line (ICPA 2039) with fertility restorer line (ICPL 87119). Genetic analysis has shown involvement of two dominant genes in regulation of restoration of fertility. In parallel, the genotyping-by-sequencing (GBS) approach has generated ~ 33 Gb data on the F2 population. GBS data have provided 2457 single nucleotide polymorphism (SNPs) segregating across the mapping population. Based on these genotyping data, a genetic map has been developed with 306 SNPs covering a total length 981.9 cM. Further QTL analysis has provided the region flanked by S8_7664779 and S8_6474381 on CcLG08 harboured major QTL explained up to 28.5% phenotypic variation. Subsequently, sequence information within the major QTLs was compared between the maintainer and the restorer lines. From this sequence information, we have developed two PCR-based markers for identification of restorer lines from non-restorer lines and validated them on parental lines of hybrids as well as on another F2 mapping population. The results obtained in this study are expected to enhance the efficiency of selection for the identification of restorer lines in hybrid breeding and may reduce traditional time-consuming phenotyping activities.
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Affiliation(s)
- Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
| | - Kishan Patel
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - C V Sameer Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - K B Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia.
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Saxena RK, Obala J, Sinjushin A, Kumar CVS, Saxena KB, Varshney RK. Characterization and mapping of Dt1 locus which co-segregates with CcTFL1 for growth habit in pigeonpea. Theor Appl Genet 2017; 130:1773-1784. [PMID: 28540572 PMCID: PMC5565653 DOI: 10.1007/s00122-017-2924-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/11/2017] [Indexed: 05/13/2023]
Abstract
We report growth habit profiling following SEM, genetic mapping and QTL analysis. Highlighted CcTFL1 , a candidate for determinacy in pigeonpea, since an Indel marker derived from this gene co-segregated with Dt1 locus. Pigeonpea (Cajanus cajan) is one of the most important legume crops grown in arid and semi-arid regions of the world. It is characterized with few unique features compared with other legume species, such as Lotus, Medicago, and Glycine. One of them is growth habit, an important agronomic trait. In the present study, identification of mutations affecting growth habit accompanied by a precise analysis of phenotype has been done which will shed more light upon developmental regulation in pigeonpea. A genetic study was conducted to examine the inheritance of growth habit and a genotyping by sequencing (GBS)-based genetic map constructed using F2 mapping population derived from crossing parents ICP 5529 and ICP 11605. Inheritance studies clearly demonstrated the dominance of indeterminate (IDT) growth habit over determinate (DT) growth habit in F2 and F2:3 progenies. A total of 787 SNP markers were mapped in the genetic map of 1454 cM map length. Growth habit locus (Dt1) was mapped on the CcLG03 contributing more than 61% of total phenotypic variations. Subsequently, QTL analysis highlighted one gene, CcTFL1, as a candidate for determinacy in pigeonpea, since an Indel marker derived from this gene co-segregated with the Dt1 locus. Ability of this Indel-derived marker to differentiate DT/IDT lines was also validated on 262 pigeonpea lines. This study clearly demonstrated that CcTFL1 is a candidate gene for growth habit in pigeonpea and a user-friendly marker was developed in the present study which will allow low-cost genotyping without need of automation.
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Affiliation(s)
- Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India.
| | - Jimmy Obala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
- University of KwaZulu-Natal, African Center for Crop Improvement, Private Bag X01, Scottsville, 3209, Pietermaritzburg, South Africa
| | - Andrey Sinjushin
- M. V. Lomonosov Moscow State University, Leninskie Gory, Moscow, 119991, Russia
| | - C V Sameer Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - K B Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India.
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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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Sinha P, Saxena KB, Saxena RK, Singh VK, Suryanarayana V, Sameer Kumar CV, Katta MAVS, Khan AW, Varshney RK. Association of nad7a Gene with Cytoplasmic Male Sterility in Pigeonpea. Plant Genome 2015; 8:eplantgenome2014.11.0084. [PMID: 33228303 DOI: 10.3835/plantgenome2014.11.0084] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/26/2015] [Indexed: 06/11/2023]
Abstract
Cytoplasmic male sterility (CMS) has been exploited in the commercial pigeonpea [Cajanus cajan (L.) Millsp.] hybrid breeding system; however, the molecular mechanism behind this system is unknown. To understand the underlying molecular mechanism involved in A4 CMS system derived from C. cajanifolius (Haines) Maesen, 34 mitochondrial genes were analyzed for expression profiling and structural variation analysis between CMS line (ICRISAT Pigeonpea A line, ICPA 2039) and its cognate maintainer (ICPB 2039). Expression profiling of 34 mitochondrial genes revealed nine genes with significant fold differential gene expression at P ≤ 0.01, including one gene, nad4L, with 1366-fold higher expression in CMS line as compared with the maintainer. Structural variation analysis of these mitochondrial genes identified length variation between ICPA 2039 and ICPB 2039 for nad7a (subunit of nad7 gene). Sanger sequencing of nad4L and nad7a genes in the CMS and the maintainer lines identified two single nucleotide polymorphisms (SNPs) in upstream region of nad4L and a deletion of 10 bp in nad7a in the CMS line. Protein structure evaluation showed conformational changes in predicted protein structures for nad7a between ICPA 2039 and ICPB 2039 lines. All above analyses indicate association of nad7a gene with the CMS for A4 cytoplasm in pigeonpea. Additionally, one polymerase chain reaction (PCR) based Indel marker (nad7a_del) has been developed and validated for testing genetic purity of A4 derived CMS lines to strengthen the commercial hybrid breeding program in pigeonpea.
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Affiliation(s)
- Pallavi Sinha
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - K B Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Vikas K Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - V Suryanarayana
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - C V Sameer Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Mohan A V S Katta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Aamir W Khan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
- School of Plant Biology and Institute of Agriculture, The Univ. of Western Australia, 35 Stirling Hwy., Crawley, WA, 6009, Australia
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Saxena RK, Saxena KB, Pazhamala LT, Patel K, Parupalli S, Sameerkumar CV, Varshney RK. Genomics for greater efficiency in pigeonpea hybrid breeding. Front Plant Sci 2015; 6:793. [PMID: 26483810 PMCID: PMC4589649 DOI: 10.3389/fpls.2015.00793] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/12/2015] [Indexed: 05/20/2023]
Abstract
Cytoplasmic genic male sterility (CGMS) based hybrid technology has demonstrated its immense potential in increasing the productivity of various crops, including pigeonpea. This technology has shown promise for breaking the long-standing yield stagnation in pigeonpea. There are difficulties in commercial hybrid seed production due to non-availability of field-oriented technologies such as time-bound assessment of genetic purity of hybrid seeds. Besides this, there are other routine breeding activities which are labor oriented and need more resources. These include breeding and maintenance of new fertility restorers and maintainer lines, diversification of cytoplasm, and incorporation of biotic and abiotic stress resistances. The recent progress in genomics research could accelerate the existing traditional efforts to strengthen the hybrid breeding technology. Marker based seed purity assessment, identification of heterotic groups; selection of new fertility restorers are few areas which have already been initiated. In this paper efforts have been made to identify critical areas and opportunities where genomics can play a leading role and assist breeders in accelerating various activities related to breeding and commercialization of pigeonpea hybrids.
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Affiliation(s)
- Rachit K. Saxena
- *Correspondence: Rachit K. Saxena, International Crops Research Institute for the Semi-Arid Tropics, Building No. 300, Center of Excellence in Genomics, ICRISAT, Patancheru, Hyderabad 502324, India,
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Tuteja R, Saxena RK, Davila J, Shah T, Chen W, Xiao YL, Fan G, Saxena KB, Alverson AJ, Spillane C, Town C, Varshney RK. Cytoplasmic male sterility-associated chimeric open reading frames identified by mitochondrial genome sequencing of four Cajanus genotypes. DNA Res 2013; 20:485-95. [PMID: 23792890 PMCID: PMC3789559 DOI: 10.1093/dnares/dst025] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The hybrid pigeonpea (Cajanus cajan) breeding technology based on cytoplasmic male sterility (CMS) is currently unique among legumes and displays major potential for yield increase. CMS is defined as a condition in which a plant is unable to produce functional pollen grains. The novel chimeric open reading frames (ORFs) produced as a results of mitochondrial genome rearrangements are considered to be the main cause of CMS. To identify these CMS-related ORFs in pigeonpea, we sequenced the mitochondrial genomes of three C. cajan lines (the male-sterile line ICPA 2039, the maintainer line ICPB 2039, and the hybrid line ICPH 2433) and of the wild relative (Cajanus cajanifolius ICPW 29). A single, circular-mapping molecule of length 545.7 kb was assembled and annotated for the ICPA 2039 line. Sequence annotation predicted 51 genes, including 34 protein-coding and 17 RNA genes. Comparison of the mitochondrial genomes from different Cajanus genotypes identified 31 ORFs, which differ between lines within which CMS is present or absent. Among these chimeric ORFs, 13 were identified by comparison of the related male-sterile and maintainer lines. These ORFs display features that are known to trigger CMS in other plant species and to represent the most promising candidates for CMS-related mitochondrial rearrangements in pigeonpea.
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Affiliation(s)
- Reetu Tuteja
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Plant and AgriBiosciences Centre (PABC), School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Rachit K. Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Jaime Davila
- Center for Plant Science Innovation, University of Nebraska, Lincoln, USA
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, USA
| | - Trushar Shah
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Wenbin Chen
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Yong-Li Xiao
- J. Craig Venter Institute (JCVI), Rockville, USA
| | - Guangyi Fan
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - K. B. Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Andrew J. Alverson
- Department of Biological Sciences, University of Arkansas, Arkansas, USA
| | - Charles Spillane
- Plant and AgriBiosciences Centre (PABC), School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | | | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- To whom correspondence should be addressed. Tel. +914030713305. Fax. +914030713071. E-mail:
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Varshney RK, Kudapa H, Roorkiwal M, Thudi M, Pandey MK, Saxena RK, Chamarthi SK, Mohan SM, Mallikarjuna N, Upadhyaya H, Gaur PM, Krishnamurthy L, Saxena KB, Nigam SN, Pande S. Advances in genetics and molecular breeding of three legume crops of semi-arid tropics using next-generation sequencing and high-throughput genotyping technologies. J Biosci 2013; 37:811-20. [PMID: 23107917 DOI: 10.1007/s12038-012-9228-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular markers are the most powerful genomic tools to increase the efficiency and precision of breeding practices for crop improvement. Progress in the development of genomic resources in the leading legume crops of the semi-arid tropics (SAT), namely, chickpea (Cicer arietinum), pigeonpea (Cajanus cajan) and groundnut (Arachis hypogaea), as compared to other crop species like cereals, has been very slow. With the advances in next-generation sequencing (NGS) and high-throughput (HTP) genotyping methods, there is a shift in development of genomic resources including molecular markers in these crops. For instance, 2,000 to 3,000 novel simple sequence repeats (SSR) markers have been developed each for chickpea, pigeonpea and groundnut. Based on Sanger, 454/FLX and Illumina transcript reads, transcriptome assemblies have been developed for chickpea (44,845 transcript assembly contigs, or TACs) and pigeonpea (21,434 TACs). Illumina sequencing of some parental genotypes of mapping populations has resulted in the development of 120 million reads for chickpea and 128.9 million reads for pigeonpea. Alignment of these Illumina reads with respective transcriptome assemblies have provided more than 10,000 SNPs each in chickpea and pigeonpea. A variety of SNP genotyping platforms including GoldenGate, VeraCode and Competitive Allele Specific PCR (KASPar) assays have been developed in chickpea and pigeonpea. By using above resources, the first-generation or comprehensive genetic maps have been developed in the three legume speciesmentioned above. Analysis of phenotyping data together with genotyping data has provided candidate markers for drought-tolerance-related root traits in chickpea, resistance to foliar diseases in groundnut and sterility mosaic disease (SMD) and fertility restoration in pigeonpea. Together with these traitassociated markers along with those already available, molecular breeding programmes have been initiated for enhancing drought tolerance, resistance to fusarium wilt and ascochyta blight in chickpea and resistance to foliar diseases in groundnut. These trait-associated robust markers along with other genomic resources including genetic maps and genomic resources will certainly accelerate crop improvement programmes in the SAT legumes.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502 324, India.
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Varshney RK, Mohan SM, Gaur PM, Gangarao NVPR, Pandey MK, Bohra A, Sawargaonkar SL, Chitikineni A, Kimurto PK, Janila P, Saxena KB, Fikre A, Sharma M, Rathore A, Pratap A, Tripathi S, Datta S, Chaturvedi SK, Mallikarjuna N, Anuradha G, Babbar A, Choudhary AK, Mhase MB, Bharadwaj C, Mannur DM, Harer PN, Guo B, Liang X, Nadarajan N, Gowda CLL. Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics. Biotechnol Adv 2013; 31:1120-34. [PMID: 23313999 DOI: 10.1016/j.biotechadv.2013.01.001] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 12/16/2012] [Accepted: 01/03/2013] [Indexed: 10/27/2022]
Abstract
Advances in next-generation sequencing and genotyping technologies have enabled generation of large-scale genomic resources such as molecular markers, transcript reads and BAC-end sequences (BESs) in chickpea, pigeonpea and groundnut, three major legume crops of the semi-arid tropics. Comprehensive transcriptome assemblies and genome sequences have either been developed or underway in these crops. Based on these resources, dense genetic maps, QTL maps as well as physical maps for these legume species have also been developed. As a result, these crops have graduated from 'orphan' or 'less-studied' crops to 'genomic resources rich' crops. This article summarizes the above-mentioned advances in genomics and genomics-assisted breeding applications in the form of marker-assisted selection (MAS) for hybrid purity assessment in pigeonpea; marker-assisted backcrossing (MABC) for introgressing QTL region for drought-tolerance related traits, Fusarium wilt (FW) resistance and Ascochyta blight (AB) resistance in chickpea; late leaf spot (LLS), leaf rust and nematode resistance in groundnut. We critically present the case of use of other modern breeding approaches like marker-assisted recurrent selection (MARS) and genomic selection (GS) to utilize the full potential of genomics-assisted breeding for developing superior cultivars with enhanced tolerance to various environmental stresses. In addition, this article recommends the use of advanced-backcross (AB-backcross) breeding and development of specialized populations such as multi-parents advanced generation intercross (MAGIC) for creating new variations that will help in developing superior lines with broadened genetic base. In summary, we propose the use of integrated genomics and breeding approach in these legume crops to enhance crop productivity in marginal environments ensuring food security in developing countries.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; CGIAR Generation Challenge Programme (GCP), c/o CIMMYT, DF 06600, Mexico; The University of Western Australia, Crawley 6009, Australia; Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou 510640, China.
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Sharma M, Ghosh R, Mangla UN, Saxena KB, Pande S. Alternaria tenuissima Causing Alternaria Blight on Pigeonpea in India. Plant Dis 2012; 96:907. [PMID: 30727370 DOI: 10.1094/pdis-01-12-0060-pdn] [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] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pigeonpea (Cajanus cajan (L.) Millsp.) is a major grain legume of the tropics and subtropics worldwide. In India, pigeonpea is the third most important food legume after chickpea and field pea. Blight symptoms on pigeonpea were observed in alarming proportion during the 2009 through 2011 crop seasons in Andhra Pradesh state in India. Disease incidence ranged from 20 to 80% irrespective of cultivars sown. Infected plants in the field showed symptoms on all aerial parts of the plant (leaves, stems, buds, and pods) irrespective of age of the plant and leaves. Symptoms on leaves were small, circular, necrotic spots that developed quickly forming typical concentric rings (1). Later, these spots coalesced and caused blighting of leaves. Spots were initially light brown and later turned dark brown. On stems, spots were sunken with concentric rings. In severe infection, defoliation and drying of infected leaves, branches, and flower buds was observed. The fungus was successfully isolated from all the infected plant parts (leaves, stem, buds, and pods) on potato dextrose agar (PDA) medium. After 4 to 5 days of incubation at 28 ± 1°C with a 12-h photoperiod, the fungus produced colonies that were regular and flat. The periphery of the colony was olive green with a black center. Monoconidial isolations were used to establish a pure culture of the fungus. Conidiophores were short, arising singly, and were 8.86 mm long and 2.97 mm thick. Conidia varied from 15.78 to 28.70 mm long and 8.03 to 13.47 mm wide. Very small beak (1.6 to 3.2 mm) or no beak was observed. Horizontal and vertical septations of conidia varied from four to six and two to four, respectively. The pathogenicity test was conducted on 8- to 10-day-old pigeonpea plants of cultivar ICPL 87119 by spraying with a conidial suspension (5 × 105 conidia/ml). Inoculated plants were covered with polythene bags and kept in a greenhouse at 28 ± 1°C with a 12-h photoperiod. After 48 h, the polythene bags were removed. Ten days after inoculation, symptoms were similar to those observed in fields. This experiment was conducted twice with two independent sets of plants. No symptoms were observed in water-inoculated control plants. The fungus was reisolated from the inoculated plants. On the basis of the morphological characteristics, the pathogen was tentatively identified as Alternaria tenuissima. The identification was further confirmed by the rDNA and internal transcribed spacer (ITS) primer. The ITS region of rDNA was amplified with ITS 1 and ITS 4 primers. Both orientation sequenced amplicons (481 bp) were submitted to GenBank (Accession No. JQ074094). A BLASTn search revealed 99% similarity to A. tenuissima (Accession No. HQ343444). To our knowledge, this is the first report of molecular identification of A. tenuissima causing Alternaria blight in pigeonpea in India. Reference: (1) Kannaiyan, J. and Nene, Y. L. 1977. Trop. Grain Legume Bull. 9:34.
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Affiliation(s)
- M Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Greater Hyderabad, Andhra Pradesh, India
| | - R Ghosh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Greater Hyderabad, Andhra Pradesh, India
| | - U N Mangla
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Greater Hyderabad, Andhra Pradesh, India
| | - K B Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Greater Hyderabad, Andhra Pradesh, India
| | - S Pande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Greater Hyderabad, Andhra Pradesh, India
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Upadhyaya HD, Kashiwagi J, Varshney RK, Gaur PM, Saxena KB, Krishnamurthy L, Gowda CLL, Pundir RPS, Chaturvedi SK, Basu PS, Singh IP. Phenotyping chickpeas and pigeonpeas for adaptation to drought. Front Physiol 2012; 3:179. [PMID: 22675307 PMCID: PMC3365634 DOI: 10.3389/fphys.2012.00179] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 05/16/2012] [Indexed: 11/28/2022] Open
Abstract
The chickpea and pigeonpea are protein-rich grain legumes used for human consumption in many countries. Grain yield of these crops is low to moderate in the semi-arid tropics with large variation due to high GxE interaction. In the Indian subcontinent chickpea is grown in the post-rainy winter season on receding soil moisture, and in other countries during the cool and dry post winter or spring seasons. The pigeonpea is sown during rainy season which flowers and matures in post-rainy season. The rainy months are hot and humid with diurnal temperature varying between 25 and 35°C (maximum) and 20 and 25°C (minimum) with an erratic rainfall. The available soil water during post-rainy season is about 200-250 mm which is bare minimum to meet the normal evapotranspiration. Thus occurrence of drought is frequent and at varying degrees. To enhance productivity of these crops cultivars tolerant to drought need to be developed. ICRISAT conserves a large number of accessions of chickpea (>20,000) and pigeonpea (>15,000). However only a small proportion (<1%) has been used in crop improvement programs mainly due to non-availability of reliable information on traits of economic importance. To overcome this, core and mini core collections (10% of core, 1% of entire collection) have been developed. Using the mini core approach, trait-specific donor lines were identified for agronomic, quality, and stress related traits in both crops. Composite collections were developed both in chickpea (3000 accessions) and pigeonpea (1000 accessions), genotyped using SSR markers and genotype based reference sets of 300 accessions selected for each crop. Screening methods for different drought-tolerant traits such as early maturity (drought escape), large and deep root system, high water-use efficiency, smaller leaflets, reduced canopy temperature, carbon isotope discrimination, high leaf chlorophyll content (drought avoidance), and breeding strategies for improving drought tolerance have been discussed.
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Affiliation(s)
- H. D. Upadhyaya
- International Crops Research Institute for the Semi Arid TropicsHyderabad, India
| | - J. Kashiwagi
- Crop Science Laboratory, Graduate School of Agriculture, Hokkaido UniversitySapporo, Japan
| | - R. K. Varshney
- International Crops Research Institute for the Semi Arid TropicsHyderabad, India
| | - P. M. Gaur
- International Crops Research Institute for the Semi Arid TropicsHyderabad, India
| | - K. B. Saxena
- International Crops Research Institute for the Semi Arid TropicsHyderabad, India
| | - L. Krishnamurthy
- International Crops Research Institute for the Semi Arid TropicsHyderabad, India
| | - C. L. L. Gowda
- International Crops Research Institute for the Semi Arid TropicsHyderabad, India
| | - R. P. S. Pundir
- International Crops Research Institute for the Semi Arid TropicsHyderabad, India
| | | | - P. S. Basu
- Indian Institute of Pulses ResearchKanpur, India
| | - I. P. Singh
- Indian Institute of Pulses ResearchKanpur, India
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Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA, Donoghue MTA, Azam S, Fan G, Whaley AM, Farmer AD, Sheridan J, Iwata A, Tuteja R, Penmetsa RV, Wu W, Upadhyaya HD, Yang SP, Shah T, Saxena KB, Michael T, McCombie WR, Yang B, Zhang G, Yang H, Wang J, Spillane C, Cook DR, May GD, Xu X, Jackson SA. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 2011; 30:83-9. [PMID: 22057054 DOI: 10.1038/nbt.2022] [Citation(s) in RCA: 421] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 10/03/2011] [Indexed: 11/08/2022]
Abstract
Pigeonpea is an important legume food crop grown primarily by smallholder farmers in many semi-arid tropical regions of the world. We used the Illumina next-generation sequencing platform to generate 237.2 Gb of sequence, which along with Sanger-based bacterial artificial chromosome end sequences and a genetic map, we assembled into scaffolds representing 72.7% (605.78 Mb) of the 833.07 Mb pigeonpea genome. Genome analysis predicted 48,680 genes for pigeonpea and also showed the potential role that certain gene families, for example, drought tolerance-related genes, have played throughout the domestication of pigeonpea and the evolution of its ancestors. Although we found a few segmental duplication events, we did not observe the recent genome-wide duplication events observed in soybean. This reference genome sequence will facilitate the identification of the genetic basis of agronomically important traits, and accelerate the development of improved pigeonpea varieties that could improve food security in many developing countries.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
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Varshney RK, Penmetsa RV, Dutta S, Kulwal PL, Saxena RK, Datta S, Sharma TR, Rosen B, Carrasquilla-Garcia N, Farmer AD, Dubey A, Saxena KB, Gao J, Fakrudin B, Singh MN, Singh BP, Wanjari KB, Yuan M, Srivastava RK, Kilian A, Upadhyaya HD, Mallikarjuna N, Town CD, Bruening GE, He G, May GD, McCombie R, Jackson SA, Singh NK, Cook DR. Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.). Mol Breed 2010; 26:393-408. [PMID: 20976284 PMCID: PMC2948155 DOI: 10.1007/s11032-009-9327-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Accepted: 08/05/2009] [Indexed: 05/18/2023]
Abstract
Pigeonpea (Cajanus cajan), an important food legume crop in the semi-arid regions of the world and the second most important pulse crop in India, has an average crop productivity of 780 kg/ha. The relatively low crop yields may be attributed to non-availability of improved cultivars, poor crop husbandry and exposure to a number of biotic and abiotic stresses in pigeonpea growing regions. Narrow genetic diversity in cultivated germplasm has further hampered the effective utilization of conventional breeding as well as development and utilization of genomic tools, resulting in pigeonpea being often referred to as an 'orphan crop legume'. To enable genomics-assisted breeding in this crop, the pigeonpea genomics initiative (PGI) was initiated in late 2006 with funding from Indian Council of Agricultural Research under the umbrella of Indo-US agricultural knowledge initiative, which was further expanded with financial support from the US National Science Foundation's Plant Genome Research Program and the Generation Challenge Program. As a result of the PGI, the last 3 years have witnessed significant progress in development of both genetic as well as genomic resources in this crop through effective collaborations and coordination of genomics activities across several institutes and countries. For instance, 25 mapping populations segregating for a number of biotic and abiotic stresses have been developed or are under development. An 11X-genome coverage bacterial artificial chromosome (BAC) library comprising of 69,120 clones have been developed of which 50,000 clones were end sequenced to generate 87,590 BAC-end sequences (BESs). About 10,000 expressed sequence tags (ESTs) from Sanger sequencing and ca. 2 million short ESTs by 454/FLX sequencing have been generated. A variety of molecular markers have been developed from BESs, microsatellite or simple sequence repeat (SSR)-enriched libraries and mining of ESTs and genomic amplicon sequencing. Of about 21,000 SSRs identified, 6,698 SSRs are under analysis along with 670 orthologous genes using a GoldenGate SNP (single nucleotide polymorphism) genotyping platform, with large scale SNP discovery using Solexa, a next generation sequencing technology, is in progress. Similarly a diversity array technology array comprising of ca. 15,000 features has been developed. In addition, >600 unique nucleotide binding site (NBS) domain containing members of the NBS-leucine rich repeat disease resistance homologs were cloned in pigeonpea; 960 BACs containing these sequences were identified by filter hybridization, BES physical maps developed using high information content fingerprinting. To enrich the genomic resources further, sequenced soybean genome is being analyzed to establish the anchor points between pigeonpea and soybean genomes. In addition, Solexa sequencing is being used to explore the feasibility of generating whole genome sequence. In summary, the collaborative efforts of several research groups under the umbrella of PGI are making significant progress in improving molecular tools in pigeonpea and should significantly benefit pigeonpea genetics and breeding. As these efforts come to fruition, and expanded (depending on funding), pigeonpea would move from an 'orphan legume crop' to one where genomics-assisted breeding approaches for a sustainable crop improvement are routine.
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Affiliation(s)
- R. K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh 502324 India
- Genomics Towards Gene Discovery Subprogramme, Generation Challenge Program (GCP), c/o CIMMYT, Int APDO Postal 6-641, 06600 Mexico DF, Mexico
| | - R. V. Penmetsa
- Department of Plant Pathology, University of California, 354 Hutchison Hall, One Shields Avenue, Davis, CA 95616-8680 USA
| | - S. Dutta
- National Research Centre on Plant Biotechnology, IARI Campus, New Delhi, 110 012 India
| | - P. L. Kulwal
- Dr. Panjabrao Deshmukh Agricultural University (PDAU), Krishinagar, Akola, Maharasthra 444 104 India
| | - R. K. Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh 502324 India
| | - S. Datta
- Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh 208024 India
| | - T. R. Sharma
- National Research Centre on Plant Biotechnology, IARI Campus, New Delhi, 110 012 India
| | - B. Rosen
- Department of Plant Pathology, University of California, 354 Hutchison Hall, One Shields Avenue, Davis, CA 95616-8680 USA
| | - N. Carrasquilla-Garcia
- Department of Plant Pathology, University of California, 354 Hutchison Hall, One Shields Avenue, Davis, CA 95616-8680 USA
| | - A. D. Farmer
- National Center for Genome Resources (NCGR), 2935 Rodeo Park Drive East, Santa Fe, NM 87505 USA
| | - A. Dubey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh 502324 India
| | - K. B. Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh 502324 India
| | - J. Gao
- Department of Plant Pathology, University of California, 354 Hutchison Hall, One Shields Avenue, Davis, CA 95616-8680 USA
| | - B. Fakrudin
- University of Agricultural Sciences, Dharwad, Karnataka 580005 India
| | - M. N. Singh
- Banaras Hindu University, Varanasi, Uttar Pradesh 221005 India
| | - B. P. Singh
- National Research Centre on Plant Biotechnology, IARI Campus, New Delhi, 110 012 India
| | - K. B. Wanjari
- Dr. Panjabrao Deshmukh Agricultural University (PDAU), Krishinagar, Akola, Maharasthra 444 104 India
| | - M. Yuan
- Tuskegee University, Tuskegee, AL 36088 USA
| | - R. K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh 502324 India
| | - A. Kilian
- Diversity Arrays Technology Pty Ltd, 1 Wilf Crane Crescent, Yarralumla, ACT 2600 Australia
| | - H. D. Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh 502324 India
| | - N. Mallikarjuna
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh 502324 India
| | - C. D. Town
- J. Craig Venter Institute (JCVI), 9704 Medical Center Drive, Rockville, MD 20850 USA
| | - G. E. Bruening
- Department of Plant Pathology, University of California, 354 Hutchison Hall, One Shields Avenue, Davis, CA 95616-8680 USA
| | - G. He
- Tuskegee University, Tuskegee, AL 36088 USA
| | - G. D. May
- National Center for Genome Resources (NCGR), 2935 Rodeo Park Drive East, Santa Fe, NM 87505 USA
| | - R. McCombie
- Cold Spring Harbor Laboratory, Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
| | - S. A. Jackson
- Department of Agronomy, Purdue University, West Lafayette, IN 47907-2054 USA
| | - N. K. Singh
- National Research Centre on Plant Biotechnology, IARI Campus, New Delhi, 110 012 India
| | - D. R. Cook
- Department of Plant Pathology, University of California, 354 Hutchison Hall, One Shields Avenue, Davis, CA 95616-8680 USA
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Dalvi VA, Saxena KB, Madrap IA, Ravikoti VK. Cytogenetic Studies in A4 Cytoplasmic-Nuclear Male-Sterility System of Pigeonpea. J Hered 2008; 99:667-70. [DOI: 10.1093/jhered/esn056] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Jones AT, Kumar PL, Saxena KB, Kulkarni NK, Muniyappa V, Waliyar F. Sterility Mosaic Disease-the "Green Plague" of Pigeonpea: Advances in Understanding the Etiology, Transmission and Control of a Major Virus Disease. Plant Dis 2004; 88:436-445. [PMID: 30812645 DOI: 10.1094/pdis.2004.88.5.436] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pigeonpea (Cajanus cajan), is a grain legume that is a very important subsistence crop in marginal farming systems adopted by millions of smallholder farmers in the Indian subcontinent. It is grown for its seed for human consumption and for income generation by trading surpluses in local and commercial markets, but is widely used for diverse purposes, including as animal fodder and for soil conservation. Sterility mosaic (SMD) is the most damaging disease of pigeonpea endemic in the Indian subcontinent. It causes yield losses of >US$300 million per annum in India and Nepal alone. SMD-affected plants show severe stunting and mosaic symptoms on leaves, with complete or partial cessation of flowering. The SMD causal agent is spread by the arthropod mite vector Aceria cajani (Acari: Eriophyidae). Cultivating SMD-resistant genotypes is the most viable way to manage this serious disease of pigeonpea. Progress in developing broad-based SMD resistant material has been hindered by the lack of knowledge of the causal agent, the absence of diagnostic tools, and factors influencing host-plant resistance. After seven decades of research, vital breakthroughs made on the identification, detection, transmission, and epidemiology of the SMD causal agent, Pigeonpea sterility mosaic virus (PPSMV), are enabling the development of broad-based durable resistant pigeonpea cultivars. These breakthroughs will contribute greatly to sustainable pigeonpea production and enhance the income and livelihood of poor farmers in the semi-arid tropics of the Indian subcontinent.
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Affiliation(s)
| | - P Lava Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India, and SCRI
| | | | - N K Kulkarni
- University of Agriculture Sciences (UAS), Bangalore, India, and ICRISAT
| | - V Muniyappa
- University of Agriculture Sciences, Bangalore, India
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Abstract
A natural male-sterile mutant was found in the population of a short-duration pigeonpea (Cajanus cajan[L.] Millsp.) cultivar ICPL 85010. This mutant is characterized by light yellow anthers of reduced size that are devoid of pollen grains. This mutant was crossed with two pigeonpea cultivars to study its inheritance. The F1, F2, and test cross data of the two crosses suggested that this male sterility trait is genetic in origin and is controlled by a single recessivegene. The F1 (mutant x ICPL 85010) plants were crossed with translucent (ms1) and arrowhead type (ms2) genetic male steriles reported earlier to study their allelic relationships. Segregation in the three-way cross F1 and F2 populations revealed that the mutant male-sterile gene was nonallelic to ms1 and ms2 loci and it is designated ms3. The new male sterility sources in pigeonpea will help in producing high-yielding hybrids and populations in diverse phenological groups.
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Affiliation(s)
- K B Saxena
- Genetic Resources and Enhancement Program, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, A. P. India.
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Swart WJ, Mathews C, Saxena KB. First Report of Leaf Rust Caused by Uredo cajani on Pigeonpea in South Africa. Plant Dis 2000; 84:1344. [PMID: 30831885 DOI: 10.1094/pdis.2000.84.12.1344b] [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] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pigeonpea (Cajanus cajan [L.] Mills.) is an important legume with potential as a dryland crop with multiple uses in the semi-arid areas of South Africa. Approximately 150 tons of dry, split seeds are imported monthly to meet the needs of South Africa. In May 2000, field trials and farmer's plots with plant ages varying from 1 to 3 years old were visited in Mpumalanga and Kwazulu-Natal to assess problems associated with pigeonpea cultivation. Rust was prevalent on more than 80% of plants on young and old leaves at all sites but was most severe at sites in Mpumalanga, where severe rust was observed on all 17 ICRISAT varieties evaluated. Leaf lesions began as chlorotic flecks that expanded and developed into necrotic spots with several orange red to brown uredinia present mostly on the abaxial sides of leaves. Urediospores were 1-celled and initially hyaline, turning dark orange, minutely echinulate, spherical with 2 to 4 circular germpores and measured 20-27 × 17 to 21μ. No telia were found and all morphological characteristics therefore correspond with the CMI description of Uredo cajani Syd. (1). In Africa, pigeonpea rust has been reported from Kenya, Nigeria, Sierra Leone, Tanzania, and Uganda. In South Africa, rust, described as Uromyces dolicholi Arthur (2), has only once been reported on pigeonpea. In the United States, U. dolicholi has also once been reported on pigeonpea (3). However, since U. dolicholi, unlike U. cajani, produces telia and occurs only on Rhyncosia spp. (4), these reports can be considered incorrect. This is therefore the first report of U. cajani on pigeonpea in South Africa. References: (1) K. H. Anahosur and J. M. Waller. 1978. No. 590: Descriptions of Plant Pathogenic Fungi and Bacteria. Commonw. Mycol. Inst., Kew, England. (2) E. M. Doidge. Bothalia 5:1-1094, 1950. (3) D. F. Farr et al. 1989. Fungi on Plants and Plant Products in the United States. American Phytopathological Society, St. Paul, MN, 1989. (4) A. Sivanesan. 1970. No. 269: Descriptions of Plant Pathogenic Fungi and Bacteria. Commonw. Mycol. Inst., Kew, England.
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Affiliation(s)
- W J Swart
- Department of Plant Pathology, University of the Free State, Bloemfontein, South Africa
| | - C Mathews
- Department of Agriculture, Conservation and Environment, Mpumalanga, South Africa
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Saxena KB, Faris DG, Singh U, Kumar RV. Relationship between seed size and protein content in newly developed high protein lines of pigeonpea. ACTA ACUST UNITED AC 1987. [DOI: 10.1007/bf01892354] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Tewari JP, Saxena KB. An appratus for recording the movements of Helminths. A short note. Indian J Med Sci 1967; 21:406-7. [PMID: 6073138] [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: 01/18/2023]
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