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Bhatnagar-Mathur P, Gupta R, Reddy PS, Reddy BP, Reddy DS, Sameerkumar CV, Saxena RK, Sharma KK. A novel mitochondrial orf147 causes cytoplasmic male sterility in pigeonpea by modulating aberrant anther dehiscence. Plant Mol Biol 2018; 97:131-147. [PMID: 29667000 DOI: 10.1007/s11103-018-0728-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 04/13/2017] [Accepted: 04/06/2018] [Indexed: 06/08/2023]
Abstract
KEY MESSAGE A novel open reading frame (ORF) identified and cloned from the A4 cytoplasm of Cajanus cajanifolius induced partial to complete male sterility when introduced into Arabidopsis and tobacco. Pigeonpea (Cajanus cajan L. Millsp.) is the only legume known to have commercial hybrid seed technology based on cytoplasmic male sterility (CMS). We identified a novel ORF (orf147) from the A4 cytoplasm of C. cajanifolius that was created via rearrangements in the CMS line and co-transcribes with the known and unknown sequences. The bi/poly-cistronic transcripts cause gain-of-function variants in the mitochondrial genome of CMS pigeonpea lines having distinct processing mechanisms and transcription start sites. In presence of orf147, significant repression of Escherichia coli growth indicated its toxicity to the host cells and induced partial to complete male sterility in transgenic progenies of Arabidopsis thaliana and Nicotiana tabacum where phenotype co-segregated with the transgene. The male sterile plants showed aberrant floral development and reduced lignin content in the anthers. Gene expression studies in male sterile pigeonpea, Arabidopsis and tobacco plants confirmed down-regulation of several anther biogenesis genes and key genes involved in monolignol biosynthesis, indicative of regulation of retrograde signaling. Besides providing evidence for the involvement of orf147 in pigeonpea CMS, this study provides valuable insights into its function. Cytotoxicity and aberrant programmed cell death induced by orf147 could be important for mechanism underlying male sterility that offers opportunities for possible translation for these findings for exploiting hybrid vigor in other recalcitrant crops as well.
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Affiliation(s)
- Pooja Bhatnagar-Mathur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India.
| | - Ranadheer Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
| | - Palakolanu Sudhakar Reddy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
| | - Bommineni Pradeep Reddy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
| | - Dumbala Srinivas Reddy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
| | - C V Sameerkumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
| | - Rachit Kumar Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
| | - Kiran K Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 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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Pazhamala L, Saxena RK, Singh VK, Sameerkumar CV, Kumar V, Sinha P, Patel K, Obala J, Kaoneka SR, Tongoona P, Shimelis HA, Gangarao NVPR, Odeny D, Rathore A, Dharmaraj PS, Yamini KN, Varshney RK. Genomics-assisted breeding for boosting crop improvement in pigeonpea (Cajanus cajan). Front Plant Sci 2015; 6:50. [PMID: 25741349 PMCID: PMC4330709 DOI: 10.3389/fpls.2015.00050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/20/2015] [Indexed: 05/18/2023]
Abstract
Pigeonpea is an important pulse crop grown predominantly in the tropical and sub-tropical regions of the world. Although pigeonpea growing area has considerably increased, yield has remained stagnant for the last six decades mainly due to the exposure of the crop to various biotic and abiotic constraints. In addition, low level of genetic variability and limited genomic resources have been serious impediments to pigeonpea crop improvement through modern breeding approaches. In recent years, however, due to the availability of next generation sequencing and high-throughput genotyping technologies, the scenario has changed tremendously. The reduced sequencing costs resulting in the decoding of the pigeonpea genome has led to the development of various genomic resources including molecular markers, transcript sequences and comprehensive genetic maps. Mapping of some important traits including resistance to Fusarium wilt and sterility mosaic disease, fertility restoration, determinacy with other agronomically important traits have paved the way for applying genomics-assisted breeding (GAB) through marker assisted selection as well as genomic selection (GS). This would accelerate the development and improvement of both varieties and hybrids in pigeonpea. Particularly for hybrid breeding programme, mitochondrial genomes of cytoplasmic male sterile (CMS) lines, maintainers and hybrids have been sequenced to identify genes responsible for cytoplasmic male sterility. Furthermore, several diagnostic molecular markers have been developed to assess the purity of commercial hybrids. In summary, pigeonpea has become a genomic resources-rich crop and efforts have already been initiated to integrate these resources in pigeonpea breeding.
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Affiliation(s)
- Lekha Pazhamala
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Rachit K. Saxena
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Vikas K. Singh
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - C. V. Sameerkumar
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Vinay Kumar
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Pallavi Sinha
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Kishan Patel
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Jimmy Obala
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-NatalScottsville, South Africa
| | - Seleman R. Kaoneka
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-NatalScottsville, South Africa
| | - P. Tongoona
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-NatalScottsville, South Africa
| | - Hussein A. Shimelis
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-NatalScottsville, South Africa
| | | | - Damaris Odeny
- International Crops Research Institute for the Semi-Arid TropicsNairobi, Kenya
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - P. S. Dharmaraj
- Agricultural Research Station, University of Agricultural SciencesGulbarga, India
| | - K. N. Yamini
- Department of Agricultural Biotechnology, Acharya N. G. Ranga Agricultural UniversityHyderabad, India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
- School of Plant Biology and Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
- *Correspondence: Rajeev K. Varshney, Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics, Building 300, Patancheru, Hyderabad 502324, India e-mail:
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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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