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Saxena RK, Jiang Y, Khan AW, Zhao Y, Kumar Singh V, Bohra A, Sonappa M, Rathore A, Kumar CVS, Saxena K, Reif J, Varshney RK. Characterization of heterosis and genomic prediction-based establishment of heterotic patterns for developing better hybrids in pigeonpea. Plant Genome 2021; 14:e20125. [PMID: 34337867 DOI: 10.1002/tpg2.20125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 05/29/2021] [Indexed: 06/13/2023]
Abstract
Whole-genome resequencing (WGRS) of 396 lines, consisting of 104 hybrid parental lines and 292 germplasm lines, were used to study the molecular basis of mid-parent heterosis (MPH) and to identify complementary heterotic patterns in pigeonpea [Cajanus cajan (L.) Millsp.] hybrids. The lines and hybrids were assessed for yield and yield-related traits in multiple environments. Our analysis showed positive MPH values in 78.6% of hybrids, confirming the potential of hybrid breeding in pigeonpea. By using genome-wide prediction and association mapping approaches, we identified 129 single nucleotide polymorphisms and 52 copy number variations with significant heterotic effects and also established a high-yielding heterotic pattern in pigeonpea. In summary, our study highlights the role of WGRS data in the study and use of heterosis in crops where hybrid breeding is expected to boost selection gain in order to ensure global food security.
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Affiliation(s)
- Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Yong Jiang
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466, Stadt Seeland, Germany
| | - Aamir W Khan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Yusheng Zhao
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466, Stadt Seeland, Germany
| | - Vikas Kumar Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Abhishek Bohra
- Indian Council of Agricultural Research - Indian Institute of Pulses Research, Kanpur, 208024, India
| | - Muniswamy Sonappa
- Zonal Agricultural Research Station, Univ. of Agricultural Sciences - Raichur, Gulbarga, Karnataka, 585101, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - C V Sameer Kumar
- Professor Jayashankar Telangana State Agricultural Univ., Rajendranagar, Hyderabad, Telangana, 500030, India
| | | | - Jochen Reif
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466, Stadt Seeland, Germany
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch Univ., Murdoch, WA, 6150, Australia
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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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Saxena RK, Kale S, Mir RR, Mallikarjuna N, Yadav P, Das RR, Molla J, Sonnappa M, Ghanta A, Narasimhan Y, Rathore A, Kumar CVS, Varshney RK. Genotyping-by-sequencing and multilocation evaluation of two interspecific backcross populations identify QTLs for yield-related traits in pigeonpea. Theor Appl Genet 2020; 133:737-749. [PMID: 31844966 DOI: 10.1007/s00122-019-03504-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
This study has identified single-nucleotide polymorphism (SNP) markers associated with nine yield-related traits in pigeonpea by using two backcross populations (BP) developed through interspecific crosses and evaluating them at two locations and 3 years. In both the populations, markers have shown strong segregation distortion; therefore, a quantitative trait locus (QTL) mapping mixed model was used. A total of 86 QTLs explaining 12-21% phenotypic variation were detected in BP-1. On the other hand, 107 QTLs explaining 11-29% phenotypic variation were detected in BP-2. Although most QTLs were environment and trait specific, few stable and consistent QTLs were also detected. Interestingly, 11 QTLs in BP-2 were associated with more than one trait. Among these QTLs, eight QTLs associated with days to 50% flowering and days to 75% maturity were located on CcLG07. One SNP "S7_14185076" marker in BP-2 population has been found associated with four traits, namely days to 50% flowering, days to 75% maturity, primary branches per plant and secondary branches per plant with positive additive effect. Hence, the present study has not only identified QTLs for yield-related traits, but also discovered novel alleles from wild species, which can be used for improvement of traits through genomics-assisted breeding.
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Affiliation(s)
- Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRSAT), Patancheru, Telangana, 502324, India
| | - Sandip Kale
- The Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Seeland, OT Gatersleben, Germany
| | - Reyazul Rouf Mir
- Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Wadura Campus, Sopore, Kashmir, 193201, India
| | - Nalini Mallikarjuna
- International Crops Research Institute for the Semi-Arid Tropics (ICRSAT), Patancheru, Telangana, 502324, India
| | - Pooja Yadav
- International Crops Research Institute for the Semi-Arid Tropics (ICRSAT), Patancheru, Telangana, 502324, India
| | - Roma Rani Das
- International Crops Research Institute for the Semi-Arid Tropics (ICRSAT), Patancheru, Telangana, 502324, India
| | - Johiruddin Molla
- International Crops Research Institute for the Semi-Arid Tropics (ICRSAT), Patancheru, Telangana, 502324, India
| | - Muniswamy Sonnappa
- Agricultural Research Station (UAS-Raichur), Gulbarga, Karnataka, 585101, India
| | - Anuradha Ghanta
- Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad, Telangana, 500030, India
| | - Yamini Narasimhan
- Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad, Telangana, 500030, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRSAT), Patancheru, Telangana, 502324, India
| | - C V Sameer Kumar
- Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad, Telangana, 500030, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRSAT), Patancheru, Telangana, 502324, India.
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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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Gopalakrishnan S, Vadlamudi S, Samineni S, Sameer Kumar CV. Plant growth-promotion and biofortification of chickpea and pigeonpea through inoculation of biocontrol potential bacteria, isolated from organic soils. Springerplus 2016; 5:1882. [PMID: 27833841 PMCID: PMC5082106 DOI: 10.1186/s40064-016-3590-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 10/20/2016] [Indexed: 11/10/2022]
Abstract
Seven strains of bacteria [Pseudomonas plecoglossicida SRI-156, Brevibacterium antiquum SRI-158, Bacillus altitudinis SRI-178, Enterobacter ludwigii SRI-211, E. ludwigii SRI-229, Acinetobacter tandoii SRI-305 and Pseudomonas monteilii SRI-360; demonstrated previously for control of charcoal rot disease in sorghum and plant growth-promotion (PGP) in rice] were evaluated for their PGP and biofortification traits in chickpea and pigeonpea under field conditions. When treated on seed, the seven selected bacteria significantly enhanced the shoot height and root length of both chickpea and pigeonpea over the un-inoculated control. Under field conditions, in both chickpea and pigeonpea, the plots inoculated with test bacteria enhanced the nodule number, nodule weight, root and shoot weights, pod number, pod weight, leaf weight, leaf area and grain yield over the un-inoculated control plots. Among the seven bacteria, SRI-229 was found to significantly and consistently enhance all the studied PGP and yield traits including nodule number (24 and 36%), nodule weight (11 and 44%), shoot weight (22 and 20%), root weight (23 and 16%) and grain yield (19 and 26%) for both chickpea and pigeonpea, respectively. When the harvested grains were evaluated for their mineral contents, iron (up to 18 and 12%), zinc (up to 23 and 5%), copper (up to 19 and 8%), manganese (up to 2 and 39%) and calcium (up to 22 and 11%) contents in chickpea and pigeonpea, respectively, were found enhanced in test bacteria inoculated plots over the un-inoculated control plots. This study further confirms that the selected bacterial isolates not only have the potential for PGP in cereals and legumes but also have the potential for biofortification of mineral nutrients.
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Affiliation(s)
- Subramaniam Gopalakrishnan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
| | - Srinivas Vadlamudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
| | - Srinivasan Samineni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
| | - C V Sameer Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
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11
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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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