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Singh VK, Khan AW, Saxena RK, Sinha P, Kale SM, Parupalli S, Kumar V, Chitikineni A, Vechalapu S, Sameer Kumar CV, Sharma M, Ghanta A, Yamini KN, Muniswamy S, Varshney RK. Indel-seq: a fast-forward genetics approach for identification of trait-associated putative candidate genomic regions and its application in pigeonpea (Cajanus cajan). Plant Biotechnol J 2017; 15:906-914. [PMID: 28027425 PMCID: PMC5466435 DOI: 10.1111/pbi.12685] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 05/05/2023]
Abstract
Identification of candidate genomic regions associated with target traits using conventional mapping methods is challenging and time-consuming. In recent years, a number of single nucleotide polymorphism (SNP)-based mapping approaches have been developed and used for identification of candidate/putative genomic regions. However, in the majority of these studies, insertion-deletion (Indel) were largely ignored. For efficient use of Indels in mapping target traits, we propose Indel-seq approach, which is a combination of whole-genome resequencing (WGRS) and bulked segregant analysis (BSA) and relies on the Indel frequencies in extreme bulks. Deployment of Indel-seq approach for identification of candidate genomic regions associated with fusarium wilt (FW) and sterility mosaic disease (SMD) resistance in pigeonpea has identified 16 Indels affecting 26 putative candidate genes. Of these 26 affected putative candidate genes, 24 genes showed effect in the upstream/downstream of the genic region and two genes showed effect in the genes. Validation of these 16 candidate Indels in other FW- and SMD-resistant and FW- and SMD-susceptible genotypes revealed a significant association of five Indels (three for FW and two for SMD resistance). Comparative analysis of Indel-seq with other genetic mapping approaches highlighted the importance of the approach in identification of significant genomic regions associated with target traits. Therefore, the Indel-seq approach can be used for quick and precise identification of candidate genomic regions for any target traits in any crop species.
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Affiliation(s)
- Vikas K. Singh
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Aamir W. Khan
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Rachit K. Saxena
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Pallavi Sinha
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Sandip M. Kale
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Swathi Parupalli
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Vinay Kumar
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Suryanarayana Vechalapu
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | | | - Mamta Sharma
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Anuradha Ghanta
- Agricultural Research Station (ARS)‐TandurProfessor Jayashankar Telangana State Agricultural University (PJTSAU)HyderabadTelangana StateIndia
| | - Kalinati Narasimhan Yamini
- Agricultural Research Station (ARS)‐TandurProfessor Jayashankar Telangana State Agricultural University (PJTSAU)HyderabadTelangana StateIndia
| | - Sonnappa Muniswamy
- Agricultural Research Station (ARS)‐GulbargaUniversity of Agricultural Sciences (UAS)RaichurKarnatakaIndia
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
- School of Plant Biology and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
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Singh VK, Khan AW, Saxena RK, Kumar V, Kale SM, Sinha P, Chitikineni A, Pazhamala LT, Garg V, Sharma M, Sameer Kumar CV, Parupalli S, Vechalapu S, Patil S, Muniswamy S, Ghanta A, Yamini KN, Dharmaraj PS, Varshney RK. Next-generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea (Cajanus cajan). Plant Biotechnol J 2016; 14:1183-94. [PMID: 26397045 PMCID: PMC5054876 DOI: 10.1111/pbi.12470] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 07/29/2015] [Accepted: 08/06/2015] [Indexed: 05/20/2023]
Abstract
To map resistance genes for Fusarium wilt (FW) and sterility mosaic disease (SMD) in pigeonpea, sequencing-based bulked segregant analysis (Seq-BSA) was used. Resistant (R) and susceptible (S) bulks from the extreme recombinant inbred lines of ICPL 20096 × ICPL 332 were sequenced. Subsequently, SNP index was calculated between R- and S-bulks with the help of draft genome sequence and reference-guided assembly of ICPL 20096 (resistant parent). Seq-BSA has provided seven candidate SNPs for FW and SMD resistance in pigeonpea. In parallel, four additional genotypes were re-sequenced and their combined analysis with R- and S-bulks has provided a total of 8362 nonsynonymous (ns) SNPs. Of 8362 nsSNPs, 60 were found within the 2-Mb flanking regions of seven candidate SNPs identified through Seq-BSA. Haplotype analysis narrowed down to eight nsSNPs in seven genes. These eight nsSNPs were further validated by re-sequencing 11 genotypes that are resistant and susceptible to FW and SMD. This analysis revealed association of four candidate nsSNPs in four genes with FW resistance and four candidate nsSNPs in three genes with SMD resistance. Further, In silico protein analysis and expression profiling identified two most promising candidate genes namely C.cajan_01839 for SMD resistance and C.cajan_03203 for FW resistance. Identified candidate genomic regions/SNPs will be useful for genomics-assisted breeding in pigeonpea.
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Affiliation(s)
- Vikas K Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Aamir W Khan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Vinay Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Sandip M Kale
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Pallavi Sinha
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Lekha T Pazhamala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Mamta Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | | | - Swathi Parupalli
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Suryanarayana Vechalapu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Suyash Patil
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Sonnappa Muniswamy
- Agricultural Research Station (ARS)-Gulbarga, University of Agricultural Sciences (UAS), Raichur, Karnataka, India
| | - Anuradha Ghanta
- Institute of Biotechnology, Professor Jayshankar Telangana State Agricultural University (PJTSAU), Telangana, India
| | - Kalinati Narasimhan Yamini
- Institute of Biotechnology, Professor Jayshankar Telangana State Agricultural University (PJTSAU), Telangana, India
| | - Pallavi Subbanna Dharmaraj
- Agricultural Research Station (ARS)-Gulbarga, University of Agricultural Sciences (UAS), Raichur, Karnataka, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
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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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Kim DH, Parupalli S, Azam S, Lee SH, Varshney RK. Comparative sequence analysis of nitrogen fixation-related genes in six legumes. Front Plant Sci 2013; 4:300. [PMID: 23986765 PMCID: PMC3749373 DOI: 10.3389/fpls.2013.00300] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 07/20/2013] [Indexed: 05/20/2023]
Abstract
Legumes play an important role as food and forage crops in international agriculture especially in developing countries. Legumes have a unique biological process called nitrogen fixation (NF) by which they convert atmospheric nitrogen to ammonia. Although legume genomes have undergone polyploidization, duplication and divergence, NF-related genes, because of their essential functional role for legumes, might have remained conserved. To understand the relationship of divergence and evolutionary processes in legumes, this study analyzes orthologs and paralogs for selected 20 NF-related genes by using comparative genomic approaches in six legumes i.e., Medicago truncatula (Mt), Cicer arietinum, Lotus japonicus, Cajanus cajan (Cc), Phaseolus vulgaris (Pv), and Glycine max (Gm). Subsequently, sequence distances, numbers of synonymous substitutions per synonymous site (Ks) and non-synonymous substitutions per non-synonymous site (Ka) between orthologs and paralogs were calculated and compared across legumes. These analyses suggest the closest relationship between Gm and Cc and the highest distance between Mt and Pv in six legumes. Ks proportional plots clearly showed ancient genome duplication in all legumes, whole genome duplication event in Gm and also speciation pattern in different legumes. This study also reports some interesting observations e.g., no peak at Ks 0.4 in Gm-Gm, location of two independent genes next to each other in Mt and low Ks values for outparalogs for three genes as compared to other 12 genes. In summary, this study underlines the importance of NF-related genes and provides important insights in genome organization and evolutionary aspects of six legume species analyzed.
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Affiliation(s)
- Dong Hyun Kim
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Swathi Parupalli
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Sarwar Azam
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Suk-Ha Lee
- Department of Plant Science, Seoul National UniversitySeoul, South Korea
- Research Institute for Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
| | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
- CGIAR Generation Challenge Programme, c/o CIMMYTMexico DF, Mexico
- *Correspondence: Rajeev K. Varshney, Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), #300 Building, Hyderabad, AP 502 324, India e-mail:
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