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Gupta S, Akhatar J, Kaur P, Sharma A, Sharma P, Mittal M, Bharti B, Banga SS. Genetic analyses of nitrogen assimilation enzymes in Brassica juncea (L.) Czern & Coss. Mol Biol Rep 2019; 46:4235-4244. [PMID: 31115836 DOI: 10.1007/s11033-019-04878-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 05/14/2019] [Indexed: 12/11/2022]
Abstract
Nitrogen (N) is a critical input for plant growth and development. A better understanding of N uptake and utilization is important to develop plant breeding strategies for improving nitrogen use efficiency (NUE). With that objective in mind, we assayed a SNP-genotyped association panel comprising 92 inbred lines for the activities of nitrate reductase (NR), nitrite reductase (NIR), glutamine synthetase (GS) and glutamate synthase (GOGAT). All these enzymes are associated with N assimilation. The experiments were carried out at two levels of N application: no added N (N0) and agrnomically recommened dose (100 kg/ha) of N application (N100). Genome wide association studies (GWAS) helped to identify several marker-trait associations (MTAs), involving chromosomes A01, A06, A08, B02, B04, B05 and B08. These explained high phenotypic variation (up to 32%). Annotation of the genomic region(s) in or around significant SNPs allowed prediction of genes encoding high affinity nitrate transporters, glutamine synthetase 1.3, myb-like transcription factor family protein, bidirectional amino acid transporter 1, auxin signaling F-box 3 and oxidoreductases. This is the first attempt to use GWAS for identification of enzyme QTLs to explain variation for nitrogen assimilation enzymes in Brassica juncea.
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Affiliation(s)
- Shilpa Gupta
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141001, India
| | - Javed Akhatar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141001, India
| | - Palminder Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141001, India
| | - Anju Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141001, India
| | - Pushp Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141001, India
| | - Meenakshi Mittal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141001, India
| | - Baudh Bharti
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141001, India
| | - Surinder Singh Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141001, India.
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Sehgal D, Skot L, Singh R, Srivastava RK, Das SP, Taunk J, Sharma PC, Pal R, Raj B, Hash CT, Yadav RS. Exploring potential of pearl millet germplasm association panel for association mapping of drought tolerance traits. PLoS One 2015; 10:e0122165. [PMID: 25970600 PMCID: PMC4430295 DOI: 10.1371/journal.pone.0122165] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 02/07/2015] [Indexed: 11/19/2022] Open
Abstract
A pearl millet inbred germplasm association panel (PMiGAP) comprising 250 inbred lines, representative of cultivated germplasm from Africa and Asia, elite improved open-pollinated cultivars, hybrid parental inbreds and inbred mapping population parents, was recently established. This study presents the first report of genetic diversity in PMiGAP and its exploitation for association mapping of drought tolerance traits. For diversity and genetic structure analysis, PMiGAP was genotyped with 37 SSR and CISP markers representing all seven linkage groups. For association analysis, it was phenotyped for yield and yield components and morpho-physiological traits under both well-watered and drought conditions, and genotyped with SNPs and InDels from seventeen genes underlying a major validated drought tolerance (DT) QTL. The average gene diversity in PMiGAP was 0.54. The STRUCTURE analysis revealed six subpopulations within PMiGAP. Significant associations were obtained for 22 SNPs and 3 InDels from 13 genes under different treatments. Seven SNPs associations from 5 genes were common under irrigated and one of the drought stress treatments. Most significantly, an important SNP in putative acetyl CoA carboxylase gene showed constitutive association with grain yield, grain harvest index and panicle yield under all treatments. An InDel in putative chlorophyll a/b binding protein gene was significantly associated with both stay-green and grain yield traits under drought stress. This can be used as a functional marker for selecting high yielding genotypes with 'stay green' phenotype under drought stress. The present study identified useful marker-trait associations of important agronomics traits under irrigated and drought stress conditions with genes underlying a major validated DT-QTL in pearl millet. Results suggest that PMiGAP is a useful panel for association mapping. Expression patterns of genes also shed light on some physiological mechanisms underlying pearl millet drought tolerance.
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Affiliation(s)
- Deepmala Sehgal
- Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom
| | - Leif Skot
- Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom
| | - Richa Singh
- Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom
- Chaudhary Charan Singh Haryana Agricultural University (CCSHAU), Department of Molecular Biology and Biotechnology, Hisar, Haryana, India
| | - Rakesh Kumar Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh, India
| | - Sankar Prasad Das
- Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom
- ICAR Research Complex for NEH Region, Tripura Centre, Lembucherra, India
| | - Jyoti Taunk
- Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom
- Chaudhary Charan Singh Haryana Agricultural University (CCSHAU), Department of Molecular Biology and Biotechnology, Hisar, Haryana, India
| | - Parbodh C. Sharma
- Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom
- Central Soil Salinity Research Institute (CSSRI), Karnal, India
| | - Ram Pal
- Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom
- National Research Centre for Orchids, Darjeeling Campus, Darjeeling, India
| | - Bhasker Raj
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh, India
| | | | - Rattan S. Yadav
- Institute of Biological, Environmental and Biological Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, United Kingdom
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Development of chromosome-specific markers with high polymorphism for allotetraploid cotton based on genome-wide characterization of simple sequence repeats in diploid cottons (Gossypium arboreum L. and Gossypium raimondii Ulbrich). BMC Genomics 2015; 16:55. [PMID: 25652321 PMCID: PMC4325953 DOI: 10.1186/s12864-015-1265-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 01/22/2015] [Indexed: 02/04/2023] Open
Abstract
Background Tetraploid cotton contains two sets of homologous chromosomes, the At- and Dt-subgenomes. Consequently, many markers in cotton were mapped to multiple positions during linkage genetic map construction, posing a challenge to anchoring linkage groups and mapping economically-important genes to particular chromosomes. Chromosome-specific markers could solve this problem. Recently, the genomes of two diploid species were sequenced whose progenitors were putative contributors of the At- and Dt-subgenomes to tetraploid cotton. These sequences provide a powerful tool for developing chromosome-specific markers given the high level of synteny among tetraploid and diploid cotton genomes. In this study, simple sequence repeats (SSRs) on each chromosome in the two diploid genomes were characterized. Chromosome-specific SSRs were developed by comparative analysis and proved to distinguish chromosomes. Results A total of 200,744 and 142,409 SSRs were detected on the 13 chromosomes of Gossypium arboreum L. and Gossypium raimondii Ulbrich, respectively. Chromosome-specific SSRs were obtained by comparing SSR flanking sequences from each chromosome with those from the other 25 chromosomes. The average was 7,996 per chromosome. To confirm their chromosome specificity, these SSRs were used to distinguish two homologous chromosomes in tetraploid cotton through linkage group construction. The chromosome-specific SSRs and previously-reported chromosome markers were grouped together, and no marker mapped to another homologous chromosome, proving that the chromosome-specific SSRs were unique and could distinguish homologous chromosomes in tetraploid cotton. Because longer dinucleotide AT-rich repeats were the most polymorphic in previous reports, the SSRs on each chromosome were sorted by motif type and repeat length for convenient selection. The primer sequences of all chromosome-specific SSRs were also made publicly available. Conclusion Chromosome-specific SSRs are efficient tools for chromosome identification by anchoring linkage groups to particular chromosomes during genetic mapping and are especially useful in mapping of qualitative-trait genes or quantitative trait loci with just a few markers. The SSRs reported here will facilitate a number of genetic and genomic studies in cotton, including construction of high-density genetic maps, positional gene cloning, fingerprinting, and genetic diversity and comparative evolutionary analyses among Gossypium species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1265-2) contains supplementary material, which is available to authorized users.
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