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Association genetics of the parameters related to nitrogen use efficiency in Brassica juncea L.

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Abstract

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Genome wide association studies allowed prediction of 17 candidate genes for association with nitrogen use efficiency. Novel information obtained may provide better understanding of genomic controls underlying germplasm variations for this trait in Indian mustard.

Abstract

Nitrogen use efficiency (NUE) of Indian mustard (Brassica juncea (L.) Czern & Coss.) is low and most breeding efforts to combine NUE with crop performance have not succeeded. Underlying genetics also remain unexplored. We tested 92 SNP-genotyped inbred lines for yield component traits, N uptake efficiency (NUPEFF), nitrogen utilization efficiency (NUTEFF), nitrogen harvest index (NHI) and NUE for two years at two nitrogen doses (No without added N and N100 added @100 kg/ha). Genotypes IC-2489-88, M-633, MCP-632, HUJM 1080, GR-325 and DJ-65 recorded high NUE at low N. These also showed improved crop performance under high N. One determinate mustard genotype DJ-113 DT-3 revealed maximum NUTEFF. Genome wide association studies (GWAS) facilitated recognition of 17 quantitative trait loci (QTLs). Environment specificity was high. B-genome chromosomes (B02, B03, B05, B07 and B08) harbored many useful loci. We also used regional association mapping (RAM) to supplement results from GWAS. Annotation of the genomic regions around peak SNPs helped to predict several gene candidates for root architecture, N uptake, assimilation and remobilization. CAT9 (At1g05940) was consistently envisaged for both NUE and NUPEFF. Major N transporter genes, NRT1.8 and NRT3.1 were predicted for explaining variation for NUTEFF and NUPEFF, respectively. Most significant amino acid transporter gene, AAP1 appeared associated with NUE under limited N conditions. All these candidates were predicted in the regions of high linkage disequilibrium. Sequence information of the predicted candidate genes will permit development of molecular markers to aid breeding for high NUE.

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Data availability

Short sequencing datasets have been deposited at the Sequence Read Archive (SRA) of NCBI under submission accession number PRJNA639209. Supply of germplasm resources will require approval of Biodiversity Authority of India.

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Acknowledgements

The studies were financially supported by the Department of Biotechnology, Government of India in the form of Centre of Excellence and Innovation in Biotechnology “Germplasm enhancement for crop architecture and defensive traits in Brassica juncea L. Czern. and Coss.” SSB also acknowledges salary support from Indian Council of Agricultural Research under ICAR National Professor Project “Broadening the genetic base of Indian mustard (Brassica juncea) through alien introgressions and germplasm enhancement”.

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  1. Neha Gupta and Mehak Gupta contributed equally to this work.

Authors and Affiliations

  1. Department of Plant Breeding and Genetics, Punjab Agricultural University, Punjab, 141004, Ludhiana, India

    Neha Gupta, Mehak Gupta, Javed Akhatar, Anna Goyal, Rimaljeet Kaur, Sanjula Sharma, Prinka Goyal, Archana Mukta, Navneet Kaur, Meenakshi Mittal, Mohini Prabha Singh, Baudh Bharti, V. K. Sardana & Surinder S. Banga

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  12. Baudh Bharti
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  14. Surinder S. Banga
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Contributions

SSB and VKS conceived the project. NG, AG and PG performed phenotypic evaluations. AM and SS conducted biochemical analysis and DNA extractions. MPS and RK compiled the results. JA, NK and BB implemented the statistical and bioinformatics software’s and performed computational analysis. MG and MM carried out annotation studies and wrote the manuscript. SSB edited the manuscript and supervised the studies.

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Correspondence to Surinder S. Banga.

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Gupta, N., Gupta, M., Akhatar, J. et al. Association genetics of the parameters related to nitrogen use efficiency in Brassica juncea L.. Plant Mol Biol 105, 161–175 (2021). https://doi.org/10.1007/s11103-020-01076-x

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  • DOI: https://doi.org/10.1007/s11103-020-01076-x

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