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GBS-SNP and SSR based genetic mapping and QTL analysis for drought tolerance in upland cotton

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Abstract

A recombinant inbred line mapping population of intra-species upland cotton was generated from a cross between the drought-tolerant female parent (AS2) and the susceptible male parent (MCU13). A linkage map was constructed deploying 1,116 GBS-based SNPs and public domain-based 782 SSRs spanning a total genetic distance of 28,083.03 cM with an average chromosomal span length of 1,080.12 cM with inter-marker distance of 10.19 cM.A total of 19 quantitative trait loci (QTLs) were identified in nine chromosomes for field drought tolerance traits. Chromosomes 3 and 8 harbored important drought tolerant QTLs for chlorophyll stability index trait while for relative water content trait, three QTLs on chromosome 8 and one QTL each on chromosome 4, 12 were identified. One QTL on each chromosome 8, 5, and 7, and two QTLs on chromosome 15 linking to proline content were identified. For the nitrate reductase activity trait, two QTLs were identified on chromosome 3 and one on each chromosome 8, 13, and 26. To complement our QTL study, a meta-analysis was conducted along with the public domain database and resulted in a consensus map for chromosome 8. Under field drought stress, chromosome 8 harbored a drought tolerance QTL hotspot with two in-house QTLs for chlorophyll stability index (qCSI01, qCSI02) and three public domain QTLs (qLP.FDT_1, qLP.FDT_2, qCC.ST_3). Identified QTL hotspot on chromosome 8 could play a crucial role in exploring abiotic stress-associated genes/alleles for drought trait improvement.

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Acknowledgements

We would like to thank Dr. Soon Joo Yap, Codon Genomics S/B, JalanDutamas 7, 43200 Seri Kembangan, Selangor, Malaysia for his kind help in data analysis and valuable suggestions. We acknowledge further Dr. A.B. Das, Utkal University and Dr. P.K. Singh to help us in improving this MS.

Funding

Director, CSIR-National Botanical Research Institute.

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Authors and Affiliations

  1. Plant Molecular Genetics Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, (U.P.), 226001, India

    Ravi Prakash Shukla, Gopal Ji Tiwari, Babita Joshi & Satya Narayan Jena

  2. School of Science, Monash University Malaysia, 46150, Bandar Sunway, Selangor, Malaysia

    Kah Song-Beng

  3. Department of Botany, D.S.B. Campus, Kumaun University, Nainital, Uttarakhand, 263002, India

    Sushma Tamta

  4. Department of Plant Biotechnology, CPMP & B, Tamil Nadu Agricultural University, Coimbatore, India

    N. Manikanda Boopathi

  5. Aakash Institute, Bhopal, Madhya Pradesh, 462011, India

    Ravi Prakash Shukla

  6. Acamedy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India

    Babita Joshi

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  1. Ravi Prakash Shukla
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  2. Gopal Ji Tiwari
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  4. Kah Song-Beng
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  7. Satya Narayan Jena
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Contributions

SNJ conceptualized the idea while RPS took it in his Ph.D. research work. All the experiments were done by RPS under the supervision of SNJ. However, SBK helped in SNP typing analysis, and GJT analyzed the genetic mapping discussing with SNJ. RPS drafted the MS with the help of GJT. SNJ, NMB, BJ, and GJT rigorously edited and revised the whole manuscript. The authors do not have any conflict of interest during the entire process of conducting the experiments, data analysis, and preparation of the manuscript.

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Correspondence to Satya Narayan Jena.

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Shukla, R.P., Tiwari, G.J., Joshi, B. et al. GBS-SNP and SSR based genetic mapping and QTL analysis for drought tolerance in upland cotton. Physiol Mol Biol Plants 27, 1731–1745 (2021). https://doi.org/10.1007/s12298-021-01041-y

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