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

Ravi Prakash Shukla; Gopal Ji Tiwari; Babita Joshi; Kah Song-Beng; Sushma Tamta; N Manikanda Boopathi; Satya Narayan Jena

doi:10.1007/s12298-021-01041-y

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

Physiol Mol Biol Plants. 2021 Aug;27(8):1731-1745. doi: 10.1007/s12298-021-01041-y. Epub 2021 Aug 20.

Authors

Ravi Prakash Shukla^{1

2}, Gopal Ji Tiwari¹, Babita Joshi^{1

3}, Kah Song-Beng⁴, Sushma Tamta⁵, N Manikanda Boopathi⁶, Satya Narayan Jena¹

Affiliations

¹ Plant Molecular Genetics Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, (U.P.) 226001 India.
² Aakash Institute, Bhopal, Madhya Pradesh 462011 India.
³ Acamedy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India.
⁴ School of Science, Monash University Malaysia, 46150 Bandar Sunway, Selangor Malaysia.
⁵ Department of Botany, D.S.B. Campus, Kumaun University, Nainital, Uttarakhand 263002 India.
⁶ Department of Plant Biotechnology, CPMP & B, Tamil Nadu Agricultural University, Coimbatore, India.

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.

Supplementary information: The online version contains supplementary material available at 10.1007/s12298-021-01041-y.

Keywords: Drought; Genetic mapping; Gossypium hirsutum; QTL cluster; SNP; SSR.