Vol.:(0123456789) 1 3 Molecular Genetics and Genomics (2021) 296:719–729 https://doi.org/10.1007/s00438-021-01779-w ORIGINAL ARTICLE Evaluation and genome‑wide association study of resistance to bacterial blight race 18 in U.S. Upland cotton germplasm Hanan Elassbli 1  · Abdelraheem Abdelraheem 1  · Yi Zhu 1  · Zonghua Teng 1  · Terry A. Wheeler 2  · Vasu Kuraparthy 3  · Lori Hinze 4  · David M. Stelly 5  · Tom Wedegaertner 6  · Jinfa Zhang 1 Received: 14 February 2021 / Accepted: 19 March 2021 / Published online: 29 March 2021 © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2021 Abstract Bacterial blight (BB), caused by Xanthomonas citri pv. malvacearum (Xcm), is a destructive disease to cotton production in many countries. In the U.S., Xcm race 18 is the most virulent and widespread race and can cause serious yield losses. Planting BB-resistant cotton cultivars is the most efective method of controlling this disease. In this study, 335 U.S. Upland cotton accessions were evaluated for resistance to race 18 using artifcial inoculations by scratching cotyledons on an individual plant basis in a greenhouse. The analysis of variance detected signifcant genotypic variation in disease incidence, and 50 accessions were resistant including 38 lines with no symptoms on either cotyledons or true leaves. Many of the resistant lines were developed in the MAR (multi-adversity resistance) breeding program at Texas A&M University, whereas others were developed before race 18 was frst reported in the U.S. in 1973, suggesting a broad base of resistance to race 18. A genome- wide association study (GWAS) based on 26,301 single nucleotide polymorphic (SNP) markers detected 11 quantitative trait loci (QTL) anchored by 79 SNPs, including three QTL on each of the three chromosomes A01, A05 and D02, and one QTL on each of D08 and D10. This study has identifed a set of obsolete Upland germplasm with resistance to race 18 and specifc chromosomal regions delineated by SNPs for resistance. The results will assist in breeding cotton for BB resistance and facilitate further genomic studies in fne mapping resistance genes to enhance the understanding of the genetic basis of BB resistance in cotton. Keywords Upland cotton · Bacterial blight · SNPs · GWAS Introduction Cotton (Gossypium spp.) is grown in over 84 countries for the textile industry. Most of the cotton crop is harvested from tetraploid Upland cotton (G. hirsutum, 2n = 4x = 52), which originated from merging of two diploid A and D genomes (Wendel et al. 1992; Wendel and Cronn 2003). There are many limiting factors in cotton production includ- ing biotic stresses such as bacterial blight (BB). BB is caused by the gram-negative bacterium Xanthomonas citri pv. mal- vacearum (Xcm). Xcm infects the aerial part of plants at all stages and generates water-soaking lesions on leaves, stems, and bolls of susceptible plants, followed by premature leaf senescence and reduced lint yield and fber quality. Using 11 diferential cotton cultivars, 22 physiological races of Xcm have been described worldwide (Hunter et al. 1968; Brink- erhof 1970; Verma and Singh 1974; Hillocks 1992; Delan- noy et al. 2005; Jalloul et al. 2015; Phillips et al. 2017). At present, race 18 is the most frequently encountered and most Communicated by Stefan Hohmann. * Jinfa Zhang jinzhang@nmsu.edu 1 Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA 2 Texas A&M AgriLife Research, 1102 E. Drew St, Lubbock, TX 79403, USA 3 Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695-7620, USA 4 Crop Germplasm Research Unit, USDA, Agricultural Research Service, College Station, TX 77845, USA 5 Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843-2474, USA 6 Cotton Incorporated, 6399 Weston Parkway, Cary, NC 27513, USA