A genome-wide association study uncovers consistent quantitative trait loci for resistance to Verticillium wilt and Fusarium wilt race 4 in the US Upland cotton

Authors: ABDELRAHEEM, ABDELRAHEEM - New Mexico State University; ELASSBLI, HANAN - New Mexico State University; ZHU, YI - New Mexico State University; KURAPARTHY, VASU - North Carolina State University; Hinze, Lori; STELLY, DAVID - Texas A&M University; WEDEGAERTNER, TOM - Cotton, Inc; ZHANG, JINFA - New Mexico State University

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/13/2019
Publication Date: 11/25/2019
Citation: Abdelraheem, A., Elassbli, H., Zhu, Y., Kuraparthy, V., Hinze, L.L., Stelly, D., Wedegaertner, T., Zhang, J. 2019. A genome-wide association study uncovers consistent quantitative trait loci for resistance to Verticillium wilt and Fusarium wilt race 4 in the US Upland cotton. Theoretical and Applied Genetics. 133:563-577. https://doi.org/10.1007/s00122-019-03487-x.
DOI: https://doi.org/10.1007/s00122-019-03487-x

Interpretive Summary: Verticillium wilt and Fusarium wilt are diseases commonly found in the soil that can cause major reductions in cotton production throughout the world. Both diseases have similar symptoms leading to yield loss, fiber quality reduction, and, if severe, plant death. Although plant resistance to diseases are commonly interconnected, the genetic basis of these two diseases and their interaction is not fully understood. In the greenhouse, plant symptoms varied from no symptoms to plant death in Upland cotton for both diseases. Resistance to these diseases was moderately heritable indicating plant breeding would be effective to incorporate resistance into new cultivars. Multiple molecular markers and genomic regions were linked to resistance for both diseases. However, the genomic regions of interest differed for each disease indicating different genetic factors are involved in resistance. These results provide important information for Verticillium wilt and Fusarium wilt resistance in cotton. The degree to which these findings can be translated to Verticillium wilt and/or Fusarium wilt field resistance will be of great interest, both agriculturally and scientifically.

Technical Abstract: Verticillium wilt (VW, caused by Verticillium dahliae Kleb.) and fusarium wilt (FW, caused by Fusarium oxysporum f.sp. vasinfectum Atk. Sny & Hans) are the most important soil-borne fungal diseases in cotton. Although resistances to biotic stresses are somewhat interconnected, the genetic basis is not fully understood due to complexity of the stress resistance and difficulties in phenotyping. To augment and refine genomic localization of VW and FW, and examine potential co-localization of major resistance factors, we conducted a genome-wide association study (GWAS) using high-density genotyping with the CottonSNP63K Array. Resistance of 376 U.S. Upland cotton accessions to a defoliating VW and FW race 4 was evaluated in six replicated greenhouse tests to identify quantitative trait loci (QTL). VW and FW resistances were respectively associated with 30 and 56 significant single nucleotide polymorphic (SNP) markers grouped into 15 and 13 resistance QTL on five (c8, c10, c16, c19, and c21) and six (c8, c14, c16, c17, c18, and c19) chromosome linkage groups. QTL on c8, c10, c16, and c21 were consistent in two or more tests for VW resistance, while two QTL on c8 and c14 were consistent for FW resistance in two tests. Two QTL clusters on c16 and c19 were observed for both VW and FW resistance, suggesting that these genomic regions may harbor genes in response for both diseases in the U.S. Upland cotton. Using the resolution afforded by the QTL and local genome annotations, 30 and 35 candidate genes were identified on four chromosomes (c8, c10, c16, and c21) for VW resistance and on three chromosomes (c14, c16, and c18) for FW resistance, respectively. These genomic regions were rich in NBS-LRR genes presented in clusters. The results create opportunities for tests to determine the correlations of field resistance with these QTL, molecular examinations of VW and FW resistances, marker-assisted selection (MAS) and eventual cloning of QTL for disease resistance in cotton.