Evaluation and genome-wide association study of Verticillium wilt resistance in a MAGIC population derived from intermating of eleven Upland cotton (Gossypium hirsutum) parents

Authors: ZHANG, JINFA - New Mexico State University; ABDELRAHEEM, ABDELRAHEEM - New Mexico State University; Thyssen, Gregory; Fang, David; Jenkins, Johnie; McCarty, Jack; WEDEGAERTNER, TOM - Cotton, Inc

Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/14/2019
Publication Date: 12/19/2019
Citation: Zhang, J., Abdelraheem, A., Thyssen, G.N., Fang, D.D., Jenkins, J.N., McCarty Jr, J.C., Wedegaertner, T. 2019. Evaluation and genome-wide association study of Verticillium wilt resistance in a MAGIC population derived from intermating of eleven Upland cotton (Gossypium hirsutum) parents. Euphytica. 216:9. https://doi.org/10.1007/s10681-019-2547-6.
DOI: https://doi.org/10.1007/s10681-019-2547-6

Interpretive Summary: Vertcillium wilt (VW) is an important fungal disease of cotton. In this study, we used a multi-parent advanced generation inter-cross (MAGIC) population of 550 recombinant inbred lines (RILs) together with their 11 Upland cotton parents and 473,516 polymorphic SNP markers to identify chromosomal regions for VW resistance based on foliar disease severity ratings (DSR). Among the 11 parents, Acala Ultima, Cocker 315, and Deltapine Acala 90 in the two tests and FiberMax 966 in one test and on average were significantly more resistant than the susceptible check parent- Phytogen PSC 355, while Paymaster HS 26, SureGrow 747, Stoneville 474, Stoneville 825, and Tamcot Pyramid performed similarly to PSC 355. Although a significant genotype × test interaction was detected for DSR, 37 MAGIC RILs were consistently resistant to VW. Of 13 and 12 VW resistance QTL declared in Test 1 and 2, respectively, through a genome-wide association study (GWAS), three QTL on chromosome A01, D02 and D08 were in common and three QTL clusters were detected on chromosome A01, A13, and D01 between the two tests. The narrow chromosomal regions for the three VW resistance QTL allowed identification of possible candidate genes for VW resistance. This greenhouse study identified VW resistant parents and RILs and common resistance QTL for VW resistance, providing useful information for developing VW resistant cultivars and further genomic studies towards the identification of VW resistance genes in cotton.

Technical Abstract: Vertcillium wilt (VW, Verticillium dahliae Kleb.) is one of the most important soil-borne fungal diseases affecting world cotton production. Numerous studies have been conducted to investigate the genetic basis of VW resistance using bi-parental or association mapping populations. In this study, a multi-parent advanced generation inter-cross (MAGIC) population of 550 recombinant inbred lines (RILs) together with their 11 Upland cotton parents with a total of 473,516 polymorphic SNP markers was used to identify chromosomal regions for VW resistance based on foliar disease severity ratings (DSR) in two replicated greenhouse tests. Among the 11 parents, Acala Ultima, Cocker 315, and Deltapine Acala 90 in the two tests and FiberMax 966 in one test and on average were significantly more resistant than the susceptible check parent- Phytogen PSC 355, while Paymaster HS 26, SureGrow 747, Stoneville 474, Stoneville 825, and Tamcot Pyramid performed similarly to PSC 355. Although a significant genotype × test interaction was detected for DSR, 37 MAGIC lines were consistently resistant to VW. Of 13 and 12 VW resistance QTL declared in Test 1 and 2, respectively, through a genome-wide association study (GWAS), three QTL on chromosome A01, D02 and D08 were in common and three QTL clusters were detected on chromosome A01, A13, and D01 between the two tests. The narrow chromosomal regions for the three VW resistance QTL allowed identification of possible candidate genes for VW resistance. This greenhouse study identified VW resistant parents and RILs and common resistance QTL for VW resistance, providing useful information for developing VW resistant cultivars and further genomic studies towards the identification of VW resistance genes in cotton.