A GWAS identified a major QTL for resistance to Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) race 4 in a MAGIC population of Upland cotton and a meta-analysis of QTLs for Fusarium wilt resistance

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

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/20/2022
Publication Date: 5/16/2022
Citation: Zhu, Y., Thyssen, G.N., Abdelraheem, A., Teng, Z., Fang, D.D., Jenkins, J.N., Mccarty Jr, J.C., Wedegaertner, T., Hake, K., Zhang, J. 2022. A GWAS identified a major QTL for resistance to Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) race 4 in a MAGIC population of Upland cotton and a meta-analysis of QTLs for Fusarium wilt resistance. Theoretical and Applied Genetics. 135:2297-2312. https://doi.org/10.1007/s00122-022-04113-z.
DOI: https://doi.org/10.1007/s00122-022-04113-z

Interpretive Summary: Fusarium wilt (FW) is one of the most important soil-borne fungal diseases affecting world cotton production. In this study, a multi-parent advanced generation inter-cross (MAGIC) population of 550 recombinant inbred lines (RILs), together with their 11 parents, was used to identify chromosomal regions for FOV race 4 (FOV4) resistance based on foliar disease severity ratings (DSR) in two replicated greenhouse tests with artificial inoculations. Among the 11 parents, Acala Ultima, M240, and Stoneville 474 were the most resistant, while Deltapine Acala 90, Coker 315, and Stoneville 825 were the most susceptible. Although a significant genotype × test interaction was detected for DSR, 22 MAGIC lines were consistently resistant to FOV4. Through a genome-wide association study (GWAS) based on 473,516 polymorphic SNP markers for the MAGIC population, a major FOV4 resistance QTL or a cluster of QTLs on chromosomes D02 (c14) was detected. The narrow chromosomal region at 0.79-0.97 Mb for the resistance QTL allowed identification of 14 possible candidate genes for FOV4 resistance. In addition, a meta-analysis of distribution of 101 published FW resistance QTLs showed a D subgenome and individual chromosome bias and no correlation between homeologous chromosome pairs. This study identified FOV4 resistant parents, MAGIC lines, and the first major QTL for FOV4 resistance, providing useful information for developing FOV4 resistant cultivars and further genomic studies towards identification of causal genes for FOV4 resistance in Upland cotton.

Technical Abstract: Fusarium wilt (FW) caused by Fusarium oxysporum f. sp. vasinfectum (FOV) 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 FW resistance using bi-parental and 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 (Gossypium hirsutum) parents, was used to identify chromosomal regions for FOV race 4 (FOV4) resistance based on foliar disease severity ratings (DSR) in two replicated greenhouse tests with artificial inoculations. Among the 11 parents, Acala Ultima, M240, and Stoneville 474 were the most resistant, while Deltapine Acala 90, Coker 315, and Stoneville 825 were the most susceptible. Although a significant genotype × test interaction was detected for DSR, 22 MAGIC lines were consistently resistant to FOV4. Through a genome-wide association study (GWAS) based on 473,516 polymorphic SNP markers for the MAGIC population, a major FOV4 resistance QTL or a cluster of QTLs on chromosomes D02 (c14) was detected. The narrow chromosomal region at 0.79-0.97 Mb for the resistance QTL allowed identification of 14 possible candidate genes for FOV4 resistance. In addition, a meta-analysis of distribution of 101 published FW resistance QTLs showed a D subgenome and individual chromosome bias and no correlation between homeologous chromosome pairs. This study further found that even 500 MAGIC lines are not enough for high resolution mapping to pinpoint a candidate gene, and high experimental errors in phenotyping cotton for FOV resistance further compromise the accuracy and precision in QTL localization and subsequent identification of candidate genes. This study identified FOV4 resistant parents, MAGIC lines, and the first major QTL for FOV4 resistance, providing useful information for developing FOV4 resistant cultivars and further genomic studies towards identification of causal genes for FOV4 resistance in Upland cotton.