A novel variant of Gh_D02G0276 is required for Root-Knot nematode resistance on chromosome 14 in Upland Cotton

Authors: Wubben, Martin; Thyssen, Gregory; Callahan, Franklin; Fang, David; Deng, Dewayne; McCarty, Jack; Li, Ping; Islam, Md; Jenkins, Johnie

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/12/2019
Publication Date: 2/11/2019
Citation: Wubben, M., Thyssen, G.N., Callahan, F.E., Fang, D.D., Deng, D.D., Mccarty Jr, J.C., Li, P., Islam, M.S., Jenkins, J.N. 2019. A novel variant of Gh_D02G0276 is required for Root-Knot nematode resistance on chromosome 14 in Upland Cotton. Theoretical and Applied Genetics. 2019)132:1425–1434. https://doi.org/10.1007/s00122-019-03289-1.
DOI: https://doi.org/10.1007/s00122-019-03289-1

Interpretive Summary: The root-knot nematode (RKN) is a serious pathogen of cotton that causes large annual yield losses. Cotton breeders have been able to determine the locations in the cotton genome that harbor RKN resistance genes; however, the exact identities of these genes remain unknown. Using a specially designed gene mapping population along with genome re-sequencing, we were successful in narrowing the resistance gene search down to just 30 Kb on cotton chromosome 14. Four genes were predicted to reside within this region and we showed that the artificial disruption of only one of these genes caused normally resistant plants to become susceptible to RKN. This gene, called D02G0276, encodes a large protein with multiple functional domains. Future research will focus on determining how D02G0276 mediates RKN resistance at the molecular level.

Technical Abstract: The southern root-knot nematode (RKN; Meloidogyne incognita) remains the primary yield-limiting biotic stress to Upland cotton (Gossypium hirsutum) throughout the southeastern United States. While useful genetic markers have been developed for two major RKN resistance loci on chromosomes 11 (A11) and 14 (D02), these markers are not completely effective since the causative mutations have not been identified. Here, we sequenced 550 lines from a multi-parent advanced generation intercross (MAGIC) population to identify five lines that had informative recombinations near the D02-RKN resistance locus. The phenotypes of these lines narrowed the D02-RKN locus to a 30-kb region with four candidate genes. We conducted virus induced gene silencing (VIGS) on each of these genes and found that Gh_D02G0276 was required for suppression of RKN egg production phenotype conferred by the D02 resistance gene. The resistant lines all possessed an allele of Gh_D02G0276 that showed non-synonymous mutations and was prematurely truncated. Furthermore, a Gh_D02G0276-specific marker for the resistant allele variant was able to identify RKN resistant germplasm from a collection of cotton accessions. The Gh_D02G0276 peptide shares similarity with domesticated hAT-like transposases with additional novel N- and C-terminal domains that resemble the target of known RKN effector molecules and a prokaryotic motif, respectively. The truncation in the resistant allele results in a loss of a plant nuclear gene specific C-terminal motif, potentially rendering this domain antigenic due to its high homology with bacterial proteins. The conclusive identification of this RKN resistance gene opens new avenues for understanding plant resistance mechanisms to RKN as well as opportunities to develop more efficient marker assisted selection in cotton breeding programs.