Genome-wide association study of the resistance of Gossypium herbaceum to reniform nematodes

Authors: Feng, Chunda; Stetina, Salliana - Sally; Erpelding, John

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 1/8/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Reniform nematode (Rotylenchulus reniformis) is an obligate parasite that feeds on the plant root system and causes severe yield losses in many crops. The annual cotton yield loss caused by reniform nematode is estimated to be 1 to 5% of the total production in the U.S. In addition, the wounds on cotton roots at the nematode feeding sites make the plants more vulnerable to some soilborne diseases such as Fusarium wilt. Nematicides and crop rotation are used to control nematodes. However, the populations of nematodes could increase quickly and dramatically during cotton growing season. Crop rotation may not be always feasible due to some economic or resource constrains. Growing resistant cultivars is the most effective way to manage this disease. However, resistance to reniform nematodes was not found in widely grown upland cotton (Gossypium hirsutum) but found in some other Gossypium species such as G. arboreum, G. longicalyx, and G. barbadense. In this study, 58 accessions of G. herbaceum were tested for resistance to reniform nematodes using a G. hirsutum cultivar Deltapine 16 (PI 529251) as the susceptible control. Nematode index (percentage of the number of female nematodes of a test line compared to that of the susceptible control) was used to evaluate resistance or susceptibility of G. herbaceum accessions. The results indicated that 27 accessions were resistant, five accessions were susceptible, and other lines had intermediate resistant or intermediate susceptible reactions. These accessions were genotyped using the genotyping-by-sequencing approach. The software TASSEL5.0 pipeline was employed to call single nucleotide polymorphisms (SNPs). After filtering, a total of 11 thousand SNPs was obtained; the number of SNPs on each chromosome ranged from 570 to 1269. Genome-wide association study of the resistance of G. herbaceum to reniform nematodes was performed using TASSEL5.0 with the general liner model. Twenty-one SNPs were found to be associated with the resistance to reniform nematodes in G. herbaceum (adjusted Bonferroni p value<0.05, FDR p<0.001). These SNPs represented 16 loci, and distributed on 11 chromosomes, including five SNPs on chromosome 2, three SNPs each on chromosomes 3 and 10, and one or two SNPs on other chromosomes. There were no SNPS found on chromosomes 6 and 11. Resistance gene analogs responsive to biotic and abiotic stresses, and transcription factors were found in the adjacent regions of the significant SNPs. More G. herbaceum accessions will be evaluated for resistance to reniform nematodes, and some of the identified SNP markers will be further tested in those accessions. The novel resistance in G. herbaceum and the potential SNP markers linked to the resistance genes identified in this research could be useful for developing upland cotton cultivars with improved resistance to this important parasite.