Abstract
BackgroundReniform nematode (Rotylenchulus reniformis) has emerged as one of the most destructive root pathogens of upland cotton (Gossypium hirsutum) in the United States. Management of R. reniformis has been hindered by the lack of resistant G. hirsutum cultivars; however, resistance has been frequently identified in germplasm accessions from the G. arboreum collection. To determine the genetic basis of reniform nematode resistance, a genome-wide association study (GWAS) was performed using 246 G. arboreum germplasm accessions that were genotyped with 7220 single nucleotide polymorphic (SNP) sequence markers generated from genotyping-by-sequencing.ResultsFifteen SNPs representing 12 genomic loci distributed over eight chromosomes showed association with reniform nematode resistance. For 14 SNPs, major alleles were shown to be associated with resistance. From the 15 significantly associated SNPs, 146 genes containing or physically close to these loci were identified as putative reniform nematode resistance candidate genes. These genes are involved in a broad range of biological pathways, including plant innate immunity, transcriptional regulation, and redox reaction that may have a role in the expression of resistance. Eighteen of these genes corresponded to differentially expressed genes identified from G. hirsutum in response to reniform nematode infection.ConclusionsThe identification of multiple genomic loci associated with reniform nematode resistance would indicate that the G. arboreum collection is a significant resource of novel resistance genes. The significantly associated markers identified from this GWAS can be used for the development of molecular tools for breeding improved reniform nematode resistant upland cotton with resistance introgressed from G. arboreum. Additionally, a greater understanding of the molecular mechanisms of reniform nematode resistance can be determined through genetic structure and functional analyses of candidate genes, which will aid in the pyramiding of multiple resistance genes.
Highlights
Reniform nematode (Rotylenchulus reniformis) has emerged as one of the most destructive root pathogens of upland cotton (Gossypium hirsutum) in the United States
Phenotypic variation in reniform nematode resistance Reniform nematode (RN) resistance based on female index (FI) values relative to the RN susceptible G. hirsutum control genotype revealed a broad range in disease response with values from 2.8 to 140.3 for the 246 G. arboreum accessions (Additional file 1: Table S1)
High-throughput GBS data integrated with phenotypic data for 246 G. arboreum accessions with diverse RN resistance levels resulted in the identification of 15 single nucleotide polymorphic (SNP) representing 12 loci distributed over eight chromosomes that significantly associated with RN resistance
Summary
Reniform nematode (Rotylenchulus reniformis) has emerged as one of the most destructive root pathogens of upland cotton (Gossypium hirsutum) in the United States. Reniform nematode (RN, Rotylenchulus reniformis) is an obligate, semi-endoparasitic nematode that feeds on the root system of upland cotton (Gossypium hirsutum) causing significant yield losses [1, 2]. Yield losses from RN typically range from 1 to 5% in the southeastern cotton producing states [2] with an estimated loss of 24,211 MT in 2015 valued at approximately US$36 million [3]. According to Robinson [1], RN has replaced root-knot nematode (Meloidogyne spp.) as the major pathogenic nematode of cotton in the mid-south region of United States. Symptoms of RN infestation include plant stunting, Li et al BMC Genetics (2018) 19:52 suppressed root growth, and reduced yield; but these symptoms are typically uniform across the field making it difficult to visually assess nematode damage [2]
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