Genome-wide association study of Gossypium arboreum resistance to reniform nematode

Li, Ruijuan; Erpelding, John E.; Stetina, Salliana R.

doi:10.1186/s12863-018-0662-3

Genome-wide association study of Gossypium arboreum resistance to reniform nematode

Journal Article · Fri Aug 03 00:00:00 EDT 2018 · BMC Genetics (Online)

DOI:https://doi.org/10.1186/s12863-018-0662-3· OSTI ID:1626783

Li, Ruijuan ^[1]; ^[2]; Stetina, Salliana R. ^[2]

Univ. of California, Davis, CA (United States). Dept. of Plant Biology; DOE/OSTI
US Dept. of Agriculture (USDA)., Stoneville, MS (United States). Crop Genetics Research Unit

Background: Reniform 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. Results: Fifteen 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. Conclusions: The 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.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge Associated Univ., Oak Ridge, TN (United States)

Sponsoring Organization:: USDA-ARS; USDOE

Grant/Contract Number:: AC05-06OR23100

OSTI ID:: 1626783

Journal Information:: BMC Genetics (Online), Journal Name: BMC Genetics (Online) Journal Issue: 1 Vol. 19; ISSN 1471-2156

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Additional file 6: of Genome-wide association study of Gossypium arboreum resistance to reniform nematode Li, Ruijuan; Erpelding, John; Stetina, Salliana https://doi.org/10.6084/M9.FIGSHARE.6933887 The current record is supplemented by this dataset	dataset	January 2018
Additional file 1: of Genome-wide association study of Gossypium arboreum resistance to reniform nematode Li, Ruijuan; Erpelding, John; Stetina, Salliana https://doi.org/10.6084/m9.figshare.6933818 The current record is supplemented by this dataset	dataset	January 2018
Additional file 1: of Genome-wide association study of Gossypium arboreum resistance to reniform nematode Li, Ruijuan; Erpelding, John; Stetina, Salliana https://doi.org/10.6084/m9.figshare.6933818.v1 The current record is supplemented by this dataset	dataset	January 2018
Additional file 2: of Genome-wide association study of Gossypium arboreum resistance to reniform nematode Li, Ruijuan; Erpelding, John; Stetina, Salliana https://doi.org/10.6084/m9.figshare.6933827 The current record is supplemented by this dataset	dataset	January 2018
Additional file 2: of Genome-wide association study of Gossypium arboreum resistance to reniform nematode Li, Ruijuan; Erpelding, John; Stetina, Salliana https://doi.org/10.6084/m9.figshare.6933827.v1 The current record is supplemented by this dataset	dataset	January 2018
Additional file 3: of Genome-wide association study of Gossypium arboreum resistance to reniform nematode Li, Ruijuan; Erpelding, John; Stetina, Salliana https://doi.org/10.6084/m9.figshare.6933851 The current record is supplemented by this dataset	dataset	January 2018
Additional file 3: of Genome-wide association study of Gossypium arboreum resistance to reniform nematode Li, Ruijuan; Erpelding, John; Stetina, Salliana https://doi.org/10.6084/m9.figshare.6933851.v1 The current record is supplemented by this dataset	dataset	January 2018
Additional file 4: of Genome-wide association study of Gossypium arboreum resistance to reniform nematode Li, Ruijuan; Erpelding, John; Stetina, Salliana https://doi.org/10.6084/m9.figshare.6933860 The current record is supplemented by this dataset	dataset	January 2018
Additional file 4: of Genome-wide association study of Gossypium arboreum resistance to reniform nematode Li, Ruijuan; Erpelding, John; Stetina, Salliana https://doi.org/10.6084/m9.figshare.6933860.v1 The current record is supplemented by this dataset	dataset	January 2018
Additional file 5 of Genome-wide association study of Gossypium arboreum resistance to reniform nematode Li, Ruijuan; Erpelding, John; Stetina, Salliana https://doi.org/10.6084/m9.figshare.6933878 The current record is supplemented by this dataset	dataset	January 2018
Additional file 5 of Genome-wide association study of Gossypium arboreum resistance to reniform nematode Li, Ruijuan; Erpelding, John; Stetina, Salliana https://doi.org/10.6084/m9.figshare.6933878.v1 The current record is supplemented by this dataset	dataset	January 2018
Additional file 6: of Genome-wide association study of Gossypium arboreum resistance to reniform nematode Li, Ruijuan; Erpelding, John; Stetina, Salliana https://doi.org/10.6084/m9.figshare.6933887.v1 The current record is supplemented by this dataset	dataset	January 2018
Genome-wide association study of Gossypium arboreum resistance to reniform nematode Li, Ruijuan; Erpelding, John; Stetina, Salliana https://doi.org/10.6084/m9.figshare.c.4188794 The current record is supplemented by this collection	collection	January 2018
Genome-wide association study of Gossypium arboreum resistance to reniform nematode Li, Ruijuan; Erpelding, John; Stetina, Salliana https://doi.org/10.6084/m9.figshare.c.4188794.v1 The current record is supplemented by this collection	collection	January 2018

Genome-wide association study of Gossypium arboreum resistance to reniform nematode

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