Analyzing genetic diversity in luffa and developing a Fusarium wilt-susceptible linked SNP marker through a single plant genome-wide association (sp-GWAS) study.

Publisher: BioMed Central Country of Publication: England NLM ID: 100967807 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2229 (Electronic) Linking ISSN: 14712229 NLM ISO Abbreviation: BMC Plant Biol Subsets: MEDLINE

Original Publication: London : BioMed Central, [2001-

Fusarium*/physiology ; Polymorphism, Single Nucleotide*/genetics ; Plant Diseases*/microbiology ; Plant Diseases*/genetics ; Genome-Wide Association Study* ; Quantitative Trait Loci* ; Disease Resistance*/genetics ; Luffa*/genetics ; Luffa*/microbiology; Genome, Plant ; Genetic Markers ; Genetic Variation

Background: Luffa (Luffa spp.) is an economically important crop of the Cucurbitaceae family, commonly known as sponge gourd or vegetable gourd. It is an annual cross-pollinated crop primarily found in the subtropical and tropical regions of Asia, Australia, Africa, and the Americas. Luffa serves not only as a vegetable but also exhibits medicinal properties, including anti-inflammatory, antidiabetic, and anticancer effects. Moreover, the fiber derived from luffa finds extensive applications in various fields such as biotechnology and construction. However, luffa Fusarium wilt poses a severe threat to its production, and existing control methods have proven ineffective in terms of cost-effectiveness and environmental considerations. Therefore, there is an urgent need to develop luffa varieties resistant to Fusarium wilt. Single-plant GWAS (sp-GWAS) has been demonstrated as a promising tool for the rapid and efficient identification of quantitative trait loci (QTLs) associated with target traits, as well as closely linked molecular markers.
Results: In this study, a collection of 97 individuals from 73 luffa accessions including two major luffa species underwent single-plant GWAS to investigate luffa Fusarium wilt resistance. Utilizing the double digest restriction site associated DNA (ddRAD) method, a total of 8,919 high-quality single nucleotide polymorphisms (SNPs) were identified. The analysis revealed the potential for Fusarium wilt resistance in accessions from both luffa species. There are 6 QTLs identified from 3 traits, including the area under the disease progress curve (AUDPC), a putative disease-resistant QTL, was identified on the second chromosome of luffa. Within the region of linkage disequilibrium, a candidate gene homologous to LOC111009722, which encodes peroxidase 40 and is associated with disease resistance in Cucumis melo, was identified. Furthermore, to validate the applicability of the marker associated with resistance from sp-GWAS, an additional set of 21 individual luffa plants were tested, exhibiting 93.75% accuracy in detecting susceptible of luffa species L. aegyptiaca Mill.
Conclusion: In summary, these findings give a hint of genome position that may contribute to luffa wild resistance to Fusarium and can be utilized in the future luffa wilt resistant breeding programs aimed at developing wilt-resistant varieties by using the susceptible-linked SNP marker.
(© 2024. The Author(s).)

Heliyon. 2019 May 07;5(5):e01634. (PMID: 31193002)
Theor Appl Genet. 2021 Mar;134(3):897-908. (PMID: 33367942)
DNA Res. 2016 Apr;23(2):145-53. (PMID: 26932983)
Genome Res. 2010 Sep;20(9):1297-303. (PMID: 20644199)
J Plant Physiol. 2017 Feb;209:84-94. (PMID: 28013174)
Braz J Otorhinolaryngol. 2015 Jul-Aug;81(4):422-30. (PMID: 26163226)
Front Plant Sci. 2017 Oct 12;8:1774. (PMID: 29075283)
Tree Physiol. 2020 Aug 29;40(9):1277-1291. (PMID: 32348504)
Front Plant Sci. 2020 Feb 27;11:206. (PMID: 32174947)
Peptides. 2002 Jun;23(6):1019-24. (PMID: 12126727)
Hortic Res. 2020 Aug 1;7(1):128. (PMID: 32821411)
Cell Res. 2012 Apr;22(4):777-81. (PMID: 22357482)
Theor Appl Genet. 2022 Jul;135(7):2297-2312. (PMID: 35577933)
Mol Plant. 2013 Sep;6(5):1616-29. (PMID: 23475998)
Development. 2015 Feb 1;142(3):444-53. (PMID: 25605779)
Sci Rep. 2017 Apr 19;7:46446. (PMID: 28422143)
Mol Ecol. 2005 Jul;14(8):2611-20. (PMID: 15969739)
Saudi J Biol Sci. 2019 Nov;26(7):1315-1324. (PMID: 31762590)
PLoS One. 2012;7(5):e37135. (PMID: 22675423)
Bioinformatics. 2007 Oct 1;23(19):2633-5. (PMID: 17586829)
BMC Plant Biol. 2014 Dec 30;14:372. (PMID: 25547028)
J Ethnopharmacol. 2019 Jan 30;229:89-96. (PMID: 30287196)
BMC Plant Biol. 2020 Jan 20;20(1):29. (PMID: 31959107)
Theor Appl Genet. 2020 Feb;133(2):563-577. (PMID: 31768602)
BMC Plant Biol. 2021 Aug 20;21(1):384. (PMID: 34416854)
Genet Mol Res. 2015 Dec 08;14(4):16255-64. (PMID: 26662419)
Theor Appl Genet. 2006 Oct;113(6):1027-36. (PMID: 16896713)
Plant Biotechnol J. 2018 Nov;16(11):1825-1835. (PMID: 29528555)
PLoS One. 2014 Aug 25;9(8):e105593. (PMID: 25153126)
Food Res Int. 2019 Feb;116:878-882. (PMID: 30717018)
Mol Ecol Resour. 2021 Jan;21(1):212-225. (PMID: 32841550)
Genes (Basel). 2021 Jun 03;12(6):. (PMID: 34205206)
Biochem Biophys Res Commun. 2003 Mar 21;302(4):635-45. (PMID: 12646216)
Front Plant Sci. 2014 Sep 30;5:484. (PMID: 25324846)
Front Plant Sci. 2012 Jan 19;2:116. (PMID: 22639630)
Plant Pathol J. 2019 Jun;35(3):200-207. (PMID: 31244566)
G3 (Bethesda). 2018 May 4;8(5):1817-1828. (PMID: 29602808)
Phytopathology. 2022 Sep;112(9):1979-1987. (PMID: 35657701)
Plant Dis. 2023 Jul;107(7):1993-2001. (PMID: 36475742)
Planta. 2010 Oct;232(5):1229-39. (PMID: 20730544)
G3 (Bethesda). 2022 Aug 25;12(9):. (PMID: 35792880)
BMC Plant Biol. 2019 Oct 8;19(1):412. (PMID: 31590656)
Front Plant Sci. 2023 Jun 09;14:1116006. (PMID: 37360710)
Plant Sci. 2012 Nov;196:125-31. (PMID: 23017907)

Keywords: Fusarium wilt; Luffa; SNP marker; Single-plant GWAS; Susceptible; ddRAD

0 (Genetic Markers)

Date Created: 20240421 Date Completed: 20240423 Latest Revision: 20240426

20240426

PMC11034075

10.1186/s12870-024-05022-7

38644483