Construction and analysis of the pangenome of Cucurbita moschata to uncover variants associated with virus resistance

Cucurbita moschata (butternut squash) is an important crop that is severely affected by several potyviruses, including Moroccan watermelon mosaic virus (MWMV), zucchini yellow mosaic virus (ZYMV), and papaya ringspot virus (PRSV). The development of molecular markers linked to virus resistance can greatly assist breeding programs through marker-assisted selection (MAS). This study aims to identify quantitative trait loci (QTLs) associated with MWMV resistance in butternut using a pangenome-assisted bulk segregant analysis (BSAseq) approach. To achieve this, a pangenome of C. moschata was first constructed using an iterative mapping and assembly strategy with resequencing data from 18 genetically diverse breeding lines from the Starke Ayres breeding program as input. The pangenome was then used to perform variant analysis, both short variants and structural variant (SV) analysis to identify genomic diversity among these lines. For trait mapping, BSAseq was carried out using DNA extracted from highly resistant F2 (second filial generation) individuals derived from a cross between a MWMV resistant parent and a MWMV susceptible parent. Reads were aligned to the newly constructed pangenome reference and the SNP index method was used to detect QTLs associated with MWMV resistance. Molecular markers were then designed within the identified QTL regions and validated in an F3 population segregating for resistance using the composite interval mapping (CIM).

Grantor dc:publisher

Stellenbosch : Stellenbosch University

Year dc:date.issued

2026

Author dc:creator

• Mafireyi, Godwin

Advisors dc:contributor.advisor

• Burger, Johan T.
• Patterton, Hugh
• Ascough, Glendon

Language dc:language.iso

en

Repository record dc:identifier.uri

https://scholar.sun.ac.za/handle/10019.1/136271

OAI identifier oai:identifier

oai:scholar.sun.ac.za:10019.1/136271