Identification and expression of gene loci underlying the quantitative trait loci of starch content in cassava

ABSTRACT

In this study, a genetic linkage map was developed based on simple sequence repeat (SSR) markers to aid in the identification and expression analysis of gene loci underlying the quantitative trait loci (QTL) of starch content (SC) in cassava (Manihot esculenta). A total of 912 polymorphic loci from 4,515 tested SSRs were mapped into 18 linkage groups. QTL analysis revealed four loci with highly significant associations with starch. Gene annotation was performed, and potential genes related to starch synthesis were identified. Of these, expression of four genes related to starch synthesis (Raffinose synthase [RS], Phosphoenolpyruvate kinase [PK], Glucose-6-phosphate [G6P], and Glycogen synthase kinase 3 [GSK-3]) was investigated by real-time PCR assays. The results found a statistically significant difference (p < 0.05) at 3 months after planting (MAP) in all the tested genes, whereas a higher expression was detected in the low-SC group with specific genotypes of linked markers. A higher level of expression was observed in the RS, PK, and G6P genes at six and nine MAP, indicating that starch accumulation mainly occurs after 3 MAP, during which the root system begins to form. The potential genes identified in this study could provide a better understanding of the starch biosynthesis mechanism, and could be useful for applications in marker-assisted selection to facilitate cassava breeding programs in the future.

KEYWORDS:

• Food productivity
• genetic linkage map
• QTL mapping
• quantitative real-time PCR
• SSR marker

Acknowledgments

This project was supported by the Institute of Molecular Biosciences, Mahidol University, Nakhon Ratchasima Research and Development Center, Department of Agriculture, Ministry of Agriculture and Cooperatives, Thailand. Financial support from the Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Thailand to SW and KT is acknowledged.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This research was funded by a grant from Mahidol University (Basic Research Fund: Fiscal Year 2021).