Validation of candidate gene-based EST-SSR markers for sugar yield in sugarcane

S Divakar; Ratnesh Kumar Jha; D N Kamat; Ashutosh Singh

doi:10.3389/fpls.2023.1273740

Validation of candidate gene-based EST-SSR markers for sugar yield in sugarcane

Front Plant Sci. 2023 Oct 27:14:1273740. doi: 10.3389/fpls.2023.1273740. eCollection 2023.

Authors

S Divakar¹, Ratnesh Kumar Jha², D N Kamat³, Ashutosh Singh²

Affiliations

¹ Department of AB&MB, CBSH, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Samastipur, Bihar, India.
² Centre for Advanced Studies on Climate Change, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Samastipur, Bihar, India.
³ Sugarcane Research Institute, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Samastipur, Bihar, India.

Abstract

Sugarcane (Saccharum spp.) is a widely cultivated crop that fulfils approximately 75% of the sucrose demand worldwide. Owing to its polyploidy and complex genetic nature, it is difficult to identify and map genes related to complex traits, such as sucrose content. However, association mapping is one of the alternatives for identifying genes or markers for marker-assisted selection. In the present study, EST-SSR primers were obtained from in silico studies. The functionality of each primer was tested using Blast2Go software, and 30 EST-SSR primers related to sugar content were selected. These markers were validated using association analysis. A total of 70 F1 diverse genotypes for sugar content were phenotypes with two check lines. All parameters related to sugar content were recorded. The results showed a significant variation between the genotypes for sugar yield traits such as Brix value, purity, and sucrose content, etc. Correlation studies revealed that the Brix%, sucrose content, and sucrose recovery were significantly correlated. An association analysis was performed using mixed linear model to avoid false positive associations. The association analysis revealed that the SEM 407 marker was significantly associated with Brix% and sucrose content. The SEM 407 primers are putatively related to diphosphate-fructose-6-phosphate 1-phosphotransferase which is associated with Brix% and sucrose content. This functional marker can be used for marker-assisted selection for sugar yield traits in sugarcane that could accelerate the sugarcane breeding program.

Keywords: EST-SSR; association mapping; candidate genes; marker-assisted selection; sugar content; sugarcane.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research was funded by Bihar government under Climate Resilient Agriculture Program (India).