ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Biotechnology
Genetic dissection of nutrient element enrichment in Saccharum officinarum L. for deciphering the food health
Provisionally accepted
Lina Fan1
Zaid Chachar1Ming Chen1Yucong Li1Jiarui Chen1Huiyi He2Jiakun Wen1Ruiqiang Lai1*
Yongwen Qi1*- 1College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- 2Institute of Nanfan and Seed Industry, Guangdong Academy of Science, Guangzhou, Guangdong, Guangzhou, China
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Sugarcane is a key global crop for sugar production, widely applied across food, industrial, and pharmaceutical sectors. Enhancing nutrient efficiency in sugarcane varieties can boost yield, ensure sugar security, and improve nutritional value. This study analyzed 109 sugarcane stem segment samples for major (e.g., magnesium, calcium, phosphorus) and trace (e.g., manganese, iron, copper) nutrient content, along with their SNP genotyping data. Two multi-model Genome-Wide Association Study (GWAS) approaches—MLM_Q+Kinship and MLM_PCA+Kinship—were used to identify SNPs linked to nutritional traits. Under a P-value threshold of <10⁻⁴, MLM_Q+Kinship identified SNPs for traits including total sugar (4), nitrogen (7), phosphorus (179), potassium (4), sulfur (41), magnesium (26), calcium (20), and silicon (66), and others. Similar results were obtained with the MLM_PCA+Kinship. A stricter threshold (P < 1.53×10⁻⁶) yielded 59 reliable "Peak" SNP loci explaining >15% of phenotypic variance. Notably, SNPs 3B_33126337 and 5C_64683842 were strongly associated with magnesium, calcium, and iron utilization. Genotypic analysis showed superior nutrient accumulation in genotypes TT (3B_33126337) and AA/AG (2D_29369331, 3B_14919731). Bioinformatics analysis identified 12 candidate genes involved in magnesium, calcium, and manganese metabolism, linked to pyruvate metabolism, purine metabolism, and glycolysis/gluconeogenesis pathways. RT-qPCR analysis further highlighted three genes (Sspon.003B0015150, Sspon.002D0013560, and Sspon.003B0007030) with significant expression differences between genotypes, suggesting their potential as key targets. These findings offer valuable genetic markers and candidate genes for the development of nutrient-efficient, high-yield sugarcane varieties that support both agricultural and nutritional advancements.
Keywords: Saccharum officinarum, Nutrient element, GWAS, genetic dissection, Food health
Received: 19 Jun 2025; Accepted: 27 Oct 2025.
Copyright: © 2025 Fan, Chachar, Chen, Li, Chen, He, Wen, Lai and Qi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Ruiqiang Lai, 2019010166@m.scnu.edu.cn
Yongwen Qi, yongwen2001@163.com
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