Mapping QTL and Identifying Candidate Genes for Resistance to Brown Stripe in Highly Allo-Autopolyploid Modern Sugarcane

Cheng, Wei; Wang, Zhoutao; Xu, Fu; Yang, Yingying; Fang, Jie; Wu, Jianxiong; Pan, Junjie; Wang, Qiaomei; Xu, Liping

doi:10.3390/horticulturae11080922

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Mapping QTL and Identifying Candidate Genes for Resistance to Brown Stripe in Highly Allo-Autopolyploid Modern Sugarcane

by

Wei Cheng

^1,2,†

,

Zhoutao Wang

^3,†,

Fu Xu

⁴,

Yingying Yang

⁵,

Jie Fang

⁶,

Jianxiong Wu

²,

Junjie Pan

⁶,

Qiaomei Wang

^1,* and

Liping Xu

^5,*

¹

Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China

²

Zhejiang Sanheyuan Agriculture Development Co., Ltd., Lishui 323000, China

³

School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, China

⁴

Maize Research Center of Crop Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China

⁵

National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China

⁶

Lishui Institute of Agriculture and Forestry Sciences, Lishui 323000, China

^*

Authors to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Horticulturae 2025, 11(8), 922; https://doi.org/10.3390/horticulturae11080922 (registering DOI)

Submission received: 9 July 2025 / Revised: 1 August 2025 / Accepted: 4 August 2025 / Published: 5 August 2025

(This article belongs to the Special Issue Disease Diagnosis and Control for Fruit Crops)

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Abstract

Disease resistance is one of the most important target traits for sugarcane genetic improvement. Sugarcane brown stripe (SBS) caused by Helminthosporium stenospilum is one of the most destructive foliar diseases, which not only reduces harvest cane yield but also sugar content. This study aimed to identify quantitative trait loci (QTL) and candidate genes associated with SBS resistance. Here, the phenotypic investigation in six field habitats showed a continuous normal distribution, revealing that the SBS resistance trait is a quantitative trait. Two high-density linkage maps based on the single-dose markers calling from the Axiom Sugarcane100K SNP chip were constructed for the dominant sugarcane cultivars YT93-159 (SBS-resistant) and ROC22 (SBS-susceptible) with a density of 2.53 cM and 2.54 cM per SNP marker, and mapped on 87 linkage groups (LGs) and 80 LGs covering 3069.45 cM and 1490.34 cM of genetic distance, respectively. A total of 32 QTL associated with SBS resistance were detected by QTL mapping, which explained 3.73–11.64% of the phenotypic variation, and the total phenotypic variance explained (PVE) in YT93-159 and ROC22 was 107.44% and 79.09%, respectively. Among these QTL, four repeatedly detected QTL (qSBS-Y38-1, qSBS-Y38-2, qSBS-R8, and qSBS-R46) were considered stable QTL. Meanwhile, two major QTL, qSBS-Y38 and qSBS-R46, could account for 11.47% and 11.64% of the PVE, respectively. Twenty-five disease resistance candidate genes were screened by searching these four stable QTL regions in their corresponding intervals, of which Soffic.01G0010840-3C (PR3) and Soffic.09G0017520-1P (DND2) were significantly up-regulated in YT93-159 by qRT-PCR, while Soffic.01G0040620-1P (EDR2) was significantly up-regulated in ROC22. These results will provide valuable insights for future studies on sugarcane breeding in combating this disease.

Keywords: sugarcane brown stripe; SBS resistance; genetic map; QTL mapping; candidate gene

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MDPI and ACS Style

Cheng, W.; Wang, Z.; Xu, F.; Yang, Y.; Fang, J.; Wu, J.; Pan, J.; Wang, Q.; Xu, L. Mapping QTL and Identifying Candidate Genes for Resistance to Brown Stripe in Highly Allo-Autopolyploid Modern Sugarcane. Horticulturae 2025, 11, 922. https://doi.org/10.3390/horticulturae11080922

AMA Style

Cheng W, Wang Z, Xu F, Yang Y, Fang J, Wu J, Pan J, Wang Q, Xu L. Mapping QTL and Identifying Candidate Genes for Resistance to Brown Stripe in Highly Allo-Autopolyploid Modern Sugarcane. Horticulturae. 2025; 11(8):922. https://doi.org/10.3390/horticulturae11080922

Chicago/Turabian Style

Cheng, Wei, Zhoutao Wang, Fu Xu, Yingying Yang, Jie Fang, Jianxiong Wu, Junjie Pan, Qiaomei Wang, and Liping Xu. 2025. "Mapping QTL and Identifying Candidate Genes for Resistance to Brown Stripe in Highly Allo-Autopolyploid Modern Sugarcane" Horticulturae 11, no. 8: 922. https://doi.org/10.3390/horticulturae11080922

APA Style

Cheng, W., Wang, Z., Xu, F., Yang, Y., Fang, J., Wu, J., Pan, J., Wang, Q., & Xu, L. (2025). Mapping QTL and Identifying Candidate Genes for Resistance to Brown Stripe in Highly Allo-Autopolyploid Modern Sugarcane. Horticulturae, 11(8), 922. https://doi.org/10.3390/horticulturae11080922

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Mapping QTL and Identifying Candidate Genes for Resistance to Brown Stripe in Highly Allo-Autopolyploid Modern Sugarcane

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