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Acta Agronomica Sinica ›› 2025, Vol. 51 ›› Issue (7): 1725-1735.doi: 10.3724/SP.J.1006.2025.44201

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

QTL mapping of tuber eye depth based on BSA-seq technique

SHAO Shun-Wei1,2,CHEN Zhuo1,LAN Zhen-Dong1,2,CAI Xing-Kui2,ZOU Hua-Fen1,LI Chen-Xi2,TANG Jing-Hua1,ZHU Xi1,ZHANG Yu1,DONG Jian-Ke2,JIN Hui1,*,SONG Bo-Tao2,*   

  1. 1Institute of South Subtropical Crop Research, Chinese Academy of Tropical Agricultural Sciences / Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs / Key Laboratory for Post-harvest Physiology and Preservation of Tropical Horticultural Products of Hainan, Zhanjiang 524091, Guangdong, China; 2 National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops / Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs / Huazhong Agricultural University, Wuhan 430070, Hubei, China
  • Received:2024-12-03 Revised:2025-04-27 Accepted:2025-04-27 Online:2025-07-12 Published:2025-05-07
  • Supported by:
    This study was supported by the Guangdong Provincial Key Areas Research and Development Program (2022B0202060001), the Special Fund for Basic Scientific Research Operating Expenses of Central-level Public Welfare Research Institutes (1630062024011), the Hainan Provincial Natural Science Foundation Youth Fund (323QN296, 323QN328), and the Regional Fund of the National Natural Science Foundation of China (32360459).

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Abstract: Eye depth is an important trait of potato tubers, significantly affecting both their appearance and processing quality. To identify quantitative trait loci (QTLs) associated with eye depth, a cross was made between the tetraploid deep-eyed variety “Hua Shu 12” (female) and the shallow-eyed advanced line “Tian 2002-4-5” (male), generating 255 clonal F1 progeny. Based on field phenotypic data collected over two consecutive years, 20 deep-eyed and 20 shallow-eyed individuals were selected to construct bulks for QTL mapping. The BSA-seq approach was employed to detect QTLs related to eye depth, and combined with traditional QTL mapping methods, a complete interval mapping analysis was conducted to construct a genetic linkage map. Two QTLs associated with eye depth were successfully identified. Phenotypic correlation analysis across both years suggested that tuber eye depth is primarily controlled by genetic factors. The LOD score for locus qEyd10.1 on chromosome 10 was 4.96, with a phenotypic variance explained (PVE) of 14.49%, while qEyd3.1 on chromosome 3 had a LOD score of 3.29 and a PVE of 10.18%. Notably, qEyd3.1 corresponds to a previously reported eye depth locus, whereas qEyd10.1 represents a novel QTL. Both loci exhibited negative additive effects, indicating that the allele responsible for reduced eye depth was inherited from the shallow-eyed parent “Tian 2002-4-5”. Through candidate gene annotation within the mapped intervals and analysis of gene structural variation between deep- and shallow-eyed materials, four candidate genes: Soltu.DM.10G029390.1, Soltu.DM.03G036540.1, Soltu.DM.03G036140.1, and Soltu.DM.03G036580.1 were preliminarily identified as potentially associated with eye depth. This study, by integrating BSA-seq with conventional QTL mapping in autotetraploid potato, provides a preliminary identification of candidate genes regulating tuber eye depth. These findings lay a foundation for future gene cloning and genetic mechanism studies, and offer a valuable reference for breeding new tetraploid potato varieties with shallower eyes.

Key words: potato, eye depth, QTL mapping, bulked segregant analysis sequencing, genetic linkage map

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