Construction of a High-Density Genetic Map and QTL Mapping Analysis for Yield, Tuber Shape, and Eye Number in Diploid Potato

Jing Yang, Chunguang Yao, Jiahao Miao, Nan Li, Faru Ji, Die Hu, Sitong Wang, Zixian Zhou, Kunyan Dai, Aie Chen and Canhui Li ()
Additional contact information
Jing Yang: Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
Chunguang Yao: Industrial Crop Research Institute, Yunnan Academy of Agricultural Science, Kunming 650205, China
Jiahao Miao: Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
Nan Li: Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
Faru Ji: Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
Die Hu: Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
Sitong Wang: Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
Zixian Zhou: Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
Kunyan Dai: Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
Aie Chen: Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China
Canhui Li: Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming 650500, China

Agriculture, 2025, vol. 15, issue 19, 1-22

Abstract: Potato ( Solanum tuberosum L.) is a globally important food crop, but its tetrasomic inheritance and diploid self-incompatibility have limited the discovery of potato genes and progress in breeding. Here, we developed an F 2 segregating population consisting of 174 lines by crossing a self-compatible genome-homozygous diploid line (Y8, female parent) with a heterozygous diploid line (IVP101, male parent), followed by selfing. Using whole-genome resequencing, we constructed a high-density genetic map containing 4464 recombinant bin markers with an average physical distance of 165.51 Kb. Phenotypic evaluation of 8 traits related to yield, tuber shape, and tuber eye number across three environments revealed significant parental differences and wide phenotypic variation within the F 2 population. QTL (Quantitative trait loci) mapping using this genetic map and multi-environment phenotypic data identified 89 QTLs, including 7 previously reported QTLs/genes. In addition, 10 QTLs were stably detected across multiple seasons (stable QTLs). Further genetic effect analysis showed that favorable alleles of these stable QTLs significantly enhanced phenotypic values. Notably, two pleiotropic QTLs were identified on chromosomes 5 and 12; the major-effect QTL on chromosome 12 ( qTY-12-6 , qTS-12-3 , and qTE-12-4 ) exhibited high phenotypic variance explained (PVE). Its favorable allele from Y8 significantly increased mean tuber weight, tuber number per plant, and promoted rounder tuber shape while reducing eye number, simultaneously improving yield and quality. Collectively, this study provides a reference for genetic mapping using homozygous and heterozygous diploid parents, and the identified QTLs offer valuable genetic resources for potato breeding and molecular mechanism research, enhancing our understanding of the genetic regulation of yield, tuber shape, and eye number in potato.

Keywords: diploid potato; yield; tuber shape; eye number; genetic map; QTL mapping (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2025
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.mdpi.com/2077-0472/15/19/2032/pdf (application/pdf)
https://www.mdpi.com/2077-0472/15/19/2032/ (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:gam:jagris:v:15:y:2025:i:19:p:2032-:d:1760094

Access Statistics for this article

Agriculture is currently edited by Ms. Leda Xuan

More articles in Agriculture from MDPI
Bibliographic data for series maintained by MDPI Indexing Manager ().