Revealing the Key Genetic Basis of Late Leaf Spot Resistance in Peanut by Combining QTL Mapping, QTL‐seq and RNA‐seq
- 1Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences Wuhan China
Abstract
Late leaf spot (LLS) is the most widespread and destructive fungal disease affecting peanut worldwide, yet relatively little is known about its genetic basis. In this study, QTL mapping using a 1327‐bin map (derived from 9533 SNP/InDel markers) and multi‐environment phenotypic data repeatedly detected two major LLS‐resistance QTLs on chromosomes A02 and B06 in the Zhonghua 5 × ICGV 86699 recombinant inbred line (RIL) population. QTL‐seq analysis confirmed qLLSA02, and integration of both mapping methods narrowed the A02 interval to a 1.0–3.4 Mb region. Transcriptome profiling identified thousands of differentially expressed genes. Through systematic investigation of variants, functional annotation, expression patterns, allelic effects and comparative genomics within this target region, we identified 10 LLS resistance candidate genes and further prioritised two of these as the most promising candidates. Two kompetitive allele‐specific PCR (KASP) markers were developed from SNPs of the two priority candidate genes, showing a strong correlation between genotype and LLS phenotype. Pathway analysis revealed that flavonoid biosynthesis, plant hormone signal transduction, and plant‐pathogen interaction pathways are involved in the response to LLS infection. This study provided insights into the genetic and molecular mechanisms underlying LLS resistance in peanut, and the two developed KASP markers can facilitate LLS resistance peanut breeding.
Related
- Genetic mapping of Citrullus amarus for resistance to gummy stem blight in watermelon
- Association mapping and genome prediction reveal a complex genetic architecture for resistance to black and frosty pod rot in cacao (Theobroma cacao L.) populations
- Combining A Massively Parallel Reporter Assay and Human Data to Elucidate Genetic Mechanisms Driving Risk for Juvenile Idiopathic Arthritis
- Colonisation history of a vector species of veterinary interest: phylogeography of Culicoides imicola (Diptera: Ceratopogonidae) in the Indian Ocean revealing low genetic structure
- Dual control of plasmid copy number in E. coli by combining temperature shifts and RNAI-based genetic circuits for tunable replication dynamics
BibTeX
@article{cui2026revealing,
title = {{Revealing the Key Genetic Basis of Late Leaf Spot Resistance in Peanut by Combining QTL Mapping, QTL‐seq and RNA‐seq}},
author = {Wenhui Cui and Pengxia Guo and Bolun Yu and Huifang Jiang and Yong Lei and Boshou Liao and Huaiyong Luo and Xin Wang and Li Huang and Nian Liu and Jianbing Guo and Weigang Chen and Xiaojing Zhou},
journal = {Plant, Cell \& Environment},
year = {2026},
month = sep,
doi = {10.1111/pce.70910},
url = {https://doi.org/10.1111/pce.70910},
note = {CC BY-NC 4.0},
}
RIS
TY - JOUR
TI - Revealing the Key Genetic Basis of Late Leaf Spot Resistance in Peanut by Combining QTL Mapping, QTL‐seq and RNA‐seq
AU - Wenhui Cui
AU - Pengxia Guo
AU - Bolun Yu
AU - Huifang Jiang
AU - Yong Lei
AU - Boshou Liao
AU - Huaiyong Luo
AU - Xin Wang
AU - Li Huang
AU - Nian Liu
AU - Jianbing Guo
AU - Weigang Chen
AU - Xiaojing Zhou
PY - 2026
DA - 2026/09/23
JO - Plant, Cell & Environment
DO - 10.1111/pce.70910
UR - https://doi.org/10.1111/pce.70910
AB - Late leaf spot (LLS) is the most widespread and destructive fungal disease affecting peanut worldwide, yet relatively little is known about its genetic basis. In this study, QTL mapping using a 1327‐bin map (derived from 9533 SNP/InDel markers) and multi‐environment phenotypic data repeatedly detected two major LLS‐resistance QTLs on chromosomes A02 and B06 in the Zhonghua 5 × ICGV 86699 recombinant inbred line (RIL) population. QTL‐seq analysis confirmed qLLSA02, and integration of both mapping methods narrowed the A02 interval to a 1.0–3.4 Mb region. Transcriptome profiling identified thousands of differentially expressed genes. Through systematic investigation of variants, functional annotation, expression patterns, allelic effects and comparative genomics within this target region, we identified 10 LLS resistance candidate genes and further prioritised two of these as the most promising candidates. Two kompetitive allele‐specific PCR (KASP) markers were developed from SNPs of the two priority candidate genes, showing a strong correlation between genotype and LLS phenotype. Pathway analysis revealed that flavonoid biosynthesis, plant hormone signal transduction, and plant‐pathogen interaction pathways are involved in the response to LLS infection. This study provided insights into the genetic and molecular mechanisms underlying LLS resistance in peanut, and the two developed KASP markers can facilitate LLS resistance peanut breeding.
SN - 0140-7791
SN - 1365-3040
ER -