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High-density bin-based genetic map reveals a 530-kb chromosome segment derived from wild peanut contributing to late leaf spot resistance

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Twenty-eight QTLs for LLS disease resistance were identified using an amphidiploid constructed mapping population, a favorable 530-kb chromosome segment derived from wild species contributes to the LLS resistance.

Abstract

Late leaf spot (LLS) is one of the major foliar diseases of peanut, causing serious yield loss and affecting the quality of kernel and forage. Some wild Arachis species possess higher resistance to LLS as compared with cultivated peanut; however, ploidy level differences restrict utilization of wild species. In this study, a synthetic amphidiploid (Ipadur) of wild peanuts with high LLS resistance was used to cross with Tifrunner to construct TI population. In total, 200 recombinant inbred lines were collected for whole-genome resequencing. A high-density bin-based genetic linkage map was constructed, which includes 4,809 bin markers with an average inter-bin distance of 0.43 cM. The recombination across cultivated and wild species was unevenly distributed, providing a novel recombination landscape for cultivated-wild Arachis species. Using phenotyping data collected across three environments, 28 QTLs for LLS disease resistance were identified, explaining 4.35–20.42% of phenotypic variation. The major QTL located on chromosome 14, qLLS14.1, could be consistently detected in 2021 Jiyang and 2022 Henan with 20.42% and 12.12% PVE, respectively. A favorable 530-kb chromosome segment derived from Ipadur was identified in the region of qLLS14.1, in which 23 disease resistance proteins were located and six of them showed significant sequence variations between Tifrunner and Ipadur. Allelic variation analysis indicating the 530-kb segment of wild species might contribute to the disease resistance of LLS. These associate genomic regions and candidate resistance genes are of great significance for peanut breeding programs for bringing durable resistance through pyramiding such multiple LLS resistance loci into peanut cultivars.

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Acknowledgements

This research is supported by National Natural Science Foundation of China (31861143009), Guangxi Science and Technology Major Project (“Peak Project” of Modern Characteristic Agriculture, GuikeAA23062004), National Key Research and Development Program of China (2022YFD1200400), Key Research and Development Project of Shandong Province (2020LZGC001, 2022LZGC007), Agricultural scientific and technological innovation project of SAAS (CXGC2023C04, CXGC2023G30), and Taishan Scholar Project of Shandong Province

Funding

This study was funded by the National Natural Science Foundation of China (31861143009), Guangxi Science and Technology Major Project (“Peak Project” of Modern Characteristic Agriculture, GuikeAA23062004), National Key Research and Development Program of China (2022YFD1200400, 2023YFD1202800), Key Research and Development Project of Shandong Province (2020LZGC001, 2022LZGC007), New 20 Policies for Universities in Jinan (202333047), Agricultural Scientific and Technological Innovation Project of SAAS (CXGC2023C04, CXGC2023G30), and Taishan Scholar Project of Shandong Province.

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Author notes

  1. Jiaowen Pan and Xiaojie Li have contributed equally.

Authors and Affiliations

  1. Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People’s Republic of China

    Jiaowen Pan, Xiaojie Li, Conghui Yu, Guanghao Wang, Ruizheng Tian, Changsheng Li, Han Xia, Shuzhen Zhao, Lei Hou, Hailing Zi, Xingjun Wang & Chuanzhi Zhao

  2. College of Life Sciences, Shandong Normal University, Jinan, 250014, People’s Republic of China

    Jiaowen Pan, Xiaojie Li, Conghui Yu, Ruizheng Tian, Han Xia, Shuzhen Zhao, Lei Hou, Xingjun Wang & Chuanzhi Zhao

  3. Weifang Academy of Agricultural Sciences, Weifang, 261071, People’s Republic of China

    Chun Fu & Xiaofeng Song

  4. Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, People’s Republic of China

    Zhenyu Wang & Meng Gao

  5. Institute of Advanced Agricultural Science, Peking University, Weifang, 261071, People’s Republic of China

    Jianxin Bian & Xiaoqin Liu

  6. Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA

    David Bertioli & Soraya Leal-Bertioli

  7. Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India

    Manish K. Pandey

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  1. Jiaowen Pan
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Contributions

CZ and XW conceived and designed the experiments. JP, XL, CF, ZW, CY, RT, XS and MG performed the experiments. CL, HX, SZ, LH, HZ, DB and SL developed the populations. JB, XL and GW provided technical assistance and some analysis. JP and CZ wrote the manuscript. MP revised the manuscript.

Corresponding author

Correspondence to Chuanzhi Zhao.

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Communicated by Reyazul Rouf Mir.

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Supplementary Information

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The number of SNPs in each chromosome.

122_2024_4580_MOESM2_ESM.pdf

Recombination bin map of 200 individual RILs. Colored tracks represent the 200 RILs of the TI population that were used for bin map construction: blue: genotype inherited from maternal parent Tifrunner, red: genotype inherited from maternal parent Ipadur, yello: genotype inherited from heterozygous genotype (Tifrunner × Ipadur) F1.

122_2024_4580_MOESM3_ESM.pdf

Collinearity analysis between genetic map and physical map. The x-axis scales the physical positions of markers based on reference sequences. The y-axis represents the genetic distance of the markers in centimorgans accordingly.

Summary of sequence information in this study.

The bin marker in 20 LGs and the genotype of 200 individual lines.

The high-density genetic map of 20 linkage groups (LG).

Genes list in the major QTL regions.

The candidate genes with sequence variations in the coding regions, intron, 5’ UTR or splice region.

Genes list in 120.78-121.31 Mb physical region of B04.

Sequence alignment analysis of disease resistance proteins genes between Tifrunner and wild species.

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Pan, J., Li, X., Fu, C. et al. High-density bin-based genetic map reveals a 530-kb chromosome segment derived from wild peanut contributing to late leaf spot resistance. Theor Appl Genet 137, 69 (2024). https://doi.org/10.1007/s00122-024-04580-6

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