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BSA‑seq and genetic mapping identified candidate genes for branching habit in peanut

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Abstract

Key Message

The candidate gene AhLBA1 controlling lateral branch angel of peanut was fine-mapped to a 136.65-kb physical region on chromosome 15 using the BSA-seq and QTL mapping.

Abstract

Lateral branch angel (LBA) is an important plant architecture trait of peanut, which plays key role in lodging, peg soil penetration and pod yield. However, there are few reports of fine mapping and quantitative trait loci (QTLs)/cloned genes for LBA in peanut. In this project, a mapping population was constructed using a spreading variety Tifrunner and the erect variety Fuhuasheng. Through bulked segregant analysis sequencing (BSA-seq), a major gene related to LBA, named as AhLBA1, was preliminarily mapped at the region of Chr.15: 150-160 Mb. Then, using traditional QTL approach, AhLBA1 was narrowed to a 1.12 cM region, corresponding to a 136.65-kb physical interval of the reference genome. Of the nine genes housed in this region, three of them were involved in hormone metabolism and regulation, including one “F-box protein” and two “2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase (2OG oxygenase)” encoding genes. In addition, we found that the level of some classes of cytokinin (CK), auxin and ethylene showed significant differences between spreading and erect peanuts at the junction of main stem and lateral branch. These findings will aid further elucidation of the genetic mechanism of LBA in peanut and facilitating marker-assisted selection (MAS) in the future breeding program.

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Acknowledgements

This research is supported by National Key Research and Development Program of China, National Natural Science Foundation of China (31861143009, 32072090), Key Research and Development Project of Shandong Province (2020LZGC001), Agricultural Scientific and Technological Innovation Project of Shandong Academy of Agricultural Sciences, and Taishan Scholar Project of Shandong Province (ts20190964).

Funding

This study was funded by National Natural Science Foundation of China (31861143009, 32072090), Key Research and Development Project of Shandong Province (2020LZGC001), Agricultural Scientific and Technological Innovation Project of Shandong Academy of Agricultural Sciences, and Taishan Scholar Project of Shandong Province (ts20190964).

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  1. Jiaowen Pan and Ximeng Zhou contributed equally for this paper.

Authors and Affiliations

  1. Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People’s Republic of China

    Jiaowen Pan, Ximeng Zhou, Naveed Ahmad, Kun Zhang, Huiling Zhao, Changsheng Li, Aiqin Li, Xianying Zhang, Jing Ma, Xiaojie Li, Ruizheng Tian, Xingjun Wang & Chuanzhi Zhao

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

    Ximeng Zhou, Huiling Zhao, Jing Ma, Xiaojie Li, Changle Ma, Xingjun Wang & Chuanzhi Zhao

  3. College of Agricultural Science and Technology, Shandong Agriculture and Engineering University, Jinan, 250100, People’s Republic of China

    Kun Zhang

  4. Cash Crop Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China

    Ronghua Tang, Jing Jiang & Liangqiong He

  5. Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, People’s Republic of China

    Mengdi Tian

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

    Manish K. Pandey

  7. State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia

    Rajeev K. Varshney

Authors
  1. Jiaowen Pan
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  2. Ximeng Zhou
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  4. Kun Zhang
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Contributions

CZ and XW conceived and designed the experiments. XZ, NA, KZ, RT, HZ, JJ and MT developed the populations. JP, CL, AL, XZ, LH, JM, XL, RT and CM performed the experiments. JP and CZ wrote the manuscript. XW, MKP and RKV revised the manuscript.

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Correspondence to Xingjun Wang or Chuanzhi Zhao.

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Communicated by Elena Bitocchi.

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Supplementary Information

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122_2022_4231_MOESM1_ESM.jpg

Fig. S1 Selecting polymorphic InDel markers between Fuhuasheng and Tifrunner. The InDel markers with polymorphism were circled out with a red ellipse. M: DNA Marker)

Fig. S2 QTL Mapping for branching habit on the genetic linkage map.

Supplementary File S1: The chromatograms of sequencing results for each InDel amplified DNA fragment. (RAR 1003 KB)

122_2022_4231_MOESM4_ESM.xlsx

Supplementary Table S1: List of SNP and InDel Sites in candidate interval in the mapping genomic region for branching habit on Chr.15. (XLSX 28 KB)

Supplementary Table S2: List of InDel primers used for mapping in this study. (XLSX 13 KB)

Supplementary Table S3: List of KASP primers used for mapping in this study. (XLSX 27 KB)

122_2022_4231_MOESM7_ESM.xlsx

Supplementary Table S4: SNPs in putative candidate genes in the mapping genomic region for branching habit on Chr.15. (XLSX 17 KB)

Supplementary Table S5: Oligonucleotide primers used in qRT-PCR (XLSX 181 KB)

Supplementary Table S6: Genetic models analysis using SEA software. (DOCX 16 KB)

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Pan, J., Zhou, X., Ahmad, N. et al. BSA‑seq and genetic mapping identified candidate genes for branching habit in peanut. Theor Appl Genet 135, 4457–4468 (2022). https://doi.org/10.1007/s00122-022-04231-8

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