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Simultaneously mapping loci related to two plant architecture traits by phenotypic recombination BSA/BSR in peanut (Arachis hypogaea L.)

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Abstract

Key message

We developed a new method phenotypic recombination BSA/BSR (PR-BSA/BSR), which could simultaneously identify the candidate genomic regions associated with two traits in a segregating population.

Abstract

Bulked segregant analysis sequencing (BSA-seq) has been widely used for identifying the genomic regions affecting a certain trait. In this study, we developed a modified BSA/bulked segregant RNA-sequencing (BSR-seq) method, which we named phenotypic recombination BSA/BSR (PR-BSA/BSR), to simultaneously identify candidate genomic regions associated with two traits in a segregating population. Lateral branch angle (LBA) and flower-branch pattern (FBP) are two important traits associated with the peanut plant architecture because they affect the planting density and light use efficiency. We generated an F6 population (with two segregating traits) derived from a cross between the inbred lines Pingdu9616 (erect and sequential; ES-type) and Florunner (spreading and alternating; SA-type). The selection of bulks with extreme phenotypes was a key step in this study. Specifically, 30 individuals with recombinant phenotypes [i.e., spreading and sequential (SS-type) and erect and alternating (EA-type)] were selected to generate two bulks. The transcriptomes of individuals were sequenced and then the loci related to LBA and FBP were simultaneously detected via a ΔSNP-index strategy, which involved the direction of positive and negative peaks in the ∆SNP-index plot. The LBA-related locus was mapped to a 6.82 Mb region (101,743,223–108,564,267 bp) on chromosome 15, whereas the FBP-related locus was mapped to a 2.16 Mb region (117,682,534–119,846,824 bp) on chromosome 12. Furthermore, the marker-based classical QTL mapping method was used to analyze the PF–F6 population, which confirmed our PR-BSA/BSR results. Therefore, the PR-BSA/BSR method produces accurate and reliable data.

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Acknowledgements

This work was supported by grants from the National Science Foundation of China (No. 31771828), the Seed Project of Shandong Province (No. 2020LZGC001).

Funding

This work was supported by grants from the National Science Foundation of China (No. 31771828), the Seed Project of Shandong Province (No. 2020LZGC001).

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  1. Xiaona Yu and Yaoyao Li have contributed equally to this work.

Authors and Affiliations

  1. Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People’s Republic of China

    Xiaona Yu, Yaoyao Li, Xinyuan Cui, Xianheng Wang, Jihua Li, Rui Guo, Fanzhuang Yan, Shaojing Zhang, Ruihua Zhao, Danlei Song, Tong Si, Xiaoxia Zou, Yuefu Wang & Xiaojun Zhang

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  1. Xiaona Yu
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Contributions

XJZ designed the research. XNY and YYL performed most of the experiments; FZY, RHZ, RG, SJZ, DLS, TS, XXZ, YFW and MLW provided technical assistance and some analysis; RG and SJZ generated the population. XJZ and XNY wrote the manuscript.

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Correspondence to Xiaojun Zhang.

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Yu, X., Li, Y., Cui, X. et al. Simultaneously mapping loci related to two plant architecture traits by phenotypic recombination BSA/BSR in peanut (Arachis hypogaea L.). Theor Appl Genet 136, 144 (2023). https://doi.org/10.1007/s00122-023-04385-z

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