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Identification of QTL and genes for pod number in soybean by linkage analysis and genome-wide association studies

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Abstract

Pod number is an important component of yield in soybean (Glycine max (L.) Merr.), and pods are unevenly distributed in the upper, middle and lower parts of the plant. Here, linkage analysis combined with genome-wide association study (GWAS) was used to identify 20 pod number-related traits in four-way recombinant inbred lines (FW-RILs) derived from crosses between the four soybean varieties (Kenfeng 14 × Kenfeng 15) × (Heinong 48 × Kenfeng 19). The results show that pod number-related traits are highly influenced by genetic factors, while the environment plays only a minor role. A total of 602 QTLs were identified, of which 52 were detected in multiple environments (over two environments). In addition, GWAS detected 26 common QTNs (identified by multiple methods or environments) in the QTL intervals. Based on gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, 11 potential candidate genes were identified that likely involved the growth and development of soybean pods. These findings will help elucidate the genetic basis of pod number traits.

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Funding

The authors gratefully acknowledge the financial support for this study provided by grants from the National Key Research and Development Program of China (2017YFD0101303-6) to W-X.L.

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Author notes

  1. Jie Song and Xu Sun contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Soybean Biology, Ministry of Education / Key Laboratory of Soybean Biology and Breeding / Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, China

    Jie Song, Xu Sun, Kaixin Zhang, Jiajing Wang, Chang Yang, Sitong Jiang, Mahfishan Siyal, Xiyu Li, Zhongying Qi, Yue Wang, Xiaocui Tian, Yanlong Fang, Wen-Xia Li & Hailong Ning

  2. State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China

    Shulin Liu & Zhixi Tian

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  1. Jie Song
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  3. Kaixin Zhang
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  4. Shulin Liu
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Contributions

W-XL and HN conceived and designed the experiments. XS, JW, CY, SJ, MS, XL ZQ, YW, XT, and YF performed the field experiments. SL and ZT performed the genome sequencing. JS, KZ, and HN analyzed and interpreted the results. JS and HN drafted the manuscript and all the authors contributed to the manuscript revision.

Corresponding authors

Correspondence to Wen-Xia Li or Hailong Ning.

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Table S1

Summary of planting conditions of 5 environments (XLSX 9 kb)

Table S2

Phenotypic data of pod number traits in 6 extreme lines (XLSX 8 kb)

Table S3

Primer sequences used in this study (XLSX 9 kb)

Table S4

Statistical analysis of pod number-related traits for FW-RILs grown in different environments (XLSX 18 kb)

Table S5

Joint ANOVA of pod numbers related traits of FW-RILs in multiple environments and heritability (XLSX 16 kb)

Table S6

Identification of QTL for soybean pod number at Multi-environment (XLSX 16 kb)

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Song, J., Sun, X., Zhang, K. et al. Identification of QTL and genes for pod number in soybean by linkage analysis and genome-wide association studies. Mol Breeding 40, 60 (2020). https://doi.org/10.1007/s11032-020-01140-w

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