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Genome-wide association study of inflorescence length of cultivated soybean based on the high-throughout single-nucleotide markers

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Abstract

As an important and complex trait, inflorescence length (IL) of soybean [Glycine max (L.) Merr.] significantly affected seed yields. Therefore, elucidating molecular basis of inflorescence architecture, especially for IL, was important for improving soybean yield potentials. Longer IL meaned to have more pod and seed in soybean. Hence, increasing IL and improving yield are targets for soybean breeding. In this study, a association panel, comprising 283 diverse samples, was used to dissect the genetic basis of IL based on genome-wide association analysis (GWAS) and haplotype analysis. GWAS and haplotype analysis were conducted through high-throughout single-nucleotide polymorphisms (SNP) developed by SLAF-seq methodology. A total of 39, 057 SNPs (minor allele frequency ≥ 0.2 and missing data ≤ 10%) were utilized to evaluate linkage disequilibrium (LD) level in the tested association panel. A total of 30 association signals were identified to be associated with IL via GWAS. Among them, 13 SNPs were novel, and another 17 SNPs were overlapped or located near the linked regions of known quantitative trait nucleotide (QTN) with soybean seed yield or yield component. The functional genes, located in the 200-kb genomic region of each peak SNP, were considered as candidate genes, such as the cell division/ elongation, specific enzymes, and signaling or transport of specific proteins. These genes have been reported to participant in the regulation of IL. Ten typical long-IL lines and ten typical short-IL lines were re-sequencing, and then, six SNPs from five genes were obtained based on candidate gene-based association. In addition, 42 haplotypes were defined based on haplotype analysis. Of them, 11 haplotypes were found to regulate long IL (> 14 mm) in soybean. The identified 30 QTN with beneficial alleles and their candidate genes might be valuable for dissecting the molecular mechanisms of IL and further improving the yield potential of soybean.

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Funding

This study was financially supported by National Key R & D Project for Crop Breeding (2016YFD0100304), the Chinese National Natural Science Foundation (31671717 and 31471517), the National Supporting Project (2014BAD22B01), the Youth Leading Talent Project of the Ministry of Science and Technology in China (2015RA228), The National Ten-thousand Talents Program, Heilongjiang Provincial Project (GX17B002, JC2018007, and C2018016), Postdoctoral Fund in Heilongjiang Province (LBH-Z15017 and LBH-Q17015), The ‘Youth Innovation Talent’ Project of the general undergraduate universities in Heilongjiang province (UNPYSCT-2016145), and the ‘Academic Backbone’ Project of Northeast Agricultural University (17XG22).

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  1. Jinyang Wang and Xue Zhao authors have contributed equally to this paper.

Authors and Affiliations

  1. Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China

    Jinyang Wang, Xue Zhao, Wei Wang, Yingfan Qu, Weili Teng, Yingpeng Han & Wenbin Li

  2. Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Lijuan Qiu

  3. Bioinformatics Division, Biomarker Technologies Corporation, Beijing, 101300, China

    Hongkun Zheng

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  1. Jinyang Wang
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  3. Wei Wang
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Correspondence to Yingpeng Han or Wenbin Li.

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Wang, J., Zhao, X., Wang, W. et al. Genome-wide association study of inflorescence length of cultivated soybean based on the high-throughout single-nucleotide markers. Mol Genet Genomics 294, 607–620 (2019). https://doi.org/10.1007/s00438-019-01533-3

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