J Integr Plant Biol. ›› 2014, Vol. 56 ›› Issue (10): 1009-1019.DOI: 10.1111/jipb.12208

• Molecular Ecology and Evolution • Previous Articles     Next Articles

Exploration of presence/absence variation and corresponding polymorphic markers in soybean genome

Yufeng Wang1†, Jiangjie Lu1†, Shouyi Chen2, Liping Shu3, Reid G. Palmer4, Guangnan Xing1, Yan Li1, Shouping Yang1, Deyue Yu1, Tuanjie Zhao1* and Junyi Gai1*   

  1. 1Soybean Research Institute/ National Center for Soybean Improvement/ MOA Key Laboratory for Biology and Genetic Improvement of Soybean (General)/ National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
    2State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
    3BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China
    4Department of Agronomy, Iowa State University, Ames, Iowa, USA
  • Received:2014-01-22 Accepted:2014-04-17 Published:2014-04-22
  • About author:These authors contributed equally to this work.
    **Correspondence: E-mail: sri@njau.edu.cn; tjzhao@njau.edu.cn


This study was designed to reveal the genome-wide distribution of presence/absence variation (PAV) and to establish a database of polymorphic PAV markers in soybean. The 33 soybean whole-genome sequences were compared to each other with that of Williams 82 as a reference genome. A total of 33,127 PAVs were detected and 28,912 PAV markers with their primer sequences were designed as the database NJAUSoyPAV_1.0. The PAVs scattered on whole genome while only 518 (1.8%) overlapped with simple sequence repeats (SSRs) in BARCSOYSSR_1.0 database. In a random sample of 800 PAVs, 713 (89.13%) showed polymorphism among the 12 differential genotypes. Using 126 PAVs and 108 SSRs to test a Chinese soybean germplasm collection composed of 828 Glycine soja Sieb. et Zucc. and Glycine max (L.) Merr. accessions, the per locus allele number and its variation appeared less in PAVs than in SSRs. The distinctness among alleles/bands of PCR (polymerase chain reaction) products showed better in PAVs than in SSRs, potential in accurate marker-assisted allele selection. The association mapping results showed SSR + PAV was more powerful than any single marker systems. The NJAUSoyPAV_1.0 database has enriched the source of PCR markers, and may fit the materials with a range of per locus allele numbers, if jointly used with SSR markers.


Wang Y, Lu J, Chen S, Shu L, Palmer RG, Xing G, Li Y, Yang S, Yu D, Zhao T, Gai J (2014) Exploration of presence/absence variation and corresponding polymorphic markers in soybean genome. J Integr Plant Biol 56: 1009–1019. doi: 10.1111/jipb.12208

Key words: Polymorphism, presence/absence variation, simple sequence repeat, soybean, whole-genome sequence

Editorial Office, Journal of Integrative Plant Biology, Institute of Botany, CAS
No. 20 Nanxincun, Xiangshan, Beijing 100093, China
Tel: +86 10 6283 6133 Fax: +86 10 8259 2636 E-mail: jipb@ibcas.ac.cn
Copyright © 2022 by the Institute of Botany, the Chinese Academy of Sciences
Online ISSN: 1744-7909 Print ISSN: 1672-9072 CN: 11-5067/Q