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

doi:10.1111/jipb.12208

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 Wang^1†, Jiangjie Lu^1†, Shouyi Chen², Liping Shu³, Reid G. Palmer⁴, Guangnan Xing¹, Yan Li¹, Shouping Yang¹, Deyue Yu¹, Tuanjie Zhao^1* and Junyi Gai^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

Abstract

Abstract:

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

Yufeng Wang, Jiangjie Lu, Shouyi Chen, Liping Shu, Reid G. Palmer, Guangnan Xing, Yan Li, Shouping Yang, Deyue Yu, Tuanjie Zhao, and Junyi Gai. Exploration of presence/absence variation and corresponding polymorphic markers in soybean genome[J]. J Integr Plant Biol., 2014, 56(10): 1009-1019.

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

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