Genome-wide patterns of large-size presence/absence variants in sorghum

doi:10.1111/jipb.12121

J Integr Plant Biol. ›› 2014, Vol. 56 ›› Issue (1): 24-37.DOI: 10.1111/jipb.12121

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Genome-wide patterns of large-size presence/absence variants in sorghum

Li-Min Zhang^1,2, Hong Luo¹, Zhi-Quan Liu¹, Yi Zhao³, Jing-Chu Luo³, Dong-Yun Hao^2,4* and Hai-Chun Jing^1*

¹The Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
²Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, China
³College of Life Sciences, Peking University, Beijing, China
⁴Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China

Received:2013-07-26 Accepted:2013-10-10 Published:2014-01-15
About author:^**Corresponding authors: Tel: +86 431 8706 3195; Fax: +86 431 8706 3080; E-mail: dyhao@cjaas.com Tel: +86 10 6283 6576; Fax: +86 10 625 90833; E-mail: hcjing@ibcas.ac.cn

Abstract

Abstract:

The presence/absence variants (PAVs) are a major source of genome structural variation and have profound effects on phenotypic and genomic variation in animals and humans. However, little is understood about PAVs in plant genomes. Our previous resequencing effort on three sorghum (Sorghum bicolour L.) genomes, each 12× coverage, uncovered 5 364 PAVs. Here, we report a detailed characterization of 51 large-size (>30 kb) PAVs. These PAVs spanned a total size of 2.92 Mb of the sorghum genome containing 202 known and predicted genes, including 38 genes annotated to encode cell death and stress response genes. The PAVs varied considerably for repeat sequences and mobile elements with DNA transposons as the major components. The frequency and distribution of these PAVs differed substantially across 96 sorghum inbred lines, and the low- and high frequency PAVs differed in their gene categories. This report shed new light on the occurrence and diversity of PAVs in sorghum genomes. Our research exemplifies a new perspective to explore genome structural variation for genetic improvement in plant breeding.

Zhang LM, Luo H, Liu ZQ, Zhao Y, Luo JC, Hao DY, Jing HC (2014) Genome‐wide patterns of large‐size presence/absence variants in sorghum. J Integr Plant Biol 56: 24–37. doi: 10.1111/jipb.12121

Key words: Breeding, genetic diversity, genomics, presence/absence variants, Sorghum bicolour

Li-Min Zhang, Hong Luo, Zhi-Quan Liu, Yi Zhao, Jing-Chu Luo, Dong-Yun Hao, and Hai-Chun Jing. Genome-wide patterns of large-size presence/absence variants in sorghum[J]. J Integr Plant Biol., 2014, 56(1): 24-37.

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Genome-wide patterns of large-size presence/absence variants in sorghum

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