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

文献类型： 外文期刊

作者： Zhang, Li-Min 1 ; Luo, Hong 1 ; Liu, Zhi-Quan 1 ; Zhao, Yi 3 ; Luo, Jing-Chu 3 ; Hao, Dong-Yun 2 ; Jing, Hai-Chun 1 ;

作者机构： 1.Chinese Acad Sci, Inst Bot, Key Lab Plant Resources, Beijing 100093, Peoples R China

2.Jilin Univ, Minist Educ, Key Lab Mol Enzymol & Engn, Changchun 130012, Peoples R China

3.Peking Univ, Coll Life Sci, Beijing 100871, Peoples R China

4.Jilin Acad Agr Sci, Inst Agr Biotechnol, Changchun 130124, Peoples R China

关键词： Breeding;genetic diversity;genomics;presence;absence variants;Sorghum bicolour

期刊名称：JOURNAL OF INTEGRATIVE PLANT BIOLOGY （ 影响因子：7.061； 五年影响因子：6.002 ）

ISSN： 1672-9072

年卷期： 2014 年 56 卷 1 期

页码：

收录情况： SCI

摘要： 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 12x coverage, uncovered 5 364 PAVs. Here, we report a detailed characterization of 51 large-size (>30kb) 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.

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