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

doi:10.1111/jipb.12121

	Genome-wide patterns of large-size presence/absence variants in sorghum
	Zhang, Li-Min ; Luo, Hong ; Liu, Zhi-Quan ; Zhao, Yi ; Luo, Jing-Chu ; Hao, Dong-Yun ; Jing, Hai-Chun
	2014
发表期刊	JOURNAL OF INTEGRATIVE PLANT BIOLOGY
ISSN	1672-9072
卷号	56 期号:1 页码:24-37
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.
关键词	Breeding genetic diversity genomics presence absence variants Sorghum bicolour
学科领域	Biochemistry & Molecular Biology ; Plant Sciences
DOI	10.1111/jipb.12121
收录类别	SCI
语种	英语
WOS关键词	COPY-NUMBER VARIATION ; SINGLE-FEATURE POLYMORPHISM ; LARGE-SCALE VARIATION ; STRUCTURAL VARIATION ; DELETION POLYMORPHISM ; GENETIC-VARIATION ; MAIZE ; ARABIDOPSIS ; REVEALS ; RESISTANCE
WOS研究方向	Biochemistry & Molecular Biology ; Plant Sciences
WOS记录号	WOS:000330853300005
出版者	WILEY
文献子类	Article
出版地	HOBOKEN
EISSN	1744-7909
资助机构	National Natural Science Foundation of China [31271797] ; National Science & Technology Support Program [2013BAD22B01] ; Knowledge Innovation Program (KIP) of the Chinese Academy of Sciences [KSCX2-YW-G-067]
作者邮箱	dyhao@cjaas.com ; hcjing@ibcas.ac.cn
引用统计	被引频次：20[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/27139
专题	中科院北方资源植物重点实验室
作者单位	1.[Zhang, Li-Min 2.Luo, Hong 3.Liu, Zhi-Quan 4.Chinese Acad Sci, Inst Bot, Key Lab Plant Resources, Beijing 100093, Peoples R China 5.Jilin Univ, Minist Educ, Key Lab Mol Enzymol & Engn, Changchun 130012, Peoples R China 6.[Zhao, Yi 7.Peking Univ, Coll Life Sci, Beijing 100871, Peoples R China 8.Jilin Acad Agr Sci, Inst Agr Biotechnol, Changchun 130124, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Li-Min,Luo, Hong,Liu, Zhi-Quan,et al. Genome-wide patterns of large-size presence/absence variants in sorghum[J]. JOURNAL OF INTEGRATIVE PLANT BIOLOGY,2014,56(1):24-37.
APA	Zhang, Li-Min.,Luo, Hong.,Liu, Zhi-Quan.,Zhao, Yi.,Luo, Jing-Chu.,...&Jing, Hai-Chun.(2014).Genome-wide patterns of large-size presence/absence variants in sorghum.JOURNAL OF INTEGRATIVE PLANT BIOLOGY,56(1),24-37.
MLA	Zhang, Li-Min,et al."Genome-wide patterns of large-size presence/absence variants in sorghum".JOURNAL OF INTEGRATIVE PLANT BIOLOGY 56.1(2014):24-37.

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