PAV markers in Sorghum bicolour: genome pattern, affected genes and pathways, and genetic linkage map construction

doi:10.1007/s00122-015-2458-4

	PAV markers in Sorghum bicolour: genome pattern, affected genes and pathways, and genetic linkage map construction
	Shen, Xin 1; Liu, Zhi-Quan ; Mocoeur, Anne 2; Xia, Yan ; Jing, Hai-Chun
	2015
发表期刊	THEORETICAL AND APPLIED GENETICS
ISSN	0040-5752
卷号	128 期号:4 页码:623-637
摘要	5,511 genic small-size PAVs in sorghum were identified and examined, including the pattern and the function enrichment of PAV genes. 325 PAV markers were developed to construct a genetic map. Presence/absence variants (PAVs) correlate closely to the phenotypic variation, by impacting plant genome sizes and the adaption to the environment. To shed more light on their genome-wide patterns, functions and the possibility of using them as molecular markers, we generated next generation genome sequencing data for four sorghum inbred lines and used associated bioinformatic pipelines to identify small-size PAVs (40-10 kb). Five thousand five hundreds and eleven genic PAVs (40-10 kb) were identified and found to affect 3,238 genes. These PAVs were mainly distributed on the sub-telomeric regions, but the highest proportions occurred in the vicinity of the centromeric regions. One of the prominent features of the PAVs is the high occurrence of long terminal repeats retrotransposons and DNA transposons. PAVs caused various alterations to gene structure, primarily including the coding sequence variants, intron variants, transcript ablation, and initiator codon changes. The genes affected by PAVs were significantly enriched in those involved in stress responses and protein modification. We used 325 PAVs polymorphic between two sorghum inbred lines Ji2731 and E-Tian, together with 49 SSR markers, and constructed a genetic map, which consisted of 10 linkage groups corresponding to the 10 chromosomes of sorghum and spanned 1,430.3 cM in length covering 97 % of the physical genome. The resources reported here should be useful for genetic study and breeding of sorghum and related species.
学科领域	Agronomy ; Plant Sciences ; Genetics & Heredity ; Horticulture
DOI	10.1007/s00122-015-2458-4
收录类别	SCI
语种	英语
WOS关键词	COPY NUMBER VARIATION ; STRUCTURAL VARIATION ; L. MOENCH ; PRESENCE/ABSENCE POLYMORPHISM ; RECOMBINATION MAP ; SHORT-READ ; SEQUENCE ; REVEALS ; SSR ; DNA
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000351437100006
出版者	SPRINGER
文献子类	Article
出版地	NEW YORK
EISSN	1432-2242
资助机构	CNSF [31271797] ; MOST [2013BAD22B01]
作者邮箱	hcjing@ibcas.ac.cn
作品OA属性	hybrid, Green Published
引用统计	被引频次：13[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/2S10CLM1/25860
专题	中科院北方资源植物重点实验室
作者单位	1.Chinese Acad Sci, Inst Bot, Key Lab Plant Resources, Beijing 100093, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 3.Univ Copenhagen, Dept Plant & Environm, Fac Sci, DK-1871 Frederiksberg, Denmark
推荐引用方式 GB/T 7714	Shen, Xin,Liu, Zhi-Quan,Mocoeur, Anne,et al. PAV markers in Sorghum bicolour: genome pattern, affected genes and pathways, and genetic linkage map construction[J]. THEORETICAL AND APPLIED GENETICS,2015,128(4):623-637.
APA	Shen, Xin,Liu, Zhi-Quan,Mocoeur, Anne,Xia, Yan,&Jing, Hai-Chun.(2015).PAV markers in Sorghum bicolour: genome pattern, affected genes and pathways, and genetic linkage map construction.THEORETICAL AND APPLIED GENETICS,128(4),623-637.
MLA	Shen, Xin,et al."PAV markers in Sorghum bicolour: genome pattern, affected genes and pathways, and genetic linkage map construction".THEORETICAL AND APPLIED GENETICS 128.4(2015):623-637.

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