PAV markers in Sorghum bicolour: genome pattern, affected genes and pathways, and genetic linkage map construction.
PAV markers in Sorghum bicolour: genome pattern, affected genes and pathways, and genetic linkage map construction.
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双色高粱中的 PAV 标记：基因组模式、受影响的基因和途径以及遗传连锁图构建
DOI：
10.1007/s00122-015-2458-4
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发表时间：
2015-04
影响因子：
5.4
通讯作者：
Jing, Hai-Chun
中科院分区：
文献类型：
--
作者：
Shen, Xin;Liu, Zhi-Quan;Mocoeur, Anne;Xia, Yan;Jing, Hai-Chun
对5,511个高粱小基因型PAV进行了鉴定和分析，包括PAV基因的模式和功能富集。共开发了325个PAV分子标记，构建了PAV遗传图谱。存在/不存在变异体（PAV）通过影响植物基因组大小和对环境的适应与表型变异密切相关。为了更多地了解它们的全基因组模式、功能以及将它们用作分子标记的可能性，我们生成了四个高粱近交系的下一代基因组测序数据，并使用相关的生物信息学管道来识别小尺寸PAV（40-10 kb）。鉴定了5511个基因PAV（40-10 kb），发现其影响3，238个基因。这些PAV主要分布在亚端粒区域，但比例最高的是着丝粒区域附近。PAV的显著特征之一是长末端重复反转录转座子和DNA转座子的高发生率。PAV引起基因结构的各种改变，主要包括编码序列变异、内含子变异、转录物消融和起始密码子改变。受PAV影响的基因显著富集在那些参与应激反应和蛋白质修饰的基因中。利用高粱自交系冀2731和鄂甜的325个PAVs和49个SSR标记，构建了一张由10个连锁群组成的遗传图谱，图谱长度为1430.3cM，覆盖了高粱基因组的97%。这些资源可为高粱及其近缘种的遗传研究和育种提供参考。
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.
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影响因子：
64.8
作者：
Gan X;Stegle O;Behr J;Steffen JG;Drewe P;Hildebrand KL;Lyngsoe R;Schultheiss SJ;Osborne EJ;Sreedharan VT;Kahles A;Bohnert R;Jean G;Derwent P;Kersey P;Belfield EJ;Harberd NP;Kemen E;Toomajian C;Kover PX;Clark RM;Rätsch G;Mott R
通讯作者：
Mott R
影响因子：
5.4
作者：
Boivin, K;Deu, M;Hamon, P
通讯作者：
Hamon, P
影响因子：
2.3
作者：
Dahlberg, JA;Zhang, X;Mullet, JE
通讯作者：
Mullet, JE
影响因子：
9.4
作者：
Arrach, Nabil;Porwollik, Steffen;McClelland, Michael
通讯作者：
McClelland, Michael
影响因子：
4.4
作者：
González VM;Aventín N;Centeno E;Puigdomènech P
通讯作者：
Puigdomènech P