Marker development using SLAF-seq and whole-genome shotgun strategy to fine-map the semi-dwarf gene ari-e in barley.
Marker development using SLAF-seq and whole-genome shotgun strategy to fine-map the semi-dwarf gene ari-e in barley.
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使用 SLAF-seq 和全基因组鸟枪策略进行标记开发，以精细绘制大麦中的半矮化基因 ari-e
DOI：
10.1186/s12864-016-3247-4
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发表时间：
2016-11-11
期刊：
影响因子：
4.4
通讯作者：
Li C
中科院分区：
文献类型：
--
作者：
Jia Q;Tan C;Wang J;Zhang XQ;Zhu J;Luo H;Yang J;Westcott S;Broughton S;Moody D;Li C
大麦半矮秆基因已被广泛探究，并在大麦育种项目中得到广泛应用。来自“金承诺”品种的半矮秆基因ari - e是一个与一些农艺性状和耐盐性相关的重要基因。虽然利用传统标记和新一代测序技术已将ari - e定位在大麦5H染色体上，但它在该染色体上尚未被精细定位。
我们综合两种方法开发用于精细定位半矮秆基因ari - e的分子标记：（1）结合混合分组分析法（BSA）的特异长度扩增片段测序（SLAF - seq）来开发单核苷酸多态性（SNP）标记，以及（2）全基因组鸟枪法测序来开发插入缺失（InDel）标记。在目标区域开发了SNP和InDel标记，并用于ari - e基因的精细定位。连锁分析表明，在双单倍体（DH）Dash×VB9104群体中，ari - e与标记InDel - 17共分离，并由两个标记（InDel - 16和DGSNP21）界定，跨度为6.8厘摩（cM）。ari - e的遗传位置在Hindmarsh×W1 DH群体中得到进一步确认，它位于InDel - 7和InDel - 17之间。结果，由InDel - 16和InDel - 17界定的两个定位群体的重叠区域在POPSEQ物理图谱上被确定为跨度为0.58兆碱基（Mb）的候选区域。
当前研究证明了用于SNP发现的SLAF - seq和用于InDel开发的全基因组鸟枪法测序是一种绘制复杂基因组区域以分离功能基因的有效方法。ari - e基因从10 Mb区间被精细定位到0.58 Mb区间。
本文的网络版（doi:10.1186/s12864 - 016 - 3247 - 4）包含补充材料，授权用户可获取。
Background:Barley semi-dwarf genes have been extensively explored and widely used in barley breeding programs. The semi-dwarf gene ari-e from Golden Promise is an important gene associated with some agronomic traits and salt tolerance. While ari-e has been mapped on barley chromosome 5H using traditional markers and next-generation sequencing technologies, it has not yet been finely located on this chromosome.Results:We integrated two methods to develop molecular markers for fine-mapping the semi-dwarf gene ari-e: (1) specific-length amplified fragment sequencing (SLAF-seq) with bulked segregant analysis (BSA) to develop SNP markers, and (2) the whole-genome shotgun sequence to develop InDels. Both SNP and InDel markers were developed in the target region and used for fine-mapping the ari-e gene. Linkage analysis showed that ari-e co-segregated with marker InDel-17 and was delimited by two markers (InDel-16 and DGSNP21) spanning 6.8 cM in the doubled haploid (DH) Dash × VB9104 population. The genetic position of ari-e was further confirmed in the Hindmarsh × W1 DH population which was located between InDel-7 and InDel-17. As a result, the overlapping region of the two mapping populations flanked by InDel-16 and InDel-17 was defined as the candidate region spanning 0.58 Mb on the POPSEQ physical map.Conclusions:The current study demonstrated the SLAF-seq for SNP discovery and whole-genome shotgun sequencing for InDel development as an efficient approach to map complex genomic region for isolation of functional gene. The ari-e gene was fine mapped from 10 Mb to 0.58 Mb interval.
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影响因子：
5.4
作者：
Chen, Wei;Yao, Jinbo;Zhang, Yongshan
通讯作者：
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