Jia Qiaojun, Tan Cong, Wang Junmei, Zhang Xiao-Qi, Zhu Jinghuan, Luo Hao, Yang Jianming, Westcott Sharon, Broughton Sue, Moody David, Li Chengdao
College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Hangzhou, 310018, China.
BMC Genomics. 2016 Nov 11;17(1):911. doi: 10.1186/s12864-016-3247-4.
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.
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.
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.
大麦半矮秆基因已得到广泛研究，并在大麦育种计划中广泛应用。来自金色承诺（Golden Promise）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。虽然已使用传统标记和新一代测序技术将ari - e定位在大麦5H染色体上，但尚未在该染色体上进行精细定位。
我们整合了两种方法来开发用于精细定位半矮秆基因ari - e的分子标记：（1）采用混合分组分析法（BSA）的特定长度扩增片段测序（SLAF - seq）来开发SNP标记，以及（2）全基因组鸟枪法测序来开发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，ari - e与标记InDel - 17共分离，并在双单倍体（DH）群体Dash × VB9104中被两个标记（InDel - 16和DGSNP21）界定，跨度为6.8厘摩（cM）。在Hindmarsh × W1 DH群体中进一步证实了ari - e的遗传位置，其位于InDel - 7和InDel - 17之间。因此，在POPSEQ物理图谱上，两个定位群体中由InDel - 16和InDel - 17侧翼的重叠区域被定义为候选区域，跨度为0.58兆碱基（Mb）。
本研究证明了用于发现SNP的SLAF - seq和用于开发InDel的全基因组鸟枪法测序是绘制复杂基因组区域以分离功能基因的有效方法。ari - e基因被精细定位在10兆碱基至0.58兆碱基的区间内。
