Highly multiplexed AmpliSeq technology identifies novel variation of flowering time-related genes in soybean (Glycine max)
Highly multiplexed AmpliSeq technology identifies novel variation of flowering time-related genes in soybean (Glycine max)
复制标题
DOI：
10.1093/dnares/dsz005
复制
发表时间：
2019-06-01
期刊：
影响因子：
4.1
通讯作者：
Ishimoto, Masao
中科院分区：
文献类型：
--
作者：
Ogiso-Tanaka, Eri;Shimizu, Takehiko;Ishimoto, Masao
全基因组重测序是检测基因变异的一种有效方法，但仅分析靶基因的成本很高。为了解决这一问题，我们尝试利用AmpliSeq技术通过目标重测序检测大豆微核心种质中开花时间相关基因及其同源物的新变异。靶向29个基因的382个扩增子的平均深度为1，237，其中99.85%的序列数据映射到参考基因组。共检测到461个变异，其中150个位点是新的，没有在dbSNP中注册。在经典成熟位点E1、E2、E3和E4中检测到已知和新的变异。此外，成功鉴定了大indel等位基因E1-nl和E3-tr。在FT 2a、MADS盒、WDR 61、光敏色素和双组分反应调节剂中发现了新的功能丧失和错义变体。多元回归分析表明，E2、E3、Dt 1和双组分响应调节因子4个基因可以解释微型核心种质开花时间变异的51.1-52.3%。其中，具有提前终止密码子的双组分反应调节子是一个新基因，尚未被报道为大豆开花时间相关基因。这些数据表明AmpliSeq技术是鉴定新等位基因的有力工具。
Whole-genome re-sequencing is a powerful approach to detect gene variants, but it is expensive to analyse only the target genes. To circumvent this problem, we attempted to detect novel variants of flowering time-related genes and their homologues in soybean mini-core collection by target re-sequencing using AmpliSeq technology. The average depth of 382 amplicons targeting 29 genes was 1,237 with 99.85% of the sequence data mapped to the reference genome. Totally, 461 variants were detected, of which 150 sites were novel and not registered in dbSNP. Known and novel variants were detected in the classical maturity loci-E1, E2, E3, and E4. Additionally, large indel alleles, E1-nl and E3-tr, were successfully identified. Novel loss-of-function and missense variants were found in FT2a, MADS-box, WDR61, phytochromes, and two-component response regulators. The multiple regression analysis showed that four genes-E2, E3, Dt1, and two-component response regulator-can explain 51.1-52.3% of the variation in flowering time of the mini-core collection. Among them, the two-component response regulator with a premature stop codon is a novel gene that has not been reported as a soybean flowering time-related gene. These data suggest that the AmpliSeq technology is a powerful tool to identify novel alleles.