Yu Xinzi, Wang Lu, Xu Kuipeng, Kong Fanna, Wang Dongmei, Tang Xianghai, Sun Bin, Mao Yunxiang
Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, China.
College of Marine Life Sciences, Ocean University of China, Qingdao, China.
Front Plant Sci. 2020 Jun 23;11:867. doi: 10.3389/fpls.2020.00867. eCollection 2020.
, commonly known as "Nori" or "Laver" is an economically important marine crop. In natural or selected populations of , coloration mutants are frequently observed. Various coloration mutants are excellent materials for genetic research and study photosynthesis. However, the candidate gene controlling the coloration phenotype remains unclear to date. QTL-seq, in combination with kompetitive allele-specific PCR (KASP) and RNA-seq, can be generally applied to population genomics studies to rapidly identify genes that are responsible for phenotypes showing extremely opposite traits. Through cross experiments between the wild line RZ and red-mutant HT, offsprings with 1-4 sectors chimeric blade were generated. Statistical analyses revealed that the red thallus coloration phenotype is conferred by a single nuclear allele. Two-pair populations, consisting of 24 and 56 wild-type/red-type single-genotype sectors from F1 progeny, were used in QTL-seq to detect a genomic region in harboring the red coloration locus. Based on a high-quality genome, we first identified the candidate region within a 3.30-Mb region at the end of chromosome 1. Linkage map-based QTL analysis was used to confirm the candidate region identified by QTL-seq. Then, four KASP markers developed in this region were used to narrow down the candidate region to a 1.42-Mb region. Finally, we conducted RNA-seq to focus on 13 differentially expressed genes and further predicted , which contains one non-synonymous SNP [A/C] in the coding region that could be regulating red thallus coloration in . Our results provide novel insights into the underlying mechanism controlling blade coloration, which is a desirable trait in algae.
通常被称为“紫菜”或“海苔”，是一种具有重要经济价值的海洋作物。在自然或选定的群体中，经常观察到颜色突变体。各种颜色突变体是遗传研究和光合作用研究的优良材料。然而，迄今为止，控制该颜色表型的候选基因仍不清楚。QTL-seq结合竞争性等位基因特异性PCR（KASP）和RNA-seq，通常可应用于群体基因组学研究，以快速鉴定负责表现出极端相反性状的表型的基因。通过野生品系RZ和红色突变体HT之间的杂交实验，产生了具有1-4个扇形嵌合叶片的后代。统计分析表明，红色叶状体颜色表型由单个核等位基因赋予。由F1后代的24个和56个野生型/红色型单基因型扇形组成的两对群体用于QTL-seq，以检测紫菜中含有红色位点的基因组区域。基于高质量基因组，我们首先在1号染色体末端的3.30-Mb区域内确定了候选区域。基于连锁图谱的QTL分析用于确认QTL-seq鉴定的候选区域。然后，在该区域开发的四个KASP标记用于将候选区域缩小到1.42-Mb区域。最后，我们进行了RNA-seq，重点关注13个差异表达基因，并进一步预测，其在编码区包含一个非同义SNP [A/C]，可能调节紫菜中的红色叶状体颜色。我们的结果为控制叶片颜色的潜在机制提供了新的见解，这是藻类中一个理想的性状。
