Wu Bo, Zhong Yun, Wu Qianqian, Chen Fangyong, Zhong Guangyan, Cui Yiping
Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, & Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences (IFTR-GDAAS), Guangzhou, China.
Citrus Research Institute of Zhejiang, Huangyan, China.
Front Plant Sci. 2020 Sep 9;11:563452. doi: 10.3389/fpls.2020.563452. eCollection 2020.
High throughput sequencing was used to reveal the distribution of whole-genome variations in cultivated (Sieb. et Zucc.). A total of 3,151,123 SNPs, 371,757 small indels, and 15,904 SVs were detected in 52 accessions. Verification by Sanger sequencing demonstrated that the positive rate of the SNPs was approximately 97.3%. Search for more genetic variations was expanded to 141 red bayberry accessions, most of which were cultivars, by sequencing 19 selected genomic segments (SEG1-19). The results showed that each segment harbored, on average, 7.8 alleles (haplotypes), a haplotype diversity of 0.42, and a polymorphic information content (PIC) of 0.40. Seventy-two different genotypes were identified from the 141 accessions, and statistical analysis showed that the accessions with duplicated genotypes were either somatic mutants or simply synonyms. Core set selection results showed that a minimum of 34 genotypes could already have covered all the alleles on the segments. A DNA fingerprinting system was developed for red bayberry, which used the diversity information of only 8 DNA segments yet still achieved a very high efficiency without losing robustness. No large clade was robustly supported by hierarchical clustering, and well-supported small clusters mainly included close relatives. These results should lead to an improved understanding of the genetic diversity of red bayberry and be valuable for future molecular breeding and variety protection.
利用高通量测序揭示栽培杨梅（Myrica rubra (Sieb. et Zucc.)）全基因组变异的分布情况。在52份材料中总共检测到3,151,123个单核苷酸多态性（SNP）、371,757个小插入缺失以及15,904个结构变异（SV）。通过桑格测序验证表明，SNP的阳性率约为97.3%。通过对19个选定的基因组片段（SEG1 - 19）进行测序，将更多遗传变异的搜索扩展到141份杨梅材料，其中大部分是栽培品种。结果表明，每个片段平均含有7.8个等位基因（单倍型），单倍型多样性为0.42，多态信息含量（PIC）为0.40。从141份材料中鉴定出72种不同的基因型，统计分析表明，具有重复基因型的材料要么是体细胞突变体，要么只是同义词。核心种质选择结果表明，最少34种基因型就已经能够覆盖这些片段上的所有等位基因。开发了一种用于杨梅的DNA指纹识别系统，该系统仅使用8个DNA片段的多样性信息，却在不损失稳健性的情况下仍实现了非常高的效率。层次聚类没有强有力地支持任何大的分支，得到良好支持的小簇主要包括亲缘关系较近的材料。这些结果将有助于加深对杨梅遗传多样性的理解，并对未来的分子育种和品种保护具有重要价值。
