Development and application of novel InDel markers in flax (Linum usitatissimum L.) through whole-genome re-sequencing
Development and application of novel InDel markers in flax (Linum usitatissimum L.) through whole-genome re-sequencing
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通过全基因组重测序在亚麻 (Linum usitatissimum L.) 中开发和应用新型 InDel 标记
DOI：
10.1007/s10722-021-01313-2
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发表时间：
2022-01-18
影响因子：
2
通讯作者：
Chen，Anguo
中科院分区：
文献类型：
--
作者：
Jiang，Hui;Pan，Gen;Chen，Anguo
亚麻是北方欧洲、加拿大、印度和中国种植的重要油料和纤维作物。分子标记技术的发展，加快了亚麻分子育种的进程，提高了亚麻的产量和品质。目前，亚麻全基因组的SSR和SNP标记已发展成熟。然而，亚麻插入/缺失（InDel）标记的发展还没有报道。通过对两份材料（87-3和84-3）的全基因组重测序数据与参考基因组的比较，共鉴定出17,110个InDel标记。InDels的长度范围为1 ~ 277 bp，其中1-15 bp的比例最高（95.55%）。在亚麻染色体中，最常见的InDels为单核苷酸（8840）、二核苷酸（3700）和三核苷酸（1349），其中Ch 2（1505）的InDels数量最多，而Ch 10（913）的数量最少。从17,110个InDel标记中筛选出90个在亚麻基因组中分布均匀的引物。在2份亚麻材料中共检测到32对多态性引物，多态性率为40.70%。利用32对多态性引物对69份亚麻材料进行遗传多样性分析、群体结构分析和主成分分析，将其分为油料亚麻和纤维亚麻两大类。相关分析表明，InDel-26和InDel-81与亚麻含油量性状相关，与InDel-26和InDel-81紧密连锁的两个候选基因lus 10031535和lus 10025284可能与亚麻油脂合成和代谢有关。这项研究是第一个基于亚麻重新测序开发InDel标记的研究，并将这些材料聚集成油和纤维两个完全分离的组。结果表明，所开发的InDel标记可用于亚麻种质鉴定、遗传多样性分析和分子标记辅助育种。
Flax is an important oil and fibre crop grown in Northern Europe, Canada, India, and China. The development of molecular markers has accelerated the process of flax molecular breeding and has improved yield and quality. Presently, simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in the whole genome have been developed for flax. However, the development of flax insertion/deletion (InDel) markers have not been reported. A total of 17,110 InDel markers were identified by comparing whole-genome re-sequencing data of two accessions (87-3 and 84-3) with the flax reference genome. The length of InDels ranged from 1 to 277 bp, with 1–15 bp accounting for the highest rate (95.55%). The most common InDels were in the form of a single nucleotide (8840), dinucleotide (3700), and trinucleotide (1349), and Ch2 (1505) showed the highest number of InDels among flax chromosomes, while Ch10 (913) presented with the lowest number. From 17,110 InDel markers, 90 primers that were evenly distributed in the flax genome were selected. Thirty-two pairs of polymorphic primers were detected in two flax accessions, and the polymorphism rate was 40.70%. Furthermore, genetic diversity analysis, population structure and principal component analysis (PCA) divided 69 flax accessions into two categories, namely oilseed flax and fibre flax using thirty-two pairs of polymorphic primers. Additionally, correlation analysis showed that InDel-26 and InDel-81 were associated with oil content traits, and two candidate genes (lus10031535andlus10025284) tightly linked to InDel-26 and InDel-81, might be involved in flax lipid biosynthesis and lipid metabolism. This study is the first to develop InDel markers based on re-sequencing in flax and clustered the accessions into two well-separated groups for oil and fibre. The results demonstrated that InDel markers developed herein could be used for flax germplasm identification, genetic diversity analysis, and molecular marker-assisted breeding.