菜头肾ddRAD测序与抗逆种质挖掘研究

Study on ddRAD Sequencing and Mining of Stress-Resistant Germplasm in Championella sarcorrhiza C. Ling

摘要: 本研究以菜头肾(Championella sarcorrhiza C. Ling)在中国最主要资源地浙江省台州、温州的收集整理为基础，分析它们的遗传结构和亲缘关系，从而明确主要类型，挖掘抗逆优质资源，为种质创新创造条件。研究将收集的13份菜头肾材料采用ddRAD简化基因组测序技术进行亲缘关系分析。该测序获得整理数据19.71 Gb，Q30质量均值为92.13%，GC均值为38.71%。总SNP 1,996,340个，其中高一致性的836,840个用于后续分析。组装得到序列平均深度19.2，平均杂合度0.1808、平均纯合度0.81392。群体平均期望纯合度为0.74287；平均杂合度为0.2571。群体的平均核酸多态性π值0.27257；群体的平均近交系数0.29036。各材料间的遗传距离在0.095~1.974，可分成4类。对此以树状图的形式予以表达。研究结合形态鉴别，基本明确收集材料有雌株、雌雄同株(两性花)、雄株三大类型，从中最多的是营养系雌株。在资源挖掘中，发现了稀缺的雄株与雌雄同株种质，表明亲本优株育成对于抗逆育种具有重要的潜在价值。

Abstract: This study was based on an investigation and collection of Championella sarcorrhiza C. Ling from Taizhou and Wenzhou in Zhejiang Province, the primary resource area of this species in China. The aim was to analyze the genetic structure and phylogenetic relationships of the collected materials, clarify the main types, and identify stress-resistant, high-quality resources to facilitate germplasm innovation. Phylogenetic analysis was performed on 13 collected accessions using ddRAD simplified genome sequencing. The sequencing produced 19.71 Gb of clean data, with an average Q30 score of 92.13% and an average GC content of 38.71%. A total of 1,996,340 SNPs were identified, of which 836,840 high-confidence SNPs were used for subsequent analysis. The assembled sequences had an average depth of 19.2, with an average heterozygosity of 0.1808 and an average homozygosity of 0.81392. The population’s average expected homozygosity was 0.74287, and the expected heterozygosity was 0.2571. The average nucleotide diversity (π) was 0.27257, and the average inbreeding coefficient was 0.29036. Genetic distances among accessions ranged from 0.095 to 1.974, divided into four categories, visualized using a phylogenetic tree. Combined with morphological identification, the collected materials were classified into three main types: female plants, hermaphroditic plants, and male plants, with vegetative female lines being the most common. The discovery of rare male and hermaphroditic germplasm indicates that breeding superior parental plants holds significant potential for stress-resistant breeding.