89份西瓜种质资源表型鉴定和遗传多样性分析

Phenotypic characterization and genetic diversity analysis of 89 watermelon germplasm resources

摘要

以89份西瓜种质资源为材料，利用形态学标记和西瓜SNP高效液相芯片，结合多样性分析、群体结构分析、聚类分析和主成分分析等方法，对其遗传多样性进行系统全面的研究。结果表明，49个表型性状Shannon多样性指数的变化范围是0.42~3.00，平均值为2.32，其中描述型性状平均值为1.28，数量性状为2.82；33个数量性状的变异系数变化范围为5.45%~72.59%，平均值为28.00%，变异系数最大的是果实质量(72.59%)，其次是第一雌花节位(64.21%)和第一雄花节位(58.59%)。利用液相芯片对这89份种质资源进行DNA测序，得到60.2 Gb的原始数据和401.3 Mb的raw_reads数据，质控后得到53.1 Gb的数据和399.7 Mb的clean_reads数据，比对到参考基因组上的reads数为332.4 Mb, 平均比对率为82.97%，平均测序深度为923.7 X。群体结构分析显示89份材料的最优群体结构数为2，主成分分析和系统发育树结果显示，在89份材料中，药西瓜与饲用西瓜亲缘关系最近，栽培西瓜与饲用西瓜亲缘关系次之。长期的选择驯化使西瓜遗传背景变得十分狭窄，通过发掘野生西瓜资源，进而拓宽西瓜遗传背景，对西瓜抗病、抗逆以及株型改良等分子育种具有重要意义。

Abstract

The genetic diversity of 89 watermelon germplasm resources was studied by morphological markers, SNP high-performance liquid chip, diversity analysis, population structure analysis, cluster analysis and principal component analysis. The results showed that the Shannon diversity index of 49 phenotypic traits ranged from 0.42 to 3.00 with an average value of 2.32, among which the mean value of descriptive traits was 1.28 and the mean value of quantitative traits was 2.82. The coefficient of variation of the 33 quantitative traits ranged from 5.45%-72.59%, and the mean value was 28.00%. The highest coefficient of variation was fruit mass (72.59%), followed by the first female flower node (64.21%) and the first male flower node (58.59%). In terms of plant type, the variation coefficient of 30 d lateral branches was also large. Liquid chip sequencing yielded 60.2 Gb of raw data and 53.1 Gb of data after quality control. The number of raw_reads and clean_reads after quality control were 401.3 Mb, 399.7 Mb, and 332.4 Mb of reads were compared to the reference genome, with an average comparison rate of 82.97%. The average sequencing depth was 923.7 X. Population structure analysis showed that the optimal population structure number of 89 materials was 2. Principal component analysis and phylogenetic tree showed that among 89 materials, the relationship between medicinal watermelon and forage watermelon was the closest, while that between cultivated watermelon and forage watermelon was the second. Long-term selection and domestication have narrowed the genetic background of watermelon. By exploring wild watermelon resources and broadening the genetic background, this study is of great significance for molecular breeding of watermelon disease resistance, stress resistance and plant type improvement.

关键词

西瓜 / 种质资源 / 群体结构分析

Key words

Watermelon / Germplasm resources / Population structure analysis

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基金资助

国家自然科学基金项目(32172602)

国家自然科学基金项目(32172574)

国家自然科学基金项目(32102389)

河南省农业良种联合攻关项目(2022010503)

河南省重大科技专项(221100110400)

河南省科技攻关项目(242102111124)