Evaluation of genetic diversity and population structure of Fragaria nilgerrensis using EST-SSR markers
Evaluation of genetic diversity and population structure of Fragaria nilgerrensis using EST-SSR markers
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利用EST-SSR标记评价草莓遗传多样性和种群结构
DOI：
10.1016/j.gene.2021.145791
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发表时间：
2021-07-02
期刊：
影响因子：
3.5
通讯作者：
Qiao, Qin
中科院分区：
文献类型：
--
作者：
Lu, Jie;Zhang, Yichen;Qiao, Qin
草莓是我国西南地区广泛分布的一种二倍体野生草莓。其白色的果实色泽和“桃香”的果实香味是栽培草莓遗传改良的重要性状。其强大的生物和非生物抗性和耐受性也使其能够在野外不同生境中生存。本研究对16个群体169个个体的遗传变异水平进行了分析。利用16个新开发的EST-SSR（expressed sequence tag-simple sequence repeats）标记，对黑稻瘟病菌（nilgerrensis）的EST-SSR分子标记进行了分析。结果表明，该种虽然具有自交亲和性和克隆繁殖性，但其遗传多样性较高，根据Nei’s遗传多样性指数（0.26）和多态位点数（0.41）计算，其遗传多样性较高。AMOVA分析表明，种群间存在显著的遗传分化（Fst = 0.34），表明种群间的基因流很小（Nm = 0.43）。尼尔格龙属系统发育树表明，同一种群的个体大多聚在一起。这些群体没有根据地理距离进行分组，与Mantel检验结果一致（R2 = 0.0063，P > 0.05）。所有的种群被分配到两个祖先群体，与一些个体混合，这表明祖先基因流发生在这两个群体之间。利用我们开发的EST-SSR分子标记，分析了黑木耳的遗传多样性和群体结构。nilgerrensis在育种过程中对遗传改良很重要。此外，具有高度遗传多样性的种群将是收集和保护的优先事项。
Fragaria nilgerrensis is a diploid wild strawberry widely distributed in Southwest China. Its white color and "peach-like" fragrance of fruits are valuable characters for the genetic improvement of cultivated strawberry plants. Its strong biotic and abiotic resistance and tolerance also enable it to survive in different habitats in the field. In this study, we evaluated the level of genetic variation within and between 16 populations with 169 individuals of F. nilgerrensis using 16 newly developed EST-SSR (expressed sequence tag-simple sequence repeats) markers. The results show that the genetic diversity of this species was high, based on Nei's genetic diversity (0.26) and polymorphic loci (0.41), although it is self-compatible and has clonal propagation. Significant genetic differentiation among populations was also detected by AMOVA analysis (Fst = 0.34), which could be indicative of little gene flow (Nm = 0.43) in F. nilgerrensis. The phylogenetic tree indicates that most of individuals from the same population have clustered together. These populations were not grouped based on the geographical distance, consistent with the Mantel test result (R2 = 0.0063, P > 0.05). All the populations were assigned into two ancestral groups, with some individuals admixed, suggesting ancestral gene flow had occurred between these two groups. Our developed EST-SSR markers as well as the genetic diversity and population structure analysis of F. nilgerrensis are important for genetic improvement in the breeding process. Moreover, the populations that contain high genetic diversity would be a priority for collection and conservation.