Duan Baohua, Mu Shumei, Guan Yueqiang, Liu Weibiao, Kang Tongxu, Cheng Yana, Li Zejian, Tian Yang, Kang Xianjiang
College of Life Sciences, Hebei University, Baoding, China.
Bureau of Agricultural and Rural Affairs of Huanghua City, Huanghua, China.
Front Genet. 2022 Jul 18;13:932173. doi: 10.3389/fgene.2022.932173. eCollection 2022.
is an economically important mariculture species in China. Evaluating its genetic diversity and population structure can contribute to the exploration of germplasm resources and promote sustainable aquaculture production. In this study, a total of 246,243 SSRs were generated by transcriptome sequencing of . Among the examined 254,746 unigenes, 66,331 had more than one SSR. Among the different SSR motif types, dinucleotide repeats (110,758, 44.98%) were the most abundant. In 173 different base repeats, A/T (96.86%), AC/GT (51.46%), and ACC/GGT (26.20%) were dominant in mono-, di-, and trinucleotide, respectively. GO annotations showed 87,079 unigenes in 57 GO terms. Cellular process, cell, and binding were the most abundant terms in biological process, cellular component, and molecular function categories separately. A total of 34,406 annotated unigenes were classified into 26 functional categories according to the functional annotation analysis of KOG, of which "general function prediction only" was the biggest category (6,028 unigenes, 17.52%). KEGG pathway annotations revealed the clustering of 34,715 unigenes into 32 different pathways. Nineteen SSRs were identified as polymorphic and, thus, used to assess the genetic diversity and structure of 240 individuals from four populations in the Bohai Sea. Genetic parameter analysis showed a similar level of genetic diversity within wild populations, and the cultured population indicated a reduction in genetic diversity compared with wild populations. The pairwise values were between 0.001 and 0.04 with an average of 0.0205 ( < 0.05), suggesting a low but significant level of genetic differentiation among the four populations. Structure analysis demonstrated that the four populations were classified into two groups including the cultured group and other populations. The phylogenetic tree and PCA revealed that a vast number of samples were clustered together and that cultivated individuals were distributed more centrally than wild individuals. The findings contribute to the further assessment of germplasm resources and assist to provide valuable SSRs for marker-assisted breeding of in the future.
是中国一种具有重要经济价值的海水养殖物种。评估其遗传多样性和种群结构有助于种质资源的探索，并促进水产养殖的可持续生产。在本研究中，通过对……的转录组测序共产生了246,243个SSR。在所检测的254,746个单基因中，66,331个含有一个以上的SSR。在不同的SSR基序类型中，二核苷酸重复序列（110,758个，占44.98%）最为丰富。在173种不同的碱基重复中，A/T（占96.86%）、AC/GT（占51.46%）和ACC/GGT（占26.20%）分别在单核苷酸、二核苷酸和三核苷酸中占主导地位。GO注释显示57个GO术语中有87,079个单基因。细胞过程、细胞和结合分别是生物过程、细胞组成和分子功能类别中最丰富的术语。根据KOG的功能注释分析，共有34,406个注释单基因被分类为26个功能类别，其中“仅一般功能预测”是最大的类别（6,028个单基因，占17.52%）。KEGG通路注释显示34,715个单基因聚集在32条不同的通路中。鉴定出19个多态性SSR，因此用于评估来自渤海四个种群的240个个体的遗传多样性和结构。遗传参数分析表明野生种群内的遗传多样性水平相似，养殖种群与野生种群相比遗传多样性有所降低。成对……值在0.001至0.04之间，平均为0.0205（……<0.05），表明四个种群之间存在低但显著的遗传分化。结构分析表明四个种群分为两组，包括养殖组和其他种群。系统发育树和主成分分析表明大量样本聚集在一起，养殖个体比野生个体分布更集中。这些发现有助于进一步评估种质资源，并有助于为未来……的分子标记辅助育种提供有价值的SSR。
