柽柳群体遗传变异研究 英文标题:Study on the Genetic Variation of Tamarix Chinensis Lour. Populations

柽柳具有很高的抗盐碱能力和耐水湿能力，是沿海滩涂最适宜发展的树种之一。本研究以柽柳主要分布区形成一定规模的9个天然群体及1个当地起源的群体为材料，从扦插生长特性到核基因组及叶绿体基因组水平上进行了较为系统的遗传变异研究，以期为柽柳遗传多样性保护及利用策略提供依据。主要结果如下：柽柳扦插具有较高的成活率，将是今后柽柳良种繁育的主要途径。柽柳不同种源(群体)扦插苗在扦插成活率、生长量、分枝数、最粗枝直径等性状均存在变异，有的差异在群体间达到显著或极显著水平，在无性系间差异更大。在柽柳良种选育中，既要注重种源间的差异，更要利用无性系间的变异。柽柳无性系3年生时的生长表现与1年生时有明显区别，说明无性系的速生性需要一定的时间才能体现，柽柳无性系选育需经过多年的栽培试验。利用柽柳属植物22724条EST序列拼接得到8490条无冗余独立基因序列，通过PRIMER5.0软件设计了引物164对，随机合成75对，在柽柳中有40对SSR引物能扩增出清晰条带，可用于柽柳遗传变异的检测，其中14对在本研究材料中具有多态性。14对由EST序列开发来的SSR引物和2对由核基因组富集文库得来gSSR在10个群体中共扩增出70个等位基因，每个位点平均扩增出等位基因(A)4.3750个，有效等位基因数(Ne)平均为2.7580个，平均期望杂合度(He)为0.5916，Nei多样性指数(h)为0.5906，Shannon多样性指数(Ⅰ)平均为1.0689，柽柳具有较高的遗传多样性。群体水平上各群体遗传多样性相近，最高为浙江慈溪群体2，为0.5759，最低的为浙江海盐群体为0.5512。柽柳遗传变异主要存在于群体内，群体间遗传分化系数较低，仅有5%左右的变异存在于群体间(Gst平均为0.0503，Fst=0.0512)。基因流Nm为4.7635。群体平均观察杂合度(Ho)为0.5257，低于平均期望杂合度，表明群体中纯合子过量，群体平均固定指数为0.0765。经Hardy-Weinberg平衡检验，尽管在种水平上16个位点中大多数位点(12个)显著偏离平衡，但在群体水平上大多位点处于平衡状态，所有群体均超过10个以上位点达到平衡。瓶颈效应分析发现所研究群体近期均经历过瓶颈事件。少量哑等位基因的检出可以部分解释有的群体不平衡位点过多现象。基于Mantel检验发现群体的遗传距离和地理距离仅成弱度正相关(r=0.2903)，且未达到显著水平(p>0.05.)，然而根据群体遗传距离的聚类结果却具有明显的地理区域性，即相同区域内的群体间遗传距离明显小于区域间。76对cpSSR引物中有47对在柽柳中能扩增出产物，但仅有3对标记在10个群体中表现出多态性。基于3对cpSSR引物在10个群体共检测到6个单倍型，具有较明显的地理分布结构，南方群体和北方群体单倍型有明显差异，表明南、北方群体可能起源于不同的区域。黄河上游群体(内蒙)的单倍型明显比黄河下游丰富，北方群体扩散方向可能沿黄河流向；南方群体单倍型有部分与北方群体相同，可能来源于黄河流域，其它单倍型的来源及扩散路径尚不能推断。

Tamarix has high salt-alkali tolerance and waterlogging resistance, making it one of the most suitable tree species for development in coastal tidal flats. In this study, nine natural populations that have formed a certain scale in the main distribution areas of Tamarix and one local-origin population were used as materials. A relatively systematic study on genetic variation was conducted from the growth characteristics of cuttings to the nuclear and chloroplast genome levels, aiming to provide a basis for the conservation and utilization strategies of Tamarix genetic diversity.

The main results are as follows: Tamarix cuttings have a relatively high survival rate, which will be the main approach for improved variety breeding of Tamarix in the future. There are variations in traits such as cutting survival rate, growth increment, number of branches, and diameter of the thickest branch among cuttings from different provenances (populations) of Tamarix. Some differences reach significant or extremely significant levels among populations, and the differences among clones are even greater. In the breeding of improved Tamarix varieties, attention should be paid to the differences among provenances, and more utilization of the variations among clones is needed. The growth performance of 3-year-old Tamarix clones is significantly different from that of 1-year-old clones, indicating that the fast-growing trait of clones requires a certain period of time to manifest, so the breeding of Tamarix clones needs to undergo multi-year cultivation experiments.

A total of 22,724 EST sequences of Tamarix genus plants were assembled into 8,490 non-redundant independent gene sequences. Using PRIMER 5.0 software, 164 pairs of primers were designed, among which 75 pairs were randomly synthesized. Of these, 40 pairs of SSR primers could amplify clear bands in Tamarix, which can be used for detecting Tamarix genetic variation, and 14 pairs showed polymorphism in the materials used in this study. The 14 pairs of SSR primers developed from EST sequences and 2 pairs of gSSR primers derived from nuclear genome enrichment libraries amplified a total of 70 alleles across the 10 populations, with an average of 4.3750 alleles (A) per locus, an average effective number of alleles (Ne) of 2.7580, an average expected heterozygosity (He) of 0.5916, a Nei's diversity index (h) of 0.5906, and an average Shannon's diversity index (I) of 1.0689, indicating that Tamarix has a relatively high level of genetic diversity.

At the population level, the genetic diversity of each population is relatively similar, with the highest being the Zhejiang Cixi population 2 at 0.5759, and the lowest being the Zhejiang Haiyan population at 0.5512. Most of the genetic variation of Tamarix exists within populations, and the genetic differentiation coefficient among populations is relatively low, with only about 5% of the variation existing among populations (average Gst = 0.0503, Fst = 0.0512). The gene flow Nm is 4.7635. The average observed heterozygosity (Ho) of the populations is 0.5257, which is lower than the average expected heterozygosity, indicating an excess of homozygotes in the populations, with an average population fixation index of 0.0765. Through Hardy-Weinberg equilibrium tests, although most loci (12 out of 16) at the species level significantly deviate from equilibrium, most loci are in equilibrium at the population level, and all populations have more than 10 loci reaching equilibrium. Bottleneck effect analysis found that all the studied populations have experienced recent bottleneck events. The detection of a small number of silent alleles can partially explain the phenomenon of excessive unbalanced loci in some populations.

Based on the Mantel test, it was found that there is only a weak positive correlation between the genetic distance and geographic distance of the populations (r=0.2903), which does not reach a significant level (p>0.05). However, the clustering results based on population genetic distance have obvious geographic regionality, that is, the genetic distance among populations within the same region is significantly smaller than that between regions.

Among the 76 pairs of cpSSR primers, 47 pairs could amplify products in Tamarix, but only 3 pairs of markers showed polymorphism in the 10 populations. Based on the 3 pairs of cpSSR primers, a total of 6 haplotypes were detected in the 10 populations, which have an obvious geographic distribution structure. The haplotypes of southern and northern populations have significant differences, indicating that southern and northern populations may originate from different regions. The haplotypes of the upper Yellow River population (Inner Mongolia) are significantly more abundant than those of the lower Yellow River population, and the diffusion direction of northern populations may follow the flow of the Yellow River. Some haplotypes of southern populations are the same as those of northern populations, which may originate from the Yellow River basin, while the sources and diffusion paths of other haplotypes cannot yet be inferred.

搜集汇总

背景与挑战

背景概述

该数据集针对柽柳的10个天然及当地起源群体，从扦插生长到基因组水平开展了系统的遗传变异研究。研究发现柽柳具有较高的遗传多样性，遗传变异主要存在于群体内部，并揭示了南北方群体可能具有不同的起源及扩散路径。