羊草叶绿体非编码区多态性标记筛选及群体遗传多样性

doi:10.11686/cyxb2018022

摘要/Abstract

摘要： 为筛选多态性丰富的羊草叶绿体非编码区片段,本研究以9个不同地理位置的羊草居群为材料,通过对12个叶绿体非编码区DNA片段测序及其序列间变异分析试图从中找出有遗传差异的叶绿体DNA(cpDNA)片段,并利用有多态性的cpDNA片段进行遗传多样性分析。结果表明,序列ndhF-rpl32、trnL-trnF、trnC-ycf6、aptI-aptH具有比较丰富的变异,可作为下一步研究野生羊草群体遗传学和谱系地理学较为理想的分子标记。在37个羊草个体4条非编码区片段的合并序列中,共检测到15种单倍型,单倍型多态性(Hd)为0.928,核苷酸多态性(Pi)为0.00101;遗传分化指数(Fst)为0.58884,基因流(Nm)为0.17,基因流较小;中性检验Tajima’s D(-1.08542)和Fu’s Fs(-5.301)均为负值,且差异不显著(P>0.10),推测羊草遵循中性进化理论,可能经历过种群扩张;AMOVA结果显示,65%的分子变异出现在居群间,35%出现在居群内;Mantel检验得到,遗传距离与地理距离具有显著相关性(r=0.449,P<0.05);居群分化值Nst 0.386(0.1865)大于Gst 0.234(0.1506),差异显著(P<0.05),表明羊草居群存在分子谱系地理结构。通过系统发育树分析得到,羊草15个单倍型分为两大分支,H2和H10聚为一支,它们与别的居群个体亲缘关系较远,其余单倍型聚为另一支;单倍型网络图显示,H2和H12、H10和H12亲缘关系较远,与系统发育树分析结果基本一致。本研究为羊草的种质资源保护、谱系地理学研究等工作奠定了基础。

关键词: 羊草, 叶绿体非编码区片段, 多态性标记, 单倍型, 遗传多样性

Abstract: The aim of this research was to screen for and classify polymorphic loci of chloroplast non-coding fragments in Leymus chinensis. The study evaluated 9 L. chinensis populations from different geographical locations to identify polymorphic loci from 12 chloroplast DNA (cpDNA) non-coding fragments, and then genetic diversity of the polymorphic cpDNA fragments was analyzed. The results showed that the polymorphic loci of ndhF-rpl32, trnL-trnF, trnC-ycf6 and aptI-aptH were rich, and they had a relatively fast evolution rate. Hence, they could be regarded as ideal molecular markers for future research on population genetics and phylogeography. Based on combined sequences there were 15 haplotypes identified. The haplotype diversity (Hd) and nucleotide diversity (Pi) were 0.928 and 0.00101 respectively. The genetic differentiation coefficient Fst was 0.58884 with the low gene flow (Nm=0.17). Tajima’s D and Fu’s Fs values of neutrality tests were negative (Tajima’s D=-1.0854; Fu’s Fs=-5.301), indicating that L. chinensis had experienced historical population expansion. Analysis of molecular variance showed that most of genetic variation was distributed among populations. The Mantel test showed a significantly positive correlation between genetic and geographical distance (r=0.449, P<0.05). The genetic differentiation coefficients Nst (0.386)>Gst (0.234) implied a significant phylogeographic structure for the populations. The neighbor-joining tree based on combined sequences showed that all haplotypes divided into two major clades, H2 and H10 clustered into a category. The network for cpDNA haplotypes based on combined sequence data showed that the relationships among H2 and H12, and H10 and H12 were further than others, which was similar to the pattern identified by the neighbor-joining tree. These results will be useful for future research on germplasm resources and phylogeography.

Key words: Leymus chinensis, chloroplast non-coding fragment, polymorphic locus, haplotype, genetic diversity

杨艳婷, 侯向阳, 魏臻武, 乔志宏, 常春, 任卫波, 武自念. 羊草叶绿体非编码区多态性标记筛选及群体遗传多样性[J]. 草业学报, 2018, 27(10): 147-157.

YANG Yan-ting, HOU Xiang-yang, WEI Zhen-wu, QIAO Zhi-hong, CHANG Chun, REN Wei-bo, WU Zi-nian. Screening and genetic diversity analysis of chloroplast non-coding regions in Leymus chinensis[J]. Acta Prataculturae Sinica, 2018, 27(10): 147-157.

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