利用线粒体DNA标记分析中国东南沿海拟穴青蟹种群遗传结构

为研究我国东南沿海拟穴青蟹(Scylla paramamosain)的种群遗传结构,对10个地理种群130只拟穴青蟹的线粒体DNA（mitochondrial DNA,mtDNA）细胞色素氧化酶亚基I（COI）基因片段序列进行分析。522bp的DNA片段共发现17个变异位点,定义了21种单倍型,其中单倍型2为10个地方种群的共享单倍型,占个体总数的56.15％,而大部分单倍型为稀有单倍型,只在少数种群的个别个体中出现。10个种群的单倍型多样性水平为h=0.6738,核苷酸多样性水平为π=0.1987%,基本呈由南到北递减的趋势。10个种群的总体遗传分化程度较低（FST＝0.05左右）,但是极为显著（P<0.005）。基于单倍型频率和序列遗传距离法分析的共同结果,广西北海种群与大多数种群的遗传分化显著,而海南三亚种群分别与海南红树林和广东台山种群遗传分化显著。Mantel检验显示种群间的遗传分化程度与地理距离没有显著的相关性。分子进化中性检验结果表明自然选择在分子进化过程中起了重要作用,并暗示该物种在最近经历了一个快速的种群爆发及扩张事件。     

Single-marker and haplotype-based association analysis of anthracnose (Colletotrichum dematium) resistance in spinach (Spinacia oleracea)

Anthracnose (Colletotrichum dematium) is an important disease in spinach (Spinacia oleracea). Sources of resistance must be identified, and molecular tools must be developed to expedite cultivar development. In this study, a diverse collection of 276 spinach accessions was scored for anthracnose disease severity. We then evaluated marker identification approaches by testing how well haplotype-based trait modelling compares to single markers in identifying strong association signals. Alleles in linkage disequilibrium were tagged in haplotype blocks, and anthracnose-associated molecular markers were identified using single-SNP (sSNP), pairwise haplotype (htP) and multi-marker haplotype (htM) SNP tagging approaches. We identified 49 significantly associated markers distributed on several spinach chromosomes using all methods. The sSNP approach identified 13 markers, while htP identified 24 (~63% more) and htM 34 (~162% more). Of these markers, four were uniquely identified by the sSNP approach, nine by htP and nineteen by htM. The results indicate that resistance to anthracnose is polygenic and that haplotype-based analysis may have more power than sSNP. Using a combination of these methods can improve the identification of molecular markers for spinach breeding.     

入侵云南草地贪夜蛾的分子鉴定

草地贪夜蛾Spodoptera frugiperda(J.E. Smith)是一种原产于美洲热带和亚热带地区的重要农业入侵害虫,目前已从缅甸进入我国云南西南部地区,且呈现蔓延之势。对入侵物种快速准确鉴定是早期预警和监测预防的关键。本研究采用分子标记手段,对采自云南5个县(市)的83份样品进行鉴定,通过PCR扩增细胞色素C氧化酶第Ⅰ亚基(COⅠ)和磷酸甘油醛异构酶(Tpi)两个基因片段并进行序列测定分析。结果表明,基于COⅠ基因片段的序列比对能够对草地贪夜蛾进行准确的物种鉴定,并且能够对其近源种甜菜夜蛾等进行鉴定。基于Tpi基因序列的特异单倍型位点比较分析,确认入侵我国的草地贪夜蛾均为"玉米型"。该研究为草地贪夜蛾的快速识别提供了方法支持,同时为进一步的虫源地解析和遗传溯源积累了宝贵的前期数据。     

青海马铃薯晚疫病菌线粒体DNA单倍型鉴定及分析

 为查明青海地区晚疫病菌单倍型分布情况,本研究对青海不同地区采自2006～2007年的70个晚疫病菌材料的线粒体单倍型进行了分析,结果表明：94.3%的菌株为Ⅱa型,5.7%的菌株为Ⅱb型,其中Ⅱb型均分离自番茄。这说明青海地区马铃薯晚疫病菌群体类型比较单一,主要为Ⅱa型,线粒体单倍型不存在多态性。     

基于线粒体DNA控制区(mtDNA D-loop)序列分析贵妃鸡的遗传多样性

采用PCR产物直接测序技术对30只贵妃鸡样品的线粒体DNA控制区(mtDNA D-loop)第Ⅰ高变区序列进行了分析。结果表明,在所分析的D-loop区部分序列中(520 bp),A、G、C、T平均含量分别为26.8%、13.0%、31.1%和29.1%;共发现13个核苷酸多态位点,均为转换位点,未检测到插入/缺失和颠换,核苷酸多样度(Pi)为0.0059,单倍型变异度(Hd)为0.538,中性检验Tajima’s D值为-0.67065。通过群体构建的NJ聚类图分子系统树发现,贵妃鸡起源于红原鸡。     

基于线粒体D-loop序列的白头鹤越冬种群遗传结构研究(英文)

白头鹤(Grus monacha)是我国长江中下游湿地的越冬水鸟,湿地退化导致栖息地逐渐丧失,影响越冬种群的稳定,开展种群遗传结构研究对越冬白头鹤的有效保护具有积极意义。本研究共采集安徽菜子湖、升金湖、江西鄱阳湖、上海崇明东滩4个白头鹤越冬地粪便样品221份、羽毛样品9份和肌肉样品4份,从中获得了72份样品的mtDNA控制区(D-loop)1103-1104bp序列。结合从GenBank获得的两个来自日本的白头鹤个体序列(GenBank AB017625、AB023813),对越冬种群进行了遗传结构分析。长江中下游4个越冬种群共发现26个变异位点,定义了23种单倍型。遗传多样性分析结果显示,白头鹤单倍型多样性(h)为0.823±0.042,核苷酸多样性(π)为0.00157±0.00021。各个种群FST值表明我国长江中下游各种群之间无显著的遗传分化。两种中性检验(Tajima’sD = 2.10951, p < 0.05;Fu’s FS=19.351, p < 0.01)分析结果表明,白头鹤在进化史上可能经历了种群扩张。     

云南致病疫霉交配型、甲霜灵敏感性、mtDNA单倍型及其群体演替研究

【目的】对致病疫霉群体特征的认识，是控制晚疫病危害的必要前提。【方法】对云南32个马铃薯和番茄产区的致病疫霉群体的交配型、甲霜灵敏感性、mtDNA单倍型进行了研究。【结果】云南马铃薯致病疫霉群体主要由A1交配型组成，番茄致病疫霉全部为A1交配型。A2 交配型和自育型菌株总体发生频率较低，分别为3.4％和4.4％。自从2002年以后，致病疫霉的群体结构发生了明显的变化，没有检测到A2交配型或自育型菌株。致病疫霉对甲霜灵敏感性的离体测定显示马铃薯和番茄上均存在抗性、中抗和敏感菌株。甲霜灵抗性、中抗、敏感菌株分别占测定菌株的13.2％ 、9.4％和 77.4％。分离自番茄的甲霜灵抗性菌株比例高于分离自马铃薯的菌株。Ⅰa 、Ⅱa 和 Ⅰb 三种mtDNA 单倍型被检测到，马铃薯致病疫霉有Ⅰa 和 Ⅱa 两种单倍型，全部为第二次全球迁移后出现的“新”群体。Ⅰa 单倍型在群体中的比例为96％，分布于所有马铃薯产区；番茄致病疫霉则为Ⅰa 和Ⅰb 两种单倍型，“新”、“旧”群体共存。【结论】马铃薯和番茄致病疫霉群体的遗传结构有明显差异；致病疫霉“新”、“旧”群体在云南已发生演替，马铃薯致病疫霉“新”群体已成功替代了“旧”群体；迁移和有限的有性生殖可能在云南致病疫霉群体的演替中担当了重要的作用。     

Genome‐wide association studies in elite varieties of German winter barley using single‐marker and haplotype‐based methods

Genome‐wide association studies (GWAS) became a widely used method to map qualitative and quantitative traits in plants. We compared existing single‐marker and haplotype‐based methods for GWAS with a focus on barley. Based on German winter barley cultivars, four different single‐marker and haplotype‐based methods were tested for their power to detect significant associations in a large genome with a limited number of markers. We identified significant associations for yield and quality‐related traits using the iSelect array with 3886 mapped single nucleotide polymorphism (SNP) markers in a structured population consisting of 109 genotypes. Genome simulations with different numbers of genotypes, marker densities and marker effects were used to compare different GWAS methods. Results of simulations revealed a higher power in detecting significant associations for haplotype‐ than for single‐marker approaches, but showed a higher false discovery rate for SNP detection, due to lack of correction for population structure. Our simulations revealed that a population size of about 500 individuals is required to detect QTLs explaining a small trait variance (<10%).     

Distribution of S haplotypes in commercial cultivars of Brassica rapa

Self‐incompatibility in Brassicaceae plants is sporophytically controlled by a single multi‐allelic locus (S locus), which contains at least three highly polymorphic genes expressed in the stigma (SLG and SRK) and in the pollen (SCR/SP11). Using polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) analysis with SXG‐specific primer pairs, the S haplotypes of F₁ hybrid and open‐pollinated commercial cultivars of Brassica rapa were identified. The number of S haplotypes detected in the F₁ hybrid cultivars of Chinese cabbage, komatsuna, pak‐choi, turnip, open‐pollinated cultivars of Chinese cabbage and turnip were 9, 9, 4, 11, 13 and 12, respectively. Nine of them had different PCR‐RFLP profiles from those of the S‐tester lines that determined the SLG sequences. Four SLG sequences in the F₁ hybrid cultivars were determined and named S⁵³, S⁵⁴, S⁵⁵ and S⁵⁶, respectively. It is demonstrated that the PCR‐RFLP analysis using specific primer pairs of SLG and SRK is useful for identification of the S haplotypes, in both, S homozygous and S heterozygous plants of B. rapa. The possibility of using this method routinely in breeding programmes, and in the evaluation of F₁ hybrid seed purity, is discussed.