珍稀濒危树种毛红椿微卫星DNA分离及SSR反应体系优化

本研究以江西宜丰种源毛红椿为材料,成功提取其基因组DNA。利用改良的链亲和素磁珠法亲和捕捉出毛红椿基因组微卫星DNA片断,并构建了富含微卫星的基因组文库。从构建的基因组文库中随机挑选了63个单克隆进行测序,其中50个单克隆成功测序,含有微卫星的单克隆有18个,并根据测序结果设计并合成SSR引物18对。利用所合成的引物优化SSR反应体系,对影响SSR反应的各个因子进行了探讨。确定了模板DNA浓度最适浓度为30ng;dNTP的最适浓度为0.3mmol·L-1;0.3μmol·L-1是引物在反应体系中的最合适浓度。建立了重复性好、稳定性好的SSR反应体系,为下一步进行毛红椿群体遗传结构和遗传变异研究提供了技术支持。     

Multilocus genotypes from Charles Darwin's finches: biodiversity lost since the voyage of the Beagle

Genetic analysis of museum specimens offers a direct window into a past that can predate the loss of extinct forms. We genotyped 18 Galápagos finches collected by Charles Darwin and companions during the voyage of the Beagle in 1835, and 22 specimens collected in 1901. Our goals were to determine if significant genetic diversity has been lost since the Beagle voyage and to determine the genetic source of specimens for which the collection locale was not recorded. Using ‘ancient’ DNA techniques, we quantified variation at 14 autosomal microsatellite loci. Assignment tests showed several museum specimens genetically matched recently field-sampled birds from their island of origin. Some were misclassified or were difficult to classify. Darwin''s exceptionally large ground finches (Geospiza magnirostris) from Floreana and San Cristóbal were genetically distinct from several other currently existing populations. Sharp-beaked ground finches (Geospiza difficilis) from Floreana and Isabela were also genetically distinct. These four populations are currently extinct, yet they were more genetically distinct from congeners than many other species of Darwin''s finches are from each other. We conclude that a significant amount of the finch biodiversity observed and collected by Darwin has been lost since the voyage of the Beagle.     

鹅掌楸配子选择与雄性繁殖适合度

在多父本等量花粉混合授粉的交配实验设计基础上, 利用SSR分子标记对其子代进行父本分析, 研究鹅掌楸的配子选择与雄性繁殖适合度。参试亲本为鹅掌楸2个种的5个单株（鹅掌楸（Liriodendron chinense）2株, 即FY和LS; 北美鹅掌楸（L. tulipifera）3株, 即LYS、MSL和NK）。结果表明： 鹅掌楸的配子选择个体间差异较大。作为母本, NK和LYS倾向于选择异种雄配子, 而MSL和LS则倾向于选择同种雄配子; 在同种雄配子的选择中, NK、LYS和LS倾向于自交, 而MSL则倾向于异交。以北美鹅掌楸为母本时, 北美鹅掌楸与鹅掌楸的雄性繁殖贡献率分别为45.5%和54.5%, 北美鹅掌楸的雄性繁殖适合度为鹅掌楸的0.556倍。以鹅掌楸为母本时, 二者的繁殖贡献率分别为15.6%和84.4%, 北美鹅掌楸的雄性繁殖适合度为鹅掌楸的0.123倍。总体上看, 鹅掌楸的雄性繁殖适合度高于北美鹅掌楸, 鹅掌楸与北美鹅掌楸均表现为自交亲和。     

塔玛亚历山大藻遗传多样性的微卫星分析

应用12个微卫星标记对9株来自欧洲和中国等不同海域的塔玛亚历山大藻(Alexandrium tamarense)进行了遗传多样性分析,探讨了不同地理藻株之间的遗传分化程度和基因流水平,分析了我国沿海塔玛亚历山大藻的遗传多样性。结果表明：9株塔玛亚历山大藻共检测出26个等位基因,其中9个位点具有多态性,多态比率75%。有效等位基因数1.3243～3.2667,平均为1.8774。塔玛亚历山大藻种内基因多样性为0.3630。9株塔玛亚历山大藻大致可以分为3个进化支,进化支与藻株的地理位置相关联。其中,中国海域的塔玛亚历山大藻至少可分为2个进化支。不同地理分布的塔玛亚历山大藻的遗传分化水平较高,达0.7522。种群间的基因流估算水平较低,提示3个种群间可能不存在基因交流。     

60Co-γ辐射诱变小麦M3代品质性状的遗传变异分析

用300 Gy的60Co-γ射线辐射小麦品种涡9722的干种子,对M3代341个株行的蛋白质含量、湿面筋含量、沉降值和硬度4个品质性状进行了遗传变异分析和SSR分子鉴定.结果表明,以超过均值±2×标准差确定变异株行,在 M3代群体中,蛋白质含量有15个株行发生正向变异,8个株行发生负向变异;湿面筋含量有11个株行发生正向变异, 4个株行发生负向变异;沉降值有13个株行发生正向变异,15个株行发生负向变异;硬度有4个株行发生正向变异,14个株行发生负向变异.相关分析表明,M3群体4个品质性状间呈极显著正相关,表现出平行变异的趋势.初步筛选出蛋白质含量和湿面筋含量符合国家强筋小麦标准的株行15个,符合国家弱筋小麦标准的株行1个.经SSR分子标记检测,以上16个变异株行控制蛋白质的基因位点发生了变异.     

56个杂交水稻骨干亲本SSR指纹图谱的构建及遗传相似性分析

以中国56个杂交水稻骨干亲本为研究材料,包括水稻雄性不育系和恢复系。从国标中公布的48对水稻SSR引物中筛选出14对稳定性好、多态性高、杂带少且在染色体上分布均匀的引物作为核心引物,建立56个杂交水稻骨干亲本的SSR指纹图谱,结果表明：14对SSR引物在56份材料中共扩增出48个多态性片段,平均每对引物可以检测3．43个等位基因。聚类分析得出56个品种间的遗传相似性系数在0．63～0．98之间,基本上反映了不同品种间的亲缘关系。     

Evidences of introgression from cultivated rice to Oryza rufipogon (Poaceae) populations based on SSR fingerprinting: implications for wild rice differentiation and conservation

Crop-to-wild introgression may play an important role in evolution of wild species. Asian cultivated rice (Oryza sativa L.) is of a particular concern because of its cross-compatibility with the wild ancestor, O. rufipogon Griff. The distribution of cultivated rice and O. rufipogon populations is extensively sympatric, particularly in Asia where many wild populations are surrounded by rice fields. Consequently, gene flow from cultivated rice may have a potential to alter genetic composition of wild rice populations in close proximity. In this study, we estimated introgression of cultivated rice with O. rufipogon based on analyses of 139 rice varieties (86 indica and 53 japonica ecotypes) and 336 wild individuals from 11 O. rufipogon populations in China. DNA fingerprinting based on 17 selected rice simple sequence repeat (SSR) primer pairs was adopted to measure allelic frequencies in rice varieties and O. rufipogon samples, and to estimate genetic associations between wild and cultivated rice through cluster analysis. We detected consanguinity of cultivated rice in O. rufipogon populations according to the admixture model of the STRUCTURE program. The analyses showedz that four wild rice populations, DX-P1, DX-P2, GZ-P2, and HL-P, contained some rare alleles that were commonly found in the rice varieties examined. In addition, the four wild rice populations that scattered among the rice varieties in the cluster analysis showed a closer affinity to the cultivars than the other wild populations. This finding supports the contention of substantial gene flow from crop to wild species when these species occur close to each other. The introgressive populations had slightly higher genetic diversity than those that were isolated from rice. Crop-to-wild introgression may have accumulative impacts on genetic variations in wild populations, leading to significant differentiation in wild species. Therefore, effective measure should be taken to avoid considerable introgression from cultivated rice, which may influence the effective in-situ conservation of wild rice species.     

Genetic diversity and origin of weedy rice (Oryza sativa f. spontanea) populations found in North-eastern China revealed by simple sequence repeat (SSR) markers

BACKGROUND AND AIMS: Weedy rice (Oryza sativa f. spontanea) is one of the most notorious weeds occurring in rice-planting areas worldwide. The objectives of this study are to determine the genetic diversity and differentiation of weedy rice populations from Liaoning Province in North-eastern China and to explore the possible origin of these weedy populations by comparing their genetic relationships with rice varieties (O. sativa) and wild rice (O. rufipogon) from different sources. METHODS: Simple sequence repeat (SSR) markers were used to estimate the genetic diversity of 30 weedy rice populations from Liaoning, each containing about 30 individuals, selected rice varieties and wild O. rufipogon. Genetic differentiation and the relationships of weedy rice populations were analysed using cluster analysis (UPGMA) and principle component analysis (PCA). KEY RESULTS: The overall genetic diversity of weedy rice populations from Liaoning was relatively high (H(e) = 0.313, I = 0.572), with about 35 % of the genetic variation found among regions. The Liaoning weedy rice populations were closely related to rice varieties from Liaoning and japonica varieties from other regions but distantly related to indica rice varieties and wild O. rufipogon. CONCLUSIONS: Weedy rice populations from Liaoning are considerably variable genetically and most probably originated from Liaoning rice varieties by mutation and intervarietal hybrids. Recent changes in farming practices and cultivation methods along with less weed management may have promoted the re-emergence and divergence of weedy rice in North-eastern China.     

Plastid genome characterisation in Brassica and Brassicaceae using a new set of nine SSRs

The objective of the present study was to identify favourable exotic Quantitative Trait Locus (QTL) alleles for the improvement of agronomic traits in the BC₂DH population S42 derived from a cross between the spring barley cultivar Scarlett and the wild barley accession ISR42-8 (Hordeum vulgare ssp. spontaneum). QTLs were detected as a marker main effect and/or a marker × environment interaction effect (M × E) in a three-factorial ANOVA. Using field data of up to eight environments and genotype data of 98 SSR loci, we detected 86 QTLs for nine agronomic traits. At 60 QTLs the marker main effect, at five QTLs the M × E interaction effect, and at 21 QTLs both the effects were significant. The majority of the M × E interaction effects were due to changes in magnitude and are, therefore, still valuable for marker assisted selection across environments. The exotic alleles improved performance in 31 (36.0%) of 86 QTLs detected for agronomic traits. The exotic alleles had favourable effects on all analysed quantitative traits. These favourable exotic alleles were detected, in particular on the short arm of chromosome 2H and the long arm of chromosome 4H. The exotic allele on 4HL, for example, improved yield by 7.1%. Furthermore, the presence of the exotic allele on 2HS increased the yield component traits ears per m² and thousand grain weight by 16.4% and 3.2%, respectively. The present study, hence, demonstrated that wild barley does harbour valuable alleles, which can enrich the genetic basis of cultivated barley and improve quantitative agronomic traits.     

Functional characterization of gynodioecy in Fragaria vesca ssp. bracteata (Rosaceae)

Background and Aims

Gynodioecy is a phylogenetically widespread and important sexual system where females coexist with hermaphrodites. Because dioecy can arise from gynodioecy, characterization of gynodioecy in close relatives of dioecious and sub-dioecious species can provide insight into this transition. Thus, we sought to determine whether Fragaria vesca ssp. bracteata, a close relative to F. chiloensis and F. virginiana, exhibits the functional and population genetic hallmarks of a gynodioecious species.

Methods

We compared reproductive allocation of females and hermaphrodites grown in the greenhouse and estimated genetic diversity (allelic diversity, heterozygosity) and inbreeding coefficients for field-collected adults of both sexes using simple sequence repeat (SSR) markers. We estimated mating system and early seed fitness from open-pollinated families of both sex morphs.

Key Results

Under greenhouse conditions, females and hermaphrodites allocated similarly to all reproductive traits except flower number, and, as a consequence, females produced 30 % fewer seeds per plant than hermaphrodites. Under natural conditions, hermaphrodites produce seeds by self-fertilization approx. 75 % of the time, and females produced outcrossed seeds with very little biparental inbreeding. Consistent with inbreeding depression, seeds from open-pollinated hermaphrodites were less likely to germinate than those from females, and family-level estimates of hermaphrodite selfing rates were negatively correlated with germination success and speed. Furthermore, estimates of inbreeding depression based on genetic markers and population genetic theory indicate that inbreeding depression in the field could be high.

Conclusions

The joint consideration of allocation and mating system suggests that compensation may be sufficient to maintain females given the current understanding of sex determination. Fragaria vesca ssp. bracteata exhibited similar sex morph-dependent patterns of mating system and genetic diversity, but less reproductive trait dimorphism, than its sub-dioecious and dioecious congeners.