Novel microsatellite markers for Begonia maxwelliana and transferability to 23 Begonia species of Peninsular Malaysia

Begonias are hyper-diverse and important horticultural plants. Six polymorphic microsatellite markers were developed from CT- and GT-enriched libraries of Begonia maxwelliana. The number of alleles per locus ranged from 2 to 12 and the observed heterozygosity ranged from 0.036 to 0.813. Null alleles were detected in one locus (Bma161) after Bonferroni correction. All the six markers were amplifiable in 23 selected Begonia species with the success rates of 17–100%. On average, species of the same section as B. maxwelliana (i.e. sect. Platycentrum) yielded higher transferability (91%). These markers will be useful for population genetic studies of the genus Begonia.     

近缘种扩增法对黑叶猴微卫星位点的筛选及特征分析(英文)

微卫星位点近缘种筛选法使得在探讨各种灵长类种群遗传结构和生殖策略上更加便捷。我们利用138条人类微卫星引物在黑叶猴中进行筛选,得到了23个具有多态性位点。在28个检测个体中,每个位点的等位基因数为3到9个,期望杂合度为0.62,观测杂合度为0.50,其中有7个位点偏离Hardy-Weinberg平衡,9个位点存在无效等位基因现象。但是各位点之间均未检测到连锁不平衡现象。这些位点将在黑叶猴种群遗传结构的研究中发挥重要作用。     

母女猫叫综合征患者的遗传分析

猫叫综合征患者不仅可以活到成年, 而且可有生育能力,可将缺失染色体直接传给其子女使其患同样的疾病。早产是该综合征重要临床表现之一。     

Reverse ascertainment bias in microsatellite allelic diversity in owls (Aves, Strigiformes)

A rich source of markers may be overlooked by screening for polymorphism in the source species only. We screened 129 microsatellite loci isolated from the powerful owl (Ninox strenua) against two closely related species; Ninox connivens and Ninox novaeseelandiae. From the screening effort 20 polymorphic markers were isolated, including six loci which were originally discarded as they were monomorphic in the source species. Further cross-species amplification of all 20 loci across species from two families, Strigidae and Tytonidae, revealed unusually high levels of polymorphism within closely related species, and limited success within phylogenetically distant species. Routine screening of multiple species during the marker development phase can yield a wider range of polymorphic markers which can subsequently enhance cross-species amplification attempts.     

Individual assignment tests proved genetic boundaries in a species complex of Pacific abalone (genus <Emphasis Type="Italic">Haliotis</Emphasis>)

We conducted this study to find genetic evidence to distinguish the members of Pacific abalone species complex (Haliotis discus hannai, H. discus discus, H. madaka, and H. gigantea) based on microsatellite DNA markers, illustrating the potential of microsatellites for species-assignment. First, we addressed the transferability of H. discus hannai microsatellites to the three other members of Pacific abalone and five additional species (H. diversicolor aquatilis, H. midae, H. corrugata, H. fulgens, and H. rubra). Second, using the microsatellites we applied two types of individual assignment testing (the distance-based assignment and Bayesian model-based clustering) to individuals from the Pacific abalone species. A total of 24 microsatellites were subjected to PCR trials for nine Haliotis species, and the cross-species amplification performance of these markers turned out to drop precipitously even for less divergent congeners. Within the Pacific abalone species complex, four of the 24 markers were not transferable to H. gigantea, suggesting a solid genetic boundary between H. gigantea and H. discus hannai, H. discus discus, and H. madaka. Among the three latter abalones, both assignment tests achieved approximately 90% or more success rate of assignment. The feasibility of the microsatellite markers to classify species sheds light on the genetic management of the Pacific abalone species complex. Electronic Supplementary Material  Supplementary material is available in the online version of this article at and is accessible for authorized users.

SSR和STS标记在花生栽培品种鉴定中的应用研究

采用10份花生品种材料,对通过数据库查询设计合成的SSR引物和其他作者发表的SSR引物及STS引物进行了评估,并基于品种间简单匹配系数做了聚类分析。获得62个能产生多态性片段的SSR和STS引物对,总共获得427条带,其中291条（68．1％）为多态性带。平均每对引物产生6．88条带,4．69条为多态性带;多态性条带比率为16.7％～100％,PIC值为0．254～0．952,平均为0．760。9对SSR／STS引物,即Lec-1、Ah4-26、Ah4-4、SsS14、SHPAL-1、PG71、PG43、PM36、PG22,对所采用的10份花生品种区分率达到10096。说明SSR和STS标记应用于花生品种鉴定有效。     

Development of an STS map of an interspecific progeny of Malus

Simple sequence repeat (SSR) markers developed from Malus, as well as Prunus, Pyrus and Sorbus, and some other sequence-tagged site (STS) loci were analysed in an interspecific F₁ apple progeny from the cross ‘Fiesta’ × ‘Totem’ that segregated for several agronomic characters. A linkage map was constructed using 259 STS loci (247 SSRs, four SCARs and eight known-function genes) and five genes for agronomic traits—scab resistance (Vf), mildew resistance (Pl-2), columnar growth habit (Co), red tissues (Rt) and green flesh background colour (Gfc). Ninety SSR loci and three genes (ETR1, Rt and Gfc) were mapped for the first time in apple. The transferability of markers from other Maloideae to Malus was found to be around 44%. The loci are spread across 17 linkage groups, corresponding to the basic chromosome number of Malus and cover 1,208 cM, approximately 85% of the estimated length of the apple genome. Interestingly, we have extended the top of LG15 with eight markers covering 25 cM. The average map density is 4.7 cM per marker; however, marker density varies greatly between linkage groups, from 2.5 in LG14 to 8.9 in LG7, with some areas of the genome still in need of further STS markers for saturation. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. An erratum to this article can be found at     

鲤科鱼蓝黑鲮微卫星位点的种间扩增(英文)

本研究使用105对微卫星引物对7种鲤科鱼类进行跨越种间PCR扩增,共得到14个多态性微卫星位点.其中9个扩增效果较好的位点用于分析来自帕吉勒提河(Bhagirathi, n=20)和戈达瓦里河(Godavari, n=25)的蓝黑鲮(Labeo calbasu)样品的遗传多样性.结果显示,前者在每个位点的平均等位基因数为7.33,而后者为8 1,期望杂合度介于0.795(Bhagirathi)和0.801(Godavari)之间;4个位点MFW11* (Godavari)、R1*(Godavari)、R3* (Bhagirathi) 和 Lr38*(Bhagirathi和Godavari)都表现出明显的杂合子缺失和哈迪温伯格平衡偏离;而任意两位点间都未观测到连锁不平衡现象;位点R3*极可能存在无效等位基因.上述结果表明这些多态性微卫星位点作为共显性标记在蓝黑鲮群体遗传学研究中有着较好的应用前景.     

用gFM31探针进行谷子品种的指纹分析

用高度多态性探针ｇＦＭ３１对５９个谷子（ＳｅｔａｒｉａｉｔａｒｌｉｃａＢｅａｕｖ．）品种（包括地方品种、育成品种及品系）进行ＤＮＡ指纹分析,共鉴别出５８种类型,而黑谷和黑粒１５１６给出完全相同的带型,二者有可能是同一材料。通过对ｇＦＭ３１ＤＮＡ序列分析,未发现其中有小卫星ＤＮＡ和微卫星ＤＮＡ序列。该探针虽在谷子品种中显示很高的多态性,但与禾谷类的其他物种的ＤＮＡ杂交信号微弱,表现出较强的谷子基因组特异性。     

利用SLAF-seq技术开发带鱼(Trichiurus japonicus)微卫星标记以及跨物种扩增检测

带鱼(Trichiurus japonicus)是广泛分布于东亚大陆架海域的暖温性近底层鱼类,长期位居我国单鱼种渔获量第一位。自上世纪70年代以来,持续过度捕捞和海洋环境变化导致中国近海带鱼资源基础和遗传多样性受到严重影响,但有关带鱼种群的微卫星DNA标记研究却较为缺乏,不利于该物种遗传资源评估和保护。为此,本研究采用基于高通量测序平台的SLAF-seq技术,从带鱼的195 308个SLAF标签中识别出25 704个二至六碱基重复微卫星位点。经过引物扩增验证,最终筛选出36个具有多态性的微卫星标记。各位点等位基因数4～35,均值14.47。观测杂合度0.214～1.000,期望杂合度0.456～0.979,均值分别为0.620和0.803。所有位点的多态信息含量值均大于0.25。经Bonferroni校正,21个位点符合哈迪-温伯格平衡,且各位点间不存在连锁不平衡。这21个多态性微卫星标记可为带鱼的种群遗传资源研究提供新的有效分子标记和技术支撑。Bottleneck分析结果表明,宁波近海带鱼群体未检测到近期的遗传瓶颈效应,这可能与目前东海区带鱼野生群体数量还比较庞大、遗传变异仍然较为丰富有关。跨物种扩增结果显示,分别有12、16、4和3个带鱼微卫星标记在带鱼属(Trichiurus)、沙带鱼(Lepturacanthus savala)、窄颅带鱼(Tentoriceps cristatus)及小带鱼(Eupleurogrammus muticus)中具有较好的通用性,这些微卫星标记为今后带鱼科相应属、种的系统进化关系研究提供新的分析手段和契机。     

Cross transferability of SSR markers to endangered Cedrela species that grow in Argentinean subtropical forests,as a valuable tool for population genetic studies

Species of Cedrela with a high economic value from Northwest and Northeastern Argentina are severely exploited. This work evaluates whether 51 nuclear SSRs, developed to study phylogenetically close species in the Meliaceae family (Cedrela odorata, Cedrela fissilis, Swietenia humilis and Swietenia macrophylla), can be used to study C. fissilis, Cedrela balansae, Cedrela saltensis and Cedrela angustifolia. A 62.8% of the total of 194 SSRs/species combinations showed a successful, homologous and cross-species amplification. As expected, a great success in SSRs transferability among Cedrela species was observed. Twenty-one screened SSRs showed a successful amplification pattern in all target species and many of them were polymorphic (9, 13, 13 and 7 SSRs for C. fissilis, C. balansae, C. saltensis and C. angustifolia, respectively). The high number of evaluated SSRs from the Cedrela genus and Meliaceae family, allowed us to obtain a suitable set of validated markers that are highly variable and easily scored, and also identify those which were less sturdy. We were able to retain a useful set of markers for three of the target species, but not for C. angustifolia. This could be due to its greater phylogenetic and morphological distances to the other three species. The lack of SSRs developed for our target species, transforms the transferred SSRs reported here in a valuable tool to monitor the genetic consequences of forest overexploitation on Cedrela species.     

Isolation and characterization of polymorphic microsatellite loci from a dinucleotide-enriched genomic library of starry flounder (Platichthys stellatus) and cross-species amplification

Starry flounder (Platichthys stellatus) is a rare fish species in China. Here, we reported 12 polymorphic microsatellite loci isolated from a dinucleotide-enriched genomic library of starry flounder (P. stellatus). The number of alleles, observed and expected heterozygosity per locus in 30 individuals ranged from two to six, from 0.2500 to 1.0000 and from 0.4512 to 0.7667, respectively. One locus significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction and no significant linkage disequilibrium between pairs of loci was found. Cross-species amplification of these microsatellite loci in additional three fish species was performed. These polymorphic microsatellite loci would be useful for investigating genetic population structure and construction of genetic linkage map in P. stellatus. Guidong Miao and Changwei Shao have contributed equally.     

Development of microsatellite loci for Pelophylax plancyi and cross-amplification in other ranid species

Thirteen polymorphic microsatellite loci were obtained from the gold-striped pond frog, Pelophylax plancyi. The number of alleles per locus ranged from 5 to 13 with an average of 8.38. The observed and expected heterozygosities (H _O and H _E) ranged from 0.533 to 0.890 and from 0.620 to 0.897, with averages of 0.686 and 0.751, respectively. In order to assess interspecific amplification, all primer pairs were tested with the same PCR conditions on three other Pelophylax species: Pelophylax hubeiensis, Pelophylax fukienensis, Pelophylax nigromaculata and two species from the genus Hylarana and Hoplobatrachus, respectively. All of these loci can be amplified successfully in the Pelophylax species, with eight loci amplified in all species tested.     

Development of microsatellite markers for the endangered grassland perennial herb Vincetoxicum atratum (Apocynaceae–Asclepiadoideae)

Eight microsatellite markers were developed for the endangered grassland perennial herb Vincetoxicum atratum. The number of alleles ranged from 4 to 14, and the expected heterozygosities were from 0.575 to 0.933 in a population of V. atratum. Five of the eight loci did not significantly deviated from the Hardy–Weinberg equilibrium. All eight loci were tested for cross-species amplification in five other species of Vincetoxicum in Japan. These microsatellite loci will be useful for conservation genetics of V. atratum and other species of Vincetoxicum.     

长江水系草鱼遗传多样性的微卫星DNA分析

利用已发表的鲤微卫星引物在草鱼中进行PCR扩增,结果有5对引物(6个座位)能成功扩增并且有较高多态性,等位基因数在3-7个之间。这些异种扩增的草鱼微卫星符合孟德尔遗传规律。测序证明草鱼中的微卫星核心重复序列部分与鲤中的原始核心序列相似,也有一些变化。随后用这6个多态微卫星座位研究了来自长江水系的四个草鱼群体的遗传结构,结果显示每个群体的平均等位基因数在38与48之间,平均观测杂合度(Ho)在04000与05741之间,平均期望杂合度(HE)在04773与06489之间,有多个座位在不同的群体中偏离哈代-温伯格平衡。遗传距离分析表明四川群体与洞庭湖群体遗传距离最远,而嘉鱼群体与鄱阳湖群体遗传距离较近。分子变异分析(AMOVA)表明,群体内遗传变异与群体间遗传变异分别占总遗传变异的9560%与440%,固定系数(FST)为0044,这表明长江水系草鱼目前的群体分化很微弱。     

基于SSR标记的越橘亲缘关系分析及品种鉴定

利用SSR标记对22个越橘栽培品种进行遗传差异及亲缘关系分析,并建立一套稳定的越橘品种鉴定体系,以期为越橘种质资源评价、鉴定、管理及越橘新品种培育奠定基础。本试验优化了一套越橘SSR-PCR反应体系,筛选出15个条带清晰、重复性好、多态性高的SSR标记,对22个越橘栽培品种进行亲缘关系分析,聚类结果与各品种的遗传背景以及表型呈现高度的一致性。从以上15个SSR标记中筛选出可用于越橘品种鉴定的SSR核心引物NA961和NA1040,核心引物组合能够完全区分22个越橘品种。用核心引物制作了参照分子量标记,构建了22个越橘品种的指纹图谱,建立了一套完整的越橘品种鉴定体系。实践验证SSR标记用于越橘品种鉴别的方法可行、结果可靠。     

Characterization of novel microsatellite loci in rare minnow (<Emphasis Type="Italic">Gobiocypris rarus</Emphasis>) and amplification in closely related species in Gobioninae

Rare minnow (Gobiocypris rarus) is an endangered small fish endemic to upper reach of the Yangtze River. From a (GT)n enriched genomic library, 32 microsatellites were isolated and characterized. Nineteen of these loci were polymorphic in a test population with alleles ranging from 2–7, and observed and expected heterozygosities from zero to 0.8438, and 0.2679 to 0.8264, respectively. In the cross-species amplifications, 13 out of 19 polymorphic loci were found to be also polymorphic in at least one of the 7 closely related species of the subfamily Gobioninae. These polymorphic microsatellite loci should provide sufficient level of genetic diversity to evaluate the fine-scale population structure in rare minnow and its closely related species for the conservation purpose.