Population structure,seasonal genotypic differentiation,and clonal diversity of weedy dandelions in three Boston area populations (Taraxacum sp.)

Weedy dandelions have a worldwide distribution and thrive in urban environments despite a lack of sexual reproduction throughout most of its range. North American dandelions, introduced from Eurasia, are believed to be primarily, if not exclusively, apomictic triploids. In some European populations, apomicts co‐occur with diploid sexual individuals and hybridizations can create genetically unique apomicts, which may subsequently disperse and establish new populations globally. Using six nuclear microsatellite markers and a cpDNA intergenic spacer, we investigate the impact of this unusual natural history on population structure and diversity in three urban Boston area dandelion populations. Our results show high levels of genetic diversity within populations, spatial population structure, and seasonal genotypic differentiation in flowering times. We find evidence that sexual reproduction and recombination, presumably in Europe, and extensive gene flow drive these patterns of diversity and create the appearance of panmixia despite the lack of evidence for local sexual reproduction.     

Hybridization of Bombina bombina and B. variegata (Anura, Discoglossidae) at a sharp ecotone in western Ukraine: comparisons across transects and over time

Abstract Bombina bombina and B. variegata are two anciently diverged toad taxa that have adapted to different breeding habitats yet hybridize freely in zones of overlap where their parapatric distributions meet. Here, we report on a joint genetic and ecological analysis of a hybrid zone in the vicinity of Stryi in western Ukraine. We used five unlinked allozyme loci, two nuclear single nucleotide polymorphisms and a mitochondrial DNA haplotype as genetic markers. Parallel allele frequency clines with a sharp central step occur across a sharp ecotone, where transitions in aquatic habitat, elevation, and terrestrial vegetation coincide. The width of the hybrid zone, estimated as the inverse of the maximum gradient in allele frequency, is 2.3 km. This is the smallest of four estimates derived from different clinal transects across Europe. We argue that the narrow cline near Stryi is mainly due to a combination of habitat distribution and habitat preference. Adult toads show a preference for either ponds ( B. bombina ) or puddles ( B. variegata ), which is known to affect the distribution of genotypes within the hybrid zones. At Stryi, it should cause a reduction of the dispersal rate across the ecotone and thus narrow the cline. A detailed comparison of all five intensively studied Bombina transects lends support to the hypothesis that habitat distribution plus habitat preference can jointly affect the structure of hybrid zones and, ultimately, the resulting barriers to gene flow between differentiated gene pools. This study also represents a resampling of an area that was last studied more than 70 years ago. Our allele-frequency clines largely coincide with those that were described then on the basis of morphological variation. However, we found asymmetrical introgression of B. variegata genes into B. bombina territory along the bank of a river.     

Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases

Sugarcane (Saccharum spp.) is a clonally propagated outcrossing polyploid crop of great importance in tropical agriculture. Up to now, all sugarcane genetic maps had been developed using either full-sib progenies derived from interspecific crosses or from selfing, both approaches not directly adopted in conventional breeding. We have developed a single integrated genetic map using a population derived from a cross between two pre-commercial cultivars (‘SP80-180’ × ‘SP80-4966’) using a novel approach based on the simultaneous maximum-likelihood estimation of linkage and linkage phases method specially designed for outcrossing species. From a total of 1,118 single-dose markers (RFLP, SSR and AFLP) identified, 39% derived from a testcross configuration between the parents segregating in a 1:1 fashion, while 61% segregated 3:1, representing heterozygous markers in both parents with the same genotypes. The markers segregating 3:1 were used to establish linkage between the testcross markers. The final map comprised of 357 linked markers, including 57 RFLPs, 64 SSRs and 236 AFLPs that were assigned to 131 co-segregation groups, considering a LOD score of 5, and a recombination fraction of 37.5 cM with map distances estimated by Kosambi function. The co-segregation groups represented a total map length of 2,602.4 cM, with a marker density of 7.3 cM. When the same data were analyzed using JoinMap software, only 217 linked markers were assigned to 98 co-segregation groups, spanning 1,340 cM, with a marker density of 6.2 cM. The maximum-likelihood approach reduced the number of unlinked markers to 761 (68.0%), compared to 901 (80.5%) using JoinMap. All the co-segregation groups obtained using JoinMap were present in the map constructed based on the maximum-likelihood method. Differences on the marker order within the co-segregation groups were observed between the two maps. Based on RFLP and SSR markers, 42 of the 131 co-segregation groups were assembled into 12 putative homology groups. Overall, the simultaneous maximum-likelihood estimation of linkage and linkage phases was more efficient than the method used by JoinMap to generate an integrated genetic map of sugarcane. E.A. Kido, A.N. Meza and H.M.B. Souza contributed equally to this work.     

Phylogeography of Haplotypes of Five Microsatellites Located in a Low-recombination Region of the X Chromosome: Studies Worldwide and in Brazilian Populations

We studied five microsatellites (DXS995, DXS8076, DXS8114, DXS1002 and DXS1050) located in a region of very low recombination rate in the long arm of the human X chromosome (Xq13.3–Xq21.3). No recombination was seen in 291 meioses in CEPH families. To test whether haplotypes composed of the five microsatellites could differentiate among distinct human continental populations, we studied an international panel containing 72 males from Africa, Europe, Asia and the America. Haplotypic diversity was very high within these groups and no haplotypes were shared among them. This led to the hope that we might be able to identify continent-specific lineages. However, in a median joining network there was no clear discrimination of the different continental groups. We then tested whether we could identify X chromosomal lineages from different continental origins in Brazilians. We typed 180 white Brazilians from four different geographical regions and examined their proportions of haplotype sharing with Africans, Asians, Europeans and Amerindians. No phylogeographical patterns emerged from the data. Moreover, there were several instances of the same haplotype being shared by many (and in one instance all) groups, suggesting that recombination might be occurring. We thus studied pairwise the level of linkage disequilibrium (LD) between the microsatellites. No detectable linkage disequilibrium between the most external loci DXS995 and DXS1050 was observed. Thus, even though recombination may be absent on short time spans, as seen in the CEPH pedigrees, on a long term basis it occurs often enough to dissipate all linkage disequilibrium. On the other hand, we observed very strong linkage disequilibrium between the pairs DXS995/DXS8076 and DXS1002/DXS8114, raising the possibility of resequencing the segment between them to identify single nucleotide polymorphisms (SNPs) in their intervals. The combination of X-linked microsatellites and SNPs in strong linkage disequilibrium might provide a powerful new tool to investigate human demographic history.     

Molecular structure and linkage isomerization of isothiocyanato(3-thiapentane-1,5-dithiolato)oxorhenium(V) complex

The properties of isothiocyanato(3-thiapentane-1,5-dithiolato)oxorhenium(V) [ReO(SSS)NCS, (1a), (3+1) type], where isothiocyanato occupies the fifth position, have been studied. Two linkage isomers, i.e., ReO(SSS)NCS (1a) and ReO(SSS)SCN (1b), were found to be formed during syntheses. The sufficient quantities of 1a were isolated in the solid state, and characterized by X-ray crystallography and IR spectroscopy. From ¹H and ¹⁵N NMR measurements, it was found that 1a is in equilibrium with 1b in liquid state. In the solvents with low dielectric constant such as CH₂Cl₂, only 1a isomer was detected, while in the solvents with high such as CH₃CN, both 1a and 1b isomers were observed. We have obtained the equilibrium constant (K_iso) for the linkage isomerization reaction in CD₃CN by measuring ¹⁵N NMR spectra at various temperatures. The values of K_iso at 25 °C, the standard enthalpy (ΔH^°), and the standard entropy (ΔS^°) for the isomerization equilibrium were evaluated as 0.409, 14.4 kJ mol⁻¹, and 40.9 J K⁻¹ mol⁻¹, respectively.     

An association mapping approach to identify flowering time genes in natural populations of Lolium perenne (L.)

We describe an association mapping approach using natural populations of perennial ryegrass (Lolium perenne L.) to identify molecular markers associated with heading date, an important trait affecting seasonal production, tillering, digestibility and grassland management regimes. Twenty-three natural populations originating from throughout Europe, with heading date phenotypes ranging from very early to very late, as well as three synthetic populations (varieties) were used for molecular marker genotyping using AFLP. In total, 589 polymorphic markers were identified. Hierarchical clustering, principal coordinate and other statistical analyses identified four outlying populations forming a clearly distinct sub-group. Removal of those four populations from the subsequent analysis reduced population sub-structure twofold. However, this made relatively little difference to the result of the association analysis. Linear regression identified three markers whose frequency of occurrence correlated with the heading date phenotype. Moreover, these markers were shown to be closely linked to each other within a major QTL on Chromosome 7, explaining 70% of the total variation in heading date. Pairwise linkage disequilibrium among them was also significant. These results suggest that association mapping approaches may be feasible in L. perenne, and that the use of natural populations could provide a useful source of genetic variation in traits of importance in crop improvement.     

中国人群中STK15基因内两种非同义SNP的连锁不平衡和单体型分析

STK15基因编码一种丝氨酸苏氨酸蛋白激酶,哺乳动物细胞中其过量表达将导致中心体扩增、染色体不稳定和细胞癌变。STK15基因外显子3中有3种非同义单核苷酸多态(SNP),即：91A→T(131F)、169G→A(V571)和311C→T(S104L)。新近研究发现,91A→T与人类肿瘤遗传易感性相关。应用PCR-RFLP技术确定了91A→T(131F)和169G→A(V571)两种SNP在中国人群中的基因型和单体型。采用巢式PCR方法扩增了193例正常个体的DNA样品,通过错配正向巢式内引物引入EcoRⅠ酶切位点。巢式PCR扩增产物用限制性内切酶EcoRⅠ和ACCⅡ双酶切消化,其中EcoRⅠ能酶切91A,AccⅡ能切开169G,用聚丙烯酰胺凝胶电泳银染法鉴定双酶切结果,发现了4种可能的单体型中的3种,其单体型频率分别为：p(91A-169G)=68．65％,p(91T-169A)=10．88％,p(91T-169G)=20．47％,p(91A-169A)=0％;它们组成的6种基因型及频率分别为：91A-169G／91A-169G(46．11％),91A-169G／91T-169A(14．51％),91A-169G／91T-169G(30．57％)．91T-169G／91T-169G(3．11％),91T-169G／91T-169A(4．15％),91T-169A／91T-169A(1．55％)。等位基因及单体型数据分析结果表明,91A→T(131F)和169G→A(V571)之间存在连锁不平衡。     

基于“HY-LM”的生态廊道与生态节点综合识别研究

传统的生态网络或生态安全格局构建研究中,多基于最小累积阻力模型（MCR）提取最小费用路径作为生态廊道,并人工判别生态节点,这种方式缺少对生态过程中能量流、信息流等交换过程的考虑,导致生态网络在结构、功能上存在一定的缺失。以福建省上杭县为例,以上杭县森林公园、湿地保护区、自然保护区等为主要生态源地,从陆生动物迁移特征出发选取土地覆被类型、距道路距离、地形起伏度、坡度、距水域距离、NDVI植被指数等因素为阻力因子,利用熵权法获得权重加权叠加生成综合阻力面,运用水文分析原理Hydrology （HY）和Linkage Mapper工具箱（LM）中电路理论等方法综合识别生态廊道和生态节点,运用重力模型对生态廊道重要性进行评价并对生态廊道和生态节点划分等级。研究结果如下：（1）基于LM方法共提取187条生态廊道,生态夹点52个,生态障碍点55个,基于HY方法共提取生态廊道240条,生态节点133个;（2） LM和HY提取的生态廊道和生态节点进行叠加,共提取生态廊道197条,辐射道30条,生态节点283个;（3）运用重力模型提取关键生态廊道103条（含辐射道30条）,一般生态廊道124条,同时判别关键生态节点97个,一般生态节点186个,关键生态廊道和关键生态节点主要集中在高阻力和较高阻力值集中的区域,关键生态节点多分布在生态源地周围;（4）对关键生态廊道、关键生态节点缓冲区所在区域土地覆被类型构成进行分析,森林、耕地和草地等土地覆被类型占比具有绝对优势,并从生态连通性和生境质量角度针对各土地覆被类型提出了优化及生态建设策略。研究结果可为区域生态网络安全格局构建、国土空间规划与生态系统修复等研究提供参考,同时也为生物多样性保护与生态文明建设提供科学依据。     

APOE ɛ4 allele and TOMM40‐APOC1 variants jointly contribute to survival to older ages

Age‐related diseases characteristic of post‐reproductive life, aging, and life span are the examples of polygenic non‐Mendelian traits with intricate genetic architectures. Polygenicity of these traits implies that multiple variants can impact their risks independently or jointly as combinations of specific variants. Here, we examined chances to live to older ages, 85 years and older, for carriers of compound genotypes comprised of combinations of genotypes of rs429358 (APOE ɛ4 encoding polymorphism), rs2075650 (TOMM40), and rs12721046 (APOC1) polymorphisms using data from four human studies. The choice of these polymorphisms was motivated by our prior results showing that the ɛ4 carriers having minor alleles of the other two polymorphisms were at exceptionally high risk of Alzheimer''s disease (AD), compared with non‐carriers of the minor alleles. Consistent with our prior findings for AD, we show here that the adverse effect of the ɛ4 allele on survival to older ages is significantly higher in carriers of minor alleles of rs2075650 and/or rs12721046 polymorphisms compared with their non‐carriers. The exclusion of AD cases made this effect stronger. Our results provide compelling evidence that AD does not mediate the associations of the same compound genotypes with chances to survive until older ages, indicating the existence of genetically heterogeneous mechanisms. The survival chances can be mainly associated with lipid‐ and immunity‐related mechanisms, whereas the AD risk, can be driven by the AD‐biomarker‐related mechanism, among others. Targeting heterogeneous polygenic profiles of individuals at high risks of complex traits is promising for the translation of genetic discoveries to health care.     

Tetra-primer ARMS-PCR identifies the novel genetic variations of bovine HNF-4α gene associating with growth traits

Hepatocyte nuclear factor-4α (HNF-4α), a member of the hepatocyte nuclear factor family, plays an important role in regulating the expression of genes involved in the development, differentiation and normal function of liver and pancreatic β cells, as well as the maintenance of glucose homeostasis. Tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) is a new method offering fast detection and extreme simplicity at a negligible cost for SNP genotyping. In this paper, we characterize the polymorphisms of the bovine HNF-4α gene in three Chinese indigenous cattle breeds (n = 660). Six novel SNPs were identified including 1 mutation in the coding region and others in introns. The statistical analyses indicated that 4 SNPs (g.T53729C, g.A53861G, g.A65188C and g.T65444C) affected growth traits markedly (P < 0.05) in Qinchuan cattle (2 years after birth). Besides, haplotypes involving these 4 SNP sites in the bovine HNF-4α gene were identified and their effects on growth traits were also analyzed. The results showed that haplotypes 2, 7, 9 and 11 were predominant and accounted for 73.2%, 59.6%, and 67.1% in Qinchuan, Nanyang and Jiaxian cattle breeds, respectively. Hap9 (TAAT) was extremely predominant in all test populations, which suggested that individuals with Hap9 were more adapted to the environment. Furthermore, 4 combined haplotypes were constructed to guarantee the reliability of analysis results in Qinchuan cattle. There were also significant differences in body length (P < 0.05). These findings will benefit for the application of DNA marker related to the growth traits on marker-assisted selection (MAS), and improve the performance of beef cattle.