QTL Mapping for Frond Length and Width in Laminaria japonica Aresch (Laminarales, Phaeophyta) Using AFLP and SSR Markers

In Laminaria japonica Aresch breeding practice, two quantitative traits, frond length (FL) and frond width (FW), are the most important phenotypic selection index. In order to increase the breeding efficiency by integrating phenotypic selection and marker-assisted selection, the first set of QTL controlling the two traits were determined in F-2 family using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. Two prominent L. japonicas inbred lines, one with "broad and thin blade" characteristics and another with "long and narrow blade" characteristics, were applied in the hybridization to yield the F-2 mapping population with 92 individuals. A total of 287 AFLP markers and 11 SSR markers were used to construct a L. japonica genetic map. The yielded map was consisted of 28 linkage groups (LG) named LG1 to LG28, spanning 1,811.1 cM with an average interval of 6.7 cM and covering the 82.8% of the estimated genome 2,186.7 cM. While three genome-wide significant QTL were detected on LG1 (two QTL) and LG4 for "FL," explaining in total 42.36% of the phenotypic variance, two QTL were identified on LG3 and LG5 for the trait "FW," accounting for the total of 36.39% of the phenotypic variance. The gene action of these QTL was additive and partially dominant. The yielded linkage map and the detected QTL can provide a tool for further genetic analysis of two traits and be potential for maker-assisted selection in L. japonica breeding.

Extreme weathering/erosion during the Miocene Climatic Optimum: Evidence from sediment record in the South China Sea

Investigating the interplay between continental weathering and erosion, climate, and atmospheric CO2 concentrations is significant in understanding the mechanisms that force the Cenozoic global cooling and predicting the future climatic and environmental response to increasing temperature and CO2 levels. The Miocene represents an ideal test case as it encompasses two distinct extreme climate periods, the Miocene Climatic Optimum (MCO) with the warmest time since 35 Ma in Earth's history and the transition to the Late Cenozoic icehouse mode with the establishment of the east Antarctic ice sheet. However the precise role of continental weathering during this period of major climate change is poorly understood. Here we show changes in the rates of Miocene continental chemical weathering and physical erosion, which we tracked using the chemical index of alteration ( CIA) and mass accumulation rate ( MAR) respectively from Ocean Drilling Program (ODP) Site 1146 and 1148 in the South China Sea. We found significantly increased CIA values and terrigenous MARs during the MCO (ca. 17-15 Ma) compared to earlier and later periods suggests extreme continental weathering and erosion at that time. Similar high rates were revealed in the early-middle Miocene of Asia, the European Alps, and offshore Angola. This suggests that rapid sedimentation during the MCO was a global erosion event triggered by climate rather than regional tectonic activity. The close coherence of our records with high temperature, strong precipitation, increased burial of organic carbon and elevated atmospheric CO2 concentration during the MCO argues for long-term, close coupling between continental silicate weathering, erosion, climate and atmospheric CO2 during the Miocene. Citation: Wan, S., W. M. Kurschner, P. D. Clift, A. Li, and T. Li (2009), Extreme weathering/ erosion during the Miocene Climatic Optimum: Evidence from sediment record in the South China Sea, Geophys. Res. Lett., 36, L19706, doi: 10.1029/2009GL040279.

海湾扇贝遗传图谱构建及壳色基因、生长相关QTL的定位研究

本研究利用AFLP和微卫星标记，以海湾扇贝杂交F1为作图群体，构建了海湾扇贝的遗传连锁图谱，并对壳色决定基因和与生长性状相关的QTL进行了定位。 共用55对AFLP引物组合对亲本和88个子代个体进行扩增，共得到了2424个位点，多态性位点为392个，占所有标记的16.17％。其中，母本标记121个，父本标记196个，共有标记75个。经卡方检验，共有331个标记（84.4%）符合孟德尔分离比，61个标记（15.6％）出现偏分离现象。偏分离标记中，36个（59％）为纯合子缺失。从35对微卫星引物中筛选出了10对多态性引物，得到了5个母本标记和6个父本标记。另外，将表现为质量性状的壳色标记作为形态标记一同进行连锁图谱构建。 分别利用母本和父本标记构建了海湾扇贝雌性和雄性连锁图谱。其中，共有包括109个AFLP标记、5个微卫星标记和1个壳色标记组成了雌性图谱的框架图，分布于16个连锁群。图谱总长度为338.8cM，平均间隔为5.29cM，图谱覆盖率为65.82％。雄性连锁图谱框架图共定位了186个标记，包括181个AFLP标记、5个微卫星标记，壳色标记未实现定位。图谱包括17个连锁群，总长度为780.3cM，平均间隔为6.56cM，图谱覆盖率为78.11％。通过SSR12位点的定位结果，可以将雌性图谱第7连锁群与雄性图谱17连锁群对应起来。 壳色标记定位在了雌性图谱第九连锁群上，说明橙色基因位点为杂合。我们将壳色基因命名为Orange1，两个标记——F1f335和D8f420与这一基因之间图距为0。在家系和群体中初步验证，这两个标记与壳色基因紧密或完全连锁。 共定位了16个与生长相关的QTL，它们分布于雌性图谱的2、3、5连锁群和雄性图谱的4、5、6、7、8连锁群上。每个QTL均发现了与其图距非常接近的分子标记（0.01-2.51％）。其中壳长、壳高、壳宽三个长度指标QTL成簇分布或部分重叠，可一同作为选择性指标，壳重和全湿重QTL位点也比较相近。只有软体部重位点单独分布，可能具有相对独立的遗传基础。

凡纳滨对虾分子标记筛选、连锁图谱构建和QTL定位

利用AFLP和微卫星标记，以凡纳滨对虾F1全同胞家系为作图群体，构建了凡纳滨对虾的雌性和雄性遗传连锁图谱并对生长相关性状体长和体重进行了QTL分析。利用经过筛选的108对AFLP引物组合，对亲本和94个子代个体进行了分离分析。共得到2041个多态AFLP标记（1:1分离）。平均每个引物组合产生20个多态片段。有826个AFLP标记偏离孟德尔遗传（40.5%, P<0.05）。所筛选的100个微卫星标记中有30个在家系中有作图信息，分别有24个和20个位点可以用于母本和父本的作图。对父母本β-1，3-葡聚糖结合蛋白(BGBP)，脂多糖和葡聚糖结合蛋白(LGBP)和蜕皮抑制激素（MIH）等基因片段进行序列分析得到一些可用于构建连锁图谱的SNP标记。 对所有的分离标记进行了连锁分析，分别绘制了凡纳滨对虾的雌性和雄性连锁图谱。雌性连锁图谱的框架图有319个遗传标记组成，分布于45个连锁群，其中AFLP标记300个，微卫星位点18个，性别标记一个，连锁群长度从29.5cM到260.0cM, 每个连锁群含4－16个标记。图谱长度为4134.4 cM, 各连锁群平均图距在7.6到25.9 cM之间，总平均图距为15.1 cM。有267个标记（含14个微卫星）整合到雄性框架图上。 雄性框架图也含45个连锁群，长度从14.2cM到161.1cM, 图谱长度为3220.9 cM, 各连锁群平均图距在4.1到25.5 cM之间，总平均图距为14.5 cM。 作图群体所有个体的性别均作为标记整合到雌雄分离信息中，在94个F1个体中，54个为雌虾，40个是雄虾。在雌性图谱第29连连锁群上，性别与三个微卫星标记紧密连锁（v1f148, v145f120, v95f166）, 图距分别为6.6, 8.6 和8.6cM, 相应LOD值分别为17.8 14.3 和 16.4。 与雌性图相对应的是，雄性图谱未发现任何与性别连锁的标记。推测凡纳滨对虾的性别决定机制可能是ZW型，其中雌性为异配性别。 体长和体重均显示出连续变异的特点，显示这些与生长相关的性状都是典型的数量性状或多基因遗传。体重和体长符合正态分布且两性状之间存在着显著的相关性（P<0.001），Pearson 相关系数为0.95。在凡纳滨对虾雌性图谱和雄性图谱上，共定位了6个与体长和体重等生长性状相关的QTL，可解释的表型变异从15.1％到21.3％。共检测到3个与体长相关的QTL，包括两个正向效应的QTL和一个负向的QTL，分别定位到雌性的第6连锁群和雄性的第4和11 连锁群上。体重也检测到3个QTL，其中一个QTL加性效应是正向的，分别位于雌性的第6和7连锁群及雄性的第11连锁群上。QTL主要集中在雌性图谱的Fc6和Fc7及雄性图的Mc4和Mc11上。体长和体重的QTL定位结果中各有两个是十分相似的，其相邻的标记位点完全一样，只是相应的LOD值略有差异，还各存在两性状特异的一个QTL。大多QTL与相邻标记之间的距离只有0.1cM(仅Wfc7的距离较大)，为进一步的精细定位奠定了基础。 分子标记筛选、遗传图谱的构建及生长相关性状的QTL定位为我们下一步从事分子标记辅助选择育种,QTL精细定位和比较基因作图打下基础，并最终推动凡纳滨对虾的遗传改良。

Genetic mapping of size-related quantitative trait loci (QTL) in the bay scallop (Argopecten irradians) using AFLP and microsatellite markers

We constructed genetic linkage maps for the bay scallop Argopecten irradians using AFLP and microsatellite markers and conducted composite interval mapping (CIM) of body-size-related traits. Three hundred seventeen AFLP and 10 microsatellite markers were used for map construction. The female parent map contained 120 markers in 15 linkage groups, spanning 479.6 cM with an average interval of 7.0 cM. The male parent map had 190 markers in 17 linkage groups, covering 883.8 cM at 7.2 cM per marker. The observed coverage was 70.4% for the female and 81.1% for the male map. Markers that were distorted toward the same direction were closely linked to each other on the genetic maps, suggesting the presence of genes important for survival. Six size-related traits, shell length, shell height, shell width, total weight, soft tissue weight, and shell weight, were measured for QTL mapping. The size data were significantly correlated with each other. We subjected the data, log transformed firstly, to a principle component analysis and use the first principle component for QTL mapping. CIM analysis revealed one significant QTL (LOD=2.69, 1000 permutation, P<0.05) in linkage group 3 on the female parent map. The mapping of size-related QTL in this study raises the possibility of improving the growth of bay scallops through marker-assisted selection. (c) 2007 Published by Elsevier B.V.

Principles and prejudice: The erosion of fairness in admissibility determinations relating to historic child sexual abuse trials in Ireland

This thesis interrogates the construction of fairness to the accused in historic child sexual abuse trials in Ireland. The protection of fairness is a requirement of any trial that claims to adhere to the rule of law. Historic child sexual abuse trials, in which the charges relate to events that are alleged to have taken place decades previously, present serious challenges to the ability of the trial process to safeguard fairness. They are a litmus test of the courts’ commitment to fairness. The thesis finds that in historic abuse trials fairness to the accused has been significantly eroded and that therefore the Irish Courts have failed to respect the core of the rule of law in these most serious of prosecutions. The thesis scrutinises two bodies of case law, both of which deal with the issue of whether evidence should reach the jury. First, it examines the decisions on applications brought by defendants seeking to prohibit their trial. The courts hearing prohibition applications face a dilemma: how to ensure the defendant is not put at risk of an unfair trial, while at the same time recognising that delay in reporting is a defining feature of these cases. The thesis traces the development of the prohibition case law and tracks the shifting interpretations given to fairness by the courts. Second, the thesis examines what fairness means in the superior courts’ decisions regarding the admissibility of the following kinds of evidence, each of which presents particular challenges to the ability of the trial to safeguard fairness: evidence of multiple complainants; evidence of recovered memories and evidence of complainants’ therapeutic records. The thesis finds that in both bodies of case law the Irish courts have hollowed out the meaning of fairness. It makes proposals on how fairness might be placed at the heart of courts’ decisions on admissibility in historic abuse trials. The thesis concludes that the erosion of fairness in historic abuse trials is indicative of a move away from the liberal model of criminal justice. It cautions that unless fairness is prioritised in historic child sexual abuse trials the legitimacy of these trials and that of all Irish criminal trials will be contestable.

Two genes on A/J chromosome 18 are associated with susceptibility to Staphylococcus aureus infection by combined microarray and QTL analyses.

Although it has recently been shown that A/J mice are highly susceptible to Staphylococcus aureus sepsis as compared to C57BL/6J, the specific genes responsible for this differential phenotype are unknown. Using chromosome substitution strains (CSS), we found that loci on chromosomes 8, 11, and 18 influence susceptibility to S. aureus sepsis in A/J mice. We then used two candidate gene selection strategies to identify genes on these three chromosomes associated with S. aureus susceptibility, and targeted genes identified by both gene selection strategies. First, we used whole genome transcription profiling to identify 191 (56 on chr. 8, 100 on chr. 11, and 35 on chr. 18) genes on our three chromosomes of interest that are differentially expressed between S. aureus-infected A/J and C57BL/6J. Second, we identified two significant quantitative trait loci (QTL) for survival post-infection on chr. 18 using N(2) backcross mice (F(1) [C18A]xC57BL/6J). Ten genes on chr. 18 (March3, Cep120, Chmp1b, Dcp2, Dtwd2, Isoc1, Lman1, Spire1, Tnfaip8, and Seh1l) mapped to the two significant QTL regions and were also identified by the expression array selection strategy. Using real-time PCR, 6 of these 10 genes (Chmp1b, Dtwd2, Isoc1, Lman1, Tnfaip8, and Seh1l) showed significantly different expression levels between S. aureus-infected A/J and C57BL/6J. For two (Tnfaip8 and Seh1l) of these 6 genes, siRNA-mediated knockdown of gene expression in S. aureus-challenged RAW264.7 macrophages induced significant changes in the cytokine response (IL-1 beta and GM-CSF) compared to negative controls. These cytokine response changes were consistent with those seen in S. aureus-challenged peritoneal macrophages from CSS 18 mice (which contain A/J chromosome 18 but are otherwise C57BL/6J), but not C57BL/6J mice. These findings suggest that two genes, Tnfaip8 and Seh1l, may contribute to susceptibility to S. aureus in A/J mice, and represent promising candidates for human genetic susceptibility studies.

Identificación de QTL para dormición y análisis molecular de la interacción ABA-GAs en cariopses de sorgo granífero

El objetivo de esta tesis fue contribuir a la dilucidación de los mecanismos moleculares y genéticos que participan en la expresión de la dormición de semillas de cereales, utilizando Sorghum bicolor (L.) Moench como sistema modelo. Para ello se utilizaron dos aproximaciones complementarias: la identificación de QTL para el carácter dormición y la evaluación de la ocurrencia de interacciones in vitro entre componentes de la señalización del ácido abscísico (ABA) y el catabolismo de las giberelinas (GAs), candidatos a tener un rol importante durante la expresión de la dormición en granos de sorgo inmaduros (i.e. antes de madurez fisiológica). Los resultados obtenidos permitieron identificar tres QTL (qDOR-5; qDOR-9 y qDOR-10) que explican una proporción de la variabilidad que se observa en el patrón de expresión de dormición de granos de sorgo maduros (i.e. después de madurez fisiológica). Un análisis in silico de las secuencias abarcadas por estos QTL mostró que ninguno ellos incluye genes considerados como candidatos para dormición de sorgo. En ese sentido, esta tesis aportó nuevas regiones genómicas que contienen genes hasta ahora desconocidos, que serían importantes en la expresión del carácter dormición en granos maduros. Por otra parte, los análisis de unión in vitro realizados mostraron que las proteínas SbABI4 y SbABI5 (componentes de la señalización del ABA) pueden interactuar de manera específica con el ABRC (complejo de respuesta al ABA) del promotor del gen SbGA2ox3, responsable de la degradación de giberelinas activas. Este mecanismo de cross-talk ABA-GAs podría ser uno de los responsables del mantenimiento de la dormición en cariopses inmaduros resistentes al brotado pre-cosecha. Más aún, el ABRC del promotor de SbGA2ox3, involucrado en las interacciones, se encontró además en los promotores de genes GA2ox de otras especies monocotiledóneas como Brachypodium y arroz (Oryza sativa), pero no así en las dicotiledóneas analizadas, sugiriendo que el cross-talk ABA-GAs podría tener lugar en otras especies además de sorgo. Los resultados de esta tesis en forma conjunta aportaron nuevas evidencias acerca del rol preponderante que tienen ciertas regiones del genoma o genes puntuales en la expresión de la dormición tanto en granos maduros como inmaduros de sorgo granífero.

Identificación de QTL para dormición y análisis molecular de la interacción ABA-GAs en cariopses de sorgo granífero

El objetivo de esta tesis fue contribuir a la dilucidación de los mecanismos moleculares y genéticos que participan en la expresión de la dormición de semillas de cereales, utilizando Sorghum bicolor (L.)Moench como sistema modelo. Para ello se utilizaron dos aproximaciones complementarias: la identificación de QTL para el carácter dormición y la evaluación de la ocurrencia de interacciones in vitro entre componentes de la señalización del ácido abscísico (ABA)y el catabolismo de las giberelinas (GAs), candidatos a tener un rol importante durante la expresión de la dormición en granos de sorgo inmaduros (i.e. antes de madurez fisiológica). Los resultados obtenidos permitieron identificar tres QTL (qDOR-5; qDOR-9 y qDOR-10)que explican una proporción de la variabilidad que se observa en el patrón de expresión de dormición de granos de sorgo maduros (i.e. después de madurez fisiológica). Un análisis in silico de las secuencias abarcadas por estos QTL mostró que ninguno ellos incluye genes considerados como candidatos para dormición de sorgo. En ese sentido, esta tesis aportó nuevas regiones genómicas que contienen genes hasta ahora desconocidos, que serían importantes en la expresión del carácter dormición en granos maduros. Por otra parte, los análisis de unión in vitro realizados mostraron que las proteínas SbABI4 y SbABI5 (componentes de la señalización del ABA)pueden interactuar de manera específica con el ABRC (complejo de respuesta al ABA)del promotor del gen SbGA2ox3, responsable de la degradación de giberelinas activas. Este mecanismo de cross-talk ABA-GAs podría ser uno de los responsables del mantenimiento de la dormición en cariopses inmaduros resistentes al brotado pre-cosecha. Más aún, el ABRC del promotor de SbGA2ox3, involucrado en las interacciones, se encontró además en los promotores de genes GA2ox de otras especies monocotiledóneas como Brachypodium y arroz (Oryza sativa), pero no así en las dicotiledóneas analizadas, sugiriendo que el cross-talk ABA-GAs podría tener lugar en otras especies además de sorgo. Los resultados de esta tesis en forma conjunta aportaron nuevas evidencias acerca del rol preponderante que tienen ciertas regiones del genoma o genes puntuales en la expresión de la dormición tanto en granos maduros como inmaduros de sorgo granífero.

Comparison between weight loss of bends in a pneumatic conveyor and erosion rate obtained in a centrifugal erosion tester for the same materials

In order to find a link between results obtained from a laboratory erosion tester and tests carried out on a pneumatic conveyor, a comparison has been made between weight loss from bends on an industrial-scale pneumatic conveyor and erosion rates obtained in a small centrifugal erosion tester, for the same materials. Identical test conditions have been applied to both experiments so that comparable test results have been obtained. The erosion rate of mild steel commonly used as the wall material of conveyor pipes and pipe bends was determined individually on both test rigs. A relationship between weight loss from the bends and erosion rate determined from the tester has been developed. A discussion based on the results and their applicability to the prediction of wear in pneumatic conveyors concludes the paper.

Effect of particle concentration on erosion rate of mild steel bends in a pneumatic conveyor

Particle concentration is known as a main factor that affects erosion rate of pipe bends in pneumatic conveyors. With consideration of different bend radii, the effect of particle concentration on weight loss of mild steel bends has been investigated in an industrial scale test rig. Experimental results show that there was a significant reduction of the specific erosion rate for high particle concentrations. This reduction was considered to be as a result of the shielding effect during the particle impacts. An empirical model is given. Also a theoretical study of scaling on the shielding effect, and comparisons with some existing models, are presented. It is found that the reduction in specific erosion rate (relative to particle concentration) has a stronger relationship in conveying pipelines than has been found in the erosion tester.

Effect of bend orientation on life and puncture point location due to solid particle erosion of a high concentration flow in pneumatic conveyors

An investigation into predicting failure of pneumatic conveyor pipe bends due to hard solid particle impact erosion has been carried out on an industrial scale test rig. The bend puncture point locations may vary with many factors. However, bend orientation was suspected of being a main factor due to the biased particle distribution pattern of a high concentration flow. In this paper, puncture point locations have been studied with different pipe bend orientations and geometry (a solids loading ratio of 10 being used for the high concentration flow). Test results confirmed that the puncture point location is indeed most significantly influenced by the bend orientation (especially for a high concentration flow) due to the biased particle distribution and biased particle flux distribution.