Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication

Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication(1,2). To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf. Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA sequence data(3). Furthermore, we find a surprising correspondence between genetic and phenotypic/functional breed groupings but there are exceptions that suggest phenotypic diversification depended in part on the repeated crossing of individuals with novel phenotypes. Our results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages. More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity.

小麦抗禾谷孢囊线虫（ Heterodera avenae）相关基因的研究

禾谷孢囊线虫严重影响禾谷类作物的产量，在小麦中由禾谷孢囊线虫引起的产量损失可达30-100%。尤其在澳大利亚、欧洲、印度和中东危害严重，目前禾谷孢囊线虫已成为危害我国作物的主要病源。控制禾谷孢囊线虫的方法主要有：作物轮作、杀线虫剂、寄主抗性等等，其中基因工程方法培育抗线虫小麦品种被认为是最经济有效的方法。分离抗禾谷类孢囊线虫基因对揭示抗性基因结构与功能及其表达调控具有重要意义。 尽管小麦是重要的粮食作物，在小麦中已发现的抗禾谷孢囊线虫的基因很少，而比其近缘属如节节麦、易变山羊草、偏凸山羊草中含有丰富的抗源。目前已鉴定出禾谷孢囊线虫抗性位点Cre，并发现了9个禾谷孢囊线虫抗性基因(Cre1,2, 3, 4, 5, 6, 7, 8, and R) ，其中只有Cre1和Cre8直接从普通小麦中获得。从节节麦中获得的Cre3基因能最有效的控制线虫数量，其次是Cre1和Cre8。这些基因的克隆对于了解禾谷孢囊线虫抗性机制及进一步的育种应用都是非常关键的。然而，目前为止仅有Cre3基因通过图位克隆的方法从节节麦中被分离得到。该基因已被克隆得到的多数线虫抗性基因一样均属于核苷酸结合位点区（NBS）－亮氨酸重复序列区（LRR）基因家族。目前，已有很多抗性基因被分离，这些已知的NBS-LRR类抗性基因的保守序列为应用PCR的方法克隆新的抗性基因提供了可能。 因此本课题的目的是采用保守区同源克隆、3′RACE 和5′RACE 等方法从抗禾谷孢囊线虫小麦-易变山羊草小片段易位系E10 中克隆小麦抗禾谷孢囊线虫基因全序列，进而通过半定量PCR 和荧光定量PCR 研究该基因的表达模式。同时通过mRNA 差别显示技术和任意引物PCR（RAP-PCR）技术分离克隆植物禾谷孢囊线虫抗性基因及其相关基因，为阐明植物抗病性分子机制以及改良作物抗病性和作物育种提供基础，为通过分子标记辅助育种和基因工程方法实现高效、定向转移抗病基因到优良小麦品种奠定了重要的理论和物质基础。主要研究结果： 1． 本实验根据此前从抗禾谷孢囊线虫材料E-10 扩增得到的与来自节节麦的抗禾谷孢囊线虫Cre3 基因及其他的NBS-LRR 类抗性基因的NBS 和LRR 保守区序列设计了两对特异性引物，从E10 中扩增到532bp 和1175bp 的两个目标条带，它们有一个32bp 的共同序列，连接构成总长为1675bp 的NBS-LRR 编码区（命名为RCCN）。根据RCCN设计引物，利用NBS-LRR区序列设计引物，通过5′RACE 和3′RACE 技术采用3′-Full RACE Core Set(TaKaRa)和5'-Full RACE Kit (TaKaRa)试剂盒，反转录后通过嵌套引物GSP1 和GSP2 分别进行两轮基因特异性扩增，分别将NBS_LRR 区向5′端和3′端延伸了1173bp 和449bp，并包含了起始密码子和终止密码子。根据拼接的得到的序列重新设计引物扩增进行全基因扩增的结果与上面获得的一致。拼接后得到全长2775 bp 的基因序列（记作CreZ, GenBank 号：EU327996）。CreZ 基因包括完整的开放阅读框，全长2775 bp，编码924个氨基酸。序列分析表明它与已知的禾谷孢囊线虫抗性基因Cre3的一致性很高，并且它与已经报到的NBS-LRR 类疾病抗性基因有着相同的保守结构域。推测CreZ基因可能是一个新的NBS-LRR 类禾谷孢囊线虫抗性基因，该基因的获得为通过基因工程途径培育抗禾谷孢囊线虫小麦新品种奠定了基础，并为抗禾谷孢囊线虫基因的调控表达研究提供了参考。 2． 通过半定量PCR和SYBR Green荧光定量PCR技术对CreZ基因的相对表达模式进行了研究。以α-tubulin 2作为参照，采用半定量PCR 分析CreZ 基因在不同接种时期1d, 5d, 10, 15d 的E-10的根和叶的的表达情况。在内参扩增一致的条件下，CreZ 在E-10的根部随着侵染时间的增加表达量有明显的增加，在没有侵染的E-10的根部其表达量没有明显变化，而在叶中没有检测表达，说明该基因只在抗性材料的根部表达。SYBR Green定量PCR分析接种前后E10根部基因CreZ基因的表达水平为检测CreZ基因的表达建立了一套灵敏、可靠的SYBRGreen I 荧光定量PCR 检测方法。接种禾谷孢囊线虫后E10根内CreZ基因的相对表达水平显著高于接种前。随接种时间的延长持续增加，最终CreZ基因的相对表达量达到未接种的对照植株的10.95倍。小麦禾谷孢囊线虫抗性基因CreZ的表达量与胁迫呈正相关，表明其与小麦的的禾谷孢囊线虫抗性密切相关，推测CreZ基因可能是一个新的禾谷孢囊线虫候选抗性基因。 3． 针对小麦基因组庞大、重复序列较多，禾谷孢囊线虫抗性基因及其相关基因的片断难以有效克隆的问题，通过mRNA 差别显示技术及RAP-PCR 技术分离克隆植物禾谷孢囊线虫抗性及其相关基因。试验最终得到154 条差异表达条带，将回收得到的差异条带的二次PCR 扩增产物经纯化后点到带正电的尼龙膜上，进行反向Northern 杂交筛选，最终筛选得到102 个阳性差异点。将其中81 个进行测序，并将序列提交到Genbank 中的dbEST 数据库，分别获得登录号(FE192210 -FE192265，FE193048- FE193074 )。序列比对分析发现，其中26 个序列与已知功能的基因序列同源；有28 条EST 序列在已有核酸数据库中未找到同源已知基因和EST，属新的ESTs 序列；另外27 个EST 序列与已知核酸数据库中的ESTs 具有一定相似性，但功能未知。其所得ESTs 序列补充了Genbank ESTs 数据库，为今后进一步开展抗禾谷类孢囊线虫基因研究工作打下了基础。结合本试验功能基因的相关信息，对小麦接种禾谷孢囊线虫后产生的抗性机制进行了探讨。接种禾谷孢囊线虫后植物在mRNA 水平上的应答是相当复杂的，同时植物的抗病机制是一个复杂的过程，涉及到多个代谢途径的相互作用。 The cereal cyst nematode (CCN), Heterodera avenae Woll, causes severe yieldreductions in cereal crops. The losses caused by CCN can be up to 30-100% in somewheat fields. At present, cereal cyst nematode has become the major disease sourcein China and it also damaged heavily in Australia, Europe, India and Middle East.The damage caused by CCN can be mitigated through several methods, includingcrop rotation, nematicide application, cultural practice, host resistance, and others.Of these methods, incorporating resistance genes into wheat cultivars and breedingresistant lines is considered to be the most cost-effective control measure forreducing nematode populations. Although wheat is an economically important crop around the world, far fewergenes resistant to CCN were found in wheat than were detected in its relatives, suchas Aegilops taucchi, Aegilops variabilis and Aegilops ventricosa. Cloning these genesis essential for understanding the mechanism of this resistance and for furtherapplication in breeding. Because of the huge genome and high repeat sequencescontent, the efficient methods to clone genes from cereal crops, are still lacking. A resistance locus, Cre, has been identified and 9 genes resistant to CCN (designatedCre1, 2, 3, 4, 5, 6, 7, 8, and R) have been described, in which Cre1 and Cre8 werederived directly from common wheat. The Cre3 locus, which was derived from Ae.tauschii, has the greatest impact on reducing the number of female cysts, followed byCre1 and Cre8. Cloning these genes is essential for understanding the mechanism ofthis resistance and for further application in breeding. However, to this point, only Cre3, a NBS-LRR disease resistance gene, has been obtained through mappingcloning in Ae. tauschii. The majority of nematode resistance genes cloned so far belong to a super familywhich contains highly conserved nucleotide-binding sites (NBS) and leucine-richrepeat (LRR) domains. To date, many NBS-LRR resistance genes have been isolated.The conserved sequences of these recognized NBS-LRR resistance genes provide thepossibility to isolate novel resistance genes using a PCR-based strategy. The aim of the present study was to clone the resistance gene of CCN fromWheat/Aegilops variabilis small fragment chromosome translocation line E10 whichis resistant to CCN and investigate the espression profiles of this gene withsemi-quantitative PCR and real-time PCR. Another purpose of this study is cloningthe relational resistance gene for CCN by mRNA differential display PCR andRAP-PCR. These works will offer a foundation for disease defence of crop andbreeding and directional transferring resistance gene into wheat with geneengineering. Primary results as following: 1．According to the conversed motif of NBS and LRR region of cereal cystnematode resistance gene Cre3 from wild wheat (Triticum tauschlii) and the knownNBS-LRR group resistance genes, we designed two pairs of specific primers for NBSand LRR region respectively. One band of approximately 530bp was amplified usingthe specific primers for conversed NBS region and one band of approximately 1175bpwas amplified with the specific primers for conversed LRR region. After sequencing,we found that these two sequences included 32bp common nucleotide having 1675bpin total, which was registered as RCCN in the Genbank. Based on the conservedregions of known resistance genes, a NBS-LRR type CCN resistance gene analog wasisolated from the CCN resistant line E-10 of the wheat near isogenic lines (NILs), by5′RACE and 3′ RACE.designated as CreZ (GenBank accession number: EU327996) .It contained a comlete ORF of 2775 bp and encoded 924 amino acids. Sequencecomparison indicated that it shared 92% nucleotide and 87% amino acid identitieswith those of the known CCN-resistance gene Cre3 and it had the same characteristic of the conserved motifs as other established NBS-LRR disease resistance genes. 2． Usingα-tubulin 2 as exoteric reference, semi-quantitative PCR and real-timePCR analysis were conducted. The expression profiling of CreZ indicated that it wasspecifically expressed in the roots of resistant plants and its relative expression levelincreased sharply when the plants were inoculated with cereal cyst nematodes. therelative expression level of the 15days-infected E10 is the 10.95 times as that ofuninfected E10,ultimately. It was inferred that the CreZ gene be a novel potentialresistance gene to CCN. 3．We cloned the relational resistance gene for CCN by mRNA differentialdisplay PCR and arbitrarily primed PCR fingerprinting of RNA from wheat whichpossess huge and high repeat sequence content genomes. Total 154 differentialexpression bands were separated and second amplified by PCR. The products werenylon membrane. The 102 positive clones were filtrated by reverse northern dot blotand 81 of those were sent to sequence. The EST sequences were submitted toGenbank (Genbank accession: FE192210 - FE192265, FE193048 - FE193074). Thesequences alignment analysis indicated 26 of them were identical with known genes;28 were not found identical sequence in nucleic acid database; another 27 ests wereidentical with some known ests, but their functions were not clear. These ESTsenriched Genbank ESTs database and offered foundation for further research ofresistance gene of CCN.

南海大陆边缘地壳结构与盆地形成机制--以珠江口－琼东南盆地为例

South China Sea is located in the convergence of Eurasian plate, the Pacific Ocean plate and Indian Ocean-Australia plate. The total area is about 3,500,000 km2, the geologic structure is complicated, and the structure line cut off reciprocal is the marginal sea taking form by that the seafloor spreads during the middle Oligocene. South China Sea continental margin have developed more than 10 large oil-gas bearing basins and a number of medium-small sized basins. These basins contain abundant mineral resources such as oil & gas. The marginal deepwater area in the north part of South China Sea has become our country’s strategic energy prospecting frontier. The deepwater area of Zhujiangkou and Qiongdongnan basins is the research target in this thesis. The thesis studied deep structure and the earth dynamics of the north part of South China Sea margin, and these researches provide scientific basis for oil-gas resources strategic investigation and valuation in deepwater sea area of north part slope of South China Sea. In order to develop the research of rebuilding velocities and density architecture of earth shell in region of interest, in marginal deepwater area in the north part of South China, we adopted 14 long-cable seismic reflection profile data of 3556.41 kilometers in total, the gravity measurement data along profiles (3851.44 kilometers in total), the magnetic observation along profiles (3838.4 kilometers in total) and depth measurement along profile, the logging data of 11 wells in project, the interpreted fault parameter and preexisting geologic and geophysical research achievement. This thesis has carried out concretely studying research as follows: 1. Overlay-velocity data sampling and analysis, interval velocity calculation, time-depth conversion, model building of earth shell velocity and layering character of earth shell are studied on 14 deep sections. Velocity structure in region of interest has revealed: Changchang is the sag with thinnest crust in Qiongdongnan basin; the sedimentary thickness lowers gradually from north to south, and the thickness change from west to east is milder. The sags’ sedimentary velocities in Qiongdongnan basin have obvious demarcation. The velocity of the 8000 meters sedimentary rocks is 4700 m/s in Shunde sag and Baiyun sag, and is the lowest; at that depth, the velocity very different in Liwan sag and Baiyun sag, which is about 800m/s. 2. Extracting gravity data and building of initial crust density model along the section; With Bouguer gravity anomaly data as constraint, revising density distributes of initial model, and building the crust density model. 3. With crust velocity and density as constraint, correcting the effect of thermobaric field and constructing constitution structure of rock in region of interest. By this research, we known that rocks in Zhujiangkou upper crustal layer are chiefly granite-gneiss, quartzite, granodiorite and basalt, however, rocks in Qiongdongnan basin upper earth shell are chiefly composed of granite-gneiss, quartzite, granodiorite, diorite and basalt. 4. Synthetically crust velocity and density structure, gaining expanding factor on crust and entire crust along section. The result is indicated: the expanding factor in every sag rises from northwest to southeast, which have reflected thinning characteristic of crust from continent to ocean. Intra-crustal deformation degree in Changchang and Ledong-Lingshui sag is bigger than that in Songnan-Baodao sag. Entire crust extension factor in Changchang and Songnan-Baodao sag is greater than that in Ledong-Lingshui sag, which can make an explanation of frequently event and longer heating process in middle-east of Qiongdongnan basin. 5. Synthesize multidisciplinary information to discuss the earth dynamics significance of discordogenic seismic profile in deepwater area of Zhujiangkou and Qiongdongnan basins.

东营凹陷沙三中亚段湖相浊积岩储层特征及油气成藏规律研究

Turbidity sandstone reservoirs have been an important field of hydrocarbon exploration and development in the basins all over the world, as well as in China. Lithologic pools are composed of turbidity sandstones and other sandstones are frequently found in the Jiyang Depression that is a Mesozoic-Cenozoic non-marine oil-bearing basin. The Dongying Sag lies in the sedimentary center of the basin. The subtle traps with turbidity reservoirs are generally difficult to be predicted and described by using current techniques. The studies on turbidity reservoirs plays thus an important theoretical and theoretical practical role in exploration and development in the Jiyang Depression. The attention is, in this thesis, focused on the petrologic properties and oil accumulating behaviors in lake turbidity sedimentary systems in the middle part of the third section of Shahejie Formation in the Dongying Sag, especially in Dongxin area, which lies on the central uplift of the Sag. The paper has disclosed the origin types of turbidity sandstones, distribution pattern and controlling factors of turbidity sandstones, and set up hydrocarbon accumulation patterns of the middle part of the third section of Shahejie Formation in Dongxin, based on nonmarine high resolution sequence stratigraphy, event sedimentology and new theories of hydrocarbon forming. By studying prediction method and technology of turbidity sandstone reservoirs, using precise geological model developing, new techniques of high resolution seismic inversion constrained by logging, the paper has forecast low permeability turbidity sandstone reservoirs and pointed out advantage exploration aims to progressive exploration and development. The paper has obtained mainly many productions and acknowledges as follows: 1.Turbidity sandstone reservoirs of the third section of Shahejie Formationin Dongying Sag are formed in such specifical geological background as rift and extension of basin. The inherited Dongying delta and transgression make up many turbidity distribution areas by overlaying and joining together. The hydrocarbon migrates from depression area to adjacent turbidity sandstone continuously. Accumulation area which is sufficient in oil is formed. 2.The paper has confirmed distinguishable sign of sequence boundary , established stratigraphic framework of Dongying Sag and realized isotime stratigraphic correlation. Es3 of Dongying delta is divided into eleven stages. Among them, the second period of the lower section in Es3, the sixth period of the middle section in Es3, the third period of the upper section in Es3 correspond to eleven sedimentary isotime surface in seismic profile, namely Es3 is classified into eleven Formations. 3.According to such the features of turbidity sandstone as deep in burial, small in area, strong in subtle property, overlaying and joining together and occurring in groups, management through fault and space variations of restriction quantum are realized and the forecast precision of turbidity sandstone by using precise geological model developing, new techniques of high resolution seismic inversion constrained by logging, based on the analysis of all kinds of interwell seismic inversion techniques. 4.According to the features of low permeable turbidity sandstone reservoirs, new method of log interpretation model is put forward. At the same time, distinguish technology of familiar low resistivity oil layer in the turbidity sandstone reservoirs is studied based on petrophysical laboratory work and "four properties" interrelationship between lithological physical Jogging and bearing hydrocarbon properties. Log interpretation model and reservoir index interpretation model of low resistivity oil layer are set up. So the log interpretation precision is improved. 5.The evolution law and its difference of the turbidity sandstone are embodies as follows: the source of sediments come from the south and east of the study area in the middle period of Es3. East source of sediments is pushed from west to east. However, the south source supply of sediments in the early and middle period of Es3 is in full, especially in Es3. subsequently, the supply is decreased gradually. Turbidity fan moves back toward the south and the size of fan is minished accordingly. The characteristic of turbidity sandstone in Dongying Sag is different in different structural positions. Dongxin in the middle-east of the central lift and Niuzhuang Sag He in Dongying delta front and prodelta deep lake subfacies. Although the turbidity sandstone of the two areas root in the Dongying delta sedimentary system, the sand body has different remarkably characteristic. 6.The sedimentary model of the turbiditys in study area have three types as follows: (1) collapse turbidity fan in respect of delta; (2) fault trench turbidity fan; (3) other types of microturbidity sandstone. Middle fan and outer fan, can be found mainly in sublacustrine fan. Middle fan includes braided channel microfacies, central microfacies and braided interchannel microfacies, which is main prospecting oil-bearing subfacies. The middle section of the third section of Shahejie Formation in study area (for example the central lift) can be divided into middle-lower and upper part. The middle-lower part is characteristic of turbidity fan. The upper part is sedimented mainly by delta-collapse fan. 7.The turbidity reservoirs of the middle part of the third section of Shahejie Formation in study area characterize by low maturity both in component and texture, strong in diagenesis and low in permeability. The reservoir can be classified into four types. Type III is the body of reservoir and comprises two types of H a and HI b. M a belongs to middle porosity - low permeability reservoir and distributes in the central lift. Hlb belongs to low porosity - low permeability and distributes in Haojia region. 8.A11 single sand body of lens turbidity reservoir of the middle part of the third section of Shahejie Formation in study area are surrounded by thick dark source rocks. The oil-water system is complex and behaves that every sandstone is single seal unit. The water body is 1/3-1-5 of the sand body. The edge water is not active. The gas exists in the top of reservoir in the form of mixed gas. For far-range turbidity fan with big scale channel, the area and volume of sand body is large and the gap is big in oil packing degree. There are lots of edge water and bottom water, and the latter increases rapidly during the course of development. 9.By exerting the modern hydrocarbon forming theories, the third section of Shahejie Formation in study area belongs to abnormally pressured fluid compartment. The lithological reservoir of the third section of Shahejie Formation is formed in the compartment. The reservoir-formed dynamic system belongs to lower self-source enclosed type. The result and the practice indicate that the form and accumulation of lithological oil reservoirs are controlled by the temperature and pressure of stratum, microfacies, thickness of sand body, fault and reservoir heterogeneity. 10. Based on studies above, the emphases focus on in south and north part of Dongying structure, west Dongxin region and south part Xinzhen structure in the application of production. The practice proves that the turbidity sandstone reservoirs in Ying 11 block and the fault-lithological reservoirs in Xin 133 block have been obtained significant breakthrough. The next target is still sandstone groups of the third section of Shahejie Formation in the bordering areas of Dongxin region for instance Xin 149 area, He 89 area, Ying 8 area etc.