EST-based gene discovery in pig: virtual expression patterns and comparative mapping to human

A molecular understanding of porcine reproduction is of biological interest and economic importance. Our Midwest Consortium has produced cDNA libraries containing the majority of genes expressed in major female reproductive tissues, and we have deposited into public databases 21,499 expressed sequence tag (EST) gene sequences from the 3 end of clones from these libraries. These sequences represent 10,574 different genes, based on sequence comparison among these data, and comparison with existing porcine ESTs and genes indicate as many as 4652 of these EST clusters are novel. In silico analysis identified sequences that are expressed in specific pig tissues or organs and confirmed the broad expression in pig for many genes ubiquitously expressed in human tissues. Furthermore, we have developed computer software to identify sequence similarity of these pig genes with their human counterparts, and to extract the mapping information of these human homologues from genome databases. We demonstrate the utility of this software for comparative mapping by localizing 61 genes on the porcine physical map for Chromosomes (Chrs) 5, 10, and 14. The following Accession numbers were assigned to our deposited sequences: BF701840 – BF704551, BF708383, BF708386 – BF713604, BG322266 – BG322271, BI398567 – BI405235, BQ597354 – BQ605166.     

长白山落叶阔叶混交林的物种多样性、种群空间分布格局及种间关联性研究

根据在吉林省蛟河实验管理局1 hm²落叶阔叶混交林样地调查结果,对落叶阔叶混交林的群落结构、物种多样性、主要树种的空间分布格局以及树木种群的种间关联进行了研究.结果表明,树木种群优势程度不明显;乔木、灌木、草本的均匀度指数、生态优势度指数都较低.对5个主要乔木种群的空间格局均呈现聚集分布;15个主要树种之间有14个种对存在着显著的种间关联,一个种独立;树种之间正关联的种对少,关联强度低,而负关联多且较高,群落结构组成不稳定,处于软阔叶林向硬阔叶林直至红松阔叶林过渡的阶段.     

A Multi-Trait,Meta-analysis for Detecting Pleiotropic Polymorphisms for Stature,Fatness and Reproduction in Beef Cattle

Polymorphisms that affect complex traits or quantitative trait loci (QTL) often affect multiple traits. We describe two novel methods (1) for finding single nucleotide polymorphisms (SNPs) significantly associated with one or more traits using a multi-trait, meta-analysis, and (2) for distinguishing between a single pleiotropic QTL and multiple linked QTL. The meta-analysis uses the effect of each SNP on each of n traits, estimated in single trait genome wide association studies (GWAS). These effects are expressed as a vector of signed t-values (t) and the error covariance matrix of these t values is approximated by the correlation matrix of t-values among the traits calculated across the SNP (V). Consequently, t''V⁻¹t is approximately distributed as a chi-squared with n degrees of freedom. An attractive feature of the meta-analysis is that it uses estimated effects of SNPs from single trait GWAS, so it can be applied to published data where individual records are not available. We demonstrate that the multi-trait method can be used to increase the power (numbers of SNPs validated in an independent population) of GWAS in a beef cattle data set including 10,191 animals genotyped for 729,068 SNPs with 32 traits recorded, including growth and reproduction traits. We can distinguish between a single pleiotropic QTL and multiple linked QTL because multiple SNPs tagging the same QTL show the same pattern of effects across traits. We confirm this finding by demonstrating that when one SNP is included in the statistical model the other SNPs have a non-significant effect. In the beef cattle data set, cluster analysis yielded four groups of QTL with similar patterns of effects across traits within a group. A linear index was used to validate SNPs having effects on multiple traits and to identify additional SNPs belonging to these four groups.     

热带尖峰岭和亚热带千岛湖六种凋落叶的分解特征

选取亚热带6个树种马尾松(Pinus massoniana)、毛竹(Phyllostachys heterocycla)、水杉(Metasequoia glyptostroboides)、木荷(Schima superba)、青冈(Cyclobalanopsis glauca)和苏铁(Cycas revoluta)的凋落物,在亚热带的千岛湖和热带的尖峰岭进行凋落物分解实验,研究不同气候带下凋落物的分解特征。两样地的年均气温和降水为主要差异,年均温差达3.0℃。结果表明:两个样地凋落物的分解速率顺序为:毛竹﹥木荷﹥青冈﹥马尾松﹥水杉﹥苏铁,尖峰岭样地6个树种95%分解所需的时间集中在3.22-8.81a,千岛湖样地95%分解所需的时间为4.61-14.27a。6种凋落物叶的分解速率尖峰岭显著大于千岛湖(P0.05)。用尖峰岭的气候条件来模拟千岛湖气候变暖后的状况,凋落物分解的分解速率将提高43.08%-95.65%,凋落物的95%分解时间将缩短30.15%-48.85%。凋落物分解的表观Q10在3.30-9.35之间。在千岛湖样地凋落物的分解速率(k值)与初始氮含量呈显著正相关(P0.05),与木质素含量呈显著负相关(P0.05);在尖峰岭样地,凋落物的分解速率与凋落物基质质量的各因子相关性均不显著。氮含量和木质素含量在中亚热带地区是预测凋落物分解和失重的良好指标,在热带地区气候因子对凋落物分解的控制作用较强于凋落物初始基质质量的控制作用。     

基于IBIS模型的1960-2006年中国陆地生态系统碳收支格局研究

定量评估区域陆地生态系统碳收支是生态系统与全球变化科学研究的重要科学问题之一。利用集成生物圈模型（IBIS）对中国陆地生态系统历史时期（1960-2006年）气候及CO₂浓度变化条件下碳收支时空变异特征和发展趋势进行了模拟分析。结果表明,1960-2006年间,中国陆地生态系统净初级生产力（NPP）总量水平约为2.46 GtC/a,总体呈上升趋势,在东南及西南地区最高,其次是长白山及大小兴安岭地区,西北内陆地区的净初级生产力水平最低;1960-2006年间,中国陆地生态系统净生态系统生产力（NEP）总量水平约为0.11 GtC/a,总体呈上升趋势,绝大部分区域表现为碳汇效应,大兴安岭、小兴安岭、长白山、东南地区及西南部分地区碳汇效应较强,西北内陆区表现出弱碳源效应,温带湿润区、高原温带区和高原寒带区碳汇效应呈显著上升趋势;中国11个气候区,NPP与降水均为正相关,除了中温带湿润区、寒温带湿润区、高原温带和高原寒带外,降水是限制植被生长的主要因子。除了高原寒带外,NEP同样表现出与降水的更强相关性,与气温的相关性较弱。经验证,IBIS模型对于中国陆地生态系统碳收支的模拟结果合理,可以为科学预测生态系统的固碳潜力和制定区域碳管理政策提供科学依据。     

长白山几种主要森林群落木本植物细根生物量及其动态

2005年在长白山北坡选择5种垂直植被带典型植物群落类型阔叶红松林、白桦林、山杨林、云冷杉林和岳桦林,利用钻取土芯法对细根分布及细根生物量进行了研究.研究结果表明,不同森林群落细根现存生物量存在一定的差异,其中白桦林最高,月平均细根现存生物量为5.1340 t/hm^2、其次为云冷杉林（5.0530 t/hm^2）、岳桦林（4.9255 t/hm^2）、阔叶红松林（4.4919 t/hm^2）和山杨林（3.9372 t/hm^2）;不同群落细根现存量月动态变化也有较大差异,月均最高最低相差阔叶红松林约为72﹪、白桦林近73﹪、山杨林26﹪、云冷杉林56﹪、岳桦林144﹪.在生长季节内不同群落细根发生和死亡也是不均匀的,春季所有群落都会产生大量的细根,一些群落在初秋（9月份）出现另一个较高的峰值,同时发现每次细根大量发生后,都随之产生大量细根的死亡,生长季末群落死亡细根生物量往往是最高的.调查群落72.9﹪以上的细根集中于土壤表层0～10cm的范围内,不同群落略有差别,在所研究的5种森林群落中,不同月份0～10cm土层中细根生物量几乎都表现出白桦林＞阔叶红松林＞云冷杉林＞岳桦林＞山杨林.     

Differential responses of litter decomposition to warming,elevated CO2, and changed precipitation regime

Plant and Soil - This study was performed to determine if the contribution of biological N2 fixation (BNF) associated with Brazilian sugarcane cultivars could be increased by the inoculation with...     

亚热带3种树种凋落叶厚度对其分解速率及酶活性的影响

对中国亚热带树种杉木(Cunninghamia lanceolata)、香樟(Cinnamomum camphora)、银杏(Ginkgo biloba)3个树种在不同凋落物厚度下凋落物分解速率和分解酶活性进行了探究.利用分解网袋法,根据浙江省的平均酸雨水平,在酸雨(pH4.0)条件下设置了凋落物40g、凋落物20g、凋落物10g 3个梯度.结果表明:凋落物分解速率随厚度的增加呈加快的趋势,杉木凋落物10、20、40g的年分解系数K分别为0.24、0.27、0.34,香樟凋落物10、20、40g的年分解系数K分别为0.25、0.3、0.32,银杏凋落物10、20、40g的年分解系数K分别为0.42、0.5、0.58;脲酶活性表现为:凋落叶40g＞凋落叶20g＞凋落叶10g,纤维素酶活性表现为:凋落叶40g、凋落叶20g＞凋落叶10g,蔗糖酶活性表现为:后期凋落叶40g＞凋落叶20g＞凋落叶10g,凋落物分解过程是多种酶共同作用的结果.     

Selection signature analysis implicates the PC1/PCSK1 region for chicken abdominal fat content

We conducted a selection signature analysis using the chicken 60k SNP chip in two chicken lines that had been divergently selected for abdominal fat content (AFC) for 11 generations. The selection signature analysis used multiple signals of selection, including long-range allele frequency differences between the lean and fat lines, long-range heterozygosity changes, linkage disequilibrium, haplotype frequencies, and extended haplotype homozygosity. Multiple signals of selection identified ten signatures on chromosomes 1, 2, 4, 5, 11, 15, 20, 26 and Z. The 0.73 Mb PC1/PCSK1 region of the Z chromosome at 55.43-56.16 Mb was the most heavily selected region. This region had 26 SNP markers and seven genes, Mar-03, SLC12A2, FBN2, ERAP1, CAST, PC1/PCSK1 and ELL2, where PC1/PCSK1 are the chicken/human names for the same gene. The lean and fat lines had two main haplotypes with completely opposite SNP alleles for the 26 SNP markers and were virtually line-specific, and had a recombinant haplotype with nearly equal frequency (0.193 and 0.196) in both lines. Other haplotypes in this region had negligible frequencies. Nine other regions with selection signatures were PAH-IGF1, TRPC4, GJD4-CCNY, NDST4, NOVA1, GALNT9, the ESRP2-GALR1 region with five genes, the SYCP2-CADH4 with six genes, and the TULP1-KIF21B with 14 genes. Genome-wide association analysis showed that nearly all regions with evidence of selection signature had SNP effects with genome-wide significance (P<10(-6)) on abdominal fat weight and percentage. The results of this study provide specific gene targets for the control of chicken AFC and a potential model of AFC in human obesity.