Genome-wide association studies of 14 agronomic traits in rice landraces

Uncovering the genetic basis of agronomic traits in crop landraces that have adapted to various agro-climatic conditions is important to world food security. Here we have identified ～ 3.6 million SNPs by sequencing 517 rice landraces and constructed a high-density haplotype map of the rice genome using a novel data-imputation method. We performed genome-wide association studies (GWAS) for 14 agronomic traits in the population of Oryza sativa indica subspecies. The loci identified through GWAS explained ～ 36% of the phenotypic variance, on average. The peak signals at six loci were tied closely to previously identified genes. This study provides a fundamental resource for rice genetics research and breeding, and demonstrates that an approach integrating second-generation genome sequencing and GWAS can be used as a powerful complementary strategy to classical biparental cross-mapping for dissecting complex traits in rice.     

Lysosomal chymotrypsin B potentiates apoptosis via cleavage of Bid

We have reported that chymotrypsin B (CtrB) is not just a digestive enzyme but is also stored in lysosomes. Herein, we demonstrated a broad distribution of CtrB and explored the involvement of CtrB in apoptosis. Exposure of RH-35 cells to H₂O₂ or palmitate induced the redistribution of lysosomal CtrB into the cytoplasm as a result of lysosomal membrane permeabilization (LMP). Suppression of CtrB significantly blocked apoptosis, while overexpression of CtrB sensitized apoptosis markedly. CtrB could cleave Bid under neutral conditions. In RH-35 cells with Bid silenced, apoptosis induced by CtrB protein was attenuated, suggesting that CtrB mediates apoptosis of RH-35 cells mainly through processing Bid. Our data also suggest that LMP occurs earlier than mitochondrial outer membrane permeabilization; Bid activation initiated by caspase-8 might be reinforced by CtrB in consequence of LMP, which causes a positive feedback loop leading to the accumulation of tBid, and results in lysosome- and mitochondrion-dependent apoptosis.     

浅论绿色无锡建设中的绿化仿生问题

本文分析了城市绿化建设中存在的共性问题及可采取的对策,从生态系统生物生产、物质循环、能量流动、信息传递以及构建和谐种群关系5个方面论述了城市绿化应以模拟自然生态系统结构与功能为途径,并指出提高城市绿化仿生水平是实现绿色无锡建设目标的关键.     

Maize HapMap2 identifies extant variation from a genome in flux

Whereas breeders have exploited diversity in maize for yield improvements, there has been limited progress in using beneficial alleles in undomesticated varieties. Characterizing standing variation in this complex genome has been challenging, with only a small fraction of it described to date. Using a population genetics scoring model, we identified 55 million SNPs in 103 lines across pre-domestication and domesticated Zea mays varieties, including a representative from the sister genus Tripsacum. We find that structural variations are pervasive in the Z. mays genome and are enriched at loci associated with important traits. By investigating the drivers of genome size variation, we find that the larger Tripsacum genome can be explained by transposable element abundance rather than an allopolyploid origin. In contrast, intraspecies genome size variation seems to be controlled by chromosomal knob content. There is tremendous overlap in key gene content in maize and Tripsacum, suggesting that adaptations from Tripsacum (for example, perennialism and frost and drought tolerance) can likely be integrated into maize.     

Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

A high-density haplotype map recently enabled a genome-wide association study (GWAS) in a population of indica subspecies of Chinese rice landraces. Here we extend this methodology to a larger and more diverse sample of 950 worldwide rice varieties, including the Oryza sativa indica and Oryza sativa japonica subspecies, to perform an additional GWAS. We identified a total of 32 new loci associated with flowering time and with ten grain-related traits, indicating that the larger sample increased the power to detect trait-associated variants using GWAS. To characterize various alleles and complex genetic variation, we developed an analytical framework for haplotype-based de novo assembly of the low-coverage sequencing data in rice. We identified candidate genes for 18 associated loci through detailed annotation. This study shows that the integrated approach of sequence-based GWAS and functional genome annotation has the potential to match complex traits to their causal polymorphisms in rice.     

Genome-wide association study of leaf architecture in the maize nested association mapping population

US maize yield has increased eight-fold in the past 80 years, with half of the gain attributed to selection by breeders. During this time, changes in maize leaf angle and size have altered plant architecture, allowing more efficient light capture as planting density has increased. Through a genome-wide association study (GWAS) of the maize nested association mapping panel, we determined the genetic basis of important leaf architecture traits and identified some of the key genes. Overall, we demonstrate that the genetic architecture of the leaf traits is dominated by small effects, with little epistasis, environmental interaction or pleiotropy. In particular, GWAS results show that variations at the liguleless genes have contributed to more upright leaves. These results demonstrate that the use of GWAS with specially designed mapping populations is effective in uncovering the basis of key agronomic traits.     

三家子矿6-2煤层瓦斯地质规律研究

通过对南票三家子煤矿瓦斯地质资料的分析,并结合煤层瓦斯含量的现场测定和实验室测试,探讨了断层、构造凹地、煤层围岩、含煤岩系沉积环境以及岩浆侵入等地质因素对6-2煤层瓦斯赋存、分布的影响;夯析了各因素与瓦斯含量的关系,即断层、岩浆侵入破坏了煤体的结构,构造凹地引起的压性应力导致6-2煤层区域性渗透率下降,这些因素对瓦斯的逸散均起了阻碍的作用,因此是影响瓦斯赋存的主控因素。绘制出瓦斯含量等值线图,进而为采掘布置和瓦斯防治工作提供了理论依据。     

Fault-Tolerant Design for Data Efficient Retransmission in WiNoC

There is a sharp decline in the network performance when the wireless link fails as a data path in the Wireless Network-on-Chip(WiNoC).To counteract this problem,we propose a fault-tolerance mechanism for the efficient retransmission of data in the WiNoC.When an error is detected in the data transmission process,this mechanism works to feed back the fault information to the source node in real time via fault signal lines.In the source node,the highest transmission priority is assigned to the backup retransmitted data,and the corresponding direct link is positioned to enable the data packet for its efficient retransmission to the destination node,thereby ensuring efficiency in fault tolerance.Additionally,we have improved the receiving port of the wireless router,added the corresponding redundant buffers and mux,and dynamically selected the retransmitted non-faulty data packets to be written to the local router in order to avoid the disorderly retransmission of the data packets.The evaluation results of this paper demonstrate that compared with the methods which are under different fault conditions,this fault-tolerant method drastically improves the data throughput rate,reduces the delay,effectively guarantees the reliability of the network,and improves the system performance.     

一种基于QVT的模型转换技术

提出一种基于查询/视图/转换(QVT)规范的模型转换技术, 并采用这种模型转换技术, 利用Kermeta语言中的模型转换功能, 通过对QVT核心分层, 设计了一种基于映射四层QVT结构的模型转换工具, 实现了Ecore元模型到Kmt元模型的转换.