2010年4—12月对南四湖大型底栖动物群落进行了季度调查，分析了底栖动物群落的时空动态，并进行了水质评价。调查期间共采集到底栖动物36种，其中寡毛类5种，软体动物10种，水生昆虫15种，其他动物6种。底栖动物的优势种为霍甫水丝蚓（Limnodrilus hoffmeisteri）、梨形环棱螺（Bellamya purificata）、长角涵螺（Alocinma longicornis）和红裸须摇蚊（Propsilocerusi akamusi），四者密度之和占总密度的88.1%。大型底栖动物的密度和生物量分别为1119 ind·m^-2和83.23 g·m^-2。底栖动物的种类数、优势种和现存量均呈现出明显的季节变化，空间分布差异亦较大。采用Shannon多样性指数、Margalef多样性指数和Hilsenhoff生物指数对南四湖的水质进行了综合评价，结果表明，南四湖总体上处于中污染状态，从季节上来看，春季和冬季的水质略好于夏季和秋季；从各湖区来看，南阳湖和昭阳湖处于重污染状态，独山湖处于中重污染状态，微山湖处于中污染状态。 

A high-density genetic linkage map is essential for the studies of comparative genomics and gene mapping, and can facilitate assembly of reference genome. Herein, we constructed a high-density genetic linkage map with 8,094 SNPs selected from 113 sequenced fish of a F1 family. Ultimately, the consensus map spanned 3818.24 cM and covered nearly the whole genome (99.4%) with a resolution of 0.47 cM. 1,457 scaffolds spanning 435.15 Mb were anchored onto 24 linkage groups, accounting for 80.7% of the draft genome assembly of the yellow drum. Comparative genomic analyses with medaka and zebrafish genomes showed superb chromosome-scale synteny between yellow drum and medaka. QTL mapping and association analysis congruously revealed 22 QTLs for growth-related traits and 13 QTLs for sex dimorphism. Some important candidate genes such as PLA2G4A, BRINP3 and P2RY1 were identified from these growth-related QTL regions. A gene family including DMRT1, DMRT2 and DMRT3 was identified from these sex-related QTL regions on the linkage group LG9. We demonstrate that this linkage map can facilitate the ongoing marker-assisted selection and genomic and genetic studies for yellow drum.

Luciobarbus brachycephalus (commonly known as the Aral barbel) represents a commercially valuable fish species in China, contributing significantly to regional aquaculture economies. High-density genetic linkage mapping coupled with quantitative trait locus (QTL) analysis has emerged as a powerful approach for elucidating the genetic mechanism of complex traits in aquatic species.

Medaka (Oryzias latipes) is widely used in research in the fields of biology, medicine, environmental science and fisheries. Zebrafish and medaka are well established as genetic model systems in which large-scale mutagenesis has been successfully performed, and for which EST data, BAC libraries, and fine linkage maps have been accumulated. Among rayfinned fish, there is a large evolutionary distance between medaka and zebrafish. In contrast, the evolutionary distance between medaka and two species of pufferfish, fugu (Takifugu rubripes), and tetraodon (Tetraodon nigroviridis), is almost comparable to that between humans and rodents, and the current genome project is showing that their genome organization is well conserved. Comparison of genome structure among teleosts and mammals helps our understanding of the orthologous gene structure and the evolution of gene families in vertebrates. In addition, gene functions have to be analyzed by both forward and reverse genetics. The Targeting Induced Local Lesions IN Genome (TILLING) system, which includes random mutagenesis, followed by screening for induced mutations in the target genes, is a powerful tool for studying the functional genomics of both medaka and zebrafish.

The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals.We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows-Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is approximately 10-20x faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package.http://maq.sourceforge.net.

Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, the massive data sets generated by NGS--the 1000 Genome pilot alone includes nearly five terabases--make writing feature-rich, efficient, and robust analysis tools difficult for even computationally sophisticated individuals. Indeed, many professionals are limited in the scope and the ease with which they can answer scientific questions by the complexity of accessing and manipulating the data produced by these machines. Here, we discuss our Genome Analysis Toolkit (GATK), a structured programming framework designed to ease the development of efficient and robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce. The GATK provides a small but rich set of data access patterns that encompass the majority of analysis tool needs. Separating specific analysis calculations from common data management infrastructure enables us to optimize the GATK framework for correctness, stability, and CPU and memory efficiency and to enable distributed and shared memory parallelization. We highlight the capabilities of the GATK by describing the implementation and application of robust, scale-tolerant tools like coverage calculators and single nucleotide polymorphism (SNP) calling. We conclude that the GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.

R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTLs) in experimental populations derived from inbred lines. It is implemented as an add-on package for the freely-available statistical software, R, and includes functions for estimating genetic maps, identifying genotyping errors, and performing single-QTL and two-dimensional, two-QTL genome scans by multiple methods, with the possible inclusion of covariates.The package is freely available at http://www.biostat.jhsph.edu/~kbroman/qtl.

Whole genome sequencing provides the most comprehensive collection of an individual's genetic variation. With the falling costs of sequencing technology, we envision paradigm shift from microarray-based genotyping studies to whole genome sequencing. We review methodologies for whole genome sequencing. There are two approaches for assembling short shotgun sequence reads into longer contiguous genomic sequences. In the de novo assembly approach, sequence reads are compared to each other, and then overlapped to build longer contiguous sequences. The reference-based assembly approach involves mapping each read to a reference genome sequence. We discuss methods for identifying genetic variation (single nucleotide polymorphisms, small indels, and copy number variants) and building haplotypes from genome assemblies, and discuss potential pitfalls. We expect methodologies to evolve rapidly as sequencing technologies improve and more human genomes are sequenced.

Understanding soybean (Glycine max) domestication and improvement at a genetic level is important to inform future efforts to further improve a crop that provides the world's main source of oilseed. We detect 230 selective sweeps and 162 selected copy number variants by analysis of 302 resequenced wild, landrace and improved soybean accessions at >11× depth. A genome-wide association study using these new sequences reveals associations between 10 selected regions and 9 domestication or improvement traits, and identifies 13 previously uncharacterized loci for agronomic traits including oil content, plant height and pubescence form. Combined with previous quantitative trait loci (QTL) information, we find that, of the 230 selected regions, 96 correlate with reported oil QTLs and 21 contain fatty acid biosynthesis genes. Moreover, we observe that some traits and loci are associated with geographical regions, which shows that soybean populations are structured geographically. This study provides resources for genomics-enabled improvements in soybean breeding.

【目的】适合机械化收获是当今油菜育种改良和遗传研究的重要目标。该研究以一个自然变异产生的油菜有限花序（denterminate inflorescence 1，di1）突变体为研究对象，通过分析有限花序的遗传模式，开展有限花序性状的基因定位和克隆，以期发掘候选基因，为培育适合机械化收获的油菜新品种提供新思路和新材料，为揭示油菜有限花序遗传机制奠定基础。【方法】以一个稳定遗传的有限花序突变株系FM8与野生型自交系FM7开展正反交，观察F1和F2后代的花序形态，分析有限花序性状的遗传模式。在F2群体中挑选20个有限花序单株和20个野生类型单株构建混合池，对混合池和亲本开展20×和10×覆盖度的全基因组重测序，定位有限花序性状的关联区间。根据关联区间对应到拟南芥基因组的共线性区段和基因注释信息，预测候选基因，并对候选基因进行同源克隆，发掘序列变异，筛选关键基因。【结果】油菜有限花序突变性状表现为初花期主花序和侧枝花序顶部形成一个或若干个顶生花，花序无限生长受阻，导致结角期主枝和侧枝有封顶特征即有限花序。有限花序突变株系与野生型正反交F1均表现为野生型，F2代无限花序与有限花序的分离比符合13﹕3，说明有限花序的遗传受2对隐性基因和1对隐性上位抑制基因互作控制。对混合池及亲本开展全基因组重测序，得到30 123个单核苷酸多态性（SNPs）标记和107 636个插入缺失标记（InDels）标记，用于有限花序性状的全基因组定位。定位结果共检测获得7个显著关联区间，分布于油菜A08、A09、A10、C08和C09共5条染色体。其中，A10染色体上的关联区间峰值最高，是控制有限花序性状的主效位点。并且，A10染色体关联区间内的14.36—15.07 Mb的区域与C09染色体2个关联区间显示高度同源性。候选基因预测发现位于A08、A09、A10、C08和C09的5个关联区间包含有8个候选基因，包括TERMINAL FLOWER 1（TFL1）、FLOWERING LOCUS C（FLC）、ATBZIP14（FD）、MULTICOPY SUPPRESSOR OF IRA1 4（FVE）和SCHLAFMUTZE（SMZ）。基因序列分析表明di1突变体TFL1、FVE和SMZ的基因编码区存在序列变异，并导致蛋白序列变异。【结论】油菜有限花序突变由2对隐性基因和1对隐性上位抑制基因互作控制。与有限花序性状显著关联的区间有7个，其中，位于染色体A10和C09的关联区间具有高度同源性。TFL1、FVE和SMZ被推断为有限花序性状的候选基因。

The effective protection and utilization of poultry resources depend on an accurate understanding of the genetic diversity and population structure. The breeding of the specialized poultry lineage “Yufen 1”, with its defined characteristics, was approved by the China Poultry Genetic Resource Committee in 2015. Thus, to investigate the relationship between the progenitor H line and other poultry breeds, the genetic diversity and population structure of “Yufen 1” H line (YF) were investigated and compared with those of 2 commercial chicken breeds, the ancestor breed Red Jungle Fowls, and 11 Chinese indigenous chicken breeds based on a whole-genome resequencing approach using 8,112,424 SNPs. The genetic diversity of YF was low, and the rate of linkage disequilibrium decay was significantly slower than that of the other Chinese indigenous breeds. In addition, it was shown that the YF population was strongly selected during intensive breeding and that genetic resources have been seriously threatened, which highlights the need to establish a systematic conservation strategy as well as utilization techniques to maintain genetic diversity within YF. Moreover, a principal component analysis, a neighbor-joining tree analysis, a structure analysis, and genetic differentiation indices indicated that YF harbors a distinctive genetic resource with a unique genetic structure separate from that of Chinese indigenous breeds at the genome level. The findings provide a valuable resource and the theoretical basis for the further conservation and utilization of YF.

The Chinese Qingyu pig breed is an invaluable indigenous genetic resource. However, few studies have investigated the genetic architecture of meat quality traits in Qingyu pigs. Here, 30 purebred Qingyu pigs were subjected to whole-genome sequencing. After quality control, 18 436 759 SNPs were retained. Genome-wide association studies (GWAS) were then performed for meat pH and color at three postmortem time points (45 min, 24 h, and 48 h) using single-marker regression analysis. In total, 11 and 69 SNPs were associated with meat pH and color of the longissimus thoracis muscle (LTM), respectively, while 54 and 29 SNPs were associated with meat pH and color of the semimembranosus muscle (SM), respectively. Seven SNPs associated with pork pH were shared by all three postmortem time points. Several candidate genes for meat traits were identified, including four genes (,,, and ) related to skeletal muscle development, regulation of Ca release in the muscle, and anaerobic respiration, which are promising candidates for selecting superior meat quality traits in Qingyu pigs. To our knowledge, this is the first study investigating the postmortem genetic architecture of pork pH and color in Qingyu pigs. Our findings further the current understanding of the genetic factors influencing meat quality.

High density genetic linkage maps are essential for QTL fine mapping, comparative genomics and high quality genome sequence assembly. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,194 SNP markers on 14,146 distinct loci for common carp based on high-throughput genotyping with the carp 250 K single nucleotide polymorphism (SNP) array in a mapping family. The genetic length of the consensus map was 10,595.94 cM with an average locus interval of 0.75 cM and an average marker interval of 0.38 cM. Comparative genomic analysis revealed high level of conserved syntenies between common carp and the closely related model species zebrafish and medaka. The genome scaffolds were anchored to the high-density linkage map, spanning 1,357 Mb of common carp reference genome. QTL mapping and association analysis identified 22 QTLs for growth-related traits and 7 QTLs for sex dimorphism. Candidate genes underlying growth-related traits were identified, including important regulators such as KISS2, IGF1, SMTLB, NPFFR1 and CPE. Candidate genes associated with sex dimorphism were also identified including 3KSR and DMRT2b. The high-density and high-resolution genetic linkage map provides an important tool for QTL fine mapping and positional cloning of economically important traits, and improving common carp genome assembly.

腹足纲是动物中仅次于昆虫纲的第二大纲。随着分子生物学技术的发展,原来基于形态学特征建立的分类不断被修正,并由此导致一些分类单元的繁殖生物学习性重新调整。现代分子生物学的发展也为腹足纲性别决定机制和性别分化机制提供有力证据和支持。本研究基于最新的腹足纲分类,对该纲部分物种从繁殖生物学的进化、性别决定机制和性别分化进行阐述,以期为腹足纲物种资源保护与利用提供参考。