The origin and evolution of sex chromosomes,revealed by sequencing of the Silene latifolia female genome

1. Download : Download high-res image (180KB)
2. Download : Download full-size image

     

Mapping genes for phosphorus utilization and correlated traits using a 4k SNP linkage map in Japanese quail (Coturnix japonica)

A large F2 cross with 920 Japanese quail was used to map QTL for phosphorus utilization, calcium utilization, feed per gain and body weight gain. In addition, four bone ash traits were included, because it is known that they are genetically correlated with the focal trait of phosphorus utilization. Trait recording was done at the juvenile stage of the birds. The individuals were genotyped genome‐wide for about 4k SNPs and a linkage map constructed, which agreed well with the reference genome. QTL linkage mapping was performed using multimarker regression analysis in a line cross model. Single marker association mapping was done within the mapped QTL regions. The results revealed several genome‐wide significant QTL. For the focal trait phosphorus utilization, a QTL on chromosome CJA3 could be detected by linkage mapping, which was substantiated by the results of the SNP association mapping. Four candidate genes were identified for this QTL, which should be investigated in future functional studies. Some overlap of QTL regions for different traits was detected, which is in agreement with the corresponding genetic correlations. It seems that all traits investigated are polygenic in nature with some significant QTL and probably many other small‐effect QTL that were not detectable in this study.     

金针菇单孢菌株菌丝生长速度QTL定位分析

本研究以已经完成基因组测序的单核菌株“6-3”与“6-21”为出发菌株,配对后获得有锁状联合的异核菌株并进行出菇,收集担孢子,单孢分离获得90个菌株构成作图群体,对作图群体的每个菌株进行二代测序并测定菌丝在PDA培养基的生长速度。分析“6-3”与“6-21”两单核菌株的SNP,获得68 914个高质量SNP标记用于遗传连锁群分析,构建了14个遗传连锁群,总长度744.32cM,平均长度为53.17cM,标记间平均遗传距离为1.88cM。QTL分析获得一个控制菌丝生长速度的基因座qMGRP1-LG7,该基因座包含134个基因,富集了与物质代谢有关的通路和基因。     

关联分析及其在真菌遗传学研究中的应用

近年来,基于连锁不平衡的关联分析被逐渐应用于解析真菌数量性状的遗传基础。本文在介绍关联分析方法的基础上,综述了关联分析在真菌遗传学中的研究进展,并对其未来的应用前景进行了展望。     

Molecular genetics of growth and development in Populus (Salicaceae). v. mapping quantitative trait loci affecting leaf variation

We examined the genetic variation of leaf morphology and development in the 2-yr-old replicated plantation of an interspecific hybrid pedigree of Populus trichocarpa T. & G. and P. deltoides Marsh. via both molecular and quantitative genetic methods. Leaf traits chosen were those that show pronounced differences between the original parents, including leaf size, shape, orientation, color, structure, petiole size, and petiole cross section. Leaves were sampled from the current terminal, proleptic, and sylleptic branches. In the F2 generation, leaf traits were all significantly different among genotypes, but with significant effects due to genotype X crown-position interaction. Variation in leaf pigmentation, petiole length. And petiole length proportion appeared to be under the control of few quantitative trait loci (QTLs). More QTLs were associated with single leaf area, leaf shape, lamina angle, abaxial color, and petiole flatness, and in these traits the number of QTLs varied among crown positions. In general, the estimates of QTL numbers from Wright's biometric method were close to those derived from molecular markers. For those traits with few underlying QTLs, a single marker interval could explain from 30 to 60% of the observed phenotypic variance. For multigenic traits, certain markers contributed more substantially to the observed variation than others. Genetic cluster analysis showed developmentally related traits to be more strongly associated with each other than with unrelated traits. This finding was also supported by the QTL mapping. For example, the same chromosomal segment of linkage group L seemed to account for 20% of the phenotypic variation of all dimension-related traits, leaf size, petiole length. and midrib angle. In both traits. the P. deltoides alleles had positive effects and were dominant to the P. trichocarpa alleles. Similar relationships were also found for lamina angle. abaxial greenness, and petiole.     

Identification of 10 882 porcine microsatellite sequences and virtual mapping of 4528 of these sequences

A total of 10 882 porcine microsatellite repeats were identified in genomic shotgun sequences from the Sino-Danish Pig Genome Sequencing Consortium (http://www.piggenome.dk). Of these, 4528 microsatellites were placed on a pig-human comparative map by blast analysis of porcine sequences against the human genome (blast cut-off threshold =1 x 10(-5)). All microsatellite sequences placed on the comparative map are accessible at http://www.animalgenome.org/QTLdb/pig.html. These sequences increase the number of identified microsatellites in the porcine genome by several orders of magnitude. They are a new resource of microsatellite sequences for generating markers to be used in linkage studies and in fine mapping and positional cloning of quantitative trait loci.     

A genome scan for serum triglyceride in obese nuclear families

Serum triglyceride (TG) levels are increased in extremely obese individuals, indicating abnormalities in lipid metabolism and insulin resistance. We carried out a genome scan for serum TG in 320 nuclear families segregating extreme obesity and normal weight. Three hundred eighty-two Marshfield microsatellite markers (Screening Set 11) were genotyped. Quantitative linkage analyses were performed using family regression and variance components methods. We found linkage on the 7q36 region [D7S3058, 174 centimorgan (cM), Logarithm of Odds (LOD) = 2.98] for log-transformed TG. We also found suggestive linkages on chromosomes 20 (D20S164, 101 cM, LOD = 2.34), 13 (111 cM, LOD = 2.00), and 9 (104 cM, LOD = 1.90) as well as some weaker trends for chromosomes 1, 3, 5, 10, 12, and 22. In 58 African American families, LOD scores of 3.66 and 2.62 were observed on two loci on chromosome 16: D16S3369 (64 cM) and MFD466 (100 cM). To verify the 7q36 linkage, we added 60 nuclear families, and the LOD score increased to 3.52 (empirical P < 0.002) on marker D7S3058.     

Integration of QTL and bioinformatic tools to identify candidate genes for triglycerides in mice

To identify genetic loci influencing lipid levels, we performed quantitative trait loci (QTL) analysis between inbred mouse strains MRL/MpJ and SM/J, measuring triglyceride levels at 8 weeks of age in F2 mice fed a chow diet. We identified one significant QTL on chromosome (Chr) 15 and three suggestive QTL on Chrs 2, 7, and 17. We also carried out microarray analysis on the livers of parental strains of 282 F2 mice and used these data to find cis-regulated expression QTL. We then narrowed the list of candidate genes under significant QTL using a "toolbox" of bioinformatic resources, including haplotype analysis; parental strain comparison for gene expression differences and nonsynonymous coding single nucleotide polymorphisms (SNP); cis-regulated eQTL in livers of F2 mice; correlation between gene expression and phenotype; and conditioning of expression on the phenotype. We suggest Slc25a7 as a candidate gene for the Chr 7 QTL and, based on expression differences, five genes (Polr3 h, Cyp2d22, Cyp2d26, Tspo, and Ttll12) as candidate genes for Chr 15 QTL. This study shows how bioinformatics can be used effectively to reduce candidate gene lists for QTL related to complex traits.     

关联分析及其在植物遗传学研究中的应用

植物的很多重要经济性状均属于复杂性状。基于连锁分析的QTL作图是研究复杂性状的有效手段, 但其尚存在一定的局限性。随着现代生物学的发展, 一种基于连锁不平衡的新剖分复杂性状方法--关联分析法, 开始应用于植物遗传学研究。与QTL作图法相比, 应用关联分析法具有不需要构建特殊的群体, 可同时对多个等位基因进行分析, 定位QTL精度可达到单基因水平等优势。该文介绍了关联分析方法学的基础和特性, 简述了其在植物遗传学研究中的进展情况, 并对其未来发展和在植物遗传学研究中的应用进行了展望。     

Expression quantitative trait loci: present and future

The last few years have seen the development of large efforts for the analysis of genome function, especially in the context of genome variation. One of the most prominent directions has been the extensive set of studies on expression quantitative trait loci (eQTLs), namely, the discovery of genetic variants that explain variation in gene expression levels. Such studies have offered promise not just for the characterization of functional sequence variation but also for the understanding of basic processes of gene regulation and interpretation of genome-wide association studies. In this review, we discuss some of the key directions of eQTL research and its implications.     

Genetic linkage map of the guppy,Poecilia reticulata,and quantitative trait loci analysis of male size and colour variation

We report construction of a genetic linkage map of the guppy genome using 790 single nucleotide polymorphism markers, integrated from six mapping crosses. The markers define 23 linkage groups (LGs), corresponding to the known haploid number of guppy chromosomes. The map, which spans a genetic length of 899 cM, includes 276 markers linked to expressed genes (expressed sequence tag), which have been used to derive broad syntenic relationships of guppy LGs with medaka chromosomes. This combined linkage map should facilitate the advancement of genetic studies for a wide variety of complex adaptive phenotypes relevant to natural and sexual selection in this species. We have used the linkage data to predict quantitative trait loci for a set of variable male traits including size and colour pattern. Contributing loci map to the sex LG for many of these traits.     

关联分析及其在植物遗传学研究中的应用

植物的很多重要经济性状均属于复杂性状。基于连锁分析的QTL作图是研究复杂性状的有效手段,但其尚存在一定的局限性。随着现代生物学的发展,一种基于连锁不平衡的新剖分复杂性状方法——关联分析法,开始应用于植物遗传学研究。与QTL作图法相比,应用关联分析法具有不需要构建特殊的群体,可同时对多个等位基因进行分析,定位QTL精度可达到单基因水平等优势。该文介绍了关联分析方法学的基础和特性,简述了其在植物遗传学研究中的进展情况,并对其未来发展和在植物遗传学研究中的应用进行了展望。     

RiceQTLPro: an integrated database for quantitative trait loci marker mapping in rice plant

The National Agricultural Biotechnology Information Center (NABIC) in South Korea reconstructed a RiceQTLPro database for gene positional analysis and structure prediction of the chromosomes. This database is an integrated web-based system providing information about quantitative trait loci (QTL) markers in rice plant. The RiceQTLPro has the three main features namely, (1) QTL markers list, (2) searching of markers using keyword, and (3) searching of marker position on the rice chromosomes. This updated database provides 112 QTL markers information with 817 polymorphic markers on each of the 12 chromosomes in rice.

Availability

The database is available for free at http://nabic.rda.go.kr/gere/rice/geneticMap/     

猪2号染色体遗传连锁图谱的构建与QTL定位分析

构建了猪2号染色体的遗传连锁图谱,并进一步进行了重要生产性状数量性状位点的定位,结果表明,7个微卫星位点均为中高度多态性位点,多态信息含量为0．40182－0．58477,可以满足遗传连锁图谱构建的要求,构建的资源家系遗传连锁图谱总长152．9cM,位点的排列顺序与USDA结果一致,但除了Sw2516与Sw1201标记区间外,所有标记区间距离均大于USDA图谱,将连锁图谱与性状记忆结合起来,进一步进行了猪数量性状位点定位的研究,在2号染色体发现了显著影响活体估测瘦肉率等活体估测性状的QTLs,此外还发现眼肌高度和背最长肌大理石纹的QTLs,其中影响活体估测瘦肉率的QTL达到了染色体显著的水平（P＜0．01）,且解释性状的表型变异达21．55％,影响眼肌高度和背最长肌大理石纹的QTLs分别可以解释10．12％和10．97％的表型变异,影响活体估测性状的QTLs加性效应与显性效应作用方向相反,影响眼肌高度的QTL加性效应与显性效应相同,在大白猪中具有增效等位基因,定位的QTLs效应较大,为在群体中开展分子标记辅助育种奠定了理论基础。     

Quantitative trait loci for growth and body size in the nine‐spined stickleback Pungitius pungitius L.

Body size is an ecologically important trait shown to be genetically variable both within and among different animal populations as revealed by quantitative genetic studies. However, few studies have looked into underlying genetic architecture of body size variability in the wild using genetic mapping methods. With the aid of quantitative trait loci (QTL) analyses based on 226 microsatellite markers, we mapped body size and growth rate traits in the nine‐spined stickleback (Pungitius pungitius) using an F₂‐intercross (n = 283 offspring) between size‐divergent populations. In total, 17 QTL locations were detected. The proportion of phenotypic variation explained by individual body size‐related QTL ranged from 3% to 12% and those related to growth parameters and increments from 3% to 10%. Several of the detected QTL affected either early or late growth. These results provide a solid starting point for more in depth investigations of structure and function of genomic regions involved in determination of body size in this popular model of ecological and evolutionary research.     

Nucleotide diversity in Silene latifolia autosomal and sex-linked genes

The plant Silene latifolia has separate sexes and sex chromosomes, and is of interest for studying the early stages of sex chromosome evolution, especially the evolution of non-recombining regions on the Y chromosome. Hitch-hiking processes associated with ongoing genetic degeneration of the non-recombining Y chromosome are predicted to reduce Y-linked genes'' effective population sizes, and S. latifolia Y-linked genes indeed have lower diversity than X-linked ones. We tested whether this represents a true diversity reduction on the Y, versus the alternative possibility, elevated diversity at X-linked genes, by collecting new data on nucleotide diversity for autosomal genes, which had previously been little studied. We find clear evidence that Y-linked genes have reduced diversity. However, another alternative explanation for a low Y effective size is a high variance in male reproductive success. Autosomal genes should then also have lower diversity than expected, relative to the X, but this is not found in our loci. Taking into account the higher mutation rate of Y-linked genes, their low sequence diversity indicates a strong effect of within-population hitch-hiking on the Y chromosome.     

Quantitative trait loci analysis of phytate and phosphate concentrations in seeds and leaves of Brassica rapa

Phytate, being the major storage form of phosphorus in plants, is considered to be an anti-nutritional substance for human, because of its ability to complex essential micronutrients. In the present study, we describe the genetic analysis of phytate and phosphate concentrations in Brassica rapa using five segregating populations, involving eight parental accessions representing different cultivar groups. A total of 25 quantitative trait loci (QTL) affecting phytate and phosphate concentrations in seeds and leaves were detected, most of them located in linkage groups R01, R03, R06 and R07. Two QTL affecting seed phytate (SPHY), two QTL affecting seed phosphate (SPHO), one QTL affecting leaf phosphate and one major QTL affecting leaf phytate (LPHY) were detected in at least two populations. Co-localization of QTL suggested single or linked loci to be involved in the accumulation of phytate or phosphate in seeds or leaves. Some co-localizing QTL for SPHY and SPHO had parental alleles with effects in the same direction suggesting that they control the total phosphorus concentration. For other QTL, the allelic effect was opposite for phosphate and phytate, suggesting that these QTL are specific for the phytate pathway.     

The Human Obesity Gene Map: The 2001 Update

This report constitutes the eighth update of the human obesity gene map, incorporating published results up to the end of October 2001. Evidence from the rodent and human obesity cases caused by single-gene mutations, Mendelian disorders exhibiting obesity as a clinical feature, quantitative trait loci (QTLs) uncovered in human genome-wide scans and in crossbreeding experiments in various animal models, association and linkage studies with candidate genes and other markers is reviewed. The human cases of obesity related in some way to single-gene mutations in six different genes are incorporated. Twenty-five Mendelian disorders exhibiting obesity as one of their clinical manifestations have now been mapped. The number of different QTLs reported from animal models currently reaches 165. Attempts to relate DNA sequence variation in specific genes to obesity phenotypes continue to grow, with 174 studies reporting positive associations with 58 candidate genes. Finally, 59 loci have been linked to obesity indicators in genomic scans and other linkage study designs. The obesity gene map depicted in Figure 1 reveals that putative loci affecting obesity-related phenotypes can be found on all chromosomes except chromosome Y. A total of 54 new loci have been added to the map in the past 12 months, and the number of genes, markers, and chromosomal regions that have been associated or linked with human obesity phenotypes is now above 250. Likewise, the number of negative studies, which are only partially reviewed here, is also on the rise.