Repeat subtraction‐mediated sequence capture from a complex genome

Sequence capture technologies, pioneered in mammalian genomes, enable the resequencing of targeted genomic regions. Most capture protocols require blocking DNA, the production of which in large quantities can prove challenging. A blocker‐free, two‐stage capture protocol was developed using NimbleGen arrays. The first capture depletes the library of repetitive sequences, while the second enriches for target loci. This strategy was used to resequence non‐repetitive portions of an approximately 2.2 Mb chromosomal interval and a set of 43 genes dispersed in the 2.3 Gb maize genome. This approach achieved approximately 1800–3000‐fold enrichment and 80–98% coverage of targeted bases. More than 2500 SNPs were identified in target genes. Low rates of false‐positive SNP predictions were obtained, even in the presence of captured paralogous sequences. Importantly, it was possible to recover novel sequences from non‐reference alleles. The ability to design novel repeat‐subtraction and target capture arrays makes this technology accessible in any species.     

Micro‐ and macrospatial scale analyses illustrates mixed mating strategies and extensive geneflow in populations of an invasive haploid pathogen

Sexual reproduction in fungi involves either a single individual (selfing) or two individuals (outcrossing). To investigate the roles that these two strategies play in the establishment of an invasive alien pathogen, the Eucalyptus leaf‐infecting fungus, Teratosphaeria (Mycosphaerella) nubilosa was studied. Specifically, the genetic diversity of the pathogen was investigated at micro and macrospatial scales. Interestingly, while data obtained at microspatial scales show clearly that selfing is the main reproductive strategy, at macrospatial scales the population genetic structure was consistent with a genetically outcrossing organism. Additional analyses were performed to explore these apparently discordant results at different spatial scales and to quantify the contribution of selfing vs. outcrossing to the genotypic diversity. The results clearly show that the fungus has a mixed mating strategy. While selfing is the predominant form of mating, outcrosses must have occurred in the pathogen that increased the genotypic diversity of the fungus over time. This mating strategy, coupled with the high levels of geneflow between distant populations of the pathogen, has created an even distribution of maximum diversity from the smallest (leaf) to largest scales (>500 km), which will make breeding for resistance difficult. These data illustrate the evolutionary potential and danger of the introduction of multiple genotypes of a potentially outcrossing pathogen, especially when it has a high dispersal potential.     

黑龙江省实验大鼠遗传学概貌分析

目的对送检的黑龙江省生产的实验大鼠遗传概貌进行分析。方法参照国家标准《实验动物近交系小鼠、大鼠生化标记检测方法》GB/T14927.1-2001,应用乙酸纤维素板,利用Akp1、Es1、Es3、Es4、Es6、Es8、Es9和Es10等8种同工酶位点,对来自编号分别为2011、2014、3026、8028和8029的5个单位的SD、Wistar、DA、PVG等4个品系的25只实验大鼠,进行生化标记位点的检测。结果除单位2014的SD大鼠在Es3存在a和b两种带型,8028和8029未检测Es10、2014和3026未检测Es6,8,9,其余各单位的大鼠在8个位点都表现出相同的带型。结论送检的黑龙江省生产的SD和Wistar大鼠符合封闭群遗传学概貌;DA和PVG大鼠样品间带型一致。     

花椰菜温敏型雄性不育系的RAPD标记

选取温敏花椰菜不育系GS-19与GS-31杂交组合的F2高可育和高不育单株构建基因池,利用100对随机引物对其进行RAPD标记。同时,采用正交设计对其反应体系及扩增条件进行优化。试验结果表明,在25μL反应体系中含dNTPs0.625mmol/L,引物0.5μmol/L,DNA模板60ng,Taq酶1.5U,超纯水14.9μL;反应条件为94℃预变性4min,然后进行94℃变性30s,36℃退火45s,72℃延伸90s,35个循环后,再72℃延伸7min,花椰菜RAPD扩增效果较好。P21-1800为花椰菜温敏雄性不育基因的连锁标记。     

利用微卫星DNA标记法进行5个肉用绵羊品种的多态性分析和杂种优势率预测

研究选择了与产肉性能相关的5个微卫星标记,分析了这5个位点在杜泊、德国美利奴、特克塞尔、道塞特和右玉本地绵羊5个品种中的遗传多态性.通过遗传分析预测了4个国外引进肉用绵羊品种与右玉本地绵羊的杂种优势,并与实际测定结果进行了比较分析.结果表明,利用微卫星DNA多态性进行品种间杂种优势预测是可行的,杜泊羊与右玉本地绵羊杂交的杂种优势最大,与实际测定结果一致.     

Somatic mosaicism in cases with small supernumerary marker chromosomes

Somatic mosaicism is something that is observed in everyday lives of cytogeneticists. Chromosome instability is one of the leading causes of large-scale genome variation analyzable since the correct human chromosome number was established in 1956. Somatic mosaicism is also a well-known fact to be present in cases with small supernumerary marker chromosomes (sSMC), i.e. karyotypes of 47,+mar/46. In this study, the data available in the literature were collected concerning the frequency mosaicism in different subgroups of patients with sSMC. Of 3124 cases with sSMC 1626 (52%) present with somatic mosaicism. Some groups like patients with Emanuel-, cat-eye- or i(18p)- syndrome only tend rarely to develop mosaicism, while in Pallister-Killian syndrome every patient is mosaic. In general, acrocentric and non-acrocentric derived sSMCs are differently susceptible to mosaicism; non-acrocentric derived ones are hereby the less stable ones. Even though, in the overwhelming majority of the cases, somatic mosaicism does not have any detectable clinical effects, there are rare cases with altered clinical outcomes due to mosaicism. This is extremely important for prenatal genetic counseling. Overall, as mosaicism is something to be considered in at least every second sSMC case, array-CGH studies cannot be offered as a screening test to reliably detect this kind of chromosomal aberration, as low level mosaic cases and cryptic mosaics are missed by that.     

Development of microsatellite markers for identifying Brazilian Coffea arabica varieties

Microsatellite markers, also known as SSRs (Simple Sequence Repeats), have proved to be excellent tools for identifying variety and determining genetic relationships. A set of 127 SSR markers was used to analyze genetic similarity in twenty five Coffea arabica varieties. These were composed of nineteen commercially important Brazilians and six interspecific hybrids of Coffea arabica, Coffea canephora and Coffealiberica. The set used comprised 52 newly developed SSR markers derived from microsatellite enriched libraries, 56 designed on the basis of coffee SSR sequences available from public databases, 6 already published, and 13 universal chloroplast microsatellite markers. Only 22 were polymorphic, these detecting 2-7 alleles per marker, an average of 2.5. Based on the banding patterns generated by polymorphic SSR loci, the set of twenty-five coffee varieties were clustered into two main groups, one composed of only Brazilian varieties, and the other of interspecific hybrids, with a few Brazilians. Color mutants could not be separated. Clustering was in accordance with material genealogy thereby revealing high similarity.     

Association between MUC1 gene polymorphism and expected progeny differences in Nelore cattle (Bos primigenius indicus)

MUC1 is a heavily glycosylated mammalian transmembrane protein expressed by mucosal secretory tissues for both protection against microbial infection and lubrication. An important characteristic of MUC1 is its variable number of tandem repeats (VNTR) containing several sites for O-glycosylation. VNTR length has been associated with many human diseases and with certain economically important traits in domestic ruminants. The aim of the present study was to correlate the length of MUC1 gene VNTR with expected progeny differences (EPDs) obtained for growth, fertility and carcass traits. Five alleles were identified, with alleles containing short VNTRs being more frequent than those with long, thereby demonstrating that Brazilian Nelore cattle are characterized by high frequencies in short MUC1 VNTRs. Statistical analyses revealed there to be no significant association between VNTR length and EPDs for weight at 120 days (W(120) ), scrotal circumference at 365 (SC (365) ) and 450 (SC (450) ) days, age at first calving (AFC), and rib eye area (REA).     

Nest composition and worker relatedness in three slave-making ants of the genus Rossomyrmex Arnoldi and their Proformica Ruzsky hosts (Hymenoptera,Formicidae)

Abstract In this paper, we analyze and compare nest composition and architecture as well as worker relatedness in three related species of slave-making ants: Rossomyrmex anatolicus, R. minuchae, and R. quandratinodum. Colony structure within nests is an important trait in ants, especially in the case of mixed societies, when host and parasite coexist in the same nest. Data for their respective free-living hosts, Proformica korbi, P. longiseta and P. sp., are also provided. For our study, we integrated a meticulous excavation procedure with a genetic method. We conclude that the average number of parasites, as well as of slaves, is species-specific, whereas nest depth depends on the nest architecture of the host. The genus Rossomyrmex seems to be monogynous and monandrous, whereas Proformica shows differences in the number of queens and mating frequency. R. quandratinodum shows different traits in nest composition (host/parasite ratio: P/R) and architecture. The difference in traits may account for some differences in parasitism: raid process or avoidance of parasitism.