A genome-wide perspective on the diversity and selection signatures in indigenous goats using 53 K single nucleotide polymorphism array

Tibetan goats, Taihang goats, Jining grey goats, and Meigu goats are the representative indigenous goats in China, found in Qinghai-Tibet Plateau, Western pastoral area, Northern and Southern agricultural regions. Very few studies have conducted a comprehensive analysis of the genomic diversity and selection of these breeds. We genotyped 96 unrelated individuals, using goat 53 K Illumina BeadChip array, of the following goat breeds: Tibetan (TG), Taihang (THG), Jining grey (JGG), and Meigu (MGG). A total of 45 951 single nucleotide polymorphisms were filtered to estimate the genetic diversity and selection signatures. All breeds had a high proportion (over 95%) of polymorphic loci. The observed and excepted heterozygosity ranged from 0.338 (MGG) to 0.402 (JGG) and 0.339 (MGG) to 0.395 (JGG), respectively. Clustering analysis displayed a genetically distinct lineage for each breed, and their Fst were greater than 0.25, indicating that they had a higher genetic differentiation between groups. Furthermore, effective population size reduced in all four populations, indicating a loss of genetic diversity. In addition, runs of homozygosity were mainly distributed in 5–10 Mb. Lastly, we identified signature genes, which were closely related to high-altitude adaptation (ADIRF) and prolificity (CNTROB, SMC3, and PTEN). This study provides a valuable resource for future studies on genome-wide perspectives on the diversity and selection signatures of Chinese indigenous goats.     

Genetic variation in three species in the Lampropholis delicata (Lacertilia: Scincidae) complex

The Lampropholis delicata complex consists of three closely related species, which have very different habitat requirements and geographic distributions. Percentage polymorphism and average heterozygosity per population are lowest in the species with the narrowest habitat requirements. Genetic differentiation between populations is also lowest in this species, which had a very limited and almost continuous distribution. For one species, which occurs in a very wide range of habitats, both natural and disturbed, genetic variability is compared between samples from disturbed and undisturbed habitats. Average heterozygosity is significantly lower in samples from disturbed than in those from undisturbed sites.     

Adaptation to salinity inHordeum jubatum L. populations studied using reciprocal transplants

Tillers and seedlings ofHordeum jubatum L. from three sites with contrasting salinity regimes in central Saskatchewan, Canada were reciprocally transplanted in order to examine the tolerance of populations of this species to salinity and related habitat factors. Survival, growth and fecundity of the three populations were controlled more by transplant site characteristics than by genetic differences, i.e. differences among populations at a site tended to be smaller than differences among sites. Survival, growth and reproduction of all three populations were best at the non-saline site. The population originating at the non-saline site showed the poorest growth in the two saline habitats, but still had substantial salt tolerance. Fecundity was greatest when the populations were grow at their site of origin.     

红原鸡与家鸡的亲缘关系研究

对中国红原鸡滇地亚种和海南亚种与我国茶花鸡,泰和鸡和寿光鸡等地方鸡种以及芦花鸡,洛岛红等外国鸡种进行了血型（３个位点,１３个等位基因）,蛋白质（酶）多态（５个位点,１１个等位基因）和ＤＮＡ指纹分析,结果表明,红原鸡与茶花鸡（原始型品种）的亲缘关系较近;与泰和鸡,寿光鸡,芦花鸡,洛岛红（进化型品种）的亲缘关系较远,呈红原鸡－茶花鸡－泰和鸡,寿光鸡或芦花鸡,洛岛红这样一个进化阶梯,以上结果与国外资料（     

Genetic tools for selective labeling of proteins with α-15N-amino acids

Summary A collection of genetic tools that can be used to manipulate amino acid metabolism in Escherichia coli is described. The set comprises 21 strains of bacteria, each containing a different genetic defect that is closely linked to a selectable transposon marker. These tools can be used to construct strains of E. coli with ideal genotypes for residue-specific, selective labeling of proteins with nearly any ¹⁵N-amino acid. By using strains which have been modified to contain the appropriate genetic lesions to control amino acid biosynthesis, dilution of the isotope by endogenous amino acid biosynthesis and scrambling of the label to other types of residues can be avoided.Abbreviations ¹⁵N-amino acid -¹⁵N-amino acid - Cam^R chloramphenicol-resistant - DPA diaminopimelic acid - Hfr high-frequency recombinant - LB Luria broth - Kan^R kanamycin resistant - P1 bacteriophage P1 - pfu plaque-forming units - Str^R streptomycin-resistant - Tet^R tetracycline-resistant     

The genetic resolution of juvenile canopy structure and function in a three-generation pedigree of Populus

 A genetic approach to the understanding of tree architecture is to cross trees of contrasting features and to study their segregating F₂ progenies. For this purpose, members of a 3-generation pedigree, combining Populus trichocarpa, P. deltoides, and their F₁ and F₂ offspring, were grown side by side in a clonally replicated plantation. At 2 and 3 years of growth, tree architecture was analyzed at the stem, branch, and leaf levels. In all generations, proleptic branches were more numerous, longer, and had more and larger leaves than sylleptics initiated in the same year. The analysis of variance revealed significant genotypic effects on growth, branch and leaf biometrics in the F₂ family, with broad-sense heritabilities (H²) ranging from 0.50 to 0.80 for most traits. For branch and leaf traits, the H² values were found to vary among branch types and crown positions. In year 2, the degree of genetic control was stronger for sylleptics than proleptics and for upper than lower crown positions. These patterns were followed in year 3, except that H² values were more a function of position within crown, as a consequence of increased competition among trees. The genetic correlations between branch/leaf morphology and stem growth were also a function of branch type and crown position. Generally, traits on proleptics or at upper positions were more tightly correlated with height growth, whereas those on sylleptics or at lower positions, with basal area growth. By year 3, proleptic traits showed increased genetic correlations with both height and radial growth. The implications of these results for the construction of ideotypes are discussed. Received: 1 December 1995     

FINGAR: A new genetic algorithm-based method for fitting NMR data

Summary A new NMR refinement method, FINGAR (FIt NMR using a Genetic AlgoRithm), has been developed, which allows one to determine a weighted set of structures that best fits measured NMR-derived data. This method shows appreciable advantages over commonly used refinement methods. FINGAR generates an ensemble of conformations whose average reproduces the experimental NMR-derived restraints. In addition, a statistical importance weight is assigned to each of the conformations in the ensemble. As a result, one is not limited to simply presenting an envelope of sampled conformers. Instead, one can subsequently focus on a select few conformers of high weight. This is critical, because many structural analyses depend on using discrete conformations, not simply averages or ensembles. The genetic algorithm used by FINGAR allows one to simultaneously and reliably fit against many restraints, and to generate solutions which include as many conformations with non-zero weights as are necessary to generate the best fit. An added benefit of FINGAR is that because the time-consuming step in this method needs only to be performed once, in the beginning of the first run, numerous FINGAR simulations can be performed rapidly.     

Covariation among floral traits in Spergularia marina (Caryophyllaceae): geographic and temporal variation in phenotypic and among-family correlations

Strong covariation among traits suggests the presence of constraints on their independent evolution due to pleiotropy, to linkage, or to selective forces that maintain particular trait combinations. We examined floral trait covariation among individuals, among maternal families within and across populations, and over time, in greenhouse-raised plants of the autogamous Spergularia marina. We had three aims. First, since the phenotype of traits expressed by modular organs often changes as individuals age, estimates of the degree of genetic covariation between such traits may also change over time. To seek evidence for this, we measured weekly (for five weeks) an array of floral traits among plants representing ～ 10 maternal families from each of four populations. The statistical significance of the phenotypic and among-family correlations among traits changed over time. Second, we compared populations with respect to trait covariation to determine whether populations or traits appear to be evolving independently of one another. Differences observed among populations suggest that they have diverged genetically. Third, we sought correlations that might reflect constraints on the independent evolution of floral traits. Investment in another and ovule production per flower vary independently among maternal families; there was no evidence for a “trade-off” between male and female investment. We propose that in autogamous taxa one should not find a negative correlation between pollen and ovule production per flower, as such taxa cannot evolve sexual specialization and should be under strong selection to maintain an efficient pollen:ovule ratio, preventing the evolution of male-biased or female-biased genotypes. We found that other pairs of floral traits, however, expressed highly signficant correlation coefficients, suggesting the presence of some evolutionary constraints, at least within some populations, although their strength depended on exactly when flowers were sampled.