Journal of Heredity

Using Seedling and Pericarp Tissues to Determine Maternal Parentage of Dispersed Valley Oak Recruits.

Publication Date: 2012 Jan 30 PMID: 22291163
Authors: Smouse, P. E. - Sork, V. L. - Scofield, D. G. - Grivet, D.
Journal: J Hered

The spatial pattern of established seedlings yields valuable information about variation in fecundity, dispersal, and spatial structure of distributed recruits, but separating maternal and paternal contributions in monoecious species has been hampered by the "2 parent" problem. It is now possible to determine the maternal parentage of established recruits with genetic assay of maternally derived tissues of the seed or fruit, but the DNA of weathered maternal tissues often yields unreliable genotypes, reducing the practical range of such assay. We develop a mixed assay of seedling and seed (pericarp) tissues and illustrate it with distributed recruits of California valley oak (Quercus lobata Nee). Detailed analysis indicates correct maternal assignment rates of canopy patch recruits of 56% (seedling assay only) versus 94% (mixed assay). For open patch recruits, maternal assignment rates were less than 50% (seedling assay only) versus 91% (mixed assay). The strategy of choice is to use seedling genotypes to identify a small set of credible parental candidates and then deploy 3-4 well-chosen pericarp/endocarp loci to reduce that list to a single obvious maternal candidate. The increase in the number of recruits available for subsequent analysis is pronounced, increasing precision and statistical power for subsequent inference.

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Computational Identification of MicroRNAs in Strawberry Expressed Sequence Tags and Validation of Their Precise Sequences by miR-RACE.

Publication Date: 2012 Jan 27 PMID: 22287696
Authors: Dong, Q. H. - Han, J. - Yu, H. P. - Wang, C. - Zhao, M. Z. - Liu, H. - Ge, A. J. - Fang, J. G.
Journal: J Hered

MicroRNAs (miRNAs) are small, endogenously expressed, nonprotein-coding RNAs that regulate gene expression at the post-transcriptional level in both animals and plants through repressing translation or inducing mRNA degradation. A comprehensive strategy to identify new miRNA homologs by mining the repository of available strawberry expressed sequence tags (ESTs) was developed. By adopting a range of filtering criteria, we identified 11 potential miRNAs belonging to 5 miRNA families from 47 890 Fragaria vesca EST sequences. Using 2 specific 5' and 3' miRNA RACE PCR reactions and a sequence-directed cloning method, we accurately determined both end sequences of 5 candidate miRNAs. Meanwhile, qRT-PCR was used to detect the expression of these 5 miRNAs in different strawberry organs and tissues at several growing stages. These newly identified F. vesca miRNAs (fve-miRNAs) and their expression information can improve our understanding of possible roles of fve-miRNAs in regulating the growth and development of F. vesca.

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Extending Pedigree Analysis for Uncertain Parentage and Diverse Breeding Systems.

Publication Date: 2012 Jan 24 PMID: 22275398
Authors: Lacy, R. C.
Journal: J Hered

Breeding programs aimed at conserving genetic diversity in populations of wildlife or rare domestic breeds rely on detailed pedigree analysis for selection of breeders that will minimize the loss of alleles, reduce the accumulation of inbreeding, and maintain gene diversity. Commonly, techniques use a matrix of kinship coefficients to derive measures of genetic variation, inbreeding, and the value of individuals as breeders. Although these techniques were first developed for use on known pedigrees of diploid individuals, the concepts and methods can be extended to apply to any entity that contains genes derived from definable sources (e.g., individual parents, social groups, colonies, gene banks) via a definable mechanism of heredity (e.g., sexual reproduction between separate sexes, hermaphroditic selfing, autozygous production of homozygous or haploid offspring, cloning). Individuals with partly unknown ancestry or multiple possible parents can also be incorporated into kinship calculations, based on probabilistic assignment of parental contributions. This paper presents the algorithms used in new PMx software to extend traditional pedigree analysis techniques used for complete pedigrees of sexually reproducing, diploid species to deal with missing information due to unknown or uncertain parentage, and other breeding systems such as clones, selfing hermaphrodites, and haploid offspring or autogamy.

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The Genetics of Cuticular Hydrocarbon Profiles in the Fruit Fly Drosophila simulans.

Publication Date: 2012 Jan 20 PMID: 22268163
Authors: Sharma, M. D. - Mitchell, C. - Hunt, J. - Tregenza, T. - Hosken, D. J.
Journal: J Hered

Female mate choice is one mechanism of sexual selection and, provided there is adequate genetic variation in the male traits that are the target of this selection, they will evolve via female choice. Cuticular hydrocarbons (CHCs) are important in Drosophila mate choice, but relatively little is known about the underlying genetic architecture of CHC profiles in Drosophila simulans. Here, we used gas chromatography-mass spectrometry to investigate patterns of genetic variation in the CHC profiles of male and female D. simulans using isofemale lines. We found substantial genetic variation for CHC profiles and individual CHC components, and individual CHCs were frequently strongly genetically correlated, with a tendency for negative covariance between long- and short-chain CHCs in males. Intersexual genetic covariances were often weak and frequently differed in sign. These findings are novel and significant, highlighting the previously unexplored genetic architecture of CHCs in D. simulans and suggest that this architecture may facilitate sex-specific CHC evolution.

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(Lack of) Genetic Diversity in Immune Genes Predates Glacial Isolation in the North American Mountain Goat (Oreamnos americanus).

Publication Date: 2012 Jan 20 PMID: 22268162
Authors: Shafer, A. B. - Fan, C. W. - Cote, S. D. - Coltman, D. W.
Journal: J Hered

The major histocompatibility complex (MHC) plays an important role in an organism's ability to respond to pathogens. Immunogenetic diversity is advantageous as it permits the recognition of more external antigens. For this reason, MHC and immune gene variation are considered a barometer for the genetic health of wild populations. Mountain goats (Oreamnos americanus) were previously shown to have little variation at the MHC Class II Oram-DRB locus, which was attributed to population bottlenecks during the last glacial maximum (LGM). In this paper, we extended the analysis of immunogenetic variability in mountain goats to 5 genes representing the 3 classes of MHC gene (Class I OLA, Class II DRA and DRB, and Class III TNF-alpha) and the natural resistance-associated macrophage protein. We sequenced approximately 3000 bp from 31 individuals sampled across the range of mountain goats and found very low levels of diversity (1-3 polymorphic sites per gene) with the exception of the Class I Oram-OLA gene. Oram-OLA was nearly 30 times more diverse than the other immune genes and appears to represent a source of increased immunogenetic diversity. This diversity may be attributed to multiple loci, mediated by pathogen exposure, or potentially influenced by social factors. The distribution of SNPs was not associated with refugial history, suggesting that the current distribution of immunogenetic diversity was present prior to the LGM. These data suggest that although they have low levels of diversity at the 4 of 5 immune loci, mountain goats may be better equipped for future climate oscillations and pathogen exposure than previously thought.

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Single-Base Substitution in P1B-ATPase Gene Is Associated with a Major QTL for Seed Cadmium Concentration in Soybean.

Publication Date: 2012 Jan 19 PMID: 22268161
Authors: Benitez, E. R. - Hajika, M. - Takahashi, R.
Journal: J Hered

Cadmium (Cd) is a pollutant metal present in soils and toxic to biologic organisms. Previous studies using recombinant inbred lines derived from a cross between soybean (Glycine max [L.] Merr.) cultivars Harosoy and Fukuyutaka revealed a major quantitative trait loci for seed Cd concentration (cd1) in chromosome 9. The genome sequence of Williams 82 suggested that a P(1B)-ATPase gene involved in the transport of metals was located in the vicinity of cd1. cDNA sequencing suggested existence of two types of transcripts: one (GmHMA1a) consisting of 9 exons and 8 introns and the other (GmHMA1b) consisting of 8 exons and 7 introns. The putative polypeptide, GmHMA1a, consisted of 885 amino acids, whereas premature termination of translation of GmHMA1b generated a putative polypeptide with 559 amino acids. GmHMA1a had a 49.8% similarity with AtHMA3, a P(1B)-ATPase of Arabidopsis. GmHMA1a of Fukuyutaka differed from that of Harosoy by a single-base substitution that led to an amino acid substitution from E to G at amino acid position 608. A derived cleaved amplified polymorphic sequence (dCAPS) marker was developed to detect the base substitution, and this dCAPS marker was successfully associated with seed Cd concentration. Transgenic experiments may be necessary to verify that GmHMA1 actually corresponds to cd1.

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A Comparison of Strategies for Selecting Breeding Pairs to Maximize Genetic Diversity Retention in Managed Populations.

Publication Date: 2012 Jan 12 PMID: 22246407
Authors: Ivy, J. A. - Lacy, R. C.
Journal: J Hered

Captive breeding programs aim to maintain populations that are demographically self-sustaining and genetically healthy. It has been well documented that the best way for managed breeding programs to retain gene diversity (GD) and limit inbreeding is to select breeding pairs that minimize a population's average kinship. We used a series of computer simulations to test 4 methods of minimizing average kinship across a variety of scenarios with varying generation lengths, mortality rates, reproductive rates, and rates of breeding pair success. "Static MK Selection" and "Dynamic MK Selection" are 2 methods for iteratively selecting genetically underrepresented individuals for breeding, whereas "Ranked MK Selection" and "Simultaneous MK Selection" are 2 methods for concurrently selecting the group of breeding individuals that produce offspring with the lowest average kinship. For populations with discrete generations (24 tested scenarios), we found that the Simultaneous and Ranked MK Selection methods were generally the best, nearly equivalent methods for selecting breeding pairs that retained GD and limited inbreeding. For populations with overlapping generations (198 tested scenarios), we found that Dynamic MK Selection was the most robust method for selecting breeding pairs. We used these results to provide guidelines for identifying which method of minimizing average kinship was most appropriate for various breeding program scenarios.

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Recent Progress in Polymorphism-Based Population Genetic Inference.

Publication Date: 2012 Jan 12 PMID: 22246406
Authors: Crisci, J. L. - Poh, Y. P. - Bean, A. - Simkin, A. - Jensen, J. D.
Journal: J Hered

The recent availability of whole-genome sequencing data affords tremendous power for statistical inference. With this, there has been great interest in the development of polymorphism-based approaches for the estimation of population genetic parameters. These approaches seek to estimate, for example, recently fixed or sweeping beneficial mutations, the rate of recurrent positive selection, the distribution of selection coefficients, and the demographic history of the population. Yet despite estimating similar parameters using similar data sets, results between methodologies are far from consistent. We here summarize the current state of the field, compare existing approaches, and attempt to reconcile emerging discrepancies. We also discuss the biases in selection estimators introduced by ignoring the demographic history of the population, discuss the biases in demographic estimators introduced by assuming neutrality, and highlight the important challenge to the field of achieving a true joint estimation procedure to circumvent these confounding effects.

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Bisprimer--A Program for the Design of Primers for Bisulfite-Based Genomic Sequencing of Both Plant and Mammalian DNA Samples.

Publication Date: 2012 Jan 13 PMID: 22246405
Authors: Kovacova, V. - Janousek, B.
Journal: J Hered

Plants and animals differ in the sequence context of the methylated sites in DNA. Plants exhibit cytosine methylation in CG, CHG, and CHH sites, whereas CG methylation is the only form present in mammals (with an exception of the early embryonic development). This fact must be taken into account in the design of primers for bisulfite-based genomic sequencing because CHG and CHH sites can remain unmodified. Surprisingly, no user-friendly primer design program is publicly available that could be used to design primers in plants and to simultaneously check the properties of primers such as the potential for primer-dimer formation. For studies concentrating on particular DNA loci, the correct design of primers is crucial. The program, called BisPrimer, includes 2 different subprograms for the primer design, the first one for mammals and the second one for angiosperm plants. Each subprogram is divided into 2 variants. The first variant serves to design primers that preferentially bind to the bisulfite-modified primer-binding sites (C to U conversion). This type of primer preferentially amplifies the bisulfite-converted DNA strands. This feature can help to avoid problems connected with an incomplete bisulfite modification that can sometimes occur for technical reasons. The second variant is intended for the analysis of samples that are supposed to consist of a mixture of DNA molecules that have different levels of cytosine methylation (e.g., pollen DNA). In this case, the aim is to minimize the selection in favor of either less methylated or more methylated molecules.

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Successful Genotyping of Microsatellites in the Woolly Mammoth.

Publication Date: 2012 Jan 10 PMID: 22235141
Authors: Ishida, Y. - Roca, A. L. - Fratpietro, S. - Greenwood, A. D.
Journal: J Hered

Genetic analyses using ancient DNA from Pleistocene and early Holocene fossils have largely relied on mitochondrial DNA (mtDNA) sequences. Among woolly mammoths, Mammuthus primigenius, mtDNA analyses have identified 2 distinct clades (I and II) that diverged 1-2 Ma. Here, we establish that microsatellite markers can be effective on Pleistocene samples, successfully genotyping woolly mammoth specimens at 2 loci. Although significant differentiation at the 2 microsatellite loci was not detected between 16 clade I and 4 clade II woolly mammoths, our results demonstrate that the nuclear population structure of Pleistocene species can be examined using fast-evolving nuclear microsatellite markers.

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