bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physical and Genetic Mapping of Chromosome 9S in Maize Using Mutations With Terminal Deficiencies
Authors: Chao Shiaoman , Gardiner Jack M , Melia-Hancock Susan , Coe Edward H 
Published: January 2021

Abstract
Deletion mapping was employed to determine the physical order of five morphological variants, pyd1, yg2, wd1, v28 and v31, with respect to restriction fragment length polymorphism (RFLP) markers located at the distal end of chromosome 9S in maize. The genetic materials used were a series of terminal-deficiency mutants, newly derived with McClintock's original stocks developed in the 1940s, via breakage-fusion-bridge cycles. A combined physical map and genetic map has been constructed based on data gathered from both genetic complementation tests and RFLP analysis. The location of v3l in relation to RFLP markers was further determined by interval mapping. The physical distance between the healed telomeric end and the most distal RFLP marker in two terminal-deficiency lines was established by using pulsed field gel electrophoresis and verified by Bal31 digestion. The results from this study set a foundation for studies on the mechanism of healing of broken chromosome ends in higher plants.
Less-Than-Additive Epistatic Interactions of Quantitative Trait Loci in Tomato
Authors: Eshed Yuval , Zamir Dani 
Published: January 2021

Abstract
Epistasis plays a role in determining the phenotype, yet quantitative trait loci (QTL) mapping has uncovered little evidence for it. To address this apparent contradiction, we analyzed interactions between individual Lycopersicon pennellii chromosome segments introgressed into an otherwise homogeneous genetic background of L. esculentum (cv. M82). Ten different homozygous introgression lines, each containing from 4 to 58 cM of introgressed DNA, were crossed in a half diallele scheme. The 45 derived double heterozygotes were evaluated in the field for four yield-associated traits, along with the 10 single heterozygotes and M82. Of 180 (45 × 4) tested interactions, 28% were epistatic (P &lt; 0.05) on both linear and geometric scales. The detected epistasis was predominately less-than-additive, i.e., the effect of the double heterozygotes was smaller than the sum of the effects of the corresponding single heterozygotes. Epistasis was also found for homozygous linked QTL affecting fruit mass and total soluble solids. Although the frequency of epistasis was high, additivity was the major component in the interaction of pairs of QTL. We propose that the diminishing additivity of QTL effects is amplified when more loci are involved; this mode of epistasis may be an important factor in phenotype canalization and in breeding.
The Heterochromatic rolled Gene of Drosophila melanogaster Is Extensively Polytenized and Transcriptionally Active in the Salivary Gland Chromocenter
Authors: Berghella Libera , Dimitri Patrizio 
Published: January 2021

Abstract
This paper reports a cytogenetic and molecular study of the structural and functional organization of the Drosophila melanogaster chromocenter. The relations between mitotic (constitutive) heterochromatin and α- and β-heterochromatin are not fully understood. In the present work, we have studied the polytenization of the rolkd (rl) locus, a 100-kb genomic region that maps to the proximal heterochromatin of chromosome 2 and has been previously thought to contribute to α-heterochromatin. We show that rolled undergoes polytenization in salivary gland chromosomes to a degree comparable to that of euchromatic genes, despite its deep heterochromatic location. In contrast, both the Bari-I sequences and the AAGAC satellite repeats, located respectively to the left and right of rl, are severely underrepresented and thus both appear to be α-heterochromatic. In addition, we found that rl is transcribed in polytene tissues. Together, the results reported here indicate that functional sequences located within the proximal constitutive heterochromatin can undergo polytenization, contributing to the formation of β-heterochromatin. The implications of this finding to chromocenter structure are discussed.
Chromosomal Distribution of Transposable Elements in Drosophila melanogaster Test of the Ectopic Recombination Model for Maintenance of Insertion Site Number
Authors: Hoogland Christine , Biémont Christian 
Published: January 2021

Abstract
Data of insertion site localization and site occupancy frequency of P, hobo, I, copia, mdg1, mdg3, 412, 297, and roo transposable elements (TEs) on the polytene chromosomes of Drosophila melanogaster were extracted from the literature. We show that TE insertion site number per chromosomal division was significantly correlated with the amount of DNA. The insertion site number weighted by DNA content was not correlated with recombination rate for all TEs except hobo, for which a positive correlation was detected. No global tendency emerged in the relationship between TE site occupancy frequency, weighted by DNA content, and recombination rate; a strong negative correlation was, however, found for the 3L arm. A possible dominant deleterious effect of chromosomal rearrangements due to recombination between TE insertions is thus not the main factor explaining the dynamics of TEs, since this hypothesis implies a negative relationship between recombination rate and both TE insertion site number and site occupancy frequency. The alternative hypothesis of selection against deleterious effects of insertional mutations is discussed.
On the Potential for Estimating the Effective Number of Breeders From Heterozygote-Excess in Progeny
Authors: Pudovkin A I , Zaykin D V , Hedgecock D 
Published: January 2021

Abstract
The important parameter of effective population size is rarely estimable directly from demographic data. Indirect estimates of effective population size may be made from genetic data such as temporal variation of allelic frequencies or linkage disequilibrium in cohorts. We suggest here that an indirect estimate of the effective number of breeders might be based on the excess of heterozygosity expected in a cohort of progeny produced by a limited number of males and females. In computer simulations, heterozygote excesses for 30 unlinked loci having various numbers of alleles and allele-frequency profiles were obtained for cohorts produced by samples of breeders drawn from an age-structured population and having known variance in reproductive success and effective number. The 95% confidence limits around the estimate contained the true effective population size in 70 of 72 trials and the Spearman rank correlation of estimated and actual values was 0.991. An estimate based on heterozygote excess might have certain advantages over the previous estimates, requiring only single-locus and single-cohort data, but the sampling error among individuals and the effect of departures from random union of gametes still need-to be explored.
The Efficiency of Meiotic Recombination Between Dispersed Sequences in Saccharomyces cerevisiae Depends Upon Their Chromosomal Location
Authors: Goldman Alastair S H , Lichten Michael 
Published: January 2021

Abstract
To examine constraints imposed on meiotic recombination by homologue pairing, we measured the frequency of recombination between mutant alleles of the ARG4 gene contained in pBR322-based inserts. Inserts were located at identical loci on homologues (allelic recombination) or at different loci on either homologous or heterologous chromosomes (ectopic recombination). Ectopic recombination between interstitially located inserts on heterologous chromosomes had an efficiency of 6-12% compared to allelic recombination. By contrast, ectopic recombination between interstitial inserts located on homologues had relative efficiencies of 47-99%. These findings suggest that when meiotic ectopic recombination occurs, homologous chromosomes are already colocalized. The efficiency of ectopic recombination between inserts on homologues decreased as the physical distance between insert sites was increased. This result is consistent with the suggestion that during meiotic recombination, homologues are not only close to each other, but also are aligned end to end. Finally, the efficiency of ectopic recombination between inserts near telomeres (within 16 kb) was significantly greater than that observed with inserts &gt;50 kb from the nearest telomere. Thus, at the time of recombination, there may be a special relationship between the ends of chromosomes not shared with interstitial regions.
The Dynein Gene Family in Chlamydomonas reinhardtii
Authors: Porter Mary E , Knott Julie A , Myster Steven H , Farlow Samuel J 
Published: January 2021

Abstract
To correlate dynein heavy chain (Dhc) genes with flagellar mutations and gain insight into the function of specific dynein isoforms, we placed eight members of the Dhc gene family on the genetic map of Chlamydomonas. Using a PCR-based strategy, we cloned 11 Dhc genes from Chlamydomonas. Comparisons with other Dhc genes indicate that two clones correspond to genes encoding the alpha and beta heavy chains of the outer dynein arm. Alignment of the predicted amino acid sequences spanning the nucleotide binding site indicates that the remaining nine clones can be subdivided into three groups that are likely to include representatives of the inner-arm Dhc isoforms. Gene-specific probes reveal that each clone represents a single-copy gene that is expressed as a transcript of the appropriate size (&gt;13 kb) sufficient to encode a high molecular weight Dhc polypeptide. The expression of all nine genes is upregulated in response to deflagellation, suggesting a role in axoneme assembly or motility. Restriction fragment length polymorphisms between divergent C. reinhardtii strains have been used to place each Dhr gene on the genetic map of Chlamydomonas. These studies lay the groundwork for correlating defects in different Dhc genes with specific flagellar mutations.
Interspecies Comparison Reveals Evolution of Control Regions in the Nematode Sex-Determining Gene tra-2
Authors: Kuwabara Patricia E 
Published: January 2021

Abstract
The Caenmhabditis elegans sexdetermining gene tra-2 promotes female development and expresses 4.7-, 1.9- and 1.8-kb mRNAs. The 4.7-kb mRNA encodes the major feminizing activity of the locus, a predicted membrane receptor that mediates cell-to-cell communication, named TRA-2A. The tra-2 gene was characterized from a close relative, C. briggsae. The Cb-tra-2 gene expresses only a 4.7-kb mRNA and alternatively spliced variants, which encode TRA-2A homologues. The Cb-TRA-2A and Ce-TRA-2A sequences are highly diverged, sharing only 43% identity, although their hydropathy profiles remain remarkably similar. Three potential regulatory sites of Ce-tra-2 activity were previously identified by analyzing tra-2(eg), tra-2(gf), and tra-2(mx) mutations. Two of these sites, the EG site and MX region, are consewed in Cb-tra-2. By contrast, the two direct repeat elements in the Ce-tra-2 3′ untranslated region, which are disrupted in tra-2(gf) mutants, are absent. Injection of Cb-tra-2 antisense RNA into C. briggsae mimics the Ce-tra-2 loss-of-function phenotype. Thus, antisense RNA permits studies of gene activity in nematodes that lack extensive genetics.
Selection on X-linked Genes During Speciation in the Drosophila athabasca Complex
Authors: Ford Michael J , Aquadro Charles F 
Published: January 2021

Abstract
We present the results of a restriction site survey of variation at five loci in Drosophila athabasca, complimenting a previous study of the period locus. There is considerably greater differentiation between the three semispecies of D. athabasca at the period locus and two other X-linked genes (neon-transient-A and E74A) than at three autosomal genes (Xdh, Adh and RC98). Using a modification of the HKA test, which uses fixed differences between the semispecies and a test based on differences in Fst among loci, we show that the greater differentiation of the X-linked loci compared with the autosomal loci is inconsistent with a neutral model of molecular evolution. We explore several evolutionary scenarios by computer simulation, including differential migration of X and autosomal genes, very low levels of migration among the semispecies, selective sweeps, and background selection, and conclude that X-linked selective sweeps in at least two of the semispecies are the best explanation for the data. This evidence that natural selection acted on the X-chromosome suggests that another X-linked trait, mating song differences among the semispecies, may have been the target of selection.
Transgene Coplacement and High Efficiency Site-Specific Recombination With the Cre/loxP System in Drosophila
Authors: Siegal Mark L , Hartl Daniel L 
Published: January 2021

Abstract
Studies of gene function and regulation in transgenic Drosophila are often compromised by the possibility of genomic position effects on gene expression. We have developed a method, called transgene coplacement, in which any two sequences can be positioned at exactly the same site and orientation in the genome. Transgene coplacement makes use of the bacteriophage P1 system of Cre/loxP site-specific recombination, which we have introduced into Drosophila. In the presence of a cre transgene driven by a dual hsp70-Mosl promoter, a white reporter gene flanked by loxP sites is excised with virtually 100% efficiency both in somatic cells and in germ cells. A strong maternal effect, resulting from Cre recombinase present in the oocyte, is observed as white or mosaic eye color in F1 progeny. Excision in germ cells of the F1 yields a strong grand-maternal effect, observed as a highly skewed ratio of eye-color phenotypes in the F2 generation. The excision reactions of Cre/loxP and the related FLP/FRT system are used to create Drosophila lines in which transgenes are at exactly allelic sites in homologous chromosomes.
Genetic Mapping of Quantitative Trait Loci Controlling Growth and Wood Quality Traits in Eucalyptus grandis Using a Maternal Half-sib Family and RAPD Markers
Authors: Grattapaglia Dario , Bertolucci Fernando L G , Penchel Ricardo , Sederoff Ronald R 
Published: January 2021

Abstract
Quantitative trait loci (QTL) mapping of forest productivity traits was performed using an open pollinated half-sib family of Eucalyptus grandis. For volume growth, a sequential QTL mapping approach was applied using bulk segregant analysis (BSA), selective genotyping (SG) and cosegregation analysis (CSA). Despite the low heritability of this trait and the heterogeneous genetic background employed for mapping, BSA detected one putative QTL and SG two out of the three later found by CSA. The three putative QTL for volume growth were found to control 13.7% of the phenotypic variation, corresponding to an estimated 43.7% of the genetic variation. For wood specific gravity five QTL were identified controlling 24.7% of the phenotypic variation corresponding to 49% of the genetic variation. Overlapping QTL for CBH, WSG and percentage dry weight of bark were observed. A significant case of digenic epistasis was found, involving unlinked QTL for volume. Our results demonstrate the applicability of the within half-sib design for QTL mapping in forest trees and indicate the existence of major genes involved in the expression of economically important traits related to forest productivity in Eucalyptus grandis. These findings have important implications for marker-assisted tree breeding.
The Effects of Variable Mutation Rates Across Sites on the Phylogenetic Estimation of Effective Population Size or Mutation Rate of DNA Sequences
Authors: Deng Hong-Wen , Fu Yun-Xin 
Published: January 2021

Abstract
Multiple hits at some sites of human mitochondrial DNA sequences suggest that the commonly assumed infinite-sites model can be violated. Under the neutral Wright-Fisher model without recombination and population subdivision, we investigated, by computer simulations, the effect of multiple hits on the estimation of the essential parameter θ = 4Neμ by Fu's UPBLUE procedure. We found that with moderate mutation rate heterogeneity, UPBLUE performs very well in terms of unbiasness and efficiency. Under extreme mutation rate heterogeneity, if sample size is reasonably large (e.g., &gt;60), UPBLUE is still very satisfactory; otherwise we developed a new correction equation. Given knowledge of the degree of mutation rate heterogeneity, the performance of UPBLUE with the new correction equation was tested to be fairly satisfactory: there is almost no bias and the sampling variance is only slightly higher than the theoretical minimum variance. Thus, with an appropriate correction, UPBLUE is relatively robust to the multiple hits. In genealogies reconstructed by UPGMA, we found that the total length of branches directly linked to the tips is underestimated, and those far away tend to be overestimated, while the total length of all branches is not biased.
Induction of Ty Recombination in Yeast by cDNA and Transcription: Role of the RAD1 and RAD52 Genes
Authors: Nevo-Caspi Yael , Kupiec Martin 
Published: January 2021

Abstract
In the yeast Saccharomyces cerevisiae ectopic recombination has been shown to occur at high frequencies for artificially created repeats, but at relatively low frequencies for a natural family of repeated sequences, the Ty family. Little is known about the mechanism(s) that prevent recombination between repeated sequences. We have previously shown that nonreciprocal recombination (gene conversion) of a genetically marked Ty can be induced either by the presence of high levels of Ty cDNA or by transcription of the marked Ty from a GAL1 promoter. These two kinds of induction act in a synergistic manner. To further characterize these two kinds of Ty recombination, we have investigated the role played by the RkD52 and RAD1 genes. We have found that the RAD52 and RAD1 gene products are essential to carry out transcription-induced Ty conversion whereas cDNA-mediated conversion can take place in their absence.
Asm-1
+, a Neurospora crassa Gene Related to Transcriptional Regulators of Fungal Development
Authors: Aramayo Rodolfo , Peleg Yoav , Addison Randolph , Metzenberg Robert 
Published: January 2021

Abstract
This report describes the identification, cloning, and molecular analysis of Asm-1 + (Ascospore maturation 1), the Neurospora crassa homologue of the Aspergillus nidulans stuA (stunted A) gene. The Asm-1 + gene is constitutively transcribed and encodes an abundant, nucleus-localized 68.5-kD protein. The protein product of Asm-1 + (ASM-1), contains a potential DNA-binding motif present in related proteins from A. nidulans (StuA), Candida albicans (EFGTF-I), and Saccharomyces cerevisiae (Phd1 and Sok2). This motif is related to the DNA binding motif of the Swi4/Mbpl/Res family of transcription factors that control the cell cycle. Deletion of Asm-1 + destroys the ability to make protoperithecia (female organs), but does not affect male-specific functions. We propose that the APSES domain (ASM-1, Phdl, StuA, EFGTF-1, and Sok2) defines a group of proteins that constitute a family of related transcription factors involved in the control of fungal development.
Trans-Suppression of Terminal Deficiency-Associated Position Effect Variegation in a Drosophila Minichromosome
Authors: Donaldson Kathryn M , Karpen Gary H 
Published: January 2021

Position effect variegation (PEV) is the clonal inactivation of euchromatic or heterochromatic genes that are abnormally positioned within a chromosome. PEV can be influenced by modifiers in trans, including single gene mutations and the total amount of heterochromatin present in the genome. Terminal deletions of a Drosophila minichromosome (Dp1187) dramatically increase PEV of a yellow + body-color gene located in cis, even when the terminal break is &gt;100 kb distal to the yellow gene. Here we demonstrate that terminal deficiency-associated PEV can be suppressed by the presence of a second minichromosome, a novel phenomenon termed “trans-suppression.” The chromosomal elements responsible for trans-suppression were investigated using a series of minichromosomes with molecularly characterized deletions and inversions. The data suggest that trans-suppression does not involve communication between transcriptional regulatory elements on the homologues, a type of transvection known to act at the yellow locus. Furthermore, trans-suppression is not accomplished by titration through the addition of extra centric heterochromatin, a general mechanism for PEV suppression. We demonstrate that trans-suppression is disrupted by significant changes in the structure of the suppressing minichromosome, including deletions of the yellow region and centric heterochromatin, and large inversions of the centric heterochromatin. We conclude that chromosome pairing plays an important role in trans-suppression and discuss the possibility that terminal deficiency-associated PEV and trans-suppression reflect changes in nuclear positioning of the chromosomes and the gene, and/or the activity and distribution of telomere-binding proteins.
Inbreeding Depression and Inferred Deleterious-Mutation Parameters in Daphnia
Authors: Deng Hong-Wen , Lynch Michael 
Published: January 2021

Abstract
Deng and Lynch recently proposed a method for estimating deleterious genomic mutation parameters from changes in the mean and genetic variance of fitness traits upon inbreeding in outcrossing populations. Such observations are readily acquired in cyclical parthenogens. Selfing and life-table experiments were performed for two such Daphnia populations. We observed a significant inbreeding depression and an increase of genetic variance for all traits analyzed. Deng and Lynch's original procedures were extended to estimate genomic mutation rate (U), mean dominance coefficient (h‒), mean selection coefficient (s‒) and scaled genomic mutational variance (Vm/Ve). On average, U^, h‒̂, s‒̂ and V^m∕Vs (^ indicates an estimate) are 0.74, 0.30, 0.14 and 4.6E-4, respectively. For the true values, the U^ and h‒̂ are lower bounds, and s‒̂ and V^m∕Ve, upper bounds. The present U^, h‒̂ and V^m∕Ve are in general concordance with earlier results. The discrepancy between the present V^m∕Ve and that from mutation-accumulation experiments in Drosophila (~0.04) is discussed. It is shown that different reproductive modes do not affect gene frequency at mutation-selection equilibrium if mutational effects on fitness are multiplicative and not completely recessive.
Epistasis in Measured Genotypes: Drosophila P-Element Insertions
Authors: Clark Andrew G , Wang Lei 
Published: January 2021

Abstract
Transposon tagging provides an opportunity to construct large numbers of strains of organisms that differ by single insertional mutations. By scoring the phenotypes of these “measured genotypes,” powerful tests of effects of mutations on phenotypic expression have been performed. Here we extend this approach by constructing with simple crosses all possible two-locus genotypes for each of eight pairs of P-element insertions. Analysis of metabolic phenotypes (fat and glycogen contents, enzyme activities, total protein, and body weight) of the resulting nine genotypes provides direct estimates of additive, dominance, and epistatic effects of the mutations. Nested two-way analysis of variance identified significant epistatic effects in 27% of the tests (35/128 of the trait × P-element combinations). Posterior contrasts were performed to partition the epistatic variance into the four orthogonal components of Cockerham, and the data exhibit a tendency toward additive × dominance and dominance × dominance epistasis, Mutations in this study have epistatic effects on metabolic traits that are on the same order of magnitude as main (additive and dominance) effects. Measured genotypes have been used in other contexts to quantify epistatic effects on phenotypic expression, and these results are also briefly reviewed.