The objectives of this study were to develop a high-density chromosome bin map of homoeologous group 7 in hexaploid wheat, to identify gene distribution in these chromosomes, and to perform comparative studies of wheat with rice and barley. We mapped 2148 loci from 919 EST clones onto group 7 chromosomes of wheat. In the majority of cases the numbers of loci were significantly lower in the centromeric regions and tended to increase in the distal regions. The level of duplicated loci (...) in this group was 24% with most of these loci being localized toward the distal regions. One hundred nineteen EST probes that hybridized to three fragments and mapped to the three group 7 chromosomes were designated landmark probes and were used to construct a consensus homoeologous group 7 map. An additional 49 probes that mapped to 7AS, 7DS, and the ancestral translocated segment involving 7BS also were designated landmarks. Landmark probe orders and comparative maps of wheat, rice, and barley were produced on the basis of corresponding rice BAC/PAC and genetic markers that mapped on chromosomes 6 and 8 of rice. Identification of landmark ESTs and development of consensus maps may provide a framework of conserved coding regions predating the evolution of wheat genomes. (shrink)

To localize wheat ESTs on chromosomes, 882 homoeologous group 6-specific ESTs were identified by physically mapping 7965 singletons from 37 cDNA libraries on 146 chromosome, arm, and sub-arm aneuploid and deletion stocks. The 882 ESTs were physically mapped to 25 regions flanked by 23 deletion breakpoints. Of the 5154 restriction fragments detected by 882 ESTs, 2043 were localized to group 6 chromosomes and 806 were mapped on other chromosome groups. The number of loci mapped was greatest on chromosome 6B and (...) least on 6D. The 264 ESTs that detected orthologous loci on all three homoeologs using one restriction enzyme were used to construct a consensus physical map. The physical distribution of ESTs was uneven on chromosomes with a tendency toward higher densities in the distal halves of chromosome arms. About 43% of the wheat group 6 ESTs identified rice homologs upon comparisons of genome sequences. Fifty-eight percent of these ESTs were present on rice chromosome 2 and the remaining were on other rice chromosomes. Even within the group 6 bins, rice chromosomal blocks identified by 1-6 wheat ESTs were homologous to up to 11 rice chromosomes. These rice-block contigs were used to resolve the order of wheat ESTs within each bin. (shrink)

A total of 1918 loci, detected by the hybridization of 938 expressed sequence tag unigenes from 26 Triticeae cDNA libraries, were mapped to wheat homoeologous group 4 chromosomes using a set of deletion, ditelosomic, and nulli-tetrasomic lines. The 1918 EST loci were not distributed uniformly among the three group 4 chromosomes; 41, 28, and 31% mapped to chromosomes 4A, 4B, and 4D, respectively. This pattern is in contrast to the cumulative results of EST mapping in all homoeologous groups, as reported (...) elsewhere, that found the highest proportion of loci mapped to the B genome. Sixty-five percent of these 1918 loci mapped to the long arms of homoeologous group 4 chromosomes, while 35% mapped to the short arms. The distal regions of chromosome arms showed higher numbers of loci than the proximal regions, with the exception of 4DL. This study confirmed the complex structure of chromosome 4A that contains two reciprocal translocations and two inversions, previously identified. An additional inversion in the centromeric region of 4A was revealed. A consensus map for homoeologous group 4 was developed from 119 ESTs unique to group 4. Forty-nine percent of these ESTs were found to be homoologous to sequences on rice chromosome 3, 12% had matches with sequences on other rice chromosomes, and 39% had no matches with rice sequences at all. Limited homology was found between wheat ESTs on homoeologous group 4 and the Arabidopsis genome. Forty-two percent of the homoeologous group 4 ESTs could be classified into functional categories on the basis of blastX searches against all protein databases. (shrink)

The focus of this study was to analyze the content, distribution, and comparative genome relationships of 996 chromosome bin-mapped expressed sequence tags accounting for 2266 restriction fragments on the homoeologous group 3 chromosomes of hexaploid wheat. Of these loci, 634, 884, and 748 were mapped on chromosomes 3A, 3B, and 3D, respectively. The individual chromosome bin maps revealed bins with a high density of mapped ESTs in the distal region and bins of low density in the proximal region of the (...) chromosome arms, with the exception of 3DS and 3DL. These distributions were more localized on the higher-resolution group 3 consensus map with intermediate regions of high-mapped-EST density on both chromosome arms. Gene ontology classification of mapped ESTs was not significantly different for homoeologous group 3 chromosomes compared to the other groups. A combined analysis of the individual bin maps using 537 of the mapped ESTs revealed rearrangements between the group 3 chromosomes. Approximately 232 of the consensus mapped ESTs matched sequences on rice chromosome 1 and revealed large- and small-scale differences in gene order. Of the group 3 mapped EST unigenes ∼21 and 32% matched the Arabidopsis coding regions and proteins, respectively, but no chromosome-level gene order conservation was detected. (shrink)

A total of 944 expressed sequence tags generated 2212 EST loci mapped to homoeologous group 1 chromosomes in hexaploid wheat. EST deletion maps and the consensus map of group 1 chromosomes were constructed to show EST distribution. EST loci were unevenly distributed among chromosomes 1A, 1B, and ID with 660, 826, and 726, respectively. The number of EST loci was greater on the long arms than on the short arms for all three chromosomes. The distribution of ESTs along chromosome arms (...) was nonrandom with EST clusters occurring in the distal regions of short arms and middle regions of long arms. Duplications of group 1 ESTs in other homoeologous groups occurred at a rate of 35.5%. Seventy-five percent of wheat chromosome 1 ESTs had significant matches with rice sequences, where large regions of conservation occurred between wheat consensus chromosome 1 and rice chromosome 5 and between the proximal portion of the long arm of wheat consensus chromosome 1 and rice chromosome 10. Only 9.5% of group 1 ESTs showed significant matches to Arabidopsis genome sequences. The results presented are useful for gene mapping and evolutionary and comparative genomics of grasses. (shrink)

The complex hexaploid wheat genome offers many challenges for genomics research. Expressed sequence tags facilitate the analysis of gene-coding regions and provide a rich source of molecular markers for mapping and comparison with model organisms. The objectives of this study were to construct a high-density EST chromosome bin map of wheat homoeologous group 2 chromosomes to determine the distribution of ESTs, construct a consensus map of group 2 ESTs, investigate synteny, examine patterns of duplication, and assess the colinearity with rice (...) of ESTs assigned to the group 2 consensus bin map. A total of 2600 loci generated from 1110 ESTs were mapped to group 2 chromosomes by Southern hybridization onto wheat aneuploid chromosome and deletion stocks. A consensus map was constructed of 552 ESTs mapping to more than one group 2 chromosome. Regions of high gene density in distal bins and low gene density in proximal bins were found. Two interstitial gene-rich islands flanked by relatively gene-poor regions on both the short and long arms and having good synteny with rice were discovered. The map locations of two ESTs indicated the possible presence of a small pericentric inversion on chromosome 2B. Wheat chromosome group 2 was shown to share syntenous blocks with rice chromosomes 4 and 7. (shrink)

This report describes the rationale, approaches, organization, and resource development leading to a large-scale deletion bin map of the hexaploid wheat genome. Accompanying reports in this issue detail results from chromosome bin-mapping of expressed sequence tags representing genes onto the seven homoeologous chromosome groups and a global analysis of the entire mapped wheat EST data set. Among the resources developed were the first extensive public wheat EST collection. Described are protocols for sequencing, sequence processing, EST nomenclature, and the assembly of (...) ESTs into contigs. These contigs plus singletons were used for selection of distinct sequence motif unigenes. Selected ESTs were rearrayed, validated by 5′ and 3′ sequencing, and amplified for probing a series of wheat aneuploid and deletion stocks. Images and data for all Southern hybridizations were deposited in databases and were used by the coordinators for each of the seven homoeologous chromosome groups to validate the mapping results. Results from this project have established the foundation for future developments in wheat genomics. (shrink)

This paper focused on analysing the three very famous ethnographic works on Pukhtun Society of Swat. First, the work of Fredrik Barth “Political Leadership among Swath Pathans, was analysed then analysis of counter work to Barth’s done by Akbar S. Ahmed, “Millennium and Charisma among Pathans”, then there was critical review of the work by Charles Lindholm “Frontier Perspectives: Essays on Comaritive Anthropology”. Works of Louis Dupree, Talal Asad and Micheal Meeker, have also consulted to critically analyse the works of (...) the mentioned authors. This paper is an effort to examine the fact that the works of Fredrik Barth, Akber S. Ahmed, and Charles Lindholm present partially true picture about the socio-economic settings of Swat Pashtuns but not a fully appropriate, impartial and correct image of that society. If one would fully depend on these works to understand the economic and political circumstances of Swat society, then it would be probably insufficient and misleading owing to a significant difference in the writings of all these writers though written from the same society. It means that all of them were writing from the different positions, from separate cultural, educational and professional backgrounds. Their backgrounds have great influence on their writing, which made their work subjective and biased. Thus, it assumes that though an anthropologist tries to remain impartial and objective while writing about any culture, he cannot be, because of his cultural restriction. So, there is an effort to give an answer to the research question by applying the idea of post-modernist approach of James Clifford “writing culture”, also getting support by the Michel Foucault ideas of “Knowledge/Power” in discourse analysis. Thus, it is supposed here that work of each above mentioned authors is a partial truth, because in an ethnographic work author plays a central role and he writes ethnography as an auto-biography (based on his/her cultural limitation). (shrink)

In lieu of an abstract, here is a brief excerpt of the content:The Peculiarly Favored Condition of GeneticsJames J. Lee, PhD (bio) and Damien Morris, MSc (bio)Turkheimer and Greer (2024) (henceforth “T&G”) make some fair points about problems in the scientific profession, including the regrettable tendency to promise practical applications of research that then never materialize. However, T&G’s sustained critique of a body of work associated with one particular researcher to make these general points struck us as uncharitable. More pressingly, (...) we feel that the far-reaching conclusions that T&G attempt to draw from the results they review from the Spit for Science (S4S) cohort are unjustified and risk misleading readers that psychiatric and behavioral genetics is in a parlous state.T&G state that S4S “produced a clear answer to the question it was designed to address,” namely, that its results “unambiguously contradict the hypothesis that alcohol-related behaviors have a meaningful genetic basis.” But S4S cannot possibly have provided affirmative evidence for the null hypothesis, because as a single cohort it lacked the statistical power to do so. Elsewhere T&G acknowledge that the sample size of S4S does not suffice for many purposes; they cannot have it both ways. When GCTA has been applied to samples of greater size, it has unambiguously supported the hypothesis that alcohol-related behaviors have a meaningful genetic basis. The UK Biobank yielded estimates exceeding 0.10 for the contribution of single nucleotide polymorphisms (SNPs) with minor allele frequency of greater than 0.05 to the heritability of drinks per week, estimates more than ten times their standard errors (Liu et al., 2019).This heritability contributed by common variants is sometimes called “SNP heritability,” and T&G disparage it for the alleged “disadvantage of being substantially smaller” than “twin and family heritabilities.” Nowhere do T&G consider what the precise numbers actually mean—an approach that can be hazardous to your scientific health, as the late John Loehlin might have said. Let us, then, consider these numbers. Under a model of pure neutrality, SNP and pedigree narrow-sense heritabilities should be fairly close, essentially as a result of factors p(1 − p) canceling in the multiplication of the numbers of SNPs to be found at a given allele frequency by the average heritability contributed per SNP (Hill, 2010). If SNP and pedigree heritabilities are not close, then natural selection must have been acting on [End Page 441] the trait, preventing new mutations of large effect from becoming common and thereby concentrating heritability at allele frequencies lower than those typically studied in genome-wide association studies (GWAS). This deduction has been abundantly confirmed: the tendency of GWAS SNPs to reside in evolutionarily conserved regions (Finucane et al., 2015; Kim et al., 2019), the younger age of GWAS SNPs when compared to control SNPs of comparable frequencies (Gazal et al., 2017), the discovery of several rare variants with larger effects than those observed in typical GWAS (Barton et al., 2021; Chen et al., 2023; Marouli et al., 2017), the directly measured deleterious fitness effects of mutations in evolutionarily constrained genes (Gardner et al., 2022), and the substantial additional genetic variance accumulated when rare variants are included in GCTA-type studies, sometimes enough to close the gap between SNP and pedigree heritabilities (Evans et al., 2018; Jang et al., 2022; Pathan et al., 2024; Wainschtein et al., 2022).The genetic architecture of a typical quantitative trait consists of many sites across the genome that can mutate to affect it, numbering potentially in the millions (Agarwala et al., 2013; Zeng et al., 2021), of which those that are common SNPs have very small effects as a result of selection. This is the message, but T&G seem to find fault with the messenger, painting “tiny” effect sizes as an embarrassment to the field of behavioral genetics as a whole. We prefer to view the finding of high polygenicity as a revelation about nature, rather than as a debating point. What is this finding telling us? If one takes the action of stabilizing selection as the initial assumption (Uyeda et al., 2011), then the extreme polygenicity revealed by GWAS becomes part of the answer to the question regarding how traits can... (shrink)