Specific end-to-end attachment of chromosomes in Ornithogalum virens

C-banding of nonhomologous chromosomes in haploid generative nuclei of Ornithogalum virens (n = 3) reveals a high degree of specificity with respect to end-to-end connexions. The centromeric end of chromosome 2 preferentially associates with the centromeric end of chromosome 3 and the telomeric end of chromosome 3 associates preferentially with the telomeric end of chromosome 1. This same association of nonhomologous chromosomes persists in prophase nuclei of diploid root tips. In addition, the telomeric ends of the 2 chromosome 2s are connected to one another as are the centromeric ends of the chromosome 1s. This results in a ring of chromosomes in which homologues lie opposite one another. Centromeric ends lie on one side of the nucleus and telomeric ends on the other. It is proposed that this specific association of chromosome ends reflects an order which was probably established at the preceding anaphase or telophase and which persists throughout interphase. The suggestion is made that the proximity of homologous ends and consequently homologous alignment may facilitate initiation of pairing at meiosis.

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Qtl mapping of some morphological traits of rice in a RILS population derived from Hashemi and modified Nemat varieties hybrid

Genetika ◽

10.2298/gensr2003087e ◽

2020 ◽

Vol 52 (3) ◽

pp. 1087-1106

Author(s):

Mona Pishnamazzadeh Emami ◽

Nasser Mohebalipour ◽

Ali Ebadi ◽

Hassan Nourafcan ◽

Jalil Ajali

Keyword(s):

Flag Leaf ◽

Block Design ◽

Rice Genome ◽

Interval Mapping ◽

Chromosome 1 ◽

Chromosome 3 ◽

First Year ◽

Chromosome 2 ◽

Chromosome 11 ◽

Second Year

In this study, QTLs controlling traits related to crop and grain yield were mapped using 140 recombinant inbred lines (F9 and F10) along with 4 control genotypes in anaugment experiment based on a randomized complete block design in 2consecutive years. Population linkage map was consisted of 170 SSR3 / 2132 centimorgan (cM) markers of rice genome, and mean distance between adjacent markers was equal to 12.47 centimorgan (cM). Composite Interval Mapping analysis was done for studying number of days to flowering in the first year, a QTL was identified on chromosome 3 and in the second year, three QTLs were identified on chromosomes 2, 3, and 7, which were common on chromosome 3 in both years. Regarding plant height in the first and second years, a QTL was mapped on chromosome 1, which was similar in both years. In terms of number of tillers in the first year, four QTLs were identified on chromosomes 4 and 12 and in the second year two QTLs were identified on chromosomes 11 and 12, and regarding panicle length in the first year, one QTL was identified on chromosome 6 and in the second year two QTLs were identified on chromosomes 2 and 4, and in terms of flag leaf length in the first year, two QTLs were identified on chromosomes 6 and 7 and in the second year two QTLs were identified on chromosome 7.With respect to flag leaf width in the first year, two QTLs were identified on chromosomes 1and 3, and in the second year, one QTL was identified on chromosome 11, and in relation to Panicle exertion in the first year, three QTLs were identified on chromosomes 1, 2, and 8, and in the second year, two QTLs were identified on chromosomes 1 and 2.In regard to yield in the first year, one QTL was identified on chromosome 2 and in the second year, two QTLs were identified on chromosome 2. Also, clusters of genes were identified by Interval Mapping in the population with respect to different traits on chromosomes 1 (two cases) and 12 (one case).

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Dissection of closely linked QTLs controlling stigma exsertion rate in rice by substitution mapping

Theoretical and Applied Genetics ◽

10.1007/s00122-021-03771-9 ◽

2021 ◽

Author(s):

Quanya Tan ◽

Chengshu Wang ◽

Xin Luan ◽

Lingjie Zheng ◽

Yuerong Ni ◽

...

Keyword(s):

Complex Trait ◽

Epistatic Effect ◽

Open Reading Frames ◽

Chromosome 3 ◽

Chromosome 2 ◽

Substitution Mapping ◽

Mapping Strategy ◽

Stigma Exsertion ◽

Important Trait ◽

Stigma Exsertion Rate

Abstract Key message Through substitution mapping strategy, two pairs of closely linked QTLs controlling stigma exsertion rate were dissected from chromosomes 2 and 3 and the four QTLs were fine mapped. Abstract Stigma exsertion rate (SER) is an important trait affecting the outcrossing ability of male sterility lines in hybrid rice. This complex trait was controlled by multiple QTLs and affected by environment condition. Here, we dissected, respectively, two pairs of tightly linked QTLs for SER on chromosomes 2 and 3 by substitution mapping. On chromosome 2, two linkage QTLs, qSER-2a and qSER-2b, were located in the region of 1288.0 kb, and were, respectively, delimited to the intervals of 234.9 kb and 214.3 kb. On chromosome 3, two QTLs, qSER-3a and qSER-3b, were detected in the region of 3575.5 kb and were narrowed down to 319.1 kb and 637.3 kb, respectively. The additive effects of four QTLs ranged from 7.9 to 9.0%. The epistatic effect produced by the interaction of qSER-2a and qSER-2b was much greater than that of qSER-3a and qSER-3b. The open reading frames were identified within the maximum intervals of qSER-2a, qSER-2b and qSER-3a, respectively. These results revealed that there are potential QTL clusters for SER in the two regions of chromosome 2 and chromosome 3. Fine mapping of the QTLs laid a foundation for cloning of the genes of SER.

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Rearrangements of the DNA in Carbon Ion-Induced Mutants of Arabidopsis thaliana

Genetics ◽

10.1093/genetics/157.1.379 ◽

2001 ◽

Vol 157 (1) ◽

pp. 379-387 ◽

Cited By ~ 1

Author(s):

Naoya Shikazono ◽

Atsushi Tanaka ◽

Hiroshi Watanabe ◽

Shigemitsu Tano

Keyword(s):

Arabidopsis Thaliana ◽

Nonhomologous End Joining ◽

Chromosome 3 ◽

Chromosome 2 ◽

Carbon Ions ◽

Induced Mutations ◽

End Joining ◽

Carbon Ion ◽

Induced Mutants ◽

Dna Strand

Abstract To elucidate the nature of structural alterations in plants, three carbon ion-induced mutations in Arabidopsis thaliana, gl1-3, tt4(C1), and ttg1-21, were analyzed. The gl1-3 mutation was found to be generated by an inversion of a fragment that contained GL1 and Atpk7 loci on chromosome 3. The size of the inverted fragment was a few hundred kilobase pairs. The inversion was found to accompany an insertion of a 107-bp fragment derived from chromosome 2. The tt4(C1) mutation was also found to be due to an inversion. The size of the intervening region between the breakpoints was also estimated to be a few hundred kilobase pairs. In the case of ttg1-21, it was found that a break occurred at the TTG1 locus on chromosome 5, and reciprocal translocation took place between it and chromosome 3. From the sequences flanking the breakpoints, the DNA strand breaks induced by carbon ions were found to be rejoined using, if present, only short homologous sequences. Small deletions were also observed around the breakpoints. These results suggest that the nonhomologous end-joining (NHEJ) pathway operates after plant cells are exposed to ion particles.

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Chromosome polymorphism in natural populations of Anopheles quadrimaculatus Say species A and B

Genome ◽

10.1139/g88-024 ◽

1988 ◽

Vol 30 (2) ◽

pp. 138-146 ◽

Cited By ~ 1

Author(s):

P. E. Kaiser ◽

J. A. Seawright ◽

B. K. Birky

Keyword(s):

X Chromosome ◽

Southeastern United States ◽

Polytene Chromosomes ◽

Natural Populations ◽

Chromosome 3 ◽

Chromosome Polymorphism ◽

Chromosome 2 ◽

Anopheles Quadrimaculatus ◽

The Right ◽

Maculipennis Complex

Ovarian polytene chromosomes from eight populations of Anopheles quadrimaculatus in the southeastern United States were observed for chromosomal polymorphisms. Two sibling species, species A and B, each with intraspecific inversions, were distinguished. Species A correlates with the previously published standard maps for salivary gland and ovarian nurse-cell polytene chromosomes. Species A was found at all eight collection sites, and five of these populations also contained species B. Three inversions on the right arm of chromosome 3 were observed in species A. Species B contained a fixed inversion on the X chromosome, one fixed and one floating inversion on the left arm of chromosome 2, and one fixed and one floating inversion on the right arm of chromosome 3. The fixed inversion on the X chromosome makes this the best diagnostic chromosome for distinguishing species A and B. An unusual dimorphism in the left arm of chromosome 3, found in both species A and B, contained two inversions. The heterokaryotypes, as well as two distinct homokaryotypes, were seen in all of the field populations. Intraspecific clinal variations in the frequencies of the species A inversions were noted. The Florida populations were practically devoid of inversions, the Georgia and Alabama populations contained some inversions, and the Arkansas population was mostly homozygous for two of the inversions. The phylogenetic relationships of species A and B to the Maculipennis complex (Nearctic) are discussed.Key words: Anopheles, inversion, populations, chromosome polymorphism, phylogenetics.

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Methylome-wide analysis reveals epigenetic marks associated with resistance to tuberculosis in HIV-infected individuals from East Africa

10.1101/2020.07.14.20153395 ◽

2020 ◽

Author(s):

Catherine Stein ◽

Penelope Bencheck ◽

Jacquelaine Bartlett ◽

Robert P Igo ◽

Rafal S Sobota ◽

...

Keyword(s):

Genome Wide Association Study ◽

Sub Saharan Africa ◽

Chromosome 1 ◽

Chromosome 2 ◽

Chromosome 5 ◽

Epigenetic Marks ◽

Genome Wide ◽

A Genome ◽

Immunodeficiency Virus ◽

Sub Saharan

Background: Tuberculosis (TB) is the most deadly infectious disease globally and highly prevalent in the developing world, especially sub-Saharan Africa. Even though a third of humans are exposed to Myocbacterium tuberculosis (Mtb), most infected immunocompetent individuals do not develop active TB. In contrast, for individuals infected with both TB and the human immunodeficiency virus (HIV), the risk of active disease is 10% or more per year. Previously, we identified in a genome-wide association study a region on chromosome 5 that was associated with resistance to TB. This region included epigenetic marks that could influence gene regulation so we hypothesized that HIV-infected individuals exposed to Mtb, who remain disease free, carry epigenetic changes that strongly protect them from active TB. To test this hypothesis, we conducted a methylome-wide study in HIV-infected, TB-exposed cohorts from Uganda and Tanzania. Results: In 221 HIV-infected adults from Uganda and Tanzania, we identified 3 regions of interest that included markers that were differentially methylated between TB cases and LTBI controls, that also included methylation QTLs and associated SNPs: chromosome 1 (RNF220, p=4x10-5), chromosome 2 (between COPS8 and COL6A3 genes, p=2.7x10-5), and chromosome 5 (CEP72, p=1.3x10-5). These methylation results colocalized with associated SNPs, methylation QTLs, and methylation x SNP interaction effects. These markers were in regions with regulatory markers for cells involved in TB immunity and/or lung. Conclusion: Epigenetic regulation is a potential biologic factor underlying resistance to TB in immunocompromised individuals that can act in conjunction with genetic variants.

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The Essential Genome of Burkholderia cenocepacia H111

Journal of Bacteriology ◽

10.1128/jb.00260-17 ◽

2017 ◽

Vol 199 (22) ◽

Cited By ~ 7

Author(s):

Steven Higgins ◽

Maria Sanchez-Contreras ◽

Stefano Gualdi ◽

Marta Pinto-Carbó ◽

Aurélien Carlier ◽

...

Keyword(s):

Minimal Medium ◽

Essential Genes ◽

Burkholderia Cenocepacia ◽

Chromosome 1 ◽

Biological Research ◽

Chromosome 2 ◽

Powerful Method ◽

Rich Medium ◽

Content Type ◽

Autonomous Growth

ABSTRACT The study of the minimum set of genes required to sustain life is a fundamental question in biological research. Recent studies on bacterial essential genes suggested that between 350 and 700 genes are essential to support autonomous bacterial cell growth. Essential genes are of interest as potential new antimicrobial drug targets; hence, our aim was to identify the essential genome of the cystic fibrosis (CF) isolate Burkholderia cenocepacia H111. Using a transposon sequencing (Tn-Seq) approach, we identified essential genes required for growth in rich medium under aerobic and microoxic conditions as well as in a defined minimal medium with citrate as a sole carbon source. Our analysis suggests that 398 genes are required for autonomous growth in rich medium, a number that represents only around 5% of the predicted genes of this bacterium. Five hundred twenty-six genes were required to support growth in minimal medium, and 434 genes were essential under microoxic conditions (0.5% O2). A comparison of these data sets identified 339 genes that represent the minimal set of essential genes required for growth under all conditions tested and can be considered the core essential genome of B. cenocepacia H111. The majority of essential genes were found to be located on chromosome 1, and few such genes were located on chromosome 2, where most of them were clustered in one region. This gene cluster is fully conserved in all Burkholderia species but is present on chromosome 1 in members of the closely related genus Ralstonia, suggesting that the transfer of these essential genes to chromosome 2 in a common ancestor contributed toward the separation of the two genera. IMPORTANCE Transposon sequencing (Tn-Seq) is a powerful method used to identify genes that are essential for autonomous growth under various conditions. In this study, we have identified a set of “core essential genes” that are required for growth under multiple conditions, and these genes represent potential antimicrobial targets. We also identified genes specifically required for growth under low-oxygen and nutrient-limited environments. We generated conditional mutants to verify the results of our Tn-Seq analysis and demonstrate that one of the identified genes was not essential per se but was an artifact of the construction of the mutant library. We also present verified examples of genes that were not truly essential but, when inactivated, showed a growth defect. These examples have identified so-far-underestimated shortcomings of this powerful method.

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A biochemical study of BAS 517 using excised corn and soybean root systems

Weed Science ◽

10.1017/s0043174500090615 ◽

1999 ◽

Vol 47 (1) ◽

pp. 28-36

Author(s):

Hwei-Yiing Li ◽

Chester L. Foy

Keyword(s):

Root System ◽

Biochemical Study ◽

Lipid Fraction ◽

Root Systems ◽

Water Soluble ◽

Root Tips ◽

Soybean Root ◽

Corn Roots ◽

Tracer Techniques ◽

High Degree

The mode of action of BAS 517 in a susceptible plant species, corn, was investigated using an excised root system and14C-tracer techniques. The root system of a tolerant species, soybean, was used for comparison. When UL-14C- glucose was used as a precursor,14C incorporation into lipids was reduced in BAS 517-treated corn roots, although14C incorporation from UL-14C-glucose into lipids was relatively low. Inhibition of14C incorporation into water-soluble compounds was not definite because of a high degree of variability. Using14C-acetate as a precursor, 49, 43, and 34% of the recovered radioactivity was found in the lipid fractions of root tips treated with 0, 1.0, and 10 μM BAS 517, respectively. In nontreated soybean root tips, 47% of the recovered radioactivity was found in the lipid fraction compared to 49% in root tips treated with 10 μM BAS 517. Further analysis of lipids showed that BAS 517 inhibited the incorporation of14C from14C-acetate into phosphatidylethanolamine, a phospholipid, whereas the labeling of sterols in treated corn roots was not adversely affected. Acetyl CoA carboxylase extracted from root systems of corn and soybean showed different sensitivity to BAS 517, suggesting its role as the herbicide target site and as a basis for the selectivity.

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Two Different Genetic Markers for High and Low Myopia

European Journal of Ophthalmology ◽

10.1177/112067219200200406 ◽

1992 ◽

Vol 2 (4) ◽

pp. 196-199 ◽

Cited By ~ 1

Author(s):

M.V. Olmedo ◽

J.I. Muñoz ◽

M.J. Rodriguez-Cid ◽

A. Carracedo ◽

F.J. Gomez-Ulla ◽

...

Keyword(s):

Acid Phosphatase ◽

High Myopia ◽

Control Population ◽

Chromosome 1 ◽

Chromosome 2 ◽

Significant Difference ◽

Hardy Weinberg Equilibrium ◽

Group 2 ◽

And Control ◽

Group 1

In myopia patients, Rh and acid phosphatase were typed in two groups: group 1 consisted of 214 patients with low myopia (−6 D or less); group 2 of 124 patients with high myopia (more than −6 D). Statistical analysis of the markers showed a good Hardy-Weinberg equilibrium for both groups. In the Rh system there was a significant difference between group 1 and the control population (p < 0.05), but not between group 2 and control (p > 0.1). In the case of ACP there was a significant difference between group 2 and the control population (p < 0.05), but not between group 1 and control (p > 0.25). We conclude that the observed association between myopia and Rh system (chromosome 1) involves low myopia, while the association between myopia and acid phosphatase (chromosome 2) involves high myopia. Further DNA researche will lead to more specific results.

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