Chromosomal Location Of Gene Research Articles

Genetic analysis of the components of winterhardiness in barley (Hordeum vulgare L.)

Winterhardiness in cereals is the consequence of a number of complex and interacting components: cold tolerance, vernalization requirement and photoperiod sensitivity. An understanding of the genetic basis of these component traits should allow for more effective selection. Genome map-based analyses hold considerable promise for dissecting complex phenotypes. A 74-point linkage map was developed from one hundred double haploid lines derived from a winter x spring barley cross and used as the basis for quantitative trait locus (QTL) analyses to determine the chromosome location of genes controlling components of winterhardiness. Despite the greater genome coverage provided by the current map, a previously-reported interval on chromosome 7 remains the only region where significant QTL effects for winter survival were detected in this population. QTLs for heading date under 24 h light map to the same region. A QTL for heading date under this photoperiod regime also maps to chromosome 2. A distinct set of QTLs mapping to chromosomes 1, 2, 3 and 5 determined heading date under 8 h light. Patterns of differential QTL expression underscore the complexity of Winterhardiness.

Mouse and Human SHPS-1: Molecular Cloning of cDNAs and Chromosomal Localization of Genes

SHPS-1 (SHP substrate-1) is a glycosylated receptor-like protein with three immunoglobulin-like domains in its extracellular region and four YXX(L/V/I) motifs, potential tyrosine phosphorylation and SRC homology 2 (SH2) domain binding sites, in its cytoplasmic region. Various mitogens and cell adhesion induce tyrosine phosphorylation of SHPS-1 and its subsequent association with SHP-2, an SH2 domain-containing protein tyrosine phosphatase, suggesting that SHPS-1 plays a role in cell signaling in response to both growth factors and cell adhesion. The mouse and human cDNAs encoding SHPS-1 have now been isolated. The deduced amino acid sequences of rat , human, and mouse SHPS-1 show identities of 65 to 81 %. In addition to the SH2 domain binding sites, a proline-rich putative SH3 domain binding site was detected in the cytoplasmic region of SHPS-1. Northern blot analysis revealed that human SHPS-1 mRNA is most abundant in brain and that the mouse mRNA is present in embryos as early as day 7. Fluorescence in situ hybridization localized the SHPS-1 gene to human chromosome 20p13 and the F3 band of mouse chromosome 2. Furthermore, interspecific backcross analysis placed the mouse SHPS-1 locus 5.0 centimorgans distal and 1.4 centimorgans proximal to the microsatellite markersD2Mit63andD2Mit19,respectively, in a region associated with the mutations coloboma (Cm), lethal milk (lm), and wellhaarig (we).

Structure, hormonal regulation, and chromosomal location of genes encoding barley (1-->4)-beta-xylan endohydrolases.

A gene encoding (1-->4)-beta-xylan xylanohydrolase (EC 3.2.1.8) isoenzyme X-I has been isolated from a barley genomic library and the nucleotide sequence of a 2704-bp fragment defined. The gene contains a single intron of 91 bp in the coding region of the mature enzyme and additional introns may be present in the 5'-untranslated region. Expression of the xylanase gene is restricted to the aleurone layer of germinated grain, where the phytohormone gibberellic acid induces both transcriptional activity of the gene and the secretion of active enzyme from the layers. Abscisic acid abolishes the gibberellic acid induction of xylanase gene expression. The hormonal responses are consistent with the presence of promoter sequences, all of which are within 150 bp of the putative transcription start site, that have been implicated as cis-acting elements within gibberellic acid response complexes in plant genes. The elements include a pyrimidine box, CTCTTTCC, together with TAACGAC and TATCCAT boxes. Three genes encode (1-->4)-beta-xylanase isoenzymes in barley and these have been mapped on the barley genome using two doubled haploid populations and seven wheat-barley addition lines. The three xylanase genes are closely linked on the long arm of chromosome 7 (5H). No recombination was detected between the genes in 234 doubled haploid lines. The genes are flanked by the RFLP markers CDO506 on the proximal side and PSR370 at the distal end.

Chromosomal locations of genes related to flavonoid and anthocyanin production in leaf sheath of shallot. Allium cepa L. Aggregatum group.

High-performance liquid chromatography (HPLC) analyses using a series of alien monosomic addition lines (AMALs) of Japanese bunching onion (Allium fistulosum L.) having extra chromosomes from shallot (A. cepa L. Aggregatum group) were performed to determine the chromosomal locations of the genes for flavonoid and anthocyanin production in leaf sheaths of A. cepa Aggregatum group. In HPLC profiles both at 360 and 520 nm, several peaks were observed in A. cepa Aggregatum group and AMAL with chromosome 5A from A. cepa Aggregatum group but no peak was observed in A. fistulosum and other AMALs. Four of the compounds observed at 360 nm were identified as known flavonoids, i.e., apigenin, kaempferol, quercetin, and rutin. Five out of the total 18 compounds at 520 nm were identified as known anthocyanins, i.e., cyanidin-3-glucoside, cyanidin-3-laminariobioside, peonidin-3-glucoside, cyanidin-3-malonylglucoside, and cyanidin-3-malonyllaminariobioside. These results reveal that a group of the genes related to the flavonoid and anthocyanin production in the leaf sheath of A. cepa Aggregatum group are located on the chromosome 5A.

Chromosomal location of genes influencing plant characters and evapotranspiration efficiency in bread wheat

Little is known of genes that influence root development and drought resistance in bread wheat. The evapotranspiration efficiency (ETE = ratio of vegetative dry weight to total water used) of spring bread wheat tall landrace ‘Chinese Spring’ is relatively high. We used 42 ditelosomic and dimonotelosomic lines of Chinese Spring to identify chromosome arms that influence plant characters and ETE. Multiple regression analyses indicated that 96% of the variation observed in ETE was explained by variation in vegetative dry weight and total water used. Variation in plant height, number of spikes (tillers), root dry weight and shoot dry weight (excluding grains) together explained 88% of the variation observed in plant vegetative dry weight. Chromosome arms involved in expression of days to heading and maturity, plant height, number of spikes, root dry weight, shoot dry weight, number of grains, grain weight, and carbon isotope discrimination (Δ) were identified. Specifically, both arms of chromosome 2A, the long arm of chromosome 2B, and the short arm of chromosome 2D might carry genes with positive effects on number of spikes, root dry weight, and shoot dry weight. None of the aneuploids produced grain yield greater than Chinese Spring. The short arms of chromosomes 6A and 4D might carry genes that suppress Δ. Chromosome 1D might carry genes that increase relative water loss. The chromosome arms belonging to homoeologous group 2 might carry genes with positive effects on ETE. The genetic basis of ETE in modern wheats could be broadened by substituting specific chromosome arms of landrace wheats carrying desired characters into their genomes.

Chromosomal locations of genes that control major RNA-degrading activities in common wheat (Triticum aestivum L.)

Seventeen RNA-degrading enzymes of common wheat, with apparent molecular masses from 42.2 kDa to 16.3 kDa, were observed by the RNA-SDS-PAGE assay. To determine their chromosome locations, all chromosome arms of common wheat except 4BS were assayed in their null condition by using a set of ditelosomic or nullitetrasomic lines of the cultivar Chinese Spring. Our results showed that only one chromosome location each was identified for the 22.8-kDa and the 21.2-kDa enzymes, as well as for the 21.6 kDa enzyme, and they are on chromosome arms 2AS and 2DS, respectively. Loci controlling the 20.1 kDa activity were on chromosome arms 2AL, 4BS, 4DS and 6BS. The locus or loci coding for the gene(s) of the 42.2-kDa, 40.9-kDa and 39.2-kDa enzymes were probably ocated on chromosome arm 5AS, and their expression, in agreement with most other RNA-degrading enzyme activities were stimulated when chromosome arm 5AL was missing, indicating a inhibiting locus on 5AL. Our data suggested that the 31.9-kDa, 30.6-kDa and 29.6-kDa enzymes were possibly products of a common precursor which might be coded by a gene(s) on chromosome arm 6BS, and that the processing is co-regulated by loci on chromosome arms 2BS, 3DS, 6AL, 6BL and 7BS. The remaining of the enzyme activities were consistently found in all of the lines tested, and thus are presumably encoded by multiple loci. The only other possibility is that, their loci may be on chromosome arm 4BS which we have not assayed in its null condition.

Chromosomal locations of genes that control major RNA-degrading activities in common wheat (Triticum aestivum L.)

Chromosomal locations of genes that control major RNA-degrading activities in common wheat (Triticum aestivum L.)

Chromosome and chromosomal arm locations of genes for resistance to Septoria glume blotch in wheat cultivar Cotipora

Septoria glume blotch, caused by Stagonospora nodorum, is an important disease of wheat (Triticum aestivum). Separate genetic mechanisms were found to control flag leaf and spike resistance. Genes for resistance to S. nodorum were located on different chromosomes in the few wheat cultivars studied. These studies only partially agree on the chromosome locations of gene in wheat for resistance to S. nodorum, and chromosomal arm locations of such genes are not known. The objectives of this study were to determine the chromosome and chromosomal arm locations of genes that significantly influence resistance to S. nodorum in wheat cultivar Cotipora. Monosomic analysis showed that flag leaf resistance was controlled by genes on chromosomes 3A, 4A, and 3B whereas the spike resistance was controlled by genes on chromosomes 3A, 4A, 7A, and 3B (P=0.01). Additionally, genes on chromosomes 6B and 5A influenced the susceptibility of the flag leaf and spike reactions, respectively (P=0.01). Telocentric analysis showed that genes on both arms of chromosome 3A, and the long arms of chromosomes 4A and 3B were involved in the flag leaf resistance whereas genes on both arms of chromosome 4A, the short arm of chromosome 3A, and the long arm of chromosome 3B conferred spike resistance.

Chromosomal location of genes controlling grain size in a large grained selection of wheat (Triticum aestivum L.)

Grain size in wheat is the most stable yield component and has a favorable effect on flour yield. To identify the chromosomes associated with the large grains of line G603-86, (grain weight over 60 mg and grain length of about 9 mm), F3 lines, extracted from F2 populations obtained from F1 monosomics of crosses between G603-86 (P1) and the monosomic set of Favorit (P2) were tested in the field. ANOVA showed significant differences among parents for grain weight and grain length, but not for grain width or the factor expressing the difference in grain form and density. Homoeologous groups had significant effects on grain weight and on all components of grain weight, while genomes were not significantly different for any of these characters. Grain weight was significantly increased by chromosomes 6D and 4A of G603-86. Grain length was significantly increased by chromosomes 4A, 4B, 2B, 3A and 1B, grain width by chromosomes 1A and 1B, and the factor form-density by chromosomes 6D and 6A. The high grain size in G603-86 results from the effects of genes located on many chromosomes which affect grain dimensions, form and density.

The development of precise genetic stocks in two wheat cultivars and their use in genetic analysis

The results of genetic studies of common wheat that have been conducted in Novosibirsk, Russia, over the past 20 years by a research team are summarized. The research strategy was to develop a collection of aneuploids and substitution lines to be further used for chromosomal localization of genes and in the study of the genetic variability of wheat. On the basis of two cultivars, namely Saratovskaya 29 and Diamant, we have developed 6 sets of aneuploids with a complete set of monosomic lines for each, plus sets of lines ditelosomic and monotelosomic for “standard” arms. Exploiting the monotelosomics, 108 single chromosome intervarietal substitutions, 13 lines with alien substitutions (mono- and disomics) and 11 addition lines have been developed. A collection of lines isogenic for dominant marker genes of morphological characters has also been developed. The genetic collection was used in chromosomal localization of 15 genes, for many of which chromosome arms have been determined. Positively or negatively, the question of allelism within some loci has been answered.

Chromosome Localization of Human Genes for Clathrin Adaptor Polypeptides AP2β and AP50 and the Clathrin-Binding Protein, VCP

Clathrin-coated vesicles, involved in endocytosis and Golgi processing, have a surface lattice containing clathrin triskelia and stoichiometric amounts of additional components termed “assembly proteins,” or APs. The AP form at the plasma membrane, AP2, is composed of two large subunits of 100–115 kDa, denoted AP2α and AP2β, a medium chain of 50 kDa, designated AP50, and a small chain. We have determined human chromosomal locations of genes for a large AP2β (CLAPB1) and a medium (CLAPM1) AP subunit and of a novel clathrin-binding protein, VCP, that binds clathrin simultaneously with APs. Chromosomalin situhybridization of a human genomic clone demonstrated that the CLAPM1 gene mapped to chromosome region 3q28. The gene for the CLAPB1 large subunit was mapped to 17q11.2–q12 by PCR amplification of an AP2β fragment from a panel of rodent–human hybrid DNAs. To map the human VCP sequence, a human-specific probe was made by RT–PCR of human mRNA using oligonucleotide primers from conserved regions of the porcine sequence. The amplified human fragment served as probe on Southern blots of hybrid DNAs to determine that the human VCP locus maps to chromosome region 9pter–q34.

Type 1 Diabetes and the Control of Dexamethazone-Induced Apoptosis in Mice Maps to the Same Region on Chromosome 6

Quantitative trait loci mapping was used to identify the chromosomal location of genes that contribute to increase the resistance to apoptosis induced in immature CD4+8+ thymocytes. An F2 intercross of the nonobese diabetic (NOD) mouse (displaying an apoptosis-resistance phenotype) and the C57BL/6 mouse (displaying a nonresistance phenotype) was phenotypically analyzed and genotyped for 32 murine microsatellite polymorphisms. Maximum likelihood methods identified a region on the distal part of chromosome 6 that is linked to dexamethazone-induced apoptosis (Iod score = 3.46) and accounts for 14% of the phenotypic variation. This chromosomal region contains the diabetes susceptibility locus Idd6, suggesting that the apoptosis-resistance phenotype constitutes a pathogenesis factor in IDDM of NOD mice.

Chromosomal location of genes for stem rust resistance derived from ‘Waldron’ wheat

The chromosomal locations of genes for resistance to stem rust (Puccinia graminis Pers.: Pers. f. sp. tritici Eriks. & E. Henn.) in the wheat (Triticum aestivum L.) cultivar 'Waldron' (WDR) were determined by monosomic analyses. Wheat lines WDR-B1, -C2, -E4, and -F1,which have single genes for resistance to stem rust derived previously from WDR sel. 'Little Club', were crossed onto a complete set of 21 'Chinese Spring' monosomics. The F2 and backcross-F1 (BC1F1) seedlings from each of the 84 crosses were tested for reaction to culture 111-SS2 (CRL-LCBB) of stem rust, and a few selected segregants were analyzed cytologically for chromosome number. The F2 from 2 crosses of WDR-C2, -E4 and -F1 and the BC1F1 from 2 crosses of WDR-F1 were tested also with culture Or11c (CRL-QBCN). Significant deviations from disomic ratios towards monosomic ratios in the F2 and BC1F1 were used to determine which chromosomes carried the genes for resistance. Cytological analyses of certain BC1F1 and susceptible F2 plants were used to help identify the location of the genes for rust resistance. WDR-B1 has a gene, herein designated Sr41, for resistance on chromosome 4D. WDR-C2 has a gene on chromosome 7 A that may be the same as one previously designated SrWld2. WDR-E4 has a gene on chromosome 2A, possibly SrWld1, which is effective against most or all North American stem rust cultures. WDR-F1 has a gene on chromosome 6B that is the same as or similar to Sr11.

Thioredoxin, a mediator of growth inhibition, maps to 9q31

The human thioredoxin gene has been provisionally mapped to 3p11–p12. Recently thioredoxin cDNA has been isolated in a procedure that detects transcripts coding for growth-suppressing proteins, and thus the chromosomal location of the gene is of particular interest. Chromosome 3 is believed to harbor several tumor suppressor genes important in the development of lung and other common epithelial tumors. To establish more firmly the chromosomal location of the human thioredoxin gene, a somatic hybrid panel was used; it identified chromosome 9 as the location of the transcribed thioredoxin gene. Fluorescence in situ hybridization of a YAC encoding the transcribed thioredoxin gene refined the localization to 9q31.

Chromosomal location of genes affecting tissue‐culture response in wheat

AbstractSix ‘Chinese Spring/Triticum spelta’ substitution lines for chromosomes 1A, 1D (duplicates), 3D (duplicates), 6D, and one ‘Chinese Spring/ Marquis’ substitution line for chromosome 2B were studied for tissue‐culture response (TCR). The results reported here indicate that chromosomes 2B and 6D are critical for TCR, whereas chromosome ID affects callus weight only. Chromosomes 1A and 3D were not found to be critical, however, these chromosomes may carry genes with minor effects.

Chromosomal Location of Genes for Stripe Rust Resistance in Spring Wheat Cultivars Compair, Fielder, Lee, and Lemhi and Interactions of Aneuploid Wheats with Races ofPuccinia striiformis

The spring wheat (Triticum aestivum) cultivar Lemhi has one gene, and cultivars Lee, Compair, and Fielder have two genes each for resistance to stripe rust, caused by Puccinia striiformis. To determine the chromosomal locations of the genes, the cultivars were crossed with susceptible disomic Chinese Spring and a set of 21 Chinese Spring aneuploids. Monosomic F 1 plants were cytologically determined, grown in a green-house, and self pollinated to produce F 2 seed. F 2 seedlings and their parents were inoculated with selected North American races of P. striiformis. The results confirmed that Yr6 in Fielder is on chromosome 7B and Yr8 in Compair is on chromosome 2D; and they show that YrLem in Lemhi is on chromosome IB, YrLel in Lee is on chromosome 4D, YrLe2 in Lee is on chromosome 6D, YrCom in Compair is on chromosome 5B, and YrFie in Fielder is on chromosome 6D. None of the Lee genes that we detected with North American races is Yr7. We propose official gene designations Yr19 for YrCom, Yr20 for YrFie, Yr21 for YrLem. Yr22 for YrLel, and Yr23 for YrLe2

Genetic analysis of the components of winterhardiness in barley (Hordeum vulgare L.)

Winterhardiness in cereals is the consequence of a number of complex and interacting component characters: cold tolerance, vernalization requirement, and photoperiod sensitivity. An understanding of the genetic basis of these component traits should allow for more-effective selection. Genome map-based analyses hold considerable promise for dissecting complex phenotypes. A 74-point linkage map was developed from 100 doubled haploid lines derived from a winter x spring barley cross and used as the basis for quantitative trait locus (QTL) analyses to determine the chromosome location of genes controlling components of winterhardiness. Despite the greater genome coverage provided by the current map, a previously-reported interval on chromosome 7 remains the only region where significant QTL effects for winter survival were detected in this population. QTLs for growth habit and heading date, under 16 h and 24 h light, map to the same region. A QTL for heading date under these photoperiod regimes also maps to chromosome 2. Contrasting alleles at these loci interact in an epistatic fashion. A distinct set of QTLs mapping to chromosomes 1, 2, 3, and 5 determined heading date under 8 h of light. Under field conditions, all QTLs identified under controlled environment conditions were determinants of heading date. Patterns of differential QTL expression, coupled with additive and additive x additive QTL effects, underscore the complexity of winterhardiness. The presence of unique phenotype combinations in the mapping population suggests that coincident QTLs for heading date and winter survival represent the effects of linkage rather than pleiotropy.

Chromosomal localization of the parathyroid hormone/parathyroid hormone-related protein receptor gene to human chromosome 3p21.1-p24.2.

The human PTH/PTH-related peptide (PTH/PTHrP) receptor could be involved in hereditary disorders of PTH or PTHrP action. Knowledge of the gene's chromosomal location would allow studies linking it to specific disease traits. Therefore, we mapped the human PTH/PTHrP receptor gene by polymerase chain reaction of human/rodent somatic cell hybrid panels using oligonucleotide primers designed to amplify a portion of the gene from genomic DNA. The PTH/PTHrP gene was unambiguously assigned to the short arm of human chromosome 3, in the region designated 3p21.1-p24.2. Analysis of a second chromosome 3-specific mapping panel suggests that the gene is located near the 3p21.2-p21.3 boundary. The availability of highly polymorphic markers located in this region will permit exploration of the PTH/PTHrP receptor locus in genetic linkage searches for the causes of bone, calcium, and other potential disorders.

Genetic control of amylose content in wheat endosperm starch and differential effects of three Wx genes

The endosperm starch of the wheat grain is composed of amylose and amylopectin. Genetic manipulation of the ratio of amylose to amylopectin or the amylose content could bring about improved texture and quality of wheat flour. The chromosomal locations of genes affecting amylose content were investigated using a monosomic series of Chinese Spring (CS) and a set of Cheyenne (CNN) chromosome substitution lines in the CS genetic background. Trials over three seasons revealed that a decrease in amylose content occurred in monosomic 4A and an increase in monosomic 7B. Allelic variation between CS and CNN was suggested for the genes on chromosomes 4A and 7B. To examine the effects of three Waxy (Wx) genes which encode a granule-bound starch synthase (Wx protein), the Wx proteins from CS monosomics of interest were analyzed using SDS-PAGE. The amount of the Wx protein coded by the Wx-B1 gene on chromosome arm 4AL was reduced in monosomic 4A, and thus accounted for its decreased amylose content. The amounts of two other Wx proteins coded by the Wx-A1 and Wx-D1 genes on chromosome arms 7AS and 7DS, respectively, showed low levels of protein in the monosomics but no effect on amylose content. The effect of chromosome 7B on the level of amylose suggested the presence of a regulator gene which suppresses the activities of the Wx genes.

Chromosomal location of genes controlling short-term and long-term somatic embryogenesis in wheat revealed by immature embryo culture of aneuploid lines

The expression of essential genes during somatic embryogenesis can be analysed by inducing aneuploid cells to undergo embryogenesis during immature embryo culture and then determining whether defects occur. Triticum aestivum disomic and aneuploid stocks, including 36 ditelosomics and 7 nullitetrasomic 'Chinese Spring' wheats, were compared for their ability to undergo somatic embryogenesis after 2 months of in vitro immature embryo culture. Their regeneration capacity was observed after 4 and 14 months of in vitro culture to determine which chromosome arms influence the process. The large range of variation found among the tested aneuploids suggested that genetic control of the somatic tissue culture ability is polygenic. Our results indicate that genes affecting somatic embryo-genesis and regeneration are located in all of the homoeologous chromosome groups. The lack of chromosome arms 1AL (DT 1AS) and 3DL (DT 3DS) practically suppresses somatic embryogenesis, demonstrating that major genes on wheat chromosome arms 1AL and 3DL control regeneration capacity. Results suggest that plants were mainly produced from somatic embryo development. Although the control of somatic embryogenesis and regeneration is polygenic, the genes located on the long arms of homoeologous group 3 chromosomes have a major effect. We also have evidence of chromosome arms that determine the time required for regeneration.