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At least 199 records · Page 11Linked to original sources
PubMed2026

Haplotype-specific expression of a terpene synthase underlies linalool variation in the grapevine cultivar Riesling.

Grapevine cultivars vary widely in monoterpenoid content, yet the genetic and regulatory mechanisms underlying this variation remain poorly characterized beyond highly aromatic Muscat types. We profiled free volatiles and monoterpenoid glycosides in a Riesling × Cabernet Sauvignon F1 mapping population, revealing extensive variation and transgressive segregation consistent with multigenic control. QTL mapping identified 70 significant loci associated with 48 volatile compounds and monoterpene glycosides, including two major QTLs explaining 33.6% and 33.4% of phenotypic variance in (3S)-linalool accumulation. Integration of haplotype-resolved transcriptomics with metabolite data, enabled by a chromosome-scale diploid Riesling genome assembly, resolved a (3S)-linalool/nerolidol synthase cluster on chromosome 10 and identified VviTPS54 as the strongest candidate underlying linalool variation. VviTPS54 exhibited haplotype-specific expression strongly correlated with (3S)-linalool accumulation across genotypes, while no QTL was detected at the 1-deoxy-D-xylulose-5-phosphate synthase 1 (VviDXS1) locus previously identified in Muscat cultivars. In addition, VviDXS1 expression was not correlated with terpene levels, indicating that regulatory variation within terpene synthase clusters, rather than methylerythritol phosphate (MEP) pathway flux, drives monoterpenoid composition in this population. These results establish regulatory variation of terpene synthases as a key mechanism underlying monoterpenoid diversity in grapevine and demonstrate that resolving such variation requires haplotype-phased genome assemblies coupled with haplotype-resolved transcriptomics to detect allele-specific expression differences at complex, heterozygous loci.

Grapevine↗
PubMed2003

Gene for gene alignment between the Brassica and Arabidopsis genomes by direct transcriptome mapping.

We report a global gene for gene alignment of the genomes of Brassica oleracea and Arabidopsis thaliana by construction of a transcriptome map based on B. oleracea cDNAs obtained from leaf tissue. cDNAs were synthesized from total RNA extracted from individual F2s of a mapping population resulting from crossing double-haploids of broccoli and cauliflower. The map consisted of 247 cDNA markers obtained by the SRAP technique. After sequencing 190 of the polymorphic cDNA bands, FASTA detected 169 sequences with similarity to genes reported in Arabidopsis. There was extensive colinearity between the two genomes for chromosomal segments rather than for whole chromosomes, often showing inversions and deletions/insertions. Large-scale duplications were observed in the B. oleracea genome, but were unevenly distributed, arguing against ancient triplication of the entire genome. The most duplicated segments corresponded to those found on Arabidopsis chromosomes 1 and 5, whereas chromosomes 2 and 4 were the least represented in Brassica. Clear differences in the similarity score value of related sequences allowed the identification of orthologs. Transcriptome mapping is an efficient approach that allows gene-for-gene alignment between a fully sequenced and a poorly characterized genome.

Arabidopsis↗
PubMed2004

High-resolution mapping and chromosome landing at the root-know nematode resistance locus Ma from Myrobalan plum using a large-insert BAC DNA library.

The Ma gene for root-knot nematode (RKN)resistance from Myrobalan plum (Prunus cerasifera L.)confers a complete-spectrum and a heat-stable resistance to Meloidogvne spp., conversely to Mi-I from tomato,which has a more restricted spectrum and a reduced efficiency at high temperature. This gene was identified from a perennial self-incompatible near-wild rootstock species and lies in cosegregation with the SCAR marker SCAFLP2 on the Prunus linkage group 7 in a 2.3 cM interval between the SCAR SCAL19 and SSR pchgms6 markers. We initiated a map-based cloning of Ma and report here the strategy that rapidly led to fine mapping and direct chromosome landing at the locus. Three pairs of bulks, totaling 90 individuals from half-sibling progenies derived from the Ma-heterozygous resistant accession P.2175, were constructed using mapping data, and saturation of the Ma region was performed by bulked segregant analysis (BSA) of 320 AFLP primer pair combinations. The closest three AFLP markers were transformed into codominant SCARs or CAPS designatedSCAFLP3, SCAFLP4 and SCAFLP5. By completing the mapping population up to 1,332 offspring from P.2175,Ma and SCAFLP2 were mapped in a 0.8 cM interval between SCAFLP3 and SCAFLP4. A large-insert bacterial artificial chromosome (BAC) DNA library of P.2175,totaling 30,720 clones with a mean insert size of 145 kb and a 14-15x Prunus haploid genome coverage was constructed and used to land on the Ma spanning interval with few BAC clones. As P.2175 is heterozygous for the gene, we constructed the resistant and susceptible physical contigs by PCR screening of the library with codominant markers. Additional microsatellite markers were then designed from BAC subcloning or BAC end sequencing. In the resistant contig, a single 280 kb BAC clone was shown to carry the Ma gene; this BAC contains two flanking markers on each side of the gene as well as two cosegregating markers. These results should allow future cloning of the Ma gene in this perennial species.

Animals↗
PubMed2005

Mapping regulatory genes as candidates for cold and drought stress tolerance in barley.

Cereal crop yield is greatly affected in many growing areas by abiotic stresses, mainly low temperature and drought. In order to find candidates for the tolerance genes for these stresses, 13 genes encoding for transcription factors and upstream regulators were screened by amplification and SSCP on six parental genotypes of three barley mapping populations ('Nure' x 'Tremois', 'Proctor' x 'Nudinka', and 'Steptoe' x 'Morex'), and mapped as newly developed STS, SNP, and SSCP markers. A new consensus function map was then drawn using the three maps above, including 16 regulatory candidate genes (CGs). The positions of barley cold and drought tolerance quantitative trait loci (QTLs) presently described in the literature were added to the consensus map to find positional candidates from among the mapped genes. A cluster of six HvCBF genes co-mapped with the Fr-H2 cold tolerance QTL, while no QTLs for the same trait were positioned on chromosome 7H, where two putative barley regulators of CBF expression, ICE1 and FRY1, found by homology search, were mapped in this work. These observations suggest that CBF gene(s) themselves, rather than their two regulators, are at present the best candidates for cold tolerance. Four out of 12 drought tolerance QTLs of the consensus map are associated with regulatory CGs, on chromosomes 2H, 5H, and 7H, and two QTLs with effector genes, on chromosomes 5H and 6H. The results obtained could be used to guide MAS applications, allowing introduction into an ideal genotype of favourable alleles of tolerance QTLs.

Chromosome Mapping↗
PubMed2001

Fine scale mapping in the sex locus region of the honey bee (Apis mellifera).

Isolating an unknown gene with fine-scale mapping is possible in a "non-model" organism. Sex determination in honey bees consists of a single locus (sex locus) with several complementary alleles. Diploid females are heterozygous at the sex locus, whereas haploid males arise from unfertilized eggs and are hemizygous. The construction of specific inbred crosses facilitates fine scale mapping in the sex locus region of the honey bee. The high recombination rate in the honey bee reduces the physical distance between markers compared with model organisms and facilitates a novel gene isolation strategy based on step-wise creation of new markers within small physical distances. We show that distances less than 25 kb can be efficiently mapped with a mapping population of only 1000 individuals. The procedure described here will accelerate the mapping, analysis and isolation of honey bee genes.

Animals↗
PubMed1995

Advanced intercross lines, an experimental population for fine genetic mapping.

An advanced intercrossed line (AIL) is an experimental population that can provide more accurate estimates of quantitative trait loci (QTL) map location than conventional mapping populations. An AIL is produced by randomly and sequentially intercrossing a population that initially originated from a cross between two inbred lines or some variant thereof. This provides increasing probability of recombination between any two loci. Consequently, the genetic length of the entire genome is stretched, providing increased mapping resolution. In this way, for example, with the same population size and QTL effect, a 95% confidence interval of QTL map location of 20 cM in the F2 is reduced fivefold after eight additional random mating generations (F10). Simulation results showed that to obtain the anticipated reduction in the confidence interval, breeding population size of the AIL in all generations should comprise an effective number of > or = 100 individuals. It is proposed that AILs derived from crosses between known inbred lines may be a useful resource for fine genetic mapping.

Animals↗
PubMed2003

Quantitative trait loci for low aflatoxin production in two related maize populations.

Aflatoxin B(1) formed by Aspergillus flavus Fr:Link has been associated with animal disease and liver cancer in humans. We performed genetic studies in progenies derived from maize inbred Tex6, associated with relatively low levels of aflatoxin production, crossed with the historically important inbred B73. (Tex6 x B73) x B73 BC(1)S(1) and Tex6 x B73 F(2:3) mapping populations were produced and evaluated in 1996 and 1997 in Champaign, Ill. Ears were inoculated 20 to 24 days after midsilk using a pinboard method and a mixture of conidia of A. flavus Link:Fr. isolates. Aflatoxin B(1) levels in harvested ears were determined using an indirect competitive ELISA. Molecular markers were assayed on the populations and used to generate maps. Molecular marker - QTL associations for lower levels of aflatoxin production were determined using multiple regression (MR) and composite interval analysis with multiple regression (CIM MR). MR revealed sets of markers associated with lower aflatoxin production in 1996 and 1997, and CIM MR detected a smaller subset of loci significant in 1997. QTLs for lower aflatoxin were attributed to both Tex6 and B73 parental sources. Environment strongly influenced the detection of QTLs for lower aflatoxin production in different years. There were very few chromosome regions associated with QTLs in more than 1 year or population with MR analysis, and none with CIM MR analysis. In 1997, QTLs for lower aflatoxin were detected with CIM MR in bins 5.01-2 and 5.04-5 in the BC(1)S(1) population, and in bins 3.05-6, 4.07-8 and 10.05-10.07 in the F(2:3) population. These QTL associations appear the most promising for further study.

Aflatoxins↗
PubMed1993

Phylogenetic distribution and genetic mapping of a (GGC)n microsatellite from rice (Oryza sativa L.).

DNA microsatellites are ubiquitously present in eukaryotic genomes and represent a vast source of highly informative markers. We describe in this article a (GGC)n microsatellite which is widely distributed in eukaryotic genomes. Using polymerase chain reaction (PCR) techniques and DNA sequencing, we demonstrated for the first time in plant species that a (GGC)n microsatellite locus is moderately polymorphic. Six alleles are present at this locus in rice and length polymorphisms are caused by variation in the number of tandem GGC repeats. By scoring a backcross mapping population, we were able to demonstrate that this locus is stably inherited and does not link to any known RFLP markers on the rice RFLP map. Our results suggest that DNA microsatellites should be useful in plants for construction of genetic linkage maps, extension of the existing genetic linkage maps, linkage analysis of disease and pest resistance genes, and the study of population genetics.

Base Sequence↗
PubMed2002

Resistance gene homologues in melon are linked to genetic loci conferring disease and pest resistance.

Genomic and cDNA fragments with homology to known disease resistance genes (RGH fragments) were cloned from Cucumis melo using degenerate-primer PCR. Fifteen homologues of the NBS-LRR gene family have been isolated. The NBS-LRR homologues show high divergence and, based on the partial NBS-fragment sequences, appear to include members of the two major subfamilies that have been described in dicot plants, one that possesses a TIR-protein element and one that lacks such a domain. Genomic organization of these sequences was explored by DNA gel-blot analysis, and conservation among other Cucurbitaceae was assessed. Two mapping populations that segregate for several disease and pest resistance loci were used to map the RGH probes onto the melon genetic map. Several NBS-LRR related sequences mapped to the vicinity of genetic loci that control resistance to papaya ringspot virus, Fusarium oxysporum race 1, F. oxysporum race 2 and to the insect pest Aphis gossypii. The utility of such markers for breeding resistant melon cultivars and for cloning the respective R-genes is discussed.

Journal Article↗
PubMed2002

Genetic mapping of 66 new microsatellite (SSR) loci in bread wheat.

In hexaploid bread wheat ( Triticum aestivum L. em. Thell), ten members of the IWMMN ( International Wheat Microsatellites Mapping Network) collaborated in extending the microsatellite (SSR = simple sequence repeat) genetic map. Among a much larger number of microsatellite primer pairs developed as a part of the WMC ( Wheat Microsatellite Consortium), 58 out of 176 primer pairs tested were found to be polymorphic between the parents of the ITMI ( International Triticeae Mapping Initiative) mapping population W7984 x Opata 85 (ITMI pop). This population was used earlier for the construction of RFLP ( Restriction Fragment Length Polymorphism) maps in bread wheat (ITMI map). Using the ITMI pop and a framework map (having 266 anchor markers) prepared for this purpose, a total of 66 microsatellite loci were mapped, which were distributed on 20 of the 21 chromosomes (no marker on chromosome 6D). These 66 mapped microsatellite (SSR) loci add to the existing 384 microsatellite loci earlier mapped in bread wheat.

Journal Article↗
PubMed2005

Genetic mapping of Z chromosome and identification of W chromosome-specific markers in the silkworm, Bombyx mori.

In the silkworm, Bombyx mori, the female is the heterogametic (ZW) sex and the male is homogametic (ZZ). The female heterogamety is a typical situation in the insect order Lepidoptera. Although the W chromosome in silkworm is strongly female determining, no W-linked gene for a morphological character has been found on it. The Z chromosome carries important traits of economic value as well as genes for various phenotypic traits, but only 2% of molecular information based on its relative size is known. Studies conducted so far indicate that the Z-linked genes are not dosage compensated. In the present study, we constructed a genetic map of randomly amplified polymorphic DNA fragments (RAPD), simple sequence repeats (SSR), and fluorescent intersimple sequence repeat PCR (FISSR) markers for the Z chromosome using a backcross mapping population. A total of 16 Z-linked markers were identified, characterized, and mapped using od, a recessive trait for translucent skin as an anchor marker yielding a total recombination map of 334.5 cM. The linkage distances obtained suggested that the markers were distributed throughout the Z chromosome. Four RAPD and four SSR markers that were linked to W chromosome were also identified. The proposed mapping approach should be useful to identify and map sex-linked traits in the silkworm. The economic and evolutionary significance of Z- and W-linked genes in silkworm, in particular, and lepidopterans, in general, is discussed.

Animals↗
PubMed2003

Saturating rye genetic map with amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) markers.

A linkage map of rye, previously developed using DS2 x RXL10 F2 mapping population, was enriched with 179 AFLP and 19 RAPD marker loci. The current map covers 1386 cM and contains 480 markers including 200 RFLPs, 179 AFLPs, 88 RAPDs, 12 protein loci and one dwarfing gene. AFLPs generated by EcoRI/MseI primer combinations were distributed over the entire genome as distinct loci or clusters of 2-14 tightly linked DNA fragments. New marker loci mapped distally to the existing framework, significantly increased coverage of chromosomes 1R, 2R and 5R. The average marker distance is now 2.9 cM, but in seven regions the closest markers are still more than 20 cM apart. A detailed description of the newly mapped AFLP and RAPD loci is presented. The relationship with other published rye maps is discussed.

Chromosomes, Plant↗
PubMed2004

Localization of a novel recessive powdery mildew resistance gene from common wheat line RD30 in the terminal region of chromosome 7AL.

Segregation analysis of resistance to powdery mildew in a F(2) progeny from the cross Chinese Spring (CS) x TA2682c revealed the inheritance of a dominant and a recessive powdery mildew resistance gene. Selfing of susceptible F(2) individuals allowed the establishment of a mapping population segregating exclusively for the recessive resistance gene. The extracted resistant derivative showing full resistance to each of 11 wheat powdery mildew isolates was designated RD30. Amplified fragment length polymorphism (AFLP) analysis of bulked segregants from F(3)s showing the homozygous susceptible and resistant phenotypes revealed an AFLP marker that was associated with the recessive resistance gene in repulsion phase. Following the assignment of this AFLP marker to wheat chromosome 7A by means of CS nullitetrasomics, an inspection of simple sequence repeat (SSR) loci evenly spaced along chromosome 7A showed that the recessive resistance gene maps to the distal region of chromosome 7AL. On the basis of its close linkage to the Pm1 locus, as inferred from connecting partial genetic maps of 7AL of populations CS x TA2682c and CS x Virest ( Pm1e), and its unique disease response pattern, the recessive resistance gene in RD30 was considered to be novel and tentatively designated mlRD30.

Ascomycota↗
PubMed1996

Simple sequence repeats for germplasm analysis and mapping in maize.

Simple sequence repeats (SSRs) are a relatively new class of DNA markers consisting of short runs of tandemly repeated sequence motifs evenly distributed throughout eukaryotic genomes. Owing to the high rate of variation in the number of repeat units, the polymorphism level shown by SSRs is high. Furthermore, they are easy to analyze by means of the polymerase chain reaction, using flanking unique sequence primers. In order to establish the utility of SSR markers for genetic mapping and for the analysis of corn germplasm, corn genomic libraries were constructed and screened for clones containing dinucleotide and trinucleotide repeats. One hundred and fifty clones were isolated and 34 of them were used in this study to analyze 15 (AG)n repeats, 15 (AC)n repeats, and 4 trinucleotide repeats. Twelve corn inbred lines, representing 87% of the RFLP alleles present in a collection of public corn cultivars, were used to assess the information content of the SSR markers. The expected heterozygosity of each SSR marker was compared with the expected heterozygosity of 100 different RFLP markers. The stability of SSRs was also tested through segregation analysis on an existing mapping population.

Alleles↗
PubMed2005

Joint analysis of two breed cross populations in pigs to improve detection and characterization of quantitative trait loci.

The purpose of this study was to develop and implement least squares interval-mapping models for joint analysis of breed cross QTL mapping populations and to evaluate the effect of joint analysis on QTL detected for economic traits in data from two breed crosses in pigs. Data on 26 growth, carcass composition, and meat quality traits from F2 crosses between commercially relevant pig breeds were used: a Berkshire x Yorkshire cross at Iowa State University (ISU) and a Berkshire x Duroc cross at the University of Illinois (UOI). All animals were genotyped for a total of 39 (ISU) and 32 (UOI) markers on chromosomes 2, 6, 13, and 18. Marker linkage maps derived from the individual and joint data were similar with regard to order and relative position, but some differences in absolute distances existed. Maps from the joint data were used in all analyses. The individual and joint data sets were analyzed using several least squares interval-mapping models: line-cross (LC) models with Mendelian and parent-of-origin effects; halfsib models (HS); and combined models (CB) that included LC and HS effects. Lack-of-fit tests between the models were used to characterize QTL for mode of expression and to identify segregation of QTL within parental breeds. A total of 26 (8), 47 (18), and 53 (16) QTL were detected at the 5% chromosome (genome)-wise level in the ISU, UOI, and joint data for the 26 analyzed traits. Of the 53 QTL detected in the joint data, only six were detected in both populations and for many, allele effects differed between the two crosses. Despite the lack of overlap between the two populations, joint analysis resulted in an increase in significance for many QTL, including detection of ten QTL that did not reach significance in either population. Confidence intervals for position also were smaller for several QTL. In contrast, 24 QTL, most of which were detected at chromosome-wise levels in the ISU or UOI population, were not detected in the joint data. Presence of paternally expressed QTL near the IGF2 region of SSC2 was confirmed, with major effects on backfat and loin muscle area, particularly in the UOI population, as well as one or more QTL for carcass composition in the distal arm of Chromosome 6. Results of this study suggest that joint analysis using a range of QTL models increases the power of QTL mapping and QTL characterization, which helps to identify genes for subsequent marker-assisted selection.

Animals↗
PubMed2003

First RFLP linkage map of red clover ( Trifolium pratense L.) based on cDNA probes and its transferability to other red clover germplasm.

We constructed a genetic linkage map of red clover ( Trifolium pratense L., 2n=2 x=14) using RFLP markers from cDNA probes of a backcrossed mapping population, and investigated the transferability of the markers to other red clover germplasm. The map contains 157 RFLP markers and one morphological marker on seven linkage groups. The total map distance was 535.7 cM and the average distance between two markers was 3.4 cM. All of the cDNA probes of the map were hybridized to the fragments of genomic DNA from 12 plants derived from three varieties, and 87% of the cDNA probes detected polymorphic bands that corresponded to those of mapping parents. This result indicated that RFLP markers on the present map were transferable to the genome analysis of other red clover germplasm. This is the first report to construct a linkage map of Trifolium species; it should provide fundamental and useful genetic information relevant to the breeding of red clover and genus Trifolium.

Chromosome Mapping↗
PubMed2000

Microsatellite repeats are not randomly distributed within Norway spruce (Picea abies K.) expressed sequences.

A Norway spruce (Picea abies K.) cDNA library obtained from vegetative bud tissue was screened for the presence of (AG)n and (AC)n microsatellite repeats. Ten (AG)n and six (AC)n microsatellites were found, with an average length of 25.5 repeat units. Most of the microsatellites are simple perfect repeats. The microsatellite distribution within the clones is clearly non-random, with different classes of repeats lying in different positions relative to the coding region and in a highly conserved orientation. An estimate of the frequency of dinucleotide microsatellites in expressed regions was obtained, showing that SSRs (simple sequence repeats) are found in genes about 20 times less frequently than in random genomic clones, with (AG)n repeats more frequent than (AC)n repeats. Potential applications of these sequences as expressed region-based molecular markers are shown by developing six SSR markers for the detection of natural variation in Norway spruce populations and testing two of them for the identification of illegitimate progenies from a mapping population.

DNA, Complementary↗
PubMed2002

Genetic linkage maps of two apricot cultivars ( Prunus armeniaca L.), and mapping of PPV (sharka) resistance.

Genetic linkage maps for two apricot cultivars have been constructed using AFLP, RAPD, RFLP and SSR markers in 81 F1 individuals from the cross 'Goldrich' x 'Valenciano'. This family segregated for resistance to 'plum pox virus' (PPV), the most-important virus affecting Prunus species. Of the 160 RAPD arbitrary primers screened a total of 44 were selected. Sixty one polymorphic RAPD markers were scored on the mapping population: 30 heterozygous in 'Goldrich', 19 heterozygous in 'Valenciano', segregating 1:1, and 12 markers heterozygous in both parents, segregating 3:1. A total of 33 and 19 RAPD markers were mapped on the 'Goldrich' and 'Valenciano' maps respectively. Forteen primer combinations were used for AFLPs and all of them detected polymorphism. Ninety five markers segregating 1:1 were identified, of which 62 were heterozygous in the female parent 'Goldrich' and 33 in the male parent 'Valenciano'. Forty five markers were present in both parents and segregated 3:1. A total of 82 and 48 AFLP markers were mapped on the 'Goldrich' and 'Valenciano' maps. Twelve RFLPs probes were screened in the population, resulting in five loci segregating in the family, one locus heterozygous for 'Valenciano' and four heterozygous for both, segregating 1:2:1. Of the 45 SSRs screened 17 segregated in the mapping family, resulting in seven loci heterozygous for the maternal parent and ten heterozygous for both, segregating 1:2:1 or 1:1:1:1. A total of 16 and 13 co-dominant markers were mapped in the female and male parent maps respectively. A total of 132 markers were placed into eight linkage groups on the 'Goldrich' map, defining 511 cM of the total map-length. The average distance between adjacent markers was 3.9 cM. A total of 80 markers were placed into seven linkage groups on the 'Valenciano' map, defining 467.2 cM of the total map-distance, with an average interval of 5.8 cM between adjacent markers. Thirty six marker loci heterozygous in both parents revealed straightforward homologies between five linkage groups in both maps. The sharka resistance trait mapped on linkage group 2. The region containing sharka resistance is flanked by two co-dominant markers that will be used for targeted SSR development employing a recently constructed complete apricot BAC library. SSRs tightly linked to sharka resistance will facilitate MAS in breeding for resistance in apricot.

Journal Article↗