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At least 1,405 records · Page 78Linked to original sources
PubMed2004

Molecular characterization of Fusarium head blight resistance in Wangshuibai with simple sequence repeat and amplified fragment length polymorphism markers.

Molecular mapping of Fusarium head blight (FHB) resistance quantitative trait loci (QTL) and marker-assisted selection of these QTL will aid in the development of resistant cultivars. Most reported FHB resistance QTL are from 'Sumai 3' and its derivatives. 'Wangshuibai' is a FHB-resistant landrace that originated from China and is not known to be related to 'Sumai 3'. A mapping population of 139 F(5:6) recombinant inbred lines was developed from a cross of 'Wangshuibai' and 'Wheaton'. This population was developed to map the FHB-resistant QTL in 'Wangshuibai' and was evaluated twice for Type II FHB resistance. A total of 1196 simple sequence repeat and amplified fragment length polymorphism markers were screened on this population, and four FHB resistance QTL were detected. A major QTL near the end of 3BS explained 37.3% of the phenotypic variation. Another QTL on 3BS, located close to the centromere, explained 7.4% of the phenotypic variation. Two additional QTL on 7AL and 1BL explained 9.8% and 11.9% of the phenotypic variation, respectively. The simple sequence repeat and amplified fragment length polymorphism markers closely linked to these QTL may be useful for stacking QTL from 'Wangshuibai' and other sources to develop cultivars with transgressive FHB resistance.

China↗
PubMed2006

Most significant genome regions involved in the control of earliness traits in bread wheat, as revealed by QTL meta-analysis.

Earliness is one of the most important adaptation traits in plant breeding. Our purpose was to identify the genome regions of bread wheat involved in the control of earliness and its three components: photoperiod sensitivity (PS), vernalization requirement (VR) and intrinsic earliness (IE). A QTL meta-analysis was carried out to examine the replicability of QTL across 13 independent studies and to propose meta-QTL (MQTL). Initial QTL were projected on a recent consensus map (2004). Quality criteria were proposed to assess the reliability of this projection. These criteria were based on the distances between markers in the QTL regions. Chromosomes of groups 2 and 5 had a greater incidence on earliness control as they carry the known, major genes Ppd and Vrn. Other chromosome regions played an intermediate role in earliness control: 4A [heading date (HD) Meta-QTL], 4B (HD MQTL), 2B (VR MQTL) and 5B (IE MQTL). Markers at this four MQTL should prove helpful in marker-assisted selection, to better control earliness.

Bread↗
PubMed2003

Identification of QTLs influencing agronomic traits in Miscanthus sinensis Anderss. I. Total height, flag-leaf height and stem diameter.

We have developed the first quantitative trait locus (QTL) analyses for agronomic traits in a cross between F(1.1) (P1) and F(1.7) (P7) entries of Miscanthus sinensis Anderss. Both lines are offspring of the cross between MS-90-2 and MS-88-110. A map based on random amplified polymorphic DNA markers previously constructed was used to perform the QTL analyses. This map was developed using a new mapping strategy that has been designated offspring cross. Eleven QTLs were detected for height, panicle height and diameter using the programme mapqtl 4.0 and the multiple QTL method. QTL significance was determined using several analyses, including Kruskal-Wallis analyses, empirical determination of LOD critical values using permutation tests, QTLs validation with field data over 2 years and co-localization of QTLs for correlated traits. The results obtained could be the first step in developing a marker-assisted selection programming in this species for biomass production.

Chromosome Mapping↗
PubMed2006

Genetic mapping of a major gene affecting onion bulb fructan content.

The non-structural dry matter content of onion bulbs consists principally of fructose, glucose, sucrose and fructans. The objective of this study was to understand the genetic basis for the wide variation observed in the relative amounts of these carbohydrates. Bulb carbohydrate composition was evaluated in progeny from crosses between high dry matter storage onion varieties and sweet, low dry matter varieties. When samples were analysed on a dry weight basis, reducing sugar and fructan content exhibited high negative correlations and bimodal segregation suggestive of the action of a major gene. A polymorphic SSR marker, ACM235, was identified which exhibited strong disequilibrium with bulb fructan content in F(2:3) families from the 'W202A' x 'Texas Grano 438' mapping population evaluated in two environments. This marker was mapped to chromosome 8 in the interspecific population 'Allium cepa x A. roylei'. Mapping in the 'Colossal Grano PVP' x 'Early Longkeeper P12' F2 population showed that a dominant major gene conditioning high-fructan content lay in the same genomic region. QTL analysis of total bulb fructan content in the intraspecific mapping population 'BYG15-23' x 'AC43' using a complete molecular marker map revealed only one significant QTL in the same chromosomal region. This locus, provisionally named Frc, may account for the major phenotypic differences in bulb carbohydrate content between storage and sweet onion varieties.

Breeding↗
PubMed2006

Genetic mapping of the gene affecting polyphenol oxidase activity in tetraploid durum wheat.

The quality of durum wheat (Triticum turgidum ssp. durum) is influenced by polyphenol oxidase(PPO) activity and its corresponding substrates. A saturated molecular-marker linkage map was constructed previously by using a set of recombinant inbred (RI) lines, derived from a cross between durum wheat cultivars Jennah Khetifa and Cham 1. Quantitative trait loci (QTL) for PPO activity in seeds were mapped in this population. PPO activity in seeds of the parents and 110 RI lines was measured spectrophotometrically. The PPO activity of Cham 1 was significantly lower than that of Jennah Khetifa. QTL analysis of these data indicated that most of PPO activity was associated with major loci on the long arm of chromosome 2A. The trait was found to be strongly associated with the SSR marker Xgwm312@2A. With this knowledge, marker-assisted selection can be used to select genotypes with lower PPO activity in durum wheat populations.

Breeding↗
PubMed1998

Mapping quantitative trait loci for milk production and health of dairy cattle in a large outbred pedigree.

Quantitative trait loci (QTL) affecting milk production and health of dairy cattle were mapped in a very large Holstein granddaughter design. The analysis included 1794 sons of 14 sires and 206 genetic markers distributed across all 29 autosomes and flanking an estimated 2497 autosomal cM using Kosambi's mapping function. All families were analyzed jointly with least-squares (LS) and variance components (VC) methods. A total of 6 QTL exceeding approximate experiment-wise significance thresholds, 24 QTL exceeding suggestive thresholds, and 34 QTL exceeding chromosome-wise thresholds were identified. Significance thresholds were determined via data permutation (for LS analysis) and chi-square distribution (for VC analysis). The average bootstrap confidence interval for the experiment-wise significant QTL was 48 cM. Some chromosomes harbored QTL affecting several traits, and these were always in coupling phase, defined by consistency with genetic correlations among traits. Chromosome 17 likely harbors 2 QTL affecting milk yield, and some other chromosomes showed some evidence for 2 linked QTL affecting the same trait. In each of these cases, the 2 QTL were in repulsion phase in those families appearing to be heterozygous for both QTL, a finding which supports the build-up of linkage disequilibrium due to selection.

Analysis of Variance↗
PubMed2006

A QTL on rat chromosome 7 modulates prepulse inhibition, a neuro-behavioral trait of ADHD, in a Lewis x SHR intercross.

BACKGROUND: Attention deficit hyperactivity disorder (ADHD) is a complex neuropsychiatric disorder with a substantial genetic component. The Spontaneously Hypertensive Rats (SHR), considered as a good animal model of ADHD, also show less anxiety-like behaviors than Lewis (LEW) rats. The use of these inbred rat strains led us to the mapping of two quantitative trait loci (QTL), named Ofil1 (on chromosome 4) and Ofil2 (on chromosome 7), related to locomotion in the central and aversive area of an open field. Herein, we examined whether LEW and SHR rats differ in the acoustic startle reflex, a test used to study the neurobiology of anxiety, and in the prepulse inhibition of the startle response, which is known to be impaired in ADHD patients. The effect of the two aforementioned loci on these behavioral responses was also studied. METHODS: For this latter purpose, rats deriving from an F2 intercross between the LEW and SHR strains were selected according to their genotype at markers flanking the QTLs and bred to obtain lines of rats homozygous LEW/LEW or SHR/SHR for each of the two loci, thus generating 4 genotypic combinations. RESULTS: The SHR rats displayed decreased startle and prepulse inhibition levels when compared to LEW rats. Ofil2 affected prepulse inhibition in female rats only. CONCLUSION: The results suggest that the LEW and SHR strains are appropriate for studying mechanisms of sensorimotor gating and indicate that the locus Ofil2 on rat chromosome 7 contain genes controlling prepulse inhibition, a neuro-behavioral trait of ADHD.

Journal Article↗
PubMed2026

Meta-QTL Analysis Reveals Consensus Genomic Regions and Candidate Genes for Resistance to Sudden Death Syndrome in Soybean.

Sudden death syndrome (SDS), caused by Fusarium virguliforme, is one of the most economically important diseases limiting soybean production worldwide. Although numerous quantitative trait loci (QTL) associated with SDS resistance have been reported, inconsistencies among mapping populations, marker systems, and experimental conditions have hindered the identification of robust resistance loci for soybean improvement. In this study, a comprehensive meta-analysis was conducted to integrate published QTL and identify stable consensus genomic regions associated with SDS resistance. After a systematic literature survey and data curation, 153 QTL derived from 14 linkage-mapping studies were analyzed using a custom R-based workflow, resulting in the identification of 23 consensus meta-QTL (MQTL) distributed across 17 chromosomes. Several MQTL, particularly those located on chromosomes 6, 8, 18, and 20, were supported by multiple independent studies and represented major genomic hotspots for SDS resistance. Physical localization and functional annotation of these MQTL identified 217 candidate genes, including genes predicted to be involved in plant defense, signal transduction, transcriptional regulation, and secondary metabolism. Gene Ontology enrichment analysis identified response to salicylic acid as the only biological process that remained significant after FDR correction, whereas Kyoto Encyclopedia of Genes and Genomes pathway analysis did not identify significantly enriched pathways. Independent support using five published genome-wide association studies further supported several MQTL, especially those on chromosomes 6, 18, and 20, thereby increasing confidence in these genomic regions. The identified MQTL and prioritized candidate genes provide potential genomic resources for future marker development, improvement applications, and functional validation aimed at improving soybean resistance to SDS.

Fusarium virguliforme↗
PubMed2004

A statistical model for high-resolution mapping of quantitative trait loci determining HIV dynamics.

Are there specific genes that control the pathogenesis of HIV infection? This question, which is of fundamental importance in designing personalized strategies of gene therapy to control HIV infection, can be examined by genetic mapping approaches. In this article, we present a new statistical model for unravelling the genetic mechanisms for the dynamic change of HIV that causes AIDS by marker-based linkage disequilibrium (LD) analyses. This new model is the extension of our functional mapping theory to integrate viral load trajectories within a genetic mapping framework. Earlier studies of HIV dynamics have led to various mathematical functions for modelling the kinetic curves of plasma virions and CD4 lymphocytes in HIV patients. Through incorporating these functions into the LD-based mapping procedure, we can identify and map individual quantitative trait loci (or QTL) responsible for viral pathogenesis. We derive a closed-form solution for estimating QTL allele frequency and marker-QTL linkage disequilibrium in the context of EM algorithm and implement the simplex algorithm to estimate the mathematical parameters describing the curve shapes of HIV pathogenesis. We performed different simulation scenarios based on currently used clinical designs in AIDS/HIV research to illustrate the utility and power of our model for genetic mapping of HIV dynamics. The implications of our model for genetic and genomic research into AIDS pathogenesis are discussed.

Acquired Immunodeficiency Syndrome↗
PubMed2002

Enhancement of Seedling Emergence in Sweet Corn by Marker-Assisted Backcrossing of Beneficial QTL.

Seedling emergence is an important trait that can limit commercialization of sweet corn hybrids. This study was designed to test what effect beneficial QTL alleles that enhance seedling emergence exert when introgressed, using marker-assisted backcrossing, into sweet corn commercial germplasm. Three RFLP marker alleles linked to QTL that enhanced seedling emergence were identified in an F(2:3) sweet corn mapping population. A recombinant inbred line (RIL, F(8)) derived from this population was used as a donor parent to backcross the marker-QTL alleles into three elite commercial sweet corn inbreds. Plants in the three segregating BC(2) populations were crossed to the non-recurrent commercial inbreds to produce three BC(2)F(1) populations with families either segregating or lacking the marker donor allele(s). These three populations were evaluated for seedling emergence under field conditions in two successive years. Across the three populations, BC(2)F(1) families segregating for the donor QTL allele linked to the marker umc139 (on chromosome 2), bnl9.08 (on chromosome 8), or php200689 (on chromosome 1) displayed 40.8, 30.2, and 28.2% increases in seedling emergence, respectively, over the unmodified F(1)s. The introgressed QTL alleles were observed to enhance seedling emergence in the BC(2)F(1) generation as was observed in the original F(2:3) mapping population. Marker-QTL associated effects were reproducible across generations and populations indicating that QTL identified in one population can exert similar effects in different genetic backgrounds. Results suggest that using DNA marker technology can help to identify and introgress beneficial QTL alleles, shortening the time and resources required to develop improved germplasm.

Journal Article↗
PubMed2004

[Comparative analyses of QTL for important agronomic traits between maize and rice].

The objective of this study was to assess syntenic relationships of quantitative trait loci (QTL) for important agronomic traits between maize and rice based on the comparative genomic map of maize and rice using two F(2:3) populations. Through the comparisons, it was observed that there were extensive conserved relationships of maize QTL affected plant height, row number, and kernels per row with rice QTL affected plant height, tillers per plant, and grains per panicle respectively. Sixteen of 45 QTL affecting five different maize traits were conserved compared with 12 of 38 QTL affecting five different rice traits, which provided some useful information for locating, isolating and cloning maize QTL by using the rice genomic data. In this study, one QTL in rice usually had two conserved QTL in maize, further supporting the hypothesis that there is a polyploidization event during maize evolution. It was interested in observing that there were QTL rich regions on chromosomes in maize and rice, where QTL affecting different traits were usually clustered. These results revealed that the QTL affected the same or similar traits in maize and rice may have the common origin. These results will be helpful to map, isolate and clone QTL in large genome crops, such as maize, by using rice genome information, as well as to understand the evolutionary forces that structured the organization of the grass genomes.

Oryza↗
PubMed2005

Molecular mapping of a quantitative trait locus for aluminum tolerance in wheat cultivar Atlas 66.

Genetic improvement of aluminum (Al) tolerance is one of the cost-effective solutions to improve wheat (Triticum aestivum) productivity in acidic soils. The objectives of the present study were to identify quantitative trait loci (QTL) for Al-tolerance and associated PCR-based markers for marker-assisted breeding utilizing cultivar Atlas 66. A population of recombinant inbred lines (RILs) from the cross Atlas 66/Century was screened for Al-tolerance by measuring root-growth rate during Al treatment in hydroponics and root response to hematoxylin stain of Al treatment. After 797 pairs of SSR primers were screened for polymorphisms between the parents, 131 pairs were selected for bulk segregant analysis (BSA). A QTL analysis based on SSR markers revealed one QTL on the distal region of chromosome arm 4DL where a malate transporter gene was mapped. This major QTL accounted for nearly 50% of the phenotypic variation for Al-tolerance. The SSR markers Xgdm125 and Xwmc331 were the flanking markers for the QTL and have the potential to be used for high-throughput, marker-assisted selection in wheat-breeding programs.

Aluminum↗
PubMed2001

The genetic architecture of quantitative traits.

Phenotypic variation for quantitative traits results from the segregation of alleles at multiple quantitative trait loci (QTL) with effects that are sensitive to the genetic, sexual, and external environments. Major challenges for biology in the post-genome era are to map the molecular polymorphisms responsible for variation in medically, agriculturally, and evolutionarily important complex traits; and to determine their gene frequencies and their homozygous, heterozygous, epistatic, and pleiotropic effects in multiple environments. The ease with which QTL can be mapped to genomic intervals bounded by molecular markers belies the difficulty in matching the QTL to a genetic locus. The latter requires high-resolution recombination or linkage disequilibrium mapping to nominate putative candidate genes, followed by genetic and/or functional complementation and gene expression analyses. Complete genome sequences and improved technologies for polymorphism detection will greatly advance the genetic dissection of quantitative traits in model organisms, which will open avenues for exploration of homologous QTL in related taxa.

Animals↗
PubMed2006

Mapping of quantitative trait loci determining NK cell-mediated resistance to MHC class I-deficient bone marrow grafts in perforin-deficient mice.

NK cells reject allogeneic and MHC class I-deficient bone marrow (BM) grafts in vivo. The mechanisms used by NK cells to mediate this rejection are not yet thoroughly characterized. Although perforin plays a major role, perforin-independent mechanisms are involved as well. C57BL/6 mice deficient in perforin (B6 perforin knockout (PKO)) reject class I-deficient TAP-1 KO BM cells as efficiently as normal B6 mice. In contrast, perforin-deficient 129S6/SvEvTac mice (129 PKO) cannot mediate this rejection while normal 129 mice efficiently reject. This suggests that in 129, but not in B6, mice, perforin is crucial for NK cell-mediated rejection of MHC class I-deficient BM grafts. To identify loci linked to BM rejection in perforin-deficient mice, we generated backcross 1 progeny by crossing (129 x B6)F(1) PKO mice to 129 PKO mice. In transplantation experiments, >350 backcross 1 progeny were analyzed and displayed a great variation in ability to reject TAP-1 KO BM grafts. PCR-based microsatellite mapping identified four quantitative trait loci (QTL) on chromosomes 2, 4, and 8, with the QTL on chromosome 8 showing the highest significance, as well as a fifth epistatic QTL on chromosome 3. This study describes the first important step toward identifying BM graft resistance gene(s).

Animals↗
PubMed2000

[Identification of quantitative trait loci associated with fruit traits in watermelon [Citullus lanantus (Thanb) Mansf] and analysis of their genetic effects].

In this study, we mapped and characterized quantitative trait loci (QTL) affecting watermelon fruit traits. A total of 118 F2 progenies derived from the cross 97103 (which is a cultivar with higher total soluble solids concentration, thin rind, susceptible to Fusarium wilt disease) x PI296341(which is a wild germplasm with lower total soluble solids concentration, thick rind, resistant to Fusarium wilt disease) were used to construct a 96-markers map in watermelon. By using interval mapping 4 QTLs for total soluble solids concentration, 5 QTLs for hardness of rind, 2 QTLs for thickness of rind, 3 QTLs for weight of simple fruit, and 6 QTLs for weight of one thousand grain seeds were identified. In addition, the explained variations, additive effects and dominance effects for all detected QTLs were analyzed.

Chromosome Mapping↗
PubMed2005

An expressed sequence tag SSR map of tetraploid alfalfa (Medicago sativa L.).

A genetic map constructed from a population segregating for a trait of interest is required for QTL identification. The goal of this study was to construct a molecular map of tetraploid alfalfa (Medicago sativa.) using simple sequence repeat (SSR) markers derived primarily from expressed sequence tags (ESTs) and bacterial artificial chromosome (BAC) inserts of M. truncatula. This map will be used for the identification of drought tolerance QTL in alfalfa. Two first generation backcross populations were constructed from a cross between a water-use efficient, M. sativa subsp. falcata genotype and a low water-use efficient M. sativa subsp. sativa genotype. The two parents and their F(1) were screened with 1,680 primer pairs designed to amplify SSRs, and 605 single dose alleles (SDAs) were amplified. In the F(1), 351 SDAs from 256 loci were mapped to 41 linkage groups. SDAs not inherited by the F(1), but transmitted through the recurrent parents and segregating in the backcross populations, were mapped to 43 linkage groups, and 44 of these loci were incorporated into the composite maps. Homologous linkage groups were joined to form eight composite linkage groups representing the eight chromosomes of M. sativa. The composite maps consist of eight composite linkage groups with 243 SDAs from M. truncatula EST sequences, 38 SDAs from M. truncatula BAC clone sequences, and five SDAs from alfalfa genomic SSRs. The total composite map length is 624 cM, with average marker density per composite linkage group ranging from 1.5 to 4.4 cM, and an overall average density of 2.2 cM. Segregation distortion was 10%, and distorted loci tended to cluster on individual homologues of several linkage groups.

Chromosome Mapping↗
PubMed2007

Cloning and characterization of the ribosomal protein L3 (RPL3) gene family from Triticum aestivum.

Plant pathogenic fungi of the genus Fusarium can cause severe diseases on small grain cereals and maize. The contamination of harvested grain with Fusarium mycotoxins is a threat to human and animal health. In wheat production of the toxin deoxynivalenol (DON), which inhibits eukaryotic protein biosynthesis, is a virulence factor of Fusarium, and resistance against DON is considered to be part of Fusarium resistance. Previously, single amino acid changes in RPL3 (ribosomal protein L3) conferring DON resistance have been described in yeast. The goal of this work was to characterize the RPL3 gene family from wheat and to investigate the potential role of naturally existing RPL3 alleles in DON resistance by comparing Fusarium-resistant and susceptible cultivars. The gene family consists of three homoeologous alleles of both RPL3A and RPL3B, which are located on chromosomes 4A (RPL3-B2), 4B (RPL3-B1), 4D (RPL3-B3), 5A (RPL3-A3), 5B (RPL3-A2) and 5D (RPL3-A1). Alternative splicing was detected in the TaRPL3-A2 gene. Sequence comparison revealed no amino acid differences between cultivars differing in Fusarium resistance. While using developed SNP markers we nevertheless found that one of the genes, namely, TaRPL3-A3 mapped close to a Fusarium resistance QTL (Qfhs.ifa-5A). The potential role of the RPL3 gene family in DON resistance of wheat is discussed.

Chromosome Mapping↗