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PubMed2000

Developing expressed sequence tags (ESTs) from polymorphic transcript-derived fragments (TDFs) in cassava (Manihot esculenta Crantz).

We applied the cDNA-AFLP (amplified fragment length polymorphism) technique to mRNA from the parents of a cassava (Manihot esculenta) genetic mapping population, and obtained more than 500 transcript-derived fragments (TDFs) that were unique in either parent. A subset of 50 TDFs were cloned and sequenced. Sequence alignment of the expressed sequence tags (ESTs) revealed mostly genes of unknown function. Six of the TDFs were mapped on to the cassava genetic map. We also demonstrated by genetic mapping of the TDFs, as RFLP (restriction fragment length polymorphism) markers, that TDFs are more polymorphic than random cDNAs. Generation of ESTs as differentially expressed sequences, in time or between different varieties, is proposed as a way of developing ESTs around specific traits for the candidate locus approach to mapping complex traits.

Chromosome Mapping↗
PubMed2002

Fine mapping in tomato using microsynteny with the Arabidopsis genome: the Diageotropica (Dgt) locus.

BACKGROUND: The Arabidopsis thaliana genome sequence provides a catalog of reference genes applicable to comparative microsynteny analysis of other species, facilitating map-based cloning in economically important crops. We have applied such an analysis to the tomato expressed sequence tag (EST) database to expedite high-resolution mapping of the Diageotropica (Dgt) gene within the distal end of chromosome 1 in tomato (Lycopersicon esculentum). RESULTS: A BLAST search of the Arabidopsis database with nucleotide sequences of markers that flank the tomato dgt locus revealed regions of microsynteny between the distal end of chromosome 1 in tomato, two regions of Arabidopsis chromosome 4, and one on chromosome 2. Tomato ESTs homeologous to Arabidopsis gene sequences within those regions were converted into co-dominant molecular markers via cleaved amplified polymorphic sequence (CAPS) analysis and scored against an informative backcross mapping population. Six new microsyntenic EST (MEST) markers were rapidly identified in the dgt region, two of which further defined the placement of the Dgt gene and permitted the selection of a candidate tomato bacterial artificial chromosome clone for sequence analysis. CONCLUSIONS: Microsynteny-based comparative mapping combined with CAPS analysis of recombinant plants rapidly and economically narrowed the dgt mapping region from 0.8 to 0.15 cM. This approach should contribute to developing high-density maps of molecular markers to target-specific regions for positional cloning and marker-assisted selection in a variety of plants.

Arabidopsis↗
PubMed2003

Narrowing down the region of the Vf locus for scab resistance in apple using AFLP-derived SCARs.

A narrow-down strategy to restrict the Vf region, which controls resistance to the fungal disease apple scab in apple, to a genetic distance of 0.4 cM is presented. Using 11 AFLP-derived SCARs and three RAPD-derived SCARs, all linked to the Vf gene, we subjected 1,412 scab-resistant individuals from 16 mapping populations to genotype analysis. Eleven recombinant individuals were identified within a genetic distance of 0.9 cM around the Vf gene. Using these 11 recombinants, we achieved fine-resolution of several AFLP-derived SCAR markers surrounding the Vf gene, resulting in the following genetic linkage map: ACS-6 and ACS are located left of the Vf gene at genetic distances of 0.2 cM and 0.1 cM, respectively; ACS-7 and ACS-9 are inseparable from the Vf gene; ACS-8, ACS-10, and ACS-4 are located to the right of the Vf gene at genetic distances of 0.1 cM, 0.4 cM, and 0.5 cM, respectively; the remaining five SCARs-ACS-11, ACS-5, ACS-2, ACS-1, and AL07-are inseparable and are located right of the Vf gene at a genetic distance of 0.7 cM. By integrating this linkage data with our previous physical map, we generated a revised map of the narrowed-down region of Vf.

Ascomycota↗
PubMed2006

Genetic mapping of hop (Humulus lupulus L.) applied to the detection of QTLs for alpha-acid content.

The map locations and effects of quantitative trait loci (QTLs) were estimated for alpha-acid content in hop (Humulus lupulus L.) using amplified fragment length polymorphism (AFLP) and microsatellite marker (simple sequence repeat (SSR)) genetic linkage maps constructed from a double pseudotestcross. The mapping population consisted of 111 progeny from a cross between the German hop cultivar 'Magnum', which exhibits high levels of alpha-acids, and a wild Slovene male hop, 2/1. The progeny segregated quantitatively for alpha-acid content determined in 2002, 2003, and 2004. The maternal map consisted of 96 markers mapped on 14 linkage groups defining 661.90 cM of total map distance. The paternal map included 70 markers assigned to 12 linkage groups covering 445.90 cM of hop genome. QTL analysis indicated 4 putative QTLs (alpha1, alpha2, alpha3, and alpha4) on linkage groups (LGs) 03, 01, 09, and 03 of the female map, respectively. QTLs explained 11.9%-24.8% of the phenotypic variance. The most promising QTL to be used in marker-assisted selection is alpha2, the peak of which colocated exactly with the AFLP marker. Three chalcone synthase-like genes (chs2, chs3, and chs4) involved in hop bitter acid synthesis mapped together on LG04 of the female map. Saturation of the maps, particularly the putative QTL regions, will be carried out using SSR markers, and the stability of the QTLs will be tested in the coming years.

Chromosome Mapping↗
PubMed2004

An analytical formula to estimate confidence interval of QTL location with a saturated genetic map as a function of experimental design.

Analytical formulae are derived for the confidence interval for location of a quantitative trait locus (QTL) using a saturated genetic map, as a function of the experimental design, the QTL allele substitution effect, and the number of individuals genotyped and phenotyped. The formulae are derived assuming evenly spaced recombination events, rather than the actual unevenly spaced distribution. The formulae are useful for determining desired sample size when designing a wide variety of QTL mapping experiments, and for evaluating a priori the potential of a given mapping population for defining the location of a QTL. The formulae do not take into account the finite number of recombination events in a given sample.

Animals↗
PubMed2004

Genetic mapping of EST-derived microsatellites from the diploid Gossypium arboreum in allotetraploid cotton.

To increase the numbers of microsatellites available for use in constructing a genetic map, and facilitate the use of functional genomics to elucidate fiber development and breeding in cotton, we sampled microsatellite sequences from expressed sequence tags (ESTs) transcribed during fiber elongation in the A-genome species Gossypium arboreum to evaluate their frequency of occurrence, level of polymorphism and distribution in the At and Dt subgenomes of tetraploid cotton. From among ESTs derived from G. arboreum fibers at 7-10 days post anthesis (dpa), 931 ESTs were found to contain simple sequence repeats (SSRs); 544 (58.4%) EST-SSR primer pairs were developed, and 468 (86%) amplified PCR products from allotetraploid cotton (G. hirsutumcv. TM-1 and G. barbadense cv. Hai7124). However, only 99 (18.2%) of these were found to be polymorphic and segregating in our interspecific BC1 mapping population [(TM-1xHai7124)xTM-1]. In these amplified and informative EST-SSRs, hexa- and tri-nucleotide repeat motifs were the most frequent, representing 40.1 and 30%, respectively, of the total. A total of 111 loci detected with these 99 EST-SSRs were integrated into our backbone map including 511 SSR loci. The distribution of the EST-SSRs appeared to be non-random, since 72 loci were anchored to the At and 37 to the Dt subgenome of allotetraploid cotton based on linkage tests. Interestingly, out of the 10 pairs of duplicate loci amplified, seven were mapped to the corresponding homologous linkage groups and/or chromosomes. BLASTX analysis revealed that 69 of the 99 ESTs showed significant similarities to known genes. Some genes important for fiber development, such as sucrose synthase, were mapped to corresponding chromosomes. These EST-SSRs provide structural and functional genomic information that will be useful for understanding cotton fiber development.

Base Sequence↗
PubMed2002

Genetic analysis of scab resistance QTL in wheat with microsatellite and AFLP markers.

Three chromosomal regions associated with scab resistance were detected in a common cultivar, Ning7840, by microsatellite and AFLP analysis. Six microsatellites on chromosome 3BS, Xgwm389, Xgwm533, Xbarc147, Xgwm493, Xbarc102, and Xbarc131, were integrated into an amplified fragment length polymorphism (AFLP) linkage group containing a major quantitative trait locus (QTL) for scab resistance in a mapping population of 133 recombinant inbred lines (RILs) derived from 'Ning7840' x 'Clark'. Based on single-factor analysis of variance of scab infection data from four experiments, Xgwm533 and Xbarc147 were the two microsatellite markers most tightly associated with the major scab resistance QTL. Interval analysis based on the integrated map of AFLP and microsatellite markers showed that the major QTL was located in a chromosome region about 8 cM in length around Xgwm533 and Xbarc147. Based on mapping of six microsatellite markers on eight 3BS deletion lines, the major QTL was located distal to breakage point 3BS-8. In total, 18 microsatellites were physically located on different subarm regions on 3BS. Two microsatellites, Xgwm120 and Xgwm614, were significantly associated with QTL for scab resistance on chromosome 2BL and 2AS, respectively. The resistance alleles on 3BS, 2BL, and 2AS were all derived from 'Ning7840'. Significant interaction between the major QTL on 3BS and the QTL on 2BL was detected based on microsatellite markers linked to them. Using these microsatellite markers would facilitate marker-assisted selection to improve scab resistance in wheat.

Chromosome Mapping↗
PubMed2005

SNP analysis of AMY2 and CTSL genes in Litopenaeus vannamei and Penaeus monodon shrimp.

Genetic studies in shrimp have focused on disease, with production traits such as growth left unexamined. Two shrimp species, Litopenaeus vannamei and Penaeus monodon, which represent the majority of US shrimp imports, were selected for single nucleotide polymorphism (SNP) discovery in alpha-amylase (AMY2) and cathepsin-l (CTSL), both candidate genes for growth. In L. vannamei, four SNPs were found in AMY2 and one SNP was found in CTSL. In P. monodon, one SNP was identified in CTSL. The CTSL gene was mapped to linkage group 28 of P. monodon using the female map developed with the Australian P. monodon mapping population. Association analyses for the AMY2 and CTSL genes with body weight (BW) were performed in two L. vannamei populations. While neither gene was found to be significantly associated with BW in these populations, there was a trend in one population towards higher BW for allele G of CTSL SNP C681G.

Animals↗
PubMed2004

One hundred and one new microsatellite loci derived from ESTs (EST-SSRs) in bread wheat.

Four hundred and seventy-eight microsatellite markers derived from expressed sequence tags (EST-SSRs) were screened among three mapping populations (W-7984xOpata 85, WOpop; LumaixHanxuan, LHpop; WenmaixShanhongmai, WSpop). The number of polymorphic EST-SSR primer pairs found in WOpop, LHpop and WSpop was 92, 58 and 29 respectively. A total of 101 EST-SSR loci amplified from 88 primer sets were distributed over the 20 chromosomes of the reference maps (no markers were located on chromosome 4B). These 101 mapped EST-SSR markers add to the existing 450 microsatellite loci previously mapped in bread wheat. Seventy-four of the 101 loci showed significant similarities to known genes, including 24 genes involved in metabolism, 4 in cellular structures, 9 in stress resistance, 12 in transcription, 2 in development, 2 transporters and 21 storage proteins. Besides gliadin and glutenin, most of the 53 genes with putative functions were mapped for the first time by EST-SSR markers in bread wheat. Sequence alignment of the mapped wheat EST-SSR loci allowed tentative assignment of functionality to the other members of grasses family. Colinearity combined with homology information offers an attractive approach to comparative genomics.

Chromosome Mapping↗
PubMed2006

Genetic mapping reveals a single major QTL for bacterial wilt resistance in Italian ryegrass (Lolium multiflorum Lam.).

Bacterial wilt caused by Xanthomonas translucens pv. graminis (Xtg) is a major disease of economically important forage crops such as ryegrasses and fescues. Targeted breeding based on seedling inoculation has resulted in cultivars with considerable levels of resistance. However, the mechanisms of inheritance of resistance are poorly understood and further breeding progress is difficult to obtain. This study aimed to assess the relevance of the seedling screening in the glasshouse for adult plant resistance in the field and to investigate genetic control of resistance to bacterial wilt in Italian ryegrass (Lolium multiflorum Lam.). A mapping population consisting of 306 F1 individuals was established and resistance to bacterial wilt was assessed in glasshouse and field experiments. Highly correlated data (r = 0.67-0.77, P < 0.01) between trial locations demonstrated the suitability of glasshouse screens for phenotypic selection. Analysis of quantitative trait loci (QTL) based on a high density genetic linkage map consisting of 368 amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers revealed a single major QTL on linkage group (LG) 4 explaining 67% of the total phenotypic variance (Vp). In addition, a minor QTL was observed on LG 5. Field experiments confirmed the major QTL on LG 4 to explain 43% (in 2004) to 84% (in 2005) of Vp and also revealed additional minor QTLs on LG 1, LG 4 and LG 6. The identified QTLs and the closely linked markers represent important targets for marker-assisted selection of Italian ryegrass.

Breeding↗
PubMed2004

Comparative mapping and rapid karyotypic evolution in the genus helianthus.

Comparative genetic linkage maps provide a powerful tool for the study of karyotypic evolution. We constructed a joint SSR/RAPD genetic linkage map of the Helianthus petiolaris genome and used it, along with an integrated SSR genetic linkage map derived from four independent H. annuus mapping populations, to examine the evolution of genome structure between these two annual sunflower species. The results of this work indicate the presence of 27 colinear segments resulting from a minimum of eight translocations and three inversions. These 11 rearrangements are more than previously suspected on the basis of either cytological or genetic map-based analyses. Taken together, these rearrangements required a minimum of 20 chromosomal breakages/fusions. On the basis of estimates of the time since divergence of these two species (750,000-1,000,000 years), this translates into an estimated rate of 5.5-7.3 chromosomal rearrangements per million years of evolution, the highest rate reported for any taxonomic group to date.

Biological Evolution↗
PubMed2003

High-resolution mapping of quantitative trait loci by selective recombinant genotyping.

Selective recombinant genotyping (SRG) is a three-stage procedure for high-resolution mapping of a QTL that has previously been mapped to a known confidence interval (target C.I.). In stage 1, a large mapping population is accessed and phenotyped, and a proportion, P, of the high and low tails is selected. In stage 2, the selected individuals are genotyped for a pair of markers flanking the target C.I., and a group of R individuals carrying recombinant chromosomes in the target interval are identified. In stage 3, the recombinant individuals are genotyped for a set of M markers spanning the target C.I. Extensive simulations showed that: (1) Standard error of QTL location (SEQTL) decreased when QTL effect (d) or population size (N) increased, but was constant for given "power factor" (PF = d(2)N); (2) increasing the proportion selected in the tails beyond 0.25 had only a negligible effect on SEQTL; and (3) marker spacing in the target interval had a remarkably powerful effect on SEQTL, yielding a reduction of up to 10-fold in going from highest (24 cM) to lowest (0.29 cM) spacing at given population size and QTL effect. At the densest marker spacing, SEQTL of 1.0-0.06 cM were obtained at PF = 500-16,000. Two new genotyping procedures, the half-section algorithm and the golden section/half-section algorithm, allow the equivalent of complete haplotyping of the target C.I. in the recombinant individuals to be achieved with many fewer data points than would be required by complete individual genotyping.

Algorithms↗
PubMed2005

Genomic characterization and linkage mapping of the apple allergen genes Mal d 2 (thaumatin-like protein) and Mal d 4 (profilin).

Four classes of apple allergens (Mal d 1, -2, -3 and -4) have been reported. By using PCR cloning and sequencing approaches, we obtained genomic sequences of Mal d 2 (thaumatin-like protein) and Mal d 4 (profilin) from the cvs Prima and Fiesta, the two parents of a European reference mapping population. Two copies of the Mal d 2 gene (Mal d 2.01 A and Mal d 2.01 B) were identified, which primarily differed in the length of a single intron (378 or 380 nt) and in one amino acid in the signal peptide. Both Mal d 2.01 A and Mal d 2.01 B were mapped at identical position on linkage group 9. Genomic characterization of four Mal d 4 genes (Mal d 4.01 A and B, Mal d 4.02 A and Mal d 4.03 A) revealed their complete gDNA sequences which varied among genes in length from 862 to 2,017 nt. They all contained three exons of conserved length: 123, 138, and 135 nt. Mal d 4.01 appeared to be duplicated in two copies and located on linkage group 9. Mal d 4.02 A and Mal d 4.03 A were single copy genes located on linkage group 2 and 8, respectively.

Allergens↗
PubMed2004

Multiple loci and epistases control genetic variation for seed dormancy in weedy rice (Oryza sativa).

Weedy rice has much stronger seed dormancy than cultivated rice. A wild-like weedy strain SS18-2 was selected to investigate the genetic architecture underlying seed dormancy, a critical adaptive trait in plants. A framework genetic map covering the rice genome was constructed on the basis of 156 BC(1) [EM93-1 (nondormant breeding line)//EM93-1/SS18-2] individuals. The mapping population was replicated using a split-tiller technique to control and better estimate the environmental variation. Dormancy was determined by germination of seeds after 1, 11, and 21 days of after-ripening (DAR). Six dormancy QTL, designated as qSD(S)-4, -6, -7-1, -7-2, -8, and -12, were identified. The locus qSD(S)-7-1 was tightly linked to the red pericarp color gene Rc. A QTL x DAR interaction was detected for qSD(S)-12, the locus with the largest main effect at 1, 11, and 21 DAR (R(2) = 0.14, 0.24, and 0.20, respectively). Two, three, and four orders of epistases were detected with four, six, and six QTL, respectively. The higher-order epistases strongly suggest the presence of genetically complex networks in the regulation of variation for seed dormancy in natural populations and make it critical to select for a favorable combination of alleles at multiple loci in positional cloning of a target dormancy gene.

Alleles↗
PubMed2003

Molecular tagging of erucic acid trait in oilseed mustard (Brassica juncea) by QTL mapping and single nucleotide polymorphisms in FAE1 gene.

Molecular mapping and tagging of the erucic acid trait (C22:1) in Brassica juncea was done by a candidate gene approach. Two QTLs underlying the variation of seed erucic acid content were assigned to two linkage groups of a B. juncea map using a doubled haploid (DH) mapping population derived from high x low erucic acid F(1) hybrid. Two consensus primers corresponding to the full-length Fatty Acid Elongase 1 ( FAE1) gene, reported to be involved in the elongation of C18:1 to C22:1, were designed. PCR amplification and subsequent cloning and sequencing identified two FAE1 genes ( FAE1.1 and FAE1.2) in both high and low erucic acid mustard lines. Sequence alignment of corresponding FAE1 genes between high and low erucic acid mustard lines identified four substitution type single nucleotide polymorphisms (SNPs) in FAE1.1 and three in FAE1.2. Using the SNuPE method of SNP genotyping, these two genes were mapped to two independent loci that co-segregated with the two QTLs governing the erucic acid trait. Association of wild ( E1E2) and mutant ( e1e2) haplotypes of two FAE1 genes with erucic acid variation in two segregating populations revealed that the e1e1e2e2 genotype identified low erucic acid individuals (<2%) and E1E1E2E2 identified individuals with highest erucic acid content (>40%). The E1e1E2e2 heterozygote was found to be intermediate in phenotype. The applicability of these SNPs in marker-assisted manipulation of the erucic acid trait was verified by genotyping a set of contrasting germplasm of B. juncea belonging to two distinct gene pools (Indian and east European) and other oil-yielding Brassica species.

Acetyltransferases↗
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↗
PubMed2002

Hordoindolines are associated with a major endosperm-texture QTL in barley (Hordeum vulgare).

Endosperm texture has a tremendous impact on the end-use quality of wheat (Triticum aestivum L.). Cultivars of barley (Hordeum vulgare L.), a close relative of wheat, also vary measurably in grain hardness. However, in contrast to wheat, little is known about the genetic control of barley grain hardness. Puroindolines are endosperm-specific proteins found in wheat and its relatives. In wheat, puroindoline sequence variation controls the majority of wheat grain texture variation. Hordoindolines, the puroindoline homologs of barley, have been identified and mapped. Recently, substantial allelic variation was found for hordoindolines among commercial barley cultivars. Our objective was to determine the influence of hordoindoline allelic variation upon grain hardness and dry matter digestibility in the 'Steptoe' x 'Morex' mapping population. This population is segregating for hordoindoline allele type, which was measured by a HinA/HinB/Gsp composite marker. One-hundred and fifty lines of the 'Steptoe' x 'Morex' population were grown in a replicated field trial. Grain hardness was estimated by near-infrared reflectance (NIR) and measured using the single kernel characterization system (SKCS). Variation attributable to the HinA/HinB/Gsp locus averaged 5.7 SKCS hardness units (SKCS U). QTL analysis revealed the presence of several areas of the genome associated with grain hardness. The largest QTL mapped to the HinA/HinB/Gsp region on the short arm of chomosome 7 (5H). This QTL explains 22% of the SKCS hardness difference observed in this study. The results indicate that the Hardness locus is present in barley and implicates the hordoindolines in endosperm texture control.

Hordeum↗
PubMed2002

Identification and mapping of a putative stress response regulator gene in barley.

Plants respond to environmental stress with a number of physiological and developmental changes. Water deficit is one of the major factors limiting plant growth and development and crop productivity. One response of plants to water deficit is accumulation of abscisic acid (ABA). An increase of ABA is responsible for the induction of many genes, presumably some of which contribute to drought tolerance. Analysis of gene expression in barley seedling shoots by differential display reverse transcriptase polymerase chain reaction (DDRT-PCR) led to the isolation of several drought-, cold- and ABA-induced partial cDNA fragments. Here we extensively characterize one of these cDNAs, designated DD6. First, a larger cDNA was extended from DD6 by 5'-RACE (rapid amplification of cDNA ends). Subsequently, the corresponding gene was isolated by screening a barley BAC library, and the sequences of the transcribed and flanking regions were determined. The deduced amino acid sequence has similarity to an Arabidopsis hypothetical protein and to a human and mouse DNA-binding protein. The corresponding gene, named Srg6 (stress-responsive gene), was mapped in a barley doubled haploid mapping population to chromosome 7H between markers ABC455 and salfp76, within a region that previously has been linked to osmotic adaptation in barley and other grass genomes.

Abscisic Acid↗