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High-resolution mapping of the Brassica napus Rfp restorer locus using Arabidopsis-derived molecular markers.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The two forms of cytoplasmic male sterility (CMS) native to the oilseed rape or canola species Brassica napus, nap and pol, have novel features that may provide insight into the molecular mechanisms through which CMS/nuclear restorer systems evolve. One such feature is the finding that the distinct nuclear restorer genes for the two systems represent different alleles or haplotypes of the same nuclear locus. Improved understanding of how these systems have evolved will require molecular cloning and characterization of this novel locus. We have employed an approach that exploits the regional co-linearity between the Ara...
Source: TAG. Theoretical and Applied Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Formanová N, Stollar R, Geddy R, Mahé L, Laforest M, Landry BS, Brown GG Tags: Theor Appl Genet Source Type: journals

Pleiotropy of the branching locus (B) masks linked and unlinked quantitative trait loci affecting seed traits in sunflower.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The discovery of unbranched, monocephalic natural variants was pivotal for the domestication of sunflower (Helianthus annuus L.). The branching locus (B), one of several loci apparently targeted by aboriginal selection for monocephaly, pleiotropically affects plant, seed and capitula morphology and, when segregating, confounds the discovery of favorable alleles for seed yield and other traits. The present study was undertaken to gain deeper insights into the genetics of branching and seed traits affected by branching. We produced an unbranched hybrid testcross recombinant inbred line (TC-RIL) population by crossing bra...
Source: TAG. Theoretical and Applied Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Bachlava E, Tang S, Pizarro G, Schuppert GF, Brunick RK, Draeger D, Leon A, Hahn V, Knapp SJ Tags: Theor Appl Genet Source Type: journals

Enriched partial correlations in genome-wide gene expression profiles of hybrids (A. thaliana): a systems biological approach towards the molecular basis of heterosis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Heterosis is a well-known phenomenon but the underlying molecular mechanisms are not yet established. To contribute to the understanding of heterosis at the molecular level, we analyzed genome-wide gene expression profile data of Arabidopsis thaliana in a systems biological approach. We used partial correlations to estimate the global interaction structure of regulatory networks. Our hypothesis states that heterosis comes with an increased number of partial correlations which we interpret as increased numbers of regulatory interactions leading to enlarged adaptability of the hybrids. This hypothesis is true for mid-par...
Source: TAG. Theoretical and Applied Genetics - November 17, 2009 Category: Genetics & Stem Cells Authors: Andorf S, Selbig J, Altmann T, Poos K, Witucka-Wall H, Repsilber D Tags: Theor Appl Genet Source Type: journals

COSII genetic maps of two diploid Nicotiana species provide a detailed picture of synteny with tomato and insights into chromosome evolution in tetraploid N. tabacum.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In conclusion, these COSII and SSR markers link the cultivated tobacco map to those of wild diploid Nicotiana species and tomato, thus providing a platform for cross-reference of genetic and genomic information among them as well as other solanaceous species including potato, eggplant, pepper and the closely allied coffee (Rubiaceae). Therefore they will facilitate genetic research in the genus Nicotiana. PMID: 19921141 [PubMed - as supplied by publisher] (Source: TAG. Theoretical and Applied Genetics)
Source: TAG. Theoretical and Applied Genetics - November 17, 2009 Category: Genetics & Stem Cells Authors: Wu F, Eannetta NT, Xu Y, Plieske J, Ganal M, Pozzi C, Bakaher N, Tanksley SD Tags: Theor Appl Genet Source Type: journals

Mixed model approaches for the identification of QTLs within a maize hybrid breeding program.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Two outlines for mixed model based approaches to quantitative trait locus (QTL) mapping in existing maize hybrid selection programs are presented: a restricted maximum likelihood (REML) and a Bayesian Markov Chain Monte Carlo (MCMC) approach. The methods use the in-silico-mapping procedure developed by Parisseaux and Bernardo (2004) as a starting point. The original single-point approach is extended to a multi-point approach that facilitates interval mapping procedures. For computational and conceptual reasons, we partition the full set of relationships from founders to parents of hybrids into two types of relations by...
Source: TAG. Theoretical and Applied Genetics - November 17, 2009 Category: Genetics & Stem Cells Authors: van Eeuwijk FA, Boer M, Totir LR, Bink M, Wright D, Winkler CR, Podlich D, Boldman K, Baumgarten A, Smalley M, Arbelbide M, Ter Braak CJ, Cooper M Tags: Theor Appl Genet Source Type: journals

Background correction of two-colour cDNA microarray data using spatial smoothing methods.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The analysis of two-colour cDNA microarray data usually involves subtracting background values from foreground values prior to normalization and further analysis. This approach has the advantage of reducing bias and the disadvantage of blowing up the variance of lower abundant spots. Whenever background subtraction is considered, it implicitly assumes locally constant background values. In practice, this assumption is often not met, which casts doubts on the usefulness of simple background subtraction. In order to improve background correction, we propose local background smoothing within the pre-processing pipeline of...
Source: TAG. Theoretical and Applied Genetics - November 15, 2009 Category: Genetics & Stem Cells Authors: Schützenmeister A, Piepho HP Tags: Theor Appl Genet Source Type: journals

Prediction of hybrid performance in maize using molecular markers and joint analyses of hybrids and parental inbreds.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The identification of superior hybrids is important for the success of a hybrid breeding program. However, field evaluation of all possible crosses among inbred lines requires extremely large resources. Therefore, efforts have been made to predict hybrid performance (HP) by using field data of related genotypes and molecular markers. In the present study, the main objective was to assess the usefulness of pedigree information in combination with the covariance between general combining ability (GCA) and per se performance of parental lines for HP prediction. In addition, we compared the prediction efficiency of AFLP an...
Source: TAG. Theoretical and Applied Genetics - November 15, 2009 Category: Genetics & Stem Cells Authors: Schrag TA, Möhring J, Melchinger AE, Kusterer B, Dhillon BS, Piepho HP, Frisch M Tags: Theor Appl Genet Source Type: journals

Systemic properties of metabolic networks lead to an epistasis-based model for heterosis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The genetic and molecular approaches to heterosis usually do not rely on any model of the genotype-phenotype relationship. From the generalization of Kacser and Burns' biochemical model for dominance and epistasis to networks with several variable enzymes, we hypothesized that metabolic heterosis could be observed because the response of the flux towards enzyme activities and/or concentrations follows a multi-dimensional hyperbolic-like relationship. To corroborate this, we used the values of systemic parameters accounting for the kinetic behaviour of four enzymes of the upstream part of glycolysis, and simulated genet...
Source: TAG. Theoretical and Applied Genetics - November 15, 2009 Category: Genetics & Stem Cells Authors: Fiévet JB, Dillmann C, de Vienne D Tags: Theor Appl Genet Source Type: journals

The International Conference on "Heterosis in Plants"Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19911155 [PubMed - as supplied by publisher] (Source: TAG. Theoretical and Applied Genetics)
Source: TAG. Theoretical and Applied Genetics - November 13, 2009 Category: Genetics & Stem Cells Authors: Melchinger AE Tags: Theor Appl Genet Source Type: journals

High congruency of QTL positions for heterosis of grain yield in three crosses of maize.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The genetic basis of heterosis in maize has been investigated in a number of studies but results have not been conclusive. Here, we compare quantitative trait loci (QTL) mapping results for grain yield, grain moisture, and plant height from three populations derived from crosses of the heterotic pattern Iowa Stiff Stalk Synthetic x Lancaster Sure Crop, investigated with the Design III, and analyzed with advanced statistical methods specifically developed to examine the genetic basis of mid-parent heterosis (MPH). In two populations, QTL analyses were conducted with a joint fit of linear transformations Z (1) (trait mea...
Source: TAG. Theoretical and Applied Genetics - November 13, 2009 Category: Genetics & Stem Cells Authors: Schön CC, Dhillon BS, Utz HF, Melchinger AE Tags: Theor Appl Genet Source Type: journals

Transcriptome-based distance measures for grouping of germplasm and prediction of hybrid performance in maize.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Grouping of germplasm and prediction of hybrid performance and heterosis are important applications in hybrid breeding programs. Gene expression analysis is a promising tool to achieve both tasks efficiently. Our objectives were to (1) investigate distance measures based on transcription profiles, (2) compare these with genetic distances based on AFLP markers, and (3) assess the suitability of transcriptome-based distances for grouping of germplasm and prediction of hybrid performance and heterosis in maize. We analyzed transcription profiles from seedlings of the 21 parental maize lines of a 7 x 14 factorial with a 46...
Source: TAG. Theoretical and Applied Genetics - November 13, 2009 Category: Genetics & Stem Cells Authors: Frisch M, Thiemann A, Fu J, Schrag TA, Scholten S, Melchinger AE Tags: Theor Appl Genet Source Type: journals

Broadening the avenue of intersubgenomic heterosis in oilseed Brassica.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Accumulated evidence has shown that each of the three basic Brassica genomes (A, B and C) has undergone profound changes in different species, and has led to the concept of the "subgenome". Significant intersubgenomic heterosis was observed in hybrids between traditional Brassica napus and first generation lines of new type B. napus. The latter were produced by the partial introgression of subgenomic components from different species into B. napus. To increase the proportion of exotic subgenomic components and thus achieve stronger heterosis, lines of first generation new type B. napus were intercrossed with each other...
Source: TAG. Theoretical and Applied Genetics - November 13, 2009 Category: Genetics & Stem Cells Authors: Zou J, Zhu J, Huang S, Tian E, Xiao Y, Fu D, Tu J, Fu T, Meng J Tags: Theor Appl Genet Source Type: journals

Molecular markers from a BAC contig spanning the Rdr1 locus: a tool for marker-assisted selection in roses.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We constructed a BAC contig of about 300 kb spanning the Rdr1 locus for black spot resistance in Rosa multiflora hybrids, using a new BIBAC library from DNA of this species. From this contig, we developed broadly applicable simple sequence repeat (SSR) markers tightly linked to Rdr1, which are suitable for genetic analyses and marker-assisted selection in roses. As a source for the high molecular weight DNA, we chose the homozygous resistant R. multiflora hybrid 88/124-46. For the assembly of the BAC contig, we made use of molecular markers derived from a previously established R. rugosa contig. In order to increase th...
Source: TAG. Theoretical and Applied Genetics - November 13, 2009 Category: Genetics & Stem Cells Authors: Biber A, Kaufmann H, Linde M, Spiller M, Terefe D, Debener T Tags: Theor Appl Genet Source Type: journals

Physical mapping and a new variant of Puroindoline b-2 genes in wheat.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Puroindoline a and b proteins soften the endosperm of wheat kernels. When the underlying puroindoline genes are altered by mutation or are deleted, kernels become harder. Thus, puroindoline a and b (Pina and Pinb) play an important role in wheat quality and utilization. Recently, additional Pinb genes have been reported. In the present report, we provide corroborating coding and additional 5' and 3' flanking sequence for three Pinb variants: Pinb-2v1, Pinb-2v2, and Pinb-2v3. Additionally, a new Pinb variant, Pinb-2v4, is reported. All four variants were physically mapped using Chinese Spring (CS) diteolosomics, nulliso...
Source: TAG. Theoretical and Applied Genetics - November 13, 2009 Category: Genetics & Stem Cells Authors: Chen F, Beecher BS, Morris CF Tags: Theor Appl Genet Source Type: journals

Variation of the parental genome contribution in segregating populations derived from biparental crosses and its relationship with heterosis of their Design III progenies.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The variation of the parental genome contribution (PGC) and its relationship with the genetic architecture of heterosis have received little attention. Our objectives were to (1) derive formulas for the variance of PGC in selfing, backcross (BC) or intermated generations produced from biparental crosses of homozygous parents, (2) investigate the correlation [Formula: see text] of the PGC [Formula: see text] estimated by a set M of markers, with Z (2) (half the trait difference between each pair of BC progenies) in the Design III, and (3) interpret experimental results on this correlation with regard to the genetic basi...
Source: TAG. Theoretical and Applied Genetics - November 13, 2009 Category: Genetics & Stem Cells Authors: Melchinger AE, Dhillon BS, Mi X Tags: Theor Appl Genet Source Type: journals

Genetic variation at bx1 controls DIMBOA content in maize.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study addressed the following objectives: to determine the QTLs involved in DIMBOA synthesis across genetically divergent maize inbreds using eight RIL families from the nested association mapping population, to check the stability of QTLs for DIMBOA content across years by evaluating two of those RIL families in 2 years, and to test the involvement of bx1 by performing association mapping with a panel of 281 diverse inbred lines. QTLs were stable across different environments. A genetic model including eight markers explained approximately 34% of phenotypic variability across eight RIL families and the position of th...
Source: TAG. Theoretical and Applied Genetics - November 13, 2009 Category: Genetics & Stem Cells Authors: Butrón A, Chen YC, Rottinghaus GE, McMullen MD Tags: Theor Appl Genet Source Type: journals

Prediction of hybrid biomass in Arabidopsis thaliana by selected parental SNP and metabolic markers.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A recombinant inbred line (RIL) population, derived from two Arabidopsis thaliana accessions, and the corresponding testcrosses with these two original accessions were used for the development and validation of machine learning models to predict the biomass of hybrids. Genetic and metabolic information of the RILs served as predictors. Feature selection reduced the number of variables (genetic and metabolic markers) in the models by more than 80% without impairing the predictive power. Thus, potential biomarkers have been revealed. Metabolites were shown to bear information on inherited macroscopic phenotypes. This pro...
Source: TAG. Theoretical and Applied Genetics - November 13, 2009 Category: Genetics & Stem Cells Authors: Steinfath M, Gärtner T, Lisec J, Meyer RC, Altmann T, Willmitzer L, Selbig J Tags: Theor Appl Genet Source Type: journals

Heterosis in early seed development: a comparative study of F1 embryo and endosperm tissues 6 days after fertilization.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we demonstrate the manifestation of heterosis in hybrid maize embryo and endosperm tissue 6 days after fertilization in crosses of several inbred lines. We provide a comparative analysis of heterosis-associated gene expression in these tissues by a combined approach of suppression subtractive hybridization and microarray hybridizations. Non-additive expression pattern indicated a trans-regulatory mechanism to act early after fertilization in hybrid embryo and endosperm although the majority of genes showed mid-parental expression levels in embryo and dosage dependent expression levels in endosperm. The consi...
Source: TAG. Theoretical and Applied Genetics - November 11, 2009 Category: Genetics & Stem Cells Authors: Jahnke S, Sarholz B, Thiemann A, Kühr V, Gutiérrez-Marcos JF, Geiger HH, Piepho HP, Scholten S Tags: Theor Appl Genet Source Type: journals

Prediction of maize single-cross hybrid performance: support vector machine regression versus best linear prediction.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Accurate prediction of the phenotypic performance of a hybrid plant based on the molecular fingerprints of its parents should lead to a more cost-effective breeding programme as it allows to reduce the number of expensive field evaluations. The construction of a reliable prediction model requires a representative sample of hybrids for which both molecular and phenotypic information are accessible. This phenotypic information is usually readily available as typical breeding programmes test numerous new hybrids in multi-location field trials on a yearly basis. Earlier studies indicated that a linear mixed model analysis ...
Source: TAG. Theoretical and Applied Genetics - November 11, 2009 Category: Genetics & Stem Cells Authors: Maenhout S, De Baets B, Haesaert G Tags: Theor Appl Genet Source Type: journals

Genetic analyses of the host-pathogen system Turnip yellows virus (TuYV)-rapeseed (Brassica napus L.) and development of molecular markers for TuYV-resistance.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The aphid transmitted Turnip yellows virus (TuYV) has become a serious pathogen in many rapeseed (Brassica napus L.) growing areas. Three-years' field trials were carried out to get detailed information on the genetics of TuYV resistance derived from the resynthesised B. napus line 'R54' and to develop closely linked markers. F(1) plants and segregating doubled-haploid (DH) populations derived from crosses to susceptible cultivars were analysed using artificial inoculation with virus-bearing aphids, followed by DAS-ELISA. Assuming a threshold of E (405) = 0.1 in ELISA carried out in December, the results led to the con...
Source: TAG. Theoretical and Applied Genetics - November 11, 2009 Category: Genetics & Stem Cells Authors: Juergens M, Paetsch C, Krämer I, Zahn M, Rabenstein F, Schondelmaier J, Schliephake E, Snowdon R, Friedt W, Ordon F Tags: Theor Appl Genet Source Type: journals

A novel approach to locate Phytophthora infestans resistance genes on the potato genetic map.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study we present and test a novel method to quickly identify to which cluster a new resistance gene belongs and to produce markers that can be used for introgression breeding. We used NBS profiling to identify markers in bulked DNA samples prepared from resistant and susceptible genotypes of small segregating populations. Markers co-segregating with resistance can be tested on individual plants and directly used for breeding. To identify the resistance gene cluster a gene belongs to, the fragments were sequenced and the sequences analyzed using bioinformatics tools. Putative map positions arising from this analysis...
Source: TAG. Theoretical and Applied Genetics - November 10, 2009 Category: Genetics & Stem Cells Authors: Jacobs MM, Vosman B, Vleeshouwers VG, Visser RG, Henken B, van den Berg RG Tags: Theor Appl Genet Source Type: journals

Combining DNA pooling with selective recombinant genotyping for increased efficiency in fine mapping.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
One of the key steps in positional cloning and marker-aided selection is to identify marker(s) tightly linked to the target gene (i.e., fine mapping). Selective genotyping such as selective recombinant genotyping (SRG) is commonly used in fine mapping for cost-saving. To further decrease genotyping effort and rapidly screen for tightly linked markers, we propose here a combined DNA pooling and SRG strategy. A two-stage pooled genotyping can be used for identifying recombinants between a pair of flanking markers more efficiently, and a joint use of bulked DNA analysis and two-stage pooling can also save cost for genotyp...
Source: TAG. Theoretical and Applied Genetics - November 8, 2009 Category: Genetics & Stem Cells Authors: Chi XF, Lou XY, Shu QY Tags: Theor Appl Genet Source Type: journals

Cloning and characterization of a putative GS3 ortholog involved in maize kernel development.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The GS3 gene was the first identified gene controlling the grain size in rice. It has been proven to be involved in the evolution of grain size during domestication. We isolated the maize ortholog, ZmGS3 and investigated its role in the evolution of maize grain size. ZmGS3 has five exons encoding a protein with 198 amino acids, and has domains in common with the rice GS3 protein. Compared with teosinte, maize has reduced nucleotide diversity at ZmGS3, and the reduction is comparable to that found in neutrally evolving maize genes. No positive selection was detected along the length of the gene using either the Hudson-K...
Source: TAG. Theoretical and Applied Genetics - November 7, 2009 Category: Genetics & Stem Cells Authors: Li Q, Yang X, Bai G, Warburton ML, Mahuku G, Gore M, Dai J, Li J, Yan J Tags: Theor Appl Genet Source Type: journals

Heterotic patterns of sugar and amino acid components in developing maize kernels.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we determined the dry matter, the levels of starch and protein components and a total of 24 low-molecular weight metabolites including sugars, sugar-phosphates, and free amino acids, in developing maize kernels between 8 and 30 days post-pollination (DPP) of the hybrid B73 x Mo17 and its parental lines. The tissue specificity of amino acid and protein content was investigated between 16 and 30 DPP. Key observations include: (1) most of the significant differences in the investigated tissue types occurred between Mo17 and the other two genotypes; (2) heterosis of dry matter and metabolite content was detectab...
Source: TAG. Theoretical and Applied Genetics - November 7, 2009 Category: Genetics & Stem Cells Authors: Römisch-Margl L, Spielbauer G, Schützenmeister A, Schwab W, Piepho HP, Genschel U, Gierl A Tags: Theor Appl Genet Source Type: journals

Correlation between parental transcriptome and field data for the characterization of heterosis in Zea mays L.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Heterosis is widely exploited in plant breeding, although its molecular basis is still not fully understood. For the characterization of this phenomenon and the development of transcriptome-based methods to predict hybrid performance (HP), we applied a microarray (46k) analysis of 21 European maize (Zea mays L.), 14 dent and 7 flint parental inbred lines. Expression profiles of the parental inbreds at the seedling stage were correlated with grain yield (GY) and grain dry matter content (GDMC) of 98 flint x dent factorial crosses at six locations. We observed highly significant correlations of the parental expression le...
Source: TAG. Theoretical and Applied Genetics - November 4, 2009 Category: Genetics & Stem Cells Authors: Thiemann A, Fu J, Schrag TA, Melchinger AE, Frisch M, Scholten S Tags: Theor Appl Genet Source Type: journals

Nucleotide diversity and molecular evolution of the PSY1 gene in Zea mays compared to some other grass species.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Phytoene synthase (PSY), which is encoded by the phytoene synthase 1 (PSY1) gene, is the first rate-limiting enzyme in the plant carotenoid biosynthetic pathway. In order to examine the genetic diversity and evolution pattern of PSY1 within the Andropogoneae, sequences of 76 accessions from 5 species (maize, teosinte, tripsacum, coix, and sorghum) of the Andropogoneae were tested, along with 4 accessions of rice (Oryza sativa L.) included as outliers. Both the number and the order of exons and introns were relatively conserved across the species tested. Three domains were identified in the coding sequence, including si...
Source: TAG. Theoretical and Applied Genetics - November 3, 2009 Category: Genetics & Stem Cells Authors: Fu Z, Yan J, Zheng Y, Warburton ML, Crouch JH, Li JS Tags: Theor Appl Genet Source Type: journals

Development of diagnostic markers for use in breeding potatoes resistant to Globodera pallida pathotype Pa2/3 using germplasm derived from Solanum tuberosum ssp. andigena CPC 2802.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we show that GpaIV ( adg ) ( s ) is also present in a breeding line called C1992/31 via genetic mapping in an F(1) population produced by crossing C1992/31 with the G. pallida susceptible cultivar Record. C1992/31 is relatively divergent from 12601ab1, confirming that GpaIV ( adg ) ( s ) is an ideal target for marker-assisted selection in currently available germplasm. To generate markers exhibiting diagnostic potential for GpaIV ( adg ) ( s ) , three bacterial artificial chromosome clones were isolated from the QTL region, sequenced, and used to develop 15 primer sets generating single-copy amplicons, which...
Source: TAG. Theoretical and Applied Genetics - November 1, 2009 Category: Genetics & Stem Cells Authors: Moloney C, Griffin D, Jones PW, Bryan GJ, McLean K, Bradshaw JE, Milbourne D Tags: Theor Appl Genet Source Type: journals

Diagnostic and co-dominant PCR markers for wheat stem rust resistance genes Sr25 and Sr26.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Wheat stem rust, caused by Puccinia graminis f. sp. tritici, is one of the most destructive diseases of wheat. A new race of the pathogen named TTKSK (syn. Ug99) and its derivatives detected in East Africa are virulent to many designated and undesignated stem rust resistance genes. The emergence and spread of those races pose an imminent threat to wheat production worldwide. Genes Sr25 and Sr26 transferred into wheat from Thinopyrum ponticum are effective against these new races. DNA markers for Sr25 and Sr26 are needed to pyramid both genes into adapted germplasm. The previously published dominant markers Gb for Sr25 ...
Source: TAG. Theoretical and Applied Genetics - October 31, 2009 Category: Genetics & Stem Cells Authors: Liu S, Yu LX, Singh RP, Jin Y, Sorrells ME, Anderson JA Tags: Theor Appl Genet Source Type: journals

Hybrid maize breeding with doubled haploids: V. Selection strategies for testcross performance with variable sizes of crosses and S(1) families.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We examined the optimum allocation of resources to maximize the selection gain DeltaG and the probability P(q) of identifying the q% best genotypes. Our specific objectives were to (1) determine the optimum number and size of crosses and S(1) families, as well as the optimum number of test environments and (2) identify the superior selection strategy. Selection was based on the evaluation of testcross progenies of (1) DH lines in both stages (DHTC) and (2) S(1) families in the first stage and of DH lines within S(1) families in the second stage (S(1)TC-DHTC) with uniform and variable sizes of crosses and S(1) families. We ...
Source: TAG. Theoretical and Applied Genetics - October 29, 2009 Category: Genetics & Stem Cells Authors: Wegenast T, Utz HF, Longin CF, Maurer HP, Dhillon BS, Melchinger AE Tags: Theor Appl Genet Source Type: journals

Identification of genetic factors influencing salt stress tolerance in white clover (Trifolium repens L.) by QTL analysis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The objective of this study was to identify quantitative trait loci (QTLs) for salinity tolerance in terms of vegetative growth under stress. Two parental genetic maps consisting of 213 and 159 marker loci and spanning 1,973.0 and 1,837.6 cM, respectively, were constructed using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers from a two-way pseudo-test cross F(1) population derived from pair-crossing of the Haifa(2) and LCL(2) genotypes. A total of 8 unique genomic regions on 8 linkage groups (LGs) of the Haifa(2) parental map and 6 unique regions on 5 LGs in the LCL(2) parental map were assoc...
Source: TAG. Theoretical and Applied Genetics - October 29, 2009 Category: Genetics & Stem Cells Authors: Wang J, Drayton MC, George J, Cogan NO, Baillie RC, Hand ML, Kearney GA, Erb S, Wilkinson T, Bannan NR, Forster JW, Smith KF Tags: Theor Appl Genet Source Type: journals

Molecular detection of genomic regions associated with grain yield and yield-related components in an elite bread wheat cross evaluated under irrigated and rainfed conditions.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Grain yield and grain weight of wheat are often decreased by water-limitation in the north-eastern cropping belt of Australia. Based on knowledge that CIMMYT lines are well-adapted in this region, a recombinant inbred line (RIL) population between two elite CIMMYT bread wheats (Seri M82 and Babax) was evaluated under water-limited environments. Fourteen productivity traits were evaluated in 192 progeny in up to eight trials. For three aggregations of the environments (all, high yield or low yield), multiple quantitative trait loci (QTL) were detected, each explaining <15% of variation. Co-location of multiple trait ...
Source: TAG. Theoretical and Applied Genetics - October 29, 2009 Category: Genetics & Stem Cells Authors: McIntyre CL, Mathews KL, Rattey A, Chapman SC, Drenth J, Ghaderi M, Reynolds M, Shorter R Tags: Theor Appl Genet Source Type: journals

Clustering, haplotype diversity and locations of MIC-3: a unique root-specific defense-related gene family in Upland cotton (Gossypium hirsutum L.).Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
MIC-3 is a recently identified gene family shown to exhibit increased root-specific expression following nematode infection of cotton plants that are resistant to root-knot nematode. Here, we cloned and sequenced MIC-3 genes from selected diploid and tetraploid cotton species to reveal sequence differences at the molecular level and identify chromosomal locations of MIC-3 genes in Gossypium species. Detailed sequence analysis and phylogenetic clustering of MIC-3 genes indicated the presence of multiple MIC-3 gene members in Gossypium species. Haplotypes of a MIC-3 gene family member were discovered by comparative analy...
Source: TAG. Theoretical and Applied Genetics - October 28, 2009 Category: Genetics & Stem Cells Authors: Buriev ZT, Saha S, Abdurakhmonov IY, Jenkins JN, Abdukarimov A, Scheffler BE, Stelly DM Tags: Theor Appl Genet Source Type: journals

Major and minor QTL and epistasis contribute to fatty acid compositions and oil concentration in high-oil maize.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
High-oil maize is a useful genetic resource for genomic investigation in plants. To determine the genetic basis of oil concentration and composition in maize grain, a recombinant inbred population derived from a cross between normal line B73 and high-oil line By804 was phenotyped using gas chromatography, and genotyped with 228 molecular markers. A total of 42 individual QTL, associated with fatty acid compositions and oil concentration, were detected in 21 genomic regions. Five major QTL were identified for measured traits, one each of which explained 42.0% of phenotypic variance for palmitic acid, 15.0% for stearic a...
Source: TAG. Theoretical and Applied Genetics - October 25, 2009 Category: Genetics & Stem Cells Authors: Yang X, Guo Y, Yan J, Zhang J, Song T, Rocheford T, Li JS Tags: Theor Appl Genet Source Type: journals

Iso-lines and inbred-lines confirmed loci that underlie resistance from cultivar 'Hartwig' to three soybean cyst nematode populations.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Soybean [Glycine max (L.) Merr.] cultivars varied in their resistance to different populations of the soybean cyst nematode (SCN), Heterodera glycines, called HG Types. The rhg1 locus on linkage group G was necessary for resistance to all HG types. However, the loci for resistance to H. glycines HG Type 1.3- (race 14) and HG Type 1.2.5- (race 2) of the soybean cyst nematode have varied in their reported locations. The aims were to compare the inheritance of resistance to three nematode HG Types in a population segregating for resistance to SCN and to identify the underlying quantitative trait loci (QTL). 'Hartwig', a s...
Source: TAG. Theoretical and Applied Genetics - October 25, 2009 Category: Genetics & Stem Cells Authors: Kazi S, Shultz J, Afzal J, Hashmi R, Jasim M, Bond J, Arelli PR, Lightfoot DA Tags: Theor Appl Genet Source Type: journals

Development and evaluation of robust molecular markers linked to disease resistance in tomato for distinctness, uniformity and stability testing.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we describe the development and/or evaluation of molecular marker assays for the Verticillium genes Ve1 and Ve2, the tomato mosaic virus Tm1 (linked marker), the tomato mosaic virus Tm2 and Tm2 ( 2 ) genes, the Meloidogyne incognita Mi1-2 gene, the Fusarium I (linked marker) and I2 loci, which are obligatory traits in PBR testing. The marker assays were evaluated for their robustness in a ring test and then evaluated in a set of varieties. Although in general, results between biological assays and marker assays gave highly correlated results, marker assays showed an advantage over biological tests in that th...
Source: TAG. Theoretical and Applied Genetics - October 24, 2009 Category: Genetics & Stem Cells Authors: Arens P, Mansilla C, Deinum D, Cavellini L, Moretti A, Rolland S, van der Schoot H, Calvache D, Ponz F, Collonnier C, Mathis R, Smilde D, Caranta C, Vosman B Tags: Theor Appl Genet Source Type: journals

Identification and mapping of molecular markers linked to the tuberculate fruit gene in the cucumber (Cucumis sativus L.).Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Warty fruit is one of the highly valuable external quality traits related to the market values of cucumber. Genetic analysis has shown that a single dominant gene, Tu (Tuberculate fruit), determines the warty fruit trait in the cucumber plant. An F(2) population (247 individuals) from the cross of S06 x S52 was used for the mapping of the Tu/tu locus. By combining bulked segregant analysis with the sequence-related amplified polymorphism (SRAP) and simple sequence repeat (SSR) markers, 15 markers (9 SRAPs and 6 SSRs) linked to the Tu/tu locus were identified. Of nine SRAP markers, three closely linked to the Tu/tu locu...
Source: TAG. Theoretical and Applied Genetics - October 21, 2009 Category: Genetics & Stem Cells Authors: Zhang W, He H, Guan Y, Du H, Yuan L, Li Z, Yao D, Pan J, Cai R Tags: Theor Appl Genet Source Type: journals

QTLs for the elongation of axile and lateral roots of maize in response to low water potential.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Changes in root architecture and the maintenance of root growth in drying soil are key traits for the adaptation of maize (Zea mays L.) to drought environments. The goal of this study was to map quantitative trait loci (QTLs) for root growth and its response to dehydration in a population of 208 recombinant inbred lines from the International Maize and Wheat Improvement Center (CIMMYT). The parents, Ac7643 and Ac7729/TZSRW, are known to be drought-tolerant and drought-sensitive, respectively. Roots were grown in pouches under well-watered conditions or at low water potential induced by the osmolyte polyethylene glycol ...
Source: TAG. Theoretical and Applied Genetics - October 21, 2009 Category: Genetics & Stem Cells Authors: Ruta N, Liedgens M, Fracheboud Y, Stamp P, Hund A Tags: Theor Appl Genet Source Type: journals

Rdr3, a novel locus conferring black spot disease resistance in tetraploid rose: genetic analysis, LRR profiling, and SCAR marker development.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The objective of the present study was to genetically analyze resistances to North American black spot races 3, 8, and 9 previously reported in tetraploid roses. Resistance to North American races 3 and 8 segregated 1:1 in multiple F(1) populations, indicating that both are conferred by dominant alleles at single loci and are present in simplex (Rrrr) configuration. Gene pyramiding was demonstrated by combining both resistances into single genotypes. Resistance to race 9 was partial and segregated in a quantitative fashion. Analysis of these populations with microsatellite markers previously developed for Rdr1 revealed tha...
Source: TAG. Theoretical and Applied Genetics - October 21, 2009 Category: Genetics & Stem Cells Authors: Whitaker VM, Bradeen JM, Debener T, Biber A, Hokanson SC Tags: Theor Appl Genet Source Type: journals

A universal core genetic map for rice.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we demonstrate that the UCGM is a useful tool for the rice genetics and breeding community, especially in strategies based on interspecific hybridisation. PMID: 19847389 [PubMed - as supplied by publisher] (Source: TAG. Theoretical and Applied Genetics)
Source: TAG. Theoretical and Applied Genetics - October 21, 2009 Category: Genetics & Stem Cells Authors: Orjuela J, Garavito A, Bouniol M, Arbelaez JD, Moreno L, Kimball J, Wilson G, Rami JF, Tohme J, McCouch SR, Lorieux M Tags: Theor Appl Genet Source Type: journals

Optimum allocation of resources for QTL detection using a nested association mapping strategy in maize.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The objective of this study was to optimize for three different fixed budgets the power of QTL detection 1 - beta* in recombinant inbred line (RIL) populations derived from a nested design by varying (1) the genetic complexity of the trait, (2) the costs for developing, genotyping, and phenotyping RILs, (3) the total number of RILs, and (4) the number of environments and replications per environment used for phenotyping. Our computer simulations were based on empirical data of 653 single nucleotide polymorphism markers of 26 diverse maize inbred lines which were selected on the basis of 100 simple sequence repeat markers o...
Source: TAG. Theoretical and Applied Genetics - October 21, 2009 Category: Genetics & Stem Cells Authors: Stich B, Utz HF, Piepho HP, Maurer HP, Melchinger AE Tags: Theor Appl Genet Source Type: journals

Vrn-D4 is a vernalization gene located on the centromeric region of chromosome 5D in hexaploid wheat.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Natural variation in wheat requirement of long exposures to cold temperatures to accelerate flowering (vernalization) is mainly controlled by the Vrn-1, Vrn-2, Vrn-3, and Vrn-4 loci. The first three loci have been well characterized, but limited information is available for Vrn-4. So far, natural variation for Vrn-4 has been detected only in the D genome (Vrn-D4), and genetic stocks for this gene are available in Triple Dirk (TDF, hereafter). We detected heterogeneity in the Vrn-1 alleles present in different TDF stocks, which may explain inconsistencies among previous studies. A correct TDF seed stock from Japan carry...
Source: TAG. Theoretical and Applied Genetics - October 21, 2009 Category: Genetics & Stem Cells Authors: Yoshida T, Nishida H, Zhu J, Nitcher R, Distelfeld A, Akashi Y, Kato K, Dubcovsky J Tags: Theor Appl Genet Source Type: journals

Identification and characterization of large-effect quantitative trait loci for grain yield under lowland drought stress in rice using bulk-segregant analysis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
An F(4:5) population of 490 recombinant inbred lines (RILs) from the cross Apo/(2*)Swarna was used to detect quantitative trait loci (QTL) with large effects on grain yield under drought stress using bulk-segregant analysis (BSA). Swarna is an important rainfed lowland rice variety grown on millions of hectares in Asia, but is highly susceptible to drought and aerobic soil conditions. Apo is an aerobic-adapted variety with moderate tolerance to drought. Two rice microsatellite (RM) markers, RM324, and RM416, located on chromosomes 2 and 3, respectively, were shown via BSA to be strongly associated with yield under lowl...
Source: TAG. Theoretical and Applied Genetics - October 16, 2009 Category: Genetics & Stem Cells Authors: Venuprasad R, Dalid CO, Del Valle M, Zhao D, Espiritu M, Sta Cruz MT, Amante M, Kumar A, Atlin GN Tags: Theor Appl Genet Source Type: journals

Accuracy of genotypic value predictions for marker-based selection in biparental plant populations.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The availability of cheap and abundant molecular markers has led to plant-breeding methods that rely on the prediction of genotypic value from marker data, but published information is lacking on the accuracy of genotypic value predictions with empirical data in plants. Our objectives were to (1) determine the accuracy of genotypic value predictions from multiple linear regression (MLR) and genomewide selection via best linear unbiased prediction (BLUP) in biparental plant populations; (2) assess the accuracy of predictions for different numbers of markers (N (M)) and progenies (N (P)) used in estimation; and (3) deter...
Source: TAG. Theoretical and Applied Genetics - October 16, 2009 Category: Genetics & Stem Cells Authors: Lorenzana RE, Bernardo R Tags: Theor Appl Genet Source Type: journals

Restriction site polymorphism-based candidate gene mapping for seedling drought tolerance in cowpea [Vigna unguiculata (L.) Walp.].Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Quantitative trait loci (QTL) studies provide insight into the complexity of drought tolerance mechanisms. Molecular markers used in these studies also allow for marker-assisted selection (MAS) in breeding programs, enabling transfer of genetic factors between breeding lines without complete knowledge of their exact nature. However, potential for recombination between markers and target genes limit the utility of MAS-based strategies. Candidate gene mapping offers an alternative solution to identify trait determinants underlying QTL of interest. Here, we used restriction site polymorphisms to investigate co-location of...
Source: TAG. Theoretical and Applied Genetics - October 15, 2009 Category: Genetics & Stem Cells Authors: Muchero W, Ehlers JD, Roberts PA Tags: Theor Appl Genet Source Type: journals

Identification and genomic location of a reniform nematode (Rotylenchulus reniformis) resistance locus (Ren ( ari )) introgressed from Gossypium aridum into upland cotton (G. hirsutum).Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this association mapping study, a tri-species hybrid, [Gossypium arboreum x (G. hirsutum x G. aridum)(2)], was crossed with MD51ne (G. hirsutum) and progeny from the cross were used to identify and map SSR markers associated with reniform nematode (Rotylenchulus reniformis) resistance. Seventy-six progeny (the 50 most resistant and 26 most susceptible) plants were genotyped with 104 markers. Twenty-five markers were associated with a resistance locus that we designated Ren ( ari ) and two markers, BNL3279_132 and BNL2662_090, mapped within 1 cM of Ren ( ari ). Because the SSR fragments associated with resistance wer...
Source: TAG. Theoretical and Applied Genetics - October 13, 2009 Category: Genetics & Stem Cells Authors: Romano GB, Sacks EJ, Stetina SR, Robinson AF, Fang DD, Gutierrez OA, Scheffler JA Tags: Theor Appl Genet Source Type: journals

A barley Hordoindoline mutation resulted in an increase in grain hardness.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Barley seed proteins, Hordoindolines, are homologues of wheat Puroindolines, which are associated with grain hardness. Barley Hordoindoline genes are known to comprise Hina and Hinb, and Hinb consists of two Hinb genes, Hinb-1 and Hinb-2. Two types of allele were found for Hina, Hinb-1 and Hinb-2 genes, respectively, among Japanese two- and six-rowed barley lines. One of the alleles of Hinb-2 (Hinb-2b) had a frame-shift mutation resulting in an in-frame stop codon. For two-rowed barley lines, grain hardness was significantly higher among lines with the Hinb-2b than those with the wild type Hinb-2 gene (Hinb-2a). Protei...
Source: TAG. Theoretical and Applied Genetics - October 13, 2009 Category: Genetics & Stem Cells Authors: Takahashi A, Ikeda TM, Takayama T, Yanagisawa T Tags: Theor Appl Genet Source Type: journals

Analysis of transposons and repeat composition of the sunflower (Helianthus annuus L.) genome.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A sample-sequencing strategy combined with slot-blot hybridization and FISH was used to study the composition of the repetitive component of the sunflower genome. One thousand six hundred thirty-eight sequences for a total of 954,517 bp were analyzed. The fraction of sequences that can be classified as repetitive using computational and hybridization approaches amounts to 62% in total. Almost two thirds remain as yet uncharacterized in nature. Of those characterized, most belong to the gypsy superfamily of LTR-retrotransposons. Unlike in other species, where single families can account for large fractions of the genome...
Source: TAG. Theoretical and Applied Genetics - October 13, 2009 Category: Genetics & Stem Cells Authors: Cavallini A, Natali L, Zuccolo A, Giordani T, Jurman I, Ferrillo V, Vitacolonna N, Sarri V, Cattonaro F, Ceccarelli M, Cionini PG, Morgante M Tags: Theor Appl Genet Source Type: journals

Multiple gene loci affecting genetic background-controlled disease resistance conferred by R gene Xa3/Xa26 in rice.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The function of bacterial-blight resistance gene Xa3/Xa26 in rice is influenced by genetic background; the Oryza sativa L. ssp. japonica background can increase Xa3/Xa26 expression, resulting in an enhanced resistance. To identify whether Xa3/Xa26 transcript level is the only factor contributing to genetic background-controlled resistance, we screened an F(2) population that was developed from a cross between Oryza sativa L. ssp. indica and japonica rice lines and was segregating for Xa3/Xa26, and compared the expression profiles of a pair of indica and japonica rice lines that both carried Xa3/Xa26. Eight quantitative...
Source: TAG. Theoretical and Applied Genetics - October 13, 2009 Category: Genetics & Stem Cells Authors: Zhou Y, Cao Y, Huang Y, Xie W, Xu C, Li X, Wang S Tags: Theor Appl Genet Source Type: journals

Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Characterization of genetic diversity is of great value to assist breeders in parental line selection and breeding system design. We screened 770 maize inbred lines with 1,034 single nucleotide polymorphism (SNP) markers and identified 449 high-quality markers with no germplasm-specific biasing effects. Pairwise comparisons across three distinct sets of germplasm, CIMMYT (394), China (282), and Brazil (94), showed that the elite lines from these diverse breeding pools have been developed with only limited utilization of genetic diversity existing in the center of origin. Temperate and tropical/subtropical germplasm cle...
Source: TAG. Theoretical and Applied Genetics - October 10, 2009 Category: Genetics & Stem Cells Authors: Lu Y, Yan J, Guimarães CT, Taba S, Hao Z, Gao S, Chen S, Li J, Zhang S, Vivek BS, Magorokosho C, Mugo S, Makumbi D, Parentoni SN, Shah T, Rong T, Crouch JH, Xu Y Tags: Theor Appl Genet Source Type: journals

Resistance to Plasmopara viticola in grapevine 'Bianca' is controlled by a major dominant gene causing localised necrosis at the infection site.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Downy mildew resistance is a quantitative trait in grapevines of the genus Vitis. The grapevine 'Bianca' has retained resistance, originally present in its North American ancestors, through several cycles of backcrossing with susceptible cultivars of Vitis vinifera followed by phenotypic selection. The genetic control of the trait was studied using 116 full-siblings from the cross 'Chardonnay' x 'Bianca' and parental genetic maps consisting of 298 and 312 markers, respectively. Ratings of resistance and histological identification of the stage of interaction, when pathogen development is impaired in resistant individua...
Source: TAG. Theoretical and Applied Genetics - October 10, 2009 Category: Genetics & Stem Cells Authors: Bellin D, Peressotti E, Merdinoglu D, Wiedemann-Merdinoglu S, Adam-Blondon AF, Cipriani G, Morgante M, Testolin R, Di Gaspero G Tags: Theor Appl Genet Source Type: journals