Showing papers in "Molecular Breeding in 2009"

Revealing the genetic architecture of FHB resistance in hexaploid wheat (Triticum aestivum L.) by QTL meta-analysis.

Abstract: Fusarium head blight (FHB) in wheat results in reduced yield and quality and in accumulation of mycotoxins. The objective of this study was to identify genomic regions in wheat involved in the control of FHB resistance applying a QTL meta-analysis approach by combining QTL of 30 mapping populations to propose independent meta-QTL (MQTL). A consensus map was created on which initial QTL were projected. Nineteen MQTL comprising 2–13 initial QTL with widely varying confidence intervals were found on 12 chromosomes. Some of them coincided with genomic regions previously identified (e.g. chromosomes 3BS, 6B), however, some MQTL were newly detected by this study. Separate analysis of populations with the same resistant parent showed a rather high consistency for the Chinese spring wheat donor ‘Sumai 3’, but little consistency for the Chinese donor ‘Wangshuibai’ and the Swiss donor ‘Arina’. According to our results breeders can in future (1) choose parents for crossing not comprising the same resistance loci or QTL intervals, (2) exploit new MQTL, and (3) select markers of some of these MQTL to be used in marker-assisted selection.

Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree ( Hevea brasiliensis )

Abstract: Expressed sequence tags derived simple sequence repeats (EST-SSRs), are different from traditional genomic SSR (gSSR) markers. They are more likely to be embedded in the functional gene sequences, less costly and time effective, and may provide abundant information. By analysis of 10,018 expressed sequence tags (ESTs) out of 10,829 for rubber tree (Hevea brasiliensis) available in public domain DNA databases, 799 SSR loci were found in the 643 non-redundant SSR-ESTs (SSR-containing ESTs), corresponding to one SSR in every 2.25 kb of the ESTs in rubber tree transcriptome. Of the total 799 SSRs in these ESTs, 673 (84.2%) contained simple repeat motifs while 126 (15.8%) represented compound motif types. Of the total EST-SSRs, 45.3% (362/799) were mononucleotide repeats (MNRs), 42.2% (337/799) were dinucleotide repeats (DNRs), 11.9% (95/799) were trinucleotide repeats (TNRs) and 0.6% (5/799) were tetranucleotide repeats (TTNRs) and hexanucleotide repeats (HNRs). The repeat motifs AAG and AG were the most abundant without regard to single nucleotide repeat. A total of 184 primer pairs were successful designed based on the non-redundant SSR-ESTs. Using 55°C as annealing temperature, 110 primer pairs successfully amplified 12 H. brasiliensis cultivated varieties and four related species. Analysis on 74 alleles amplified by 30 randomly selected primer pairs indicated the medium polymorphism of the EST-SSRs developed. Based on 272 alleles detected by 87 EST-SSR markers, an assessment of genetic diversity was carried out on 12 H. brasiliensis cultivated varieties and four related species. In addition, investigation based on five selected EST-SSRs by cloning and sequencing cross some cultivated species and related species provided evidence for cross-species/genera transferability of the EST-SSR markers developed in this study.

Inheritance of seed iron and zinc concentrations in common bean ( Phaseolus vulgaris L.)

Abstract: Micronutrients are essential elements needed in small amounts for adequate human nutrition and include the elements iron and zinc. Both of these minerals are essential to human well-being and an adequate supply of iron and zinc help to prevent iron deficiency anemia and zinc deficiency, two prevalent health concerns of the developing world. The objective of this study was to determine the inheritance of seed iron and zinc accumulation in a recombinant inbred line (RIL) population of common beans from a cross of low × high mineral genotypes (DOR364 × G19833) using a quantitative trait locus (QTL) mapping approach. The population was grown over two trial sites and two analytical methods (Inductively Coupled Plasma Spectrometry and Atomic Absorption Spectroscopy) were used to determine iron and zinc concentration in the seed harvested from these trials. The variability in seed mineral concentration among the lines was larger for iron (40.0–84.6 ppm) than for zinc (17.7–42.4 ppm) with significant correlations between trials, between methods and between minerals (up to r = 0.715). A total of 26 QTL were identified for the mineral × trial × method combinations of which half were for iron concentration and half for zinc concentration. Many of the QTL (11) for both iron (5) and zinc (6) clustered on the upper half of linkage group B11, explaining up to 47.9% of phenotypic variance, suggesting an important locus useful for marker assisted selection. Other QTL were identified on linkage groups B3, B6, B7, and B9 for zinc and B4, B6, B7, and B8 for iron. The relevance of these results for breeding common beans is discussed especially in light of crop improvement for micronutrient concentration as part of a biofortification program.

Evaluation of coffee reference genes for relative expression studies by quantitative real-time RT-PCR

Abstract: Accuracy in quantitative real-time polymerase chain reaction (qPCR) requires the use of stable endogenous controls. Normalization with multiple reference genes is the gold standard, but their identification is a laborious task, especially in species with limited sequence information. Coffee (Coffea ssp.) is an important agricultural commodity and, due to its economic relevance, is the subject of increasing research in genetics and biotechnology, in which gene expression analysis is one of the most important fields. Notwithstanding, relatively few works have focused on the analysis of gene expression in coffee. Moreover, most of these works have used less accurate techniques such as northern blot assays instead of more accurate techniques (e.g., qPCR) that have already been extensively used in other plant species. Aiming to boost the use of qPCR in studies of gene expression in coffee, we uncovered reference genes to be used in a number of different experimental conditions. Using two distinct algorithms implemented by geNorm and Norm Finder, we evaluated a total of eight candidate reference genes (psaB, PP2A, AP47, S24, GAPDH, rpl39, UBQ10, and UBI9) in four different experimental sets (control versus drought-stressed leaves, control versus drought-stressed roots, leaves of three different coffee cultivars, and four different coffee organs). The most suitable combination of reference genes was indicated in each experimental set for use as internal control for reliable qPCR data normalization. This study also provides useful guidelines for reference gene selection for researchers working with coffee plant samples under conditions other than those tested here.

A consensus list of microsatellite markers for olive genotyping

Abstract: Cultivar identification is a primary concern for olive growers, breeders, and scientists. This study was aimed at examining the SSR markers retrieved from the literature and currently used in olive study, in order to select those most effective in characterizing the olive accessions and to make possible the comparison of data obtained by different laboratories. Olive microsatellite profiles were assessed by four independent laboratories, which analyzed 37 pre-selected SSR loci on a set of 21 cultivars. These SSR markers were initially tested for their reproducibility, power of discrimination and number of amplified loci/alleles. Independent segregation was tested for each pair of SSRs in a controlled cross and the allelic error rate was quantified. Some of them were finally selected as the most informative and reliable. Most of the alleles were sequenced and their sizes were determined. Profiles of the reference cultivars and a list of alleles with their sizes obtained by sequencing are reported. Several genetic parameters have been analysed on a larger set of cultivars allowing for a deeper characterization of the selected loci. Results of this study provide a list of recommended markers and protocols for olive genotyping as well as the allelic profile of a set of reference cultivars that would be useful for the establishment of a universal database of olive accessions.

Construction of a comprehensive PCR-based marker linkage map and QTL mapping for fiber quality traits in upland cotton (Gossypium hirsutum L.)

Abstract: To facilitate marker assisted selection, there is an urgent need to construct a saturated genetic map of upland cotton (Gossypium hirsutum L.). Four types of markers including SSR, SRAP, morphological marker, and intron targeted intron–exon splice junction (IT-ISJ) marker were used to construct a linkage map with 270 F2:7 recombinant inbred lines derived from an upland cotton cross (T586 × Yumian 1). A total of 7,508 SSR, 740 IT-ISJ and 384 SRAP primer pairs/combinations were used to screen for polymorphism between the two mapping parents, and the average polymorphisms of three types of molecular markers represented 6.8, 6.6 and 7.0%, respectively. The polymorphic primer pairs/combinations and morphological markers were used to genotype 270 recombinant inbred lines, and a map including 604 loci (509 SSR, 58 IT-ISJ, 29 SRAP and 8 morphological loci) and 60 linkage groups was constructed. The map spanned 3,140.9 cM with an average interval of 5.2 cM between two markers, approximately accounting for 70.6% of the cotton genome. Fifty-four of 60 linkage groups were ordered into 26 chromosomes. Multiple QTL mapping was used to identify QTL for fiber quality traits in five environments, and thirteen QTL were detected. These QTL included four for fiber length (FL), two for fiber strength (FS), two for fiber fineness (FF), three for fiber length uniformity (FU), and two for fiber elongation (FE), respectively. Each QTL explained between 7.4 and 43.1% of phenotypic variance. Five out of thirteen QTL (FL1 and FU1 on chromosome 6, FL2, FU2 and FF1 on chromosome7) were detected in five environments, and they explained more than 20% of the phenotypic variance. Eleven QTL were distributed on A genome, while the other two on D genome.

Robust and highly informative microsatellite-based genetic identity kit for potato.

Abstract: The fingerprinting of 742 potato landraces with 51 simple sequence repeat (SSR, or microsatellite) markers resulted in improving a previously constructed potato genetic identity kit. All SSR marker loci were assayed with a collection of highly diverse landraces of all species of cultivated potato with ploidies ranging from diploid to pentaploid. Loci number, amplification reproducibility, and polymorphic information content were recorded. Out of 148 SSR markers of which 30 are new, we identified 58 new SSR marker locations on at least one of three potato genetic linkage maps. These results permitted the selection of a new potato genetic identity kit based on 24 SSR markers with two per chromosome separated by at least 10 cM, single locus, high polymorphic information content, and high quality of amplicons as determined by clarity and reproducibility. The comparison of a similarity matrix of 742 landraces obtained with the 24 SSR markers of the new kit and with the entire dataset of 51 SSR markers showed a high correlation (r = 0.94) by a Mantel test and even higher correlations (r = 0.99) regarding topological comparisons of major branches of a neighbor joining tree. This new potato genetic identity kit is able to discriminate 93.5% of the 742 landraces compared to 98.8% with 51 SSR markers. In addition, we made a marker-specific set of allele size standards that conveniently and unambiguously provide accurate sizing of all alleles of the 24 SSR markers across laboratories and platforms. The new potato genetic identity kit will be of particular utility to standardize the choice and allele sizing of microsatellites in potato and aid in collaborative projects by allowing cumulative analysis of independently generated data.

Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars

Abstract: In this study, we developed 359 detection primers for single nucleotide polymorphisms (SNPs) previously discovered within intron sequences of wheat genes and used them to evaluate SNP polymorphism in common wheat (Triticum aestivum L.). These SNPs showed an average polymorphism information content (PIC) of 0.18 among 20 US elite wheat cultivars, representing seven market classes. This value increased to 0.23 when SNPs were pre-selected for polymorphisms among a diverse set of 13 hexaploid wheat accessions (excluding synthetic wheats) used in the wheat SNP discovery project (http://wheat.pw.usda.gov/SNP). PIC values for SNP markers in the D genome were approximately half of those for the A and B genomes. D genome SNPs also showed a larger PIC reduction relative to the other genomes (P < 0.05) when US cultivars were compared with the more diverse set of 13 wheat accessions. Within those accessions, D genome SNPs show a higher proportion of alleles with low minor allele frequencies (<0.125) than found in the other two genomes. These data suggest that the reduction of PIC values in the D genome was caused by differential loss of low frequency alleles during the population size bottleneck that accompanied the development of modern commercial cultivars. Additional SNP discovery efforts targeted to the D genome in elite wheat germplasm will likely be required to offset the lower diversity of this genome. With increasing SNP discovery projects and the development of high-throughput SNP assay technologies, it is anticipated that SNP markers will play an increasingly important role in wheat genetics and breeding applications.

Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.).

Abstract: Stigma and spikelet characteristics play an essential role in hybrid seed production. A mini-core of 90 accessions developed from USDA rice core collection was phenotyped in field grown for nine traits of stigma and spikelet and genotyped with 109 DNA markers, 108 SSRs plus an indel. Three major clusters were built upon Rogers’ genetic distance, indicative of indicas, and temperate and tropical japonicas. A mixed linear model combining PC-matrix and K-matrix was adapted for mapping marker-trait associations. Resulting associations were adjusted using false discovery rate technique. We identified 34 marker-trait associations involving 22 SSR markers for eight traits. Four markers were associated with single stigma exsertion (SStgE), six with dual exsertion (DStgE) and five with total exsertion. RM5_Chr1 played major role indicative of high regression with not only DStgE but also SStgE. Four markers were associated with spikelet length, three with width and seven with L/W ratio. Numerous markers were co-associated with multiple traits that were phenotypically correlated, i.e. RM12521_Chr2 associated with all three correlated spikelet traits. The co-association should improve breeding efficiency because single marker could be used to assist breeding for multiple traits. Indica entry 1032 (cultivar 50638) and japonica entry 671 (cultivar Linia 84 Icar) with 80.65 and 75.17% of TStgE, respectively are recommended to breeder for improving stigma exsertion.

QTL mapping of aroma compounds analysed by headspace solid-phase microextraction gas chromatography in the apple progeny ‘Discovery’ × ‘Prima’

Abstract: Improving fruit quality of apple varieties is an important but complex breeding goal. Flavour is among the key factors of apple fruit quality but in spite of the analytical and biochemical knowledge about volatiles little is known about the genetic and molecular bases of apple aroma. The aim of this study was to use a saturated molecular linkage map of apple to identify QTLs for aroma compounds such as alcohols, esters and terpenes, but also for a number of unidentified volatile compounds (non-targeted analysis approach). Two parental genetic maps were constructed for the apple cultivars ‘Discovery’ and ‘Prima’ by using mainly AFLP and SSR markers. ‘Discovery’ and ‘Prima’ showed very different volatile patterns, and ‘Discovery’ mostly had the higher volatile concentrations in comparison with the Vf-scab resistant ‘Prima’ which has its origin in the small-fruited apple species Malus floribunda. About 50 putative QTLs for a total of 27 different apple fruit volatiles were detected through interval mapping by using genotypic data of 150 F1 individuals of the mapping population ‘C3’ together with phenotypic data obtained by head-space solid phase microextraction gas chromatography. QTLs for volatile compounds putatively involved in apple aroma were found on 12 out of the 17 apple chromosomes, but they were not evenly dispersed. QTLs were mainly clustered on linkage groups LG 2, 3 and 9. In a first attempt, a LOX (lipoxygenase) candidate gene, putatively involved in volatile metabolism, was mapped on LG 9, genetically associated with a cluster of QTLs for ester-type volatiles. Implications for aroma breeding in apple are discussed.

Pyramiding multiple genes for resistance to soybean mosaic virus in soybean using molecular markers

Abstract: Seven strains of Soybean mosaic virus (SMV) and three independent resistance loci (Rsv1, Rsv3, and Rsv4) have been identified in soybean. The objective of this research was to pyramid Rsv1, Rsv3, and Rsv4 for SMV resistance using molecular markers. J05 carrying Rsv1 and Rsv3 and V94-5152 carrying Rsv4 were used as the donor parents for gene pyramiding. A series of F2:3, F3:4, and F4:5 lines derived from J05 × V94-5152 were developed for selecting individuals carrying all three genes. Eight PCR-based markers linked to the three SMV resistance genes were used for marker-assisted selection. Two SSR markers (Sat_154 and Satt510) and one gene-specific marker (Rsv1-f/r) were used for selecting plants containing Rsv1; Satt560 and Satt063 for Rsv3; and Satt266, AI856415, and AI856415-g for Rsv4. Five F4:5 lines were homozygous for all eight marker alleles and presumably carry all three SMV resistance genes that would potentially provide multiple and durable resistance to SMV.

Dreb1 genes in wheat (Triticum aestivum L.): development of functional markers and gene mapping based on SNPs

Abstract: The Dreb genes are involved in abiotic stress tolerances, such as drought, salinity, low temperature and ABA. The purpose of the present research was to establish protocols for the development of genome-specific and allele specific markers in common wheat (Triticum aestivum L.) using the Dreb1 genes as an example. Based on the available sequences of Dreb1 genes in common wheat and related species, five primer pairs were designed using Primer Premier 5.0. Two primers, P25F/PR and P21F/P21R, amplified 596- and 1113-bp fragments, respectively, from the A genome, P18F/P18R amplified a 717-bp fragment from the B genome, and primers P22F/PR and P20F/P20R amplified 596- and 1193-bp fragments, respectively, from the D genome. Using these genome-specific primers and the Chinese Spring using nulli-tetrasomic lines, the Dreb1 genes were located on chromosomes 3A, 3B and 3D. Two SNPs (S646 and S770) in Dreb-B1 distinguished the Opata 85 and W7984 parents of the ITMI mapping population, but there was no polymorphism between the orthologous Dreb-A1 and Dreb-D1 sequences. By assaying the genotypes of 115 RILs with the allele-specific primer P40 based on SNP S770, Dreb-B1 was mapped between markers Xmwg818 and Xfbb117 on chromosome 3BL. This genetic mapping of Dreb-B1 on chromosome 3B may be helpful in wheat breeding programs aimed at improving drought tolerance.

Molecular mapping of wilt resistance genes in chickpea

Abstract: Fusarium wilt is a widespread and serious chickpea disease caused by the soil-borne fungus Fusarium oxysporum f.sp. ciceri (Foc). We evaluated an F9 recombinant inbred line population of chickpea for resistance to three Foc races (1, 2 and 3) in pot culture experiments and identified flanking and tightly linked DNA markers for the resistance genes. The simple sequence repeat markers H3A12 and TA110 flanked the Foc1 locus at 3.9 and 2.1 cM, respectively, while Foc2 was mapped 0.2 cM from TA96 and 2.7 cM from H3A12. The H1B06y and TA194 markers flanked the Foc3 locus at 0.2 and 0.7 cM, respectively. These markers were also validated using 16 diverse chickpea genotypes. Identification of tightly linked flanking markers for wilt resistance genes will be useful for their exploitation in breeding programs and to understand the mechanism of resistance and evolution of the genes.

A meta-QTL analysis of disease resistance traits of Theobroma cacao L.

Abstract: Theobroma cacao, is a tropical understorey tree that is a major economic resource to several tropical countries. However, the crop is under increased threat from several diseases that are responsible for 30% loss of harvest globally. Although QTL data related to the genetic determinism of disease resistance exist in cocoa, QTL mapping experiments are heterogeneous, thus making comparative QTL mapping essential for marker assisted selection (MAS). Sixteen QTL experiments were analysed, and the 76 QTLs detected were projected on a progressively established consensus map. Several hot spots, with QTLs related to different Phytophthora species and other diseases, were observed. The likely number of “real” QTLs was estimated by using a meta-analysis implemented in BioMercator software. There was a twofold reduction in average confidence interval observed when compared to the confidence interval of individual QTLs. This alternative approach confirms the existence of several sources of resistance to different diseases of cocoa which could be cumulated in new varieties to increase the sustainability of cocoa resistance using MAS strategies.

Development of single nucleotide polymorphism (SNP) markers for use in commercial maize (Zea mays L.) germplasm

Abstract: The development of single nucleotide polymorphism (SNP) markers in maize offers the opportunity to utilize DNA markers in many new areas of population genetics, gene discovery, plant breeding and germplasm identification. However, the steps from sequencing and SNP discovery to SNP marker design and validation are lengthy and expensive. Access to a set of validated SNP markers is a significant advantage to maize researchers who wish to apply SNPs in scientific inquiry. We mined 1,088 loci sequenced across 60 public inbreds that have been used in maize breeding in North America and Europe. We then selected 640 SNPs using generalized marker design criteria that enable utilization with several SNP chemistries. While SNPs were found on average every 43 bases in 1,088 maize gene sequences, SNPs that were amenable to marker design were found on average every 623 bases; representing only 7% of the total SNPs discovered. We also describe the development of a 768 marker multiplex assay for use on the Illumina® BeadArray™ platform. SNP markers were mapped on the IBM2 intermated B73 × Mo17 high resolution genetic map using either the IBM2 segregating population, or segregation in multiple parent-progeny triplets. A high degree of colinearity was found with the genetic nested association map. For each SNP presented we give information on map location, polymorphism rates in different heterotic groups and performance on the Illumina® platform.

Identification, characterisation and application of single nucleotide polymorphisms for diversity assessment in cassava (Manihot esculenta Crantz)

Abstract: To monitor genetic diversity in the field it is important that it is measured accurately. Here, we elucidate the potential of single nucleotide polymorphisms (SNPs) for measuring genetic diversity in cassava. The nature and frequency of SNPs was characterised and their utility in genetic diversity assessment compared to that of simple sequence repeats (SSRs). This was achieved by direct sequencing of amplicons in diverse cassava varieties. A total of 26 SNPs were identified from quality sequences of nine genes, giving an estimated frequency of one SNP every 121 nucleotides. Nucleotide diversity ranged from 7.8 × 10−4 to 5.6 × 10−3. Average haplotype-based polymorphic information content (PIC = 0.414) was higher than for individual SNPs (PIC = 0.228). The Mantel test indicated interdependence (r = 0.219; P < 0.001) between SNP and SSR genotypic data. Individual SNPs had lower PIC values than SSRs. For this reason larger numbers of SNPs may be necessary to achieve the same level of discrimination among genotypes provided by SSRs.

Genetic engineering of chickpea (Cicer arietinum L.) with the P5CSF129A gene for osmoregulation with implications on drought tolerance

Abstract: Abiotic stresses including water deficit severely limits crop yields in the semi-arid tropics. In chickpea, annual losses of over 3.7 million tones have been estimated to be due to water deficit conditions alone. Therefore, major efforts are needed to improve its tolerance to water deficit, and genetic engineering approaches provide an increasing hope for this possibility. We have used transgenic technology for the introduction of an osmoregulatory gene P5CSF129A encoding the mutagenized Δ1-pyrroline-5-carboxylate synthetase (P5CS) for the overproduction of proline. A total of 49 transgenic events of chickpea were produced with the 35S:P5CSF129A gene through Agrobacterium tumefaciens-mediated gene transfer through the use of axillary meristem explants. Eleven transgenic events that accumulated high proline (2–6 folds) were further evaluated in greenhouse experiments based on their transpiration efficiency (TE), photosynthetic activity, stomatal conductance, and root length under water stress. Almost all the transgenic events showed a decline in transpiration at lower values of the fraction of transpirable soil water (dryer soil), and extracted more water than their untransformed parents. The accumulation of proline in the selected events was more pronounced that increased significantly in the leaves when exposed to water stress. However, the overexpression of P5CSF129A gene resulted only in a modest increase in TE, thereby indicating that the enhanced proline had little bearing on the components of yield architecture that are significant in overcoming the negative effects of drought stress in chickpea.

Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species

Abstract: Genic microsatellites or simple sequence repeat markers derived from expressed sequence tags (ESTs), referred to as EST–SSRs, are inexpensive to develop, represent transcribed genes, and often have assigned putative function. The large apple (Malus × domestica) EST database (over 300,000 sequences) provides a valuable resource for developing well-characterized DNA molecular markers. In this study, we have investigated the level of transferability of 68 apple EST–SSRs in 50 individual members of the Rosaceae family, representing three genera and 14 species. These representatives included pear (Pyrus communis), apricot (Prunus armeniaca), European plum (P. domestica), Japanese plum (P. salicina), almond (P. dulcis), peach (P. persica), sour cherry (P. cerasus), sweet cherry (P. avium), strawberry (Fragaria vesca, F. moschata, F. virginiana, F. nipponica, and F. pentaphylla), and rose (Rosa hybrida). All 68 primer pairs gave an amplification product when tested on eight apple cultivars, and for most, the genomic DNA-derived amplification product matched the expected size based on EST (in silico) data. When tested across members of the Rosaceae, 75% of these primer pairs produced amplification products. Transferability of apple EST–SSRs across the Rosaceae ranged from 25% in apricot to 59% in the closely related pear. Besides pear, the highest transferability of these apple EST–SSRs, at the genus level, was observed for strawberry and peach/almond, 49 and 38%, respectively. Three markers amplified in at least one genotype within all tested species, while eight additional markers amplified in all species, except for cherry. These 11 markers are deemed good candidates for a widely transferable Rosaceae marker set provided their level of polymorphism is adequate. Overall, these findings suggest that transferability of apple EST–SSRs across Rosaceae is varied, yet valuable, thereby providing additional markers for comparative mapping and for carrying out evolutionary studies.

Towards improvement of marker assisted selection of apple scab resistant cultivars: Venturia inaequalis virulence surveys and standardization of molecular marker alleles associated with resistance genes

Abstract: Molecular breeding for pathogen resistance faces two major problems that delay its widespread adoption, resistance breakdown and difficulties in unambiguously identifying the alleles of the markers associated with specific resistance genes. Since the breakdown of the Rvi6 (Vf) gene in the Northern part of Europe breeders have intensified the search for new resistance sources to be introduced into their breeding programs. Alternative major genes to Rvi6 are available (e.g. Rvi2, Rvi4, Rvi5, Rvi10; Rvi11, Rvi12, Rvi13, and Rvi15, respectively Vh2, Vh4, Vm, Va, Vbj, Vb, Vd, Vr2 according to the old apple scab resistance gene nomenclature) but, with few exceptions (i.e., Rvi4, Rvi5 and, Rvi13), they have so far not been incorporated in commercial varieties. Pyramiding, i.e., combining several of these major resistance genes (R-genes) in individual plants, is one of the most promising strategies currently available to develop apple cultivars with durable apple scab resistance. But, which genes are the best suited to produce such new cultivars? Although the most interesting genes are surely those whose resistance so far has not been broken by the pathogen, genes with resistance that has been overcome coupled with only limited spread of the virulence may also be used in the pyramiding process. However, obtaining information on whether an R-gene is overcome and if so, the extent of the spread of the virulence is difficult and time consuming. Furthermore, often such reports are not up-to-date and the correctness of the data is difficult to verify. To solve these problems, the initiative “Monitoring of Venturia inaequalis virulences” has been proposed. The monitoring is based on a network of orchards of selected differential hosts. Incidence and severity of scab on these genotypes will be collected yearly; and after validation, the data will be published through the homepage of the project (www.vinquest.ch). Here, we present an outline of this initiative. A second major obstacle for broad adoption of marker assisted selection is the lack of tools to align marker analyzes performed in different laboratories to unambiguously identify the alleles linked to specific resistances. The identification of the alleles of the markers in coupling with the resistance genes is often very difficult, if the same genotype used to develop the markers is not simultaneously analyzed. In this paper we present an approach to standardize the size of the alleles in coupling with the resistance genes, using easily accessible cultivars. The proposed procedure has been applied to selected markers for the apple scab resistance genes Rvi2, Rvi4, Rvi5, Rvi6, Rvi11, Rvi12, Rvi13, Rvi14 and Rvi15 (respectively Vh2, Vh4, Vm, Vf, Vbj, Vb, Vd, Rvi14 and Vr2 according to the old nomenclature).

A genetic linkage map of the cultivated strawberry (Fragaria × ananassa) and its comparison to the diploid Fragaria reference map

Abstract: The cultivated strawberry, Fragaria × ananassa, is the most economically-important soft-fruit species, but few practical molecular tools for the purpose of marker assisted selection currently exist. As a precursor to the development of such tools, a genetic linkage map was developed from a F1 population comprising 174 seedlings derived from a cross between two F. × ananassa cultivars, ‘Redgauntlet’ × ‘Hapil’. The resultant map is composed of 315 molecular markers—218 microsatellites, 11 gene-specific markers and 86 AFLP and RAPD markers—and spans 3,116 cM. In total, 69 linkage group fragments were recovered, more than the 56 linkage groups expected for the cultivated strawberry, however, all fragments contained a transferable marker that could be associated with one of 56 linkage group scaffolds. The female (Redgauntlet) and male (Hapil) linkage maps are composed, respectively of 170 loci in 32 linkage groups covering 1,675.3 cM and 182 loci in 37 linkage groups covering 1,440.7 cM, with 37 markers common to both maps. The maximum number of markers in one linkage group was 15, the minimum was two. All linkage groups resolved contained at least one transferable marker (SSR or gene-specific) that had been mapped on the diploid Fragaria reference map (FV × FB), and therefore all linkage groups could be identified as homologous to one of the seven diploid Fragaria linkage groups. When marker order was compared to the diploid Fragaria reference map, effectively complete colinearity was observed. However, the occurrence of duplicated loci on homologues of linkage groups FG1 and FG6 provided evidence of a putative chromosomal duplication or translocation event in Fragaria. The development of this linkage map will facilitate the study and dissection of QTL associated with traits of economic importance such as disease resistance and fruit quality, and provides a foundation for the development of markers for the purpose of marker assisted breeding and selection in the cultivated strawberry, F. × ananassa.

Increased glycine betaine synthesis and salinity tolerance in AhCMO transgenic cotton lines

Abstract: Glycine betaine is an osmoprotectant that plays an important role and accumulates rapidly in many plants during salinity or drought stress. Choline monooxygenase (CMO) is a major catalyst in the synthesis of glycine betaine. In our previous study, a CMO gene (AhCMO) cloned from Atriplex hortensis was introduced into cotton (Gossypium hirsutum L.) via Agrobacterium mediation to enhance resistance to salinity stress. However, there is little or no knowledge of the salinity tolerance of the transgenic plants, particularly under saline-field conditions. In the present study, two transgenic AhCMO cotton lines of the T3 generation were used to study the AhCMO gene expression, and to determine their salinity tolerance in both greenhouse and field under salinity stress. Molecular analysis confirmed that the transgenic plants expressed the AhCMO gene. Greenhouse study showed that on average, seedlings of the transgenic lines accumulated 26 and 131% more glycine betaine than those of non-transgenic plants (SM3) under normal and salt-stress (150 mmol l−1 NaCl) conditions, respectively. The osmotic potential, electrolyte leakage and malondialdehyde (MDA) accumulation were significantly lower in leaves of the transgenic lines than in those of SM3 after salt stress. The net photosynthesis rate and Fv/Fm in transgenic cotton leaves were less affected by salinity than in non-transgenic cotton leaves. Therefore, transgenic cotton over-expressing AhCMO was more tolerant to salt stress due to elevated accumulation of glycine betaine, which provided greater protection of the cell membrane and photosynthetic capacity than in non-transgenic cotton. The seed cotton yield of the transgenic plants was lower under normal conditions, but was significantly higher than that of non-transgenic plants under salt-stressed field conditions. The results indicate that over-expression of AhCMO in cotton enhanced salt stress tolerance, which is of great value in cotton production in the saline fields.

Development, identification, and validation of markers for marker-assisted selection against the Stagonospora nodorum toxin sensitivity genes Tsn1 and Snn2 in wheat

Abstract: The wheat-Stagonospora nodorum pathosystem involves a number of pathogen-produced host-selective toxins that interact with host genes in an inverse gene-for-gene manner to cause disease. The wheat intervarietal recombinant inbred population derived from BR34 and Grandin (BG population) segregates for the toxin sensitivity genes Tsn1, Snn2, and Snn3, which confer sensitivity to the toxins ToxA, SnTox2, and SnTox3, respectively. Here, we report the addition of 141 molecular markers to the BG population linkage maps, the identification and/or development of markers tightly linked to Tsn1 and Snn2, and the validation of the markers using a set of diverse wheat accessions. The BG population maps now contain 787 markers, and new simple sequence repeat (SSR) markers closely linked to Snn2 on chromosome arm 2DS were identified. In an effort to target more markers to the Snn2 locus, STS markers were developed from 2DS bin-mapped ESTs resulting in the development and mapping of 36 markers mostly to the short arms of group 2 chromosomes. Together, SSR and EST-STS markers delineated Snn2 to a 4.0 cM interval. SSRs developed in related work for Tsn1 were mapped in the BG population and delineated the gene to a 1.0 cM interval. Evaluation of the markers for Tsn1 and Snn2 in a diverse set of wheat genotypes validated their utility for marker-assisted selection, which is particularly efficient for removing toxin sensitivity alleles from elite germplasm and varieties.

Expression of apoplastically secreted tobacco osmotin in cotton confers drought tolerance

Abstract: Osmotin or osmotin-like proteins have been shown to be induced in several plant species in response to various types of biotic and abiotic challenges. The protein is generally believed to be involved in protecting the plant against these stresses. Although some understanding of the possible mechanism underlying the defense function of osmotin against biotic stresses is beginning to emerge, its role in abiotic stress response is far from clear. We have transformed cotton plants with a tobacco-osmotin gene, lacking the sequence encoding its 20 amino acid-long, C-terminal vacuolar-sorting motif, under the control of CaMV 35S promoter. Apoplastic secretion of the recombinant protein was confirmed and the plants were evaluated for their ability to tolerate drought conditions. Under polyethylene glycol-mediated water stress, the osmotin-expressing seedlings showed better growth performance. The transformants showed a slower rate of wilting during drought and faster recovery following the termination of dry conditions in a greenhouse setting. During drought, the leaves from transgenic plants had higher relative water content and proline levels, while showing reduced H2O2 levels, lipid peroxidation and electrolyte leakage. Importantly, following a series of dry periods, the osmotin transformants performed better in terms of most growth and developmental parameters tested. Most relevant, the fiber yield of transgenic plants did not suffer as much as that of their non-transgenic counterparts under drought conditions. The results provide direct support for a protective role of osmotin in cotton plants experiencing water stress and suggest a possible way to achieve tolerance to drought conditions by means of genetic engineering.

Genetic mapping and localization of a major QTL for seedling resistance to downy mildew in Chinese cabbage ( Brassica rapa ssp. pekinensis )

Abstract: Downy mildew caused by the fungus Peronospora parisitica is a serious threat to members of the Brassicaceae family. Annually, a substantial loss of yield is caused by the widespread presence of this disease in warm and humid climates. The aim of this study was to localize the genetic factors affecting downy mildew resistance in Chinese cabbage (Brassica rapa ssp. pekinensis). To achieve this goal, we improved a preexisting genetic map of a doubled-haploid population derived from a cross between two diverse Chinese cabbage lines, 91-112 and T12-19, via microspore culture. Microsatellite simple sequence repeat (SSR) markers, isozyme markers, sequence-related amplified polymorphism markers, sequence-characterized amplified region markers and sequence-tagged-site markers were integrated into the previously published map to construct a composite Chinese cabbage map. In this way, the identities of linkage groups corresponding to the Brassica A genome reference map were established. The new map contains 519 markers and covers a total length of 1,070 cM, with an average distance between markers of 2.06 cM. All markers were designated as A1–A10 through alignment and orientation using 55 markers anchored to previously published B. rapa or B. napus reference maps. Of the 89 SSR markers mapped, 15 were newly developed from express sequence tags in Genbank. The phenotypic assay indicated that a single major gene controls seedling resistance to downy mildew, and that a major QTL was detected on linkage group A8 by both interval and MQM mapping methods. The RAPD marker K14-1030 and isozyme marker PGM flanked this major QTL in a region spanning 2.9 cM, and the SSR marker Ol12G04 was linked to this QTL by a distance of 4.36 cM. This study identified a potential chromosomal segment and tightly linked markers for use in marker-assisted selection to improve downy mildew resistance in Chinese cabbage.

Allelic variants of phytoene synthase 1 (Psy1) genes in Chinese and CIMMYT wheat cultivars and development of functional markers for flour colour

Abstract: Phytoene synthase genes influence yellow pigment (YP) content in wheat grain, and are associated with the quality of end-use products. In the present study, a suite of 217 Chinese winter wheat cultivars and 342 CIMMYT spring wheat cultivars were used to search for phytoene synthase 1 gene variations and to detect and compare their genetic effects in different genetic backgrounds. An initial focus on the Chinese winter wheat cultivars revealed four allelic variants of this gene on chromosome 7B (Psy-B1), designated as Psy-B1a, Psy-B1b, Psy-B1c and Psy-B1d. The frequencies of these four alleles were 39.6, 43.8, 15.7 and 0.9%, respectively. A co-dominant marker YP7B-1 based on a 5-bp InDel of poly C in the fifth intron of Psy-B1 amplified a 151-bp PCR fragment in accessions with the medium YP content allele Psy-B1a, and a 156-bp fragment in lower YP content accessions with Psy-B1b. Two dominant markers YP7B-2 (428 bp) and YP7B-3 (884 bp) were designed for accessions with Psy-B1c and Psy-B1d, respectively. Allele Psy-B1c was associated with high YP content, but the phenotypic effect of Psy-B1d was not determined due to the limited number of accessions. In CIMMYT spring wheat cultivars, Psy-B1a, Psy-B1b, Psy-B1d and a further allelic variant, Psy-B1e, were detected with frequencies of 50.6, 29.2, 19.6 and 0.6%, respectively. Psy-B1c was not found in the CIMMYT germplasm. However, no significant differences were detected for mean YP content among CIMMYT wheat lines with different Psy-B1 genotypes. A new allelic variant of Psy-A1, designated Psy-A1c, was identified in three CIMMYT wheat lines, and this allele was associated with higher YP content.

In silico mapping of 1758 new SSR markers developed from public genomic sequences for sorghum

Abstract: In order to develop simple sequence repeat (SSR) markers for sorghum, a total of 2,113 primer pairs were designed from 81,342 public genomic sequence contigs of sorghum [methyl-filtered sequences downloaded from SAMI (Sorghum Assembled Genomic Island)]. After screening eight sorghum lines, 1,758 primers amplifying polymorphisms were identified. Of these 1,710 SSR markers were predominantly polymorphic in the eight lines and could detect from two to eight alleles. In addition, 1,692 of the markers were mapped on to the ten sorghum chromosomes by in silico mapping. The number of markers per chromosome ranged from 107 to 285. These SSR markers will provide an ideal marker system to help with gene targeting, gene cloning, quantitative trait locus mapping, and marker-assisted selection in sorghum species.

Development of a simple functional marker for fragrance in rice and its validation in Indian Basmati and non-Basmati fragrant rice varieties

Abstract: Fragrance development in rice has been reported due to a 8-bp deletion in the exon 7 of badh2 gene located on Chromosome 8S. Multiplex markers targeting the functional InDel polymorphism was earlier reported for genotyping fragrance trait, but the marker was observed to be inconsistent and difficult to use. We have developed a simple, co-dominant, functional marker for fragrance trait, which can be resolved in an agarose gel and validated in Basmati and non-Basmati aromatic rice varieties and in a mapping population segregated for fragrance trait. The marker targets the InDel polymorphism in badh2 gene and amplifies 95 and 103 bp fragments in fragrant and non-fragrant genotypes, respectively. The newly developed marker was highly efficient in discriminating all fragrant and non-fragrant genotypes and showed perfect co-segregation with the trait of fragrance in the mapping population. We recommend the use of this simple, low-cost marker in routine genotyping for fragrance trait in large scale breeding materials and germplasm.

Field evaluation of cotton near-isogenic lines introgressed with QTLs for productivity and drought related traits

Abstract: Quantitative trait loci (QTLs) for yield and drought related physiological traits, osmotic potential (OP), carbon isotope ratio (d 13 C, an indica- tor of water use efficiency), and leaf chlorophyll content (Chl), were exchanged via marker-assisted selection (MAS) between elite cultivars of the two cotton species Gossypium barbadense cv. F-177 and G. hirsutum cv. Siv'on. The resulting near isogenic lines (NILs) were examined in two field trials, each with two irrigation regimes, in order to (1) evaluate the potential to improve cotton drought resistance by MAS and (2) test the role of physiological traits in plant productivity. NILs introgressed with QTLs for high yield rarely exhibited an advantage in yield relative to the recipient parent, whereas a considerable number of NILs exhibited the expected phenotype in terms of lower OP (5 out of 9), higher d 13 C (4 out of 6) or high Chl (2 out of 3). Several NILs exhibited considerable modifications in non-targeted traits including leaf morphology, stomatal conductance and specific leaf weight (SLW). In G. barbadense genotypes, yield was correlated negatively with d 13 C and OP and positively with stomatal conductance, SLW and Chl, whereas in G. hirsutum yield was negatively correlated with d 13 C, SLW and Chl. This dissimilarity suggests that each of the respective species has evolved different mechanisms underlying plant productivity. We conclude that the improvement of drought related traits in cotton NILs may lead to improved drought resistance via MAS, but that conventional breeding may be necessary to combine the introduced QTL(s) with high yield potential.

“Blind” mapping of genic DNA sequence polymorphisms in Lolium perenne L. by high resolution melting curve analysis

Abstract: High resolution melting curve analysis (HRM) measures dissociation of double stranded DNA of a PCR product amplified in the presence of a saturating fluorescence dye. Recently, HRM proved successful to genotype DNA sequence polymorphisms such as SSRs and SNPs based on the shape of the melting curves. In this study, HRM was used for simultaneous screening and genotyping of genic DNA sequence polymorphisms identified in the Lolium perenne F2 mapping population VrnA. Melting profiles of PCR products amplified from previously published gene loci and from a novel gene putatively involved in vernalization response successfully discriminated genotypes in absence of allelic sequence information, and allowed to determine allele segregation in VrnA. Here we introduce the concept of “blind” mapping based on HRM as a powerful, fast and cheap method to map any DNA sequence polymorphisms without prior knowledge of allelic sequences in the key grassland species perennial ryegrass (Lolium perenne L.).

Expression of Arabidopsis NDPK2 increases antioxidant enzyme activities and enhances tolerance to multiple environmental stresses in transgenic sweetpotato plants

Abstract: Transgenic sweetpotato (Ipomoea batatas L. cv. Yulmi) plants expressing the Arabidopsis nucleoside diphosphate kinase 2 (AtNDPK2) gene under the control of an oxidative stress–inducible peroxidase (SWPA2) promoter (referred to as SN plants) were developed and evaluated for enhanced tolerance of SN plants under various abiotic stress conditions. The level of AtNDPK2 expression and NDPK activity in SN plants following methyl viologen (MV) treatment was positively correlated with the plant’s tolerance to MV. Interestingly, we observed that antioxidant enzyme activities such as peroxidase, ascorbate peroxidase, and catalase increased in MV-treated SN plants. In addition, SN plants showed enhanced tolerance to cold, high salinity, and drought stresses by an increase in the activity of H2O2 scavenging enzymes. These results indicate that overexpression of AtNDPK2 in sweetpotato might efficiently modulate oxidative stress from various environmental stresses.