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Key message: Anatomical changes in and hormone roles of the exserted stigma were investigated, and localization and functional analysis of SlLst for the exserted stigma were performed using SLAF-BSA-seq, parental resequencing and overexpression of SlLst in tomato. Tomato accession T431 produces stigmas under relatively high temperatures (> 27 °C, the average temperature in Harbin, China, in June–August), so pollen can rarely reach the stigma properly. This allows the percentage of male sterility exceed 95%, making the use of this accession practical for hybrid seed production. To investigate the mechanism underlying the exserted stigma male sterility, the morphological changes of, anatomical changes of, and comparative endogenous hormone (IAA, ABA, GA3, ZT, SA) changes in flowers during flower development of tomato accessions DL5 and T431 were measured. The location and function of genes controlling exserted stigma sterility were analyzed using super SLAF-BSA-seq, parental resequencing, comparative genomics and the overexpression of SlLst in tomato. The results showed that an increase in cell number mainly caused stigma exsertion. IAA played a major role, while ABA had an opposite effect on stigma exertion. Moreover, 26 candidate genes related to the exserted stigma were found, located on chromosome 12. The Solyc12g027610.1 (SlLst) gene was identified as the key candidate gene by functional analysis. A subcellular localization assay revealed that SlLst is targeted to the nucleus and cell membrane. Phenotypic analysis of SlLst-overexpressing tomato showed that SlLst plays a crucial role during stigma exsertion. [ABSTRACT FROM AUTHOR]

Protein content (PC) is an important component of rice nutritional quality. In order to better understand the genetic basis of this trait and increase related breeding efficiency, 21 single chromosome segment substitution (SCSS) lines grown in four sites over two growing seasons (regarded as eight environments) were used to associate PC with particular chromosome segments. Segments from 15 chromosomes were found to contain quantitative trait loci (QTLs) for PC in at least one environment. These included segments from chromosome 3 and 8, in which QTLs for PC had not previously been identified. The segment of chromosome 8 in CSSL-48 had the largest positive effect across all environments. The interaction between substitution and environment was highly significant. Some substitutions had large effects in one environment, but no effect in another (i.e. CSSL-08 and CSSL-17), while some substitutions significantly increased PC in one environment but decreased it in another (i.e. CSSL-41 and CSSL-43). By biplot and clustering analysis, the eight environments were grouped into two contrasting environment types, that is, Hainan and Jiangsu. The segment of chromosome 8 in CSSL-48 had PC-enhancing QTLs in both of the environment types. The segments in CSSL-34 had QTLs which increase PC in the Jiangsu environment but have no effect in the Hainan environment. For enhancing PC, CSSL-48 could be explored in breeding for wide adaptation across all environments, while CSSL-12, CSSL-14, CSSL-17, CSSL-41 and CSSL-43, and that in CSSL-34 could be explored in breeding for specific adaptation to the Hainan and Jiangsu environments, respectively. Near isogenic lines are under development to validate the QTLs with large effects in a range of genetic backgrounds relevant to Jiangsu and Hainan breeding programs. Secondary mapping populations are also being developed for further localising the responsible QTLs in CSSL-14, CSSL-34 and CSSL-48. [ABSTRACT FROM AUTHOR]

Asr (ABA, stress, ripening) genes represent a small gene family potentially involved in drought tolerance in several plant species. To analyze their interest for rice breeding for water-limited environments, this gene family was characterized further. Genomic organization of the gene family reveals six members located on four different chromosomes and with the same exon–intron structure. The maintenance of six members of the Asr gene family, which are the result of combination between tandem duplication and whole genome duplication, and their differential regulation under water stress, involves probably some sub-functionalization. The polymorphism of four members was studied in a worldwide collection of 204 accessions of Oryza sativa L . and 14 accessions of wild relatives ( O. rufipogon and O. nivara). The nucleotide diversity of the Asr genes was globally low, but contrasted for the different genes, leading to different shapes of haplotype networks. Statistical tests for neutrality were used and compared to their distribution in a set of 111 reference genes spread across the genome, derived from another published study. Asr3 diversity exhibited a pattern concordant with a balancing selection at the species level and with a directional selection in the tropical japonica sub-group. This study provides a thorough description of the organization of the Asr family, and the nucleotide and haplotype diversity of four Asr in Oryza sativa species. Asr3 stood out as the best potential candidate. The polymorphism detected here represents a first step towards an association study between genetic polymorphisms of this gene family and variation in drought tolerance traits. [ABSTRACT FROM AUTHOR]

Fusarium graminearum Schwabe, the conidial form of Gibberella zeae, is the causal fungal pathogen responsible for Gibberella stalk rot of maize. Using a BC1F1 backcross mapping population derived from a cross between ‘1145’ (donor parent, completely resistant) and ‘Y331’ (recurrent parent, highly susceptible), two quantitative trait loci (QTLs), qRfg1 and qRfg2, conferring resistance to Gibberella stalk rot have been detected. The major QTL qRfg1 was further confirmed in the double haploid, F2, BC2F1, and BC3F1 populations. Within a qRfg1 confidence interval, single/low-copy bacterial artificial chromosome sequences, anchored expressed sequence tags, and insertion/deletion polymorphisms, were exploited to develop 59 markers to saturate the qRfg1 region. A step by step narrowing-down strategy was adopted to pursue fine mapping of the qRfg1 locus. Recombinants within the qRfg1 region, screened from each backcross generation, were backcrossed to ‘Y331’ to produce the next backcross progenies. These progenies were individually genotyped and evaluated for resistance to Gibberella stalk rot. Significant (or no significant) difference in resistance reactions between homozygous and heterozygous genotypes in backcross progeny suggested presence (or absence) of qRfg1 in ‘1145’ donor fragments. The phenotypes were compared to sizes of donor fragments among recombinants to delimit the qRfg1 region. Sequential fine mapping of BC4F1 to BC6F1 generations enabled us to progressively refine the qRfg1 locus to a ~500-kb interval flanked by the markers SSR334 and SSR58. Meanwhile, resistance of qRfg1 to Gibberella stalk rot was also investigated in BC3F1 to BC6F1 generations. Once introgressed into the ‘Y331’ genome, the qRfg1 locus could steadily enhance the frequency of resistant plants by 32–43%. Hence, the qRfg1 locus was capable of improving maize resistance to Gibberella stalk rot. [ABSTRACT FROM AUTHOR]

Root system development is an important target for improving yield in cereal crops. Active root systems that can take up nutrients more efficiently are essential for enhancing grain yield. In this study, we attempted to identify quantitative trait loci (QTL) involved in root system development by measuring root length of rice seedlings grown in hydroponic culture. Reliable growth conditions for estimating the root length were first established to renew nutrient solutions daily and supply NH4 + as a single nitrogen source. Thirty-eight chromosome segment substitution lines derived from a cross between ‘Koshihikari’, a japonica variety, and ‘Kasalath’, an indica variety, were used to detect QTL for seminal root length of seedlings grown in 5 or 500 μM NH4 +. Eight chromosomal regions were found to be involved in root elongation. Among them, the most effective QTL was detected on a ‘Kasalath’ segment of SL-218, which was localized to the long-arm of chromosome 6. The ‘Kasalath’ allele at this QTL, qRL6.1, greatly promoted root elongation under all NH4 + concentrations tested. The genetic effect of this QTL was confirmed by analysis of the near-isogenic line (NIL) qRL6.1. The seminal root length of the NIL was 13.5–21.1% longer than that of ‘Koshihikari’ under different NH4 + concentrations. Toward our goal of applying qRL6.1 in a molecular breeding program to enhance rice yield, a candidate genomic region of qRL6.1 was delimited within a 337 kb region in the ‘Nipponbare’ genome by means of progeny testing of F2 plants/F3 lines derived from a cross between SL-218 and ‘Koshihikari’. [ABSTRACT FROM AUTHOR]

The duplicated and the highly repetitive nature of the maize genome has historically impeded the development of true single nucleotide polymorphism (SNP) markers in this crop. Recent advances in genome complexity reduction methods coupled with sequencing-by-synthesis technologies permit the implementation of efficient genome-wide SNP discovery in maize. In this study, we have applied Complexity Reduction of Polymorphic Sequences technology (Keygene N.V., Wageningen, The Netherlands) for the identification of informative SNPs between two genetically distinct maize inbred lines of North and South American origins. This approach resulted in the discovery of 1,123 putative SNPs representing low and single copy loci. In silico and experimental (Illumina GoldenGate (GG) assay) validation of putative SNPs resulted in mapping of 604 markers, out of which 188 SNPs represented 43 haplotype blocks distributed across all ten chromosomes. We have determined and clearly stated a specific combination of stringent criteria (>0.3 minor allele frequency, >0.8 GenTrainScore and >0.5 Chi_test100 score) necessary for the identification of highly polymorphic and genetically stable SNP markers. Due to these criteria, we identified a subset of 120 high-quality SNP markers to leverage in GG assay-based marker-assisted selection projects. A total of 32 high-quality SNPs represented 21 haplotypes out of 43 identified in this study. The information on the selection criteria of highly polymorphic SNPs in a complex genome such as maize and the public availability of these SNP assays will be of great value for the maize molecular genetics and breeding community. [ABSTRACT FROM AUTHOR]

The gene-pool of wild emmer wheat, Triticum turgidum ssp . dicoccoides, harbors a rich allelic repertoire for disease resistance. In the current study, we made use of tetraploid wheat mapping populations derived from a cross between durum wheat (cv. Langdon) and wild emmer (accession G18-16) to identify and map a new powdery mildew resistance gene derived from wild emmer wheat. Initially, the two parental lines were screened with a collection of 42 isolates of Blumeria graminis f. sp. tritici ( Bgt) from Israel and 5 isolates from Switzerland. While G18-16 was resistant to 34 isolates, Langdon was resistant only to 5 isolates and susceptible to 42 isolates. Isolate Bgt#15 was selected to differentiate between the disease reactions of the two genotypes. Segregation ratio of F2-3 and recombinant inbreed line (F7) populations to inoculation with isolate Bgt#15 indicated the role of a single dominant gene in conferring resistance to Bgt#15. This gene, temporarily designated PmG16, was located on the distal region of chromosome arm 7AL. Genetic map of PmG16 region was assembled with 32 simple sequence repeat (SSR), sequence tag site (STS), Diversity array technology (DArT) and cleaved amplified polymorphic sequence (CAPS) markers and assigned to the 7AL physical bin map (7AL-16). Using four DNA markers we established colinearity between the genomic region spanning the PmG16 locus within the distal region of chromosome arm 7AL and the genomic regions on rice chromosome 6 and Brachypodium Bd1. A comparative analysis was carried out between PmG16 and other known Pm genes located on chromosome arm 7AL. The identified PmG16 may facilitate the use of wild alleles for improvement of powdery mildew resistance in elite wheat cultivars via marker-assisted selection. [ABSTRACT FROM AUTHOR]

We describe a novel approach for high-throughput development of genetic markers using representational oligonucleotide microarray analysis. We test the performance of the method in sugar beet ( Beta vulgaris L.) as a model for crop plants with little sequence information available. Genomic representations of both parents of a mapping population were hybridized on microarrays containing in total 146,554 custom made oligonucleotides based on sugar beet bacterial artificial chromosome (BAC) end sequences and expressed sequence tags (ESTs). Oligonucleotides showing a signal with one parental line only, were selected as potential marker candidates and placed onto an array, designed for genotyping of 184 F2 individuals from the mapping population. Utilizing known co-dominant anchor markers we obtained 511 new dominant markers (392 derived from BAC end sequences, and 119 from ESTs) distributed over all nine sugar beet linkage groups and calculated genetic maps. Further improvements for large-scale application of the approach are discussed and its feasibility for the cost-effective and flexible generation of genetic markers is presented. [ABSTRACT FROM AUTHOR]

Maize endosperm accounts for more than 80% of the grain weight. Cell division and grain filling are the two key stages for endosperm development. Previous studies showed that gene expression during differential stages in endosperm development is greatly different. However, information on systematic identification and characterization of the differentially expressed genes between the two stages are limited. In this study, suppression subtractive hybridization (SSH) was used to generate four subtracted cDNA libraries for the two stages using two maize inbreds with large and small grain. Totally, 4,784 differentially expressed sequence tags (ESTs) were sequenced and 902 were non-redundant, which consisted of 344 unique ESTs. Among them 192 had high sequence similarity to the GenBank entries and represent diverse of functional categories, such as metabolism, cell growth/division, transcription, signal transduction, protein destination/storage, protein synthesis and others. The expression patterns of 75.7% SSH-derived cDNAs were confirmed by reverse Northern blot and semi-quantitative reverse transcription polymerase chain reaction, and exhibited the similar results (75.0%). Genes differentially expressed between two key stages for the two inbreds were involved in diverse physiological process pathway, which might be responsible for the formation of grain weight. 43.8% (70 of the 160 unique ESTs) of the identified ESTs were assigned to 39 chromosome bins distributed over all ten maize chromosomes. Eleven ESTs were found to co-localize with previous detected QTLs for grain weight, which might be considered as the candidate genes of grain weight for further study. [ABSTRACT FROM AUTHOR]

We describe how the diversity arrays technology (DArT) can be coupled with chromosome sorting to increase the density of genetic maps in specific genome regions. Chromosome 3B and the short arm of chromosome 1B (1BS) of wheat were isolated by flow cytometric sorting and used to develop chromosome- and chromosome arm-enriched genotyping arrays containing 2,688 3B clones and 384 1BS clones. Linkage analysis showed that 553 of the 711 polymorphic 3B-derived markers (78%) mapped to chromosome 3B, and 59 of the 68 polymorphic 1BS-derived markers (87%) mapped to chromosome 1BS, confirming the efficiency of the chromosome-sorting approach. To demonstrate the potential for saturation of genetic maps, we constructed a consensus map of chromosome 3B using 19 mapping populations, including some that were genotyped with the 3B-enriched array. The 3B-derived DArT markers doubled the number of genetic loci covered. The resulting consensus map, probably the densest genetic map of 3B available to this date, contains 939 markers (779 DArTs and 160 other markers) that segregate on 304 genetically distinct loci. Importantly, only 2,688 3B-derived clones (probes) had to be screened to obtain almost twice as many polymorphic 3B markers (510) as identified by screening approximately 70,000 whole genome-derived clones (269). Since an enriched DArT array can be developed from less than 5 ng of chromosomal DNA, a quantity which can be obtained within 1 h of sorting, this approach can be readily applied to any crop for which chromosome sorting is available. [ABSTRACT FROM AUTHOR]

Biofortification through genetic manipulation is the best approach for improving micronutrient content of the staple food crops to alleviate hidden hunger, namely, the deficiency of Fe and Zn affecting more than two billion people worldwide. An interspecific hybridization was made between T. aestivum line Chinese Spring (CS) and Aegilops kotschyi accession 3790 selected for high grain iron and zinc concentration. The CS × Ae. kotschyi F1 hybrid with low chromosome pairing was highly male and female sterile. This was backcrossed with wheat cultivars to get seed set. The selfed BC1F1 and BC2F1 plants with high grain iron and zinc concentration were selected in subsequent generations. The selected derivatives showed 60–136% enhanced grain iron and zinc concentration and 50–120% increased iron and zinc content per seed as compared to the recipient wheat cultivars. Thirteen cytologically stable, fertile and agronomically superior plants with high grain iron and zinc concentrations were selected for molecular characterization. The application of anchored wheat SSR markers, transferable to Ae. kotschyi, to the high grain iron and zinc containing derivatives indicated introgression of group 2 and group 7 chromosomes of Ae. kotschyi. GISH and FISH analysis of some derivatives confirmed the substitution of chromosomes 2S and 7U for their homoeologues of the A genome, suggesting that some of the genes controlling high grain micronutrient content in the Ae. kotschyi accession are on these chromosomes. [ABSTRACT FROM AUTHOR]

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 F2 population (247 individuals) from the cross of S06 × 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 locus were successfully converted into sequence characterized amplified region (SCAR) markers. The Tu/ tu locus was mapped between the co-dominant SSR marker SSR16203 and the SCAR marker C_SC933, at a genetic distance of 1.4 and 5.9 cM, respectively. Then the linked SSR markers in the study were used as anchor loci to locate the Tu/ tu locus on cucumber chromosome 5. Moreover, the validity analysis of the C_SC69 and C_SC24 markers was performed with 62 cucumber lines of diverse origins, showing that the two SCAR markers can be used for marker-assisted selection (MAS) of the warty fruit trait in cucumber breeding. The information provided in this study will facilitate the map-based cloning of the Tu/ tu gene. [ABSTRACT FROM AUTHOR]

Stagonospora nodorum, casual agent of Stagonospora nodorum blotch (SNB) of wheat, produces a number of host-selective toxins (HSTs) known to be important in disease. To date, four HSTs and corresponding host sensitivity genes have been reported, and all four host–toxin interactions are significant factors in the development of disease. Here, we describe the identification and partial characterization of a fifth S. nodorum produced HST designated SnTox4. The toxin, estimated to be 10–30 kDa in size, was found to be proteinaceous in nature. Sensitivity to SnTox4 is governed by a single dominant gene, designated Snn4, which mapped to the short arm of wheat chromosome 1A in a recombinant inbred (RI) population. The compatible Snn4–SnTox4 interaction is light dependent and results in a mottled necrotic reaction, which is different from the severe necrosis that results from other host–toxin interactions in the wheat– S. nodorum pathosystem. QTL analysis in a population of 200 RI lines derived from the Swiss winter wheat varieties Arina and Forno revealed a major QTL for SNB susceptibility that coincided with the Snn4 locus. This QTL, designated QSnb.fcu-1A, explained 41.0% of the variation in disease on leaves of seedlings indicating that a compatible Snn4–SnTox4 interaction plays a major role in the development of SNB in this population. Additional minor QTL detected on the short arms of chromosomes 2A and 3A accounted for 5.4 and 6.0% of the variation, respectively. The effects of the three QTL were largely additive, and together they explained 50% of the total phenotypic variation. These results provide further evidence that host–toxin interactions in the wheat– S. nodorum pathosystem follow an inverse gene-for-gene model. [ABSTRACT FROM AUTHOR]

Resistance to Globodera pallida Rookmaker (Pa3), originating from wild species Solanum tarijense was identified by QTL analysis and can be largely ascribed to one major QTL. GpaXI explained 81.3% of the phenotypic variance in the disease test. GpaXI is mapped to the long arm of chromosome 11. Another minor QTL explained 5.3% of the phenotypic variance and mapped to the long arm of chromosome 9. Clones containing both QTL showed no lower cyst counts than clones with only GpaXI. After Mendelising the phenotypic data, GpaXI could be more precisely mapped near markers GP163 and FEN427, thus anchoring GpaXI to a region with a known R-gene cluster containing virus and nematode resistance genes. [ABSTRACT FROM AUTHOR]

A highly polymorphic core collection of bread wheat and a more narrow-based breeding material, gathered from pedigrees of seven modern cultivars, was analysed in order to compare genetic diversity indices and linkage disequilibrium (LD) patterns along the chromosome 3B with microsatellite (SSR) and Diversity Arrays Technology markers. Five ancestral gene pools could be identified within the core collection, indicating a strong geographical structure (Northwest Europe, Southeast Europe, CIMMYT–ICARDA group, Asia, Nepal). The breeding material showed a temporal structure, corresponding to different periods of breeding programmes [old varieties (from old landraces to 1919), semi-modern varieties (1920–1959), modern varieties (1960–2006)]. Basic statistics showed a higher genetic diversity in the core collection than in the breeding material, indicating a stronger selection pressure in this latter material. More generally, the chromosome 3B had a lower diversity than the whole B-genome. LD was weak in all studied materials. Amongst geographical groups, the CIMMYT–ICARDA pool presented the longest ranged LD in contrast to Asian accessions. In the breeding material, LD increased from old cultivars to modern varieties. Genitors of seven modern cultivars were found to be different; most marker pairs in significant LD were observed amongst genitors of Alexandre and Koreli varieties, indicating an important inbreeding effect. At low genetic distances (0–5 cM), the breeding material had higher LD than the core collection, but globally the two materials had similar values in all classes. Marker pairs in significant LD are generally observed around the centromere in both arms and at distal position on the short arm of the chromosome 3B. [ABSTRACT FROM AUTHOR]

Wheat powdery mildew is an economically important disease in cool and humid environments. Powdery mildew causes yield losses as high as 48% through a reduction in tiller survival, kernels per head, and kernel size. Race-specific host resistance is the most consistent, environmentally friendly and, economical method of control. The wheat ( Triticum aestivum L.) germplasm line NC06BGTAG12 possesses genetic resistance to powdery mildew introgressed from the AAGG tetraploid genome Triticum timopheevii subsp. armeniacum. Phenotypic evaluation of F3 families derived from the cross NC06BGTAG12/‘Jagger’ and phenotypic evaluation of an F2 population from the cross NC06BGTAG12/‘Saluda’ indicated that resistance to the ‘Yuma’ isolate of powdery mildew was controlled by a single dominant gene in NC06BGTAG12. Bulk segregant analysis (BSA) revealed simple sequence repeat (SSR) markers specific for chromosome 7AL segregating with the resistance gene. The SSR markers Xwmc273 and Xwmc346 mapped 8.3 cM distal and 6.6 cM proximal, respectively, in NC06BGTAG12/Jagger. The multiallelic Pm1 locus maps to this region of chromosome 7AL. No susceptible phenotypes were observed in an evaluation of 967 F2 individuals in the cross NC06BGTAG12/‘Axminster’ ( Pm1a) which indicated that the NC06BGTAG12 resistance gene was allelic or in close linkage with the Pm1 locus. A detached leaf test with ten differential powdery mildew isolates indicated the resistance in NC06BGTAG12 was different from all designated alleles at the Pm1 locus. Further linkage and allelism tests with five other temporarily designated genes in this very complex region will be required before giving a permanent designation to this gene. At this time the gene is given the temporary gene designation MlAG12. [ABSTRACT FROM AUTHOR]

Breeders can force sexual hybridisation between wheat and related grass species to produce interspecific hybrids containing a dihaploid set of wheat and related chromosomes. This facilitates the introgression of desirable genes into wheat from the secondary gene pool. However, most elite European wheat varieties carry genes that suppress crossability, making the transfer of novel traits from exotic germplasm into elite wheat varieties difficult or impossible. Previous studies have identified at least five crossability loci in wheat. Here, the crossability locus with the largest effect, Kr1 on chromosome arm 5BL, was fine-mapped by developing a series of recombinant substitution lines in which the genome of the normally non-crossable wheat variety ‘Hobbit sib’ carries a recombinant 5BL chromosome arm containing segments from the crossable variety ‘Chinese Spring’. These recombinant lines were scored for their ability to cross with rye over four seasons. Analysis revealed at least two regions on 5BL affecting crossability, including the Kr1 locus. However, the ability to set seed is highly dependent on prevailing environmental conditions. Typically, even crossable wheat lines exhibit little or no seed set when crossed with rye in winter, but show up to 90% seed set from similar crosses made in summer. By recombining different combinations of the two regions affecting crossability, wheat lines that consistently exhibit up to 50% seed set, whether crossed in the UK winter or summer conditions, were generated, thus creating a very important tool for increasing the efficiency of alien wheat transfer programmes. [ABSTRACT FROM AUTHOR]

The use of major resistance genes is a cost-effective strategy for preventing stem rust epidemics in wheat crops. The stem rust resistance gene Sr39 provides resistance to all currently known pathotypes of Puccinia graminis f. sp. tritici (Pgt) including Ug99 (TTKSK) and was introgressed together with leaf rust resistance gene Lr35 conferring adult plant resistance to P. triticina (Pt), into wheat from Aegilops speltoides. It has not been used extensively in wheat breeding because of the presumed but as yet undocumented negative agronomic effects associated with Ae. speltoides chromatin. This investigation reports the production of a set of recombinants with shortened Ae. speltoides segments through induction of homoeologous recombination between the wheat and the Ae. speltoides chromosome. Simple PCR-based DNA markers were developed for resistant and susceptible genotypes (Sr39#22r and Sr39#50s) and validated across a set of recombinant lines and wheat cultivars. These markers will facilitate the pyramiding of ameliorated sources of Sr39 with other stem rust resistance genes that are effective against the Pgt pathotype TTKSK and its variants. [ABSTRACT FROM AUTHOR]

Two quantitative trait loci ( Fr-H1 and Fr-H2) for frost tolerance (FT) have been discovered on the long arm of chromosome 5H in barley. Two tightly linked groups of CBF genes, known to play a key role in the FT regulatory network in A. thaliana, have been found to co-segregate with Fr-H2. Here, we investigate the allelic variations of four barley CBF genes ( HvCbf3, HvCbf6, HvCbf9 and HvCbf14) in a panel of European cultivars, landraces and H. spontaneum accessions. In the cultivars a reduction of nucleotide and haplotype diversities in CBFs compared with the landraces and the wild ancestor H. spontaneum, was evident. In particular, in cultivars the loss of HvCbf9 genetic variants was higher compared to other sequences. In order to verify if the pattern of CBF genetic variants correlated with the level of FT, an association procedure was adopted. The pairwise analysis of linkage disequilibrium (LD) among the genetic variants in four CBF genes was computed to evaluate the resolution of the association procedure. The pairwise plotting revealed a low level of LD in cultivated varieties, despite the tight physical linkage of CBF genes analysed. A structured association procedure based on a general liner model was implemented, including the variants in CBFs, of Vrn-H1, and of two reference genes not involved in FT ( α-Amy1 and Gapdh) and considering the phenotypic data for FT. Association analysis recovered two nucleotide variants of HvCbf14 and one nucleotide variant of Vrn-H1 as statistically associated to FT. [ABSTRACT FROM AUTHOR]

Lophopyrum elongatum (tall wheatgrass), a wild relative of wheat, can be used as a source of novel genes for improving salt tolerance of bread wheat. Sodium ‘exclusion’ is a major physiological mechanism for salt tolerance in a wheat–tall wheatgrass amphiploid, and a large proportion (~50%) for reduced Na+ accumulation in the flag leaf, as compared to wheat, was earlier shown to be contributed by genetic effects from substitution of chromosome 3E from tall wheatgrass for wheat chromosomes 3A and 3D. Homoeologous recombination between 3E and wheat chromosomes 3A and 3D was induced using the ph1b mutant, and putative recombinants were identified as having SSR markers specific for tall wheatgrass loci. As many as 14 recombinants with smaller segments of tall wheatgrass chromatin were identified and low-resolution breakpoint analysis was achieved using wheat SSR loci. Seven recombinants were identified to have leaf Na+ concentrations similar to those in 3E(3A) or 3E(3D) substitution lines, when grown in 200 mM NaCl in nutrient solution. Phenotypic analysis identified recombinants with introgressions at the distal end on the long arm of homoeologous group 3 chromosomes being responsible for Na+ ‘exclusion’. A total of 55 wheat SSR markers mapped to the long arm of homoeologous group 3 markers by genetic and deletion bin mapping were used for high resolution of wheat–tall wheatgrass chromosomal breakpoints in selected recombinants. Molecular marker analysis and genomic in situ hybridisation confirmed the 524-568 recombinant line as containing the smallest introgression of tall wheatgrass chromatin on the distal end of the long arm of wheat chromosome 3A and identified this line as suitable for developing wheat germplasm with Na+ ‘exclusion’. [ABSTRACT FROM AUTHOR]

An incompletely dominant gene conferring resistance to Puccinia hordei, Rph14, identified previously in an accession of Hordeum vulgare, confers resistance to all known pathotypes of P. hordei in Australia. Knowledge of the chromosomal location of Rph14 and the identification of DNA markers closely linked to it will facilitate combining it with other important leaf rust resistance genes to achieve long lasting resistance. The inheritance of Rph14 was confirmed using 146 and 106 F3 lines derived from the crosses ‘Baudin’/‘PI 584760’ ( Rph14) and ‘Ricardo’/‘PI 584760’ ( Rph14), respectively. Bulk segregant analysis on DNA from the parental genotypes and resistant and susceptible DNA bulks using DArT markers located Rph14 to the short arm of chromosome 2H. DArT marker bPb-1664 was identified as having the closest genetic association with Rph14. PCR based marker analysis identified a single SSR marker, Bmag692, linked closely to Rph14 at a map distance of 2.1 and 3.8 cm in the ‘Baudin’/‘PI 584760’and ‘Ricardo’/‘PI 584760’ populations, respectively. [ABSTRACT FROM AUTHOR]

Over time, many single, all-stage resistance genes to stripe rust ( Puccinia striiformis f. sp. tritici) in wheat ( Triticum aestivum L.) are circumvented by race changes in the pathogen. In contrast, high-temperature, adult-plant resistance (HTAP), which only is expressed during the adult-plant stage and when air temperatures are warm, provides durable protection against stripe rust. Our objective was to identify major quantitative trait loci (QTL) for HTAP resistance to stripe rust in the spring wheat cultivar ‘Louise’. The mapping population consisted of 188 recombinant inbred lines (RIL) from a Louise (resistant) by ‘Penawawa’ (susceptible) cross. F5:6 lines were evaluated for stripe rust reaction under natural infection in replicated field trials at five locations in the US Pacific Northwest in 2007 and 2008. Infection type (IT) and disease severity were recorded for each RIL 2–4 times per location. In all environments, Penawawa, the susceptible parent, was rated with an IT ranging from 6 to 8 at all growth stages evaluated. In contrast, Louise, the resistant parent, was rated with an IT of 2 or 3 across growth stages. Distribution of IT values was bimodal, indicating a single major gene was affecting the trait. The parents and RIL population were evaluated with 295 polymorphic simple sequence repeat and one single nucleotide polymorphism markers. One major QTL, designated QYrlo.wpg-2BS, associated with HTAP resistance in Louise, was detected on chromosome 2BS (LOD scores ranging from 5.5 to 62.3 across locations and years) within a 16.9 cM region flanked by Xwmc474 and Xgwm148. SSR markers associated with QYrlo.wpg-2BS are currently being used in marker-based forward breeding strategies to transfer the target region into adapted germplasm to improve the durability of resistance in resulting cultivars. [ABSTRACT FROM AUTHOR]

A lesion-mimic phenotype appeared in a segregating population of common wheat cross Yanzhan 1/Zaosui 30. The parents had non-lesion normal phenotypes. Shading treatment and histochemical analyses showed that the lesions were caused by light-dependent cell death and were not associated with pathogens. Studies over two cropping seasons showed that some lines with more highly expressed lesion-mimic phenotypes exhibited significantly lower grain yields than those with the normal phenotype, but there were no significant effects in the lines with weakly expressed lesion-mimic phenotypes. Among yield traits, one-thousand grain weight was the most affected by lesion-mimic phenotypes. Genetic analysis indicated that this was a novel type of lesion mimic, which was caused by interaction of recessive genes derived from each parent. The lm1 ( lesion mimic 1) locus from Zaosui 30 was flanked by microsatellite markers Xwmc674 and Xbarc133/ Xbarc147 on chromosome 3BS, at genetic distances of 1.2 and 3.8 cM, respectively, whereas lm2 from Yanzhan 1 was mapped between microsatellite markers Xgwm513 and Xksum154 on chromosome 4BL, at genetic distances of 1.5 and 3 cM, respectively. The linked microsatellite makers identified in this study might be useful for evaluating whether potential parents with normal phenotype are carriers of lesion-mimic alleles. [ABSTRACT FROM AUTHOR]

Variation in ear emergence time is critical for the adaptation of wheat ( Triticum aestivum L.) to specific environments. The aim of this study was to identify genes controlling ear emergence time in elite European winter wheat germplasm. Four doubled haploid populations derived from the crosses: Avalon × Cadenza, Savannah × Rialto, Spark × Rialto, and Charger × Badger were selected which represent diversity in European winter wheat breeding programmes. Ear emergence time was recorded as the time from 1st May to heading in replicated field trials in the UK, France and Germany. Genetic maps based on simple sequence repeat (SSR) and Diversity Arrays Technology (DArT) markers were constructed for each population. One hundred and twenty-seven significant QTL were identified in the four populations. These effects were condensed into 19 meta-QTL projected onto a consensus SSR map of wheat. These effects are located on chromosomes 1B (2 meta-QTL), 1D, 2A (2 meta-QTL), 3A, 3B (2 meta-QTL), 4B, 4D, 5A (2 meta-QTL), 5B, 6A, 6B 7A (2 meta-QTL), 7B and 7D. The identification of environmentally robust earliness per se effects will facilitate the fine tuning of ear emergence in predictive wheat breeding programmes. [ABSTRACT FROM AUTHOR]

Wheat quality depends on protein composition and grain protein content. High molecular weight glutenin subunits (HMW-GS) play an important role in determining the viscoelastic properties of gluten. In an attempt to improve the bread-making quality of hexaploid wheat by elaborating novel HMW-GS combinations, a fragment of wheat chromosome 1D containing the Glu-D1 locus encoding the Dx2+Dy12 subunits was translocated to the long arm of chromosome 1A using the ph1b mutation. The partially isohomoeoallelic line selected was characterized using cytogenetical and molecular approaches to assess the amount of chromatin introgressed in the translocated 1A chromosome. Triple-target genomic in situ hybridization indicated that the translocated 1A chromosome had a terminal 1D segment representing 25% of the length of the recombinant long arm. The translocation was also identified on the long arm using molecular markers, and its length was estimated with a minimum of 91 cM. Proteome analysis was performed on total endosperm proteins. Out of the 152 major spots detected, 9 spots were up-regulated and 4 spots were down-regulated. Most of these proteins were identified as α-, β-, γ-gliadins assigned to the chromosomes of homoeologous groups 1 and 6. Quantitative variations in the HMW-GS were only observed in subunit Dy12 in response to duplication of the Glu-D1 locus. [ABSTRACT FROM AUTHOR]

We analysed the products of male meiosis in microspore-derived progeny from a Brassica napus (AACnCn) × Brassica carinata (BBCcCc) interspecific hybrid (ABCnCc). Genotyping at 102 microsatellite marker loci and nuclear DNA contents provided strong evidence that 26 of the 28 progeny (93%) were derived from unreduced (2n) gametes. The high level of CnCc marker heterozygosity, and parallel spindles at Anaphase II in the ABCnCc hybrid, indicated that unreduced gametes were formed by first division restitution. The frequency of dyads at the tetrad stage of pollen development (2.6%) suggested that unreduced gametes were preferentially selected in microspore culture. Segregation of marker alleles in the microspore-derived progeny was consistent with homologous recombination between Cn and Cc chromosomes and homoeologous recombination involving A-, B- and C-genome chromosomes during meiosis in the ABCnCc hybrid. We discuss the potential for using microspore culture of unreduced gametes in interspecific hybrids to map Brassica centromeres through half-tetrad analysis. [ABSTRACT FROM AUTHOR]

Powdery mildew caused by Blumeria graminis f. sp. tritici is an important wheat disease in China and other parts of the world. Wild emmer ( Triticum turgidum var. dicoccoides) is the immediate progenitor of cultivated tetraploid and hexaploid wheats and thus an important resource for wheat improvement. Wild emmer accession IW2 collected from Mount Hermon, Israel, is highly resistant to powdery mildew at the seedling and adult plant stages. Genetic analysis using an F2 segregating population and F2:3 families, derived from a cross between susceptible durum cultivar Langdon and wild emmer accession IW2, indicated that a single dominant gene was responsible for the resistance of IW2. Bulked segregant and molecular marker analyses detected that six polymorphic SSR, one ISBP, and three EST-STS markers on chromosome 3BL bin 0.63–1.00 were linked to the resistance gene. Allelic variations of resistance-linked EST-STS marker BE489472 revealed that the allele was present only in wild emmer but absent in common wheat. Segregation distortion was observed for the powdery mildew resistance allele and its linked SSR markers with preferential transmission of Langdon alleles over IW2 alleles. The resistance gene was introgressed into common wheat by backcrossing and marker-assisted selection. Since no designated powdery mildew resistance gene has been found on chromosome 3BL, the resistance gene derived from wild emmer accession IW2 appears to be new one and was consequently designated Pm41. [ABSTRACT FROM AUTHOR]

We report the development of a new interspecific cotton recombinant inbred line (RIL) population of 140 lines deriving from an interspecific cross between Gossypium hirsutum ( Gh) and G. barbadense ( Gb), using the same two parents that have served for the construction of a BC1 map and for the marker-assisted backcross selection program underway at CIRAD. Two marker systems, microsatellites and AFLPs, were used. An important feature of the RIL population was its marked segregation distortion with a genome-wide bias to Gh alleles (parental genome ratio is 71/29). The RIL map displays an excellent colinearity with the BC1 map, although it is severely contracted in terms of map size. Existence of 255 loci in common (between 6 and 14 per chromosome) allowed the integration of the two data sets. A consensus BC1–RIL map based upon 215 individuals (75 BC1 + 140 RIL) was built. It consisted of 1,745 loci, spanned 3,637 cM, intermediate between the sizes of the two component maps, and constituted a solid framework to cross align cotton maps using common markers. The new RIL population will be further exploited for fiber property QTL mapping and eQTL mapping. [ABSTRACT FROM AUTHOR]

Cultivated tomato ( Solanum lycopersicum, syn. Lycopersicon esculentum) is susceptible to the necrotrophic ascomycete and causal agent of gray mold, Botrytis cinerea. Resistance to this fungal pathogen is elevated in wild relatives of tomato, including Solanum lycopersicoides. An introgression line population (IL) containing chromosomal segments of S. lycopersicoides within the background of tomato cv. VF36 was used to screen the genome for foliar resistance and susceptibility to B. cinerea. Based on this screen, putative quantitative trait loci (QTL) were identified, five for resistance and two for susceptibility. Four resistance QTL decreased infection frequency while the fifth reduced lesion diameter. One susceptibility QTL increased infection frequency whereas the other increased lesion diameter. Overlapping chromosomal segments provided strong evidence for partial resistance on chromosomes 1 and 9 and for elevated susceptibility on chromosome 11. Segregation analysis confirmed the major resistance QTL on the long arm of chromosome 1 and susceptibility on chromosome 11. Linkage of partial resistance to chromosome 9 could not be confirmed. The usefulness of these data for resistance breeding and for map-based cloning of foliar resistance to B. cinerea is discussed. [ABSTRACT FROM AUTHOR]

Yield losses caused by lodging in cereals can be partially controlled by reducing plant height. A progeny of recombinant inbred lines from a cross of two Japanese barley varieties was used to study the inheritance of culm and culm internode lengths. An unexpected QTL for reduced culm length ( qCUL), which affected mainly the length of the third and fourth culm internodes, was contributed by ‘Kanto Nakate Gold’. This QTL was also associated with reduced lodging in two experiments. A near-isogenic line (culm length 62.9–73.4 cm) in an ‘Azumamugi’ background, carrying a chromosome segment containing the qCUL allele from Kanto Nakate Gold, was significantly shorter than its recurrent parent (82.9–89.4 cm). The F2 generation from the next backcross segregated for plant height in a Mendelian monogenic ratio. The qCUL locus was shown to be tightly linked (1.2 cM) with the codominant STS marker ABG608. [ABSTRACT FROM AUTHOR]

The tomato I-3 gene introgressed from the Lycopersicon pennellii accession LA716 confers resistance to race 3 of the fusarium wilt pathogen Fusarium oxysporum f. sp. lycopersici. We have improved the high-resolution map of the I-3 region of tomato chromosome 7 with the development and mapping of 31 new PCR-based markers. Recombinants recovered from L. esculentum cv. M82 × IL7-2 F2 and (IL7-2 × IL7-4) × M82 TC1F2 mapping populations, together with recombinants recovered from a previous M82 × IL7-3 F2 mapping population, were used to position these markers. A significantly higher recombination frequency was observed in the (IL7-2 × IL7-4) × M82 TC1F2 mapping population based on a reconstituted L. pennellii chromosome 7 compared to the other two mapping populations based on smaller segments of L. pennellii chromosome 7. A BAC contig consisting of L. esculentum cv. Heinz 1706 BACs covering the I-3 region has also been established. The new high-resolution map places the I-3 gene within a 0.38 cM interval between the molecular markers RGA332 and bP23/gPT with an estimated physical size of 50–60 kb. The I-3 region was found to display almost continuous microsynteny with grape chromosome 12 but interspersed microsynteny with Arabidopsis thaliana chromosomes 1, 2 and 3. An S-receptor-like kinase gene family present in the I-3 region of tomato chromosome 7 was found to be present in the microsyntenous region of grape chromosome 12 but was absent altogether from the A. thaliana genome. [ABSTRACT FROM AUTHOR]

End-use quality is one of the priorities of modern wheat ( Triticum aestivum L.) breeding. Even though quality is a complex trait, high molecular weight (HMW) glutenins play a major role in determining the bread making quality of wheat. DNA markers developed from the sequences of HMW glutenin genes were reported in several previous studies to facilitate marker-assisted selection (MAS). However, most of the previously available markers are dominant and amplify large DNA fragments, and thus are not ideal for high throughput genotyping using modern equipment. The objective of this study was to develop and validate co-dominant markers suitable for high throughput MAS for HMW glutenin subunits encoded at the Glu-A1 and Glu-D1 loci. Indels were identified by sequence alignment of allelic HMW glutenin genes, and were targeted to develop locus-specific co-dominant markers. Marker UMN19 was developed by targeting an 18-bp deletion in the coding sequence of subunit Ax2* of Glu-A1. A single DNA fragment was amplified by marker UMN19, and was placed onto chromosome 1AL. Sixteen wheat cultivars with known HMW glutenin subunits were used to validate marker UMN19. The cultivars with subunit Ax2* amplified the 362-bp fragment as expected, and a 344-bp fragment was observed for cultivars with subunit Ax1 or the Ax-null allele. Two co-dominant markers, UMN25 and UMN26, were developed for Glu-D1 by targeting the fragment size polymorphic sites between subunits Dx2 and Dx5, and between Dy10 and Dy12, respectively. The 16 wheat cultivars with known HMW glutenin subunit composition were genotyped with markers UMN25 and UMN26, and the genotypes perfectly matched their subunit types. Using an Applied Biosystems 3130xl Genetic Analyzer, four F2 populations segregating for the Glu-A1 or Glu-D1 locus were successfully genotyped with primers UMN19, UMN25 and UMN26 labeled with fluorescent dyes. [ABSTRACT FROM AUTHOR]

Phytophthora capsici Leonian, an oomycete pathogen, is a serious problem in pepper worldwide. Its resistance in pepper is controlled by quantitative trait loci (QTL). To detect QTL associated with P. capsici resistance, a molecular linkage map was constructed using 100 F2 individuals from a cross between Capsicum annuum ‘CM334’ and C. annuum ‘Chilsungcho’. This linkage map consisted of 202 restriction fragment length polymorphisms (RFLPs), 6 WRKYs and 1 simple sequence repeat (SSR) covering 1482.3 cM, with an average interval marker distance of 7.09 cM. QTL mapping of Phytophthora root rot and damping-off resistance was performed in F2:3 originated from a cross between resistant Mexican landrace C. annuum ‘CM334’ and susceptible Korean landrace C. annuum ‘Chilsungcho’ using composite interval mapping (CIM) analysis. Four QTL explained 66.3% of the total phenotypic variations for root rot resistance and three 44.9% for damping-off resistance. Of these QTL loci, two were located close to RFLP markers CDI25 on chromosome 5 (P5) and CT211A on P9. A bacterial artificial chromosome (BAC) library from C. annuum ‘CM334’ was screened with these two RFLP probes to obtain sequence information around the RFLP marker loci for development of PCR-based markers. CDI25 and CT211 probes identified seven and eight BAC clones, respectively. Nine positive BAC clones containing probe regions were sequenced and used for cytogenetic analysis. One single-nucleotide amplified polymorphism (SNAP) for the CDI25 locus, and two SSRs and cleaved amplified polymorphic sequence (CAPS) for CT211 were developed using sequences of the positive BAC clones. These markers will be valuable for rapid selection of genotypes and map-based cloning for resistance genes against P. capsici. [ABSTRACT FROM AUTHOR]

Root elongation induced by phosphorus deficiency has been reported as one of the adaptive mechanisms in plants. Genetic differences were found in rice for the root elongation under phosphorus deficiency (REP), for which a distinct quantitative trait locus (QTL) was detected on the long arm of chromosome 6. Subsequently, the effect and position of the QTL, designated as qREP-6, were confirmed using chromosome segment substitution lines (CSSLs), in which the background of a japonica cultivar, ‘Nipponbare’ with non-REP, was partially substituted by chromosomal segments from an indica cultivar, ‘Kasalath’ with remarkable REP. Out of 54 CSSLs, two lines (CSSL28 and CSSL29) that retain a common ‘Kasalath’-derived segment on the long arm of chromosome 6 showed a significantly high REP. The high REP lines also showed high adaptabilities such as enhanced tillering ability and shoot phosphorus content. Accordingly, conditional dependencies between the related traits were assessed using a graphical Gaussian model (GGM). Direct interactions between REP and root length, and between root length and tiller number were detected under P deficiency in CSSLs. Furthermore, qREP-6 for REP and qTNP-6 for tiller number under P deficiency were fine-mapped with an F2 population of a cross between Nipponbare and CSSL29. A region containing qREP-6 accounted for more than half of the phenotypic variance, the most plausible interval of which contained 37 candidate genes. The result provides a foundation for cloning of the qREP-6 gene which will be applicable to study P deficiency-dependent response and to improve rice’s adaptability to P deficiency stress. [ABSTRACT FROM AUTHOR]

We previously mapped mRNA transcript abundance traits (expression-QTL or eQTL) using the Barley1 Affymetrix array and ‘whole plant’ tissue from 139 progeny of the Steptoe × Morex (St/Mx) reference barley mapping population. Of the 22,840 probesets (genes) on the array, 15,987 reported transcript abundance signals that were suitable for eQTL analysis, and this revealed a genome-wide distribution of 23,738 significant eQTLs. Here we have explored the potential of using these mRNA abundance eQTL traits as surrogates for the identification of candidate genes underlying the interaction between barley and the wheat stem rust fungus Puccinia graminis f. sp. tritici. We re-analysed quantitative ‘resistance phenotype’ data collected on this population in 1990/1991 and identified six loci associated with barley’s reaction to stem rust. One of these coincided with the major stem rust resistance locus Rpg1, that we had previously positionally cloned using this population. Correlation analysis between phenotype values for rust infection and mRNA abundance values reported by the 22,840 GeneChip probe sets placed Rpg1, which is on the Barley1 GeneChip, in the top five candidate genes for the major QTL on chromosome 7H corresponding to the location of Rpg1. A second co-located with the rpg4/Rpg5 stem rust resistance locus that has been mapped in a different population and the remaining four were novel. Correlation analyses identified candidate genes for the rpg4/Rpg5 locus on chromosome 5H. By combining our data with additional published mRNA profiling data sets, we identify a putative sensory transduction histidine kinase as a strong candidate for a novel resistance locus on chromosome 2H and compile candidate gene lists for the other three loci. [ABSTRACT FROM AUTHOR]

The already available comprehensive genome sequence information of model crops along with the transcriptomic resource from other crops provides an excellent opportunity for comparative genome analysis. We studied the synteny between each of the four major sorghum staygreen quantitative trait loci (QTL) regions with that in the rice genome and attempted to increase marker density around the QTL with genic-microsatellites from the sorghum transcriptomic resource using the rice genome as template. For each of the sorghum QTL regions, the reported RFLP markers were compiled, used for sequence similarity searches against the rice genome which identified syntenous regions on rice chromosome 1 for Stg1 and Stg2 QTL, on chromosome 9 for Stg3 QTL, and on chromosome 11 for Stg4 QTL. Using the Gramene genome browsing tool, 869 non-redundant sorghum expressed sequence tags (ESTs) were selected and 50 genic-microsatellites (18, 12, 15, and 5, for Stg1, Stg2, Stg3, and Stg4 QTL, respectively) could be developed. We could experimentally establish synteny of the Stg1, Stg2, Stg3, and Stg4 QTL regions with that of the rice genome by mapping ten polymorphic genic-microsatellite markers (20%) to the positions of the staygreen QTL. The simple strategy demonstrated in the present study could readily be extrapolated to other cereals of the Poaceae family. The markers developed in this study provide a basis for the isolation of genes underling these QTL using an association study or map-based gene isolation approach, and create an additional option for MAS of the staygreen trait in sorghum. [ABSTRACT FROM AUTHOR]

Quality protein maize (QPM) was created by selecting genetic modifiers that convert the starchy endosperm of an opaque2 ( o2) mutant to a hard, vitreous phenotype. Genetic analysis has shown that there are multiple, unlinked o2 modifiers ( Opm), but their identity and mode of action are unknown. Using two independently developed QPM lines, we mapped several major Opm QTLs to chromosomes 1, 7 and 9. A microarray hybridization performed with RNA obtained from true breeding o2 progeny with vitreous and opaque kernel phenotypes identified a small group of differentially expressed genes, some of which map at or near the Opm QTLs. Several of the genes are associated with ethylene and ABA signaling and suggest a potential linkage of o2 endosperm modification with programmed cell death. [ABSTRACT FROM AUTHOR]

Bread wheat ( Triticum aestivum L.) is a hexaploid species with a large and complex genome. A reference genetic marker map, namely the International Triticeae Mapping Initiative (ITMI) map, has been constructed with the recombinant inbred line population derived from a cross involving a synthetic line. But it is not sufficient for a full understanding of the wheat genome under artificial selection without comparing it with intervarietal maps. Using an intervarietal mapping population derived by crossing Nanda2419 and Wangshuibai, we constructed a high-density genetic map of wheat. The total map length was 4,223.1 cM, comprising 887 loci, 345 of which were detected by markers derived from expressed sequence tags (ESTs). Two-thirds of the high marker density blocks were present in interstitial and telomeric regions. The map covered, mostly with the EST-derived markers, approximately 158 cM of telomeric regions absent in the ITMI map. The regions of low marker density were largely conserved among cultivars and between homoeologous subgenomes. The loci showing skewed segregation displayed a clustered distribution along chromosomes and some of the segregation distortion regions (SDR) are conserved in different mapping populations. This map enriched with EST-derived markers is important for structure and function analysis of wheat genome as well as in wheat gene mapping, cloning, and breeding programs. [ABSTRACT FROM AUTHOR]

Five asymmetric hybrid plants were obtained between Medicago sativa (2 n = 4 x = 32) and Medicago arborea (2 n = 4 x = 32) through sexual reproduction and the use of a cytoplasmically male sterile M. sativa genotype. Over 2,000 pollinations were made to obtain these hybrids. Amplified fragment length polymorphism (AFLP) analysis showed that in the most studied hybrid (WA2273), 4% of the bands unique to the M. arborea parent were present, versus 72% for the unique M. sativa bands. This suggests that only a single M. arborea chromosome or chromosome parts has been transferred. WA2273 had 7% of AFLP bands which were not present in either parent, which is suggestive of chromosome rearrangements as would be expected if only chromosome parts or a single part had been transferred from M. arborea. Phenotypic evidence for hybridity was obtained for pod coiling (1.4 coils in WA2273 versus three coils in the M. sativa parent and its self and testcross populations, and one coil in M. arborea), and Colletotrichum trifolii race 2 resistance (transferred from the resistant M. arborea parent, as the M. sativa parent and the self populations were highly susceptible). The hybrids were self sterile, but were female fertile to a high level when crossed with 4 x, but not 2 x, M. sativa, indicating they were at or near 4 x. Both the pod coiling trait and anthracnose resistance segregated in the progeny of testcrosses between WA2273 and M. sativa. The work demonstrates that agronomically useful traits can be introgressed into M. sativa from M. arborea by use of male sterile M. sativa and sexual reproduction. [ABSTRACT FROM AUTHOR]

Carbon isotope composition (δ13C) and leaf water-use efficiency vary in concert in C3 plants, making δ13C useful as a proxy for plant water-use efficiency. A QTL for δ13C was detected in the Solanum pennellii chromosome fragment of IL5-4, an introgression line with S. lycopersicum cv. M82 background. M82 and IL 5-4 were crossed, and RFLP markers in the target region converted to PCR-based markers. Forty-one recombinants with an introgression fragment ranging in length from 1.1 to 11.4 cM were identified by marker assisted selection (MAS) among approximately 2000 F2 plants. A total of 29 markers were mapped within the introgression fragment unique to IL5-4. These markers divided the about 9 cM target region into nine intervals. A dominant QTL for δ13C, designated QWUE5.1 that explained 25.6% of the total phenotypic variance was mapped to an interval about 2.2 cM long. Twenty-one plants with a S. pennellii chromosome fragment shortened to a length of 2.0–9.1 cM by a second recombination event were generated by MAS of 1,125 F4 plants. Two near isogenic lines with high δ13C (small negative value) and carrying QWUE5.1 on the shortest introgression fragments (about 7.0 cM) were identified. The markers and genetic stocks developed are valuable for cloning the gene underlying QWUE5.1, MAS of QWUE5.1, and fine-mapping genes/QTL located in this region. [ABSTRACT FROM AUTHOR]

Segregation distortion (SD) is the deviation of genetic segregation ratios from their expected Mendelian fraction and is a common phenomenon found in most genetic mapping studies. In this study two segregating Lolium perenne populations were used to construct two genetic maps: an ‘F2 biomass’ consisting of 360 genotypes and an ‘F1 late flowering’ sibling based population consisting of 182 genotypes. Additionally two parental maps were generated for the ‘F1 late flowering’ population. SD was detected and p-values for SD were calculated for each marker locus. The ‘F1 late flowering’ map had only half of the extent of SD (32%) compared to the map based on the ‘F2 biomass’ population (63%). Molecular marker data have been supplemented with genomic in situ hybridization (GISH) data to show non major non-recombined segments of Fescue chromosomes within the parental inbred ryegrass lines with a Festuca × Lolium pedigree. We conclude that SD in our study is more likely caused by genetic effects rather than by population structure and marker types. Two new L. perenne mapping populations including their genetic maps are introduced; one of them is the largest reported Lolium mapping population consisting of 360 individuals. [ABSTRACT FROM AUTHOR]

New potato ( Solanum tuberosum) varieties are required to contain low levels of the toxic glycoalkaloids and a potential approach to obtain this is through marker-assisted selection (MAS). Before applying MAS it is necessary to map quantitative trait loci (QTLs) for glycoalkaloid content in potato tubers and identify markers that link tightly to this trait. In this study, tubers of a dihaploid BC1 population, originating from a cross between 90-HAF-01 ( S. tuberosum 1) and 90-HAG-15 ( S. tuberosum 2 × S. sparsipilum), were evaluated for content of α-solanine and α-chaconine (total glycoalkaloid, TGA) after field trials. In addition, tubers were assayed for TGA content after exposure to light. A detailed analysis of segregation patterns indicated that a major QTL is responsible for the TGA content in tubers of this potato population. One highly significant QTL was mapped to chromosome I of the HAG and the HAF parent. Quantitative trait loci for glycoalkaloid production in foliage of different Solanum species have previously been mapped to this chromosome. In the present research, QTLs for α-solanine and α-chaconine content were mapped to the same location as for TGA content. Similar results were observed for tubers exposed to light. The simple sequence repeat marker STM5136 was closely linked to the identified QTL. [ABSTRACT FROM AUTHOR]

Fusarium head blight (FHB) is one of the most important wheat diseases that causes yield and quality losses as well as contamination with deoxynivalenol (DON). This study aimed for marker-based introduction of three previously mapped QTLs from two German winter wheat resistance sources into an elite background unrelated to the mapping population. A double cross (DC) served as initial population that combined two resistance donor-QTL alleles from “Dream” ( Qfhs.lfl-6AL, Qfhs.lfl-7BS) and one donor-QTL allele from “G16-92” on chromosome 2BL with two high yielding, susceptible elite winter wheats (“Brando”, “LP235.1”). The initial population of 600 DC-derived F1 lines was selected with SSR markers for the respective QTLs. After two marker-selection steps, each of eight marker classes was represented by 9–22 lines possessing the respective donor-QTL allele or all possible combinations thereof in the homozygous state. The effect of the QTLs was estimated by field tests at four locations inoculated with Fusarium culmorum. Resistance was measured as the mean of multiple FHB ratings (0–100%). Marker classes incorporating only one QTL were not significantly more resistant than the class without any QTL, the combination of two donor-QTL alleles reduced FHB significantly. On average, lines with Qfhs.lfl-6AL were significantly taller than lines without this QTL. A considerable variation for FHB resistance was found in all marker classes. Marker-based introduction of two QTLs enhanced mean FHB rating by about 40 percentage points, the selected plants, however, were, on average, significantly taller. Both findings strongly support a phenotypic selection following after marker-based introduction of effective QTLs. [ABSTRACT FROM AUTHOR]

The first predominantly gene-based genetic linkage map of lentil ( Lens culinaris ssp. culinaris) was constructed using an F5 population developed from a cross between the cultivars Digger (ILL5722) and Northfield (ILL5588) using 79 intron-targeted amplified polymorphic (ITAP) and 18 genomic simple sequence repeat (SSR) markers. Linkage analysis revealed seven linkage groups (LGs) comprised of 5–25 markers that varied in length from 80.2 to 274.6 cM. The genome map spanned a total length of 928.4 cM. Clear evidence of a simple and direct macrosyntenic relationship between lentil and Medicago truncatula was observed. Sixty-six out of the 71 gene-based markers, which were previously assigned to M. truncatula genetic and physical maps, were found in regions syntenic between the Lens c. ssp. culinaris and M. truncatula genomes. However, there was evidence of moderate chromosomal rearrangements which may account for the difference in chromosome numbers between these two legume species. Eighteen common SSR markers were used to connect the current map with the most comprehensive and recent map that exists for lentil, providing the syntenic context of four important domestication traits. The composite map presented, anchored with orthologous markers mapped in M. truncatula, provides a strong foundation for the future use of genomic and genetic information in lentil genetic analysis and breeding. [ABSTRACT FROM AUTHOR]

Stigma exsertion is one of the important traits which contribute to the efficient improvement of commercial seed production in hybrid rice. In order to understand the genetic factors involved in the stigma exsertion of an indica variety—IR24—a QTL analysis was conducted using the F2 population between a japonica variety—Koshihikari—and a breeding line showing exserted stigma selected from the backcross population between IR24 as a donor and japonica varieties. As a result, a highly significant QTL ( qES3), which had been predicted in the recombinant inbred population of IR24, was confirmed at the centromeric region on chromosome 3. qES3 increases about 20% of the frequency of the exserted stigmas at the IR24 allele and explains about 32% of the total phenotypic variance. A QTL near-isogenic line for qES3 increased the frequency of the exserted stigma by 36% compared to that of Koshihikari in a field evaluation, which suggests that qES3 is a promising QTL for the development of a maternal line for hybrid rice. [ABSTRACT FROM AUTHOR]

The yellow colour of durum wheat ( Triticum turgidum L. var durum) semolina is due in part to the presence of carotenoid pigments found in the endosperm and is an important end-use quality trait. We hypothesized that variation in the genes coding for phytoene synthase ( Psy), a critical enzyme in carotenoid biosynthesis, may partially explain the phenotypic variation in endosperm colour observed among durum cultivars. Using rice sequence information, primers were designed to PCR clone and sequence the Psy genes from Kofa (high colour) and W9262-260D3 (medium colour) durum cultivars. Sequencing confirmed the presence of four Psy genes in each parent, corresponding to a two member gene family designated as Psy1-1, Psy1-2 and Psy2-1 and Psy2-2. A genetic map was constructed using 155 F1-derived doubled haploid lines from the cross W9262-260D3/Kofa with 194 simple sequence repeat and DArT® markers. Using Psy1-1 and Psy2-1 allele-specific markers and chromosome mapping, the Psy1 and Psy2 genes were located to the group 7 and 5 chromosomes, respectively. Four quantitative trait loci (QTL) underlying phenotypic variation in endosperm colour were identified on chromosomes 2A, 4B, 6B, and 7B. The Psy1-1 locus co-segregated with the 7B QTL, demonstrating an association of this gene with phenotypic variation for endosperm colour. This work is the first report of mapping Psy genes and supports the role of Psy1-1 in elevated levels of endosperm colour in durum wheat. This gene is a target for the further development of a molecular marker to enhance selection for endosperm colour in durum wheat breeding programs. [ABSTRACT FROM AUTHOR]

A genetic study is presented for traits relating to nitrogen use in wheat. Quantitative trait loci (QTLs) were established for 21 traits relating to growth, yield and leaf nitrogen (N) assimilation during grain fill in hexaploid wheat ( Triticum aestivum L.) using a mapping population from the cross Chinese Spring × SQ1. Glutamine synthetase (GS) isozymes and estimated locations of 126 genes were placed on the genetic map. QTLs for flag leaf GS activity, soluble protein, extract colour and fresh weight were found in similar regions implying shared control of leaf metabolism and leaf size. Flag leaf traits were negatively associated with days to anthesis both phenotypically and genetically, demonstrating the complex interactions of metabolism with development. One QTL cluster for GS activity co-localised with a GS2 gene mapped on chromosome 2A, and another with the mapped GSr gene on 4A. QTLs for GS activity were invariably co-localised with those for grain N, with increased activity associated with higher grain N, but with no or negative correlations with grain yield components. Peduncle N was positively correlated, and QTLs co-localised, with grain N and flag leaf N assimilatory traits, suggesting that stem N can be indicative of grain N status in wheat. A major QTL for ear number per plant was identified on chromosome 6B which was negatively co-localised with leaf fresh weight, peduncle N, grain N and grain yield. This locus is involved in processes defining the control of tiller number and consequently assimilate partitioning and deserves further examination. [ABSTRACT FROM AUTHOR]

A linkage map of Chinese cabbage ( Brassica rapa) was constructed to localize the clubroot resistance (CR) gene, Crr3. Quantitative trait loci analysis using an F3 population revealed a sharp peak in the logarithm of odds score around the sequence-tagged site (STS) marker, OPC11-2S. Therefore, this region contained Crr3. Nucleotide sequences of OPC11-2S and its proximal markers showed homology to sequences in the top arm of Arabidopsis chromosome 3, suggesting a synteny between the two species. For fine mapping of Crr3, a number of STS markers were developed based on genomic information from Arabidopsis. We obtained polymorphisms in 23 Arabidopsis-derived STS markers, 11 of which were closely linked to Crr3. The precise position of Crr3 was determined using a population of 888 F2 plants. Eighty plants showing recombination around Crr3 locus were selected and used for the mapping. A fine map of 4.74 cM was obtained, in which two markers (BrSTS-41 and BrSTS-44) and three markers (OPC11-2S, BrSTS-54 and BrSTS-61) were cosegregated. Marker genotypes of the 21 selected F2 families and CR tests of their progenies strongly suggested that the Crr3 gene is located in a 0.35 cM segment between the two markers, BrSTS-33 and BrSTS-78. [ABSTRACT FROM AUTHOR]

Rym16 Hb , a gene conferring resistance to soil-borne viruses, was introgressed from Hordeum bulbosum to barley chromosome 2HL. Mechanical inoculation with BaMMV and field tests on a plot contaminated with different viruses demonstrated that Rym16 Hb is effective against all European viruses of the soil-borne virus complex (BaMMV, BaYMV-1, -2). Genetic analysis revealed a dominant inheritance of the resistance controlled by Rym16 Hb . Using 2HL anchor markers, the size of the introgression was estimated to be about 30 M. In its proximal part, the introgression was characterized by a rearrangement of markers Xbcd266, ABC153 and ABC252, accompanied with pronounced linkage drag by factor 4 in segregating mapping populations. The introgression was found to be associated with a recessive lethality factor, l Hb , which was closely linked to the markers mentioned above. Recombination occurring within the introgressed H. bulbosum segment allowed us to separate l Hb from Rym16 Hb and to reduce the size of the introgression to 23 cM or less. [ABSTRACT FROM AUTHOR]

Avirulence of Magnaporthe grisea isolate CHL346 on rice cultivar GA25 was studied with 242 ascospore progenies derived from the cross CHL346 × CHL42. Segregation analysis of the avirulence in the progeny population was in agreement with the existence of a single avirulence ( Avr) gene, designated as AvrPi15. For mapping the Avr gene, we developed a total of 121 microsatellite DNA markers [simple sequence repeat (SSR)], which evenly distributed in the whole-genome of M. grisea through bioinformatics analysis (BIA) using the publicly available sequence. Linkage analysis of the AvrPi15 gene with these SSR markers showed that six markers on chromosome 6, MS6-1, MS6-2, MS6-3, MS6-7, MS6-8 and MS6-10, were linked to the AvrPi15 locus. To further define the chromosomal location of the AvrPi15 locus, two additional markers, MS6-17 and STS6-6, which were developed based on the sequences of telomeric region 11 (TEL11), were subjected to linkage analysis. The results showed that MS6-17 and STS6-6 were associated with the locus by 3.3 and 0.8 cM, respectively. To finely map the Avr gene, two additional candidate avirulence gene (CAG) markers, CAG6-1 and CAG6-2, were developed based on the gene annotation of the sequence of TEL 11. Linkage analysis of the Avr gene with these two markers revealed that both of them completely cosegregated with the AvrPi15 locus. Finally, this locus was physically mapped into ∼ 7.2-kb interval of the TEL11 by BIA using these sequence-ready markers. This is the key step toward positional cloning of the AvrPi15 gene. [ABSTRACT FROM AUTHOR]