QTL underlying some agronomic traits in barley detected by SNP markers

Background

Increasing the yield of barley (Hordeum vulgare L.) is a main breeding goal in developing barley cultivars. A high density genetic linkage map containing 1894 SNP and 68 SSR markers covering 1375.8 cM was constructed and used for mapping quantitative traits. A late-generation double haploid population (DH) derived from the Huaai 11 × Huadamai 6 cross was used to identify QTLs and QTL × environment interactions for ten traits affecting grain yield including length of main spike (MSL), spikelet number on main spike (SMS), spikelet number per plant (SLP), grain number per plant (GP), grain weight per plant (GWP), grain number per spike (GS), thousand grain weight (TGW), grain weight per spike (GWS), spike density (SPD) and spike number per plant (SP).

Results

In single environment analysis using composite interval mapping (CIM), a total of 221 QTLs underlying the ten traits were detected in five consecutive years (2009–2013). The QTLs detected in each year were 50, 48, 41, 41 and 41 for the year 2009 to 2013. The QTLs associated with these traits were generally clustered on chromosome 2H, 4H and 7H.

In multi-environment analysis, a total of 111 significant QTLs including 18 for MSL, 16 for SMS, 15 for SPD, 5 for SP, 4 for SLP, 14 for TGW, 5 for GP, 11 for GS, 8 for GWP, and 15 for GWS were detected in the five years. Most QTLs showed significant QTL × environment interactions (QEI), nine QTLs (qIMSL3-1, qIMSL4-1, qIMSL4-2, qIMSL6-1, qISMS7-1, qISPD2-7, qISPD7-1, qITGW3-1 and qIGWS4-3) were detected with minimal QEI effects and stable in different years. Among 111 QTLs,71 (63.40 %) QTLs were detected in both single and multiple environments.

Conclusions

Three main QTL cluster regions associated with the 10 agronomic traits on chromosome 2H, 4H and 7H were detected. The QTLs for SMS, SLP, GP and GWP were located in the region near Vrs1 on chromosome 2H. The QTLs underlying SMS, SPD and SLP were clustered on chromosome 4H. On the terminal of chromosome 7H, there was a QTL cluster associated with TGW, SPD, GWP and GWS. The information will be useful for marker-assisted selection (MAS) in barley breeding.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0409-y) contains supplementary material, which is available to authorized users.

Quantitative Trait Loci for Yield and Yield-Related Traits in Spring Barley Populations Derived from Crosses between European and Syrian Cultivars

In response to climatic changes, breeding programmes should be aimed at creating new cultivars with improved resistance to water scarcity. The objective of this study was to examine the yield potential of barley recombinant inbred lines (RILs) derived from three cross-combinations of European and Syrian spring cultivars, and to identify quantitative trait loci (QTLs) for yield-related traits in these populations. RILs were evaluated in field experiments over a period of three years (2011 to 2013) and genotyped with simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers; a genetic map for each population was constructed and then one consensus map was developed. Biological interpretation of identified QTLs was achieved by reference to Ensembl Plants barley gene space. Twelve regions in the genomes of studied RILs were distinguished after QTL analysis. Most of the QTLs were identified on the 2H chromosome, which was the hotspot region in all three populations. Syrian parental cultivars contributed alleles decreasing traits' values at majority of QTLs for grain weight, grain number, spike length and time to heading, and numerous alleles increasing stem length. The phenomic and molecular approaches distinguished the lines with an acceptable grain yield potential combining desirable features or alleles from their parents, that is, early heading from the Syrian breeding line (Cam/B1/CI08887//CI05761) and short plant stature from the European semidwarf cultivar (Maresi).

Identification of QTL underlying physiological and morphological traits of flag leaf in barley

BACKGROUND

Physiological and morphological traits of flag leaf play important roles in determining crop grain yield and biomass. In order to understand genetic basis controlling physiological and morphological traits of flag leaf, a double haploid (DH) population derived from the cross of Huaai 11 × Huadamai 6 was used to detect quantitative trait locus (QTL) underlying 7 physiological and 3 morphological traits at the pre-filling stage in year 2012 and 2013.

RESULTS

Total of 38 QTLs distributed on chromosome 1H, 2H, 3H, 4H, 6H and 7H were detected, and explained 6.53% - 31.29% phenotypic variation. The QTLs flanked by marker Bmag829 and GBM1218 on chromosome 2H were associated with net photosynthetic rate (Pn), stomatal conductance (Gs), flag leaf area (LA), flag leaf length (FLL), flag leaf width (FLW), relative chlorophyll content (SPD) and leaf nitrogen concentration (LNC).

CONCLUSION

Two QTL cluster regions associated with physiological and morphological traits, one each on the chromosome 2H and 7H, were observed. The two markers (Bmag829 and GBM1218) may be useful for marker assisted selection (MAS) in barley breeding.

A gene-derived SNP-based high resolution linkage map of carrot including the location of QTL conditioning root and leaf anthocyanin pigmentation

BACKGROUND

Purple carrots accumulate large quantities of anthocyanins in their roots and leaves. These flavonoid pigments possess antioxidant activity and are implicated in providing health benefits. Informative, saturated linkage maps associated with well characterized populations segregating for anthocyanin pigmentation have not been developed. To investigate the genetic architecture conditioning anthocyanin pigmentation we scored root color visually, quantified root anthocyanin pigments by high performance liquid chromatography in segregating F2, F3 and F4 generations of a mapping population, mapped quantitative trait loci (QTL) onto a dense gene-derived single nucleotide polymorphism (SNP)-based linkage map, and performed comparative trait mapping with two unrelated populations.

RESULTS

Root pigmentation, scored visually as presence or absence of purple coloration, segregated in a pattern consistent with a two gene model in an F2, and progeny testing of F3-F4 families confirmed the proposed genetic model. Purple petiole pigmentation was conditioned by a single dominant gene that co-segregates with one of the genes conditioning root pigmentation. Root total pigment estimate (RTPE) was scored as the percentage of the root with purple color.All five anthocyanin glycosides previously reported in carrot, as well as RTPE, varied quantitatively in the F2 population. For the purpose of QTL analysis, a high resolution gene-derived SNP-based linkage map of carrot was constructed with 894 markers covering 635.1 cM with a 1.3 cM map resolution. A total of 15 significant QTL for all anthocyanin pigments and for RTPE mapped to six chromosomes. Eight QTL with the largest phenotypic effects mapped to two regions of chromosome 3 with co-localized QTL for several anthocyanin glycosides and for RTPE. A single dominant gene conditioning anthocyanin acylation was identified and mapped.Comparative mapping with two other carrot populations segregating for purple color indicated that carrot anthocyanin pigmentation is controlled by at least three genes, in contrast to monogenic control reported previously.

CONCLUSIONS

This study generated the first high resolution gene-derived SNP-based linkage map in the Apiaceae. Two regions of chromosome 3 with co-localized QTL for all anthocyanin pigments and for RTPE, largely condition anthocyanin accumulation in carrot roots and leaves. Loci controlling root and petiole anthocyanin pigmentation differ across diverse carrot genetic backgrounds.

Development of wheat-Aegilops speltoides recombinants and simple PCR-based markers for Sr32 and a new stem rust resistance gene on the 2S#1 chromosome

Wheat- Aegilops speltoides recombinants carrying stem rust resistance genes Sr32 and SrAes1t effective against Ug99 and PCR markers for marker-assisted selection. Wild relatives of wheat are important resources for new rust resistance genes but underutilized because the valuable resistances are often linked to negative traits that prevent deployment of these genes in commercial wheats. Here, we report ph1b-induced recombinants with reduced alien chromatin derived from E.R. Sears' wheat-Aegilops speltoides 2D-2S#1 translocation line C82.2, which carries the widely effective stem rust resistance gene Sr32. Infection type assessments of the recombinants showed that the original translocation in fact carries two stem rust resistance genes, Sr32 on the short arm and a previously undescribed gene SrAes1t on the long arm of chromosome 2S#1. Recombinants with substantially shortened alien chromatin were produced for both genes, which confer resistance to stem rust races in the TTKSK (Ug99) lineage and representative races of all Australian stem rust lineages. Selected recombinants were back crossed into adapted Australian cultivars and PCR markers were developed to facilitate the incorporation of these genes into future wheat varieties. Our recombinants and those from several other labs now show that Sr32, Sr39, and SrAes7t on the short arm and Sr47 and SrAes1t on the long arm of 2S#1 form two linkage groups and at present no rust races are described that can distinguish these resistance specificities.

Marker-trait associations in Virginia Tech winter barley identified using genome-wide mapping

Genome-wide association studies (GWAS) provide an opportunity to examine the genetic architecture of quantitatively inherited traits in breeding populations. The objectives of this study were to use GWAS to identify chromosome regions governing traits of importance in six-rowed winter barley (Hordeum vulgare L.) germplasm and to identify single-nucleotide polymorphisms (SNPs) markers that can be implemented in a marker-assisted breeding program. Advanced hulled and hulless lines (329 total) were screened using 3,072 SNPs as a part of the US. Barley Coordinated Agricultural Project (CAP). Phenotypic data collected over 4 years for agronomic and food quality traits and resistance to leaf rust (caused by Puccinia hordei G. Otth), powdery mildew [caused by Blumeria graminis (DC.) E.O. Speer f. sp. hordei Em. Marchal], net blotch (caused by Pyrenophora teres), and spot blotch [caused by Cochliobolus sativus (Ito and Kuribayashi) Drechsler ex Dastur] were analyzed with SNP genotypic data in a GWAS to determine marker-trait associations. Significant SNPs associated with previously described quantitative trait loci (QTL) or genes were identified for heading date on chromosome 3H, test weight on 2H, yield on 7H, grain protein on 5H, polyphenol oxidase activity on 2H and resistance to leaf rust on 2H and 3H, powdery mildew on 1H, 2H and 4H, net blotch on 5H, and spot blotch on 7H. Novel QTL also were identified for agronomic, quality, and disease resistance traits. These SNP-trait associations provide the opportunity to directly select for QTL contributing to multiple traits in breeding programs.

Syntenic relationships between cucumber (Cucumis sativus L.) and melon (C. melo L.) chromosomes as revealed by comparative genetic mapping

BACKGROUND

Cucumber, Cucumis sativus L. (2n = 2 × = 14) and melon, C. melo L. (2n = 2 × = 24) are two important vegetable species in the genus Cucumis (family Cucurbitaceae). Both species have an Asian origin that diverged approximately nine million years ago. Cucumber is believed to have evolved from melon through chromosome fusion, but the details of this process are largely unknown. In this study, comparative genetic mapping between cucumber and melon was conducted to examine syntenic relationships of their chromosomes.

RESULTS

Using two melon mapping populations, 154 and 127 cucumber SSR markers were added onto previously reported F(2)- and RIL-based genetic maps, respectively. A consensus melon linkage map was developed through map integration, which contained 401 co-dominant markers in 12 linkage groups including 199 markers derived from the cucumber genome. Syntenic relationships between melon and cucumber chromosomes were inferred based on associations between markers on the consensus melon map and cucumber draft genome scaffolds. It was determined that cucumber Chromosome 7 was syntenic to melon Chromosome I. Cucumber Chromosomes 2 and 6 each contained genomic regions that were syntenic with melon chromosomes III+V+XI and III+VIII+XI, respectively. Likewise, cucumber Chromosomes 1, 3, 4, and 5 each was syntenic with genomic regions of two melon chromosomes previously designated as II+XII, IV+VI, VII+VIII, and IX+X, respectively. However, the marker orders in several syntenic blocks on these consensus linkage maps were not co-linear suggesting that more complicated structural changes beyond simple chromosome fusion events have occurred during the evolution of cucumber.

CONCLUSIONS

Comparative mapping conducted herein supported the hypothesis that cucumber chromosomes may be the result of chromosome fusion from a 24-chromosome progenitor species. Except for a possible inversion, cucumber Chromosome 7 has largely remained intact in the past nine million years since its divergence from melon. Meanwhile, many structural changes may have occurred during the evolution of the remaining six cucumber chromosomes. Further characterization of the genomic nature of Cucumis species closely related to cucumber and melon might provide a better understanding of the evolutionary history leading to modern cucumber.

Linkage map construction involving a reciprocal translocation

This paper is concerned with a novel statistical-genetic approach for the construction of linkage maps in populations obtained from reciprocal translocation heterozygotes of barley (Hordeum vulgare L.). Using standard linkage analysis, translocations usually lead to 'pseudo-linkage': the mixing up of markers from the chromosomes involved in the translocation into a single linkage group. Close to the translocation breakpoints recombination is severely suppressed and, as a consequence, ordering markers in those regions is not feasible. The novel strategy presented in this paper is based on (1) disentangling the "pseudo-linkage" using principal coordinate analysis, (2) separating individuals into translocated types and normal types and (3) separating markers into those close to and those more distant from the translocation breakpoints. The methods make use of a consensus map of the species involved. The final product consists of integrated linkage maps of the distal parts of the chromosomes involved in the translocation.

A second generation genetic map of the bumblebee Bombus terrestris (Linnaeus, 1758) reveals slow genome and chromosome evolution in the Apidae

Background

The bumblebee Bombus terrestris is an ecologically and economically important pollinator and has become an important biological model system. To study fundamental evolutionary questions at the genomic level, a high resolution genetic linkage map is an essential tool for analyses ranging from quantitative trait loci (QTL) mapping to genome assembly and comparative genomics. We here present a saturated linkage map and match it with the Apis mellifera genome using homologous markers. This genome-wide comparison allows insights into structural conservations and rearrangements and thus the evolution on a chromosomal level.

Results

The high density linkage map covers ~ 93% of the B. terrestris genome on 18 linkage groups (LGs) and has a length of 2'047 cM with an average marker distance of 4.02 cM. Based on a genome size of ~ 430 Mb, the recombination rate estimate is 4.76 cM/Mb. Sequence homologies of 242 homologous markers allowed to match 15 B. terrestris with A. mellifera LGs, five of them as composites. Comparing marker orders between both genomes we detect over 14% of the genome to be organized in synteny and 21% in rearranged blocks on the same homologous LG.

Conclusions

This study demonstrates that, despite the very high recombination rates of both A. mellifera and B. terrestris and a long divergence time of about 100 million years, the genomes' genetic architecture is highly conserved. This reflects a slow genome evolution in these bees. We show that data on genome organization and conserved molecular markers can be used as a powerful tool for comparative genomics and evolutionary studies, opening up new avenues of research in the Apidae.

A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

Background

Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut).

Results

A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher.

Conclusion

We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.

Genetic linkage mapping for molecular dissection of chilling requirement and budbreak in apricot (Prunus armeniaca L.)

Commercial production of apricot is severely affected by sensitivity to climatic conditions, an adaptive feature essential for cycling between vegetative or floral growth and dormancy. Yield losses are due to late winter or early spring frosts and inhibited vegetative or floral growth caused by unfulfilled chilling requirement (CR). Two apricot cultivars, Perfection and A.1740, were selected for high and low CR, respectively, to develop a mapping population of F1 individuals using a two-way pseudo-testcross mapping strategy. High-density male and female maps were constructed using, respectively, 655 and 592 markers (SSR and AFLP) spanning 550.6 and 454.9 cM with average marker intervals of 0.84 and 0.77 cM. CR was evaluated in two seasons on potted trees forced to break buds after cold treatments ranging from 100 to 900 h. A total of 12 putative CR quantitative trait loci (QTLs) were detected on six linkage groups using composite interval mapping and a simultaneous multiple regression fit. QTL main effects of additive and additive x additive interactions accounted for 58.5% +/- 6.7% and 66.1% +/- 5.8% of the total phenotypic variance in the Perfection and A.1740 maps, respectively. We report two apricot high-density maps and QTLs corresponding to map positions of differentially expressed transcripts and suggested candidate genes controlling CR.

A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome

BACKGROUND

The construction of genetic linkage maps for cultivated peanut (Arachis hypogaea L.) has and continues to be an important research goal to facilitate quantitative trait locus (QTL) analysis and gene tagging for use in a marker-assisted selection in breeding. Even though a few maps have been developed, they were constructed using diploid or interspecific tetraploid populations. The most recently published intra-specific map was constructed from the cross of cultivated peanuts, in which only 135 simple sequence repeat (SSR) markers were sparsely populated in 22 linkage groups. The more detailed linkage map with sufficient markers is necessary to be feasible for QTL identification and marker-assisted selection. The objective of this study was to construct a genetic linkage map of cultivated peanut using simple sequence repeat (SSR) markers derived primarily from peanut genomic sequences, expressed sequence tags (ESTs), and by "data mining" sequences released in GenBank.

RESULTS

Three recombinant inbred lines (RILs) populations were constructed from three crosses with one common female parental line Yueyou 13, a high yielding Spanish market type. The four parents were screened with 1044 primer pairs designed to amplify SSRs and 901 primer pairs produced clear PCR products. Of the 901 primer pairs, 146, 124 and 64 primer pairs (markers) were polymorphic in these populations, respectively, and used in genotyping these RIL populations. Individual linkage maps were constructed from each of the three populations and a composite map based on 93 common loci were created using JoinMap. The composite linkage maps consist of 22 composite linkage groups (LG) with 175 SSR markers (including 47 SSRs on the published AA genome maps), representing the 20 chromosomes of A. hypogaea. The total composite map length is 885.4 cM, with an average marker density of 5.8 cM. Segregation distortion in the 3 populations was 23.0%, 13.5% and 7.8% of the markers, respectively. These distorted loci tended to cluster on LG1, LG3, LG4 and LG5. There were only 15 EST-SSR markers mapped due to low polymorphism. By comparison, there were potential synteny, collinear order of some markers and conservation of collinear linkage groups among the maps and with the AA genome but not fully conservative.

CONCLUSION

A composite linkage map was constructed from three individual mapping populations with 175 SSR markers in 22 composite linkage groups. This composite genetic linkage map is among the first "true" tetraploid peanut maps produced. This map also consists of 47 SSRs that have been used in the published AA genome maps, and could be used in comparative mapping studies. The primers described in this study are PCR-based markers, which are easy to share for genetic mapping in peanuts. All 1044 primer pairs are provided as additional files and the three RIL populations will be made available to public upon request for quantitative trait loci (QTL) analysis and linkage map improvement.

Multipoint-likelihood maximization mapping on 4 segregating populations to achieve an integrated framework map for QTL analysis in pot azalea (Rhododendron simsii hybrids)

Background

Azalea (Rhododendron simsii hybrids) is the most important flowering pot plant produced in Belgium, being exported world-wide. In the breeding program, flower color is the main feature for selection, only in later stages cultivation related plant quality traits are evaluated. As a result, plants with attractive flowering are kept too long in the breeding cycle. The inheritance of flower color has been well studied; information on the heritability of cultivation related quality traits is lacking. For this purpose, QTL mapping in diverse genetic backgrounds appeared to be a must and therefore 4 mapping populations were made and analyzed.

Results

An integrated framework map on four individual linkage maps in Rhododendron simsii hybrids was constructed. For genotyping, mainly dominant scored AFLP (on average 364 per population) and MYB-based markers (15) were combined with co-dominant SSR (23) and EST markers (12). Linkage groups were estimated in JoinMap. A consensus grouping for the 4 mapping populations was made and applied in each individual mapping population. Finally, 16 stable linkage groups were set for the 4 populations; the azalea chromosome number being 13. A combination of regression mapping (JoinMap) and multipoint-likelihood maximization (Carthagène) enabled the construction of 4 maps and their alignment. A large portion of loci (43%) was common to at least two populations and could therefore serve as bridging markers. The different steps taken for map optimization and integration into a reference framework map for QTL mapping are discussed.

Conclusions

This is the first map of azalea up to our knowledge. AFLP and SSR markers are used as a reference backbone and functional markers (EST and MYB) were added as candidate genes for QTL analysis. The alignment of the 4 maps on the basis of framework markers will facilitate in turn the alignment of QTL regions detected in each of the populations. The approach we took is thoroughly different than the recently published integrated maps and well-suited for mapping in a non-model crop.

The construction of a genetic linkage map of non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino)

Non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino) is one of the most important vegetables in eastern China. A genetic linkage map was constructed using 127 doubled haploid (DH) lines, and the DH population was derived from a commercial hybrid "Hanxiao" (lines SW-13 x L-118). Out of the 614 polymorphic markers, 43.49% were not assigned to any of the linkage groups(LGs). Chi-square tests showed that 42.67% markers were distorted from expected Mendelian segregation ratios, and the direction of distorted segregation was mainly toward the paternal parent L-118. After sequentially removing the markers that had an interval distance smaller than 1 cM from the upper marker, the overall quality of the linkage map was increased. Two hundred and sixty-eight molecular markers were mapped into 10 LGs, which were anchored to the corresponding chromosome of the B. rapa reference map based on common simple sequence repeat (SSR) markers. The map covers 973.38 cM of the genome and the average interval distance between markers was 3.63 cM. The number of markers on each LG ranged from 18 (R08) to 64 (R07), with an average interval distance within a single LG from 1.70 cM (R07) to 6.71 cM (R06). Among these mapped markers, 169 were sequence-related amplified polymorphism (SRAP) molecular markers, 50 were SSR markers and 49 were random amplification polymorphic DNA (RAPD) markers. With further saturation to the LG, the current map offers a genetic tool for loci analysis for important agronomic traits.

A consensus linkage map identifies genomic regions controlling fruit maturity and beta-carotene-associated flesh color in melon (Cucumis melo L.)

The nutritional value and yield potential of US Western Shipping melon (USWS; Cucumis melo L.) could be improved through the introgression of genes for early fruit maturity (FM) and the enhancement of the quantity of beta-carotene (QbetaC) in fruit mesocarp (i.e., flesh color). Therefore, a set of 116 F(3) families derived from the monoecious, early FM Chinese line 'Q 3-2-2' (no beta-carotene, white mesocarp) and the andromonoecious, late FM USWS line 'Top Mark' (possessing beta-carotene, orange mesocarp) were examined during 2 years in Wisconsin, USA to identify quantitative trait loci (QTL) associated with FM and QbetaC. A 171-point F(2-3) based map was constructed and used for QTL analysis. Three QTL associated with QbetaC were detected, which explained a significant portion of the observed phenotypic variation (flesh color; R (2) = 4.0-50.0%). The map position of one QTL (beta-carM.E.9.1) was uniformly aligned with one carotenoid-related gene (Orange gene), suggesting its likely role in QbetaC in this melon population and putative relationship with the melon white flesh (wf) gene. Two major (FM.6.1 and FM.11.1; R (2) >or= 20%) and one minor QTL (FM.2.1; R (2) = 8%) were found to be associated with FM. This map was then merged with a previous recombinant inbred line (RIL)-based map used to identify seven QTL associated with QbetaC in melon fruit. This consensus map [300 molecular markers (187 co-dominant melon and 14 interspecific; 10 LG)] provides a framework for the further dissection and cloning of published QTL, which will consequently lead to more effective trait introgression in melon.

A new interspecific, Gossypium hirsutum x G. barbadense, RIL population: towards a unified consensus linkage map of tetraploid cotton

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 BC(1) 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 BC(1) 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 BC(1)-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.

A reference integrated map for cultivated grapevine (Vitis vinifera L.) from three crosses, based on 283 SSR and 501 SNP-based markers

We have developed an integrated map from five elite cultivars of Vitis vinifera L.; Syrah, Pinot Noir, Grenache, Cabernet Sauvignon and Riesling which are parents of three segregating populations. A new source of markers, SNPs, identified in ESTs and unique BAC-end sequences was added to the available IGGP reference set of SSRs. The complete integrated map comprises 1,134 markers (350 AFLP, 332 BESs, 169 ESTs, 283 SSRs) spanning 1,443 cM over 19 linkage groups and shows a mean distance between neighbouring loci of 1.27 cM. Marker order was mainly conserved between the integrated map and the highly dense SyrahxPinot Noir consensus map except for few inversions. Moreover, the marker order has been validated through the assembled genome sequence of Pinot Noir. We have also assessed the transferability of SNP-based markers among five V. vinifera varieties, enabling marker validation across different genotypes. This integrated map can serve as a fundamental tool for molecular breeding in V. vinifera and related species and provide a basis for studies of genome organization and evolution in grapevines.

Dissection of the barley 2L1.0 region carrying the 'Laevigatum' quantitative resistance gene to leaf rust using near-isogenic lines (NIL) and subNIL

Partial resistance to leaf rust (Puccinia hordei G. H. Otth) in barley is a quantitative resistance that is not based on hypersensitivity. This resistance hampers haustorium formation, resulting in a long latency period in greenhouse tests. The three most consistent quantitative trait loci (QTL) uncovered in the L94 x 'Vada' mapping population were introgressed by marker-assisted backcrossing into the susceptible L94 background to obtain near-isogenic lines (NIL). We also developed the reciprocal Vada-NIL for the susceptibility alleles of those QTL. The QTL Rphq2 affected latency period of P. hordei more than the QTL Rphq3 and Rphq4. The NIL confirmed the contribution of Rphq2 to partial resistance by prolonging the latency period by 28 h on L94-Rphq2 and shortening the latency period by 23 h on Vada-rphq2. On the basis of flanking restriction fragment length polymorphism-based markers, Rphq2 appeared to be located near the telomeric end of the long arm of chromosome 2H, in a physical region of high recombination, making it the target QTL for map-based cloning. Microscopic observations on the NIL confirmed the nonhypersensitive nature of the resistance conferred by Rphq2. A high-resolution genetic map of the Rphq2 region was constructed using a population of 38 subNIL with overlapping L94 introgressions in Vada background across the region. Rphq2 mapped approximately 2 centimorgans (cM) proximal from the MlLa locus. By bulked segregant analysis and use of synteny with rice, we developed additional markers and fine-mapped Rphq2 to a genetic interval of 0.11 cM that corresponds to a stretch of sequence of, at most, 70 kb in rice. Analysis of this rice sequence revealed predicted genes encoding two proteins with unknown function, retrotransposon proteins, peroxidase proteins, and a protein similar to a mitogen-activated protein kinase kinase kinase (MAP3K). Possible homologs of those peroxidases and MAP3K in barley are candidates for the gene that contributes to partial resistance to P. hordei.

A high-density, integrated genetic linkage map of lettuce (Lactuca spp.)

An integrated map for lettuce comprising of 2,744 markers was developed from seven intra- and inter-specific mapping populations. A total of 560 markers that segregated in two or more populations were used to align the individual maps. 2,073 AFLP, 152 RFLP, 130 SSR, and 360 RAPD as well as 29 other markers were assigned to nine chromosomal linkage groups that spanned a total of 1,505 cM and ranged from 136 to 238 cM. The maximum interval between markers in the integrated map is 43 cM and the mean interval is 0.7 cM. The majority of markers segregated close to Mendelian expectations in the intra-specific crosses. In the two L. saligna x L. sativa inter-specific crosses, a total of 155 and 116 markers in 13 regions exhibited significant segregation distortion. Data visualization tools were developed to curate, display and query the data. The integrated map provides a framework for mapping ESTs in one core mapping population relative to phenotypes that segregate in other populations. It also provides large numbers of markers for marker assisted selection, candidate gene identification, and studies of genome evolution in the Compositae.

The reference genetic linkage map for the multinational Brassica rapa genome sequencing project

We describe the construction of a reference genetic linkage map for the Brassica A genome, which will form the backbone for anchoring sequence contigs for the Multinational Brassica rapa Genome Sequencing Project. Seventy-eight doubled haploid lines derived from anther culture of the F(1) of a cross between two diverse Chinese cabbage (B. rapa ssp. pekinensis) inbred lines, 'Chiifu-401-42' (C) and 'Kenshin-402-43' (K) were used to construct the map. The map comprises a total of 556 markers, including 278 AFLP, 235 SSR, 25 RAPD and 18 ESTP, STS and CAPS markers. Ten linkage groups were identified and designated as R1-R10 through alignment and orientation using SSR markers in common with existing B. napus reference linkage maps. The total length of the linkage map was 1,182 cM with an average interval of 2.83 cM between adjacent loci. The length of linkage groups ranged from 81 to 161 cM for R04 and R06, respectively. The use of 235 SSR markers allowed us to align the A-genome chromosomes of B. napus with those of B. rapa ssp. pekinensis. The development of this map is vital to the integration of genome sequence and genetic information and will enable the international research community to share resources and data for the improvement of B. rapa and other cultivated Brassica species.

Linkage maps for Arabidopsis lyrata subsp. lyrata and Arabidopsis lyrata subsp. petraea combining anonymous and Arabidopsis thaliana-derived markers

Arabidopsis lyrata, a close relative of the model plant Arabidopsis thaliana, is 1 of a few plant species for which the genome is to be entirely sequenced, which promises to yield important insights into genome evolution. Only 2 sparse linkage maps have been published, and these were based solely on markers derived from the A. thaliana genome. Because the genome of A. lyrata is practically twice as large as that of A. thaliana, the extent of map coverage of the A. lyrata genome remains uncertain. In this study, a 2-way pseudo-testcross strategy was used to construct genetic linkage maps of A. lyrata subsp. petraea and A. lyrata subsp. lyrata, using simple sequence repeat (SSR) and cleaved amplified polymorphic sequence (CAPS) markers from the A. thaliana genome, and anonymous amplified fragment length polymorphism (AFLP) markers that could potentially uncover regions unique to the A. lyrata genome. The SSR and CAPS markers largely confirmed the relationships between linkage groups in A. lyrata and A. thaliana. AFLP markers slightly increased the coverage of the A. lyrata maps, but mostly increased marker density on the linkage groups. We noted a much lower level of polymorphism and a greater segregation distortion in A. lyrata subsp. lyrata markers. The implications of these findings for the sequencing of the A. lyrata genome are discussed.

A high density barley microsatellite consensus map with 775 SSR loci

A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations 'Igri x Franka', 'Steptoe x Morex', 'OWB(Rec) x OWB(Dom)', 'Lina x Canada Park', 'L94 x Vada' and 'SusPtrit x Vada'. Segregation data for microsatellite markers from different research groups including SCRI (Bmac, Bmag, EBmac, EBmag, HVGeneName, scsssr), IPK (GBM, GBMS), WUR (GBM), Virginia Polytechnic Institute (HVM), and MPI for Plant Breeding (HVGeneName), generated in above mapping populations, were used in the computer program RECORD to order the markers of the individual linkage data sets. Subsequently, a framework map was constructed for each chromosome by integrating the 496 "bridge markers" common to two or more individual maps with the help of the computer programme JoinMap 3.0. The final map was calculated by following a "neighbours" map approach. The integrated map contained 775 unique microsatellite loci, from 688 primer pairs, ranging from 93 (6H) to 132 (2H) and with an average of 111 markers per linkage group. The genomic DNA-derived SSR marker loci had a higher polymorphism information content value (average 0.61) as compared to the EST/gene-derived SSR loci (average 0.48). The consensus map spans 1,068 cM providing an average density of one SSR marker every 1.38 cM. Such a high-density consensus SSR map provides barley molecular breeding programmes with a better choice regarding the quality of markers and a higher probability of polymorphic markers in an important chromosomal interval. This map also offers the possibilities of thorough alignment for the (future) physical map and implementation in haplotype diversity studies of barley.

A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defence gene homologues

A consensus map of barley was constructed based on three reference doubled haploid (DH) populations and three recombinant inbred line (RIL) populations. Several sets of microsatellites were used as bridge markers in the integration of those populations previously genotyped with RFLP or with AFLP markers. Another set of 61 genic microsatellites was mapped for the first time using a newly developed fluorescent labelling strategy, referred to as A/T labelling. The final map contains 3,258 markers spanning 1,081 centiMorgans (cM) with an average distance between two adjacent loci of 0.33 cM. This is the highest density of markers reported for a barley genetic map to date. The consensus map was divided into 210 BINs of about 5 cM each in which were placed 19 quantitative trait loci (QTL) contributing to the partial resistance to barley leaf rust (Puccinia hordei Otth) in five of the integrated populations. Each parental barley combination segregated for different sets of QTLs, with only few QTLs shared by any pair of cultivars. Defence gene homologues (DGH) were identified by tBlastx homology to known genes involved in the defence of plants against microbial pathogens. Sixty-three DGHs were located into the 210 BINs in order to identify candidate genes responsible for the QTL effects. Eight BINs were co-occupied by a QTL and DGH(s). The positional candidates identified are receptor-like kinase, WIR1 homologues and several defence response genes like peroxidases, superoxide dismutase and thaumatin.

The genetics of nitrogen use in hexaploid wheat: N utilisation, development and yield

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 x 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.

The genetic map of finger millet, Eleusine coracana

Restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), expressed-sequenced tag (EST), and simple sequence repeat (SSR) markers were used to generate a genetic map of the tetraploid finger millet (Eleusine coracana subsp. coracana) genome (2n = 4x = 36). Because levels of variation in finger millet are low, the map was generated in an inter-subspecific F(2) population from a cross between E. coracana subsp. coracana cv. Okhale-1 and its wild progenitor E. coracana subsp. africana acc. MD-20. Duplicated loci were used to identify homoeologous groups. Assignment of linkage groups to the A and B genome was done by comparing the hybridization patterns of probes in Okhale-1, MD-20, and Eleusine indica acc. MD-36. E. indica is the A genome donor to E. coracana. The maps span 721 cM on the A genome and 787 cM on the B genome and cover all 18 finger millet chromosomes, at least partially. To facilitate the use of marker-assisted selection in finger millet, a first set of 82 SSR markers was developed. The SSRs were identified in small-insert genomic libraries generated using methylation-sensitive restriction enzymes. Thirty-one of the SSRs were mapped. Application of the maps and markers in hybridization-based breeding programs will expedite the improvement of finger millet.

Mapping of major spot-type and net-type net-blotch resistance genes in the Ethiopian barley line CI 9819

Net blotch of barley ( Hordeum vulgare L.), caused by the fungal phytopathogen Pyrenophora teres Drechs. f. teres Smedeg., constitutes one of the most serious constraints to barley production worldwide. Two forms of the disease, the net form, caused by P. teres f. teres, and the spot form, caused by P. teres f. maculata, are differentiated by the type of symptoms on leaves. Several barley lines with major gene resistance to net blotch have been identified. Earlier, one of these was mapped in the Rolfi × CI 9819 cross to barley chromosome 6H, using a mixture of 4 Finnish isolates of P. teres f. teres. In this study, we used the same barley progeny to map resistance to 4 spot-type isolates and 4 net-type isolates of P. teres. With all net-type isolates, a major resistance gene was located on chromosome 6H, in the same position as described previously, explaining up to 88% of the phenotypic variation in infection response in the progeny. We designate this gene Rpt5. Several minor resistance genes were located on chromosomes 1H, 2H, 3H, 5H, and 7H. These minor genes were not genuinely isolate-specific, but their effect varied among isolates and experiments. When the spot-type isolates were used for infection, a major isolate-specific resistance gene was located on chromosome 5H, close to microsatellite marker HVLEU, explaining up to 84% of the phenotypic variation in infection response in the progeny. We designate this gene Rpt6. No minor gene effects were detected in spot-type isolates. The Ethiopian 2-rowed barley line CI 9819 thus carries at least 2 independent major genes for net-blotch resistance: Rpt5, active against net-type isolates; and Rpt6, active against specific spot-type isolates.

Mapping of Rym16Hb, the second soil-borne virus-resistance gene introgressed from Hordeum bulbosum

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.

A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits

BACKGROUND

Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers.

RESULTS

The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 +/- 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 +/- 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits.

CONCLUSION

Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations.

A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits

BACKGROUND

Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers.

RESULTS

The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 +/- 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 +/- 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits.

CONCLUSION

Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations.

Molecular mapping of Loci conferring resistance to different pathotypes of the spot blotch pathogen in barley

ABSTRACT Spot blotch, caused by Cochliobolus sativus, is an important disease of barley in many production areas and is best controlled through the deployment of resistant cultivars. Information on the genetics of resistance in various sources can be useful in developing effective breeding strategies. Parents of the doubled haploid mapping population Calicuchima-sib/ Bowman-BC (C/B) exhibit a differential reaction to pathotypes 1 and 2 of C. sativus. To elucidate the genetics of spot blotch resistance in this population, C/B progeny were evaluated with both pathotypes at the seedling stage in the greenhouse and at the adult plant stage in the field. At the seedling stage, progeny segregated 84 resistant to 26 susceptible based on the qualitative analysis of infection response (IR) data to pathotype 1. This fit best to a 3:1 ratio, indicating that two genes were involved in conferring resistance. Quantitative analysis of the raw IR data to pathotype 1 revealed a single quantitative trait locus (QTL) on chromosome 4(4H) explaining 14% of the phenotypic variance. Adult plant resistance to pathotype 1 was conferred by QTL on chromosome 2(2H) and chromosome 3(3H), explaining 21 and 32% of the phenotypic variation, respectively. Bowman contributed the resistance alleles on chromosome 3(3H) and chromosome 4(4H), whereas Calicuchima-sib contributed the resistance allele on chromosome 2(2H). Resistance to pathotype 2 was conferred by a single gene (designated Rcs6) on chromosome 5(1H) based on qualitative analysis of data. Rcs6 was effective at both the seedling and adult plant stages and was contributed by Calicuchima-sib. This result was corroborated in the quantitative analysis of raw IR (seedling stage) and disease severity (adult plant stage) data as a single major effect (r(2) = 0.93 and 0.88, respectively) QTL was identified on chromosome 5(1H). Progeny with resistance to both pathotypes were identified in the C/B population and may be useful in programs breeding for spot blotch resistance.

Candidate genes for barley mutants involved in plant architecture: an in silico approach

To individuate candidate genes (CGs) for a set of barley developmental mutants, a synteny approach comparing the genomes of barley and rice has been introduced. Based on map positions of mutants, sequenced RFLP markers linked to the target loci were selected. The markers were mapped in silico by BLAST searches against the rice genome sequence and chromosomal regions syntenous to barley target intervals were identified. Rice syntenous regions were defined for 15 barley chromosomal intervals hosting 23 mutant loci affecting plant height (brh1; brh2; sld4), shoot and inflorescence branching (als; brc1; cul-2, -3, -5, -15, -16; dub1; mnd6; vrs1), development of leaves (lig) and leaf-like organs (cal-b19, -C15, -d4; lks5; suKD-25; suKE-74; suKF-76; trd; trp). Annotation of 110 Mb of rice genomic sequence made it possible to screen for putative CGs which are listed together with the reasons supporting mutant-gene associations. For two loci, CGs were identified with a clear probability to represent the locus considered. These include FRIZZY PANICLE, a candidate for the brc1 barley mutant, and the rice ortholog of maize Liguleless1 (Lg1), a candidate for the barley lig locus on chromosome 2H. For this locus, the validity of the approach was supported by the PCR-amplification of a genomic fragment of the orthologous barley sequence. SNP mapping located this fragment on chromosome 2H in the region hosting the lig genetic locus.

Map-based analysis of genes affecting the brittle rachis character in tetraploid wheat (Triticum turgidum L.)

The mature spike rachis of wild emmer [Triticum turgidum L. ssp. dicoccoides (Körn. ex Asch. and Graebner) Thell.] disarticulates spontaneously between each spikelet leading to the dispersion of wedge-type diaspores. By contrast, the spike rachis of domesticated emmer (Triticum turgidum L. ssp. turgidum) fails to disarticulate and remains intact until it is harvested. This major distinguishing feature between wild and domesticated emmer is controlled by two major genes, brittle rachis 2 (Br-A2) and brittle rachis 3 (Br-A3) on the short arms of chromosomes 3A and 3B, respectively. Because of their biological and agricultural importance, a map-based analysis of these genes was undertaken. Using two recombinant inbred chromosome line (RICL) populations, Br-A2, on chromosome 3A, was localized to a approximately 11-cM region between Xgwm2 and a cluster of linked loci (Xgwm666.1, Xbarc19, Xcfa2164, Xbarc356, and Xgwm674), whereas Br-A3, on chromosome 3B, was localized to a approximately 24-cM interval between Xbarc218 and Xwmc777. Comparative mapping analyses suggested that both Br-A2 and Br-A3 were present in homologous regions on chromosomes 3A and 3B, respectively. Furthermore, Br-A2 and Br-A3 from wheat and Btr1/Btr2 on chromosome 3H of barley (Hordeum vulgare L.) also were homologous suggesting that the location of major determinants of the brittle rachis trait in these species has been conserved. On the other hand, brittle rachis loci of wheat and barley, and a shattering locus on rice chromosome 1 did not appear to be orthologous. Linkage and deletion-based bin mapping comparisons suggested that Br-A2 and Br-A3 may reside in chromosomal areas where the estimated frequency of recombination was approximately 4.3 Mb/cM. These estimates indicated that the cloning of Br-A2 and Br-A3 using map-based methods would be extremely challenging.

Quantitative trait loci controlling vernalisation requirement, heading time and number of panicles in meadow fescue (Festuca pratensis Huds.)

The "BF14/16xHF2/7" mapping population of meadow fescue (Festuca pratensis Huds.) was characterised for number of panicles produced by non-vernalised plants in the field, vernalisation requirement (number of weeks at 6 degrees C and 8 h photoperiod), as well as days to heading, number of panicles and proportion of shoots heading after a 12 weeks vernalisation treatment. Quantitative trait loci (QTLs) were identified and compared to QTLs and genes related to the induction of flowering in cereals and grasses. A region on chromosome 1F affected days to heading and the proportion of shoots heading. Chromosome 4F appeared to have several genes with a strong effect on vernalisation requirement. The strongest effects were located in the proximal end of 4F and may correspond to the earliness per se (eps) QTL eps6L.2 in barley and a heading time QTL in perennial ryegrass. A part of the meadow fescue orthologue of VRN1 was sequenced and mapped to another region of 4F that also had a strong effect on vernalisation requirement. The proximal end of chromosome 5F had QTLs for days to heading and proportion of heading shoots. Syntenic regions in wheat and barley contain eps-loci. A QTL for number of panicles in the field and a QTL for proportion of heading shoots were present on chromosome 6. A region on 7F affected the variation in number of panicles among plants without a vernalisation requirement, and is syntenic to regions in perennial ryegrass, barley and rice containing orthologues of Arabidopsis thaliana CO.

Comprehensive genetic analyses reveal differential expression of spot blotch resistance in four populations of barley

Spot blotch, caused by Cochliobolus sativus, is an important disease of barley in the Upper Midwest region of the United States. The resistance of six-rowed malting cultivars like Morex has remained effective for over 40 years and is considered durable. Previous research on Steptoe/Morex (S/M), a 6x6-rowed doubled haploid (DH) population, showed that seedling resistance is controlled by a single gene (Rcs5) on chromosome 1(7H) and adult plant resistance by two quantitative trait loci (QTL): one of the major effect on chromosome 5(1H) explaining 62% of the phenotypic variance and a second of minor effect on chromosome 1(7H) explaining 9% of the phenotypic variance. To corroborate these results in a 2x6-rowed DH population, composite interval mapping (CIM) was performed on Harrington/Morex (H/M). As in the S/M population, a single major gene (presumably Rcs5) on chromosome 1(7H) conferred resistance at the seedling stage. However, at the adult plant stage, the results were markedly different as no chromosome 5(1H) effect whatsoever was detected. Instead, a QTL at or near Rcs5 on chromosome 1(7H) explained nearly all of the phenotypic variance (75%) for disease severity. To determine whether this result might be due to the genetic background of the two-rowed susceptible parent Harrington, we analyzed another DH population that included the same resistance donor (Morex) and another six-rowed susceptible cultivar Dicktoo (D/M). Three QTL conferred seedling resistance in the D/M population: one near Rcs5 on chromosome 1(7H) explaining 30%, a second near the centromere of chromosome 1(7H) explaining 9%, and a third on the short arm of chromosome 3(3H) explaining 19% of the phenotypic variation. As in the H/M population, no chromosome 5(1H) QTL was detected for adult plant resistance in the D/M population. Instead, three QTL on other chromosomes explained most of the variation: one on the short arm of chromosome 3(3H) explaining 36%, a second on the long arm of chromosome 3(3H) explaining 11%, and a third at or near Rcs5 on chromosome 1(7H) explaining 20% of the phenotypic variation. These data demonstrate the complexity of expression of spot blotch resistance in different populations and have important implications in breeding for durable resistance.

A composite linkage map from two crosses for the species complex Picea mariana x Picea rubens and analysis of synteny with other Pinaceae

Four individual linkage maps were constructed from two crosses for the species complex Picea mariana (Mill.) B.S.P. x Picea rubens Sarg in order to integrate their information into a composite map and to compare with other Pinaceae. For all individual linkage maps, 12 major linkage groups were recovered with 306 markers per map on average. Before building the composite linkage map, the common male parent between the two crosses made it possible to construct a reference linkage map to validate the relative position of homologous markers. The final composite map had a length of 2,319 cM (Haldane) and contained a total of 1,124 positioned markers, including 1,014 AFLPs, 3 RAPDs, 53 SSRs, and 54 ESTPs, assembled into 12 major linkage groups. Marker density of the composite map was statistically homogenous and was much higher (one marker every 2.1 cM) than that of the individual linkage maps (one marker every 5.7 to 7.1 cM). Synteny was well conserved between individual, reference, and composite linkage maps and 94% of homologous markers were colinear between the reference and composite maps. The combined information from the two crosses increased by about 24% the number of anchor markers compared to the information from any single cross. With a total number of 107 anchor markers (SSRs and ESTPs), the composite linkage map is a useful starting point for large-scale genome comparisons at the intergeneric level in the Pinaceae. Comparisons of this map with those in Pinus and Pseudotsuga allowed the identification of one breakdown in synteny where one linkage group homologous to both Picea and Pinus corresponded to two linkage groups in Pseudotsuga. Implications for the evolution of the Pinaceae genome are discussed.

Microsatellite and AFLP markers in the Prunus persica [L. (Batsch)]xP. ferganensis BC(1)linkage map: saturation and coverage improvement

A set of 146 single sequence repeats (SSRs) and 14 amplified fragment length polymorphism (AFLP) primer combinations were used to enrich a previously developed linkage map obtained from a (Prunus persicaxP. ferganensis)xP. persica BC(1) progeny. Forty-one SSR primer pairs gave polymorphic patterns detecting 42 loci. The restriction/selective primer AFLP combinations produced a total of 79 segregating fragments. The resulting map is composed of 216 loci covering 665 cM with an average distance of 3.1 cM. Novel regions were covered by the newly mapped loci for a total of 159 cM. Eight linkage groups were assembled instead of the earlier 10 as two small groups (G1a and G8b), previously independent, were joined to their respective major groups (G1b and G8a). Several gaps were also reduced resulting in an improved saturation of the map. Twelve gaps >or=10 cm are still present. A comparative analysis against the Prunus reference map (71 anchor loci) pointed out an almost complete synteny and colinearity. Six loci were not syntenic and only two were not colinear. Genetic distances were significantly longer in our map than in the reference one.

Approaching the self-incompatibility locus Z in rye (Secale cereale L.) via comparative genetics

Using barley and wheat expressed sequence tags as well as rice genomic sequence and mapping information, we revisited the genomic region encompassing the self-incompatibility (SI) locus Z on rye chromosome 2RL applying a comparative approach. We were able to arrange 12 novel sequence-tagged site (STS) markers around Z, spanning a genetic distance of 32.3 cM, with the closest flanking markers mapping at a distance of 0.5 cM and 1.0 cM from Z, respectively, and one marker cosegregating with Z, in a testcross population of 204 progeny. Two overlapping rice bacterial artifical chromosomes (BACs), OSJNBa0070O11 and OSJNBa0010D21, were found to carry rice orthologs of the three rye STS markers from the 1.5-cM interval encompassing Z. The STS-marker orthologs on these rice BACs span less than 125,000 bp of the rice genome. The STS marker TC116908 cosegregated with Z in a mapping population and revealed a high degree of polymorphism among a random sample of rye plants of various origin. TC116908 was shown via Southern hybridization to correspond to gene no. 10 (OSJNBa0070O11.10) on rice BAC OSJNBa0070O11. Reverse transcription-PCR with a TC116908-specific primer pair resulted in the amplification of a fragment of the expected size from the rye pistil but not from leaf cDNA. OSJNBa0070O11.10 was found to show a highly significant sequence similarity to AtUBP22, a ubiquitin-specific protease (UBP). TC116908 likely represents a putative UBP gene that is specifically expressed in rye pistils and cosegregates with Z. Given that the ubiquitination of proteins is emerging as a general mechanism involved in different SI systems of plants, TC116908 appears to be a promising target for further investigation with respect to its relation to the SI system of the grasses.

Molecular cytogenetic identification of nullisomy 5B induced homoeologous recombination between wheat chromosome 5D and barley chromosome 5H

Chromosome 5H of Hordeum vulgare 'New Golden' (NG) carries a gene(s) that accelerates heading in a wheat background. To introduce the early heading gene(s) of NG barley into the wheat genome, we attempted to induce homoeologous recombination between wheat and NG 5H chromosomes by 5B nullisomy. A nullisomic 5B, trisomic 5A, monosomic 5H plant (2n = 42) was produced from systematic crosses between aneuploid stocks of wheat group 5 chromosomes. A total of 656 F2 plants produced by self-fertilization were screened for recombinants by a PCR assay with 3 5H-specific amplicon markers. Twelve plants (1.8%) were selected as putative wheat-barley 5H recombinants. Five of them were inviable or sterile and the remaining 7 were fertile and subjected to the progeny test. Cytological analyses using fluorescence in situ hybridization and C-banding revealed that 6 of the 7 progeny lines are true homoeologous recombinants between the long arms of chromosomes 5D and 5H, but that the other one was not a recombinant having an aberrant barley telosome. The 6 cytologically confirmed recombinant lines included only 2 types (3 lines each), which were reciprocal products derived from exchanges at the same distal interval defined by two flanking markers. One type had a small 5HL segment translocated to the 5DL terminal, and the other type had a small terminal 5DL segment translocated to the 5HL terminal. In the latter type, the physical length of translocated barley segments slightly differed among lines. Homoeologous recombinants obtained in this study should be useful for further chromosome manipulation to introgress a small interstitial 5HL chromosome segment with the early heading gene(s) to wheat. Preferential occurrence of restricted types of recombinants is discussed in relation to homoeologous relationships between wheat and barley chromosomes.

Construction of an integrated map of rose with AFLP, SSR, PK, RGA, RFLP, SCAR and morphological markers

A high-density genetic map with a number of anchor markers has been created to be used as a tool to dissect genetic variation in rose. Linkage maps for the diploid 94/1 population consisting of 88 individuals were constructed using a total of 520 molecular markers including AFLP, SSR, PK, RGA, RFLP, SCAR and morphological markers. Seven linkage groups, putatively corresponding to the seven haploid rose chromosomes, were identified for each parent, spanning 487 cM and 490 cM, respectively. The average length of 70 cM may cover more than 90% of the rose genome. An integrated map was constructed by incorporating the homologous parental linkage groups, resulting in seven linkage groups with a total length of 545 cM. The present linkage map is currently the most advanced map in rose with regard to marker density, genome coverage and with robust markers, giving good perspectives for QTL mapping and marker-assisted breeding in rose. The SSR markers, together with RFLP markers, provide good anchor points for future map alignment studies in rose and related species. Codominantly scored AFLP markers were helpful in the integration of the parental maps.

Resistance to barley scald (Rhynchosporium secalis) in the Ethiopian donor lines ‘Steudelli’ and ‘Jet’, analyzed by partial least squares regression and interval mapping

The resistance of barley (Hordeum vulgare L.) to Rhynchosporium secalis (scald) has been investigated in two crosses between the susceptible cv. 'Ingrid' and two resistant Ethiopian landraces, 'Steudelli' and 'Jet'. Doubled haploids were inoculated in replicated tests using two isolates of R. secalis, '4004' and 'WRS1872'. Expression of resistance differed widely between replicated tests. AFLP, SSR and RFLP markers were used to develop chromosome maps. Results have been analysed using partial least squares regression (PLSR) and interval mapping. In PLSR the major covariance structures or 'latent variables' between X (markers) and Y (isolates, tests) are modelled as principal components and their optimal number determined by cross-validation. In 'Steudelli' two QTL were detected, one on each of chromosomes 3H and 7H, in 4 out of 5 tests, while in 'Jet' only one (different) allele at the 3H locus was found. The validated R(2) varied between 11.0% and 64.9% in the replicated tests with '4004'.With isolate 'WRS1872' the 7H locus and another 3H locus were detected. By interval mapping the QTL detected were less stable and generally gave lower R(2) values than PLSR. PLSR does not depend on maps, but interval mapping based on values predicted by PLSR had R(2) around 90%. It is suggested that PLSR may be a useful tool in QTL analysis.

An integrated genetic map and a new set of simple sequence repeat markers for pearl millet, Pennisetum glaucum

Over the past 10 years, resources have been established for the genetic analysis of pearl millet, Pennisetum glaucum (L.) R. Br., an important staple crop of the semi-arid regions of India and Africa. Among these resources are detailed genetic maps containing both homologous and heterologous restriction fragment length polymorphism (RFLP) markers, and simple sequence repeats (SSRs). Genetic maps produced in four different crosses have been integrated to develop a consensus map of 353 RFLP and 65 SSR markers. Some 85% of the markers are clustered and occupy less than a third of the total map length. This phenomenon is independent of the cross. Our data suggest that extreme localization of recombination toward the chromosome ends, resulting in gaps on the genetic map of 30 cM or more in the distal regions, is typical for pearl millet. The unequal distribution of recombination has consequences for the transfer of genes controlling important agronomic traits from donor to elite pearl millet germplasm. The paper also describes the generation of 44 SSR markers from a (CA)n-enriched small-insert genomic library. Previously, pearl millet SSRs had been generated from BAC clones, and the relative merits of both methodologies are discussed.

High-resolution mapping of theSandZloci ofPhalaris coerulescens

Self incompatibility (SI) in Phalaris coerulescens is gametophytically determined by two unlinked multi allelic loci (S and Z). Neither the S nor Z genes have yet been cloned. As part of a map-based cloning strategy, high-resolution maps of the S and Z regions were generated from distorted segregating populations using RFLP probes from wheat, barley, oat, and Phalaris. The S locus was delimited to 0.26 cM with two boundary markers (Xwg811 and Xpsr168) and cosegregated with Xbm2 and Xbcd762. Xbcd266 was the closest marker linked to Z (0.9 cM). A high level of colinearity in the S and Z regions was found in both self-incompatible and -compatible species. The S locus was localized to the subcentromere region of chromosome 1 and the Z locus to the long arm end of chromosome 2. Several rice BAC clones orthologous to the S and Z locus regions were identified. This opens the possibility of using the rice genome sequence data to generate more closely linked markers and identify SI candidate genes. These results add further support to the conservation of gene order in the S and Z regions of the grass genomes.Key words: Phalaris coerulescens, self-incompatibility, distorted segregation, mapping, map-based cloning, synteny mapping.

A microsatellite map of white clover

The white clover ( Trifolium repens) nuclear genome (n = 2x = 16) is an important yet under-characterised genetic environment. We have developed simple sequence repeat (SSR) genetic markers for the white clover genome by mining an expressed sequence tag (EST) database and by isolation from enriched genomic libraries. A total of 2,086 EST-derived SSRs (EST-SSRs) were identified among 26,480 database accessions. Evaluation of 792 EST-SSR primer pairs resulted in 566 usable EST-SSRs. Of these, 335 polymorphic EST-SSRs, used in concert with 30 genomic SSRs, detected 493 loci in the white clover genome using 92 F1 progeny from a pair cross between two highly heterozygous genotypes--364/7 and 6525/5. Map length, as estimated using the joinmap algorithm, was 1,144 cM and spanned all 16 homologues. The R (red leaf) locus was mapped to linkage group B1 and is tightly linked to the microsatellite locus prs318c. The eight homoeologous pairs of linkage groups within the white clover genome were identified using 96 homoeologous loci. Segregation distortion was detected in four areas (groups A1, D1, D2 and H2). Marker locus density varied among and within linkage groups. This is the first time EST-SSRs have been used to build a whole-genome functional map and to describe subgenome organisation in an allopolyploid species, and T. repens is the only Trifolieae species to date to be mapped exclusively with SSRs. This gene-based microsatellite map will enable the resolution of quantitative traits into Mendelian characters, the characterisation of syntenic relationships with other genomes and acceleration of white clover improvement programmes.

Structure and evolution of cereal genomes

The cereal species, of central importance to our diet, began to diverge 50-70 million years ago. For the past few thousand years, these species have undergone largely parallel selection regimes associated with domestication and improvement. The rice genome sequence provides a platform for organizing information about diverse cereals, and together with genetic maps and sequence samples from other cereals is yielding new insights into both the shared and the independent dimensions of cereal evolution. New data and population-based approaches are identifying genes that have been involved in cereal improvement. Reduced-representation sequencing promises to accelerate gene discovery in many large-genome cereals, and to better link the under-explored genomes of 'orphan' cereals with state-of-the-art knowledge.

Optimal sampling of a population to determine QTL location, variance, and allelic number

In a population intended for breeding and selection, questions of interest relative to a specific segregating QTL are the variance it generates in the population, and the number and effects of its alleles. One approach to address these questions is to extract several inbreds from the population and use them to generate multiple mapping families. Given random sampling of parents, sampling strategy may be an important factor determining the power of the analysis and its accuracy in estimating QTL variance and allelic number. We describe appropriate multiple-family QTL mapping methodology and apply it to simulated data sets to determine optimal sampling strategies in terms of family number versus family size. Genomes were simulated with seven chromosomes, on which 107 markers and six QTL were distributed. The total heritability was 0.60. Two to ten alleles were segregating at each QTL. Sampling strategies ranged from sampling two inbreds and generating a single family of 600 progeny to sampling 40 inbreds and generating 40 families of 15 progeny each. Strategies involving only one to five families were subject to variation due to the sampling of inbred parents. For QTL where more than two alleles were segregating, these strategies did not sample QTL alleles representative of the original population. Conversely, strategies involving 30 or more parents were subject to variation due to sampling of QTL genotypes within the small families obtained. Given these constraints, greatest QTL detection power was obtained for strategies involving five to ten mapping families. The most accurate estimation of the variance generated by the QTL, however, was obtained with strategies involving 20 or more families. Finally, strategies with an intermediate number of families best estimated the number of QTL alleles. We conclude that no overall optimal sampling strategy exists but that the strategy adopted must depend on the objective.

Development of a composite map in Vicia faba, breeding applications and future prospects

A composite map of the Vicia faba genome based on morphological markers, isozymes, RAPDs, seed protein genes and microsatellites was constructed. The map incorporates data from 11 F(2) families for a total of 654 individuals all sharing the common female parent Vf 6. The integrated map is arranged in 14 major linkage groups (five of which were located in specific chromosomes). These linkage groups include 192 loci and cover 1559 cM with an overall average marker interval of 8 cM. By joining data of a new F(2) population segregating for resistance to ascochyta, broomrape and others traits of agronomic interest, have been saturated new areas of the genome. The combination of trisomic segregation, linkage analysis among loci from different families with a recurrent parent, and the analysis of new physically located markers, has allowed the establishment of the present status of the V. faba map with a wide coverage. This map provides an efficient tool in breeding applications such as disease-resistance mapping, QTL analyses and marker-assisted selection.

The gibberellic-acid insensitive dwarfing gene sdw3 of barley is located on chromosome 2HS in a region that shows high colinearity with rice chromosome 7L

In this study, comparative high resolution genetic mapping of the GA-insensitive dwarfing gene sdw3 of barley revealed highly conserved macrosynteny of the target region on barley chromosome 2HS with rice chromosome 7L. A rice contig covering the sdw3-orthologous region was identified and subsequently exploited for marker saturation of the target interval in barley. This was achieved by (1) mapping of rice markers from the orthologous region of the rice genetic map, (2) mapping of rice ESTs that had been physically localized on the rice contig, or (3) mapping of barley ESTs that show strong sequence similarity to coding sequences present in the rice contig. Finally, the sdw3 gene was mapped to an interval of 0.55 cM in barley, corresponding to a physical distance of about 252 kb in rice, after employing orthologous EST-derived rice markers. Three putative ORFs were identified in this interval in rice, which exhibited significant sequence similarity to known signal regulator genes from different species. These ORFs can serve as starting points for the map-based isolation of the sdw3 gene from barley.