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Bambara groundnut ( Vigna subterranea (L.) Verdc.) is an indigenous underutilized legume that has the potential to improve food security in semi-arid Africa. So far, there are a lack of reports of controlled breeding populations that could be used for variety development and genetic studies. We report here the construction of the first genetic linkage map of bambara groundnut using a F3 population derived from a 'narrow' cross between two domesticated landraces (Tiga Nicuru and DipC) with marked divergence in phenotypic traits. The map consists of 238 DArT array and SSR based markers in 21 linkage groups with a total genetic distance of 608.3 cM. In addition, phenotypic traits were evaluated for a quantitative trait loci (QTL) analysis over two generations. A total of 36 significant QTLs were detected for 19 traits. The phenotypic effect explained by a single QTL ranged from 11.6% to 49.9%. Two stable QTLs were mapped for internode length and growth habit. The identified QTLs could be useful for marker-assisted selection in bambara groundnut breeding programmes. [ABSTRACT FROM AUTHOR]

Turnip mosaic virus (TuMV) is the major virus infecting crops of the genus Brassica worldwide. A dominant resistance gene, TuRB01b, that confers immunity to the virus isolate UK 1 (a representative pathotype 1 isolate of TuMV) on Brassica rapa was identified in the Chinese cabbage cultivar Tropical Delight. The TuRB01b locus was mapped to a 2.9-cM interval on B. rapa chromosome 6 (A6) that was flanked by RFLP markers pN101e1 and pW137e1. This mapping used a first backcross (B1) population segregating for the resistance gene at TuRB01b and sets of RFLP markers employed in previous mapping experiments in Brassica. Virus-plant interaction phenotypes were assayed in inbred progeny derived from B1 individuals to allow different virus isolates to be tested. Comparative mapping confirmed that A6 of B. rapa was equivalent to chromosome 6 of Brassica napus (A6) and that the map position of TuRB01b in B. rapa could be identical to that of TuRB01 in B. napus. Detailed evaluation of plant-virus interactions showed that TuRB01 and TuRB01b had indistinguishable specificities to a range of TuMV isolates. The possibility that TuRB01 and TuRB01b represent similar or identical alleles at the same A genome resistance locus suggests that B. napus acquired TuRB01 from the B. rapa gene pool. [ABSTRACT FROM AUTHOR]

The brown planthopper (BPH, Nilaparvata lugens Stål) is still considered a major threat to rice farmers. Exploring novel resistance genes that relate to the BPH population in the targeted rice-growing area might be a suitable solution. We identified and mapped the gene locus using 175 lines of F 2:3 populations derived from Balamawee × PD601. Genomic analysis was then used to identify the candidate gene governing the resistance toward BPH. We discovered a novel genetic locus for BPH resistance in the long arm of chromosome 4 linked to markers Q31 and RM17007 at 4.76 and 5.42 cM, respectively, with total phenotypic variation reaching 52.21% at LOD 29.68. The tolerance mechanism influences the nature of this resistance, as shown by the Functional Plant Loss Index. The resistance level, mechanism of resistance, and physical mapping reveal that the resistance genes in this study differ from the previous study, therefore, we propose this novel gene as Bph44 .

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Genetic linkage maps are used to localize markers on the genome based on the recombination frequency. Most often, these maps are based on the segregation observed within a single biparental population of limited size ( n  < 300) where relatively few recombination events are sampled and in which some genomic regions are monomorphic because both parents carry the same alleles. Together, these two limitations affect both the resolution and extent of genome coverage of such maps. Consensus genetic maps overcome the limitations of individual genetic maps by merging the information from multiple segregating populations derived from a greater diversity of parental combinations, thus increasing the number of recombination events and reducing the number of monomorphic regions. The aim of this study was to construct a high-density consensus genetic map for single nucleotide polymorphism (SNP) markers obtained through a genotyping-by-sequencing (GBS) approach. Individual genetic maps were generated from six F 4:5 mapping populations ( n  = 278-365), totaling 1857 individuals. The six linkage maps were then merged to produce a consensus map comprising a total of 16 311 mapped SNPs that jointly cover 99.5% of the soybean genome with only two gaps larger than 10 cM. Compared to previous soybean consensus maps, it offers a more extensive and uniform coverage.

The short petiole trait is valuable for the development of plant ideotypes with high yield by improving the plant canopy. The soybean breeding line SS98206SP has shown extremely short petioles in the greenhouse and fields. A new single recessive gene designated as lps3 confers the short petiole trait in SS98206SP. The objectives of this study were to map the short petiole gene in SS98206SP with PCR-based markers. In total, 187 F2 plants and their F2:3 families from a cross between the short petiole line SS98206SP and the long petiole cultivar 'Taekwang' along with the two parental lines were evaluated for their petiole lengths in a greenhouse. An SSR marker from each 10-cM section of a consensus soybean map was selected for bulked segregant analysis (BSA) to identify the tentative genomic location of the gene. The BSA technique was useful to localize the gene to a genomic region in the soybean linkage group F (chromosome 13). A linkage map with six SSR and two SNP markers flanking the gene was constructed. We positioned the gene between two SSR markers, Sat_234 and Sct_033, at distances of 8.5 and 3.5 cM from the marker, respectively. The makers flanking the gene ( lps3) were located within 3-4 cM of the gene. These markers will be useful for maker-assisted selection in the development of new ideotype soybean plants. [ABSTRACT FROM AUTHOR]

The article presents a research study which analyzed the genetic mapping and quantitative trait loci (QTL) in Sorghum (S.) bicolor x S. sudanese hybrid. The female parent sorghum 314A and male parent Sudan grass 2002GZ-1 showed polymorphism for ten agronomic characters including plant height, stem diameter and leaf number. The correlation between detectable QTL and the argonomic traits and the genetic map can allegedly be used in improving relevant characters in Sorghum bicolor x S. sudanese hybrid.

Septoria speckled leaf blotch (SSLB), caused by Septoria passerinii, is one of the most important foliar diseases of barley (Hordeum vulgare L.) in North America. The primary problem caused by this disease is substantial yield loss. The objective of this study was to determine the chromosomal location of SSLB resistance genes in the barley accession PI 643302. A recombinant inbred line population was developed from the cross Zhenongda 7/PI 643302. PI 643302 is resistant while Zhenongda 7 is susceptible to SSLB. The population was phenotyped for SSLB resistance in five experiments in the greenhouse. A linkage map comprising 113 molecular markers was constructed and simplified composite interval mapping was performed. Two QTLs, designated QrSp-1H and QrSP-2H, were found. QrSp-1H was found on the short arm of chromosome 1H (1HS) in all five experiments and showed a large effect against SSLB. Based on the location of QrSp-1H, it is likely the SSLB resistance gene Rsp2. The QTL QrSp-2H mapped to the distal region on the long arm of chromosome 2H (2HL), had a smaller effect than QrSp-1H, and was also detected consistently in all five experiments. A QTL for SSLB resistance in the same region on chromosome 2H has not been reported previously in either cultivated or wild barley; thus, QrSp-2H is a new QTL for SSLB resistance in barley. [ABSTRACT FROM AUTHOR]

Identification and genetic mapping of loci conferring resistance to polycyclic pathogens such as the rust fungi depends on accurate measurement of disease resistance. We converted an absolute quantification assay of Puccinia coronata DNA to a relative assay by adding a TaqMan® primers/probe set specific to the oat β-actin gene to simplify and improve quantification of fungal infection. The new multiplex assay estimates the amount of fungal DNA in a sample relative to the amount of host DNA and requires fewer and less labour-intensive steps than previous assays. The relative fungal DNA assay (RFDNA) reliably detected and quantified both host and pathogen DNA over five orders of magnitude and was at least as sensitive as either digital image analysis (DLA) or absolute estimation of fungal DNA (AFDNA) in repeated greenhouse studies using 12 oat cultivars with different resistance responses to P. coronata isolate LGCG. Measuring crown rust resistance to LGCG using DLA, AFDNA and RFDNA in a P8669/P94163 recombinant inbred line population produced segregation ratios that did not differ from the 1:1 Mendelian ratio expected for a single gene. Compared to the AFDNA assessment method, the RFDNA assay is equally sensitive, yet faster and much easier to use than the AFDNA method for precise quantification of the crown rust pathogen in oat leaves. The method will be especially useful for streamlining measurement of partial resistance, since uncovering small differences in resistance requires phenotypic evaluation of large populations. [ABSTRACT FROM AUTHOR]

A high-density genetic linkage map of papaya, previously developed using an F2 mapping population derived from the intraspecific cross AU9 × SunUp, was enriched with AFLP markers. The comprehensive genetic map presented here spans 945.2 cM and covers 9 major and 5 minor linkage groups containing 712 SSR, 277 AFLP, and 1 morphological markers. The average marker density for the 9 major linkage groups is 0.9 cM between adjacent markers, and the total number of gaps >5 cM was reduced from 48 to 27 in the current map. AFLPs generated by EcoRI/MseI primer combinations were distributed throughout the 14 linkage groups and resulted in several large locus order rearrangements within the 9 major linkage groups. Integration of AFLP markers provided tighter linkage association between loci, leading to a reduction in map distance on LGs 1, 2, and 4, which were inflated in the previous map, and correction of the marker order on LG8. Suppression of recombination in the male-specific Y region (MSY) of LG1 is further validated by the addition of 27 sex co-segregating AFLP markers. A large region of distorted segregation surrounding the MSY spans 54.4 cM and represents ~71% of the linkage group. This comprehensive high-density genetic map provides a framework for mapping quantitative trait loci and for fine mapping as well as for comparative genomic studies of crop plant development and evolution. [ABSTRACT FROM AUTHOR]

Stripe rust, caused by Puccinia striiormis Westend f. sp. tritici, is one of the most important foliar diseases of wheat (Triticum aestivum L.) worldwide. Stripe rust resistance genes Yr27, Yr31, YrSp, YrV23, and YrCN19 on chromosome 2BS confer resistance to some or all Chinese P. striiormis f. sp. tritici races CYR31, CYR32, SY11-4, and SY11-14 in the greenhouse. To screen microsatellite (SSR) markers linked with YrCN19, F1, F2, and F3 populations derived from cross Ch377/CN19 were screened with race CYR32 and 35 SSR primer pairs. Linkage analysis indicated that the single dominant gene YrCN19 in cultivar CN19 was linked with SSR markers Xgwm410, Xgwm374, Xwmc477, and Xgwm382 on chromosome 2BS with genetic distances of 0.3, 7.9, 12.3, and 21.2 cM, respectively. Crosses of CN19 with wheat lines carrying other genes on chromosome 2B showed that all were located at different loci. YrCN19 is thus different from the other reported Yr genes in chromosomal location and resistance response and was therefore named Yr41. Prospects and strategies of using Yr41 and other Yr genes in wheat improvement for stripe rust resistance are discussed. [ABSTRACT FROM AUTHOR]

Scab, caused by the fungal pathogen Venturia inaequalis, is the most common disease of cultivated apple (Malus ×domestica). The fungal races 6 and 7 have now overcome the major resistance gene Vf, which is widely used in apple breeding programmes. New breeding strategies to achieve durable resistance are thus necessary. The aim of this study was to determine the genetic basis of quantitative resistance of the apple cultivar ‘Dülmener Rosenapfel’, known to be scab resistant under different environmental conditions. An F1 progeny derived from the cross between the susceptible cultivar ‘Gala’ and ‘Dülmener Rosenapfel’ was tested in a greenhouse with a multi-isolate inoculum of V. inaequalis. Rvi14, a new major gene that conditions a chlorotic-type reaction, was mapped on linkage group (LG) 6 in a genomic region not known to be involved in disease resistance. A further three quantitative trait loci (QTL) for resistance were identified. One co-localized with Rvi14 on LG6, whereas the remaining two were detected on LG11 and LG17, in genomic regions already reported to carry broad-spectrum QTL in other genetic backgrounds. Since a selective genotyping approach was used to detect QTL, an expectation-maximization (EM) computation was used to estimate the corrected QTL contributions to phenotypic variation and was validated by entire progeny genotyping. La tavelure, causée par le champignon pathogène Venturia inaequalis, est la maladie du pommier cultivé (Malus ×domestica) la plus répandue. Les races 6 et 7 du champignon ont maintenant contourné le gène majeur de résistance Vf, largement utilisé dans les programmes d’amélioration du pommier. De nouvelles stratégies d’amélioration sont alors nécessaires en vue d’une résistance durable. Le but de cette étude était d’étudier le déterminisme génétique de la résistance quantitative de la variété de pommier ‘Dülmener Rosenapfel’, connue pour être résistante à la tavelure dans différentes conditions environnementales. Une descendance F1 issue du croisement entre la variété sensible ‘Gala’ et ‘Dülmener Rosenapfel’ a été testée en serre avec un inoculum multi-souches de V. inaequalis. Un nouveau gène majeur, Rvi14, déterminant une réaction de type chlorotique, a été localisé sur le groupe de liaison (GL) 6 dans une région génomique pas encore connue pour être impliquée dans la résistance aux maladies. Trois QTL (« quantitative trait loci ») de résistance ont été identifiés. Un a co-localisé avec Rvi14 sur le GL6 alors que les deux autres ont été détectés sur le GL11 et le GL17, dans des régions génomiques déjà connues pour porter des QTL à large spectre dans d’autres fonds génétiques. Les QTL ayant été détectés par génotypage sélectif, leur contribution à la variation phénotypique a été corrigée par maximum de vraisemblance; cette méthode corrective a ensuite été validée par le génotypage de la population entière. [ABSTRACT FROM AUTHOR]

A spontaneously mutated male-sterile material was found among the offspring of the indica restorer line Jinhuiyihao. To understand the status and function of the related gene and clone the gene, a near-isogenic line (NIL) of the male sterility was bred, and characterization of the mutant and gene mapping were performed. The results indicated that there are obvious differences between the male-sterile NIL and the indica maintainer line II-32B. The anther size of the NIL is smaller than that of II-32B, and the anther color is white in the NIL but yellow in II-32B. No pollen from the matured anther in the NIL was observed to be stained using KI-I2 solution. In transverse sections of the sterile anther, at early microspore stage the cytoplasm of the tapetum concentrates but the tapetum itself does not degenerate after microspores are released from the tetrads; the tapetum then desquamates from the anther wall and enwraps microspores; subsequently, the surrounded microspores collapse completely at late microspore and early bicellular pollen stages. Inheritance analysis showed that the male sterility was controlled by a single recessive gene, ostd (t). This gene was mapped between the SSR markers RM7434 and RM275 on chromosome 6, and the physical distance from RM7434 to RM275 is about 389 kb. [ABSTRACT FROM AUTHOR]

xs1 is a male-sterile rice mutant derived from a spontaneous mutation. The floret of the mutant, consisting of 6 stamens and 1 pistil, looks the same as that of the wild type except that the filaments are long and thin and the anthers are withered in white transparence. It is confirmed that xs1 is a no-pollen type of male-sterile mutant, for no pollen grains can be stained with I2-KI solution and the anther locules are always hollow. Anther transverse sections indicate that the mutant microspores are abnormally condensed and agglomerated to form a deeply stained cluster at the late microspore stage, which results in cessation of the vacuolation process of microspores, and, therefore, the mutant forms no functional pollens for reproduction. Genetic analysis of 4 F2 populations and 3 BC1F1 populations revealed that the mutation is controlled by a single recessive gene, termed VR1 (Vacuolation retardation 1). Screening of 432 F2 mutant individuals derived from the cross of xs1 × G603 with simple sequence repeat markers revealed that VR1 is located between the molecular markers RM17411 and RM5030, at distances of 0.7 and 1.5 cM, respectively, on chromosome 4. VR1 is a new male fertility controlling gene located on chromosome 4 in rice. [ABSTRACT FROM AUTHOR]

A dynamically rolled leaf mutant (rl10) was identified from a spontaneous mutation in an Oryza sativa L. subsp. indica line, II-32B. The leaf chlorophyll content of rl10 is higher than that of the wild type. Genetic analysis using 3 F2 segregating populations derived from crosses between rl10 and the rice lines Mian5B, II-32B, and D62B, respectively, confirmed that the rolled leaf trait of rl10 is controlled by a single recessive gene. Of 719 SSR primer pairs that showed polymorphism between D62B and rl10, 151 were adopted to map the RL10(t) gene using an F2 segregating population of the cross rl10 × D62B, which contained 352 recessive plants. RL10(t) was primarily mapped on the long arm of chromosome 9, 5.09 cM from marker RM105 and 5.13 cM from marker RM3912. Using a novel set of 22 primer pairs between RM105 and RM3912, RL10(t) was further mapped between markers rlc3 (0.72 cM in distance) and rlc12 (0.1 cM in distance) using an F2/F3 population containing 1172 recessive individuals. Mapped position analysis and homology analysis of the 20 genes within the 194-kb region between these 2 markers both indicated that a gene encoding a Myb-like domain transcription factor with homology to Arabidopsis KANADI (annotated in PAC clone AP005904) is the most probable candidate for RL10(t). This study enables further investigation of whether KANADI-like Myb genes are involved in leaf polarity modeling in monocots, as they are in dicots. Un mutant à enroulement foliaire actif (rl10) a été identifié suite à une mutation spontanée chez la lignée II-32B de l’Oryzasativa L. subsp. indica. La teneur en chlorophylle foliaire chez rl10 est plus élevée que chez le type sauvage. Une analyse génétique, effectuée sur trois populations F2 dérivées de croisement entre rl10 et Mian5B, II-32B et D62B, a confirmé que l’enroulement foliaire actif présente une hérédité monogénique récessive. Les 151 microsatellites (parmi 719) qui étaient polymorphes entre D62B et rl10 ont été employés pour situer le gène RL10(t) au sein d’une population F2rl10 × D62B comptant 352 individus récessifs. RL10(t) a d’abord été situé sur le bras long du chromosome 9, à 5,09 cM de RM105 et à 5,13 cM de RM3912. À l’aide d’un nouveau jeu de 22 microsatellites situés entre RM105 et RM3912, RL10(t) a été positionné entre rlc3 (à 0,72 cM) et rlc12 (à 0,1 cM) en utilisant une population F2/F3 comprenant 1172 individus récessifs. L’analyse de la position cartographique et de l’homologie des 20 gènes situés dans l’intervalle de 194 kb qui sépare ces deux marqueurs suggèrent tous deux qu’un gène codant pour un facteur de transcription à domaine Myb et présentant une homologie avec le gène KANADI (annoté dans le clone PAC AP005904) serait le candidat le plus probable pour RL10(t). Cela permettra d’examiner si des gènes Myb ressemblant à KANADI sont également impliqués dans l’établissement de la polarité foliaire chez les monocotylédones comme chez les dicotylédones. [ABSTRACT FROM AUTHOR]

Black spot disease, which is caused by the Japanese pear pathotype of Alternaria alternata (Fr.) Keissler, is one of the most harmful diseases in Japanese pear cultivation. We identified the exact positions and linkage groups (LGs) of the genes for susceptibility to black spot in the Japanese pear (Pyrus pyrifolia Nakai) cultivars ‘Osa Nijisseiki’ (gene Ani) and ‘Nansui’ (gene Ana). Segregation of susceptibility and resistance fitted the expected ratio of 1:1 in progeny of ‘Nansui’ but showed a slight distortion in progeny of ‘Osa Nijisseiki’. We mapped the genes for susceptibility to black spot in both populations using a genome scanning approach. The simple sequence repeat (SSR) markers CH04h02 and CH03d02 showed tight linkage to Ani and Ana. Although Ani and Ana are derived from different sources, both genes are located at the top region of LG 11. Information about the positions of the susceptibility genes and the molecular markers linked to them will be useful for marker-assisted selection in pear breeding programs. La tache alternarienne, causée par l’Alternariaalternata (Fr.) Keissler pathotype poirier japonais, constitue l’une des maladies les plus dommageables pour la culture de la poire au Japon. Les auteurs ont identifié la position et le groupe de liaison (« LGs ) des gènes qui confèrent la sensibilité à la tache alternarienne chez les poiriers japonais (Pyrus pyrifolia Nakai) ‘Osa Nijsseiki’ (gène Ani) et ‘Nansui’ (gène Ana). La ségrégation de la sensibilité et de la résistance était conforme à l’attente 1:1 chez la progéniture de ‘Nansui’, alors qu’elle montrait une légère distorsion au sein de la progéniture de ‘Osa Nijsseiki’. Les gènes de sensibilité ont été cartographiés chez les deux populations à l’aide de marqueurs couvrant la totalité du génome. Les marqueurs microsatellites (« SSR ») CH04h02 et CH03d02 montraient une liaison étroite avec les gènes Ani et Ana. Bien que les gènes de sensibilité chez ‘Osa Nijsseiki’ et ‘Nansui’ soient dérivés de sources différentes, les deux gènes sont situés dans la moitié supérieure du groupe de liaison LG 11. Cette information concernant la position des gènes de sensibilité et la disponibilité de marqueurs moléculaires vont faciliter la sélection assistée chez le poirier. [ABSTRACT FROM AUTHOR]

Fruit size and seedlessness are highly relevant traits in many fruit crop species, and both are primary targets of breeding programs for table grapes. In this work we performed a quantitative genetic analysis of size and seedlessness in an F1 segregating population derived from the cross between a classical seeded (Vitis vinifera L. ‘Dominga’) and a newly bred seedless (‘Autumn Seedless’) cultivar. Fruit size was scored as berry weight (BW), and for seedlessness we considered both seed fresh weight (SFW) and the number of seeds and seed traces (SN) per berry. Quantitative trait loci (QTL) analysis of BW detected 3 QTLs affecting this trait and accounting for up to 67% of the total phenotypic variance. QTL analysis for seedlessness detected 3 QTLs affecting SN (explaining up to 35% of total variance) and 6 affecting SFW (explaining up to 90% of total variance). Among them, a major effect QTL explained almost half of the phenotypic variation for SFW. Comparative analysis of QTLs for these traits reduced the number of grapevine genomic regions involved, one of them being a major effect QTL for seedlessness. Association analyses showed that microsatellite locus VMC7F2, closely linked to this QTL, is a useful marker for selection of seedlessnes. [ABSTRACT FROM AUTHOR]

A PCR approach with degenerate primers designed from conserved NBS–LRR (nucleotide binding site – leucine-rich repeat) regions of known disease-resistance (R) genes was used to amplify and clone homologous sequences from 5 faba bean (Vicia faba) lines and 2 chickpea (Cicer arietinum) accessions. Sixty-nine sequenced clones showed homologies to various R genes deposited in the GenBank database. The presence of internal kinase-2 and kinase-3a motifs in all the sequences isolated confirm that these clones correspond to NBS-containing genes. Using an amino-acid sequence identitiy of 70% as a threshold value, the clones were grouped into 10 classes of resistance-gene analogs (RGA01 to RGA10). The number of clones per class varied from 1 to 30. RGA classes 1, 6, 8, and 9 were comprised solely of clones isolated from faba bean, whereas classes 2, 3, 4, 5, and 7 included only chickpea clones. RGA10, showing a within-class identity of 99%, was the only class consisting of both faba bean and chickpea clones. A phylogenetic tree, based on the deduced amino-acid sequences of 12 representative clones from the 10 RGA classes and the NBS domains of 6 known R genes (I2 and Prf from tomato, RPP13 from Arabidopsis, Gro1–4 from potato, N from tobacco, L6 from flax), clearly indicated the separation between TIR (Toll/interleukin-1 receptor homology: Gro1–4, L6, N, RGA05 to RGA10)- and non-TIR (I2, Prf, RPP13, RGA01 to RGA04)-type NBS–LRR sequences. The development of suitable polymorphic markers based on cloned RGA sequences to be used in genetic mapping will facilitate the assessment of their potential linkage relationships with disease-resistance genes in faba bean and chickpea. This work is the first to report on faba bean RGAs. [ABSTRACT FROM AUTHOR]

A number of mutations affecting seed development in barley (Hordeum vulgare L.) have been known for many years; however, to date, no research has been reported that elucidates the molecular structure of the causal genes. As a first step, we initiated the linkage mapping of the two shrunken endosperm genes seg8 and sex1 using microsatellite markers. The recessive gene seg8 was mapped in the centromeric region of chromosome 7H to a 4.6 cM interval flanked by markers GBM1516 and Bmag341. The recessive sex1 gene showed xenia effects and was located in the centromeric region of barley chromosome 6H, which is in accordance to the previously reported chromosomal location in the classical linkage map. It was flanked by markers GBM5012 and GBM1063 in a 4.2 cM interval. EST-derived microsatellite markers were used to establish the syntenic relationships to the genomic rice sequences. Two orthologous sites on rice chromosome 2 flanking a 4.1 Mb sequence had homology to the respective barley markers in the sex1 region. For the markers in the seg8 region orthologous sites on rice chromosome 6 were detected. [ABSTRACT FROM AUTHOR]

Apple scab, caused by the fungus Venturia inaequalis, is the major production constraint in temperate zones with humid springs. Normally, its control relies on frequent and regular fungicide applications. Because this control strategy has come under increasing criticism, major efforts are being directed toward the breeding of scab-resistant apple cultivars. Modern apple breeding programs include the use of molecular markers, making it possible to combine several different scab-resistance genes in 1 apple cultivar (pyramiding) and to speed up the breeding process. The apple scab-resistance gene Vb is derived from the Siberian crab apple ‘Hansen’s baccata #2’, and is 1 of the 6 “historical” major apple scab-resistance genes (Vf, Va, Vr, Vbj, Vm, and Vb). Molecular markers have been published for all these genes, except Vr. In testcross experiments conducted in the 1960s, it was reported that Vb segregated independently from 3 other major resistance genes, including Vf. Recently, however, Vb and Vf have both been mapped on linkage group 1, a result that contrasts with the findings from former testcross experiments. In this study, simple sequence repeat (SSR) markers were used to identify the precise position of Vb in a cross of ‘Golden Delicious’ (vbvb) and ‘Hansen’s baccata #2’ (Vbvb). A genome scanning approach, a fast method already used to map apple scab-resistance genes Vr2 and Vm, was used, and the Vb locus was identified on linkage group 12, between the SSR markers Hi02d05 and Hi07f01. This finding confirms the independent segregation of Vb from Vf. With the identification of SSR markers linked to Vb, another major apple scab-resistance gene has become available; breeders can use it to develop durable resistant cultivars with several different resistance genes. [ABSTRACT FROM AUTHOR]

Brachypodium is well suited as a model system for temperate grasses because of its compact genome and a range of biological features. In an effort to develop resources for genome research in this emerging model species, we constructed 2 bacterial artificial chromosome (BAC) libraries from an inbred diploid Brachypodium distachyon line, Bd21, using restriction enzymes HindIII and BamHI. A total of 73 728 clones (36 864 per BAC library) were picked and arrayed in 192 384-well plates. The average insert size for the BamHI and HindIII libraries is estimated to be 100 and 105 kb, respectively, and inserts of chloroplast origin account for 4.4% and 2.4%, respectively. The libraries individually represent 9.4- and 9.9-fold haploid genome equivalents with combined 19.3-fold genome coverage, based on a genome size of 355 Mb reported for the diploid Brachypodium, implying a 99.99% probability that any given specific sequence will be present in each library. Hybridization of the libraries with 8 starch biosynthesis genes was used to empirically evaluate this theoretical genome coverage; the frequency at which these genes were present in the library clones gave an estimated coverage of 11.6- and 19.6-fold genome equivalents. To obtain a first view of the sequence composition of the Brachypodium genome, 2185 BAC end sequences (BES) representing 1.3 Mb of random genomic sequence were compared with the NCBI GenBank database and the GIRI repeat database. Using a cutoff expectation value of E  × 10-10, only 3.3% of the BESs showed similarity to repetitive sequences in the existing database, whereas 40.0% had matches to the sequences in the EST database, suggesting that a considerable portion of the Brachypodium genome is likely transcribed. When the BESs were compared with individual EST databases, more matches hit wheat than maize, although their EST collections are of a similar size, further supporting the close relationship between Brachypodium and the Triticeae. Moreover, 122 BESs have significant matches to wheat ESTs mapped to individual chromosome bin positions. These BACs represent colinear regions containing the mapped wheat ESTs and would be useful in identifying additional markers for specific wheat chromosome regions. [ABSTRACT FROM AUTHOR]

Leaf (brown) and stripe (yellow) rusts, caused by Puccinia triticina and Puccinia striiformis, respectively, are fungal diseases of wheat (Triticum aestivum) that cause significant yield losses annually in many wheat-growing regions of the world. The objectives of our study were to characterize genetic loci associated with resistance to leaf and stripe rusts using molecular markers in a population derived from a cross between the rust-susceptible cultivar 'Avocet S' and the resistant cultivar 'Pavon76'. Using bulked segregant analysis and partial linkage mapping with AFLPs, SSRs and RFLPs, we identified 6 independent loci that contributed to slow rusting or adult plant resistance (APR) to the 2 rust diseases. Using marker information available from existing linkage maps, we have identified additional markers associated with resistance to these 2 diseases and established several linkage groups in the 'Avocet S' × 'Pavon76' population. The putative loci identified on chromosomes 1BL, 4BL, and 6AL influenced resistance to both stripe and leaf rust. The loci on chromosomes 3BS and 6BL had significant effects only on stripe rust, whereas another locus, characterized by AFLP markers, had minor effects on leaf rust only. Data derived from Interval mapping indicated that the loci identified explained 53% of the total phenotypic variation (R2) for stripe rust and 57% for leaf rust averaged across 3 sets of field data. A single chromosome recombinant line population segregating for chromosome 1B was used to map Lr46/Yr29 as a single Mendelian locus. Characterization of slow-rusting genes for leaf and stripe rust in improved wheat germplasm would enable wheat breeders to combine these additional loci with known slow-rusting loci to generate wheat cultivars with higher levels of slow-rusting resistance. [ABSTRACT FROM AUTHOR]

A novel floral organ mutant of rice (Oryzasativa L. subsp. indica), termed pistilloid-stamen (ps) here, has flowers with degenerated lemma and palea, with some stamens transformed into pistils and pistil–stamen chimeras. Genetic analysis confirmed that the ps trait is controlled by a single recessive gene. F2 and F3 segregation populations derived from PS ps heterozygote crossed with Oryza sativa subsp. indica 'Luhui-17' (PS PS) were used for molecular mapping of the gene using simple sequence repeat (SSR) markers. With 97 recessive individuals from an F2 segregation population, the ps locus was preliminarily mapped 6.2 cM distal to marker RM6324 and 3.1 cM proximal to marker RM6340 in the terminal region of the short arm of chromosome 1. With a large F3 segregation population, the gene was fine-mapped between markers RM6470 and RM1141, at distances of 0.10 and 0.03 cM to each marker, respectively. The position of the ps gene was finally located within a 20 kb physical region containing 3 annotated putative genes. One of them, encoding a protein with a single C2H2 zinc-finger domain, may be the candidate gene for PS. [ABSTRACT FROM AUTHOR]

Barramundi (Lates calcarifer) is an important marine food fish species in Southeast Asia and Australia. Seventy-four novel microsatellites were isolated from a genomic DNA library enriched for CA repeats and were characterized in 24 unrelated individuals. Among the 74 microsatellites, 71 were polymorphic, with an average allele number of 7.0 ± 3.6/locus. The average expected heterozygosity of these polymorphic markers was 0.66. Sixty-three of the 71 polymorphic microsatellites conformed to Hardy–Weinberg equilibrium. Linkage analyses were conducted in a reference family, leading to the assignment of 34 novel microsatellites and 16 published markers in 16 linkage groups. The novel microsatellites developed in this study will contribute significantly to the construction of a first-generation linkage map for mapping of quantitative trait loci in Barramundi, and supply a large choice of markers for studies on population genetics, stock management, and pedigree reconstruction. [ABSTRACT FROM AUTHOR]

The fleshless berry (flb) mutation of grapevine (Vitis vinifera L. 'Ugni Blanc') impairs the differentiation and division of inner mesocarp cells responsible for flesh in grapevine berries. In order to study the inheritance of the mutation and to map the flb locus, 5 segregating populations were created. Progeny plants were classified as mutant or wild type by scoring for the presence of an ovary phenotype associated with the Flb– phenotype at anthesis. Phenotypic segregation revealed the involvement of a single dominant allele that was heterozygous in the original mutant. Through bulk segregant analysis, microsatellite (simple sequence repeat (SSR)) markers linked to the mutation were identified, and the flb locus was assigned to linkage group 18. The locus position was then refined by analyzing individual progeny and the segregation of SSR markers in the target region with the closest marker 5.6 cM distant from the flb locus. All progeny with the Flb– ovary phenotype differed from the original fleshless berry mutant in that no berries formed after anthesis. Our data suggest that the original mutant plant was a chimera with the mutated allele present in only 1 cell layer (L2 layer) of the ovary and berry. [ABSTRACT FROM AUTHOR]

The article discusses the avirulence genes AVR-Pia and AVR-Pii partial mapping in the rice blast fungus Magnaporthe oryzae. The study utilized 31 restriction fragment length polymorphism (RFLP) markers from existing M. oryzae genetic maps in constructing genetic map based on a cross between fertile isolates. The genetic linkage between AVR-Pii or AVR-Pia and RFLP markers is determined, in which gene AVR-Pii was found linked to two markers and AVR-Pia was linked to three markers.

In an effort to expand the Gossypium hirsutum L. (cotton) expressed sequence tag (EST) database, ESTs representing a variety of tissues and treatments were sequenced. Assembly of these sequences with ESTs already in the EST database (dbEST, GenBank) identified 9675 cotton sequences not present in GenBank. Statistical analysis of a subset of these ESTs identified genes likely differentially expressed in stems, cotyledons, and drought-stressed tissues. Annotation of the differentially expressed cDNAs tentatively identified genes involved in lignin metabolism, starch biosynthesis and stress response, consistent with pathways likely to be active in the tissues under investigation. Simple sequence repeats (SSRs) were identified among these ESTs, and an inexpensive method was developed to screen genomic DNA for the presence of these SSRs. At least 69 SSRs potentially useful in mapping were identified. Selected amplified SSRs were isolated and sequenced. The sequences corresponded to the EST containing the SSRs, confirming that these SSRs will potentially map the gene represented by the EST. The ESTs containing SSRs were annotated to help identify the genes that may be mapped using these markers. [ABSTRACT FROM AUTHOR]

A genetic linkage map of an intraspecific cross between 2 Silene vulgaris s.l. ecotypes is presented. Three-hundred AFLP markers from 2 different restriction enzyme combinations were used to genotype an F2 mapping population. Maternal and paternal pure-coupling phase maps with 114 and 186 markers on 12 and 13 linkage groups, respectively, were constructed. Total map length of the paternal and maternal maps are 547 and 446 Kosambi cM, respectively. Nearly half of the markers (49%) exhibited significant transmission ratio distortion. Genome coverage and potential causes of the observed segregation ratio distortions are discussed. The maps represent a first step towards the identification of quantitative trait loci associated with habitat adaptation in the non-model species Silene vulgaris. [ABSTRACT FROM AUTHOR]

The dominant male sterility gene Ms-cd1 (c, cabbage; d, dominant) was identified as a spontaneous mutation in the spring cabbage line 79-399-3. The Ms-cd1 gene is successfully applied in hybrid seed production of several Brassica oleracea cultivars in China. Amplified fragment length polymorphism (AFLP) technology was used to identify markers linked to the Ms-cd1 gene in bulks of male-sterile and male-fertile individuals of a segregating BC3 population and in a near-isogenic population of 25 male-sterile plants. Twelve markers within a 20-cM interval proximal to the Ms-cd1 gene were identified, 5 of which can be used to select homozygous male-sterile Ms-cd1/ Ms-cd1 plants. Three AFLP markers and 3 sequence characterized amplified region markers that were linked to MS-cd1 mapped onto linkage group O9, corresponding to chromosome 3 of B. oleracea. This region corresponds to the top of chromosome 5 in Arabidopsis thaliana. [ABSTRACT FROM AUTHOR]

A set of differential isolates of Blumeria graminis f.sp. tritici was used to identify 10 alleles at the Pm3 locus on the short arm of chromosome 1A. Three F3 populations were used to map Pm3h in Abessi, Pm3i in line N324, and Pm3j alleles in GUS 122 relative to microsatellite markers. In total, 13 marker loci were mapped on chromosome 1AS and 1 marker on 1AL. The order of marker loci in the 3 mapping populations is consistent with previously published maps. All 3 alleles were mapped in the distal region of chromosome 1AS. The present study indicated that microsatellite markers are an ideal marker system for comparative mapping of alleles at the same gene locus in different mapping populations. The linkage distances of the closest microsatellite marker, Xgwm905–1A, to Pm3h, Pm3i, and Pm3j were 3.7 cM, 7.2 cM, and 1.2 cM, respectively. The microsatellite marker Xgwm905–1A cannot be used to distinguish between Pm3 alleles. The development of specific markers for individual Pm3 alleles is discussed on the basis of the recently cloned Pm3b allele. [ABSTRACT FROM AUTHOR]

Wide hybrids have been used in generating genetic maps of many plant species. In this study, genetic and physical mapping was performed on phlb-induced recombinants of rye chromosome 2R in wheat (Triticum aestivum L.). All recombinants were single breakpoint translocations. Recombination 2RS-2BS was absent from the terminal and the pericentric regions and was distributed randomly along an intercalary segment covering approximately 65°10 of the arm's length. Such a distribution probably resulted from structural differences at the telomeres of 2RS and wheat 2BS arm that disrupted telomeric initiation of pairing. Recombination 2RL-2BL was confined to the terminal 25% of the arm's length. A genetic map of homoeologous recombination 2R-2B was generated using relative recombination frequencies and aligned with maps of chromosomes 2B and 2R based on homologous recombination. The alignment of the short arms showed a shift of homoeologous recombination toward the centromere. On the long arms, the distribution of homoeologous recombination was the same as that of homologous recombination in the distal halves of the maps, but the absence of multiple crossovers in homoeologous recombination eliminated the proximal half of the map. The results confirm that homoeologous recombination in wheat is based on single exchanges per arm, indicate that the distribution of these single homoeologous exchanges is similar to the distribution of the first (distal) crossovers in homologues, and suggest that successive crossovers in an arm generate specific portions of genetic maps. A difference in the distribution of recombination between the short and long arms indicates that the distal crossover localization in wheat is not dictated by a restricted distribution of DNA sequences capable of recombination but by the pattern of pairing initiation, and that can be affected by structural differences. Restriction of homoeologous recombination to single crossovers in the distal part... [ABSTRACT FROM AUTHOR]

Recent advances in DNA sequence analysis and the establishment of high-throughput assays have provided the framework for large-scale discovery and analysis of DNA sequence variation. In this context, single nucleotide polymorphisms (SNPs) are of particular interest. To initiate a systematic approach to develop an SNP map of barley (Hordeum vulgare L.), we have employed denaturing high-performance liquid chromatography (DHPLC) to analyse segregating SNP patterns in a doubled-haploid (DH) mapping population. To this end, SNPs between the parental genotypes were identified using a direct sequencing approach. Once a SNP was established between the parents, the optimal melting temperature of the PCR fragment containing the SNP was predicted for its analysis by DHPLC. Following the detection of the optimal temperature, the DH lines were analysed for the presence of either of the alleles. To test the utility of the analysis, data from previously mapped RFLP markers from which these SNPs were derived were compared. Results from these experiments indicate that DHPLC can be efficiently employed in analysing SNPs on a high-throughput scale.Key words: denaturing high performance liquid chromatography, doubled-haploid lines, restriction fragment length polymorphism, genetic mapping, molecular markers.Les récents progrès en matière d'analyse de séquences d'ADN et la mise au point de méthodologies à haut débit ont rendu possible l'identification et l'analyse de la variation nucléotidique à grande échelle. Dans ce contexte, les marqueurs SNP (polymorphisme mononucléotidique) présentent un intérêt particulier. Afin d'initier une approche systématique visant la mise au point d'une carte SNP chez l'orge (Hordeum vulgare L.), les auteurs ont employé la chromatographie haute performance en phase liquide dénaturante (DHPLC) pour analyser la ségrégation de SNP au sein d'une population de cartographie constituée d'haploïdes doublés (HD). Pour cela, des SNP entre les génotypes parentaux ont été identifiés au moyen d'une approche de séquençage direct. Lorsqu'un SNP était confirmé, la température optimale de dénaturation de l'amplicon contenant le SNP a été prédite en vue de son analyse par DHPLC. Suite à la détermination de la température optimale, les lignées HD ont été analysées pour la présence de l'un ou l'autre des allèles. Afin de vérifier l'utilité de cette analyse, les données provenant de marqueurs RFLP précédemment cartographiés, et desquels sont dérivés les SNP, ont été comparées aux données obtenues avec les SNP. Les résultats de ces expériences montrent que la DHPLC peut être employée de façon efficace dans l'analyse à haut débit des SNP.Mots clés : chromatographie haute performance en phase liquide dénaturante, haploïdes doublés, polymorphisme de longueur des fragments de restriction, cartographie génétique, marqueurs moléculaires.[Traduit par la Rédaction] [ABSTRACT FROM AUTHOR]

The Wilms' tumor suppressor (WT1) gene plays an important role in the development and functioning of the genitourinary system, and mutations in this gene are associated with nephroblastoma formation in humans. Rainbow trout (Oncorhynchus mykiss) is one of the rare animal models that readily form nephroblastomas, yet trout express three distinct WT1 genes, one of which is duplicated and inherited tetrasomically. Sequence analyses suggest an ancient gene duplication in the common ancestor of bony fishes resulted in the formation of two WT1 gene families, that conserve the splicing variations of tetrapod WT1, and a second duplication event occurred in the trout lineage. The WT1 genes of one family map to linkage groups 6 and 27 in the trout genome map. Reverse transcribed polymerase chain reaction (RT-PCR) expression analysis demonstrated little difference in WT1 tissue expression pattern between genes.Key words: tumor suppressor, nephroblastoma, RT-PCR expression, kidney, cancer, cDNA, gene mapping.Le gène de suppression de tumeur de Wilm (WT1) joue un rôle important dans le développement et le fonctionnement du système génito-urinaire et des mutations dans ce gène sont associées avec la formation de néphroblastomes chez les humains. La truite arc-en-ciel (Oncorhynchus mykiss) est l'une des rares espèces modèles animales qui produit aisément des néphroblastomes. Pourtant, la truite exprime trois gènes WT1 différents dont un est dupliqué et montre une hérédité tétrasomique. Des analyses de séquence suggèrent qu'une duplication génique ancienne chez l'ancêtre des poissons osseux a produit deux familles des gènes WT1, lesquels conservent les variations au niveau de l'épissage comme chez les tétrapodes, tandis qu'une seconde duplication se serait produite dans l'embranchement des truites. Les gènes WT1 d'une famille sont situés sur les groupes de liaison 6 et 27 de la carte génétique de la truite. Des analyses RT-PCR ont montré qu'il existait peu de différences entre l'expression des différents gènes WT1 au sein de divers tissus.Mots clés : suppresseur de tumeur, néphroblastome, expression RT-PCR, rein, cancer, ADNc, cartographie génétique.[Traduit par la Rédaction] [ABSTRACT FROM AUTHOR]

A population of 100 F[sub 6] -derived recombinant inbred lines was developed from the cross of two diploid (2n = 14) Avena accessions, CI3815 (A. strigosa) and CI1994 (A. wiestii). Restriction fragment length polymorphism (RFLP) probes previously mapped in other grass species were used to develop a framework linkage map suitable for comparative genetics. Nine linkage groups were identified among the 181 loci mapped, with an average interlocus distance of 5 cM, and a total genetic map length of 880 cM. A cluster of five tightly linked crown rust resistance genes (Pca) was localized on the map, as were five loci identified by disease resistance gene analogs from maize, sorghum, and wheat. None of the five loci identified by the gene analogs were linked to the Pca locus. The linkage map was compared with previously published diploid and hexaploid linkage maps in an attempt to identify homologous or homoeologous chromosomes between populations. Locus orders and linkage relationships were poorly conserved between the A. strigosa × A. wiestii map and other Avena maps. In spite of mapping complications due to duplications within a basic genome as well as the allopolyploid constitution of many Avena species, such map comparisons within Avena provide further evidence of substantial chromosomal rearrangement between species within Avena.Key words: grasses, oat, genetic mapping, homoeology.Une population constituée de 100 lignées recombinantes fixées dérivées en F[sub 6] a été produite à partir d'un croisement entre deux accessions diploïdes (2n = 14) de l'Avena : CI3815 (A. strigosa) et CI1994 (A. wiestii). Des sondes RFLP précédemment utilisées pour la cartographie chez d'autres graminées ont été employées pour développer une carte cadre comparer l'organisation des génomes. Neuf linkats ont été identifiés parmi les 181 locus étudiés. La densité moyenne des marqueurs était de 5 cM et la taille totale de la carte était de 880 cM. Un îlot dense de cinq gènes conférant la résistance à la rouille couronnée (Pca) a été localisé sur la carte tout comme cinq locus correspondant à des analogues de gènes de résistance en provenance du maïs, du sorgho et du blé. Aucun des cinq locus identifiés n'était lié au locus Pca. La carte génétique a été comparée à des cartes publiées antérieurement pour des avoines diploïdes ou hexaploïdes afin d'identifier des chromosomes homologues ou homéologues entre populations. L'ordre des locus et les distances étaient très mal conservés entre la carte tirée du croisement A. strigosa × A. wiestii et les autres cartes pour le genre Avena. En dépit des complications qu'entraînent les duplications au sein du génome de base et l'allopolyploïdie de plusieurs espèces d'Avena, de telles comparaisons de cartes génétiques procurent des évidences additionnelles quant à l'existence d'importantes différences au niveau de l'arrangement des chromosomes parmi les espèces du genre Avena.Mots clés : graminées, avoine, cartographie génétique, homéologie. [ABSTRACT FROM AUTHOR]