Inheritance and molecular mapping of a downy mildew resistance gene, Pl 13 in cultivated sunflower (Helianthus annuus L.)

The inheritance of resistance to sunflower downy mildew (SDM) derived from HA-R5 conferring resistance to nine races of the pathogen has been determined and the new source has been designated as Pl ₁₃ . The F₂ individuals and F₃ families of the cross HA-R5 (resistant) × HA 821 (susceptible) were screened against the four predominant SDM races 300, 700, 730, and 770 in separate tests which indicated dominant control by a single locus or a cluster of tightly linked genes. Bulked segregant analysis (BSA) was carried out on 116 F₂ individuals with 500 SSR primer pairs that resulted in the identification of 10 SSR markers of linkage groups 1 (9 markers) and 10 (1 marker) of the genetic map (Tang et al. in Theor Appl Genet 105:1124–1136, 2002) that distinguished the bulks. Of these, the SSR marker ORS 1008 of linkage group 10 was tightly linked (0.9 cM) to the Pl ₁₃ gene. Genotyping the F₂ population and linkage analysis with 20 polymorphic primer pairs located on linkage group 10 failed to show linkage of the markers with downy mildew resistance and the ORS 1008 marker. Nevertheless, validation of polymorphic SSR markers of linkage group 1 along with six RFLP-based STS markers of linkage group 12 of the RFLP map of Jan et al. (Theor Appl Genet 96:15–22, 1998) corresponding to linkage group 1 of the SSR map, mapped seven SSR markers (ORS 965-1, ORS 965-2, ORS 959, ORS 371, ORS 716, and ORS 605) including ORS 1008 and one STS marker (STS10D6) to linkage group 1 covering a genetic distance of 65.0 cM. The Pl ₁₃ gene, as a different source with its location on linkage group 1, was flanked by ORS 1008 on one side at a distance of 0.9 cM and ORS 965-1 on another side at a distance of 5.8 cM. These closely linked markers to the Pl ₁₃ gene provide a valuable basis for marker-assisted selection in sunflower breeding programs.     

Molecular mapping of the Rf 3 fertility restoration gene to facilitate its utilization in breeding confection sunflower

The inheritance of a previously identified dominant Rf gene in the confection sunflower line RHA 280 has been determined and designated as Rf ₃ . This study reports the mapping of the Rf ₃ locus using an F2 population of 227 individuals derived from CMS HA 89-3149 × RHA 280. Bulked segregant analysis with 624 pairs of simple sequence repeat (SSR) primers and sequence tagged site (STS) primers identified two polymorphic SSR markers each of linkage groups (LGs) 7 and 11 from a previous map. Results on 90 F2 individuals with 42 polymorphic markers of LGs 7 and 11 indicated that the Rf ₃ gene was linked with eight markers on LG 7, including five SSR markers (ORS328, ORS331, ORS928, ORS966, and ORS1092) and three expressed sequence tag (EST)-SSR markers (HT619-1, HT619-2, and HT1013). Further analysis of the total F2 population of 227 individuals identified a co-dominant marker, ORS328, linked to Rf ₃ at a genetic distance of 0.7 cM on one side, and a female-dominant marker HT1013 at 12.6 cM proximal to Rf ₃ on the other side; a genetic distance of 47.1 cM for LG 7 was covered. This is the first report of an Rf gene from the confection sunflower. The closely linked marker to Rf ₃ will facilitate marker-assisted selection, and provide a basis for cloning of this gene.     

Molecular analysis of the high stearic acid content in sunflower mutant CAS-14

Increasing the stearic acid content to improve sunflower (Helianthus annuus L.) oil quality is a desirable breeding objective for food-processing applications. CAS-14 is a sunflower mutant line with a high stearic acid content in its seed oil (>35% vs. <6% in currently grown sunflower hybrids), which is controlled by the Es3 gene. However, the expression of the high stearic acid character in CAS-14 is strongly influenced by temperature during seed maturation and it is not uniform along the seed. The objectives of this study were (1) to identify PCR-based molecular markers linked to the Es3 gene from CAS-14, (2) to map this gene on the sunflower genetic map, and (3) to characterize the interaction between CAS-14 and CAS-3, a sunflower high stearic acid (about 26%) mutant line with the Es1 and Es2 genes determining this trait. Two F₂ mapping populations were developed from crosses between CAS-14 and P21, a nuclear male sterile line with the Ms₁₁ gene controlling this character, and between CAS-14 and CAS-3. One hundred and thirty-three individuals from P21×CAS-14, and 164 individuals from CAS-3×CAS-14 were phenotyped in F₂ and F₃ seed generations for fatty acid composition using gas–liquid chromatography, and they were then genotyped with microsatellite [simple sequence repeat (SSR)] and insertion–deletion (INDEL) markers. Bulk segregant analysis in the P21×CAS-14 population identified two markers on LG 8 putatively linked to Es3. A large linkage group was identified using additional markers mapping to LG 8. Es3 mapped to the distal half of LG 8 and was flanked by the SSR markers ORS243 and ORS1161 at genetic distances of 0.5, and 3.9 cM, respectively. The Ms₁₁ gene was also mapped to LG 8 and genetic distance between this gene and Es3 was found to be 7.4 cM. In the CAS-3×CAS-14 population, two QTLs were identified on LG 1 and LG 8, which underlie the Es1 gene from CAS-3 and the Es3 gene from CAS-14, respectively. A significant epistatic interaction between these two QTLs was found. Results from this study provided a basis for determining CAS-14 efficient breeding strategies.     

Chromosome location, DNA markers and rust resistance of the sunflower gene R 5

Sunflower rust, caused by the fungus Puccinia helianthi Schwein., was not a serious problem for many decades because of successful deployment of effective resistance genes in commercial sunflower (Helianthus annuus L.) hybrids in North America. In the 1980s and early 1990s, however, a shift in virulence of the rust race population in North America rendered most of the commercial hybrids susceptible to new virulent races. A germplasm line, HA-R2, carrying the rust resistance gene R ₅ was released as a multi-race rust-resistant line in 1985 but has not been widely used in commercial hybrid production. R ₅ remains effective against the prevalent rust races of sunflower in North America. This gene was previously reported to be associated with two simple sequence repeat (SSR) markers, ORS316 and ORS630, which were mapped to linkage group (LG) 13 of sunflower. However, out of the 63 markers of LG13 screened in the present study, only 18, including ORS316 and ORS630, were polymorphic. These markers, which covered all of LG 13, were assayed in 94 individual F2 progenies derived from the cross of HA 89 with HA-R2. All failed to detect any locus in LG13 associated with the gene R ₅ . Subsequently, a bulked segregant analysis was employed with an additional 510 SSR markers selected from the remaining 16 LGs of the sunflower genome. This analysis demonstrated that the LG2 markers showed association with rust resistance. Genotyping of the 94 F2 individuals with 23 polymorphic SSR markers from LG2 confirmed the R ₅ location on LG2, flanked by two SSR markers, ORS1197-2 and ORS653a, at 3.3 and 1.8?cM of genetic distance, respectively. The markers for R ₅ developed in this study will provide a useful tool for speeding up deployment of the R ₅ gene in commercial sunflower hybrid production.     

Molecular mapping of a nuclear male-sterility gene in sunflower (Helianthus annuus L.) using TRAP and SSR markers

A nuclear male-sterile mutant, NMS 360, induced by streptomycin from an inbred maintainer line HA 89, possesses a single recessive gene, ms9, controlling male sterility. The present study identified DNA markers linked to the ms9 gene in an F₂ population derived from the cross of NMS 360 × RHA 271 and maps the ms9 gene to an existing sunflower SSR linkage map. Bulked segregant analysis was performed using the target region amplification polymorphism (TRAP) marker technique and the simple sequence repeats (SSR) technique. From 444 primer combinations, six TRAP markers linked with the ms9 gene were amplified. Two markers, Ts4p03-202 and Tt3p09-529, cosegregated with the ms9 gene. The other four markers, To3d14-310, Tt3p17-390, Ts4p23-300, and Tt3p09-531, linked with ms9 at a distance of 1.2, 3.7, 10.3, and 22.3 cM, respectively. Thirty SSR primers from 17 linkage groups of a PHA × PHB cultivated sunflower linkage map were screened among the two parents and the F₂ population. SSR primer ORS 705 of linkage group 10 was tightly linked to ms9 at a distance of 1.2 cM. The ms9 gene was subsequently mapped to linkage group 10 of the public sunflower SSR linkage map. The markers that were tightly linked with the ms9 gene will be useful in marker-assisted selection of male-sterile plants among segregating populations, and will facilitate the isolation of the ms9 gene by map-based cloning.     

Mapping minor QTL for increased stearic acid content in sunflower seed oil

Increased stearic acid (C18:0) content in the seed oil of sunflower would improve the oil quality for some edible uses. The sunflower line CAS-20 (C18:0 genotype Es1Es1es2es2), developed from the high C18:0 mutant line CAS-3 (C18:0 genotype es1es1es2es2; 25% C18:0), shows increased C18:0 levels in its seed oil (8.6%). The objective of this research was to map quantitative trait loci (QTL) conferring increased C18:0 content in CAS-20 in an F₂ mapping population developed from crosses between HA-89 (wild type Es1Es1Es2Es2; low C18:0) and CAS-20, which segregates independently of the macromutation Es1 controlling high C18:0 content in CAS-3. Seed oil fatty acid composition was measured in the F₂ population by gas-liquid chromatography. A genetic linkage map of 17 linkage groups (LGs) comprising 80 RFLP and 19 SSR marker loci from this population was used to identify QTL controlling fatty acid composition. Three QTL affecting C18:0 content were identified on LG3, LG11, and LG13, with all alleles for increased C18:0 content inherited from CAS-20. In total, these QTL explained 43.6% of the C18:0 phenotypic variation. Additionally, four candidate genes (two stearate desaturase genes, SAD6 and SAD17, and a FatA and a FatB thioesterase gene) were placed on the QTL map. On the basis of positional information, QTL on LG11 was suggested to be a SAD6 locus. The results presented show that increased C18:0 content in sunflower seed oil is not a simple trait, and the markers flanking these QTL constitute a powerful tool for plant breeding programs.     

<Emphasis Type="Italic">Pl</Emphasis><Subscript><Emphasis Type="Italic">Arg</Emphasis></Subscript> from <Emphasis Type="Italic">Helianthus argophyllus</Emphasis> is unlinked to other known downy mildew resistance genes in sunflower

The Pl _Arg locus in the sunflower (Helianthus annuus L.) inbred line Arg1575-2 conferring resistance to at least four tested races (300, 700, 730, 770) of downy mildew (Plasmopara halstedii) was localized by the use of simple sequence repeat (SSR) markers. Bulked segregant analysis (BSA) was conducted on 126 individuals of an F₂ progeny from a cross between a downy mildew susceptible line, CmsHA342, and Arg1575-2. Twelve SSR markers linked to the Pl _Arg locus were identified. All markers were located proximal to Pl _Arg on linkage group LG1 based on the map of Yu et al. (2003) in a window of 9.3 cM. Since Pl _Arg was mapped to a linkage group different from all other Pl genes previously mapped with SSRs, it can be concluded that Pl _Arg provides a new source of resistance against P. halstedii in sunflower.     

An enhanced microsatellite map of diploid Fragaria

A total of 45 microsatellites (SSRs) were developed for mapping in Fragaria. They included 31 newly isolated codominant genomic SSRs from F. nubicola and a further 14 SSRs, derived from an expressed sequence tagged library (EST-SSRs) of the cultivated strawberry, F. × ananassa. These, and an additional 64 previously characterised but unmapped SSRs and EST-SSRs, were scored in the diploid Fragaria interspecific F₂ mapping population (FV×FN) derived from a cross between F. vesca 815 and F. nubicola 601. The cosegregation data of these 109 SSRs, and of 73 previously mapped molecular markers, were used to elaborate an enhanced linkage map. The map is composed of 182 molecular markers (175 microsatellites, six gene specific markers and one sequence-characterised amplified region) and spans 424 cM over seven linkage groups. The average marker spacing is 2.3 cM/marker and the map now contains just eight gaps longer than 10 cM. The transferability of the new SSR markers to the cultivated strawberry was demonstrated using eight cultivars. Because of the transferable nature of these markers, the map produced will provide a useful reference framework for the development of linkage maps of the cultivated strawberry and for the development of other key resources for Fragaria such as a physical map. In addition, the map now provides a framework upon which to place transferable markers, such as genes of known function, for comparative mapping purposes within Rosaceae.     

Molecular tagging and candidate gene analysis of the high gamma-tocopherol trait in safflower (<Emphasis Type="Italic">Carthamus tinctorius</Emphasis> L.)

Genetic control of the synthesis of high gamma-tocopherol (gamma-T) content in the seed oil of safflower (Carthamus tinctorius L.) and development of highly reliable molecular markers for this trait were determined through molecular tagging and candidate gene approaches. An F2 population was developed by crossing the high gamma-T natural mutant IASC-1 with the CL-1 line (standard, high alpha-T profile). This population segregated for the partially recessive gene Tph2. Bulked segregant analysis with random amplified polymorphic DNA (RAPD) and microsatellite (SSR) markers revealed linkage of eight RAPD and one SSR marker loci to the Tph2 gene and allowed the construction of a Tph2 linkage map. RAPD fragments closest to the Tph2 gene were transformed into sequence-characterized amplified region markers. A gamma-T methyltransferase (gamma-TMT) locus was found to co-segregate with Tph2. The locus/band was isolated, cloned and sequenced and it was confirmed as a gamma-TMT gene. A longer partial genomic DNA sequence from this gene was obtained. IASC-1 and CL-1 sequence alignment showed one non-synonymous and two synonymous nucleotide mutations. Intron fragment length polymorphism and insertion-deletion markers based on the gamma-TMT sequence diagnostic for the Tph2 mutation were developed and tested across 22 safflower accessions, cultivars, and breeding lines. The results from this study provide strong support for the role of the gamma-TMT gene in determining high gamma-T content in safflower and will assist introgression of thp2 alleles into elite safflower lines to develop varieties with improved tocopherol composition for specific market niches.     

Identification of QTLs for resistance to powdery mildew and SSR markers diagnostic for powdery mildew resistance genes in melon (Cucumis melo L.)

Powdery mildew caused by Podosphaera xanthii is an important foliar disease in melon. To find molecular markers for marker-assisted selection, we constructed a genetic linkage map of melon based on a population of 93 recombinant inbred lines derived from crosses between highly resistant AR 5 and susceptible ‘Earl’s Favourite (Harukei 3)’. The map spans 877 cM and consists of 167 markers, comprising 157 simple sequence repeats (SSRs), 7 sequence characterized amplified region/cleavage amplified polymorphic sequence markers and 3 phenotypic markers segregating into 20 linkage groups. Among them, 37 SSRs and 6 other markers were common to previous maps. Quantitative trait locus (QTL) analysis identified two loci for resistance to powdery mildew. The effects of these QTLs varied depending on strain and plant stage. The percentage of phenotypic variance explained for resistance to the pxA strain was similar between QTLs (R ² = 22–28%). For resistance to pxB strain, the QTL on linkage group (LG) XII was responsible for much more of the variance (41–46%) than that on LG IIA (12–13%). The QTL on LG IIA was located between two SSR markers. Using an independent population, we demonstrated the effectiveness of these markers. This is the first report of universal and effective markers linked to a gene for powdery mildew resistance in melon.     

Genetic linkage maps of rose constructed with new microsatellite markers and locating QTL controlling flowering traits

New microsatellites markers [simple sequence repeat (SSR)] have been isolated from rose and integrated into an existing amplified fragment-length polymorphism genetic map. This new map was used to identify quantitative trait locus (QTL) controlling date of flowering and number of petals. From a rose bud expressed sequence tag (EST) database of 2,556 unigenes and a rose genomic library, 44 EST-SSRs and 20 genomic-SSR markers were developed, respectively. These new rose SSRs were used to expand genetic maps of the rose interspecific F₁ progeny. In addition, SSRs from other Rosaceae genera were also tested in the mapping progeny. Genetic maps for the two parents of the progeny were constructed using pseudo-testcross mapping strategy. The maps consist of seven linkage groups of 105 markers covering 432 cM for the maternal map and 136 markers covering 438 cM for the paternal map. Homologous relationships among linkage groups between the maternal and paternal maps were established using SSR markers. Loci controlling flowering traits were localised on genetic maps as a major gene and QTL for the number of petals and a QTL for the blooming date. New SSR markers developed in this study will provide tools for the establishment of a consensus linkage map for roses that combine traits and markers in various rose genetic maps.     

Molecular mapping of the rust resistance gene <Emphasis Type="Italic">R</Emphasis><Subscript><Emphasis Type="Italic">4</Emphasis></Subscript> to a large NBS-LRR cluster on linkage group 13 of sunflower

Rust is a serious fungal disease in the sunflower growing areas worldwide with increasing importance in North America in recent years. Several genes conferring resistance to rust have been identified in sunflower, but few of them have been genetically mapped and linked to molecular markers. The rust resistance gene R ₄ in the germplasm line HA-R3 was derived from an Argentinean open-pollinated variety and is still one of most effective genes. The objectives of this study were to determine the chromosome location of the R ₄ gene and the allelic relationship of R ₄ with the R _adv rust resistance gene. A total of 63 DNA markers previously mapped to linkage group (LG) 13 were used to screen for polymorphisms between two parental lines HA 89 and HA-R3. A genetic map of LG 13 was constructed with 21 markers, resulting in a total map length of 93.8 cM and an average distance of 4.5 cM between markers. Two markers, ZVG61 and ORS581, flanked the R ₄ gene at 2.1 and 0.8 cM, respectively, and were located on the lower end of LG 13 within a large NBS-LRR cluster identified previously. The PCR pattern generated by primer pair ZVG61 was unique in the HA-R3 line, compared to lines HA-R1, HA-R4, and HA-R5, which carry other R ₄ alleles. A SCAR marker linked to the rust resistance gene R _adv mapped to LG 13 at 13.9 cM from the R ₄ locus, indicating that R _adv is not an allele of the R ₄ locus. The markers tightly linked to the R ₄ gene will facilitate gene pyramiding for rust resistance breeding of sunflower.     

Identification and mapping of microsatellite markers linked to a root-knot nematode resistance gene (rkn1) in Acala NemX cotton (Gossypium hirsutum L.)

Host-plant resistance is the most economic and effective strategy for root-knot nematode (RKN) Meloidogyne incognita control in cotton (Gossypium hirsutum L.). Molecular markers linked to resistance are important for incorporating resistance genes into elite cultivars. To screen for microsatellite markers (SSR) closely linked to RKN resistance in G. hirsutum cv. Acala NemX, F₁, F₂, BC₁F₁, and F_2:7 recombinant inbred lines (RILs) from intraspecific crosses and an F₂ from an interspecific cross with G. barbadense cv. Pima S-7 were used. Screening of 284 SSR markers, which cover all the known identified chromosomes and most linkage groups of cotton, was performed by bulked segregant analysis, revealing informative SSRs. The informative SSRs were then mapped on the above populations. One co-dominant SSR marker CIR316 was identified tightly linked to a major resistance gene (designated as rkn1), producing amplified DNA fragments of approximately 221 bp (CIR316a) and 210 bp (CIR316c) in Acala NemX and susceptible Acala SJ-2, respectively. The linkage between CIR316a marker and resistance gene rkn1 in Acala NemX had an estimated distance of 2.1–3.3 cM depending on the population used. Additional markers, including BNL1231 with loose linkage to rkn1 (map distance 25.1–27.4 cM), BNL1066, and CIR003 allowed the rkn1 gene to be mapped to cotton linkage group A03. This is the first report in cotton with a closely linked major gene locus determining nematode resistance, and informative SSRs may be used for marker-assisted selection.     

Exploitation of pepper EST–SSRs and an SSR-based linkage map

As genome and cDNA sequencing projects progress, a tremendous amount of sequence information is becoming publicly available. These sequence resources can be exploited for gene discovery and marker development. Simple sequence repeat (SSR) markers are among the most useful because of their great variability, abundance, and ease of analysis. By in silico analysis of 10,232 non-redundant expressed sequence tags (ESTs) in pepper as a source of SSR markers, 1,201 SSRs were found, corresponding to one SSR in every 3.8 kb of the ESTs. Eighteen percent of the SSR–ESTs were dinucleotide repeats, 66.0% were trinucleotide, 7.7% tetranucleotide, and 8.2% pentanucleotide; AAG (14%) and AG (12.4%) motifs were the most abundant repeat types. Based on the flanking sequences of these 1,201 SSRs, 812 primer pairs that satisfied melting temperature conditions and PCR product sizes were designed. 513 SSRs (63.1%) were successfully amplified and 150 of them (29.2%) showed polymorphism between Capsicum annuum ‘TF68’ and C. chinense ‘Habanero’. Dinucleotide SSRs and EST–SSR markers containing AC-motifs were the most polymorphic. Polymorphism increased with repeat length and repeat number. The polymorphic EST–SSRs were mapped onto the previously generated pepper linkage map, using 107 F₂ individuals from an interspecific cross of TF68 × Habanero. One-hundred and thirtynine EST–SSRs were located on the linkage map in addition to 41 previous SSRs and 63 RFLP markers, forming 14 linkage groups (LGs) and spanning 2,201.5 cM. The EST–SSR markers were distributed over all the LGs. This SSR-based map will be useful as a reference map in Capsicum and should facilitate the use of molecular markers in pepper breeding.Gibum Yi and Je Min Lee equally contributed to this work.     

Quantitative trait loci and candidate gene mapping of aluminum tolerance in diploid alfalfa

Aluminum (Al) toxicity in acid soils is a major limitation to the production of alfalfa (Medicago sativa subsp. sativa L.) in the USA. Developing Al-tolerant alfalfa cultivars is one approach to overcome this constraint. Accessions of wild diploid alfalfa (M. sativa subsp. coerulea) have been found to be a source of useful genes for Al tolerance. Previously, two genomic regions associated with Al tolerance were identified in this diploid species using restriction fragment length polymorphism (RFLP) markers and single marker analysis. This study was conducted to identify additional Al-tolerance quantitative trait loci (QTLs); to identify simple sequence repeat (SSR) markers that flank the previously identified QTLs; to map candidate genes associated with Al tolerance from other plant species; and to test for co-localization with mapped QTLs. A genetic linkage map was constructed using EST-SSR markers in a population of 130 BC₁F₁ plants derived from the cross between Al-sensitive and Al-tolerant genotypes. Three putative QTLs on linkage groups LG I, LG II and LG III, explaining 38, 16 and 27% of the phenotypic variation, respectively, were identified. Six candidate gene markers designed from Medicago truncatula ESTs that showed homology to known Al-tolerance genes identified in other plant species were placed on the QTL map. A marker designed from a candidate gene involved in malic acid release mapped near a marginally significant QTL (LOD 2.83) on LG I. The SSR markers flanking these QTLs will be useful for transferring them to cultivated alfalfa via marker-assisted selection and for pyramiding Al tolerance QTLs.     

Molecular mapping of the Pl 16 downy mildew resistance gene from HA-R4 to facilitate marker-assisted selection in sunflower

The major genes controlling sunflower downy mildew resistance have been designated as Pl genes. Ten of the more than 20 Pl genes reported have been mapped. In this study, we report the molecular mapping of gene Pl(16) in a sunflower downy mildew differential line, HA-R4. It was mapped on the lower end of linkage group (LG) 1 of the sunflower reference map, with 12 markers covering a distance of 78.9 cM. One dominant simple sequence repeat (SSR) marker, ORS1008, co-segregated with Pl(16), and another co-dominant expressed sequence tag (EST)-SSR marker, HT636, was located 0.3 cM proximal to the Pl(16) gene. The HT636 marker was also closely linked to the Pl(13) gene in another sunflower differential line, HA-R5. Thus the Pl(16) and Pl(13) genes were mapped to a similar position on LG 1 that is different from the previously reported Pl(14) gene. When the co-segregating and tightly linked markers for the Pl(16) gene were applied to other germplasms or hybrids, a unique band pattern for the ORS1008 marker was detected in HA-R4 and HA-R5 and their F(1) hybrids. This is the first report to provide two tightly linked markers for both the Pl(16) and Pl(13) genes, which will facilitate marker-assisted selection in sunflower resistance breeding, and provide a basis for the cloning of these genes.     

Soybean molecular linkage group B1 corresponds to classical linkage group 16 based on map location of the <Emphasis Type="Italic">lf</Emphasis><Subscript>2</Subscript> gene

The seven-leaflet character of soybean [Glycine max L. (Merr.)] is a single recessive trait conditioned by the lf ( 2 ) gene. The lf ( 2 ) gene is located on linkage group (LG) 16 of the classical soybean genetic map, but it has not been placed on the molecular map. The objective of this research was to identify the location of the lf ( 2 ) gene on the soybean molecular map using simple sequence repeat (SSR) markers. A backcross breeding method was used to create three- and seven-leaflet near-isogenic lines in genetic backgrounds of 'Traill', 'MN1401', and 'MN1801'. Eight mapping populations were derived from eight single heterozygous Lf ( 2 ) lf ( 2 ) plants. A total of 482 SSR markers that covered approximately every 10-20 cM of all soybean molecular LG were used to screen the mapping populations for polymorphisms. For the 115 SSRs that were identified as polymorphic, possible linkage between the lf ( 2 ) gene and the polymorphic SSR markers was determined. One SSR marker from the LG B1, Sat_272, was linked (LOD > 4.0) to the lf ( 2 ) gene in the Traill and MN1401 derived populations, with map distances ranging from 2.8 to 11.2 cM. Two additional markers (a SSR, Sat_270 and a SNP, A588c) located on LG B1 were also polymorphic and were identified as linked to the lf ( 2 ) gene in one of the populations. This research was successful in mapping the lf ( 2 ) gene to LG B1 of the soybean molecular map and therefore, provides evidence that molecular LG B1 corresponds to classical LG 16.     

Development of simple sequence repeat DNA markers and their integration into a barley linkage map

Simple sequence repeats (SSRs), or microsatellites, are a new class of PCR-based DNA markers for genetic mapping. The objectives of the present study were to develop SSR markers for barley and to integrate them into an existing barley linkage map. DNA sequences containing SSRs were isolated from a barley genomic library and from public databases. It is estimated that the barley genome contains one (GA)_n repeat every 330 kb and one (CA)_n repeat every 620 kb. A total of 45 SSRs were identified and mapped to seven barley chromosomes using doubled-haploid lines and/or wheat-barley addition-line assays. Segregation analysis for 39 of these SSRs identified 40 loci. These 40 markers were placed on a barley linkage map with respect to 160 restriction fragment length polymorphism (RFLP) and other markers. The results of this study demonstrate the value of SSRs as markers in genetic studies and breeding research in barley.     

Development of SSR markers located in the G1 linkage group of apricot (Prunus armeniaca L.) using a bacterial artificial chromosome library

Sixteen simple sequence repeats (SSRs) of apricot (Prunus armeniaca L.) were isolated from a bacterial artificial chromosome (BAC) library. Twelve restriction fragment length polymorphism (RFLP) probes mapped on LG1 of the Prunus general map were hybridized to the BAC library in order to select clones belonging to G1 linkage group of apricot. Selected BACs were digested, subcloned and hybridized with probes containing repeat motifs (GA)₁₀ and (TA)₁₀. Sequencing of the positive subclones revealed 18 unique SSR sequences of which 16 allowed the design of primers flanking the SSR. From the 16 primer pairs, 10 amplified polymorphic markers with an average of observed and expected heterozygosities of 0.44 and 0.68, respectively. The procedure described here proves to be a useful technique for obtaining markers in target areas of a genome.     

Genetic linkage maps of Populus nigra L. including AFLPs, SSRs, SNPs, and sex trait

Black poplar (Populus nigra L.) is a tree of ecological and economic interest. A better knowledge of P. nigra genome is needed for an effective protection and use of its genetic resources. The main objective of this study is the construction of a highly informative genetic map of P. nigra species including genes of adaptive and economic interest. Two genotypes originated from contrasted natural Italian populations were crossed to generate a F₁ mapping pedigree of 165 individuals. Amplification fragment length polymorphism (AFLP), simple sequence repeat (SSR), and single nucleotide polymorphism (SNP) markers were used to genotype 92 F₁ individuals, and the pseudo-test-cross strategy was applied for linkage analysis. The female parent map included 368 markers (274 AFLPs, 91 SSRs, and 3 SNPs) and spanned 2,104 cM with 20 linkage groups, and the male parent map, including 317 markers (205 AFLPs, 106 SSRs, 5 SNPs, and sex trait), spanned 2,453 cM with 23 main linkage groups. The sex, as morphological trait, was mapped on the linkage group XIX of the male parent map. The generated maps are among the most informative in SSRs when compared to the Populus maps published so far and allow a complete alignment with the 19 haploid chromosomes of Populus sequence genome. These genetic maps provide informative tools for a better understanding of P. nigra genome structure and genetic improvement of this ecologically and economically important European tree species. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.