Male and female genetic linkage map of hops, Humulus lupulus

A male and female linkage map of hop has been constructed using 224 DNA polymorphisms (106 amplified fragment length polymorphisms (AFLPs), three random amplified polymorphic DNAs (RAPDs), one RAPD‐sequence‐tagged‐site (STS), and three microsatellite (STSs) segregating in an F₁ population of the English cultivar ‘Wye Target’‐the German male breeding line ‘85/54/15’. Linkage between these loci was estimated using JOINMAP Version 2.0. The final map for the female parent consisted of 110 loci assigned to eight linkage groups covering a distance of 346.7 cM. For the male map, 57 loci could be mapped on nine linkage groups spanning over 227.4 cM. One of these male linkage groups (Gr09‐M) presumably represents the Y chromosome, since all markers assigned (10 AFLPs, three RAPDs and one STS) were closely linked to the male sex (M). Because of their sex‐specific segregation, 10 doubly heterozygous AFLPs spanning a distance of 18.7 cM could be identified as markers describing the X chromosome, which is part of the male and female map. Three STMSs, which had already proved useful in hop genotyping, could be integrated as codominant locus‐specific markers and thus allowed to produce reliable allelic bridges between the female and male counterparts.     

Genetic mapping of AFLP markers in Japanese bunching onion (<Emphasis Type="Italic">Allium fistulosum</Emphasis>)

Summary The first genetic linkage map of Japanese bunching onion (Allium fistulosum) based primarily on AFLP markers was constructed using reciprocally backcrossed progenies. They were 120 plants each of (P₁)BC₁ and (P₂)BC₁ populations derived from a cross between single plants of two inbred lines: D1s-15s-22 (P₁) and J1s-14s-20 (P₂). Based on the (P₂)BC₁ population, a linkage map of P₁ was constructed. It comprises 164 markers – 149 amplified fragment length polymorphisms (AFLPs), 2 cleaved amplified polymorphic sequences (CAPSs), and 12 simple sequence repeats (SSRs) from Japanese bunching onion, and 1 SSR from bulb onion (A. cepa) – on 15 linkage groups covering 947 centiMorgans (cM). The linkage map of P₂ was constructed with the (P₁)BC₁ population and composed of 120 loci – 105 AFLPs, 1 CAPS, and 13 SSRs developed from Japanese bunching onion and 1 SSR from bulb onion – on 14 linkage groups covering 775 cM. Both maps were not saturated but were considered to cover the majority of the genome. Nine linkage groups in P₂ map were connected with their counterparts in P₁ map using co-dominant anchor markers, 13 SSRs and 1 CAPS.     

A genetic linkage map of Physocarpus,a member of the Spiraeoideae (Rosaceae), based on RAPD,AFLP, RGA,SSR and gene specific markers

Physocarpus opulifolius is a deciduous shrub native to North America belonging to the Spiraeoideae subfamily of the Rosaceae. The cultivars ‘Luteus’ and ‘Diabolo’ are grown in gardens for their ornamental foliage, golden and purple respectively. We developed a linkage map of P. opulifolius with a view to detecting markers for the leaf colour genes, which are under major gene control. A total of 162 molecular markers (128 RAPDs, 27 AFLPs, three RGA, three STS markers and one SSR) and the leaf colour genes Pur and Aur were scored in the Physocarpus progeny and used to create a linkage map covering 586.1 cM over nine linkage groups. There was an average of 18.2 markers per linkage group and a mean linkage group length of 65.1 cM. Both leaf colour genes were mapped. This is the first reported linkage map of a member of the Spireaeoideae and the mapping of a small number of transferable markers has demonstrated its utility to comparative mapping, which will complement existing comparative mapping efforts in other rosaceous subfamilies.     

Genetic linkage map construction for white jute (Corchorus capsularis L.) using SRAP,ISSR and RAPD markers

White jute (Corchorus capsularis) and dark jute (Corchorus olitorius) are two important cultivated crops that are used for natural fibre production. Some genetic maps have been developed for dark jute, but the genetic map information for white jute (C. capsularis) is limited. In this study, a linkage map comprising 44 sequence‐related amplified polymorphisms (SRAPs), 57 intersimple sequence repeats (ISSRs) and 18 randomly amplified polymorphic DNA (RAPD) covering 2185.7 cM with a mean density of 18.7 cM per locus was constructed in an F₂ population consisting of 185 individuals derived from a cross between two diverse genotypes of ‘Xinxuan No. 1’ and ‘Qiongyueqing’ in white jute. These markers were evenly distributed in the linkage groups without any clustering. This genetic linkage map construction will facilitate the mapping of agronomic traits and marker‐assisted selection breeding in white jute.     

A high-density integrative linkage map for <Emphasis Type="Italic">Gossypium hirsutum</Emphasis>

Sequence-related amplified polymorphism (SRAP) combined with SSRs, RAPDs, and RGAPs was used to construct a high density genetic map for a F₂ population derived from the cross DH962 (G. hirsutum accession) × Jimian5 (G. hirsutum cultivar). A total of 4,096 SRAP primer combinations, 6310 SSRs, 600 RAPDs, and 10 RGAPs produced 331, 156, 17 and 2 polymorphic loci, respectively. Among the 506 loci obtained, 471 loci (309 SRAPs, 144 SSRs, 16 RAPDs and 2 RGAPs) were assigned to 51 linkage groups. Of these, 29 linkage groups were assigned to corresponding chromosomes by SSR markers with known chromosome locations. The map covered 3070.2 cM with a mean density of 6.5 cM per locus. The segregation distortion in this population was 9.49%, and these distorted loci tend to cluster at the end of linkage groups or in minor clusters on linkage groups. The majority of SRAPs in this map provided an effective tool for map construction in G. hirsutum despite of its low polymorphism. This high-density linkage map will be useful for further genetic studies in Upland cotton, including mapping of loci controlling quantitative traits, and comparative and integrative analysis with other interspecific and intraspecific linkage maps in cotton.     

A skeletal linkage map of Hordeum bulbosum L. and comparative mapping with barley (H. vulgare L.)

A restriction fragment length polymorphism (RFLP) based linkage map of a cross between two diploid Hordeum bulbosum (2n = 2x = 14) clones, PB1 and PB11, was constructed from 46 recombinant progeny clones. Since both parents are heterozygous, separate and combined parental maps were constructed. All of the RFLP markers screened had previously been mapped in barley (H. vulgare L.) so that comparative maps could be produced. The PB1 linkage map consists of 20 RFLP marker loci assigned to four linkage groups covering 94.3 cM. The PB11 linkage map consists of 27 RFLP marker loci assigned to six linkage groups covering 149.1 cM. Thirteen markers polymorphic in both parents were used as ‘anchors’ to create a combined linkage map consisting of 38 loci assigned to six linkage groups and covering a genetic distance of 198 cM. Marker order was highly conserved in a comparison with the linkage map of H. vulgare (Laurie etal., 1995). However, in contrast, the genetic distances for the same markers were very different being 649 cM and 198 cM respectively, a genetic distance ratio of 1: 3.3. Thus although the map was short, it can be presumed to cover half the genome of H. bulbosum. This study provides further confirmation of the close relationship between the two species and gives a basis for the development of marker mediated introgression through interspecific hybridisation between the two species. This revised version was published online in July 2006 with corrections to the Cover Date.     

The first genetic linkage map of crape myrtle (Lagerstroemia) based on amplification fragment length polymorphisms and simple sequence repeats markers

Lagerstroemia (crape myrtle) are famous ornamental plants with large pyramidal racemes, long flower duration and diverse colours. Genetic maps provide an important genomic resource of basic and applied significance. A genetic linkage map was developed by genotyping 192 F₁ progeny from a cross between L. caudata (female) and L. indica (‘Xiang Xue Yun’) (male) with a combination of amplification fragment length polymorphisms (AFLP) and simple sequence repeats (SSR) markers in a double pseudo‐testcross mapping strategy. A total of 330 polymorphic loci consisting of 284 AFLPs and 46 SSRs showing Mendelian segregation were generated from 383 AFLP primer combinations and 150 SSR primers. The data were analysed using JoinMap 4.0 (evaluation version) to construct the linkage map. The map consisted of 20 linkage groups of 173 loci (160 AFLPs and 13 SSRs) covering 1162.1 cM with a mean distance of 10.69 cM between adjacent markers. The 20 linkage groups contained 2–49 loci and ranged in length from 7.38 to 163.57 cM. This map will serve as a framework for mapping QTLs and provide reference information for future molecular breeding work.     

Construction of integrated linkage map of a recombinant inbred line population of white lupin (Lupinus albus L.)

We report the development of a Diversity Arrays Technology (DArT) marker panel and its utilisation in the development of an integrated genetic linkage map of white lupin (Lupinus albus L.) using an F₈ recombinant inbred line population derived from Kiev Mutant/{"type":"entrez-protein","attrs":{"text":"P27174","term_id":"14195583","term_text":"P27174"}}P27174. One hundred and thirty-six DArT markers were merged into the first genetic linkage map composed of 220 amplified fragment length polymorphisms (AFLPs) and 105 genic markers. The integrated map consists of 38 linkage groups of 441 markers and spans a total length of 2,169 cM, with an average interval size of 4.6 cM. The DArT markers exhibited good genome coverage and were associated with previously identified genic and AFLP markers linked with quantitative trait loci for anthracnose resistance, flowering time and alkaloid content. The improved genetic linkage map of white lupin will aid in the identification of markers for traits of interest and future syntenic studies.     

A high‐resolution einkorn (Triticum monococcum L.) linkage map involving wild,domesticated and feral einkorn genotypes

A high‐resolution consensus linkage map of Triticum monococcum was assembled from two separate maps involving domesticated, feral and wild einkorn wheat accessions. The genotyping‐by‐sequencing (GBS) approach based on DArTseq markers yielded overstretched maps. Deleting all markers with missing data and then converting dubious singletons to missing data produced two maps of about 1,380 cM, close to the published genome size. The consensus map spanned 1,562 cM, had one bin mapped every 0.92 cM and showed only one gap > 10 cM. Chromosome length varied between 151 cM (chromosome 4) and 270 cM (chromosome 7). The consensus map was compared to other A‐genome maps, and the sequences of genetically mapped DArTseq were used to anchor contigs of the T. monococcum, T. urartu and T. aestivum draft genomes based on sequence homology to assess colinearity and to assign mapped markers to the seven chromosomes of the bread wheat A‐genome. Finally, an in silico functional characterization of the sequences was performed. This high‐resolution map will facilitate QTL and association analysis and assist the genome assembly of the einkorn genome.     

Genetic linkage map of cassava (Manihot esculenta Crantz) based on AFLP and SSR markers

To generate a genetic linkage map of cassava ( Manihot esculenta Crantz), 58 F₁ progenies from a cross between Rayong 90 (female) and Rayong 5 (male) were examined in amplification fragment length polymorphism (AFLP) and simple sequence repeat (SSR) analyses. A total of 469 polymorphic markers consisting of 378 AFLPs generated from 76 primer combinations and 91 SSRs were identified. These markers were analyzed using the joinmap ^® 3.0 package program to construct a genetic linkage map. A total of 33 linkage groups of a common map were constructed from 119 AFLPs and 18 SSRs, spanning 1095 cM with an average of 7.99 cM between markers. The genetic linkage map generated in this study will be useful for genetic studies in cassava particularly for the identification of genetic markers linked to traits of interest, although the complex cassava genome suggests that maybe a long term objective.     

The first genetic maps of cashew (Anacardium occidentale L.)

Cashew (Anacardium occidentale) is a widespread tropical tree crop that is grown primarily for its nuts and has a global production of over 2 million Mt. In spite of its economic importance to many countries, however, no linkage map containing STS anchor sites has yet been produced for this species. This is largely attributable to a prolonged juvenile phase of the tree (limiting mapping to F₁ progenies) and difficulty in effecting sufficient hand-pollinations to create mapping populations of effective size. Here, we produce an F₁ mapping population of 85 individuals from a cross between CP 1001 (dwarf commercial clone) and CP 96 (giant genotype), and use it to generate two linkage genetic maps comprising of 205 genetic markers (194 AFLP and 11 SSR markers). The female map (CP 1001) contains 122 markers over 19 linkage groups and the male map (CP 96) comprises 120 markers assembled over 23 linkage groups. The total map distance of the female map is 1050.7 cM representing around 68% genome coverage, whereas the male map spans 944.7 cM (64% coverage). The average map distance between markers is 8.6 cM in the female map and 7.9 cM in the male map. Homology between the two maps was established between 13 linkage groups of the female map and 14 of the male map using 46 bridging markers that include 11 SSR markers. These maps represent a platform from which to identify loci controlling economically important traits in this crop.     

Clustering of amplified fragment length polymorphism markers in a linkage map of rye

Amplified fragment length polymorphisms (AFLPs) are now widely used in DNA fingerprinting and genetic diversity studies, the construction of dense genetic maps and in fine mapping of agronomically important traits. The AFLP markers have been chosen as a source to extend and saturate a linkage map of rye, which has previously been generated by means of restriction fragment length polymorphism, random amplified polymorphic DNA, simple sequence repeat and isozyme markers. Gaps between linkage groups, which were known to be part of chromosome 2R, have been closed, thus allowing the determination of their correct order. Eighteen EcoRI‐MseI primer combinations were screened for polymorphism and yielded 148 polymorphic bands out of a total of 1180. The level of polymorphism among the different primer combinations varied from 5.7% to 33.3%. Eight primer combinations, which revealed most polymorphisms, were further analysed in all individuals of the F₂ mapping population. Seventy‐one out of 80 polymorphic loci could be integrated into the linkage map, thereby increasing the total number of markers to 182. However, 46% of the mapped AFLP markers constituted four major clusters located on chromosomes 2R, 5R and 7R, predominantly in proximity to the centromere. The integration of AFLP markers caused an increase of 215 cM, which resulted in a total map length of almost 1100 cM.     

A genetic linkage map of <Emphasis Type="Italic">Populus adenopoda</Emphasis> Maxim. × <Emphasis Type="Italic">P. alba</Emphasis> L. hybrid based on SSR and SRAP markers

Populus adenopoda Maxim. and P. alba L. [section Populus (aspen), genus Populus] are two tree species of ecological and economic value. To date, no high-density genetic maps are available for these two species. In this study, 1100 interspecific hybrids were obtained by controlled crossing and embryo culture. Simple sequence repeat (SSR) and sequence-related amplified polymorphisms (SRAP) were used to genotype 189 F₁ individuals. The genetic linkage map of P. adenopoda × P. alba generated from this study includes 212 markers (192 SSRs and 50 SRAPs) and consists of 26 linkage groups spanning 2178.5 cM, with an average distance of 11.7 cM between markers. This is the first SSR- and SRAP-containing genetic linkage map for aspen. The SSRs on the map will serve both as bridges for comparison with the poplar maps published to date and as a direct link to the Populus genomic sequence. Future studies focusing on the data presented here should enhance the density and precision of the map for identifying and localizing quantitative trait loci and promote genomic research on the genus.     

Mapping genes for double podding and other morphological traits in chickpea

Seed traits are important considerations for improving yield and product quality of chickpea (Cicer arietinum L.). The purpose of this study was to construct an intraspecific genetic linkage map and determine map positions of genes that confer double podding and seed traits using a population of 76 F₁₀ derived recombinant inbred lines (RILs) from the cross of ‘ICCV-2’ (large seeds and single pods) × ‘JG-62’ (small seeds and double podded). We used 55 sequence-tagged microsatellite sites (STMS), 20 random amplified polymorphic DNAs (RAPDs), 3inter-simple sequence repeats (ISSR) and 2 phenotypic markers to develop a genetic map that comprised 14 linkage groups covering297.5 cM. The gene for double podding (s) was mapped to linkage group 6 and linked to Tr44 and Tr35 at a distance of7.8 cM and 11.5 cM, respectively. The major gene for pigmentation, C, was mapped to linkage group 8 and was loosely linked to Tr33 at a distance of 13.5 cM. Four QTLs for 100 seed weight (located on LG4 and LG9), seed number plant^-1 (LG4), days to 50% flower (LG3) were identified. This intraspecific map of cultivated chickpea is the first that includes genes for important morphological traits. Synteny relationships among STMS markers appeared to be conserved on six linkage groups when our map was compared to the interspecific map presented by Winter et al. (2000). This revised version was published online in August 2006 with corrections to the Cover Date.     

Mapping of quantitative trait loci controlling partial resistance against rust incited by <Emphasis Type="Italic">Uromyces pisi</Emphasis> (Pers.) Wint. in a <Emphasis Type="Italic">Pisum fulvum</Emphasis> L. intraspecific cross

A quantitative trait loci (QTL) associated with resistance to pea rust, caused by the fungus Uromyces pisi (Pers.) Wint., has been identified in a F₂ population derived from an intraspecific cross between two wild pea (Pisum fulvum L.) accessions, IFPI3260 (resistant) and IFPI3251 (susceptible). Both parental lines and all the segregating population displayed a fully compatible interaction (high infection type), which indicates absence of hypersensitive response. Nevertheless, differences on the percentage of symptomatic area of the whole plant (disease severity) were observed. A genetic map was developed covering 1283.3 cM and including 146 markers (144 random amplified polymorphic DNA (RAPDs) and two sequence tagged sites (STSs) markers) distributed in 9 linkage groups. A QTL explaining 63% of the total phenotypic variation was located in linkage group 3. RAPDs markers (OPY11₁₃₁₆ and OPV17₁₀₇₈) flanking this QTL should allow, after their conversion in SCARs, a reliable marker-assisted selection for rust resistance.     

A new citrus linkage map based on SRAP,SSR, ISSR,POGP, RGA and RAPD markers

Sequence-related amplified polymorphism (SRAP), simple sequence repeats (SSR), inter-simple sequence repeat (ISSR), peroxidase gene polymorphism (POGP), resistant gene analog (RGA), randomly amplified polymorphic DNA (RAPD), and a morphological marker, Alternaria brown spot resistance gene of citrus named as Cabsr caused by (Alternaria alternata f. sp. Citri) were used to establish genetic linkage map of citrus using a population of 164 F₁ individuals derived between ‘Clementine’ mandarin (Citrus reticulata Blanco ‘Clementine) and ‘Orlando’ tangelo’ (C. paradisi Macf. ‘Duncan’ × C. reticulata Blanco ‘Dancy’). A total of 609 markers, including 385 SRAP, 97 RAPD, 95 SSR, 18 ISSR, 12 POGP, and 2 RGA markers were used in linkage analysis. The ‘Clementine’ linkage map has 215 markers, comprising 144 testcross and 71 intercross markers placed in nine linkage groups. The ‘Clementine’ linkage map covered 858 cM with and average map distance of 3.5 cM between adjacent markers. The ‘Orlando’ linkage map has 189 markers, comprising 126 testcross and 61 intercross markers placed in nine linkage groups. The ‘Orlando’ linkage map covered 886 cM with an average map distance of 3.9 cM between adjacent markers. Segregation ratios for Cabsr were not significantly different from 1:1, suggesting that this trait is controlled by a single locus. This locus was placed in ‘Orlando’ linkage group 1. The new map has an improved distribution of markers along the linkage groups with fewer gaps. Combining different marker systems in linkage mapping studies may give better genome coverage due to their chromosomal target site differences, therefore fewer gaps in linkage groups.     

Linkage map construction and mapping QTL for cotton fibre quality using SRAP, SSR and RAPD

Tetraploid cotton is one of the most extensively cultivated species. Two tetraploid species, Gossypium hirsutum L. and G. barbadense L., dominate the world's cotton production. To better understand the genetic basis of cotton fibre traits for the improvement of fibre quality, a genetic linkage map of tetraploid cotton was constructed using sequence‐related amplified polymorphisms (SRAPs), simple sequence repeats (SSRs) and random amplified polymorphic DNAs (RAPDs). A total of 238 SRAP primer combinations, 368 SSR primer pairs and 600 RAPD primers were used to screen polymorphisms between G. hirsutum cv. Handan208 and G. barbadense cv. Pima90 which revealed 749 polymorphic loci in total (205 SSRs, 107 RAPDs and 437 SRAPs). Sixty‐nine F₂ progeny from the interspecific cross of ‘Handan208’בPima90’ were genotyped with the 749 polymorphic markers. A total of 566 loci were assembled into 41 linkage groups with at least three loci in each group. Twenty‐eight linkage groups were assigned to corresponding chromosomes by SSR markers with known chromosome locations. The map covered 5141.8 cM with a mean interlocus space of 9.08 cM. A × test for significance of deviations from the expected ratio (1: 2: 1 or 3: 1) identified 135 loci (18.0%) with skewed segregation, most of which had an excess of maternal parental alleles. In total, 13 QTL associated with fibre traits were detected, among which two QTL were for fibre strength, four for fibre length and seven for micronaire value. These QTL were on nine linkage groups explaining 16.18‐28.92% of the trait variation. Six QTL were located in the A subgenome, six QTL in the D subgenome and one QTL in an unassigned linkage group. There were three QTL for micronaire value clustered on LG1, which would be very useful for improving this trait by molecular marker‐assisted selection.     

Construction of a high-density reference linkage map of tea (Camellia sinensis)

A few linkage maps of tea have been constructed using pseudo-testcross theory based on dominant marker systems. However, dominant markers are not suitable as landmark markers across a wide range of materials. Therefore, we developed co-dominant SSR markers from genomic DNA and ESTs and constructed a reference map using these co-dominant markers as landmarks. A population of 54 F₁ clones derived from reciprocal crosses between ‘Sayamakaori’ and ‘Kana-Ck17’ was used for the linkage analysis. Maps of both parents were constructed from the F₁ population that was taken for BC₁ population. The order of most of the dominant markers in the parental maps was consistent. We constructed a core map by merging the linkage data for markers that detected polymorphisms in both parents. The core map contains 15 linkage groups, which corresponds to the basic chromosome number of tea. The total length of the core map is 1218 cM. Here, we present the reference map as a central core map sandwiched between the parental maps for each linkage group; the combined maps contain 441 SSRs, 7 CAPS, 2 STS and 674 RAPDs. This newly constructed linkage map can be used as a basic reference linkage map of tea.     

High resolution map of eggplant (Solanum melongena) reveals extensive chromosome rearrangement in domesticated members of the Solanaceae

A linkage map of eggplant was constructed for an interspecific F₂ population derived from a cross between Solanum linnaeanum MM195 and S. melongena MM738. The map contains 400 AFLP^® (amplified fragment length polymorphism), 348 RFLP (restriction fragment length polymorphism) and 116 COSII (conserved ortholog set) markers. The 864 mapped markers encompass 12 linkage groups, span 1,518 cM and are spaced at an average interval of 1.8 cM. Use of orthologous markers allowed confirmation of the established syntenic relationships between eggplant and tomato chromosomes and helped delineate the nature of the 33 chromosomal rearrangements and 11 transpositions distinguishing the two species. This genetic map provides a 2- to 3-fold improvement in marker density compared to previously published interspecific maps. Because the interspecific mapping population is rich in morphological variation, this greater genome saturation will be useful for QTL (quantitative trait locus) analyses. The recent release of the tomato genome sequence will provide additional opportunities for exploiting this map for comparative genomics and crop improvement.