Genetic map of artichoke × wild cardoon: toward a consensus map for <Emphasis Type="Italic">Cynara cardunculus</Emphasis>

An integrated consensus linkage map is proposed for globe artichoke. Maternal and paternal genetic maps were constructed on the basis of an F₁ progeny derived from crossing an artichoke genotype (Mola) with its progenitor, the wild cardoon (Tolfa), using EST-derived SSRs, genomic SSRs, AFLPs, ten genes, and two morphological traits. For most genes, mainly belonging to the chlorogenic acid pathway, new markers were developed. Five of these were SNP markers analyzed through high-resolution melt technology. From the maternal (Mola) and paternal (Tolfa) maps, an integrated map was obtained, containing 337 molecular and one morphological markers ordered in 17 linkage groups (LGs), linked between Mola and Tolfa. The integrated map covers 1,488.8 cM, with an average distance of 4.4 cM between markers. The map was aligned with already existing maps for artichoke, and 12 LGs were linked via 31 bridge markers. LG numbering has been proposed. A total of 124 EST-SSRs and two genes were mapped here for the first time, providing a framework for the construction of a functional map in artichoke. The establishment of a consensus map represents a necessary condition to plan a complete sequencing of the globe artichoke genome.     

Identification of unique expression signatures and therapeutic targets in esophageal squamous cell carcinoma

Background

The Asteraceae species Cynara cardunculus (2n?=?2x?=?34) includes the two fully cross-compatible domesticated taxa globe artichoke (var. scolymus L.) and cultivated cardoon (var. altilis DC). As both are out-pollinators and suffer from marked inbreeding depression, linkage analysis has focussed on the use of a two way pseudo-test cross approach.

Results

A set of 172 microsatellite (SSR) loci derived from expressed sequence tag DNA sequence were integrated into the reference C. cardunculus genetic maps, based on segregation among the F₁ progeny of a cross between a globe artichoke and a cultivated cardoon. The resulting maps each detected 17 major linkage groups, corresponding to the species?? haploid chromosome number. A consensus map based on 66 co-dominant shared loci (64 SSRs and two SNPs) assembled 694 loci, with a mean inter-marker spacing of 2.5?cM. When the maps were used to elucidate the pattern of inheritance of head production earliness, a key commercial trait, seven regions were shown to harbour relevant quantitative trait loci (QTL). Together, these QTL accounted for up to 74% of the overall phenotypic variance.

Conclusion

The newly developed consensus as well as the parental genetic maps can accelerate the process of tagging and eventually isolating the genes underlying earliness in both the domesticated C. cardunculus forms. The largest single effect mapped to the same linkage group in each parental maps, and explained about one half of the phenotypic variance, thus representing a good candidate for marker assisted selection.     

Construction of a reference molecular linkage map of globe artichoke (<Emphasis Type="Italic">Cynara cardunculus</Emphasis> var. <Emphasis Type="Italic">scolymus</Emphasis>)

The genome organization of globe artichoke (Cynara cardunculus var. scolymus), unlike other species belonging to Asteraceae (=Compositae) family (i.e. sunflower, lettuce and chicory), remains largely unexplored. The species is highly heterozygous and suffers marked inbreeding depression when forced to self-fertilize. Thus a two-way pseudo-testcross represents the optimal strategy for linkage analysis. Here, we report linkage maps based on the progeny of a cross between globe artichoke (C. cardunculus var. scolymus) and cultivated cardoon (C. cardunculus var. altilis). The population was genotyped using a variety of PCR-based marker platforms, resulting in the identification of 708 testcross markers suitable for map construction. The male map consisted of 177 loci arranged in 17 major linkage groups, spanning 1,015.5 cM, while female map was built with 326 loci arranged into 20 major linkage groups, spanning 1,486.8 cM. The presence of 84 loci shared between these maps and those previously developed from a cross within globe artichoke allowed for map alignment and the definition of 17 homologous linkage groups, corresponding to the haploid number of the species. This will provide a favourable property for QTL scanning; furthermore, as 25 mapped markers (8%) correspond to coding regions, it has an additional value as functional map and might represent an important genetic tool for candidate gene studies in globe artichoke.     

Mapping the genomic regions encoding biomass-related traits in <Emphasis Type="Italic">Cynara cardunculus</Emphasis> L

Cynara cardunculus, a member of the Asteraceae family, comprises the three taxa var. scolymus (globe artichoke), var. altilis (cultivated cardoon) and the ancestral var. sylvestris (wild cardoon). The substantial quantities of lignocellulosic biomass produced by these plants (up to 30.0 t/ha year^?1 dry matter by the cultivated cardoon) can be used either as a source of bioenergy and/or as raw material for paper pulp production. Here, genotyping-by-sequencing to an F₁ population derived from a cross between a globe artichoke (C3) and a cultivated cardoon (ALT) genotypes has been used to perform a genome-wide linkage analysis, leading to the elaboration of a pair of highly dense genetic maps, each derived from one of the two highly heterozygous parental genotypes. In both maps, the number of linkage groups (17) matched the species’ haploid chromosome number. The F₁ population was phenotyped over two seasons with respect to plant height, stem number, capitulum number, leaf and stem fresh weight, and the dry weight of the whole plant, the leaves, the stems, the capitula and the achenes. The phenotypic data were combined with the linkage maps to identify 81 quantitative trait loci, of which 50 were placed on the C3 map and 31 on the ALT map. The loci were scattered over 13 linkage groups, and were clustered within 27 genomic regions, 22 of which harboured two or more QTL. Ten of these regions were specific to the C3 map and six to the ALT map, while the other 11 were represented on both maps. The 27 regions harboured in all 1960 genes, 83% of which could be functionally annotated. An enrichment for certain gene ontology terms was noted for the gene content of the genomic regions harbouring loci influencing seed yield and the number/weight of stems.     

Retrotransposon-based S-SAP as a platform for the analysis of genetic variation and linkage in globe artichoke.

A high copy number of retrotransposon sequences are present and widely dispersed in plant genomes. Their activity generates a considerable degree of sequence polymorphism. Here, we report the cloning of CYRE-5, a long-terminal repeat carrying retrotransposon-like sequence in Cynara cardunculus L., and its exploitation to develop a DNA fingerprinting assay across 22 accessions, including both cultivated (globe artichoke and cultivated cardoon) and wild (wild cardoon) types. The effectiveness of the sequence-specific amplified polymorphism (S-SAP) platform is compared with that of amplified fragment length polymorphism (AFLP). A genetic linkage analysis, based on a hybrid population between 2 globe artichoke varietal types, resulted in the inclusion of 29 S-SAP loci in the core genetic map, confirming their dispersed distribution across the globe artichoke genome.     

Constructing genetic linkage maps for Pinus elliottii var. elliottii and Pinus caribaea var. hondurensis using SRAP, SSR, EST and ISSR markers

A total of 122 F₁ individuals from a single full-sib interspecific hybrid family crossed between Pinus elliottii var. elliottii (PEE) and P. caribaea var. hondurensis (PCH) were used to construct a detailed genetic linkage maps using four types of molecular markers: sequence-related amplified polymorphism (SRAP), microsatellite (SSR), expressed sequence tag polymorphism (ESTP) and inter-simple sequence repeat (ISSR). There were 381 SRAP, 108 SSR, 25 ESTP and 32 ISSR loci, segregating in the interspecific F₁ hybrid individuals. Framework maps were constructed at a LOD score threshold of 4.0 using the JoinMap^® 3.0. The map for the male parent (PCH) had 108 markers in 16 linkage groups (LGs), with a total length of 1,065.9 cM (Kosambi) and an average marker interval of 9.87 cM. The map for the female parent (PEE) contained 93 markers in 19 LGs, with a total length of 1,006.7 cM (Kosambi) and an average marker interval of 10.82 cM. The maps for PCH and PEE covered 56.5 and 70.3 % of their respective genomes. Based on the position of 36 loci segregating in both parents, 8 homologous LGs between PEE and PCH were identified.     

An SSR- and AFLP-based genetic linkage map of tall fescue (Festuca arundinacea Schreb.)

Tall fescue (Festuca arundinacea Schreb.) is commonly grown as forage and turf grass in the temperate regions of the world. Here, we report the first genetic map of tall fescue constructed with PCR-based markers. A combination of amplified fragment length polymorphisms (AFLPs) and expressed sequence tag-simple sequence repeats (EST-SSRs) of both tall fescue and those conserved in grass species was used for map construction. Genomic SSRs developed from Festuca × Lolium hybrids were also mapped. Two parental maps were initially constructed using a two-way pseudo-testcross mapping strategy. The female (HD28-56) map included 558 loci placed in 22 linkage groups (LGs) and covered 2,013 cM of the genome. In the male (R43-64) map, 579 loci were grouped in 22 LGs with a total map length of 1,722 cM. The marker density in the two maps varied from 3.61 cM (female parent) to 2.97 (male parent) cM per marker. These differences in map length indicated a reduced level of recombination in the male parent. Markers that revealed polymorphism within both parents and showed 3:1 segregation ratios were used as bridging loci to integrate the two parental maps as a bi-parental consensus. The integrated map covers 1,841 cM on 17 LGs, with an average of 54 loci per LG, and has an average marker density of 2.0 cM per marker. Homoeologous relationships among linkage groups of six of the seven predicted homeologous groups were identified. Three small groups from the HD28-56 map and four from the R43-64 map are yet to be integrated. Homoeologues of four of those groups were detected. Except for a few gaps, markers are well distributed throughout the genome. Clustering of those markers showing significant segregation distortion (23% of total) was observed in four of the LGs of the integrated map.Electronic Supplementary Material Supplementary material is available for this article at     

Construction of Commercial Sweet Cherry Linkage Maps and QTL Analysis for Trunk Diameter

A cross between the sweet cherry (Prunus avium) cultivars ‘Wanhongzhu’ and ‘Lapins’ was performed to create a mapping population suitable for the construction of a linkage map. The specific-locus amplified fragment (SLAF) sequencing technique used as a single nucleotide polymorphism (SNP) discovery platform and generated 701 informative genotypic assays; these, along with 16 microsatellites (SSRs) and the incompatibility (S) gene, were used to build a map which comprised 8 linkage groups (LGs) and covered a genetic distance of 849.0 cM. The mean inter-marker distance was 1.18 cM and there were few gaps > 5 cM in length. Marker collinearity was maintained with the established peach genomic sequence. The map was used to show that trunk diameter (TD) is under the control of 4 loci, mapping to 3 different LGs. Different locus influenced TD at a varying stage of the tree’s development. The high density ‘W×L’ genetic linkage map has the potential to enable high-resolution identification of QTLs of agronomically relevant traits, and accelerate sweet cherry breeding.     

Development of genetic maps of the citrus varieties ‘Murcott’ tangor and ‘Pêra’ sweet orange by using fluorescent AFLP markers

The progeny of 87 BC(1) hybrids of 'Murcott' tangor and 'Pera' sweet orange, genotyped with fluorescent amplified fragment length polymorphism (fAFLP) markers, was used for the construction of genetic maps for both citrus varieties. Mapping strategies, considering the progeny as a result of backcrossing and cross-pollination, were exploited in Mapmaker 2.0 (LOD score >or= 3.0 and or= 3.0 and theta 相似文献   

Mapping of RFLP and qualitative trait loci in Brassica rapa and comparison to the linkage maps of B. napus,B. oleracea,and Arabidopsis thaliana

A linkage map of restriction fragment length polymorphisms (RFLPs) was constructed for oilseed, Brassica rapa, using anonymous genomic DNA and cDNA clones from Brassica and cloned genes from the crucifer Arabidopsis thaliana. We also mapped genes controlling the simply inherited traits, yellow seeds, low seed erucic acid, and pubescence. The map included 139 RFLP loci organized into ten linkage groups (LGs) and one small group covering 1785 cM. Each of the three traits mapped to a single locus on three different LGs. Many of the RFLP loci were detected with the same set of probes used to construct maps in the diploid B. oleracea and the amphidiploid B. napus. Comparisons of the linkage arrangements between the diploid species B. rapa and B. oleracea revealed six LGs with at least two loci in common. Nine of the B. rapa LGs had conserved linkage arrangements with B. napus LGs. The majority of loci in common were in the same order among the three species, although the distances between loci were largest on the B. rapa map. We also compared the genome organization between B. rapa and A. thaliana using RFLP loci detected with 12 cloned genes in the two species and found some evidence for a conservation of the linkage arrangements. This B. rapa map will be used to test for associations between segregation of RFLPs, detected by cloned genes of known function, and traits of interest.     

Construction of an RAPD linkage map and localization of QTLs for oleic acid level using recombinant inbreds in mustard (Brassica juncea).

RAPD markers were employed for construction of a linkage map and localization of QTLs for oleic acid level using a set of 94 recombinant inbred lines (RILs) of mustard (Brassica juncea L.) as a mapping population. Only 30% of the 235 random primers used were useful in terms of polymorphism detected and the reproducibility of those patterns. Normal Mendelian segregation was observed for the majority of the 130 markers obtained with 71 informative primers; only 13.1% deviated (P < 0.01) from the expected 1:1 ratio. One-hundred and fourteen markers were assigned to 21 linkage groups (LGs) covering a total length of 790.4 cM with an average distance of 6.93 cM between markers. Two quantitative trait loci (QTL) for oleic acid level were mapped to 14- and 10.6-cM marker intervals on two different LGs. Both loci together explained 32.2% of phenotypic variance. One major QTL explained 28.5% of the trait variance observed in this species.     

A Consensus Microsatellite-Based Linkage Map for the Hermaphroditic Bay Scallop (Argopecten irradians) and Its Application in Size-Related QTL Analysis

Bay scallop (Argopecten irradians) is one of the most economically important aquaculture species in China. In this study, we constructed a consensus microsatellite-based genetic linkage map with a mapping panel containing two hybrid backcross-like families involving two subspecies of bay scallop, A. i. irradians and A. i. concentricus. One hundred sixty-one microsatellite and one phenotypic (shell color) markers were mapped to 16 linkage groups (LGs), which corresponds to the haploid chromosome number of bay scallop. The sex-specific map was 779.2 cM and 781.6 cM long in female and male, respectively, whereas the sex-averaged map spanned 849.3 cM. The average resolution of integrated map was 5.9 cM/locus and the estimated coverage was 81.3%. The proportion of distorted markers occurred more in the hybrid parents, suggesting that the segregation distortion was possibly resulted from heterospecific interaction between genomes of two subspecies of bay scallop. The overall female-to-male recombination rate was 1.13∶1 across all linked markers in common to both parents, and considerable differences in recombination also existed among different parents in both families. Four size-related traits, including shell length (SL), shell height (SH), shell width (SW) and total weight (TW) were measured for quantitative trait loci (QTL) analysis. Three significant and six suggestive QTL were detected on five LGs. Among the three significant QTL, two (qSW-10 and qTW-10, controlling SW and TW, respectively) were mapped on the same region near marker AiAD121 on LG10 and explained 20.5% and 27.7% of the phenotypic variance, while the third (qSH-7, controlling SH) was located on LG7 and accounted for 15.8% of the phenotypic variance. Six suggestive QTL were detected on four different LGs. The linkage map and size-related QTL obtained in this study may facilitate marker-assisted selection (MAS) in bay scallop.     

Genetic linkage map of the guppy,Poecilia reticulata,and quantitative trait loci analysis of male size and colour variation

We report construction of a genetic linkage map of the guppy genome using 790 single nucleotide polymorphism markers, integrated from six mapping crosses. The markers define 23 linkage groups (LGs), corresponding to the known haploid number of guppy chromosomes. The map, which spans a genetic length of 899 cM, includes 276 markers linked to expressed genes (expressed sequence tag), which have been used to derive broad syntenic relationships of guppy LGs with medaka chromosomes. This combined linkage map should facilitate the advancement of genetic studies for a wide variety of complex adaptive phenotypes relevant to natural and sexual selection in this species. We have used the linkage data to predict quantitative trait loci for a set of variable male traits including size and colour pattern. Contributing loci map to the sex LG for many of these traits.     

SRAP-based mapping and QTL detection for inflorescence-related traits in chrysanthemum (Dendranthema morifolium)

Chrysanthemum (Dendranthema morifolium) is an economically important ornamental species and comprises a large proportion of the flower industry in south-east Asian and European countries. In this study, a segregating population of 142 F₁ progeny of the cross between the two chrysanthemum cultivars ??Yuhualuoying?? and ??Aoyunhanxiao?? was used to construct two separate genetic linkage maps via a double pseudo-testcross mapping strategy. Genotyping was performed using 500 SRAP primer combinations, of which about 50% were informative. This allowed the definition of 896 SRAP loci, of which about 23% showed some segregation distortion. The ??Yuhualuoying?? map consisted of 333 testcross markers arranged into 57 linkage groups (LGs). It covered >1,900 cM with a mean inter-marker distance of 6.9 cM. The map constructed from ??Aoyunhanxiao?? comprised 342 test cross markers arranged into 55 LGs. It spanned nearly 1,900 cM, with a mean inter-marker distance of 6.6 cM. The markers were distributed rather uniformly along both maps. A quantitative trait loci analysis was conducted to investigate the pattern of inheritance of three inflorescence traits. This led to the detection of 12 putative loci at a LOD score >2.5, of which four each specified flower diameter, ray floret layer number, and ray floret length. This study provides molecular mapping information on marker-assisted selection programs for the improvement of multiple traits of interest.     

Linkage analysis and identification of quantitative trait loci associated with freeze tolerance and turf quality traits in St. Augustinegrass

St. Augustinegrass [Stenotaphrum secundatum (Walt.) Kuntze] is a warm-season turfgrass commonly grown in the southern USA. In this study, the first linkage map for all nine haploid chromosomes of the species was constructed for cultivar ‘Raleigh’ and cultivar ‘Seville’ using a pseudo-F₂ mapping strategy. A total of 160 simple sequence repeat markers were mapped to nine linkage groups (LGs) covering a total distance of 1176.24 cM. To demonstrate the usefulness of the map, quantitative trait loci (QTL) were mapped controlling field winter survival, laboratory-based freeze tolerance, and turf quality traits. Multiple genomic regions associated with these traits were identified. Moreover, overlapping QTL were found for winterkill and spring green up on LG 3 (99.21 cM); turf quality, turf density, and leaf texture on LG 3 (68.57–69.50 cM); and surviving green tissue and regrowth on LGs 1 (38.31 cM), 3 (77.70 cM), 6 (49.51 cM), and 9 (34.20 cM). Additional regions, where QTL identified in both field and laboratory-based/controlled environment freeze testing co-located, provided strong support that these regions are good candidates for true gene locations. These results present the first complete linkage map produced for St. Augustinegrass, providing a template for further genetic mapping. Additionally, markers linked to the QTL identified may be useful to breeders for transferring these traits into new breeding lines and cultivars.     

Evidence of Allopolyploidy in Urochloa humidicola Based on Cytological Analysis and Genetic Linkage Mapping

The African species Urochloa humidicola (Rendle) Morrone & Zuloaga (syn. Brachiaria humidicola (Rendle) Schweick.) is an important perennial forage grass found throughout the tropics. This species is polyploid, ranging from tetra to nonaploid, and apomictic, which makes genetic studies challenging; therefore, the number of currently available genetic resources is limited. The genomic architecture and evolution of U. humidicola and the molecular markers linked to apomixis were investigated in a full-sib F₁ population obtained by crossing the sexual accession H031 and the apomictic cultivar U. humidicola cv. BRS Tupi, both of which are hexaploid. A simple sequence repeat (SSR)-based linkage map was constructed for the species from 102 polymorphic and specific SSR markers based on simplex and double-simplex markers. The map consisted of 49 linkage groups (LGs) and had a total length of 1702.82 cM, with 89 microsatellite loci and an average map density of 10.6 cM. Eight homology groups (HGs) were formed, comprising 22 LGs, and the other LGs remained ungrouped. The locus that controls apospory (apo-locus) was mapped in LG02 and was located 19.4 cM from the locus Bh027.c.D2. In the cytological analyses of some hybrids, bi- to hexavalents at diakinesis were observed, as well as two nucleoli in some meiocytes, smaller chromosomes with preferential allocation within the first metaphase plate and asynchronous chromosome migration to the poles during anaphase. The linkage map and the meiocyte analyses confirm previous reports of hybridization and suggest an allopolyploid origin of the hexaploid U. humidicola. This is the first linkage map of an Urochloa species, and it will be useful for future quantitative trait locus (QTL) analysis after saturation of the map and for genome assembly and evolutionary studies in Urochloa spp. Moreover, the results of the apomixis mapping are consistent with previous reports and confirm the need for additional studies to search for a co-segregating marker.     

Construction of a SSR-based genetic map and identification of QTL for domestication traits using recombinant inbred lines from a cross between wild and cultivated cowpea (<Emphasis Type="Italic">V. unguiculata</Emphasis> (L.) Walp.)

Cowpea (Vigna unguiculata (L.) Walp.) is a grain legume commonly grown and consumed in many parts of the tropics and subtropics. A genetic linkage map was constructed using simple sequence repeat (SSR) markers and a recombinant inbred (RI) population of159 individuals derived from a cross between the breeding line 524B, a California Blackeye, and 219-01, a perennial wild cowpea from Kenya. Out of 912 primer combinations predicted to amplify SSRs in cowpea, 639 reliably produced amplification products in PCR assays and 202 (31.6%) were polymorphic between the two parents. These polymorphic SSRs were used to construct a genetic map consisting of 11 linkage groups (LGs) spanning 677 cM, with an average distance between markers of 3 cM. Agronomic traits related to domestication (seed weight, pod shattering) were analyzed together with the genotypic data. Six quantitative trait loci (QTL) for seed size were revealed with the phenotypic variation ranging from 8.9 to 19.1%. Four QTL for pod shattering were identified with the phenotypic variation ranging from 6.4 to 17.2%. The QTL for seed size and pod shattering mainly cluster in two areas of LGs 1 and 10, facilitating the use of marker-assisted selection to eliminate undesirable wild phenotypes in breeding activities involving introgression of traits from wild germplasm. The generation of an SSR-based molecular map and additional trait-linked markers also contributes to the expanding tool kit available to cowpea breeders, especially in Africa.     

Genetic linkage map of the loach <Emphasis Type="Italic">Misgurnus anguillicaudatus</Emphasis> (Teleostei: Cobitidae)

In the present study, the first genetic linkage map of the loach Misgurnus anguillicaudatus was constructed with 164 microsatellite markers and a color locus, and it included 155 newly developed markers. A total of 159 microsatellite markers and a color locus were mapped in 27 linkage groups (LGs). The female map covered 784.5 cM with 153 microsatellite markers and a color locus, whereas the male map covered 662.2 cM with 119 microsatellite markers. The centromeric position in each LG was estimated by marker-centromere mapping based on half-tetrad analysis. In 4 LGs (LG2, LG3, LG4, and LG5), the centromere was estimated at the intermediate region. In LG1, LG11, and LG12, the centromere was estimated to shift from the sub-intermediate region to the end (telomeric). The number of these LGs (7) was identical to the collective number of bi-arm metacentric (5) and sub-metacentric chromosome (2) of the haploid chromosome set (n = 5) of the loach. In the other LGs, the position of the centromere was estimated at the end or outside. These results indicate satisfactory compliance between the linkage map and the chromosome set. Our map would cover approximately almost the entire loach genome because most markers were successfully mapped.     

Genetic maps of SSR and SRAP markers in diploid orchardgrass (Dactylis glomerata L.) using the pseudo-testcross strategy

Orchardgrass (Dactylis glomerata L.) is one of the most important cool-season forage grasses commonly grown throughout the temperate regions of the world. The objective of this work was to construct a diploid (2n = 2x = 14) orchardgrass genetic linkage map useful as a framework for basic genetic studies and plant breeding. A combination of simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) molecular markers were used for map construction. The linkage relationships among 164 SSRs and 108 SRAPs, assayed in a pseudo-testcross F1 segregating population generated from a cross between two diploid parents, were used to construct male (01996) and female (YA02-103) parental genetic maps. The paternal genetic map contains 90 markers (57 SSRs and 33 SRAPs) over 9 linkage groups (LGs), and the maternal genetic map is composed of 87 markers (54 SSRs and 33 SRAPs) assembled over 10 LGs. The total map distance of the male map is 866.7 centimorgans (cM), representing 81% genome coverage, whereas the female map spans 772.0 cM, representing 75% coverage. The mean map distance between markers is 9.6 cM in the male map and 8.9 cM in the female map. About 14% of the markers remained unassigned. The level of segregation distortion observed in this cross was 15%. Homology between the two maps was established between five LGs of the male map and five LGs of the female map using 10 bridging markers. The information presented in this study establishes a foundation for extending genetic mapping in this species, serves as a framework for mapping quantitative trait loci (QTLs), and provides basic information for future molecular breeding studies.     

Linkage Maps of Lowland and Upland Tetraploid Switchgrass Ecotypes

Switchgrass (Panicum virgatum L.) is a native perennial warm season (C₄) grass that has been identified as a promising species for bioenergy research and production. Consequently, biomass yield and feedstock quality improvements are high priorities for switchgrass research. The objective of this study was to develop a switchgrass genetic linkage map using a full-sib pseudo-testcross mapping population derived from a cross between two heterozygous genotypes selected from the lowland cultivar ‘Alamo’ (AP13) and the upland cultivar ‘Summer’ (VS16). The female parent (AP13) map consists of 515 loci in 18 linkage groups (LGs) and spans 1,733 cM. The male parent (VS16) map arranges 363 loci in 17 LGs and spans 1,508 cM. No obvious cause for the lack of one LG in VS16 could be identified. Comparative analyses between the AP13 and VS16 maps showed that the two major ecotypic classes of switchgrass have highly colinear maps with similar recombination rates, suggesting that chromosomal exchange between the two ecotypes should be able to occur freely. The AP13 and VS16 maps are also highly similar with respect to marker orders and recombination levels to previously published switchgrass maps. The genetic maps will be used to identify quantitative trait loci associated with biomass and quality traits. The AP13 genotype was used for the whole genome-sequencing project and the map will thus also provide a tool for the anchoring of the switchgrass genome assembly.