Development and characterisation of simple sequence repeat (SSR) markers for white clover (Trifolium repens L.)

Highly informative molecular markers, such as simple sequence repeats (SSRs), can greatly accelerate breeding programs. The aim of this study was to develop and characterise a comprehensive set of SSR markers for white clover (Trifolium repens L.), which can be used to tag genes and quantitative trait loci controlling traits of agronomic interest. Sequence analysis of 1123 clones from genomic libraries enriched for (CA) _n repeats yielded 793 clones containing SSR loci. The majority of SSRs consisted of perfect dinucleotide repeats, only 7% being trinucleotide repeats. After exclusion of redundant sequences and SSR loci with less than 25 bp of flanking sequence, 397 potentially useful SSRs remained. Primer pairs were designed for 117 SSR loci and PCR products in the expected size range were amplified from 101 loci. These markers were highly polymorphic, 88% detecting polymorphism across seven white clover genotypes with an average allele number of 4.8. Four primer pairs were tested in an F₂ population revealing Mendelian segregation. Successful cross-species amplification was achieved in at least one out of eight legume species for 46 of 54 primer pairs. The rate of successful amplification was significantly higher for Trifolium species when compared to species of other genera. The markers developed in this study not only provide valuable tools for molecular breeding of white clover but may also have applications in related taxa. Received: 3 April 2000 / Accepted: 12 May 2000     

A high-density molecular map for ryegrass (Lolium perenne) using AFLP markers

AFLP markers have been successfully employed for the development of a high-density linkage map of ryegrass (Lolium perenne L.) using a progeny set of 95 plants from a testcross involving a doubled-haploid tester. This genetic map covered 930 cM in seven linkage groups and was based on 463 amplified fragment length polymorphism (AFLP) markers using 17 primer pairs, three isozymes and five EST markers. The average density of markers was approximately 1 per 2.0 cM. However, strong clustering of AFLP markers was observed at putative centromeric regions. Around these regions, 272 markers covered about 137 cM whereas the remaining 199 markers covered approximately 793 cM. Most genetic distances between consecutive pairs of markers were smaller than 20 cM except for five gaps on groups A, C, D, F and G. A skeletal map with a uniform distribution of markers can be extracted from this high-density map, and can be applied to detect and map QTLs. We report here the application of AFLP markers to genome mapping, in Lolium as a prelude to quantitative trait locus (QTL) identification for diverse agronomic traits in ryegrass and for marker-assisted plant breeding. Received: 4 November 1998 / Accepted:15 March 1999     

Expressed sequence tag-derived microsatellite markers of perennial ryegrass (Lolium perenne L.)

An expressed sequence tag (EST) library of the key grassland species perennial ryegrass (Lolium perenne L.) has been exploited as a resource for microsatellite marker development. Out of 955 simple sequence repeat (SSR) containing ESTs, 744 were used for primer design. Primer amplification was tested in eight genotypes of L. perenne and L. multiflorum representing (grand-) parents of four mapping populations and resulted in 464 successfully amplified EST-SSRs. Three hundred and six primer pairs successfully amplified products in the mapping population VrnA derived from two of the eight genotypes included in the original screening and revealed SSR polymorphisms for 143 ESTs. Here, we report on 464 EST-derived SSR primer sequences of perennial ryegrass established in laboratory assays, providing a dedicated tool for marker assisted breeding and comparative mapping within and among forage and turf grasses. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Simple sequence repeat (SSR) markers survey of the cassava (Manihot esculenta Crantz) genome: towards an SSR-based molecular genetic map of cassava

The development of PCR-based, easily automated molecular genetic markers, such as SSR markers, are required for realistic cost-effective marker-assisted selection schemes. This paper describes the development and characterization of 172 new SSR markers for the cassava genome. The placement of 36 of these markers on the existing RFLP framework map of cassava is also reported. Two similar enrichment methods were employed. The first method yielded 35 SSR loci, for which primers could be designed, out of 148 putative DNA clones. A total of 137 primer pairs could be designed from 544 putative clones sequenced for the second enrichment. Most of the SSRs (95%) were di-nucleotide repeats, and 21% were compound repeats. A major drawback of these methods of SSR discovery is the redundancy – 20% duplication; in addition, primers could not be designed for many SSR loci that were too close to the cloning site – 45% of the total. All 172 SSRs amplified the corresponding loci in the parents of the mapping progeny, with 66% of them revealing a unique allele in at least one of the parents, and 26% having unique alleles in both of the parents. Of the 36 SSRs that have been mapped, at least 1 was placed on 16 out of the 18 linkage groups of the framework map, indicating a broad coverage of the cassava genome. This preliminary mapping of the 36 markers has led to the joining of a few small groups and the creation of one new group. The abundance of allelic bridges as shown by these markers will lead to the development of a consensus map of the male- and female-derived linkage groups. In addition, the relatively higher number of these allelic bridges, 30% as against 10% for RFLPs in cassava, underscores SSR as the marker of choice for cassava. The 100% primer amplification obtained for this set of primers also confirms the appropriateness of SSR markers for use in cassava genome analysis and the transferability of the technology as a low-cost approach to increasing the efficiency of cassava breeding. Current efforts are geared towards the generation of more SSR markers to attain a goal of 200 SSR markers, or 1 SSR marker every 10 cM. Received: 15 November 1999 / Accepted: 14 April 2000     

Characterization and analysis of simple sequence repeat (SSR) loci in seashore paspalum (Paspalum vaginatum Swartz)

A size-fractionated TaqI genomic library of seashore paspalum (Paspalum vaginatum Swartz) was screened for the presence of (GA) _n and (CA) _n simple sequence repeats (SSRs). A total of 54 clones with a positive signal were detected among 13,000 clones screened. Forty-seven clones having repeats of n 3 were identified, of which 85% were perfect, 13% were imperfect and 2% were compound repeat sequences. Five of ten primer pairs synthesized to amplify selected loci resulted in a product in the expected size range and were subsequently used to examine SSR polymorphisms among 46 ecotypes of P. vaginatum. The number of alleles resolved on agarose or polyacrylamide gels were similar and ranged from 6 to 16 with an average of 14 per locus. Phenetic analysis of SSR polymorphisms revealed genetic relationships among the P. vaginatum ecotypes that were in general agreement with relationships determined previously by RAPD analysis of the same plant materials. Further screening of the genomic library did not identify (AT) _n , trimeric or tetrameric repeats. Hybridization of an (ATT)₈ oligonucleotide probe to genomic DNA isolated from I. batatas, E. coli, Citrullis lanatus and P. vaginatum suggested that the P. vaginatum genome contained significantly fewer ATT repeats than either the I. batatas or C. lanatus genome.     

Development and characterization of simple sequence repeats for flowering dogwood (Cornus florida L.)

Abundant, codominant simple sequence repeats (SSRs) markers can be used for constructing genetic linkage maps and in marker-assisted breeding programs. Enrichment methods for SSR motifs were optimized with the ultimate aim of developing numerous loci in flowering dogwood (C. florida L.) genome. Small insert libraries using four motifs (GT, CT, TGG, and AAC) were constructed with C. florida ‘Cherokee Brave’ deoxyribonucleic acid (DNA). Colony polymerase chain reaction (PCR) of 2,208 selected clones with three primers we reported previously indicated that 47% or 1,034 of the clones harbored one of the four targeted SSR motifs. Sequencing the putative positive clones confirmed that nearly 99% (1,021 of 1,034) of them contained the desired motifs. Of the 871 unique SSR loci, 617 were dinucleotide repeats (70.8%), and 254 were trinucleotide or longer repeats (29.2%). In total, 379 SSR loci had perfect structure, 237 had interrupted, and 255 had compound structure. Primer pairs were designed from 351 unique sequences. The ability of the 351 SSR primer pairs to amplify specific loci was evaluated with genomic DNA of ‘Appalachian Spring’ and ‘Cherokee Brave’. Of these primers, 311 successfully amplified product(s) with ‘Cherokee Brave’ DNA, 21 produced weak or faint products, and 19 did not amplify any products. Additionally, 218 of the 311 primers pairs revealed polymorphisms between the two cultivars, and 20 out of 218 primers detected an average of 13.7 alleles from 38 selected Cornus species and hybrids. These SSR loci constitute a valuable resource of ideal markers for both genetic linkage mapping and gene tagging of flowering dogwood. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Effects of sheath tube length on leaf development in perennial ryegrass (Lolium perenne L.)

Position in and contribution of leaf laminae to the canopy of forage grasses are important both in determining herbage growth rates and intake rate by grazing animals. These canopy characteristics are controlled by the way dry matter is apportioned between sheath and lamina in growing leaves. The objective of this work was to determine how the development of individual leaves is affected by altering the effective length of the psuedostem tube, on the assumption that the light environment within the tube varied. The development of a leaf from initiation at the apex to maturity was followed by successive destructive dissections of tillers. Vertical incisions were made in the pseudostem of each tiller to three different depths. The three treatments imposed were — no incision (control), moderate and severe incision of the sheath length. Destructive harvests of tillers followed 3, 6, 12 and 24 days after imposition of treatments. Incision resulted in the length of the monitored leaf being reduced significantly at all harvests, and differentiation of the sheath beginning earlier. The length reduction reflected a reduction in both cell size and cell number and the effects were evident at the earliest harvest. The data support the theory that leaf size and timing of onset of sheath development are influenced by the environment of the developing leaf. The present results indicate that sheath tube length affects leaf development and suggests that the effects are substantially explained by a direct light effect on the location and depth of the elongation zone.     

Ultrastructural features of a Stagonospora species (Ascomycotina) in senescent tissues of perennial ryegrass (Lolium perenne L.)

The pycnidium of a Stagonospora sp. observed in degenerating leaf sheath and blade tissues of Lolium perenne L. contained concentric bodies similar to those found in the mycobiont of several lichens and a few other free-living ascomycetes. These bodies occurred in vegetative hyphae, hyphae of the pycnidial wall, in conidiogenous cells and in conidia and comprised a central electron-translucent core surrounded by a granular zone and an outer radially orientated fibrillar or lamellar zone. In some cases the entire body was surrounded by a translucent halo. A second feature of the interwoven hyphae of the pycnidial wall was the occurrence of pores connecting adjacent hyphae. These lateral pores appeared identical to pores in septa between cells of individual hyphae, and like them, were associated with Woronin bodies.     

Development of a genomic microsatellite library in perennial ryegrass (Lolium perenne) and its use in trait mapping

Background and Aims: Perennial ryegrass (Lolium perenne) is one of the key forageand amenity grasses throughout the world. In the UK it accountsfor 70 % of all agricultural land use with an estimated farmgate value of £6 billion per annum. However, in termsof the genetic resources available, L. perenne has lagged behindother major crops in Poaceae. The aim of this project was thereforethe construction of a microsatellite-enriched genomic libraryfor L. perenne to increase the number of genetic markers availablefor both marker-assisted selection in breeding programmes andgene isolation. Methods: Primers for 229 non-redundant microsatellite markers were designedand used to screen two L. perenne genotypes, one amenity andone forage. Of the 229 microsatellites, 95 were found to showpolymorphism between amenity and forage genotypes. A selectionof microsatellite primers was selected from these 95 and usedto screen two mapping populations derived from intercrossingand backcrossing the two forage and amenity grass genotypes. Key Results and Conclusions: The utility of the resulting genetic maps for analysis of thegenetic control of target traits was demonstrated by the mappingof genes associated with heading date to linkage groups 4 and7.     

Identification,characterisation and mapping of simple sequence repeat (SSR) markers from raspberry root and bud ESTs

Raspberry breeding is a long, slow process in this highly heterozygous out-breeder. Selections for complex traits like fruit quality are broad-based and few simple methodologies and resources are available for glasshouse and field screening for key pest and disease resistances. Additionally, the timescale for selection of favourable agronomic traits requires data from different seasons and environmental locations before any breeder selection can proceed to finished cultivar. Genetic linkage mapping offers the possibility of a more knowledge-based approach to breeding through linking favourable traits to markers and candidate genes on genetic linkage maps. To further increase the usefulness of existing maps, a set of 25 polymorphic SSRs derived from expressed sequences (EST-SSRs) have been developed in red raspberry (Rubus idaeus). Two different types of expressed sequences were targeted. One type was derived from a root cDNA library as a first step in assessing sequences which may be involved in root vigour and root rot disease resistance and the second type were ESTs from a gene discovery project examining bud dormancy release and seasonality. The SSRs detect between 2 and 4 alleles per locus and were assigned to linkage groups on the existing ‘Glen Moy’ × ‘Latham’ map following genotyping of 188 progeny and examined for association with previously mapped QTL. The loci were also tested on a diverse range of Rubus species to determine transferability and usefulness for germplasm diversity studies and the introgression of favourable alleles.     

干旱胁迫下内生真菌感染对黑麦草叶内几种同工酶的影响

以内生真菌感染(endophyte-infected,EI)与不感染(endophyte-free,EF)的黑麦草(Lolium perenne L．)种子建立实验种群,分别对其施加长时间不同强度的干旱胁迫,通过比较黑麦草体内过氧化物酶(POD)、超氧化物歧化酶(SOD)、多酚氧化酶(PPO)活性及其同工酶谱的变化以探讨保护酶系统在内生真菌——植物共生体的抗旱性方面所作的贡献。研究结果表明,水分胁迫和内生真菌对黑麦草3种酶的影响不仅表现在总量上而且表现在同工酶的酶谱及各区带的酶活力上。就总酶活力而言,EI和EF植株中POD、SOD和PPO的活性均随着干旱胁迫强度的增加而增加,进一步将EI和EF植株的酶活力进行比较,发现与EF植株相比,EI植株中POD和PPO的活性相对较低,而SOD的活性相对较高。从同工酶的谱带数量和强弱来看,POD同工酶各区带活力均随干旱胁迫强度的增加而增加,EI植株叶片增加的幅度高于EF叶片,而且EI叶片在重度胁迫下出现了1条新带SOD同工酶各区带活力在EI叶片中有随干旱胁迫增加而增加的趋势,而在EF叶片中有些区带酶活力增强,有些区带酶活力减弱,且EI叶片在中度胁迫下出现了1条新带;PPO同工酶随干旱胁迫的增强,EI和EF叶片均表现为有些区带酶活力增强,有些区带酶活力减弱。总之,内生真菌的感染虽然没有显著提高宿主植物黑麦草POD、SOD和PPO的活性,但使宿主黑麦草对干旱胁迫的反应更为迅速,其中既包括POD、SOD等酶活力的迅速升高,也包括新酶带的产生。     

A comparative study of molecular and morphological methods of describing relationships between perennial ryegrass (Lolium perenne L.) varieties

A sample set of registered perennial ryegrass varieties was used to compare how morphological characterisation and AFLP^® (AFLP^® is a registered trademark of Keygene N.V.) and STS molecular markers described variety relationships. All the varieties were confirmed as morphologically distinct, and both the STS and AFLP markers exposed sufficient genetic diversity to differentiate these registered ryegrass varieties. Distances obtained by each of the approaches were compared, with special attention given to the coincidences and divergences between the methods. When correlations between morphological, AFLP and STS distances were calculated and the corresponding scatter-plots constructed, the variety relationships appeared to be rather inconsistent across the methods, especially between morphology and the molecular markers. However, some consistencies were found for closely related material. An implication could be that these molecular-marker techniques, while not yet suited to certain operations in the traditional registration of new varieties, could be suitable methods for investigating disputable distinctness situations or possible EDV (EDV= essentially derived variety. An EDV is a variety being clearly distinct from, but conforming in the expression of the essential characteristics of, an ’initial variety’ (IV) from which it is found to have been predominantly derived) relationships, subject to establishing standardised protocols and statistical techniques. Some suggestions for such a protocol, including a statistical test for distinctness, are given.     

Targeted isolation of simple sequence repeat markers through the use of bacterial artificial chromosomes

 Simple sequence repeats (SSRs) are versatile DNA markers that are readily assayed and highly informative. Unfortunately, non-targeted approaches to SSR development often leave large genomic regions without SSR markers. In some cases these same genomic regions are already populated by other types of DNA markers, especially restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNAs (RAPDs), and amplified fragment length polymorphisms (AFLPs). To identify SSR markers in such regions, bacterial artificial chromosome (BAC) clones can be used as intermediaries. First, one or more BAC clones in a region of interest are identified through the use of an existing DNA marker. BAC clones uncovered in this initial step are then used to create a small insert DNA library that can be screened for the presence of SSR-containing clones. Because BAC inserts are often 100-kb pairs or more in size, most contain one or more SSRs. This strategy was applied to two regions of the soybean genome near genes that condition resistance to the soybean cyst nematode on molecular linkage groups G and A2. This targeted approach to identifying new DNA markers can readily be extended to other types of DNA markers, including single nucleotide polymorphisms. Received: 13 August 1998 / Accepted: 13 October 1998     

Two simple sequence repeat markers to select for soybean cyst nematode resistance coditioned by the rhg1 locus

The soybean cyst nematode (SCN) (Heterodera glycines Inchinoe) is the most economically significant soybean pest. The principal strategy to reduce or eliminate damage from this pest is the use of resistant cultivars. Identifying resistant segregants in a breeding program is a difficult and expensive process which is complicated by the oligogenic nature of the resistance and genetic variability in the pathogen. Fortunately, resistance at one SCN-resistance locus, rhg1, is generally accepted as a necessity for the development of resistant genotypes using any source of resistance and when challenged by any SCN race. Thus, the development of SCN resistant cultivars would be expedited if an effective and rapid system were available to identify breeding lines carrying a resistance allele at the rhg1 locus. In this study we report two simple sequence repeat (SSR) or microsatellite loci that cosegregate and map 0.4 cM from rhg1. Allelic variation at the first of these loci, BARC-Satt309, distinguished most, if not all, SCN-susceptible genotypes from those carrying resistance at rhg1 derived from the important SCN-resistance sources ’Peking’, PI 437654, and PI 90763. BARC-Satt309 was also effective in distinguishing SCN resistance sources PI 88788 and PI 209332 from many, but not all, susceptible genotypes. BARC-Satt309 cannot be used in marker-assisted selection in populations developed from typical southern US cultivars crossed with the important resistance sources PI 88788 or PI 209332 because these genotypes all carry the identical allele at the BARC-Satt309 locus. A second SSR locus, BARC-Sat_168, was developed from a bacterial artificial chromosome (BAC) clone that was identified using the primers to BARC-Satt309. BARC-Sat_168 distinguished PI 88788 and PI 209332 from southern US cultivars such as ’Lee’, ’Bragg’ and ’Essex’. Both BARC-Satt309 and BARC-Sat_168 were used to assay lines from SCN-susceptible×SCN-resistant crosses and proved to be highly effective in identifying lines carrying rhg1 resistance from those carrying the allele for SCN susceptibility at the rhg1 locus. Received: 5 November 1998 / Accepted: 3 February 1999     

Field performance of cell-suspension-derived Lolium perenne L. regenerants and their progenies

 Two sets of plants (Lb and Lc), regenerated from different single-genotype-derived embryogenic suspension cultures of Lolium perenne cv Citadel, were evaluated for agronomic traits in a modified polycross design in the field. Seed from the primary regenerated plants was harvested to evaluate morphological and phenological traits of corresponding progenies in a replicated field experiment. When compared to seed-grown plants of the same cultivar, primary regenerants of the Lb set showed a significant delay in ear emergence and a more-erect growth habit, while primary regenerants from the Lc set showed a significantly higher seed yield. However, progenies of regenerated plants did not differ from those of seed-grown plants. Embryogenic suspension cells of L. perenne have the potential for producing fertile, well-performing, material which can be integrated into breeding programs. Received: 3 November 1997 / Accepted: 25 November 1997     

Partitioning of sugars in Lolium perenne (perennial ryegrass) during drought and on rewatering

Simulated swards of perennial ryegrass ( Lolium perenne ) growing in 1-m³ soil blocks in the glasshouse were either well watered or deprived of water for 57 d and then rewatered. The first aim was to measure effects of drought on sugar (water-soluble carbohydrate) composition of laminae and sheaths of mature laminae, and bases and laminae of young (growing) leaves. The second aim was to use pulse labelling with ¹⁴CO₂ to follow the partitioning of recently-fixed assimilates, and the assembly and consumption of reserve sugars (fructans). Over the last 7 d of drought growth almost stopped, old leaves died faster than they were replaced, and total sugar (which had doubled in concentration during drought) was rapidly consumed. Leaf laminae had lower content of total sugars and of large fructan (DP>5) than did growing bases and sheaths. Drought greatly reduced the rate at which sugar was exported from the laminae to the sheaths and growing leaf bases, and the rate at which it was converted to fructan. Nevertheless, fructan accumulated over the first 50 d of drought. Rewatering did not result in depolymerization and remobilization of sugars that had been formed during the last 7 d of drought, but stimulated their further assembly into high-DP fructans. Our hypothesis, that accumulation of neo-kestose (a DP-3 fructan) in droughted laminae was a symptom of sugar remobilization just before death, was disproved. It is concluded that sugar reserves contribute to drought resistance only under extreme conditions. The specific role of fructan in dry environments might be to improve regrowth when drought is relieved, rather than to enhance growth during drought.