Genetic diversity within Pisum sativum using protein- and PCR-based markers

Agro-morphological characterization of Pakistani maize accessions using qualitative and quantitative traits

Abstract Agro-morphological characterizations offer robust and vigorous means for the precise characterization of germplasm to be used in breeding programs. Here, agro-morphological features-based analyses were considered to figure out the genetic variability within 99 maize accessions and five (5) check varieties including Azam, W. Islamabad, Haq Nawaz, Ev-5 and Evr197. A total of 28 important agro-morphological traits were accounted in the field trails at Hazara University Mansehra Pakistan, during spring 2015. The maximum variation was detected in grain weight per cob (53.43), followed by number of kernels per row (38.64) and flag leaf area (cm2), (38.09%). Cluster analysis divided the 99 maize accession with five check varieties of maize accessions into 7 clusters following the hierarchical clustering. Cluster II recorded 29 genotypes with maximum grain yield per cob, and highest flag leaf length, followed by cluster IV. Lowest grain yield per cob was noted for accessions of cluster I. Similarly, cluster VII consisted of accession with the longest cob length. Moreover, the investigations also revealed that the primary constituent among first five principal components with an eigen value about more than 0.98 in relation to 68.75% of the total variants. PCI accounted for 25.53%, PCII contributed 18.31%, and PCIII is 9.88% of the overall morphological variability were significant contributors were grain weight per cob, number of kernel per row, 1000 grain weight. The identification of a significant level of genetic diversity during the present investigation having implications for maize germplasm characterisation, conservation, and breeding programs aiming at developing improvement maize cultivars.

Genomic prediction and allele mining of agronomic and morphological traits in pea (Pisum sativum) germplasm collections

Well-performing genomic prediction (GP) models for polygenic traits and molecular marker sets for oligogenic traits could be useful for identifying promising genetic resources in germplasm collections, setting core collections, and establishing molecular variety distinction. This study aimed at (i) defining GP models and key marker sets for predicting 15 agronomic or morphological traits in germplasm collections, (ii) verifying the GP model usefulness also for selection in breeding programs, (iii) investigating the consistency between molecular and phenotypic diversity patterns, and (iv) identifying genomic regions associated with to the target traits. The study was based on phenotyping data and over 41,000 genotyping-by-sequencing-generated SNP markers of 220 landraces or old cultivars belonging to a world germplasm collection and 11 modern cultivars. Non-metric multi-dimensional scaling (NMDS) and an analysis of population genetic structure indicated a high level of genetic differentiation of material from Western Asia, a major West-East diversity gradient, and quite limited genetic diversity of the improved germplasm. Mantel's test revealed a low correlation (r = 0.12) between phenotypic and molecular diversity, which increased (r = 0.45) when considering only the molecular diversity relative to significant SNPs from genome-wide association analyses. These analyses identified, inter alia, several areas of chromosome 6 involved in a largely pleiotropic control of vegetative or reproductive organ pigmentation. We found various significant SNPs for grain and straw yield under severe drought and onset of flowering, and one SNP on chromosome 5 for grain protein content. GP models displayed moderately high predictive ability (0.43 to 0.61) for protein content, grain and straw yield, and onset of flowering, and high predictive ability (0.76) for individual seed weight, based on intra-population, intra-environment cross-validations. The inter-population, inter-environment assessment of the models trained on the germplasm collection for breeding material of three recombinant inbred line (RIL) populations, which was challenged by much narrower diversity of the material, over eight-fold less available markers and quite different test environments, led to an overall loss of predictive ability of about 40% for seed weight, 50% for protein content and straw yield, and 60% for onset of flowering, and no prediction for grain yield. Within-RIL population predictive ability differed among populations.

Morphological, Biochemical, and Molecular Characterization of Exotic Brassica Germplasm

Oilseed rape (Brassica napus L.) is an important oilseed crop. We examined the diversity of germplasm expressed at three distinct levels (i.e., morphological, biochemical, and DNA levels). In this study, 150 B. napus L. accessions with three check varieties were provided by Bioresources Conservation Institute. The germplasm was grown in field conditions for data collection of 15 quantitative and nine qualitative agro-morphological traits. The result indicated that for 15 quantitative agro-morphological traits, the highest coefficient of variation was recorded for plant height and days to flowering initiation. For nine qualitative traits, most of the accessions have a spatulate leaf, brown color seeds, yellow flowers, and erect silique attitude. The best adoptable genetically diverse exotic Brassica germplasms were selected, i.e., accessions 24178, 24881, 24199, 24214, 24242, and 24192. Based on biochemical analysis for high oil content and high oleic acid content, chakwal sarsoon and accession 24192 were selected. For high oleic and linoleic acids, accession 24181 performed best, for low erucic acid accessions 24177 and 24195. Based on molecular (SSR) markers, the top 50 selected genotypes were evaluated with 30 SSR markers. The 47 genotypes with three check varieties were clustered in six major groups; the coefficient of similarity ranged between 0.18 and 1.00. Based on SSR data, the germplasms accession 24178 and Abasin were the most diverse genotypes. These genotypes have the capacity and could be used in future breeding programs. High genetic variations were investigated through the SSR among the studied genotypes of Brassica napus L. The present study also concluded that SSR is a better technique for intraspecific genetic diversity. Other modern techniques should be applied such as SNIP for the investigation of a high level of genetic diversity among crop plants in the future.

Five Regions of the Pea Genome Co-Control Partial Resistance to D. pinodes, Tolerance to Frost, and Some Architectural or Phenological Traits

Evidence for reciprocal links between plant responses to biotic or abiotic stresses and architectural and developmental traits has been raised using approaches based on epidemiology, physiology, or genetics. Winter pea has been selected for years for many agronomic traits contributing to yield, taking into account architectural or phenological traits such as height or flowering date. It remains nevertheless particularly susceptible to biotic and abiotic stresses, among which Didymella pinodes and frost are leading examples. The purpose of this study was to identify and resize QTL localizations that control partial resistance to D. pinodes, tolerance to frost, and architectural or phenological traits on pea dense genetic maps, considering how QTL colocalizations may impact future winter pea breeding. QTL analysis revealed five metaQTLs distributed over three linkage groups contributing to both D. pinodes disease severity and frost tolerance. At these loci, the haplotypes of alleles increasing both partial resistance to D. pinodes and frost tolerance also delayed the flowering date, increased the number of branches, and/or decreased the stipule length. These results question both the underlying mechanisms of the joint control of biotic stress resistance, abiotic stress tolerance, and plant architecture and phenology and the methods of marker-assisted selection optimizing stress control and productivity in winter pea breeding.

SSR-Based Molecular Identification and Population Structure Analysis for Forage Pea (Pisum sativum var. arvense L.) Landraces

Plant genetic diversity has a significant role in providing traits that can help meet future challenges, such as the need to adapt crops to changing climatic conditions or outbreaks of disease. Our aim in this study was to evaluate the diversity of 61 forage pea specimens (P. sativum ssp. arvense L.) collected from the northeastern Anatolia region of Turkey using 28 simple sequence repeat (SSR) markers. These primers generated a total of 82 polymorphic bands. The number of observed alleles (Na) per primer varied from 2 to 4 with a mean of 2.89 alleles/locus. The mean value of expected heterozygosity (Exp-Het = 0.50) was higher than the mean value of observed heterozygosity (Obs-Het = 0.22). The mean of polymorphic information content (PIC) was 0.41 with a range of 0.03-0.70. The mean number of effective alleles (Ne) was found to be 2.15, Nei's expected heterozygosity (H) 0.49, and Shannon's information index (I) 0.81. Cluster analysis through the unweighted pair-group mean average (UPGMA) method revealed that 61 forage pea landraces were divided into three main clusters. Genetic dissimilarity between the genotypes, calculated with the use of NTSYS-pc software, varied between 0.10 (G30 and G34) and 0.66 (G1 and G32). Principal coordinate analysis (PCoA) revealed that three principal coordinates explained 51.54% of the total variation. Moreover, population structure analysis showed that all genotypes formed three sub-populations. Expected heterozygosity values varied between 0.2669 (the first sub-population) and 0.3223 (third sub-population), with an average value of 0.2924. Average population differentiation measurement (Fst) was identified as 0.2351 for the first sub-population, 0.3838 for the second sub-population, and 0.2506 for the third sub-population. In general, current results suggest that SSR markers could be constantly used to illuminate the genetic diversity of forage pea landraces and can potentially be incorporated into future studies that examine the diversity within a larger collection of forage pea genotypes from diverse regions.

Trait Expression and Environmental Responses of Pea (Pisum sativum L.) Genetic Resources Targeting Cultivation in the Arctic

In the Arctic part of the Nordic region, cultivated crops need to specifically adapt to adverse and extreme climate conditions, such as low temperatures, long days, and a short growing season. Under the projected climate change scenarios, higher temperatures and an earlier spring thaw will gradually allow the cultivation of plants that could not be previously cultivated there. For millennia, Pea (Pisum sativum L.) has been a major cultivated protein plant in Nordic countries but is currently limited to the southern parts of the region. However, response and adaptation to the Arctic day length/light spectrum and temperatures are essential for the productivity of the pea germplasm and need to be better understood. This study investigated these factors and identified suitable pea genetic resources for future cultivation and breeding in the Arctic region. Fifty gene bank accessions of peas with a Nordic landrace or cultivar origin were evaluated in 2-year field trials at four Nordic locations in Denmark, Finland, Sweden, and Norway (55° to 69° N). The contrasting environmental conditions of the trial sites revealed differences in expression of phenological, morphological, crop productivity, and quality traits in the accessions. The data showed that light conditions related to a very long photoperiod partly compensated for the lack of accumulated temperature in the far north. A critical factor for cultivation in the Arctic is the use of cultivars with rapid flowering and maturation times combined with early sowing. At the most extreme site (69°N), no accession reached full maturation. Nonetheless several accessions, predominantly landraces of a northern origin, reached a green harvest state. All the cultivars reached full maturation at the sub-Arctic latitude in northern Sweden (63°N) when plants were established early in the season. Seed yield correlated positively with seed number and aboveground biomass, but negatively with flowering time. A high yield potential and protein concentration of dry seed were found in many garden types of pea, confirming their breeding potential for yield. Overall, the results indicated that pea genetic resources are available for breeding or immediate cultivation, thus aiding in the northward expansion of pea cultivation. Predicted climate changes would support this expansion.

Characterization of phenolic compounds in two novel lines of Pisum sativum L. along with their in vitro antioxidant potential

Like other vegetables, Pisum sativum L. also faces storage and degradation problems. To enhance their resistance and make them enable to cope with the deterioration problems during storage, the current study was designed to develop two resistant lines of P. sativum in terms of phenolic contents and genotypes. The phenolic compounds generally have antioxidant properties and deterioration during storage which are usually due to oxidation caused by free radicals. Thus, if a variety has high phenolic contents these problems will be coped in a better way. The genotype of a plant is also important in this regard, and the best adopted species would survive in unfavorable conditions. First, the phenolic and flavonoid contents were determined in the crude extract using the Folin-Ciocalteu method. Then, the identification and quantification of phenolic compounds were carried out in the developed lines of selected plants PL-04 and PL-05, as well as in the parental varieties [Climax (female) and Falan (male)] via HPLC. DPPH assay was used to determine the free radical scavenging capabilities of the extracts of the developed verities. The genotypic differences were confirmed by DNA fingerprinting using advanced simple sequence repeat (SSR) markers. The HPLC analysis of PL-04 confirmed the presence of three phenolic compounds in an appreciable amount which exhibited a higher antioxidant activity against DPPH radicals, while in the parental varieties, two phenolic compounds were identified and exhibited lower antioxidant activities. PL-04 was found rich in phenolic compounds and affectively scavenge-free radicals which would therefore be resistant to oxidation and degradation caused by free radicals. Comparing the present findings with our previous one, P-04 was found to be resistant to powdery mildew; it was concluded that the most probable reason of the resistance was the high phenolic contents and thus long shelf life.

Molecular Evidence for Two Domestication Events in the Pea Crop

Pea, one of the founder crops from the Near East, has two wild species: Pisum sativum subsp. elatius, with a wide distribution centered in the Mediterranean, and P. fulvum, which is restricted to Syria, Lebanon, Israel, Palestine and Jordan. Using genome wide analysis of 11,343 polymorphic single nucleotide polymorphisms (SNPs) on a set of wild P. elatius (134) and P. fulvum (20) and 74 domesticated accessions (64 P. sativum landraces and 10 P. abyssinicum), we demonstrated that domesticated P. sativum and the Ethiopian pea (P. abyssinicum) were derived from different P. elatius genepools. Therefore, pea has at least two domestication events. The analysis does not support a hybrid origin of P. abyssinicum, which was likely introduced into Ethiopia and Yemen followed by eco-geographic adaptation. Both P. sativum and P. abyssinicum share traits that are typical of domestication, such as non-dormant seeds. Non-dormant seeds were also found in several wild P. elatius accessions which could be the result of crop to wild introgression or natural variation that may have been present during pea domestication. A sub-group of P. elatius overlaps with P. sativum landraces. This may be a consequence of bidirectional gene-flow or may suggest that this group of P. elatius is the closest extant wild relative of P. sativum.

Patterns of Genetic Structure and Linkage Disequilibrium in a Large Collection of Pea Germplasm

Pea (Pisum sativum, L.) is a major pulse crop used both for animal and human alimentation. Owing to its association with nitrogen-fixing bacteria, it is also a valuable component for low-input cropping systems. To evaluate the genetic diversity and the scale of linkage disequilibrium (LD) decay in pea, we genotyped a collection of 917 accessions, gathering elite cultivars, landraces, and wild relatives using an array of ∼13,000 single nucleotide polymorphisms (SNP). Genetic diversity is broadly distributed across three groups corresponding to wild/landraces peas, winter types, and spring types. At a finer subdivision level, genetic groups relate to local breeding programs and type usage. LD decreases steeply as genetic distance increases. When considering subsets of the data, LD values can be higher, even if the steep decay remains. We looked for genomic regions exhibiting high level of differentiation between wild/landraces, winter, and spring pea, respectively. Two regions on linkage groups 5 and 6 containing 33 SNPs exhibit stronger differentiation between winter and spring peas than would be expected under neutrality. Interestingly, QTL for resistance to cold acclimation and frost resistance have been identified previously in the same regions.

A community resource for exploring and utilizing genetic diversity in the USDA pea single plant plus collection

Globally, pea (Pisum sativum L.) is an important temperate legume crop for food, feed and fodder, and many breeding programs develop cultivars adapted to these end-uses. In order to assist pea development efforts, we assembled the USDA Pea Single Plant Plus Collection (PSPPC), which contains 431 P. sativum accessions with morphological, geographic and taxonomic diversity. The collection was characterized genetically in order to maximize its value for trait mapping and genomics-assisted breeding. To that end, we used genotyping-by-sequencing-a cost-effective method for de novo single-nucleotide polymorphism (SNP) marker discovery-to generate 66 591 high-quality SNPs. These data facilitated the identification of accessions divergent from mainstream breeding germplasm that could serve as sources of novel, favorable alleles. In particular, a group of accessions from Central Asia appear nearly as diverse as a sister species, P. fulvum, and subspecies, P. sativum subsp. elatius. PSPPC genotypes can be paired with new and existing phenotype data for trait mapping; as proof-of-concept, we localized Mendel's A gene controlling flower color to its known position. We also used SNP data to define a smaller core collection of 108 accessions with similar levels of genetic diversity as the entire PSPPC, resulting in a smaller germplasm set for research screening and evaluation under limited resources. Taken together, the results presented in this study along with the release of a publicly available SNP data set comprise a valuable resource for supporting worldwide pea genetic improvement efforts.

Aggressiveness Changes in Populations of Didymella pinodes over Winter and Spring Pea Cropping Seasons

Ascochyta blight, caused by the necrotrophic ascomycete Didymella pinodes, is responsible for severe losses in winter and spring pea crops. Despite different climatic conditions, epidemics on winter and spring crops are due to a single population of D. pinodes, suggesting gene flow either between the two crops or from reservoir sources during the cropping season. This should lead to similar pathogenicity characteristics in isolates sampled from the two crops. However, these hypotheses have never been formally tested. We therefore sampled a total of 520 D. pinodes strains throughout a growing season from winter and spring pea plots (WP and SP, respectively) and from winter and spring trap plants (TWP and TSP). Amplified fragment length polymorphism (AFLP) markers revealed high genetic diversity within subpopulations, whereas pathogenicity tests showed that mean aggressiveness increases over the course of an epidemic. These results support the idea that alloinoculum contributes to the carryover of epidemics between winter and spring crops and that the most aggressive isolates are selected as an epidemic progresses.

IMPORTANCE

Ascochyta blight, caused by Didymella pinodes, is responsible for severe losses in pea crops. While previous studies have shown that ascochyta blight epidemics on winter and spring crops are due to a single population of D. pinodes, suggesting that isolates from the two crops present similar pathogenicity characteristics, that hypothesis have never been tested. Genetic analysis of subpopulations sampled throughout a growing season from winter and spring pea plots revealed high genetic diversity within subpopulations, whereas pathogenicity tests showed that mean aggressiveness increases over the course of an epidemic.

Genomic Tools in Pea Breeding Programs: Status and Perspectives

Pea (Pisum sativum L.) is an annual cool-season legume and one of the oldest domesticated crops. Dry pea seeds contain 22-25% protein, complex starch and fiber constituents, and a rich array of vitamins, minerals, and phytochemicals which make them a valuable source for human consumption and livestock feed. Dry pea ranks third to common bean and chickpea as the most widely grown pulse in the world with more than 11 million tons produced in 2013. Pea breeding has achieved great success since the time of Mendel's experiments in the mid-1800s. However, several traits still require significant improvement for better yield stability in a larger growing area. Key breeding objectives in pea include improving biotic and abiotic stress resistance and enhancing yield components and seed quality. Taking advantage of the diversity present in the pea genepool, many mapping populations have been constructed in the last decades and efforts have been deployed to identify loci involved in the control of target traits and further introgress them into elite breeding materials. Pea now benefits from next-generation sequencing and high-throughput genotyping technologies that are paving the way for genome-wide association studies and genomic selection approaches. This review covers the significant development and deployment of genomic tools for pea breeding in recent years. Future prospects are discussed especially in light of current progress toward deciphering the pea genome.

Assessment of genetic diversity in Ethiopian field pea (Pisum sativum L.) accessions with newly developed EST-SSR markers

BACKGROUND

Field pea (Pisum sativum L.) is among the prominent crops in the world as food and feed. There are relatively few simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs) in P. sativum.

RESULTS

In the present study, 15 new EST-SSR markers were developed from publicly available ESTs. These markers have successfully amplified their target loci across seven Pisum sativum subsp. sativum accessions. Eleven (73%) of these SSRs were trinucleotide repeats, two (13%) dinucleotide and two (13%) were hexanucleotide repeats. Across-taxa transferability of these new markers was also tested on other subspecies of Pisum as well as on P. fulvum, Vicia faba and Lens culinaris. In Pisum sativum subsp. sativum, 13 of the 15 markers were polymorphic and 12 of them subsequently used for genetic diversity analysis. Forty six accessions, of which 43 were from Ethiopia, were subjected to genetic diversity analysis using these newly developed markers. All accessions were represented by 12 individuals except two (NGB103816 and 237508) that were represented by 9 and 11 individuals, respectively. A total of 37 alleles were detected across all accessions. PS10 was the most polymorphic locus with six alleles, and the average number of alleles per locus over the 12 polymorphic loci was 3.1. Several rare and private alleles were also revealed. The most distinct accession (32048) had private alleles at three loci with 100% frequency.

CONCLUSION

These newly developed EST-SSR primer-pairs successfully amplified expected loci in P. sativum subsp. sativum as well as in other subspecies of the genus Pisum and related genera. High levels of genetic variation were detected in field pea accessions from Ethiopia using these markers. This result implies the potential of the Ethiopian field pea gene pool for improvement of field peas in various desirable traits. In addition, these markers could be a valuable asset in resolving the inconsistency in the taxonomic status of the different subspecies of genus Pisum as well as for characterization of field pea accessions in different gene banks around the world for breeding and conservation purposes.

Variability within a pea core collection of LEAM and HSP22, two mitochondrial seed proteins involved in stress tolerance

LEAM, a late embryogenesis abundant protein, and HSP22, a small heat shock protein, were shown to accumulate in the mitochondria during pea (Pisum sativum L.) seed development, where they are expected to contribute to desiccation tolerance. Here, their expression was examined in seeds of 89 pea genotypes by Western blot analysis. All genotypes expressed LEAM and HSP22 in similar amounts. In contrast with HSP22, LEAM displayed different isoforms according to apparent molecular mass. Each of the 89 genotypes harboured a single LEAM isoform. Genomic and RT-PCR analysis revealed four LEAM genes differing by a small variable indel in the coding region. These variations were consistent with the apparent molecular mass of each isoform. Indels, which occurred in repeated domains, did not alter the main properties of LEAM. Structural modelling indicated that the class A α-helix structure, which allows interactions with the mitochondrial inner membrane in the dry state, was preserved in all isoforms, suggesting functionality is maintained. The overall results point out the essential character of LEAM and HSP22 in pea seeds. LEAM variability is discussed in terms of pea breeding history as well as LEA gene evolution mechanisms.

Precision assessment of some supervised and unsupervised algorithms for genotype discrimination in the genus Pisum using SSR molecular data

For the first time, prediction accuracies of some supervised and unsupervised algorithms were evaluated in an SSR-based DNA fingerprinting study of a pea collection containing 20 cultivars and 57 wild samples. In general, according to the 10 attribute weighting models, the SSR alleles of PEAPHTAP-2 and PSBLOX13.2-1 were the two most important attributes to generate discrimination among eight different species and subspecies of genus Pisum. In addition, K-Medoids unsupervised clustering run on Chi squared dataset exhibited the best prediction accuracy (83.12%), while the lowest accuracy (25.97%) gained as K-Means model ran on FCdb database. Irrespective of some fluctuations, the overall accuracies of tree induction models were significantly high for many algorithms, and the attributes PSBLOX13.2-3 and PEAPHTAP could successfully detach Pisum fulvum accessions and cultivars from the others when two selected decision trees were taken into account. Meanwhile, the other used supervised algorithms exhibited overall reliable accuracies, even though in some rare cases, they gave us low amounts of accuracies. Our results, altogether, demonstrate promising applications of both supervised and unsupervised algorithms to provide suitable data mining tools regarding accurate fingerprinting of different species and subspecies of genus Pisum, as a fundamental priority task in breeding programs of the crop.

Genetic diversity and trait genomic prediction in a pea diversity panel

BACKGROUND

Pea (Pisum sativum L.), a major pulse crop grown for its protein-rich seeds, is an important component of agroecological cropping systems in diverse regions of the world. New breeding challenges imposed by global climate change and new regulations urge pea breeders to undertake more efficient methods of selection and better take advantage of the large genetic diversity present in the Pisum sativum genepool. Diversity studies conducted so far in pea used Simple Sequence Repeat (SSR) and Retrotransposon Based Insertion Polymorphism (RBIP) markers. Recently, SNP marker panels have been developed that will be useful for genetic diversity assessment and marker-assisted selection.

RESULTS

A collection of diverse pea accessions, including landraces and cultivars of garden, field or fodder peas as well as wild peas was characterised at the molecular level using newly developed SNP markers, as well as SSR markers and RBIP markers. The three types of markers were used to describe the structure of the collection and revealed different pictures of the genetic diversity among the collection. SSR showed the fastest rate of evolution and RBIP the slowest rate of evolution, pointing to their contrasted mode of evolution. SNP markers were then used to predict phenotypes -the date of flowering (BegFlo), the number of seeds per plant (Nseed) and thousand seed weight (TSW)- that were recorded for the collection. Different statistical methods were tested including the LASSO (Least Absolute Shrinkage ans Selection Operator), PLS (Partial Least Squares), SPLS (Sparse Partial Least Squares), Bayes A, Bayes B and GBLUP (Genomic Best Linear Unbiased Prediction) methods and the structure of the collection was taken into account in the prediction. Despite a limited number of 331 markers used for prediction, TSW was reliably predicted.

CONCLUSION

The development of marker assisted selection has not reached its full potential in pea until now. This paper shows that the high-throughput SNP arrays that are being developed will most probably allow for a more efficient selection in this species.

Genetic diversity and population structure among pea (Pisum sativum L.) cultivars as revealed by simple sequence repeat and novel genic markers

Field pea (Pisum sativum L.) is an important cool season legume crop widely grown around the world. This research provides a basis for selection of pea germplasm across geographical regions in current and future breeding and genetic mapping efforts for pea improvement. Eleven novel genic markers were developed from pea expressed sequence tag (EST) sequences having significant similarity with gene calls from Medicago truncatula spanning at least one intron. In this study, 96 cultivars widely grown or used in breeding programs in the USA and Canada were analyzed for genetic diversity using 31 microsatellite or simple sequence repeat (SSR) and 11 novel EST-derived genic markers. The polymorphic information content varied from 0.01-0.56 among SSR markers and 0.04-0.43 among genic markers. The results showed that SSR and EST-derived genic markers displayed one or more highly reproducible, multi-allelic, and easy to score loci ranging from 200 to 700 bp in size. Genetic diversity was assessed through unweighted neighbor-joining method, and 96 varieties were grouped into three main clusters based on the dissimilarity matrix. Four subpopulations were determined through STRUCTURE analysis with no significant geographic separation of the subpopulations. The findings of the present study can be used to select diverse genotypes to be used as parents of crosses aimed for breeding improved pea cultivars.

Transcriptome sequencing for high throughput SNP development and genetic mapping in Pea

BACKGROUND

Pea has a complex genome of 4.3 Gb for which only limited genomic resources are available to date. Although SNP markers are now highly valuable for research and modern breeding, only a few are described and used in pea for genetic diversity and linkage analysis.

RESULTS

We developed a large resource by cDNA sequencing of 8 genotypes representative of modern breeding material using the Roche 454 technology, combining both long reads (400 bp) and high coverage (3.8 million reads, reaching a total of 1,369 megabases). Sequencing data were assembled and generated a 68 K unigene set, from which 41 K were annotated from their best blast hit against the model species Medicago truncatula. Annotated contigs showed an even distribution along M. truncatula pseudochromosomes, suggesting a good representation of the pea genome. 10 K pea contigs were found to be polymorphic among the genetic material surveyed, corresponding to 35 K SNPs.We validated a subset of 1538 SNPs through the GoldenGate assay, proving their ability to structure a diversity panel of breeding germplasm. Among them, 1340 were genetically mapped and used to build a new consensus map comprising a total of 2070 markers. Based on blast analysis, we could establish 1252 bridges between our pea consensus map and the pseudochromosomes of M. truncatula, which provides new insight on synteny between the two species.

CONCLUSIONS

Our approach created significant new resources in pea, i.e. the most comprehensive genetic map to date tightly linked to the model species M. truncatula and a large SNP resource for both academic research and breeding.

Twentieth-century changes in the genetic composition of Swedish field pea metapopulations

Landrace crops are formed by local adaptation, genetic drift and gene flow through seed exchange. In reverse, the study of genetic structure between landrace populations can reveal the effects of these forces over time. We present here the analysis of genetic diversity in 40 Swedish field pea (Pisum sativum L.) populations, either available as historical seed samples from the late nineteenth century or as extant gene bank accessions assembled in the late twentieth century. The historical material shows constant high levels of within-population diversity, whereas the extant accessions show varying, and overall lower, levels of within-population diversity. Structure and principal component analysis cluster most accessions, both extant and historical, in groups after geographical origin. County-wise analyses of the accessions show that the genetic diversity of the historical accessions is largely overlapping. In contrast, most extant accessions show signs of genetic drift. They harbor a subset of the alleles found in the historical accessions and are more differentiated from each other. These results reflect how, historically present metapopulations have been preserved during the twentieth century, although as genetically isolated populations.

Exploring chloroplastic changes related to chilling and freezing tolerance during cold acclimation of pea (Pisum sativum L.)

Pea (Pisum sativum L.) productivity is linked to its ability to cope with abiotic stresses such as low temperatures during fall and winter. In this study, we investigate the chloroplast-related changes occurring during pea cold acclimation, in order to further lead to genetic improvement of its field performance. Champagne and Térèse, two pea lines with different acclimation capabilities, were studied by physiological measurements, sub-cellular fractionation followed by relative protein quantification and two-dimensional DIGE. The chilling tolerance might be related to an increase in protein related to soluble sugar synthesis, antioxidant potential, regulation of mRNA transcription and translation through the chloroplast. Freezing tolerance, only observed in Champagne, seems to rely on a higher inherent photosynthetic potential at the beginning of the cold exposure, combined with an early ability to start metabolic processes aimed at maintaining the photosynthetic capacity, optimizing the stoichiometry of the photosystems and inducing dynamic changes in carbohydrate and protein synthesis and/or turnover.

A single, plastic population of Mycosphaerella pinodes causes ascochyta blight on winter and spring peas (Pisum sativum) in France

Plant diseases are caused by pathogen populations continuously subjected to evolutionary forces (genetic flow, selection, and recombination). Ascochyta blight, caused by Mycosphaerella pinodes, is one of the most damaging necrotrophic pathogens of field peas worldwide. In France, both winter and spring peas are cultivated. Although these crops overlap by about 4 months (March to June), primary Ascochyta blight infections are not synchronous on the two crops. This suggests that the disease could be due to two different M. pinodes populations, specialized on either winter or spring pea. To test this hypothesis, 144 pathogen isolates were collected in the field during the winter and spring growing seasons in Rennes (western France), and all the isolates were genotyped using amplified fragment length polymorphism (AFLP) markers. Furthermore, the pathogenicities of 33 isolates randomly chosen within the collection were tested on four pea genotypes (2 winter and 2 spring types) grown under three climatic regimes, simulating winter, late winter, and spring conditions. M. pinodes isolates from winter and spring peas were genetically polymorphic but not differentiated according to the type of cultivars. Isolates from winter pea were more pathogenic than isolates from spring pea on hosts raised under winter conditions, while isolates from spring pea were more pathogenic than those from winter pea on plants raised under spring conditions. These results show that disease developed on winter and spring peas was initiated by a single population of M. pinodes whose pathogenicity is a plastic trait modulated by the physiological status of the host plant.

Transcriptome analysis in pea allows to distinguish chilling and acclimation mechanisms

In order to distinguish chilling and freezing tolerance mechanisms in pea, responses to cold exposure were compared between the freezing tolerant line Champagne and the sensitive line Terese. Global gene expression was considered in the two lines and associated with morphological, histological and biochemical approaches. The chilling tolerance in both lines was related to responses of the CBF, COR and LEA genes belonging to the CBF regulon, with greater earliness of expression in the Champagne genotype. The freezing tolerance, only observed in Champagne, was associated with acclimation processes such as cellular osmotic stabilization, photosynthesis modifications, antioxidants production, modifications in hormone metabolism, cell wall composition and dynamics.

Genetic diversity in European Pisum germplasm collections

The distinctness of, and overlap between, pea genotypes held in several Pisum germplasm collections has been used to determine their relatedness and to test previous ideas about the genetic diversity of Pisum. Our characterisation of genetic diversity among 4,538 Pisum accessions held in 7 European Genebanks has identified sources of novel genetic variation, and both reinforces and refines previous interpretations of the overall structure of genetic diversity in Pisum. Molecular marker analysis was based upon the presence/absence of polymorphism of retrotransposon insertions scored by a high-throughput microarray and SSAP approaches. We conclude that the diversity of Pisum constitutes a broad continuum, with graded differentiation into sub-populations which display various degrees of distinctness. The most distinct genetic groups correspond to the named taxa while the cultivars and landraces of Pisum sativum can be divided into two broad types, one of which is strongly enriched for modern cultivars. The addition of germplasm sets from six European Genebanks, chosen to represent high diversity, to a single collection previously studied with these markers resulted in modest additions to the overall diversity observed, suggesting that the great majority of the total genetic diversity collected for the Pisum genus has now been described. Two interesting sources of novel genetic variation have been identified. Finally, we have proposed reference sets of core accessions with a range of sample sizes to represent Pisum diversity for the future study and exploitation by researchers and breeders.

ISSR: a reliable and cost-effective technique for detection of DNA polymorphism

With the emergence of more and more molecular markers as useful tools in plethora of population genetic and phylogenetic studies, choice of marker system for a particular study has become mind boggling. These marker systems differ in their advantages and disadvantages, so it is imperative to keep in mind all the pros and cons of the technique while selecting one for the problem to be addressed.Here, we have shed light on the ISSR (intersimple sequence repeat) technique, as a marker of choice if one wants to go for properties such as reliability, simplicity, cost effectiveness, and speed, in addition to assessing genetic diversity between closely related individuals. We have outlined here the whole methodology of this technique with an example of Tribulus terrestris as case study.

Use of SSR, RAPD markers and protein profiles based analysis to differentiate Eleusine coracana genotypes differing in their protein content

Fifty-two genotypes of Eleusine coracana collected from Uttarakhand hills were subjected to simple sequence repeat (SSR), random amplified polymorphic DNA (RAPD)-PCR and protein profiling analysis to investigate the variation in protein content. The main objective of the present study was to detect variability among E. coracana and also assess the discriminating ability of these three molecular methods. A total of 21 RAPD and 24 SSR primers were assayed for their specificity in detecting genetic variability in E. coracana, of which 20 RAPD and 21 SSR primers were highly reproducible and were found suitable for use in PCR analysis. Assessing genetic diversity among E. coracana genotypes by RAPD-PCR using 20 polymorphic primers yielded 56 different RAPD markers which clustered the genotypes into different groups on the basis of protein content. Similarly, SSR-PCR with 21 polymorphic primers clustered the genotypes into different groups. On the other hand, biochemical typing of E. coracana using whole seed proteins generated profiles that showed no major difference indicating the technique to be not useful in typing genotypes of this crop. However, a few of the genotypes showed the presence of a unique band of 32 kDa that needs to be further investigated to understand the role of the protein from nutritional point of view, if any. In the present study, significant negative correlation (r = -0.69*) was found between the protein and calcium content of finger millet genotypes. Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis based seed storage proteins generated profiles showed no major differences in banding pattern among 52 finger millet genotypes while quantitative estimation of seed storage protein fractions using Lowry method revealed that glutelin was highest followed by prolamin, globulin and albumin.

Estimation of pea (Pisum sativum L.) microsatellite mutation rate based on pedigree and single-seed descent analyses

Microsatellites, or simple sequence repeats (SSRs) are widespread class of repetitive DNA sequences, used in population genetics, genetic diversity and mapping studies. In spite of the SSR utility, the genetic and evolutionary mechanisms are not fully understood. We have investigated three microsatellite loci with different position in the pea (Pisum sativum L.) genome, the A9 locus residing in LTR region of abundant retrotransposon, AD270 as intergenic and AF016458 located in 5'untranslated region of expressed gene. Comparative analysis of a 35 pair samples from seven pea varieties propagated by single-seed descent for ten generations, revealed single 4 bp mutation in 10th generation sample at AD270 locus corresponding to stepwise increase in one additional ATCT repeat unit. The estimated mutation rate was 4.76 × 10(-3) per locus per generation, with a 95% confidence interval of 1.2 × 10(-4) to 2.7 × 10(-2). The comparison of cv. Bohatýr accessions retrieved from different collections, showed intra-, inter-accession variation and differences in flanking and repeat sequences. Fragment size and sequence alternations were also found in long term in vitro organogenic culture, established at 1983, indicative of somatic mutation process. The evidence of homoplasy was detected across of unrelated pea genotypes, which adversaly affects the reliability of diversity estimates not only for diverse germplasm but also highly bred material. The findings of this study have important implications for Pisum phylogeny studies, variety identification and registration process in pea breeding where mutation rate influences the genetic diversity and the effective population size estimates.

Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea

BACKGROUND

Single Nucleotide Polymorphisms (SNPs) can be used as genetic markers for applications such as genetic diversity studies or genetic mapping. New technologies now allow genotyping hundreds to thousands of SNPs in a single reaction.In order to evaluate the potential of these technologies in pea, we selected a custom 384-SNP set using SNPs discovered in Pisum through the resequencing of gene fragments in different genotypes and by compiling genomic sequence data present in databases. We then designed an Illumina GoldenGate assay to genotype both a Pisum germplasm collection and a genetic mapping population with the SNP set.

RESULTS

We obtained clear allelic data for more than 92% of the SNPs (356 out of 384). Interestingly, the technique was successful for all the genotypes present in the germplasm collection, including those from species or subspecies different from the P. sativum ssp sativum used to generate sequences. By genotyping the mapping population with the SNP set, we obtained a genetic map and map positions for 37 new gene markers.

CONCLUSION

Our results show that the Illumina GoldenGate assay can be used successfully for high-throughput SNP genotyping of diverse germplasm in pea. This genotyping approach will simplify genotyping procedures for association mapping or diversity studies purposes and open new perspectives in legume genomics.

Genetic dissection of nitrogen nutrition in pea through a QTL approach of root, nodule, and shoot variability

Pea (Pisum sativum L.) is the third most important grain legume worldwide, and the increasing demand for protein-rich raw material has led to a great interest in this crop as a protein source. Seed yield and protein content in crops are strongly determined by nitrogen (N) nutrition, which in legumes relies on two complementary pathways: absorption by roots of soil mineral nitrogen, and fixation in nodules of atmospheric dinitrogen through the plant-Rhizobium symbiosis. This study assessed the potential of naturally occurring genetic variability of nodulated root structure and functioning traits to improve N nutrition in pea. Glasshouse and field experiments were performed on seven pea genotypes and on the 'Cameor' x 'Ballet' population of recombinant inbred lines selected on the basis of parental contrast for root and nodule traits. Significant variation was observed for most traits, which were obtained from non-destructive kinetic measurements of nodulated root and shoot in pouches, root and shoot image analysis, (15)N quantification, or seed yield and protein content determination. A significant positive relationship was found between nodule establishment and root system growth, both among the seven genotypes and the RIL population. Moreover, several quantitative trait loci for root or nodule traits and seed N accumulation were mapped in similar locations, highlighting the possibility of breeding new pea cultivars with increased root system size, sustained nodule number, and improved N nutrition. The impact on both root or nodule traits and N nutrition of the genomic regions of the major developmental genes Le and Af was also underlined.

Genetic characterization of pea (Pisum sativum) germplasm from Turkey using morphological and SSR markers

The need for the conservation of plant genetic resources has been widely accepted. Germplasm characterization and evaluation yield information for more efficient utilization of these valuable resources. The aim of the present study was to characterize the pea germplasm conserved at the Aegean Agricultural Research Institute of Turkey using morphological and simple sequence repeat (SSR)-based molecular approaches. Genetic characterization of 30 pea genotypes collected from different regions of Turkey and 10 commercial pea cultivars was performed using the criteria of the International Union for the Protection of New Varieties of Plants (UPOV) (TG 7/9 Pisum sativum), and with 10 SSR markers. We originally tested 15 SSR markers; 10 of these markers were selected on the basis of high polymorphism information content in the molecular assays. Sixty-one alleles were detected at the 10 loci. The number of alleles per SSR locus ranged from 3 (PVSBE2) to 12 (AB53), with a mean of 6.1 alleles. The most informative loci were AB53 (12 alleles), AA355 (9 alleles), AD270 (8 alleles), A9 (7 alleles), AD61 (7 alleles), and AB25 (6 alleles). The UPGMA dendrogram defined by SSR markers revealed genetic relatedness of the pea genotypes. These findings can be used to guide future breeding studies and germplasm management of these pea genotypes.

The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis

BACKGROUND

The genetic diversity of crop species is the result of natural selection on the wild progenitor and human intervention by ancient and modern farmers and breeders. The genomes of modern cultivars, old cultivated landraces, ecotypes and wild relatives reflect the effects of these forces and provide insights into germplasm structural diversity, the geographical dimension to species diversity and the process of domestication of wild organisms. This issue is also of great practical importance for crop improvement because wild germplasm represents a rich potential source of useful under-exploited alleles or allele combinations. The aim of the present study was to analyse a major Pisum germplasm collection to gain a broad understanding of the diversity and evolution of Pisum and provide a new rational framework for designing germplasm core collections of the genus.

RESULTS

3020 Pisum germplasm samples from the John Innes Pisum germplasm collection were genotyped for 45 retrotransposon based insertion polymorphism (RBIP) markers by the Tagged Array Marker (TAM) method. The data set was stored in a purpose-built Germinate relational database and analysed by both principal coordinate analysis and a nested application of the Structure program which yielded substantially similar but complementary views of the diversity of the genus Pisum. Structure revealed three Groups (1-3) corresponding approximately to landrace, cultivar and wild Pisum respectively, which were resolved by nested Structure analysis into 14 Sub-Groups, many of which correlate with taxonomic sub-divisions of Pisum, domestication related phenotypic traits and/or restricted geographical locations. Genetic distances calculated between these Sub-Groups are broadly supported by principal coordinate analysis and these, together with the trait and geographical data, were used to infer a detailed model for the domestication of Pisum.

CONCLUSIONS

These data provide a clear picture of the major distinct gene pools into which the genus Pisum is partitioned and their geographical distribution. The data strongly support the model of independent domestications for P. sativum ssp abyssinicum and P. sativum. The relationships between these two cultivated germplasms and the various sub-divisions of wild Pisum have been clarified and the most likely ancestral wild gene pools for domesticated P. sativum identified. Lastly, this study provides a framework for defining global Pisum germplasm which will be useful for designing core collections.

Analysis of a diverse global Pisum sp. collection and comparison to a Chinese local P. sativum collection with microsatellite markers

Twenty-one informative microsatellite loci were used to assess and compare the genetic diversity among Pisum genotypes sourced from within and outside China. The Chinese germplasm comprised 1243 P. sativum genotypes from 28 provinces and this was compared to 774 P. sativum genotypes that represented a globally diverse germplasm collection, as well as 103 genotypes from related Pisum species. The Chinese P. sativum germplasm was found to contain genotypes genetically distinct from the global gene pool sourced outside China. The Chinese spring type genotypes were separate from the global gene pool and from the other main Chinese gene pool of winter types. The distinct Chinese spring gene pool comprised genotypes from Inner Mongolia and Sha'anxi provinces, with those from Sha'anxi showing the greatest diversity. The other main gene pool within China included both spring types from other northern provinces and winter types from central and southern China, plus some accessions from Inner Mongolia and Sha'anxi. A core collection of Chinese landraces chosen to represent molecular diversity was compared both to the wider Chinese collection and to a geographically diverse core collection of Chinese landraces. The average gene diversity and allelic richness per locus of both the micro-satellite based core and the wider collection were similar, and greater than the geographically diverse core. The genetic diversity of P. sativum within China appears to be quite different to that detected in the global gene pool, including the presence of several rare alleles, and may be a useful source of allelic variation for both major gene and quantitative traits.

Genetic diversity and population structure of pea (Pisum sativum L.) varieties derived from combined retrotransposon, microsatellite and morphological marker analysis

One hundred and sixty-four accessions representing Czech and Slovak pea (Pisum sativum L.) varieties bred over the last 50 years were evaluated for genetic diversity using morphological, simple sequence repeat (SSR) and retrotransposon-based insertion polymorphism (RBIP) markers. Polymorphic information content (PIC) values of 10 SSR loci and 31 RBIP markers were on average high at 0.89 and 0.73, respectively. The silhouette method after the Ward clustering produced the most probable cluster estimate, identifying nine clusters from molecular data and five to seven clusters from morphological characters. Principal component analysis of nine qualitative and eight quantitative morphological parameters explain over 90 and 93% of total variability, respectively, in the first three axes. Multidimensional scaling of molecular data revealed a continuous structure for the set. To enable integration and evaluation of all data types, a Bayesian method for clustering was applied. Three clusters identified using morphology data, with clear separation of fodder, dry seed and afila types, were resolved by DNA data into 17, 12 and five sub-clusters, respectively. A core collection of 34 samples was derived from the complete collection by BAPS Bayesian analysis. Values for average gene diversity and allelic richness for molecular marker loci and diversity indexes of phenotypic data were found to be similar between the two collections, showing that this is a useful approach for representative core selection.

The flowering locus Hr colocalizes with a major QTL affecting winter frost tolerance in Pisum sativum L

An understanding of the genetic determinism of frost tolerance is a prerequisite for the development of frost tolerant cultivars for cold northern areas. In legumes, it is not known to which extent vernalization requirement or photoperiod responsiveness are necessary for the development of frost tolerance. In pea (Pisum sativum L.) however, the flowering locus Hr is suspected to influence winter frost tolerance by delaying floral initiation until after the main winter freezing periods have passed. The objective of this study was to dissect the genetic determinism of frost tolerance in pea by QTL analysis and to assess the genetic linkage between winter frost tolerance and the Hr locus. A population of 164 recombinant inbred lines (RILs), derived from the cross Champagne x Terese was evaluated both in the greenhouse and in field conditions to characterize the photoperiod response from which the allele at the Hr locus was inferred. In addition, the population was also assessed for winter frost tolerance in 11 field conditions. Six QTL were detected, among which three were consistent among the different experimental conditions, confirming an oligogenic determinism of frost tolerance in pea. The Hr locus was found to be the peak marker for the highest explanatory QTL of this study. This result supports the hypothesis of the prominent part played by the photoperiod responsiveness in the determinism of frost tolerance for this species. The consistency of three QTL makes these positions interesting targets for marker-assisted selection.

Analysis of genetic diversity through AFLP, SAMPL, ISSR and RAPD markers in Tribulus terrestris, a medicinal herb

Tribulus terrestris is well known for its medicinal importance in curing urino-genital disorders. Amplified fragment length polymorphism (AFLP), selective amplification of microsatellite polymorphic loci (SAMPL), inter-simple sequence repeat (ISSR) and randomly amplified polymorphic DNA (RAPD) markers were used for the first time for the detection of genetic polymorphism in this medicinal herb from samples collected from various geographical regions of India. Six assays each of AFLP and SAMPL markers and 21 each of ISSR and RAPD markers were utilized. AFLP yielded 500 scorable amplified products, of which 82.9% were polymorphic. SAMPL primers amplified 488 bands, 462 being polymorphic (94.7%). The range of amplified bands was 66 [(TC)(8)G + M-CAG] to 98 [(CA)(6)AG + M-CAC] and the percentage polymorphism, 89.9 [from (CT)(4)C (AC)(4)A + M-CTG] to 100 [from (GACA)(4) + M-CTA]. The ISSR primers amplified 239 bands of 0.4-2.5 kb, 73.6% showed polymorphism. The amplified products ranged from 5 to 16 and the percentage polymorphism 40-100. RAPD assays produced 276 bands, of which 163 were polymorphic (59%). Mantel test employed for detection of goodness of fit established cophenetic correlation values above 0.9 for all the four marker systems. The dendrograms and PCA plots derived from the binary data matrices of the four marker systems are highly concordant. High bootstrap values were obtained at major nodes of phenograms through WINBOOT software. The relative efficiency of the four molecular marker systems calculated on the basis of multiplex ratio, marker index and average heterozygosity revealed SAMPL to be the best. Distinct DNA fingerprinting profile, unique to every geographical region could be obtained with all the four molecular marker systems. Clustering can be a good indicator for clear separation of genotypes from different regions in well-defined groups that are supported by high bootstrap values.

Gene-based sequence diversity analysis of field pea (Pisum)

Sequence diversity of 39 dispersed gene loci was analyzed in 48 diverse individuals representative of the genus Pisum. The different genes show large variation in diversity parameters, suggesting widely differing levels of selection and a high overall diversity level for the species. The data set yields a genetic diversity tree whose deep branches, involving wild samples, are preserved in a tree derived from a polymorphic retrotransposon insertions in an identical sample set. Thus, gene regions and intergenic "junk DNA" share a consistent picture for the genomic diversity of Pisum, despite low linkage disequilibrium in wild and landrace germplasm, which might be expected to allow independent evolution of these very different DNA classes. Additional lines of evidence indicate that recombination has shuffled gene haplotypes efficiently within Pisum, despite its high level of inbreeding and widespread geographic distribution. Trees derived from individual gene loci show marked differences from each other, and genetic distance values between sample pairs show high standard deviations. Sequence mosaic analysis of aligned sequences identifies nine loci showing evidence for intragenic recombination. Lastly, phylogenetic network analysis confirms the non-treelike structure of Pisum diversity and indicates the major germplasm classes involved. Overall, these data emphasize the artificiality of simple tree structures for representing genomic sequence variation within Pisum and emphasize the need for fine structure haplotype analysis to accurately define the genetic structure of the species.

Assessment of genetic and epigenetic stability in long-term in vitro shoot culture of pea (Pisum sativum L.)

In vitro clonal propagation of plants should generate identical copies of the selected genotype. However, associated stress might result in a breakdown of control mechanisms and consequent instability of the genome. We have used several molecular methods to assess the genetic stability of long-term propagated (24 years) multiple shoot in vitro culture of pea (Pisum sativum L.). We focused on assessing the stability of repetitive sequences, such as simple sequence repeats (SSR) and retrotransposons, both comprising a large part of genome. No differences were found when seedlings (Co-2004) or original seed (Co-1982) controls and long-term or newly established in vitro (one subculture cycle) samples were investigated by the SSR, inter-repeats (ISSR) or inter-retrotransposon amplified polymorphism (IRAP) method. However, the more global amplified fragment length polymorphism (AFLP) and particularly the methylation sensitive MSAP methods detected 11 and 18% polymorphism among samples, respectively. Interestingly, investigation of the global cytosine methylation status by HPCE measurement revealed no statistically significant differences. Some evidence of retrotransposon re-arrangement was observed by sequence-specific amplification polymorphism. This occurred mostly in the abundant Ty3-gypsy type Cyclop element and to a smaller extent in the Ogre element. Alternatively, no polymorphism was detected among the PDR-1 element of the Ty1-copia type retrotransposon. Based on these results, multiple shoot culture of pea maintained over a long period may be considered as a true to type multiplication method of the original genotype.

A strategy on constructing core collections by least distance stepwise sampling

A strategy was proposed for constructing core collections by least distance stepwise sampling (LDSS) based on genotypic values. In each procedure of cluster, the sampling is performed in the subgroup with the least distance in the dendrogram during constructing a core collection. Mean difference percentage (MD), variance difference percentage (VD), coincidence rate of range (CR) and variable rate of coefficient of variation (VR) were used to evaluate the representativeness of core collections constructed by this strategy. A cotton germplasm collection of 1,547 accessions with 18 quantitative traits was used to construct core collections. Genotypic values of all quantitative traits of the cotton collection were unbiasedly predicted based on mixed linear model approach. By three sampling percentages (10, 20 and 30%), four genetic distances (city block distance, Euclidean distance, standardized Euclidean distance and Mahalanobis distance) combining four hierarchical cluster methods (nearest distance method, furthest distance method, unweighted pair-group average method and Ward's method) were adopted to evaluate the property of this strategy. Simulations were conducted in order to draw consistent, stable and reproducible results. The principal components analysis was performed to validate this strategy. The results showed that core collections constructed by LDSS strategy had a good representativeness of the initial collection. As compared to the control strategy (stepwise clusters with random sampling strategy), LDSS strategy could construct more representative core collections. For LDSS strategy, cluster methods did not need to be considered because all hierarchical cluster methods could give same results completely. The results also suggested that standardized Euclidean distance was an appropriate genetic distance for constructing core collections in this strategy.