Indicators to assess temporal genetic diversity in the French Catalogue: no losses for maize and peas

The aim of this study, led by the GEVES (Research and Control Group for Varieties and Seeds), was to suggest indicators to assess the diversity available to farmers since the French Official Catalogue for Plant Varieties and Species was initiated. The largest datasets of 1990 inbred maize lines and 578 pea lines from the last 50 years were analysed using morphological and enzymatic parameters. Lines were grouped into three to five periods. Genetic diversity was estimated in each period from morphological and enzymatic markers by computing numerous indices, such as the number of classes of scores for each characteristic, allelic richness or genetic diversity index (H _e ). Population differentiation parameters (G_ST, G_ST′, F_ST, Q_ST) were also estimated between periods. While genetic diversity computed from distinction, uniformity, stability traits was more marked for maize (0.66) than for garden peas (0.35) or feed peas (0.29), the opposite trend was observed with enzymes, resulting in a genetic diversity of 0.43, 0.35 and 0.22 for garden peas, feed peas and maize, respectively. However, no significant changes in genetic diversity were observed over time, and genetic differentiation was slight between periods. All our results demonstrated that no significant reduction in the diversity available to farmers had been observed since initiation of the French Catalogue. The H _e was a good indicator providing a quantitative estimate of genetic diversity, but it should be interpreted alongside a more precise indicator such as allelic richness or the number of classes for morphological characteristics.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Development of pea bacterial blight caused by Pseudomonas syringae pv. pisi in winter and spring cultivars of combining peas (Pisum sativum) with different sowing dates

Pea bacterial blight occurred by natural infection in a field trial on peas in 1995. Disease development in the winter cultivars Rafale, Frilene and Froidure was compared with that in the spring cultivars Baccara, Conquest and Bohatyr, each sown on six dates in October, November, December, mid-March, late March and April. Disease incidence had reached 100% plants affected in all treatments by mid-July. Disease severity was greater in winter-sown (October, November or December) than in spring-sown peas of each cultivar at each assessment. Significant (P < 0.05) differences in disease severity occurred between cultivars in the winter-sown plots in May and June and the spring cultivars were affected more severely than the winter cultivars. Comparison of areas under the disease progress curves for both disease incidence and severity also showed that the winter-sown peas were more affected by disease than spring-sown peas and that spring cultivars were more severely affected than winter cultivars. Yield was strongly correlated with disease severity. A linear regression model suggested that, for peas sown in October, November or December, a yield loss of 0.5 tha^-1 occurred for each 10% increase in canopy area affected by pea bacterial blight.     

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.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1266-1) contains supplementary material, which is available to authorized users.     

Assessing the genetic diversity of Panicum coloratum var. makarikariense using agro‐morphological traits and microsatellite‐based markers

Panicum coloratum var. makarikariense is a perennial C₄ grass native to South Africa with relatively good forage production under limited‐resource conditions. Genetic characterisation and breeding efforts have been scant, thus limiting its use in cattle raising systems. The goal of the present study was to assess the genetic diversity of a collection of P. coloratum var. makarikariense using agro‐morphological traits and molecular markers, in comparison with one accession of var. coloratum and one population of Panicum bergii. Agro‐morphological variability between and within accessions of var. makarikariense in a common garden setting was observed, showing that there is still opportunity for selection. Some accessions performed better than the commercialised material in relation to potential forage production. A total of 117 ISSR bands and 48 SSR alleles allowed the detection of genetic variability between and within accessions. The presence of accession‐specific bands suggested distinctness and limited gene flow. The genetic variability encountered in the commercialised material suggested that it is a stabilised population which has not undergone a strong selection process. Low correlation between agro‐morphologic and molecular variability was observed indicating that both approaches provide complementary information. Both morphological and molecular markers reveal genetic differentiation between varieties and species. This study provides a set of new SSR markers available for diversity assessment and valuable information that can be applied directly in collection management for breeding and conservation programmes.     

Marker assisted pea breeding: <Emphasis Type="Italic">eIF4E</Emphasis> allele specific markers to <Emphasis Type="Italic">pea seed-borne mosaic virus</Emphasis> (PSbMV) resistance

Traditional plant breeding relies upon crosses and subsequent selection of genotypes to meet desirable traits. The incorporation of marker-assisted selection into breeding strategies would result in a reduction in the number of offspring to be propagated, selected and tested. In the case of pea (Pisum sativum L.), the testing of resistance to viral pathogens such as pea seed-borne mosaic virus (PSbMV) is included in the breeding process. Resistance to the common strains of PSbMV is conferred by a single recessive gene (eIF4E), localized on LG VI (sbm-1 locus). We have analyzed for variation in the eIF4E genomic sequences from 43 pea varieties and breeding lines, reported as donors of resistance. This enabled a comprehensive investigation of the eIF4E gene structure and mutations responsible for PSbMV resistance were identified. Subsequently, PCR-based and gene-specific single nucleotide polymorphism and co-dominant amplicon length polymorphism markers were developed. All together 60 accessions were analyzed using sequence data and/or allele specific DNA markers. Developed allele specific markers were reproducibly amplified across a broad spectra of pea varieties and breeding lines. These were found to be 100% accurate in detecting the presence of the respective alleles when compared to symptomology and ELISA, testing (74% reliable). Hence, these molecular markers will substantially speed-up PSbMV diagnosis and resistance breeding processes in pea.     

Identification of quantitative trait loci for specific mechanisms of resistance to <Emphasis Type="Italic">Orobanche crenata</Emphasis> Forsk. in pea (<Emphasis Type="Italic">Pisum sativum</Emphasis> L.)

Crenate broomrape (Orobanche crenata) is the major constraint for pea cultivation in the Mediterranean Basin and Middle East. Cultivation of resistant varieties would be the most efficient, economical and environmentally friendly way to control this parasite. However, little resistance is available within cultivated pea. Promising sources of resistance have been identified in wild peas but their use in breeding programs is hampered by the polygenic nature of the resistance. The identification of molecular markers linked to the resistance would allow tracking of the underlying genes, facilitating their introgression into pea cultivars. The main objective of this study was the identification of genomic regions associated with resistance to O. crenata. A RIL (Recombinant Inbred Lines) population derived from a cross between a resistant accession of the wild pea Pisum sativum ssp. syriacum, and a susceptible pea variety was screened for resistance to O. crenata under field conditions during two seasons. In addition, resistance reactions at different stages of the O. crenata infection cycle were assessed using a Petri dish method. The approach allowed the identification of four Quantitative Trait Loci (QTL) associated with field resistance, assessed as the number of emerged broomrape shoots per pea plant under field conditions. These identified QTLs explained individually from 10 to 17% of the phenotypic variation. In addition QTLs governing specific mechanisms of resistance, such as low induction of O. crenata seed germination, lower number of established tubercles per host root length unit, and slower development of tubercles were also identified. Identified QTLs explained individually from 8 to 37% of the variation observed depending on the trait. Host plant aerial biomass and root length were also assessed and mapped. Both traits were correlated with the level of O. crenata infection and three out of the four QTLs controlling resistance under field conditions co-localized with QTLs controlling plant aerial biomass or root length. The relationship observed among these traits and resistance is discussed.     

Genetic diversity assessment of bittersweet (Solanum dulcamara,Solanaceae) germplasm using conserved DNA‐derived polymorphism and intron‐targeting markers

Bittersweet (Solanum dulcamara), a European native weed, is widespread across a variety of habitats and often occurs as a coloniser of open, disturbed, ephemeral environments or wetlands, although it is also found in mountain habitats and on forest edges. As recent studies have shown the potential utility of the species in plant breeding programs, we assembled a collection of bittersweet germplasm from natural populations found in Europe. This collection was analysed with conserved DNA‐derived polymorphism (CDDP) and intron‐targeting (IT) markers to assess genetic diversity found within and among the populations. We found that there is limited genetic variability within the collected S. dulcamara accessions, with a greater proportion of allelic variation distributed among populations and considerably greater population structure at higher regional levels. Although bittersweet is an outcrossing species, its population structure might be affected by its perennial self‐compatible nature, reducing genetic diversity within regional populations and enhancing inbreeding leading to high interpopulation or spatial differentiation. We found that populations have been separated by local selection of alleles, resulting in regional differentiation. This has been accompanied by concurrent loss of genetic diversity within populations, although this process has not affected species‐level genetic diversity. Germplasm collecting strategies should be aimed at preserving overall genetic diversity in bittersweet nightshade by expanding sampling to southern Europe and to smaller regional geographic levels in northern and central Europe.     

Genetic analysis of Spanish melon (<Emphasis Type="Italic">Cucumis melo</Emphasis> L.) germplasm using a standardized molecular-marker array and geographically diverse reference accessions

Genetic relationships among 125 Spanish melon (Cucumis melo L.) accessions from a Spanish germplasm collection were assessed using a standard molecular-marker array consisting of 34 random amplified polymorphic DNA (RAPD) markers bands (19 primers) and 72 reference accessions drawn from previous studies. The reference accession array consisted of a broad range [Japanese (19) Crete (17), African (15), and USA and Europe (US/EU, 21)] of horticultural groupings (Group Cantalupensis, Group Conomon, Group Inodorus, Group Flexuosus, and Group Chito), and of melon market classes (e.g., Charentais, U.S. Western and European Shipper types, Ogen, and Galia, Honeydew, and Casaba). Spanish melon accessions (largely Casaba, Group Inodorus) were genetically distinct from the reference accessions and other Group Inodorus melons of different origins. Most African accessions showed common genetic affinities, and grouped with the Group Chito and the Group Conomon accessions examined. Those accession groupings were distinct from all other accessions belonging to Group Cantalupensis, Flexuosus, and Inodorus accessions originating from Crete, Japan, Europe, and the U.S. Genetic diversity was highest in accessions of African origin and lowest in accessions of Spanish origin. Additional RAPD markers (49 primers, 141 bands) and 22 selected agronomic traits (quantitative and qualitative) were then used to assess the genetic diversity among Spanish accessions. While cluster analysis using fruit characteristics grouped accessions into cultivars, RAPD-based genetic-distance estimate did not provide consistent accession groupings either by cultivar or geographic origin. While the highest level of polymorphism was detected among melons originating from the central region of Spain, and in the Rochet cultivar, accessions from the Andalucía region and Green cultivars were comparatively less diverse. These results indicate that the Spanish melon accessions could be used to broaden the genetic base of local and foreign Casaba germplasm, to enhance the genetic diversity of U.S and European commercial melon germplasm, and to delineate collection strategies for acquisition of additional Spanish landraces.Communicated by C. MöllersMention of trade name, proprietary product, or specific equipment does not constitute a guarantee or warranty by the USDA and does not imply its approval to the exclusion of other products that may be suitable.     

1063. Lathyrus oleraceus Lam.: Leguminosae

A wild relative of the garden pea, formerly called Pisum sativum L., but now included in the genus Lathyrus, is illustrated, and its relationship to cultivated peas is discussed. Recent studies of the DNA of Pisum and Lathyrus have led to the change of name for this common species.     

Molecular and cytological characterization of the global <Emphasis Type="Italic">Musa</Emphasis> germplasm collection provides insights into the treasure of banana diversity

Bananas (Musa spp.) are one of the main fruit crops grown worldwide. With the annual production reaching 144 million tons, their production represents an important contribution to the economies of many countries in Asia, Africa, Latin-America and Pacific Islands. Most importantly, bananas are a staple food for millions of people living in the tropics. Unfortunately, sustainable banana production is endangered by various diseases and pests, and the breeding for resistant cultivars relies on a far too small base of genetic variation. Greater diversity needs to be incorporated in breeding, especially of wild species. Such work requires a large and thoroughly characterized germplasm collection, which also is a safe depository of genetic diversity. The largest ex situ Musa germplasm collection is kept at the International Transit Centre (ITC) in Leuven (Belgium) and currently comprises over 1500 accessions. This report summarizes the results of systematic cytological and molecular characterization of the Musa ITC collection. By December 2015, 630 accessions have been genotyped. The SSR markers confirmed the previous morphological based classification for 84% of ITC accessions analyzed. The remaining 16% of the genotyped entries may need field verification by taxonomist to decide if the unexpected classification by SSR genotyping was correct. The ploidy level estimation complements the molecular data. The genotyping continues for the entire ITC collection, including newly introduced accessions, to assure that the genotype of each accession is known in the largest global Musa gene bank.     

Combining focused identification of germplasm and core collection strategies to identify genebank accessions for central European soybean breeding

Environmental adaptation of crops is essential for reliable agricultural production and an important breeding objective. Genebanks provide genetic variation for the improvement of modern varieties, but the selection of suitable germplasm is frequently impeded by incomplete phenotypic data. We address this bottleneck by combining a Focused Identification of Germplasm Strategy (FIGS) with core collection methodology to select soybean (Glycine max) germplasm for Central European breeding from a collection of >17,000 accessions. By focussing on adaptation to high-latitude cold regions, we selected an “environmental precore” of 3,663 accessions using environmental data and compared the Donor opulation of Environments (DPE) in Asia and the Target Population of Environments (TPE) in Central Europe in the present and 2070. Using single nucleotide polymorphisms, we reduced the precore into two diverse core collections of 183 and 366 accessions to serve as diversity panels for evaluation in the TPE. Genetic differentiation between precore and non-precore accessions revealed genomic regions that control maturity, and novel candidate loci for environmental adaptation, demonstrating the potential of diversity panels for studying adaptation. Objective-driven core collections have the potential to increase germplasm utilization for abiotic adaptation by breeding for a rapidly changing climate, or de novo adaptation of crops to expand cultivation ranges.     

Development of SCAR markers linked to <Emphasis Type="Italic">sin</Emphasis>-<Emphasis Type="Italic">2</Emphasis>, the stringless pod trait in pea (<Emphasis Type="Italic">Pisum sativum</Emphasis> L.)

With increasing consumer demand for vegetables, edible-podded peas have become more popular. Stringlessness is one of most important traits for snap peas. A single recessive gene, sin-2, controls this trait. Because pollen carrying the stringless gene is less competitive than pollen carrying the stringy gene, there are fewer than expected stringless plants recovered in segregating generations. Marker-assisted selection (MAS) is a valuable tool to identify plants with the traits of interest at an early stage in the breeding process. The objective of this study was to identify robust, user-friendly molecular markers tightly linked to sin-2. A total of 144 target region amplification polymorphism (TRAP) primer combinations were used to screen four DNA bulks, which were constructed from 32 pea breeding lines based on their phenotypes. Sixty polymorphic TRAP primer combinations were identified between bulks of stringless and stringy pods. Five primer combinations, F6_Trap03_168, F6_SA12_145, F10_ODD8_130, F11_GA5_850, and F12_SA12_190, showed more than 90 % association with the stringless phenotype in 32 pea breeding lines. Two of the TRAP markers, F10_ODD8_130 and F12_SA12_190, were cloned, sequenced, and successfully converted to sequence characterized amplified region (SCAR) markers. These two SCAR markers were validated using 20 F₅ recombinant inbred lines derived from a cross between Bohatyr (a dry pea variety with strings) and S1188 (a stringless snap pea variety) and showed strong marker-trait association. The results will have direct application in MAS of stringless edible-podded peas.     

Challenges in pea breeding for tolerance to drought: Status and prospects

Drought is increasingly frequent in the context of climate change and is considered a major constraint for crop yield. Water scarcity can impair growth, disturb plant water relations and reduce water use efficiency. Pea (Pisum sativum) is a temperate grain legume rich in protein, fibre, micronutrients and bioactive compounds that can benefit human health. In reducing pea yield because of drought, the intensity and duration of stress are critical. This review describes several drought resistance mechanisms in pea based on morphology, physiology and biochemical changes during/after the water deficit period. Drought tolerance of pea can be managed by adopting strategies such as screening, breeding and marker-assisted selection. Therefore, various biotechnological approaches have led to the development of drought-tolerant pea cultivars. Finally, the main objective of the current research is to point out some useful traits for drought tolerance in peas and also, mention the methods that can be useful for future studies and breeding programmes.     

The patterns of population differentiation in a <Emphasis Type="Italic">Brassica rapa</Emphasis> core collection

With the recent advances in high throughput profiling techniques the amount of genetic and phenotypic data available has increased dramatically. Although many genetic diversity studies combine morphological and genetic data, metabolite profiling has yet to be integrated into these studies. For our study we selected 168 accessions representing the different morphotypes and geographic origins of Brassica rapa. Metabolite profiling was performed on all plants of this collection in the youngest expanded leaves, 5 weeks after transplanting and the same material was used for molecular marker profiling. During the same season a year later, 26 morphological characteristics were measured on plants that had been vernalized in the seedling stage. The number of groups and composition following a hierarchical clustering with molecular markers was highly correlated to the groups based on morphological traits (r = 0.420) and metabolic profiles (r = 0.476). To reveal the admixture levels in B. rapa, comparison with the results of the programme STRUCTURE was needed to obtain information on population substructure. To analyze 5546 metabolite (LC–MS) signals the groups identified with STRUCTURE were used for random forests classification. When comparing the random forests and STRUCTURE membership probabilities 86% of the accessions were allocated into the same subgroup. Our findings indicate that if extensive phenotypic data (metabolites) are available, classification based on this type of data is very comparable to genetic classification. These multivariate types of data and methodological approaches are valuable for the selection of accessions to study the genetics of selected traits and for genetic improvement programs, and additionally provide information on the evolution of the different morphotypes in B. rapa.     

ATP-dependent cell-free transfer of membrane lipids from nuclei to Golgi apparatus of germinating axes of garden pea

Summary ATP-dependent cell-free transfer of membrane constituents radiolabeled with [¹⁴C]acetate, primarily lipids, was demonstrated between isolated nuclei in suspension and purified Golgi apparatus immobilized on nitrocellulose strips prepared from garden pea (Pisum sativum) in the presence of pea cytosol. The ATP-dependent transfer correlated with the ability of the nuclear envelope to form 50–70 nm vesicles and blebs in an ATP-dependent manner. Specific transfer, transfer at 23°C minus transfer at 4°C, was approximately doubled by addition of ATP and was greater for peas germinated for 2 days than for peas germinated for 3 days. ATP plus cytosol-dependent transfer could not be demonstrated using radiolabeled pea nuclei as donor with purified endoplasmic reticulum, plasma membrane, nuclei, mitochondria or amyloplasts as acceptors. The results provide a second example, in addition to transfer between endoplasmic reticulum and Golgi apparatus, where ATP-and temperature-dependent transfer via 50–70 nm transition vesicles can be demonstrated in a cell-free system.     

Genetic diversity and structure of the zombi pea (<Emphasis Type="Italic">Vigna vexillata</Emphasis> (L.) A. Rich) gene pool based on SSR marker analysis

Zombi pea (Vigna vexillata (L.) A. Rich) is an underutilized legume species and a useful gene source for resistance to biotic and abiotic stresses, although there is little understanding on its genetic diversity and structure. In this study, 422 (408 wild and 14 cultivated) accessions of zombi pea from diverse origins (201 from Africa, 126 from America, 85 from Australia, 5 from Asia and 5 from unknown origin) were analyzed with 20 simple sequence repeat (SSR) markers to determine its genetic diversity and genetic structure. The SSR markers detected 273 alleles in total with a mean of 13.6 alleles per locus. Polymorphism information content values of the markers varied from 0.58 to 0.90 with an average of 0.76. Overall gene diversity was 0.715. Gene diversity and average allelic richness was highest in Africa (0.749 and 8.08, respectively) and lowest in America (0.435 and 4.10, respectively). Nei’s genetic distance analysis revealed that the highest distance was between wild Australia and cultivated Africa (0.559), followed by wild West Africa and wild Australia (0.415). STRUCTURE, neighbor-joining (NJ), and principal coordinate analyses consistently showed that these zombi pea accessions were clustered into three major groups, viz. America, Africa and Asia, and Australia. NJ tree also suggested that American and Australian accessions are originated from East African zombi peas, and that the cultivated accessions from Africa and Asia were genetically distinct, while those from America were clustered with some cultivated accessions from Africa. These results suggest that Africa is the center of origin and diversity of zombi pea, and that domestication of this pea took place more than once in different regions.     

Delineating the effects of a plant trait on interactions among associated insects

Plant traits can affect ecological interactions between plants, herbivores, and predators. Our study tests whether reduced leaf wax in peas alters the interaction between the pea aphid ( Acyrthosiphon pisum), a foliar-foraging predator (a lady beetle, Hippodamia convergens) and a ground-foraging predator (a ground beetle, Poecilus scitulus). We performed a 2×2×2 factorial experiment in which wax level, presence of H. convergens, and presence of P. scitulus were manipulated. Experimental arenas consisted of a cage surrounding three pea plants. One plant in each cage was stocked with 15 pea aphids. In greenhouse and field cage experiments, we assessed the effect of each factor and their interactions on aphid density. As in previous studies, H. convergens foraged for aphids more effectively on reduced wax peas than on normal peas. Other interactions among H. convergens, P. scitulus , and A. pisum were the same on both types of peas. We consider how aphid movement, plant growth, and a high frequency of predation by P. scitulus on H. convergens influenced pea aphid density.     

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.