Genetic diversity analysis of Solanum accessions from Czech collections of potato genetic resources using nuclear SSR markers

Malus sylvestris (Mill.) is the only indigenous wild apple species in Central Europe. Agriculture, forestry, and urbanization increasingly endanger Malus sylvestris natural habitats. In addition, the risks of cross‐hybridization associated with increase in the cultivation of the domesticated apple Malus × domestica (Borkh.) threaten the genetic integrity of M. sylvestris. The present study investigated the number of hybrids, genetic diversity, and genetic structure of 292 putative M. sylvestris that originate from five different natural M. sylvestris populations in Saxony, Germany. All samples were genetically analyzed using nine nuclear microsatellite markers (ncSSR) and four maternally inherited chloroplast markers (cpDNA) along with 56 apple cultivars commonly cultivated in Saxony. Eighty‐seven percent of the wild apple accessions were identified as pure M. sylvestris. The cpDNA analysis showed six private haplotypes for M. sylvestris, whereas three haplotypes were present in M. sylvestris and M. × domestica. The analysis of molecular variance (AMOVA) resulted in a moderate (ncSSR) and great (cpDNA) variation among pure M. sylvestris and M. × domestica individuals indicating a low gene flow between both species. The genetic diversity within the pure M. sylvestris populations was high with a weak genetic structure between the M. sylvestris populations indicating an unrestricted genetic exchange between these M. sylvestris populations. The clear distinguishing of M. sylvestris and M. ×domestica confirms our expectation of the existence of pure M. sylvestris accessions in this area and supports the argument for the implementation of preservation measures to protect the M. sylvestris populations in Saxony.

BACKGROUNDPlant resistance to insects can be reduced by crop domestication which means their wild ancestors could provide novel sources of resistance. Thus, crossing wild ancestors with domesticated crops can potentially enhance their resistance against insects. However, a prerequisite for this is identification of sources of resistance. Here, we investigated the response of three wild potato (Solanum stoloniferum Schltdl.) accessions and cultivated potato (Solanum tuberosum) to aphid (Myzus persicae Sulzer) herbivory.RESULTSResults revealed that there was a significant reduction in aphid survival and reproduction on wild potato accessions (CGN18333, CGN22718, CGN23072) compared to cultivated (Desiree) potato plants. A similar trend was observed in olfactometer bioassay; the wild accessions had a repellent effect on adult aphids. In contrast, among the tested wild potato accessions, the parasitoid Diaeretiella rapae (M'Intosh) was significantly attracted to volatiles from CGN18333. Volatile analysis showed that wild accessions emitted significantly more volatiles compared to cultivated potato. Principal component analysis (PCA) of volatile data revealed that the volatile profiles of wild and cultivated potato are dissimilar. β‐Bisabolene, (E)‐β‐farnesene, trans‐α‐bergamotene, d‐limonene, (E,E)‐4,8,12‐trimethyl‐1,3,7,11‐tridecatetraene (TMTT), and p‐cymen‐7‐ol were the main volatiles contributing to the emitted blends, suggesting possible involvement in the behavioural response of both M. persicae and D. rapae.CONCLUSIONOur findings show that the tested wild accessions have the potential to be used to breed aphid‐resistant potatoes. This opens new opportunities to reduce the aphid damage and to enhance the recruitment of natural enemies. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

The objectives of this study were investigated the variations of agronomic traits, developmental progress, and genotype makeup in Taiwan wild rice. The materials were collected from germplasm nursery of Taiwan Agriculture and Research Institute. All of the 48 tested survival lines could be divided to three different plant types by appearance phenotype. Type Ⅰ was similar to Type Ⅲ except the color of leaf sheath. Type Ⅰ had purple brown sheath and Type Ⅲ showed pale green sheath, and they had a smaller angle between tillers and ground. The phenotype of Type Ⅱ was similar to that of culture varieties and angle between tillers and ground was near 90 degree. The color of leaf and leaf sheath of type Ⅱ lines were green. The heading day of wild rice in Taiwan was longer than that of culture varieties. Average days from transplant to heading of wild rice in Taiwan was 132. Among the three types, Type Ⅲ had the stronger growth vigor in the traits of plant height, tiller number per plant and leaf number of main stem. The variation of spikelet fertility was the largest among the components of yield. A total of 10 DNA simple sequence repeat (SSR) primer pairs were selected to detect genotype polymorphisms among 48 Taiwan wild rice lines, 9 culture varieties, and 7 wild rice accession lines from IRRI. Ten SSR primers amplified a total of 38 polymorphic bands. The average number of alleles per SSR locus was 3.8 with a range 2 to 6. UPGMA cluster analysis proposed that the 64 rice materials could be divided into 6 groups. Although almost all of Taiwan wild rice lines were clustered into the same group, considerable DNA polymorphism was found among these lines. The present results revealed that Taiwan wild rice may be a high heterogenous population with respect to agronomic traits and genetic background. This population also showed some Japonica-like traits, suggesting introgression might occur during long period of coexistence with other cultivars. Most of modern crop cultivars are domestication from their wild ancestors. Oryza sativa L., the most widely cultivated and important rice species in the world is recognized to be evolved from Oryza rufipogon. And Oryza rufipogon is also an important genetic resource for the breeding improvement of the present rice cultivars. Because of the civilization and urbanization, more and more wild species have gradually lost their habitats and have been becoming extinct. In Taiwan wild rice species was first discovered around Taoyuan and Shinchu areas, but because of the reasons mentioned above, they have become endangered species. So far, only limited scientists had done preliminary researches on Taiwan wild rice, and very few knowledge about the agronomic and quality traits of Taiwan wild rice have been documented. This study was aimed to make serial investigations on morphological characteristics, amylose content, crude-protein content, and storage protein of grains of Taiwan wild rice. In addition, protein electrophoresis based proteomic approach was utilized to study the expression specialty of storage proteins in the wild rice. In grain morphological traits, different grain colors from gray black to light yellow were found within wild rice population. The long grain shape of Taiwan wild rice was found to be closed to that of modern Indica type cultivars. The modern cultivar-like grain morphological traits appeared within Taiwan rice population might be due to the high cross-pollination rate of the wild rice and the long coexistence between the wild rice and modern cultivars in the field. In grain chemical properties, apparent variations in amylase, crude protein content, and storage protein contents were found in Taiwan wild rice population. Amylose contents of Taiwan wild rice lines were ranged between 12.3% and 28.4%. Crude protein content varied between 9.64% and 16.64%. The low amylase and high protein contents suggest that Taiwan wild rice are prominent breeding resources for the improvement of protein or amylase content of modern rice cultivars. Regarding expressions of grain storage proteins revealed by 1D and 2D electrophoresis, Taiwan wild rice accumulated higher amount of glutelins and prolamines than modern cultivars. Expression patterns of urea soluble proteins on 1D gel, mainly glutelins and prolamins, were closer to that of modern cultivars. Differential expressions of some proteins were observed within the wild rice population. In addition, profiles of 2D gels showed polymorphism in the expressions of glutelins and prolamines within the wild rice population. The present results suggest that Taiwan wild rice is a heterogeneous population which may harbor a certain number of traits/genes from cultivars. Results of the current study may offer valuable information for both maintenance and utilization of Taiwan wild rice.

Comparison of the use of morphological, protein and DNA markers in the genetic characterization of Iranian wild Prunus species

Genetic succession and spatial genetic structure in a natural old growth Cryptomeria japonica forest revealed by nuclear and chloroplast microsatellite markers

To determine whether populations of Phytophthora infestans attacking wild and cultivated potatoes in the highlands of Peru are specialized on their hosts of origin, we characterized isolates using several neutral markers, metalaxyl resistance and for aggressiveness in a detached leaf assay. One hundred and fifty-three isolates were collected from the northern and central highlands of Peru from different potato cultivars (both modern and native cultivars) and from different species of wild, tuber-bearing potatoes. All the isolates analyzed belonged to one of four clonal lineages that had been described previously in Peru: EC-1, US-1, PE-3 and PE-7. The EC-1 lineage (n = 133) was dominant and present in similar frequencies on wild and cultivated potatoes. PE-3 (n = 14) was found primarily on cultivated potatoes, with only one isolate coming from a wild host. US-1 (n = 2) and PE-7 (n = 4) were rare; all but one (PE-7) occurred on wild potatoes. Isolates from the EC-1 lineage from modern cultivars were compared in three separate detached leaf inoculation assays with EC-1 isolates from the wild potato species S. sogarandinum, S. bill-hookerii or S. huancabambense, respectively. No significant interactions between isolate type (from wild or cultivated potato) and host type (wild or cultivated) were measured for any assay. It appears that the pathogen genotypes in the EC-1 lineage indiscriminately attack both wild and cultivated tuber-bearing solanaceous hosts in Peru, and breeders should be able to select for resistance using the common EC-1 lineage.

Long-term conservation of Plant Genetic Resources (PGR) is a key priority for guaranteeing food security and sustainability of agricultural systems for current and future generations. The need for the secure conservation of genetic resources collections ex situ is critical, due to rapid and extreme climatic changes which are threatening and reducing biodiversity in their natural environments. The International Potato Center (CIP) conserves one of the most complete and diverse genetic resources collections of potato, with more than 7500 accessions composed of 4900 cultivated potato and 2600 potato wild relative accessions. The clonal conservation of cultivated potato, principally landraces, through in vitro or field collections is indispensable to maintain fixed allelic states, yet it is costly and labor-intensive. Cryopreservation, the conservation of biological samples in liquid nitrogen (-196°C), is considered the most reliable and cost-efficient long-term ex-situ conservation method for clonal crops. Over the last decade, CIP has built one of the largest potato cryobanks worldwide, cyopreserving more than 4000 cultivated potato accessions which represents 84% of the total cultivated potato collection currently conserved at CIP. In approximately, four years the entire potato collection will be cryopreserved. The development of an applied, robust cryopreservation protocol for potato, serves as a model for other clonally maintained crop collections. The CIP cryobank designs experiments with a high number of genetically diverse genotypes (70-100 accessions, seven cultivated species), to obtain reliable results that can be extrapolated over the collection as genotypes can often respond variably to the same applied conditions. Unlike most published reports on cryopreservation of plants, these large-scale experiments on potato are unique as they examine the acclimatization process of in vitro plants prior to, as well as during cryopreservation on up to ten times the number of genotypes conventionally reported in the published literature. As a result, an operational cryopreservation protocol for potato has advanced that works well across diverse potato accessions, not only with reduced processing time and costs, but also with an increased average full-plant recovery rate from 58% to 73% (+LN) for routine cryopreservation. The present article describes the composition of CIP's cryobank, the cryopreservation protocol, methodology for the dynamic improvement of the operational protocol, as well as data collected on regeneration from long term cryopreserved potatoes.

Availability of standardized morphological and molecular characterization data is essential for the efficient development of breeding programmes in emerging crops. Pepino (Solanum muricatum) is an increasingly important vegetatively propagated vegetable crop for which concurrent data on morphological descriptors and molecular markers are not available. We evaluated 58 morphological traits, using a collection of 14 accessions of pepinos (including local Andean varieties and modern cultivars) and 8 of wild relatives, using the IPGRI and COMAV descriptors lists coupled with 20 EST-SSRs from tomato. High morphological diversity was found in both cultivated and wild accessions; all morphological traits except three were variable. Cultivated pepino and wild relatives were significantly different for 26 traits. Also, local varieties and modern cultivars of pepino were different from each other for 13 morphological traits and were clearly separated in a principal components analysis. Fourteen of the 20 tomato EST-SSRs were polymorphic, with an average number of alleles per locus of 4.07 and a polymorphic information content value of 0.4132. This revealed a high degree of transferability from tomato to pepino and wide molecular diversity in the collection. Cultivated materials manifest high levels of observed heterozygosity, suggesting that it is related to heterosis for yield associated with heterozygosis. SSR data clearly differentiated cultivated and wild materials. Furthermore, for pepinos, the modern varieties were genetically much less diverse than the traditional local varieties. However, both groups of cultivated material expressed a low degree of genetic differentiation. A strong correlation (r = 0.673) between morphological and molecular distances was found. Our results provide foundational information for programmes of germplasm conservation, and that can be used to enhance breeding for this emerging crop.

To assess the genetic relations in Pisum genus and to examine putative duplicate accessions, 20 pea varieties ( Pisum sativum L.) with 57 accessions from wild Pisum species fulvum , subspecies (subsp.) asiaticum , elatius , thebaicum, abyssinicum, transcaucasicum and arvense were analyzed using 10 out of 20 microsatellite primer pairs. We genotyped all accessions. In total, 59 alleles were identified in whole collection. The maximum number of alleles (8 alleles) was obtained from the PEACPLHPP, AF004843, and AA43090 loci. The maximum number of private alleles (4) in the wild collection was detected in AF004843 locus but in the cultivar collection, it was detected in AA430902 and PSBLOX13.2 loci. Cluster analysis and principal coordinate analysis located accessions in 3 groups and cultivated varieties were obviously separated from the wild accessions. Analysis of molecular variance (AMOVA) revealed that the intergroups component of variance (29%) is lower than the intragroups component of variance (71%). The lowest value of genetic differentiation ( Pisum genus and to examine putative duplicate accessions, 20 pea varieties ( Pisum sativum L.) with 57 accessions from wild Pisum species fulvum , subspecies (subsp.) asiaticum , elatius , thebaicum, abyssinicum, transcaucasicum and arvense were analyzed using 10 out of 20 microsatellite primer pairs. We genotyped all accessions. In total, 59 alleles were identified in whole collection. The maximum number of alleles (8 alleles) was obtained from the PEACPLHPP, AF004843, and AA43090 loci. The maximum number of private alleles (4) in the wild collection was detected in AF004843 locus but in the cultivar collection, it was detected in AA430902 and PSBLOX13.2 loci. Cluster analysis and principal coordinate analysis located accessions in 3 groups and cultivated varieties were obviously separated from the wild accessions. Analysis of molecular variance (AMOVA) revealed that the intergroups component of variance (29%) is lower than the intragroups component of variance (71%). The lowest value of genetic differentiation ( Pisum genus and to examine putative duplicate accessions, 20 pea varieties ( Pisum sativum L.) with 57 accessions from wild Pisum species fulvum , subspecies (subsp.) asiaticum , elatius , thebaicum, abyssinicum, transcaucasicum and arvense were analyzed using 10 out of 20 microsatellite primer pairs. We genotyped all accessions. In total, 59 alleles were identified in whole collection. The maximum number of alleles (8 alleles) was obtained from the PEACPLHPP, AF004843, and AA43090 loci. The maximum number of private alleles (4) in the wild collection was detected in AF004843 locus but in the cultivar collection, it was detected in AA430902 and PSBLOX13.2 loci. Cluster analysis and principal coordinate analysis located accessions in 3 groups and cultivated varieties were obviously separated from the wild accessions. Analysis of molecular variance (AMOVA) revealed that the intergroups component of variance (29%) is lower than the intragroups component of variance (71%). The lowest value of genetic differentiation (
PT = 0.27) of pair wise collections between wild and variety collections, was detected in ssp. elatius . Assignment test on the basis of log-likelihood to estimate the likelihood that an individual belongs to a given group, showed that 96% of accessions being assigned correctly to their groups. This study showed that genetic probability profiles of accessions can corroborate clustering analyses while providing additional information as a powerful tool for assigning accessions into their related groups.

The genetic resources available for the improvement of the cultivated potato (Solanum tuberosum) are reviewed along with progress in their utilisation. The conclusions are as follows. The wild and cultivated species of potato have been utilised in potato breeding to good effect, but only a very small sample of the available biodiversity has been exploited. New knowledge and technology will open possibilities for much greater use of these genetic resources in breeding. The strategy for utilising the cultivars native to Latin America will either be the introgression of desirable genes or the direct use of parents from improved populations, depending on how far modern S. tuberosum cultivars have genetically diverged from them and the extent to which S. tuberosum cultivars have been improved in the process. Molecular marker-assisted selection will be used for faster introgression of desirable genes from wild species, and the possibility exists of moving genes directly from wild species to cultivated potato with transgenic methods. New cultivars will continue to come from crosses between pairs of parents with complementary features but adapted to local growing conditions. However, increasingly these parents will possess desirable genes which have been introgressed from wild species and may also be from complementary groups of cultivated germplasm to exploit hybrid vigour. Successful cultivars may be genetically modified, if consumers see benefits in the use of the technology, to introduce genes not present in cultivated potatoes and their wild relatives to achieve novel biochemistry and further desirable improvements.

Sympatric hybridizing oak species provide a model system for studying local adaptation. Disjunct populations of Quercus rubra L. and Quercus ellipsoidalis E. J. Hill at the northern edge of their distribution may harbor important reservoirs of adaptive genetic variation. Genic (expressed sequence tag- simple sequence repeat = EST-SSR) and non-genic nuclear microsatellite (nuclear SSR = nSSR) markers were used to estimate neutral and potentially adaptive genetic variation in these two supposedly interfertile oak species showing different adaptations to drought. Eleven populations of putative Q. rubra and Q. ellipsoidalis located in the Western Upper Peninsula of Michigan were characterized using seven EST-SSRs and eight nSSRs. Bayesian cluster analysis revealed two distinct groups corresponding to each species with evidence of low levels of potential introgression. A comparison of the genetic structure of adult trees and seedlings revealed no evidence for selection against hybrids. Overall, similar levels of genetic variation and differentiation between populations and species were found at both EST-SSRs and nSSRs indicating that most EST-SSRs chosen reflect neutral variation. Two loci, 3A05 (nSSR) and GOT021 (EST-SSR, putative histidine kinase 4-like), were identified as putative outlier loci between species showing largely reduced variation in Q. ellipsoidalis. Future analyses of an increased number of EST-SSRs located in functional genes will allow the identification of genes involved in the reproductive isolation between both species.

Coffee is an important beverage crop in the world and has a significant contribution to Kenya’s economy. Here, we analyzed the genome-wide distribution of microsatellites in the Coffea canephora genome. A total of 159,041 SSRs were identified, with an overall density of 308 SSRs per Mb. Tetra-nucleotide repeats are the most abundant, accounting for 32 % of the total SSRs. AT-rich motifs are dominant across all SSR repeat units, while GC-rich motifs were generally rare. A set of 100 SSRs was selected to amplify 96 coffee accessions, including 10 wild accessions collected from Mt. Marsabit (Kenya). Of these SSRs, 33 % generated clear polymorphic bands among all tested accessions, with an average of 3.9 alleles per SSR locus. Wild coffee species from Mt. Marsabit showed a close genetic similarity with cultivated accessions in Kenya, suggesting that the wild species in Mt. Marsabit played an important role in the domestication of cultivated coffee in Kenya. Significantly low pairwise genetic divergence was observed between cultivated and wild accessions in Kenya, suggesting a relatively narrow level of genetic basis among coffee germplasm in Kenya. In addition, cultivated and wild coffee accessions in Kenya show a great divergence from those in other countries. Our results not only provide molecular tools for genetic studies in coffee but are also helpful for conservation and coffee breeding programs in Kenya.

BackgroundThe mountainous region between the Caucasus and China is considered to be the center of domestication for grapevine. Despite the importance of Central Asia in the history of grape growing, information about the extent and distribution of grape genetic variation in this region is limited in comparison to wild and cultivated grapevines from around the Mediterranean basin. The principal goal of this work was to survey the genetic diversity and relationships among wild and cultivated grape germplasm from the Caucasus, Central Asia, and the Mediterranean basin collectively to understand gene flow, possible domestication events and adaptive introgression.ResultsA total of 1378 wild and cultivated grapevines collected around the Mediterranean basin and from Central Asia were tested with a set of 20 nuclear SSR markers. Genetic data were analyzed (Cluster analysis, Principal Coordinate Analysis and STRUCTURE) to identify groups, and the results were validated by Nei’s genetic distance, pairwise FST analysis and assignment tests. All of these analyses identified three genetic groups: G1, wild accessions from Croatia, France, Italy and Spain; G2, wild accessions from Armenia, Azerbaijan and Georgia; and G3, cultivars from Spain, France, Italy, Georgia, Iran, Pakistan and Turkmenistan, which included a small group of wild accessions from Georgia and Croatia. Wild accessions from Georgia clustered with cultivated grape from the same area (proles pontica), but also with Western Europe (proles occidentalis), supporting Georgia as the ancient center of grapevine domestication. In addition, cluster analysis indicated that Western European wild grapes grouped with cultivated grapes from the same area, suggesting that the cultivated proles occidentalis contributed more to the early development of wine grapes than the wild vines from Eastern Europe.ConclusionsThe analysis of genetic relationships among the tested genotypes provided evidence of genetic relationships between wild and cultivated accessions in the Mediterranean basin and Central Asia. The genetic structure indicated a considerable amount of gene flow, which limited the differentiation between the two subspecies. The results also indicated that grapes with mixed ancestry occur in the regions where wild grapevines were domesticated.

Potato (Solanum tuberosum L.) breeders are interested in developing chipping cultivars that can be stored at cold temperatures to reduce storage losses and increase profitability for potato producers. Commercial cultivars accumulate reducing sugars during cold storage, resulting in unacceptably dark chips when processed. In this study, we have identified diploid wild Solanum species accessions that are resistant to cold‐induced sweetening at very low storage temperatures (2°C). Selected accessions were crossed as males to haploids (2n = 2x) of S. tuberosum to produce adapted hybrids, some of which produce acceptable chips following 3 mo of storage at 2°C. Reconditioning for 6 d at 20 to 22°C increased the number of clones with acceptable chip scores by threefold. The best wild species parents were S. raphanifolium 296126, 310998, and 210048. While parental chip scores help to predict offspring performance, progeny testing is important to identify the best cross combinations. The best hybrids have been introgressed into diploid and tetraploid breeding clones. These hybrids produce good tuber type and low levels of reducing sugars under extremely low storage temperatures.

The origin of cultivated potatoes has remaining questions. In this study, 237 accessions of all cultivated species and 155 accessions of wild species closely related to cultivated potatoes, including their putative ancestors, were analyzed using 15 plastid microsatellites (SSRs) to investigate genetic diversity and their relationships with the wild species. We here used polymorphic plastid SSRs we developed from potato plastid genome sequences as well as already known plastid SSR markers. All 15 loci were polymorphic and identified a total of 127 haplotypes. Dramatic decreases in levels of genetic diversity were revealed in landraces in comparison with wild ancestor species. The plastid SSR results showed a decrease in haplotype number and diversity from Peru to both north and south. Phylogenetic analysis revealed two distinct groups. One of them, group A, contained the majority of accessions of cultivated species of the Solanum tuberosum Andigenum group including all accessions of cultivated diploid and triploid cytotypes of this group (S. chaucha, S. phureja, and S. stenotomum by a former taxonomic system) and most of tetraploid accessions of the S.tuberosum Andigenum group (S. tuberosum subsp. andigenum), and the majority of accessions of wild ancestors from the northern members of the S. brevicaule complex. Another group B comprised most of the wild species accessions and almost exclusively hybrid cultivated species which have introgressed plastid genomes from the other wild gene pools. Lack of clustering of traditional cultivated species (as used above) support a revised group classification of S. tuberosum.