The Enigma of <Emphasis Type="Italic">Solanum maglia</Emphasis> in the Origin of the Chilean Cultivated Potato, <Emphasis Type="Italic">Solanum tuberosum</Emphasis> Chilotanum Group<Superscript>1</Superscript>

The Enigma of Solanum maglia in the Origin of the Chilean Cultivated Potato, Solanum tuberosum Chilotanum Group. Landrace potato cultivars occur in two broad geographic regions: the high Andes from western Venezuela south to northern Argentina (Solanum tuberosum Andigenum Group, “Andigenum”), and lowland south-central Chile (S. tuberosum Chilotanum Group, “Chilotanum”), with a coastal desert and 560 km between southernmost populations of Andigenum and Chilotanum. Unlike Andigenum landraces, Chilotanum landraces are adapted to long days and carry a 241 base pair plastid DNA deletion. However, Andigenum and Chilotanum landraces are morphologically similar. We investigated a hypothesis that Chilotanum landraces arose from Solanum maglia, a rare tuber-bearing species found in Chile and Argentina. This hypothesis was formulated first based on morphological analyses of starch grains of extant and preserved (12,500 years before present) S. maglia, and on putative sympatry of extant S. maglia and Chilotanum landraces. Our new starch grain analyses fail to support this hypothesis; we could find no evidence of current sympatric distributions, and S. maglia lacks the 241-bp plastid deletion. However, microsatellite data group all accessions of S. maglia exclusively with Chilotanum, which is supported by our previous observation at the single locus of the waxy gene. These results could be interpreted in various ways, but all explanations have problems. One explanation is that S. maglia is a progenitor of Chilotanum. However, the plastid deletion in Chilotanum but not S. maglia cannot be easily explained. Another explanation is that Chilotanum was formed by hybridization between S. maglia and pre-Chilotanum, but this conflicts with prior cladistic analyses. These new data shed light on aspects of this question and highlight various evolutionary scenarios, but the origin of Chilotanum and the involvement of S. maglia in its origin remain an enigma.     

Ecogeography of ploidy variation in cultivated potato (Solanum sect. Petota)

? Premise of the study: The taxonomy of cultivated potatoes has been highly controversial, with estimates of species numbers ranging from 3 to 17. Ploidy level has been one of the most important taxonomic characters to recognize cultivated potato species, containing diploid (2n = 2x = 24), triploid (2n = 3x = 36), tetraploid (2n = 4x = 48), and pentaploid (2n = 5x = 60) cultivars. We tested the environmental associations of different ploidy levels in cultivated potato species that traditionally have been recognized as Linnaean taxa to see whether, in combination with prior morphological, molecular, and crossing data, some of the ploidy variants can be recognized as distinct taxa. ? Methods: We summarize 2780 chromosome counts of landrace cultivated potatoes, provide georeferences to 2048 of them, and analyze these data for 20 environmental variables at 10-min resolution using the randomForest algorithm to explore associations with taxa and ploidy variants. ? Key results: Except for the S. tuberosum Chilotanum Group and extreme northern and southern range extensions of the Andigenum Group, it is impossible to find distinct habitats for the ploidy variants of the S. tuberosum Andigenum Group. ? Conclusions: Our distributional and ecological data, in combination with prior results from morphology, microsatellites, and crossing data, provide yet additional data to support a major reclassification of cultivated potato species. A rational, stable, and universally accepted taxonomy of this major crop plant will greatly aid all users of wild and cultivated potatoes from breeders to gene bank managers to ecologists and evolutionary biologists.     

Hybrid origins of cultivated potatoes

Solanum section Petota is taxonomically difficult, partly because of interspecific hybridization at both the diploid and polyploid levels. The taxonomy of cultivated potatoes is particularly controversial. Using DNA sequence data of the waxy gene, we here infer relationships among the four species of cultivated potatoes accepted in the latest taxonomic treatment (S. ajanhuiri, S. curtilobum, S. juzepczukii and S. tuberosum, the latter divided into the Andigenum and Chilotanum Cultivar Groups). The data support prior ideas of hybrid origins of S. ajanhuiri from the S. tuberosum Andigenum Group (2x = S. stenotomum) × S. megistacrolobum; S. juzepczukii from the S. tuberosum Andigenum Group (2x = S. stenotomum) × S. acaule; and S. curtilobum from the S. tuberosum Andigenum Group (4x = S. tuberosum subsp. andigenum) × S. juzepczukii. For the tetraploid cultivar-groups of S. tuberosum, hybrid origins are suggested entirely within much more closely related species, except for two of three examined accessions of the S. tuberosum Chilotanum Group that appear to have hybridized with the wild species S. maglia. Hybrid origins of the crop/weed species S. sucrense are more difficult to support and S. vernei is not supported as a wild species progenitor of the S. tuberosum Andigenum Group.     

Reclassification of landrace populations of cultivated potatoes (Solanum sect. Petota)

Cultivated potatoes have been classified as species under the International Code of Botanical Nomenclature (ICBN) and as cultivar-groups under the International Code of Nomenclature of Cultivated Plants (ICNCP); both classifications are still widely used. This study examines morphological support for the classification of landrace populations of cultivated potatoes, using representatives of all seven species and most subspecies as outlined in the latest taxonomic treatment. These taxa are S. ajanhuiri, S. chaucha, S. curtilobum, S. juzepczukii, S. phureja subsp. phureja, S. stenotomum subsp. stenotomum, S. stenotomum subsp. goniocalyx, S. tuberosum subsp. andigenum, and S. tuberosum subsp. tuberosum. The results show some phenetic support for S. ajanhuiri, S. chaucha, S. curtilobum, S. juzepczukii, and S. tuberosum subsp. tuberosum, but little support for the other taxa. Most morphological support is by using a suite of characters, all of which are shared with other taxa (polythetic support). These results, combined with their likely hybrid origins, multiple origins, evolutionary dynamics of continuing hybridization, and our classification philosophy, leads us to recognize all landrace populations of cultivated potatoes as a single species, S. tuberosum, with the eight cultivar-groups: Ajanhuiri Group, Andigenum Group, Chaucha Group, Chilotanum Group, Curtilobum Group, Juzepczukii Group, Phureja Group, and Stenotomum Group. We defer classification of modern cultivars, traditionally classified in Tuberosum Group, to a later study.     

An extreme cytoplasmic bottleneck in the modern European cultivated potato (Solanum tuberosum) is not reflected in decreased levels of nuclear diversity

We have used the polymorphic chloroplast (cp) and nuclear simple sequence repeats (SSRs) to analyse levels of cytoplasmic and nuclear diversity in the gene pool of the European cultivated potato (Solanum tuberosum ssp. tuberosum). Primers designed from the complete chloroplast sequence of tobacco (Nicotiana tabacum) were used to amplify polymorphic products in a range of potato cultivars. Combining the data from seven polymorphic cpSSR loci gave 26 haplotypes, one of which (haplotype A) accounted for 151 out of the 178 individuals studied and corresponded to the T-type cytoplasm previously identified in cultivated potatoes using chloroplast restriction fragment length polymorphism analysis. Phylogenetic and diversity analyses of the relationships between cpSSR haplotypes confirmed much higher levels of cytoplasmic diversity outwith the T-type group. Diversity levels at eight nuclear SSR loci, however, were not significantly different between cytoplasmic groups, suggesting a severe maternal bottleneck in the evolution of the modern cultivated potato. These results highlight the importance in quantifying levels of cytoplasmic as well as nuclear diversity and confirm the need for a change in breeding practices to increase levels of non-T-type cytoplasm in the cultivated gene pool, thus helping reduce problems associated with pollen sterility. This may be facilitated by germplasm analysis using cpSSRs, which will allow efficient selection of diverse cytoplasm donors.     

Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers

Retrotransposon segments were characterized and inter-retrotransposon amplified polymorphism (IRAP) markers developed for cultivated flax (Linum usitatissimum L.) and the Linum genus. Over 75 distinct long terminal repeat retrotransposon segments were cloned, the first set for Linum, and specific primers designed for them. IRAP was then used to evaluate genetic diversity among 708 accessions of cultivated flax comprising 143 landraces, 387 varieties, and 178 breeding lines. These included both traditional and modern, oil (86), fiber (351), and combined-use (271) accessions, originating from 36 countries, and 10 wild Linum species. The set of 10 most polymorphic primers yielded 141 reproducible informative data points per accession, with 52% polymorphism and a 0.34 Shannon diversity index. The maximal genetic diversity was detected among wild Linum species (100% IRAP polymorphism and 0.57 Jaccard similarity), while diversity within cultivated germplasm decreased from landraces (58%, 0.63) to breeding lines (48%, 0.85) and cultivars (50%, 0.81). Application of Bayesian methods for clustering resulted in the robust identification of 20 clusters of accessions, which were unstratified according to origin or user type. This indicates an overlap in genetic diversity despite disruptive selection for fiber versus oil types. Nevertheless, eight clusters contained high proportions (70?C100%) of commercial cultivars, whereas two clusters were rich (60%) in landraces. These findings provide a basis for better flax germplasm management, core collection establishment, and exploration of diversity in breeding, as well as for exploration of the role of retrotransposons in flax genome dynamics.     

Potato Glycoalkaloids: A Burden or a Blessing?

Steroidal glycoalkaloids (SGAs) are produced following the general steroid biosynthesis pathway, starting from acetyl-coenzyme A and followed by the intermediates mevalonic acid, squalene, cycloartenol, and cholesterol. α-Chaconine and α-solanine are the main SGAs of the cultivated potato (Solanum tuberosum), whereas many other SGAs are known in the wild potato species. Low concentrations of SGAs improve the taste of potato, but concentrations greater than 200 mg/kg can have toxic effects on animals and humans. SGAs have antimicrobial activity and confer resistance to some insects, but many such pests of potato are not greatly affected. Certain environmental conditions and wounding enhance SGA accumulation in tubers in the field and storage. Low production of SGAs is a dominant character inherited in a relatively simple manner and can be selected for in potato-breeding programs, whereas the use of wild potato germplasm tends to increase the SGA accumulation in the breeding lines. Further efforts are likely to be directed toward the reduction of the SGA content in the edible potato products through breeding and biotechnological methodologies, whereas potato genotypes with high SGA production may be developed for use in the pharmaceutical industry.     

苦玄参40个株系表型性状遗传多样性分析

植物遗传多样性一直以来是种质资源研究的热点。为揭示苦玄参栽培种质的遗传多样性,该研究从苦玄参常年栽培种中根据形态学性状差异选择40个株系,以产量、药效物质含量及茎、叶、花等形态学性状为指标,进行物种变异和遗传多样性分析,并对其进行聚类分析,获取各株系遗传亲缘关系。结果表明:苦玄参苷IA和IB含量的遗传变异系数较高,分别为24.225%和17.853%;遗传多样性指数高,分别为1.920和2.075。产量遗传变异系数较低,仅为3.637%,但遗传多样性指数较高,达到1.884。其余表型性状指标遗传变异系数均较高,其中花色高达127.794%。数值型性状具有较高的遗传多样性,均大于1,但描述型指标遗传多样性指标较低,均小于1。聚类分析可将供试材料分为4个大的类群:第Ⅰ类群共有7个株系,此类群产量性状及相关指标平均数较高;第Ⅱ类群有8个株系,茎节长度最长,其余指标中等偏下;第Ⅲ类群数量最多,有20个株系,各指标均较低;第Ⅳ类群有5个株系,苦玄参苷含量和产量均较高,综合指标比较优。相关分析结果表明,苦玄参苷IA的含量与叶缘性状具有显著相关,产量性状与茎节长度、一级分枝和末级分枝数具有极显著相关,选择优良种质应注重该4个性状的选择。该研究结果表明目前苦玄参栽培种具有广泛的变异和较高的遗传多样性,为苦玄参资源的利用提供了参考依据。     

Potential for the improvement of Salicornia bigelovii through selective breeding

Salicornia bigelovii Torr. is an annual salt marsh plant that produces seed oils, protein meal, fresh salad greens and forage on seawater irrigation. We compared S. bigelovii lines produced in two breeding programs with wild germplasm in greenhouse trials on brackish water (10 ppt NaCl) irrigation. S. bigelovii is an out-crossing species that is also capable of selfing, and the breeding programs showed it is possible to use both hybridization and pedigree breeding to improve the germplasm. Lines selected in a breeding program carried out in Eritrea, Africa, had smaller plant size and lower biomass yields than the starting germplasm, due to the need to compress the growth cycle within the cool months of the year in that hot climate, but seed yields and harvest index were improved. Lines produced from wild germplasm by mass selection and hybridization in Tucson, Arizona had higher biomass yield than starting germplasm. We conclude that S. bigelovii has sufficient genetic diversity among wild accessions and cultivars to support a crop improvement program.     

Allelic reduction and genetic shift in the Canadian hard red spring wheat germplasm released from 1845 to 2004

Analysis of genetic diversity changes in existing gene pools of cultivated crops is important for understanding the impact of plant breeding on crop genetic diversity and developing effective indicators for genetic diversity of cultivated plants. The objective of this study was to assess genetic diversity changes in 75 Canadian hard red wheat (Triticum aestivum L.) cultivars released from 1845 to 2004 using 31 simple sequence repeats (SSRs) markers. A total of 267 SSR alleles were detected, and their allelic frequencies ranged from 0.01 to 0.97, with an average of 0.14. Significant allelic reduction was observed at only four SSR loci for the cultivars released from 1970 onwards. However, 51 alleles (about 19%) present in pre-1910 cultivars were undetected in cultivars released after 1990 and were spread over 27 SSR loci. The proportion of SSR variation accounted for by six breeding periods was 12.5%, by four ancestral families, 16.5%, and by eight breeding programs, 8.4%. The average genetic diversity measured by three different band-sharing methods did not change significantly among cultivars released from different breeding periods, breeding programs, and ancestral families. However, genetic shift was obvious in the cultivars released over the six breeding periods, reflecting well the various breeding efforts over years. These results clearly show the allelic reduction and genetic shift in the Canadian hard red spring wheat germplasm released over time. Consequently, more effort needs to be made to broaden the wheat breeding base and conserve wheat germplasm.     

Polymorphic simple sequence repeat markers in chloroplast genomes of Solanaceous plants

PCR-based markers were developed from mononucleotide simple-sequence repeats in the chloroplast genome of Nicotiana tabacum and applied to the analysis of genetic diversity. These markers were found to detect high levels of polymorphism at three taxonomic levels in Solanaceous plants. Of 36 chloroplast loci examined, 26 show some degree of polymorphism among potato accessions. Among a set of 30 tetraploid potato cultivars it is apparent that a single chloroplast haplotype is prevalent, presumably a result of the widespread use as a female parent of the imported US cultivar Rough Purple Chili in the latter half of the 19th century. Nonetheless, there is considerable chloroplast diversity in the cultivated potato, and it is clear that a large proportion of this variability has arisen through the use of wild or primitive cultivated species of potato in introgression programmes. This variability should be used in future breeding programmes. An examination of single accessions from 24 potato species, as well as representatives from tobacco and other members of the Solanaceae, reveals high levels of inter-specific chloroplast DNA variation. These data, and the ease of use and potential for multiplexing of these markers, suggest that cpSSRs will be of great utility in population genetics, germplasm management, evolutionary and phylogenetic studies as well as in, the analysis of material from introgression and somatic-fusion experiments. Interestingly, the polymorphism arising from one of the more-polymorphic chloroplast loci examined, does not originate solely from the SSR, and is due to variation in the copy number of two tandemly arrayed sequence elements. Received: 15 December 1998 / Accepted: 9 February 1999     

Trends in genetic diversity among European maize cultivars and their parental components during the past 50 years

It has been claimed that the system that delivers the products of plant breeding reduces the diversity of cultivated varieties leading to an increased genetic vulnerability. The main goal of our study was to monitor the temporal trends in genetic diversity over the past five decades among maize cultivars with the largest acreage in Central Europe. Our objectives were to (1) investigate how much of the genetic diversity present in important adapted open-pollinated varieties (OPVs) has been captured in the elite flint germplasm pool, (2) examine changes in the genetic diversity among the most important commercial hybrids as well as in their dent and flint parents, (3) analyze temporal changes in allele frequencies between the dent and flint parental inbreds, and (4) investigate linkage disequilibrium (LD) trends between pairs of loci within the set of parental dent and flint lines. We examined 30 individuals of five prominent OPVs from Central Europe, 85 maize hybrids of economic importance, and their dent and flint parental components with 55 SSRs. LD was significant at probability level P=0.01 for 20.2% of the SSR marker pairs in the 82 dent lines and for 17.2% in the 66 flint lines. The dent and flint heterotic groups were clearly separated already at the beginning of hybrid breeding in Central Europe. Furthermore, the genetic variation within and among varieties decreased significantly during the five decades. The five OPVs contain numerous unique alleles that were absent in the elite flint pool. Consequently, OPVs could present useful sources for broadening the genetic base of elite maize breeding germplasm.     

Diversity of wild and cultivated pearl millet accessions (Pennisetum glaucum [L.] R. Br.) in Niger assessed by microsatellite markers

Genetic diversity of crop species in sub-Sahelian Africa is still poorly documented. Among such crops, pearl millet is one of the most important staple species. In Niger, pearl millet covers more than 65% of the total cultivated area. Analyzing pearl millet genetic diversity, its origin and its dynamics is important for in situ and ex situ germplasm conservation and to increase knowledge useful for breeding programs. We developed new genetic markers and a high-throughput technique for the genetic analysis of pearl millet. Using 25 microsatellite markers, we analyzed genetic diversity in 46 wild and 421 cultivated accessions of pearl millet in Niger. We showed a significantly lower number of alleles and lower gene diversity in cultivated pearl millet accessions than in wild accessions. This result contrasts with a previous study using iso-enzyme markers showing similar genetic diversity between cultivated and wild pearl millet populations. We found a strong differentiation between the cultivated and wild groups in Niger. Analyses of introgressions between cultivated and wild accessions showed modest but statistically supported evidence of introgressions. Wild accessions in the central region of Niger showed introgressions of cultivated alleles. Accessions of cultivated pearl millet showed introgressions of wild alleles in the western, central, and eastern parts of Niger.Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.Cedric Mariac and Viviane Luong have contributed equally to this work.     

The genetic diversity and evolution of field pea (<Emphasis Type="Italic">Pisum</Emphasis>) 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.     

RETRACTED ARTICLE: An analysis of population structure and linkage disequilibrium using multilocus data in 187 maize inbred lines

This study analyzes population structure and linkage disequilibrium (LD) among 187 commonly used Chinese maize inbred lines, representing the genetic diversity among public, commercial and historically important lines for corn breeding. Seventy SSR loci, evenly distributed over 10 chromosomes, were assayed for polymorphism. The identified 290 alleles served to estimate population structure and analyze the genome-wide LD. The population of lines was highly structured, showing 6 subpopulations: BSSS (American BSSS including Reid), PA (group A germplasm derived from modern U.S. hybrids in China), PB (group B germplasm derived from modern U.S. hybrid in China), Lan (Lancaster Surecrop), LRC (derivative lines from Lvda Reb Cob, a Chinese landrace) and SPT (derivative lines from Si-ping-tou, a Chinese landrace). Forty lines, which formerly had an unknown and/or miscellaneous origin and pedigree record, were assigned to the appropriate group. Relationship estimates based on SSR marker data were quantified in a Q matrix, and this information will inform breeder’s decisions regarding crosses. Extensive inter- and intra-chromosomal LD was detected between 70 microsatellite loci for the investigated maize lines (2109 loci pairs in LD with D′ > 0.1 and 93 out of them at P < 0.01).This suggests that rapidly evolving microsatellites may track recent population structure. Interlocus LD decay among the diverse maize germplasm indicated that association studies in QTLs and/or candidate genes might avoid nonfunctional and spurious associations since most of the LD blocks were broken between diverse germplasm. The defined population structure and the LD analysis present the basis for future association mapping. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Reproductive ecology and genetic variability in natural populations of the wild potato,Solanum kurtzianum

The cultivated potato (Solanum tuberosum ssp. tuberosum) has more than 200 related wild species distributed along the Andes, adapted to a wide range of geographical and ecological areas. Since the last century, several collection expeditions were carried out to incorporate genetic variability into the potato germplasm around the world. However, little is known about the reproductive ecology and genetic population structure of natural potato population from field studies. The aim of this work is to study, in the field, the genetic variability and reproductive strategies of populations of one of the most widely distributed potato species in Argentina, Solanum kurtzianum, growing in Mendoza province. AFLP markers showed that the genetic variability is mainly present among plants within populations, indicating that in the sampled populations, sexual reproduction is more relevant than clonal multiplication (by tubers). Additional evidence was obtained evaluating the genetic diversity in populations with a distribution in patches, where several genotypes were always detected. From a field study performed in the Villavicencio Natural Reserve, we found that the average number of plump seeds per fruit was 94.3, identified and calculated the foraging distance of four insect pollinators, and demonstrated the seed dispersal by storm water channels. We argue that the breeding system, the two modes of reproduction and the ecological interaction described here may have a prominent role in determining the genetic structure of S. kurtzianum populations, and discuss the importance of field studies on population genetics, reproductive biology and ecology to design collections and conservation strategies.     

Leveraging natural diversity: back through the bottleneck

Plant breeders have long recognized the existence of useful genetic variation in the wild ancestors of our domesticated crop species. In cultivated rice (Oryza sativa), crosses between high-yielding elite cultivars and low-yielding wild accessions often give rise to superior offspring, with wild alleles conferring increased performance in the context of the elite cultivar genetic background. Because the breeding value of wild germplasm cannot be determined by examining the performance of wild accessions, a phylogenetic approach is recommended to determine which interspecific combinations are most likely to be useful in a breeding program. As we deepen our understanding of how genetic diversity is partitioned within and between cultivated and wild gene pools of Oryza, breeders will have increased power to make predictions about the most efficient strategies for utilizing wild germplasm for rice improvement.     

Population Structure and Diversity in Finger Millet (Eleusine coracana) Germplasm

A genotypic analysis of 79 finger millet accessions (E. coracana subsp. coracana) from 11 African and five Asian countries, plus 14 wild E. coracana subsp. africana lines collected in Uganda and Kenya was conducted with 45 SSR markers distributed across the finger millet genome. Phylogenetic and population structure analyses showed that the E. coracana germplasm formed three largely distinct subpopulations, representing subsp. africana, subsp. coracana originating from Africa and subsp. coracana originating from Asia. A few lines showed admixture between the African and Asian cultivated germplasm pools and were the result of either targeted or accidental intercrossing. Evidence of gene flow was also seen between the African wild and cultivated subpopulations, indicating that hybridizations among subspecies occur naturally where both species are sympatric. The genotyping, combined with phylogenetic and population structure analyses proved to be very powerful in predicting the origin of breeding materials. The genotypic study was complemented by a phenotypic evaluation. The wild and cultivated accessions differed by a range of domestication-related characters, such as tiller number, plant height, peduncle length, seed color and grain yield. Significant differences in plant architecture and yield were also identified between the Asian and African subpopulations. The observed population structure within cultivated finger millet is consistent with the theory that, after the introduction of finger millet from Africa into India via the trade routes some 3000 years ago, the two germplasm pools remained largely isolated until recent times. The significantly lower diversity present within the Asian subpopulation also suggests that it arose from a relatively small number of founder plants.