Extensive introgression of Middle American germplasm into Chilean common bean cultivars

Summary The genetic diversity of 95. representative Chilean common bean (Phaseolus vulgaris L.) landraces was analyzed using phaseolin seed protein and eight isozyme systems as genetic markers. Four types of phaseolin were found, “C”, “T”, “S” and “H”, in decreasing order of frequency. Each type had a different distribution between the Northern and Southern regions of the country. Nei’s genetic distance based on isozyme diversity indicated that a high percentage of the total variation found in this sample occurred between landraces and only a small percentage of the variation was detected within populations. Cluster analysis based on Nei’s genetic distance and a principal component analysis of isozyme frequencies did not detect a clear association between the geographic distribution of the landraces and their isozyme constitution. However, Nei’s genetic distance analysis clustered the bean landraces into two major groups which had a specific isozyme pattern, seed color, and seed size. The genetic analysis also detected a rare polymorphism for theMdh-2 locus, a null allele at theDiap-2 locus, and polymorphism for theAco-2 locus. The principal component analysis of isozyme frequencies showed that only 30% of the genotypes analyzed were similar to the Andean check and 5% of the samples were similar to Middle American check. This finding suggests a high frequency of hybridization between the Middle America and Andean gene pools in cultivated common bean from Chile.     

Morphotype relationships in Lima bean (Phaseolus lunatus L.) deduced from variation of the evolutionary marker phaseolin

Summary Variation of the seed storage protein phaseolin was analysed in a collection of 100 accessions of Phaseolus lunatus L. using one-dimensional SDS/PAGE. Cultivated small-seeded genotypes belonging to Sieva and Potato morphotypes and intermediate Sieva-Potato and Sieva-Big Lima morphotypes showed the M (Mesoamerican) pattern, confirming their origin in the same gene pool. Cultivated Big Lima morphotypes showed the A (Andean) pattern, confirming that they belong to a distinct gene pool.     

A note on the variation of phaseolin among common bean landraces collected in Eastern Asia

Summary Phaseolin seed protein was used as a marker to reveal the origin, Mesoamerican or Andean, of common bean (Phaseolus vulgaris) accessions cultivated in some countries (Korea, China, and Japan) of eastern Asia. Andean cultivars (T and C phaseolin patterns) are predominant in this geographical area. Introductions from Middle America, represented by cultivars with S phaseolin type, also occurred at lower rate. In all cases, genotypes with larger seeds have been favoured.     

Genetic Analysis of Egyptian Date (<Emphasis Type="Italic">Phoenix dactylifera</Emphasis> L.) Accessions Using AFLP Markers

Forty-seven samples of date palm (Phoenix dactylifera L.) collected from eight locations in Egypt were studied using four sets of amplified fragment length polymorphism (AFLP) markers with near infrared fluorescence labeled primers. These samples belonged to 21 named accessions and 9 of unknown pedigrees. A total of 350 bands were scored and 233 (66.6%) were polymorphic. Twenty-seven Egyptian accessions and ‘Medjool’and ‘Deglet Noor’accessions from California could beclassified into the major cluster. This major cluster may represent a major group of date palm germplasm in North Africa. There were four other clusters, each containing one or two accessions. The variety ‘Halawy’and one accession of unknown provenance were most likely from hybridization between two clusters. Six groups of accessions of which had the same names, revealed similar but not identical AFLP profiles suggesting these accessions might derive from seedlings rather thanthrough clonal offshoot propagation.     

Identification of European and Asian pears using EST-SSRs from <Emphasis Type="Italic">Pyrus</Emphasis>

Ten EST-SSRs previously isolated from Pyrus were used to identify 81 P. communis, 13 P. pyrifolia and 20 P. ussuriensis or P. × bretschneideri accessions. Cross-transference of these EST-SSRs was high in these species. PYC-008 and PYC-004 were the least informative SSRs in each of the pear species and were monomorphic in P. pyrifolia while PYC-013, PYC-002 and PYC-009b were the most informative in all species. EST-SSRs were very valuable for identification of incorrectly identified accessions, failed grafts and sets of synonyms in each of the species. Unsuspected relationships were uncovered, including a parental relationship between ‘Anjou’ and ‘Farmingdale’, a clonal relationship between ‘Berger’ and ‘Bartlett’, and a very close relationship between ‘Beurre Superfin’ and ‘Doyenne du Comice’. One SSR marker was different in one of three sports of ‘Doyenne du Comice’ (‘Doyenne du Comice Crimson Gem’) and in one of two sports of ‘Anjou’ (‘Gebhard Red’ red skin sport of ‘Anjou’). UPGMA cluster analysis separated the pear accessions into a large European cluster and an Asian group mostly according to common ancestry, geographical origin or time of ripening. High cross-transference of EST-SSRs in Pyrus species is very valuable for germplasm management in such a highly diverse collection as found at the NCGR Pyrus genebank in Corvallis, OR.     

Phaseolin diversity in wild Lima bean (Phaseolus lunatus L.) in American centres of origin

Summary Phaseolin variability was analyzed in 86 wild Phaseolus lunatus accessions, representing a wide geographical distribution from Mexico to Argentina, to determine geographical patterns of variability. The collection can be divided into two major groups. One group consists of accessions from Mexico, Central America, Cuba, Columbia, Argentina showing two Mesoamerican (M) phaseolin pattern types, already described in cultivated materials, as well as a variety of additional banding patterns. This suggests that at least two genotypes in the Mesoamerican gene pool were involved in a domestication process and spread throughout the world. The other group, consisting of wild Andean (A) forms from Northern Peru and belonging to the Andean gene pool, showed, among others, two A pattern types comparable to those found in cultivated large-seeded accessions.     

Marker-assisted sampling of the cultivated Andean potato Solanum phureja collection using RAPD markers

The potato crop originated in the Andean highlands where numerous farmer's varieties and non-cultivated wild species exist. An Andean potato collection is held in trust at the International Potato Center (CIP) to preserve the biodiversity of this crop and ensure the supply of germplasm for potato improvement worldwide. A core collection representing the biodiversity of the Andean potato germplasm is under construction using morphological, molecular, and geographic data. One of the eight cultivated potato species, Solanum phureja, has been genotyped using the RAPD technique. A protocol suitable for large germplasm collection genotyping has been developed to process numerous samples at reasonable costs. From 106 RAPD primers evaluated, we have selected 12 primers yielding 102 polymorphic markers, which unambiguously discriminated all 128 accessions but 2 that are possible duplicates. The S. phureja germplasm collected throughout the Andean countries appears to have a homogeneous genetic constitution. There was no clear geographic pattern as indicated by cluster analysis of the RAPD data. A sub-group of 20 accessions has been identified on the basis of the marker data and selected to maximize molecular (RAPD) variance and polymorphism. The probability of capturing equal amounts of marker polymorphism in this sub-group of 20 accessions by random sampling is less than 40%. This set accessions represents our first group of accessions that may constitute a core of the S. phureja collection. This tentative core will be challenged for diversity content by alternate markers and agronomic traits. Hence, the methodology for sampling less than 10% of the base collection, proposed for core collections by Brown (1989), can be based on molecular marker data provided cost-efficient fingerprints are developed.     

Phenotypic diversity of the big seed type subcollection of wild soybean (Glycine soja Sieb. et Zucc.) in China

Wild soybean (Glycine soja), the progenitor of soybeans, has become an important germplasm source for soybean breeding. The Chinese G. soja germplasm collection includes two subcollections, one typical wild soybean (G. soja) and the other ‘big seed type’ (semi-wild soybean, G. gracilis). In order to understand the nature of this big seed type subcollection, a considerable number of 1,185 accessions were investigated focusing on phenotypes, compositional structure and genetic diversity of this subcollection. The results showed that there were 617 combined morphotypes formed by six major morphological traits. The morphotype number and diversity gradually decreased among four sections from small to large 100-seed weight sizes. The big seed subcollection accumulated distinctly high frequencies for white flower, grey pubescence, seed non-bloom and four seed coat colours (green, yellow, brown and black), differing from the typical G. soja. Between the two subcollections, only the compositional structures of leaf shapes were almost in agreement. A rare strip-shaped leaf only appeared in typical G. soja and small-seeded grade (100-seed wt) of the big seed type. Seed non-bloom trait showed that the increased frequencies were concomitant with the augmenting of 100-seed weight. The data suggested that white flower accumulated rapidly in the big seed type, followed by seed non-bloom, while the slowest rate of accumulation was grey pubecence, and that the ‘large-seeded type (2.51–3 g 100-seed wt)’ of typical G. soja and the ‘smallest-seeded type (3.01–3.5 g 100-seed wt)’ of the big seed type could have a closer genetic relationship. The morphotype number and genetic diversity showed reduced values with increased 100-seed weights. The geographical distribution of genetic diversity indicated two tendencies: decreased from north to south and also from east to west. Our results suggested that Northeast China was the first centre of morphological diversity for the big seed type, and the North was the secondary centre in China.     

Genic SSRs for European and North American hop (Humulus lupulus L.)

Eight genic SSR loci were evaluated for genetic diversity assessment and genotype identification in Humulus lupulus L. from Europe and North America. Genetic diversity, as measured by three diversity indices, was significantly lower in European cultivars than in North American wild accessions. Neighbor Joining cluster analysis separated the hop genotypes into European and North American groups. These eight SSRs were useful in uniquely identifying each accession with the exception of two sets of European landraces and a pair of Japanese cultivars, ‘Shinshuwase’ and ‘Kirin II’. An accession from Manitoba grouped with the European (EU) cluster reflecting the group’s genetic similarity to older Manitoba germplasm used to develop ‘Brewer's Gold’ and the gene pool arising from this cultivar. Cultivars grouped closely with one of their immediate parents. ‘Perle’ grouped with its parent ‘Northern Brewer and ‘Willamette’ grouped with its parent ‘Fuggle H’. Wild American accessions were divided into two subgroups: a North Central group containing mostly H. lupulus var. lupuloides and a Southwestern group containing H. lupulus var. neomexicanus accessions. These eight SSRs will be valuable for genotype identification in European and wild American germplasm and may potentially prove useful for marker-assisted selection in hop. PCR products from four previously reported primer pairs that amplify the same intronic SSR regions as do the genic SSRs in this study were compared in eight common cultivars. Different primer pairs generated robust markers at the chs2 and chi loci. However, only the HLC-004B and HLC-006 primer pairs amplified successfully at the chs3 and chs4 loci. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Development of Core Collection in Pigeonpea [<Emphasis Type="Italic">Cajanus cajan</Emphasis> (L.) Millspaugh] using Geographic and Qualitative Morphological Descriptors

Pigeonpea is an important pulse crop grown by smallholder farmers in the semi-arid tropics. Most of the pigeonpea cultivars grown to date are selections from the landraces, with a narrow genetic base. With the expansion of the crop to newer areas, problems of local importance are to be addressed. Hence, an economically feasible and faster germplasm evaluation mechanism, such as a core collection, is required. This article describes the development of core collection from 12,153 pigeonpea accessions collected from 56 countries and maintained at ICRISAT, Patancheru, India. The germplasm accessions from 56 countries were placed under 14 clusters based primarily on geographic origin. Data on 14 qualitative morphological traits were used for cluster formation by Ward’s method. From each cluster ≈10% accessions were randomly selected to constitute a core collection comprising 1290 accessions. Mean comparisons using Newman–Keuls test, variances’ comparisons by Levene’s test, and comparison of frequency distribution by χ²-test indicated that the core collection was similar to that of the entire collection for various traits and the genetic variability available in the entire collection is preserved in the core collection. The Shannon–Weaver diversity index for different traits was also similar for both entire and core collection. All the important phenotypic associations between different traits available in the entire collection were preserved in the core collection. The core collection constituted in the present study facilitates identification of useful traits economically and expeditiously for use in pigeonpea improvement.     

Collection of Lupinus angustifolius L. Germplasm and Characterisation of Morphological and Molecular Diversity

Lupinus angustifolius L. is a Mediterranean species, domesticated in the 20th century, representing an important grain legume crop in Australia and other countries. This work is focused on the collection of wild germplasm and on the characterisation of morphological and molecular diversity of germplasm accessions. It reports the collection of 81 wild L. angustifolius accessions from the South and Centre of Portugal, available at the ‘Instituto Superior de Agronomia Gene Bank’, with subsequent morphological and molecular characterisation of a selection of these and other accessions. A multivariate analysis of morphological traits on 88 L. angustifolius accessions (including 59 wild Portuguese accessions, 15 cultivars and 14 breeding lines) showed a cline of variation on wild germplasm, with plants from Southern Portugal characterised by earlier flowering, higher vegetative development and larger seeds. AFLP and ISSR molecular markers grouped modern cultivars as sub-clusters within the wider diversity of wild germplasm, revealing the narrow pool of genetic diversity on which domesticated accessions are based. The importance of preserving, characterising and using wild genetic resources for L. angustifolius crop improvement is outlined by the results obtained.     

Structure of genetic diversity among common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.) varieties of mesoamerican and andean origins using new developed microsatellite markers

A common bean genomic library was constructed using the ‘IAC-UNA’ variety enriched for (CT) and (GT) for microsatellite motifs. From 1,209 sequenced clones, 714 showed microsatellites distributed over 471 simple and 243 compound motifs. GA/CT and GT/CA were the most frequent motifs found among these sequences. A total of 123 microsatellites has been characterized. Out of these, 87 were polymorphic (73.7%), 33 monomorphic (26.8%), and 3 (2.4%) did not amplify at all. In a sample of 20 common bean materials selected from the Agronomic Institute Germplasm Bank, the number of alleles per locus varied 2–9, with an average of 2.82. The polymorphic information content (PIC) of each marker varied from 0.05 to 0.83, with a 0.45 average value. Cluster and principal coordinate analysis of the microsatellite data were consistent with the original assignment of the germplasm accessions into the Andean and Mesoamerican gene pools of common bean. Low polymorphism levels detected could be associated with the domestication process. These microsatellites could be a valuable resource for the bean community because of their use as new markers for genetic studies. Electronic supplementary material The online version of this article (doi: ) contains supplementary material, which is available to authorized users. An erratum to this article can be found at     

Molecular Markers for the Classification of Switchgrass (Panicum virgatum L.) Germplasm and to Assess Genetic Diversity in Three Synthetic Switchgrass Populations

Information regarding the amount of genetic diversity is necessary to enhance the effectiveness of breeding programs and germplasm conservation efforts. Genetic variation between 21 switchgrass genotypes randomly selected from two lowland (‘Alamo’ and ‘Kanlow’) and one upland (‘Summer’) synthetic cultivars were estimated using restriction fragment length polymorphism (RFLP) markers. Comparison of 85 RFLP loci revealed 92% polymorphism between at least two genotypes from the upland and lowland ecotypes. Within ecotypes, the upland genotypes showed higher polymorphism than lowland genotypes (64% vs. 56%). ‘Kanlow’ had a lower percent of polymorphic loci than ‘Alamo’ (52% vs. 60%). Jaccard distances revealed higher genetic diversity between upland and lowland ecotypes than between genotypes within each ecotype. Hierarchical cluster analysis using Ward's minimum variance grouped the genotypes into two major clusters, one representing the upland group and the other the lowland group. Phylogenetic analysis of chloroplast non-coding region trnL (UAA) intron sequences from 34 switchgrass accessions (6 upland cultivars, 2 lowland cultivars, and 26 accessions of unknown affiliation) produced a neighbor-joining dendrogram comprised of two major clusters with 99% bootstrap support. All accessions grouped in the same cluster with the lowland cultivars (‘Alamo’ and ‘Kanlow’) had a deletion of 49 nucleotides. Phenotypic identification of greenhouse-grown plants showed that all accessions with the deletion are of the lowland type. The deletion in trnL (UAA) sequences appears to be specific to lowland accessions and should be useful as a DNA marker for the classification of upland and lowland germplasm.     

The Sierra Norte of Madrid: an agrobiodiversity refuge for common bean landraces

At the mountain area close to the city of Madrid, common beans were one of the main food crops present in everyday diet until 1960. This paper describes the morphological diversity, for forty-six phenological and morphological traits, found in forty-three traditional varieties of common beans collected in this area and seven commercial varieties used as reference. That comparison suggests that common bean breeding programs have led to later varieties with a higher production of straight pods. Quantitative traits showed also similar values when compared to the Iberian common bean collection, except for the phenological and seed size characters. The phenological differences could suggest an ecological adaptation of the studied landraces to the regional environmental conditions. The different seed size averages of both collections might correspond to the scarce presence of smaller seed-type common beans in Madrid collection. All the accessions collected in the Sierra Norte of Madrid belong to any of the groups included in the Spanish core collection. Madrilenian collection is also composed by indeterminate growth habit varieties, while the presence of bush accessions is relatively uncommon. Most of the Madrilenian landraces have a remarkable fitness for green-pod consumption (42 %) and their seeds are mainly white (30 %), ovate-shape (49 %) and medium-large (40 %). The study of seed storage protein allowed to classify the landraces according to their domesticated gene pools. Most of them (72 %), with T and C phaseolin type, seem to belong to Andean germplasm, while the remaining (28 %), with S and B phaseolin type, to Mesoamerican one. The remarkable morphological diversity of common beans found in this small area is a symptom of a broad genetic base despite genetic erosion, what indicates a widespread crop in the past. Therefore, it is advisable to design agro-environmental policies to promote the production and commercialization of common bean landraces in Sierra Norte of Madrid.     

AFLP similarities among historic Danish cultivars of fodder beet (<Emphasis Type="Italic">Beta vulgaris</Emphasis> L. subsp. <Emphasis Type="Italic">vulgaris</Emphasis>var. <Emphasis Type="Italic">rapacea</Emphasis> Koch)

Dead seeds of a fodder beet cultivar ‘Elvetham’ stored under ambient conditions since 1880 were compared to a homonymous sample preserved in an on-farm situation in Denmark. DNA was isolated from single seeds and successfully applied to Amplified Fragment Length Polymorphism (AFLP) analysis of the accessions. Six primer pairs were used to determine the similarity between the two accessions based on 112 polymorphic bands. Furthermore, similarity among seven cultivars of fodder beets representing the main types used in Scandinavia at the end of the 19th century was determined. This analysis was based on 152 polymorphic bands. Differentiation among the seven cultivars was determined to a mean G _ST value of 0.438, while G _ST between the two ‘Elvetham’ accessions was 0.266. A principal coordinate analysis based on jaccards similarity index illustrates that the two ‘Elvetham’ accessions are different from each other. The differentiation is higher than the value found between two separate ‘Eckerndorfer’ accessions. The results indicate that the cultivated accession has changed. Additionally, the value of applying old dead seed material for documentation in gene banks is demonstrated. During the analysis it was found that DNA isolated from seeds and leaves behaved differently in the AFLP process, however, the two fractions assigned to their common accession.     

A note on the evolution of kabuli chickpeas as shown by induced mutations in <Emphasis Type="Italic">Cicer reticulatum</Emphasis> Ladizinsky

Two distinct chickpeas of the domestic chickpea, C. arietinum L., exist and are referred to as ‘desi’ or microsperma and ‘kabuli’ or macrosperma. Cicer reticulatum Ladiz. is considered to be the wild progenitor of the domestic chickpea. However, the morphological variation in 18 original accessions of C. reticulatum is narrower than those of the domestic chickpeas. The aim of the study is to increase the variability in C. reticulatum. In M₂ generation, a mutant with white flower color was isolated despite of the fact that the parent has the pink flower. Although seed coat color of the parent was dark brown, the mutant was cream like ‘kabuli’ chickpea. It is commonly accepted that the large seeded domestic ‘kabuli’ chickpeas originated from the small seeded ‘desi’ chickpeas, but the induced mutants (white flower and cream seed coat color) of C. reticulatum may suggest an additional path for the evolution of ‘kabuli’ chickpea. ‘Kabuli’ chickpeas could have originated from spontaneous mutants of C. reticulatum. In M₃ generation, multipinnate leaf, erect growth habit, green seed and double-podded chickpeas were isolated. Among these progenies, morphologic variability increased and approached domesticated chickpea. Based on historical records and the induced mutants obtained from this study, the domestic ‘kabuli’ chickpea could have directly emerged from C. reticulatum in ancient Eastern Turkey.     

Molecular characterisation of common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.) accessions from Southwestern Uganda reveal high levels of genetic diversity

Common bean (Phaseolus vulgaris L.) was introduced to East Africa over 400 years ago and is today a fundamental part of food and income security of many smallholder farmers in the region. East Africa is among the top three bean producing and consuming regions of Africa with Uganda, Rwanda and Kenya being leaders in production. The leading common bean producing region in Uganda is the Southwestern (SW) highlands. Production is subsistent and farmers grow mixed varieties (accessions) to minimize losses. The aim of this study was to investigate the impact of farmer selection and production practices on genetic diversity of common bean in SW Uganda. 100 accessions were assembled from SW Uganda and assayed with 6 DNA simple sequence repeat (SSR) markers. A total of 41 alleles were detected giving an overall average gene diversity of 0.299 (30%) in both districts. The accessions clustered into two major gene pools i.e., Mesoamerican and Andean. Within each gene pool there was evidence of clonal populations suggesting wide distribution of certain accessions. Kabale district had a higher average gene diversity (38%) compared to Kisoro district (22%). Detection of Andean phaseolin in a clone set of Mesoamerican gene pool suggests introgession between the two groups.     

Genetic Diversity and Relationships of Japanese Peach (<Emphasis Type="Italic">Prunus persica</Emphasis> L.) Cultivars Revealed by AFLP and Pedigree Tracing

To evaluate the genetic diversity and to clarify the genetic relationships of Japanese peach cultivars, we analyzed the amplified fragment length polymorphism (AFLP) and traced the pedigree of 17 Japanese commercial peach cultivars and six traditional accessions. Sixteen AFLP primer combinations produced a total of 837 fragments and 146 polymorphic bands with a polymorphism percentage of 17.5%. All of the peach accessions could be identified from differences in at least 10 polymorphic bands. A cluster analysis showed that all the Japanese commercial peach cultivars, except ‘Kiyomi’ and ‘Jichigetsuto’, formed a major group consisting of three sub-groups. Of the six traditional accessions, four were genetically distant from the Japanese commercial peach cultivars while two accessions from China were classified into the Japanese commercial peach cultivars group. Both the AFLP analysis and pedigree tracing suggested that Japanese commercial peach cultivars are mainly derived from ‘Shanhai Suimitsuto’, one of the traditional accessions from China. Although the genetic relationships revealed by AFLP were generally in agreement with those shown by the pedigree information, some contradictions were found. Combining the AFLP results and pedigree information can provide a better understanding of the genetic relationships of Japanese peach cultivars.