The Use of Molecular and Biochemical Markers in Crop Evolution Studies

Predictive genotype-phenotype relations using genetic diversity in African yam bean (Sphenostylis stenocarpa (Hochst. ex. A. Rich) Harms)

BACKGROUND

African Yam Bean (AYB) is an understudied and underutilized tuberous legume of tropical West and Central African origin. In these geographical regions, both seeds and tubers of AYB are important components of people's diets and a potential target as a nutritional security crop. The understanding of the genetic diversity among AYB accessions is thus an important component for both conservation and potential breeding programs.

RESULTS

In this study, 93 AYB accessions were obtained from the International Institute of Tropical Agriculture (IITA) genebank and genotyped using 3722 SNP markers based on Restriction site-Associated DNA sequencing (RAD-Seq). Genetic data was analysed using multiple clustering methods for better understanding the distribution of genetic diversity across the population. Substantial genetic variability was observed in the present set of AYB accessions and different methodologies demonstrated that these accessions are divided into three to four main groups. The accessions were also analysed for important agronomic traits and successfully associated with their genetic clusters where great majority of accessions shared a similar phenotype.

CONCLUSIONS

To our knowledge, this is the first study on predicting genotypic-phenotypic diversity relationship analysis in AYB. From a breeding perspective, we were able to identify specific diverse groups with precise phenotype such as seed or both seed and tuber yield purpose accessions. These results provide novel and important insights to support the utilization of this germplasm in AYB breeding programs.

A comparative analysis of the complete chloroplast genome sequences of four peanut botanical varieties

Background

Arachis hypogaea L. is an economically important oilseed crop worldwide comprising six botanical varieties. In this work, we characterized the chloroplast (cp) genome sequences of the four widely distributed peanut varieties.

Methods

The cp genome data of these four botanical varieties (var. hypogaea, var. hirsuta, var. fastigiata, and var. vulgaris) were obtained by next-generation sequencing. These high-throughput sequencing reads were then assembled, annotated, and comparatively analyzed.

Results

The total cp genome lengths of the studied A. hypogaea varieties were 156,354 bp (var. hypogaea), 156,878 bp (var. hirsuta), 156,718 bp (var. fastigiata), and 156,399 bp (var. vulgaris). Comparative analysis of theses cp genome sequences revealed that their gene content, gene order, and GC content were highly conserved, with only a total of 46 single nucleotide polymorphisms and 26 insertions/deletions identified. Most of the variations were restricted to non-coding sequences, especially, the trnI-GAU intron region was detected to be highly variable and will be useful for future evolutionary studies.

Discussion

The four cp genome sequences acquired here will provide valuable genetic resources for distinguishing A. hypogaea botanical varieties and determining their evolutionary relationship.

Leaf crinkle disease in urdbean (Vigna mungo L. Hepper): An overview on causal agent, vector and host

Urdbean leaf crinkle disease (ULCD) is an economically significant widespread and devastating disease resulting in extreme crinkling, puckering and rugosity of leaves inflicting heavy yield losses annually in major urdbean-producing countries of the world. This disease is caused by urdbean leaf crinkle virus (ULCV). Urdbean (Vigna mungo L. Hepper) is relatively more susceptible than other pulses to leaf crinkle disease. Urdbean is an important and useful crop cultivated in various parts of South-East Asia and well adapted for cultivation under semi-arid and subtropical conditions. Aphids, insects and whiteflies have been reported as vectors of the disease. The virus is also transmitted through sap inoculation, grafting and seed. The loss in seed yield in ULCD-affected urdbean crop ranges from 35 to 81%, which is dependent upon type of genotype location and infection time. The diseased material and favourable climatic conditions contribute for the widespread viral disease. Anatomical and biochemical changes take place in the affected diseased plants. Genetic variations have been reported in the germplasm screening which suggest continuous screening of available varieties and new germplasm to search for new traits (new genes) and identify new sources of disease resistance. There are very few reports on breeding programmes for the development and release of varieties tolerant to ULCD. Mostly random amplified polymorphic DNA (RAPD) as well as inter-simple sequence repeat (ISSR) molecular markers have been utilized for fingerprinting of blackgram, and a few reports are there on sequence-tagged micro-satellite site (STMS) markers. There are so many RNA viruses which have also developed strategies to counteract silencing process by encoding suppressor proteins that create hindrances in the process. But, in the case of ULCV, there is no report available indicating which defence pathway is operating for its resistance in the plants and whether same silencing suppression strategy is also followed by this virus causing leaf crinkle disease in urdbean. The antiviral principles (AVP) present in leaf extracts of several plants are known to inhibit infection by many viruses. Many chemicals have been reported as inhibitors of virus replication in plants. Raising the barrier crops also offers an effective solution to control the spread of virus.

Development and characterization of microsatellite markers for Morus spp. and assessment of their transferability to other closely related species

BACKGROUND

Adoption of genomics based breeding has emerged as a promising approach for achieving comprehensive crop improvement. Such an approach is more relevant in the case of perennial species like mulberry. However, unavailability of genomic resources of co-dominant marker systems has been the major constraint for adopting molecular breeding to achieve genetic enhancement of Mulberry. The goal of this study was to develop and characterize a large number of locus specific genic and genomic SSR markers which can be effectively used for molecular characterization of mulberry species/genotypes.

RESULT

We analyzed a total of 3485 DNA sequences including genomic and expressed sequences (ESTs) of mulberry (Morus alba L.) genome. We identified 358 sequences to develop appropriate microsatellite primer pairs representing 222 genomic and 136 EST regions. Primers amplifying locus specific regions of Dudia white (a genotype of Morus alba L), were identified and 137 genomic and 51 genic SSR markers were standardized. A two pronged strategy was adopted to assess the applicability of these SSR markers using mulberry species and genotypes along with a few closely related species belonging to the family Moraceae viz., Ficus, Fig and Jackfruit. While 100% of these markers amplified specific loci on the mulberry genome, 79% were transferable to other related species indicating the robustness of these markers and the potential they hold in analyzing the molecular and genetic diversity among mulberry germplasm as well as other related species. The inherent ability of these markers in detecting heterozygosity combined with a high average polymorphic information content (PIC) of 0.559 ranging between 0.076 and 0.943 clearly demonstrates their potential as genomic resources in diversity analysis. The dissimilarity coefficient determined based on Neighbor joining method, revealed that the markers were successful in segregating the mulberry species, genotypes and other related species into distinct clusters.

CONCLUSION

We report a total of 188 genomic and genic SSR markers in Morus alba L. A large proportion of these markers (164) were polymorphic both among mulberry species and genotypes. A substantial number of these markers (149) were also transferable to other related species like Ficus, Fig and Jackfruit. The extent of polymorphism revealed and the ability to detect heterozygosity among the cross pollinated mulberry species and genotypes render these markers an invaluable genomic resource that can be utilized in assessing molecular diversity as well as in QTL mapping and subsequently mulberry crop improvement through MAS.

Genetic diversity of Pleurotus pulmonarius revealed by RAPD, ISSR, and SRAP fingerprinting

Pleurotus pulmonarius is one of the most widely cultivated and popular edible fungi in the genus Pleurotus. Three molecular markers were used to analyze the genetic diversity of 15 Chinese P. pulmonarius cultivars. In total, 21 random amplified polymorphic DNA (RAPD), 20 inter-simple sequence repeat (ISSR), and 20 sequence-related amplified polymorphism (SRAP) primers or primer pairs were selected for generating data based on their clear banding profiles produced. With the use of these RAPD, ISSR, and SRAP primers or primer pairs, a total of 361 RAPD, 283 ISSR, and 131 SRAP fragments were detected, of which 287 (79.5 %) RAPD, 211 (74.6 %) ISSR, and 98 (74.8 %) SRAP fragments were polymorphic. Unweighted Pair-Group Method with Arithmetic Mean (UPGMA) trees of these three methods were structured similarly, grouping the 15 tested strains into four clades. Subsequently, visual DNA fingerprinting and cluster analysis were performed to evaluate the resolving power of the combined RAPD, ISSR, and SRAP markers in the differentiation among these strains. The results of this study demonstrated that each method above could efficiently differentiate P. pulmonarius cultivars and could thus be considered an efficient tool for surveying genetic diversity of P. pulmonarius.

Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops

Domesticated food crops are derived from a phylogenetically diverse assemblage of wild ancestors through artificial selection for different traits. Our understanding of domestication, however, is based upon a subset of well-studied 'model' crops, many of them from the Poaceae family. Here, we investigate domestication traits and theories using a broader range of crops. We reviewed domestication information (e.g. center of domestication, plant traits, wild ancestors, domestication dates, domestication traits, early and current uses) for 203 major and minor food crops. Compiled data were used to test classic and contemporary theories in crop domestication. Many typical features of domestication associated with model crops, including changes in ploidy level, loss of shattering, multiple origins, and domestication outside the native range, are less common within this broader dataset. In addition, there are strong spatial and temporal trends in our dataset. The overall time required to domesticate a species has decreased since the earliest domestication events. The frequencies of some domestication syndrome traits (e.g. nonshattering) have decreased over time, while others (e.g. changes to secondary metabolites) have increased. We discuss the influences of the ecological, evolutionary, cultural and technological factors that make domestication a dynamic and ongoing process.

Some like it hot, some like it warm: phenotyping to explore thermotolerance diversity

Plants have evolved overlapping but distinct cellular responses to different aspects of high temperature stress. These responses include basal thermotolerance, short- and long-term acquired thermotolerance, and thermotolerance to moderately high temperatures. This 'thermotolerance diversity' means that multiple phenotypic assays are essential for fully describing the functions of genes involved in heat stress responses. A large number of genes with potential roles in heat stress responses have been identified using genetic screens and genome wide expression studies. We examine the range of phenotypic assays that have been used to characterize thermotolerance phenotypes in both Arabidopsis and crop plants. Three major variables differentiate thermotolerance assays: (1) the heat stress regime used, (2) the developmental stage of the plants being studied, and (3) the actual phenotype which is scored. Consideration of these variables will be essential for deepening our understanding of the molecular genetics of plant thermotolerance.

Landscape management and domestication of Stenocereus pruinosus (Cactaceae) in the Tehuacán Valley: human guided selection and gene flow

BACKGROUND

Use of plant resources and ecosystems practiced by indigenous peoples of Mesoamerica commonly involves domestication of plant populations and landscapes. Our study analyzed interactions of coexisting wild and managed populations of the pitaya Stenocereus pruinosus, a columnar cactus used for its edible fruit occurring in natural forests, silviculturally managed in milpa agroforestry systems, and agriculturally managed in homegardens of the Tehuacán Valley, Mexico. We aimed at analyzing criteria of artificial selection and their consequences on phenotypic diversity and differentiation, as well as documenting management of propagules at landscape level and their possible contribution to gene flow among populations.

METHODS

Semi-structured interviews were conducted to 83 households of the region to document perception of variation, criteria of artificial selection, and patterns of moving propagules among wild and managed populations. Morphological variation of trees from nine wild, silviculturally and agriculturally managed populations was analyzed for 37 characters through univariate and multivariate statistical methods. In addition, indexes of morphological diversity (MD) per population and phenotypic differentiation (PD) among populations were calculated using character states and frequencies.

RESULTS

People recognized 15 pitaya varieties based on their pulp color, fruit size, form, flavor, and thorniness. On average, in wild populations we recorded one variety per population, in silviculturally managed populations 1.58 ± 0.77 varieties per parcel, and in agriculturally managed populations 2.19 ± 1.12 varieties per homegarden. Farmers select in favor of sweet flavor (71% of households interviewed) and pulp color (46%) mainly red, orange and yellow. Artificial selection is practiced in homegardens and 65% of people interviewed also do it in agroforestry systems. People obtain fruit and branches from different population types and move propagules from one another. Multivariate analyses showed morphological differentiation of wild and agriculturally managed populations, mainly due to differences in reproductive characters; however, the phenotypic differentiation indexes were relatively low among all populations studied. Morphological diversity of S. pruinosus (average MD = 0.600) is higher than in other columnar cacti species previously analyzed.

CONCLUSIONS

Artificial selection in favor of high quality fruit promotes morphological variation and divergence because of the continual replacement of plant material propagated and introduction of propagules from other villages and regions. This process is counteracted by high gene flow influenced by natural factors (pollinators and seed dispersers) but also by human management (movement of propagules among populations), all of which determines relatively low phenotypic differentiation among populations. Conservation of genetic resources of S. pruinosus should be based on the traditional forms of germplasm management by local people.

Evaluation of genetic diversity among Chinese Pleurotus eryngii cultivars by combined RAPD/ISSR marker

Pleurotus eryngii (DC. Ex. Fr.) Quél is a rare precious edible fungus which belongs to the family Pleurotaceae. This mushroom has highly nutritional, pharmaceutical, economic and ecological values. In the present study, combined randomly amplified polymorphic DNA (RAPD)/inter-simple sequence repeat (ISSR) was used to assess the genetic diversity of P. eryngii strains cultivated in China. For the RAPD and ISSR analyses, 404 and 392 polymorphic bands were obtained from 32 P. eryngii strains using 28 and 24 selected primers, respectively. A combined RAPD/ISSR dendrogram grouped the 32 strains into five clades with coefficient of 0.770. The comparison of RAPD and ISSR was also elucidated in the present study. The results of our study obtained by combined RAPD/ISSR analysis contributed to a better understanding of the genetic relationships among the P. eryngii strains and provide orientation for the strain improvement of P. eryngii species.

Molecular characterization of mulberry (Morus spp.) genotypes via RAPD and ISSR

BACKGROUND

In recent years, DNA-based markers have been used quite extensively because of their many advantages over the traditional morphological and biochemical markers. Many studies have shown that molecular markers are useful in delineating the genetic relationships among closely related mulberry genotypes and cultivars. Thus, in the present study, polymer chain reaction based DNA fingerprinting techniques were used to investigate the genetic relationships among mulberry genotypes growing in different agro-climatic regions of Turkey.

RESULTS

20 RAPD primers generated a total of 173 bands, of which 157 (90.75%) were polymorphic. As for 11 ISSR primers, 124 bands (96.55%) were polymorphic in a total of 128. The similarity index for RAPD technique ranged between 0.24-0.98; 25İs203 with 25İs112 were found to be the closest genotypes, while 24Ke10 and 25İs123 were the most distant ones. According to the ISSR result, the genetic similarity index changed between 0.21-095; 25İs203 with 25İs112 genotypes were the closest, while 25İs08 and 01KaD2 were the most distant ones.

CONCLUSION

The RAPD and ISSR markers were found to be promising for assessing genetic diversity in mulberry genotypes.

Estimation of genetic distance based on RAPDs between 11 cotton accessions varying in heat tolerance

The genetic distance of 11 cotton genotypes varying in heat tolerance was studied using RAPD markers. Fifty-three random decamer primers were used for the estimation of genetic distance. Among the 53 RAPD primers, which were custom synthesized by GeneLink Inc., UK, 32 were polymorphic and 21 were monomorphic. The 32 polymorphic primers produced 273 fragments, with a mean of 8.3 fragments per primer. The number of polymorphic bands produced in the 11 cotton accessions ranged from 1 to 31. Primer GLC-20 produced 31 polymorphic bands, while two primers, GLB-5 and GLC-12, produced one polymorphic band each. A range of 88.89 to 42.48% genetic similarity was observed among the 11 cotton accessions. The highest genetic similarity was observed between FH-945 and BH-160 (88.89%), whereas the lowest value was found between NIAB-801/2 and FH-945 (42.48%). Unique amplification profiles were produced by most of the cultivars; the differences were sufficient to distinguish them from other genotypes. This confirms the efficacy of RAPD markers for the identification of plant genotypes. An accumulative analysis of amplified products generated by RAPDs was sufficient to assess the genetic diversity among the genotypes. This information should be helpful for formulating breeding and genome mapping programs.

Assessment of genetic diversity and relationships among maize (Zea mays L.) Italian landraces by morphological traits and AFLP profiling

In the present study we have analyzed the genetic diversity pattern in a sample of 54 Italian maize landraces, using morphological traits and molecular markers. Although the 54 landraces surveyed in this study were restricted to Lombardy, the core region of maize production in Italy, our data revealed a large genetic heterogeneity for both morphological and molecular traits in the accessions analyzed. Additionally, our data confirm that the AFLP markers produced a high frequency of polymorphic bands and were able to unequivocally fingerprint each of the landraces considered. Cluster analysis based on AFLP markers displayed a clearer separation of the accessions in comparison to morphological data. Different populations were divided into four major clusters reflecting the geographical origin and seasonal employment of the landraces analyzed. Molecular analysis of variance showed significant (P < 0.01) differences among groups, among populations within groups, and among individuals within populations. Approximately 74% of the total variance could be attributed to differences within populations. Conversely, a lower level of differentiation was detected among groups (approximately 4%). Regarding population structures, the genetic distance between populations (FST = 0.25 +/- 0.3) and the degree of inbreeding within groups (FSC = 0.22 +/- 0.2), did not diverge significantly, while both significantly differed from the degree of relatedness between markers within groups (FCT = 0.04 +/- 0.03). Results are discussed in relation to a suitable conservation method.

Assessment of genetic variation within Indian mustard (Brassica juncea) germplasm using random amplified polymorphic DNA markers

Genetic diversity among 45 Indian mustard (Brassica juncea L.) genotypes comprising 37 germplasm collections, five advance breeding lines and three improved cultivars was investigated at the DNA level using the random amplified polymorphic DNA (RAPD) technique. Fifteen primers used generated a total of 92 RAPD fragments, of which 81 (88%) were polymorphic. Of these, 13 were unique to accession 'Pak85559'. Each primer produced four to nine amplified products with an average of 6.13 bands per primer. Based on pairwise comparisons of RAPD amplification products, Nei and Li's similarity coefficients were calculated to evaluate the relationships among the accessions. Pairwise similarity indices were higher among the oilseed accessions and cultivars showing narrow ranges of 0.77-0.99. An unweighted pair-group method with arithmetic averages cluster analysis based on these genetic similarities placed most of the collections and oilseed cultivars close to each other, showing a low level of polymorphism between the accessions used. However, the clusters formed by oilseed collections and cultivars were comparatively distinct from that of advanced breeding lines. Genetically, all of the accessions were classified into a few major groups and a number of individual accessions. Advanced breeding lines were relatively divergent from the rest of the accessions and formed independent clusters. Clustering of the accessions did not show any pattern of association between the RAPD markers and the collection sites. A low level of genetic variability of oilseed mustard was attributed to the selection for similar traits and horticultural uses. Perhaps close parentage of these accessions further contributed towards their little diversity. The study demonstrated that RAPD is a simple and fast technique to compare the genetic relationship and pattern of variation among the gene pool of this crop.

Genetic analysis of the cultivated potato Solanum tuberosum L. Phureja Group using RAPDs and nuclear SSRs

The Solanum tuberosum L. Phureja Group consists of potato landraces widely grown in the Andes from western Venezuela to central Bolivia, and forms an important breeding stock due to their excellent culinary properties and other traits for developing modern varieties. They have been distinguished by short-day adaptation, diploid ploidy (2n = 2x = 24), and lack of tuber dormancy. This nuclear simple sequence repeat (nSSR or microsatellite) study complements a prior random amplified polymorphic DNA (RAPD) study to explore the use of these markers to form a core collection of cultivar groups of potatoes. Like this prior RAPD study, we analyzed 128 accessions of the Phureja Group using nuclear microsatellites (nSSR). Twenty-six of the 128 accessions were invariant for 22 nSSR markers assayed. The nSSR data uncovered 25 unexpected triploid and tetraploid accessions. Chromosome counts of the 102 accessions confirmed these nSSR results and highlighted seven more triploids or tetraploids. Thus, these nSSR markers (except 1) are good indicators of ploidy for diploid potatoes in 92% of the cases. The nSSR and RAPD results: (1) were highly discordant for the remaining 70 accessions that were diploid and variable in nSSR, (2) show the utility of nSSRs to effectively uncover many ploidy variants in cultivated potato, (3) support the use of a cultivar-group (rather than a species) classification of cultivated potato, (4) fail to support a relationship between genetic distance and geographic distance, (5) question the use of any single type of molecular marker to construct core collections.

Genetic variability and genetic structure of wild and semi-domestic populations of tasar silkworm (Antheraea mylitta ) ecorace Daba as revealed through ISSR markers

The genetic diversity in the wild and semi-domestic populations of Daba ecorace of Antheraea mylitta was studied to ascertain the distribution of variability within and among populations of semi-domestic bivoltine (DB), trivoltine (DT) and nature grown wild populations (DN) with inter-simple sequence repeat (ISSR) markers. A total of 138 markers were produced among 56 individuals of the three populations, of which 98% were polymorphic. For the individual populations, the percentage polymorphism was 58.69, 52.9 and 77.54 for DB, DT and DN, respectively. Average number of observed (1.791+/- 0.408) and effective alleles (1.389+/-0.348) was also high in the wild populations in comparison to the bivoltine and trivoltine semi-domestic populations. Genetic diversity (H(t)) in DB, DT and DN was 0.180+/- 0.033, 0.153+/- 0.032 and 0.235+/- 0.033, respectively and within-population genetic diversity (H(s)) ranged from 0.166 to 0.259 with a mean of 0.189. Mean gene differentiation (G(ST)) was found to be 0.25. Shanon's diversity index was 0.278, 0.237 and 0.361 for DB, DT and DN and overall it was 0.391. Gene flow (N(m)) among the populations was 1.509. The dendrogram produced by UPGMA with Dice's genetic distance matrices resulted in the formation of three major clusters separating the three populations. Considerable intra- and inter-population variability is found in all three populations. The population structure analysis further suggests that the semi-domestic populations of Daba ecorace are at the threshold of differentiating themselves. The high genetic variability present within wild Daba population of A. mylitta is of much importance for conservation as well as utilization in systematic breeding program.

Quantitative evaluation of the petal shape variation in Primula sieboldii caused by breeding process in the last 300 years

Primula sieboldii: (E. Morren) has been a popular garden plant at least since the Edo period, about 300 years ago. We compared petal form between cultivars and wild populations in order to characterise the changes that have occurred during domestication. The comparison was made using EF-PCA analysis, which describes overall petal shape mathematically by transforming petal contour coordinates into elliptic Fourier descriptors; it subsequently summarises these descriptors by principal component analysis (PCA). Rearing cultivars in a common-garden experiment identified the PCs with a substantial genetic element. A clear heritable component was detected for the PCs characterising symmetrical variation in flower shape, but not the asymmetrical variation. Wild populations of this species have become endangered owing to habitat destruction by human activity, and many lowland floodplain habitats have been lost. Variation within the remaining wild populations was significantly lower than in the cultivars for PC1 (aspect ratio), PC3 (curvature of proximal and distal parts) and petal area; but not for PC2 (depth of head notch) and PC4 (position of the centre of gravity). The shifts in petal form from the wild populations to the cultivars parallel those seen in other crop-types following domestication, including an increase in size and diversity of forms: cultivars have shallower head notches, more fan-shaped petals and larger petals than do wild P. sieboldii.

Possible effects of (trans)gene flow from crops on the genetic diversity from landraces and wild relatives

Gene flow is a potential concern associated with the use of transgenic crops because it could affect genetic diversity of related landraces and wild relatives. This concern has taken on added importance with the looming introduction of transgenic crops in centers of crop domestication (Mexico, China) and those producing pharmaceutical compounds. For gene flow to take place among cultivars and their wild relatives, several steps have to be fulfilled, including the presence of cultivars or wild relatives within pollen or seed dispersal range, the ability to produce viable and fertile hybrids, at least partial overlap in flowering time, actual gene flow by pollen or seed, and the establishment of crop genes in the domesticated or wild recipient populations. In contrast with domestication genes, which often make crops less adapted to natural ecosystems, transgenes frequently represent gains of function, which might release wild relatives from constraints that limit their fitness. In most sexually reproducing organisms, the chromosomal region affected by selection of a single gene amounts to a small percentage of the total genome size. Because of gene flow, the level of genetic diversity present in the domesticated gene pool becomes a crucial factor affecting the genetic diversity of the wild gene pool. For some crops, such as cotton and maize, the introduction of transgenic technologies has led to a consolidation of the seed industry and a reduction in the diversity of the elite crop gene pool. Thus, diversity in improved varieties grown by farmers needs to be monitored. Several areas deserve further study, such as the actual magnitude of gene flow and its determinants in different agroecosystems, the long-term effects of gene flow on genetic diversity both across gene pools and within genomes, the expression of transgenes in new genetic backgrounds, and the effects of socio-economic factors on genetic diversity.

Using molecular markers to assess the effect of introgression on quantitative attributes of common bean in the Andean gene pool

Progress in bean breeding programs requires the exploitation of genetic variation that is present among races or through introgression across gene pools of Phaseolus vulgaris L. Of the two major common bean gene pools, the Andean gene pool seems to have a narrow genetic base, with about 10% of the accessions in the CIAT core collection presenting evidence of introgression. The objective of this study was to quantify the degree of spontaneous introgression in a sample of common bean landraces from the Andean gene pool. The effects of introgression on morphological, economic and nutritional attributes were also investigated. Homogeneity analysis was performed on molecular marker data from 426 Andean-type accessions from the primary centres of origin of the CIAT common bean core collection and two check varieties. Quantitative attribute diversity for 15 traits was studied based on the groups found from the cluster analysis of marker prevalence indices computed for each accession. The two-group summary consisted of one group of 58 accessions (14%) with low prevalence indices and another group of 370 accessions (86%) with high prevalence indices. The smaller group occupied the outlying area of points displayed from homogeneity analysis, yet their geographic origin was widely distributed over the Andean region. This group was regarded as introgressed, since its accessions displayed traits that are associated with the Middle American gene pool: high resistance to Andean disease isolates but low resistance to Middle American disease isolates, low seed weight and high scores for all nutrient elements. Genotypes generated by spontaneous introgression can be helpful for breeders to overcome the difficulties in transferring traits between gene pools.

Molecular phylogeny of date palm (Phoenix dactylifera L.) cultivars from Saudi Arabia by DNA fingerprinting

Genetic diversity among 13 different cultivars of date palm (Phoenix dactylifera L.) of Saudi Arabia was studied using random amplified polymorphic DNA (RAPD) markers. The screening of 140 RAPD primers allowed selection of 37 primers which revealed polymorphism, and the results were reproducible. All 13 genotypes were distinguishable by their unique banding patterns produced by 37 selected primers. Cluster analysis by the unweighted paired group method of arithmetic mean (UPGMA) showed two main clusters. Cluster A consisted of five cultivars (Shehel, Om-Kobar, Ajwa, Om-Hammam and Bareem) with 0.59-0.89 Nei and Li's coefficient in the similarity matrix. Cluster B consisted of seven cultivars (Rabeeha, Shishi, Nabtet Saif, Sugai, Sukkary Asfar, Sukkary Hamra and Nabtet Sultan) with a 0.66-0.85 Nei and Li's similarity range. Om-Hammam and Bareem were the two most closely related cultivars among the 13 cultivars with the highest value in the similarity matrix for Nei and Li's coefficient (0.89). Ajwa was closely related with Om-Hammam and Bareem with the second highest value in the similarity matrix (0.86). Sukkary Hamra and Nabtet Sultan were also closely related, with the third highest value in the similarity matrix (0.85). The cultivar Barny did not belong to any of the cluster groups. It was 34% genetically similar to the rest of the 12 cultivars. The average similarity among the 13 cultivars was more than 50%. As expected, most of the cultivars have a narrow genetic base. The results of the analysis can be used for the selection of possible parents to generate a mapping population. The variation detected among the closely related genotypes indicates the efficiency of RAPD markers over the morphological and isozyme markers for the identification and construction of genetic linkage maps.

Microsatellite variation in cassava (Manihot esculenta, Euphorbiaceae) and its wild relatives: further evidence for a southern Amazonian origin of domestication

Genetic variation at five microsatellite loci was used to investigate the evolutionary and geographical origins of cassava (Manihot esculenta subsp. esculenta) and the population structure of cassava's wild relatives. Two hundred and twelve individuals were sampled, representing 20 crop accessions, 27 populations of cassava's closest wild relative (M. esculenta subsp. flabellifolia), and six populations of a potentially hybridizing species (M. pruinosa). Seventy-three alleles were observed across all loci and populations. These data indicate the following on cassava's origin: (1) genetic variation in the crop is a subset of that found in the wild M. esculenta subspecies, suggesting that cassava is derived solely from its conspecific wild relative. (2) Phenetic analyses group cassava with wild populations from the southern border of the Amazon basin, indicating this region as the likely site of domestication. (3) Manihot pruinosa, while closely related to M. esculenta (and possibly hybridizing with it where sympatric), is probably not a progenitor of the crop. Genetic differentiation among the wild populations is moderately high (F:(ST) = 0.42, rho(ST) = 0.54). This differentiation has probably arisen primarily through random genetic drift (rather than mutation) following recent population divergence.

Evidence on the origin of cassava: phylogeography of Manihot esculenta

Cassava (Manihot esculenta subsp. esculenta) is a staple crop with great economic importance worldwide, yet its evolutionary and geographical origins have remained unresolved and controversial. We have investigated this crop's domestication in a phylogeographic study based on the single-copy nuclear gene glyceraldehyde 3-phosphate dehydrogenase (G3pdh). The G3pdh locus provides high levels of noncoding sequence variation in cassava and its wild relatives, with 28 haplotypes identified among 212 individuals (424 alleles) examined. These data represent one of the first uses of a single-copy nuclear gene in a plant phylogeographic study and yield several important insights into cassava's evolutionary origin: (i) cassava was likely domesticated from wild M. esculenta populations along the southern border of the Amazon basin; (ii) the crop does not seem to be derived from several progenitor species, as previously proposed; and (iii) cassava does not share haplotypes with Manihot pruinosa, a closely related, potentially hybridizing species. These findings provide the clearest picture to date on cassava's origin. When considered in a genealogical context, relationships among the G3pdh haplotypes are incongruent with taxonomic boundaries, both within M. esculenta and at the interspecific level; this incongruence is probably a result of lineage sorting among these recently diverged taxa. Although phylogeographic studies in animals have provided many new evolutionary insights, application of phylogeography in plants has been hampered by difficulty in obtaining phylogenetically informative intraspecific variation. This study demonstrates that single-copy nuclear genes can provide a useful source of informative variation in plants.

Genetic diversity evaluation of some elite cotton varieties by RAPD analysis

Random amplified polymorphic DNA (RAPD) analysis was used to evaluate the genetic diversity of elite commercial cotton varieties. Twenty two varieties belonging to Gossypium hirsutum L. and one to G. arboreum L. were analyzed with 50 random decamer primers using the polymerase chain reaction (PCR). Forty nine primers detected polymorphism in all 23 cotton varieties, while one produced monomorphic amplification profiles. A total of 349 bands were amplified, 89.1% of which were polymorphic. Cluster analysis by the unweighted pair group method of arithmetic means (UPGMA) showed that 17 varieties can be placed in two groups with a similarity ranging from 81.51% to 93.41%. G. hirsutum L. varieties S-12, V3 and MNH-93 showed a similarity of 78.12, 74.46 and 69.56% respectively with rest of the varieties. One variety, CIM-1100, showed 57.02% similarity and was quite distinct. The diploid cotton G. arboreum L. var. Ravi was also very distinct from rest of its tetraploid counterparts and showed only 55.7% similarity. The analysis revealed that the intervarietal genetic relationships of several varieties is related to their center of origin. As expected, most of the varieties have a narrow genetic base. The results obtained can be used for the selection of possible parents to generate a mapping population. The results also reveal the genetic relationship of elite commercial cotton varieties with some standard "Coker" varieties and the diploid G. arboreum L. var. Ravi (old world cotton).

Colombian Common and Lima Beans: Views on their Origin and Evolutionary Significance

<p>This article reviews the geographical distribution of wild common and lima beans in the Neotropics, their morphological and ecological attributes, and their biochemical and molecular variation along their ranges. These facts reveal the organization of the genetic diversity into three major gene pools, with one being considered ancestral, and additional subdivisions within the derived ones. The relationships between the ancestral branch and related species are discussed. Colombia appears to he more than a place of contact between gene pools of cultivated materials, but the transit place of the ancestral branches, and a possible place of domestication as well. </p><p> </p><p><strong>Los Fríjoles Colombianos Lima y Común: Puntos de Vista de su Origen y el Significado de su Evolución</strong></p><p>Se presenta una revisión de la distribución geográfica de las formas silvestres del frijol común y del frijol lima en el Neotrópico, de sus características morfológicas y ecológicas, y de la variación bioquímica y molecular a lo largo de esta distribución. Estos hechos muestran que la diversidad genética viene organizada en tres acervos o grupos de genes, uno de ellos siendo ancestral, y con subdivisiones adicionales dentro de los acervos derivados. Se discuten las relaciones filogenéticas entre este ramal ancestral y las especies afines. Más que lugar de contacto entre acervos de materiales cultivados, Colombia aparece como corredor biológico donde transitaron las ramas ancestrales, y como lugar de posible domesticación.</p><p> </p><p> </p>

Evolution of genetic diversity during the domestication of common-bean (Phaseolus vulgaris L.)

M13 DNA fingerprinting was used to determine evolutionary changes that occurred in Latin American germ plasm and USA cultivars of commonbean (Phaseolus vulgaris L.) during domestication. Linkage mapping experiments showed that M13-related sequences in the common-bean genome were either located at the distal ends of linkage groups or that they were unlinked to each other or to any previously mapped markers. Levels of polymorphism observed by hybridization with M13 (1 probe-enzyme combination) were comparable to those observed by hybridization with single-copy random PstI genomic probes (36 enzyme-probe combinations) but were higher than those observed for isozymes (10 loci). Results indicated that the wild ancestor had diverged into two taxa, one distributed in Middle America (Mexico, Central America, and Colombia) and the other in the Andes (Peru and Argentina); they also suggested separate domestications in the two areas leading to two cultivated gene pools. Domestication in both areas led to pronounced reductions in diversity in cultivated descendants in Middle America and the Andes. The marked lack of polymorphism within commercial classes of USA cultivars suggests that the dispersal of cultivars from the centers of origin and subsequent breeding of improved cultivars led to high levels of genetic uniformity. To our knowledge, this is the first crop for which this reduction in diversity has been documented with a single type of marker in lineages that span the evolution between wild ancestor and advanced cultivars.