Landraces of Phaseolus vulgaris (Fabaceae) in Northern Malawi. II. Generation and maintenance of variability

Bean (Phaseolus vulgaris) landraces in northern Malawi were found to be heterogeneous for many qualitative and quantitative traits. An earlier 21- character evaluation of 25 lines in 15 landraces found significant differences in all characters among lines and among landraces. The present study has concentrated on two factors that are likely to be involved in the generation and maintenance of this heterogeneity: seed- handling practices and natural outcrossing. Seed- handling practices during harvest, storage, and marketing at the village, local market, and national levels were found to result in physical and usually nonselective mixing of many seed types. Experiments determined that outcrossing does occur at a low level among beans in Malawi and can result in the generation of many new seed phenotypes. A scenario was developed integrating seed- handling practices and outcrossing that lays a foundation for understanding the generation and maintenance of variability in these bean landraces. The process whereby landrace heterogeneity arises and the ways it is maintained, if understood, should assist plant breeders in the development of improved germplasm for subsistence farmers.     

Molecular characterisation of wild populations and landraces of common bean from northwestern Argentina

Abstract

Information on the variability of wild bean populations and landraces is essential to set conservation strategies and design breeding programmes aimed at enlarging the genetic base of commercial beans. Nineteen Argentinean common bean landraces and wild populations were characterised and their diversity was analysed by means of inter‐simple sequence repeat (ISSR) markers and seed proteins. Populations were successfully identified as belonging to the Andean gene pool of origin by phaseolin electrophoresis, whereas ISSR markers revealed high levels of inter‐ and intra‐population variability. Four of 10 primers produced polymorphic and reproducible DNA profiles, which were used to generate UPGMA (unweighted pair group method with arithmetical averages) and NJ (neighbour‐joining) trees. ISSR markers revealed a high level of variability both within wild bean populations and landraces. Genetic variability of wild samples was associated with their geographic distribution. By contrast, landraces were clustered, at least to some degree, based on their seed colour and shape, showing no clear discrimination among sites. The results presented here suggest that, to a certain extent, hybridisation between wild beans and landraces occurs in the wild, a hypothesis that needs to be tested through further analyses.     

Role of seed flow on the pattern and dynamics of pearl millet (<Emphasis Type="Italic">Pennisetum glaucum</Emphasis> [L.] R. Br.) genetic diversity assessed by AFLP markers: a study in south-western Niger

We studied the regional genetic diversity and seed exchange dynamics of pearl millet landraces in south-western Niger. The genetic study was based on AFLP markers. We found significant genetic differentiation between landraces in different geographical areas of south-western Niger. However, the degree of differentiation was low insofar as only 1.9% of the total molecular diversity was due to regional differentiation, suggesting a relatively high gene flow. Anthropologic studies on farming practices have suggested that seed exchanges between farmers on a large geographical scale probably make a considerable contribution to this result. In order to test this hypothesis, the effects of seed exchange on the genetic diversity of landraces was analyzed on seed samples from two distant villages in contrasting areas of south-western Niger. Seeds imported by farmers into the southern village of Sina Koara did not differ significantly from locally grown landraces. By contrast, in the northern village of Alzou, several samples were genetically different from locally grown landraces and closer to southern accessions. These data suggest that the seed flow is preferentially from south to north, i.e. from an area with more favorable rainfall conditions. The potential consequences for the genetic diversity and adaptation of northern pearl millet landraces are discussed.     

Biochemical and molecular characterization of cowpea landraces using seed storage proteins and SRAP marker patterns

Seven landraces of cowpea [Vigna unguiculata (L.) Walp.] were assessed for genetic variability in total proteins, protein fractions viz. albumins, globulins, prolamins, and glutelins by SDS-polyacrylamide gel electrophoresis and DNA polymorphism using sequence-related amplified polymorphisms (SRAP) markers. The solubility-based protein fractionation data indicated that the salt soluble fraction (globulin) and water-soluble fraction (albumin) proteins were the predominant fractions in cowpea seeds comprising 45–50.3% and 31.2–35.5% of total soluble proteins, respectively. The electrophoretic pattern revealed the molecular heterogeneity among total proteins as well as different protein fractions. The molecular weights of protein bands obtained by SDS-PAGE varied between 10 to 250, 15 to 110, 15 to 150, and 15 to 130?kDa for total proteins, albumins, globulins, and glutelins, respectively. A large number of bands were found common to the various landraces, indicative of their close relationship with one another. However, a few bands distinctive to some specific landraces were also detected, indicating varietal differences. A 34 SRAP primer pair combination generated a total of 1003 amplicons (loci) showed 100% polymorphism with an average of 0.93 polymorphism information content (PIC) value. Landraces displayed an average 0.50 similarity coefficient which clustered the landraces corresponding to their growth habit in main clusters and to their geographical origin in subcultures. Molecular and biochemical analysis were correlated with a medium level (Mantel test, r?=?0.56, P?<?0.02). These findings revealed that seed proteins and DNA polymorphism provide valuable information regarding the variability among landraces and this information could be utilized for breeding purposes in the enhancement of protein quality and quantity in grain legumes.     

Farmers Drive Genetic Diversity of Thai Purple Rice (Oryza sativa L.) Landraces

Purple or black rice (Oryza sativa L.) is a culturally important germplasm in Asia with a long history of cultivation in northern Thailand. Purple rice is identified by the color of the rice pericarp, which varies from purple to black with the accumulation of phenolic acids, flavonoids, and anthocyanins. In the present study, we assessed molecular variation within and between wetland purple rice landraces germplasm from northern and northeastern Thailand using 12 microsatellite loci. All purple rice varieties surveyed showed high levels of homozygosity within varieties and strong genetic differentiation among varieties, indicating the fixation of genetic differences among them. This pattern is consistent with purple rice farming practices in northern Thailand, where a small portion of harvested seed is selected and replanted based on farmers’ preferences. The reduced genetic diversity and high homozygosity observed for purple rice is also consistent with patterns expected for this inbreeding crop. Genetic differentiation among the varieties showed some degree of structuring based on their geographical origin. Taken together, these data highlight that the genetic diversity and structure of wetland purple rice landraces is shaped by farmer utilization and cultivation through local cultural practices, and that conservation should focus on ex situ conservation across its cultivation range, along with on-farm, in situ conservation based on farmers’ seed-saving practices. In situ conservation may prove especially valuable for preserving the genetic identity of local varieties and promote adaptation to local environments.

     

Agricultural Biodiversity in Northwest Somalia – an Assessment Among Selected Somali Sorghum(<Emphasis Type="Italic">Sorghum bicolor</Emphasis> (L.) Moench) Germplasm

The seed sector situation in Northwest Somalia is critical. The availability of food has decreased and many people are at risk of hunger. Food security can be restored by enhancing the local genetic resources and creating an efficient seed sector. Sorghum is important as a food and fodder crop in this region. It is close to Ethiopia, which is considered as the probable origin and domestication of Sorghum. Twelve morphological and productive characteristics were chosen to assess the phenotypic variability of 16 accessions of sorghum from Northwest Somalia. Univariate (analysis of variance and G test) and multivariate (discriminant and cluster analysis) methods were used to assess the morphological variation within the accession and to group the 16 accessions into clusters based upon quantitative and qualitative characters. Elmi Jama Cas, Masego Cas, Masego Cad and Carabi clearly represent distinct landraces with specific features suitable for different purpose, such as grain and/or forage production. Each landrace tested is able to grow under harsh environmental conditions, thus ensuring a low, but stable production for small poor resources farmers. Knowledge and conservation of local landraces will provide a broad base of genetic variability from which improved sorghum varieties can be developed, thus aiding in the stabilisation of a secure and sustainable food supply for farmers of Northwest Somalia.     

Estimating maize genetic erosion in modernized smallholder agriculture

Replacement of crop landraces by modern varieties is thought to cause diversity loss. We studied genetic erosion in maize within a model system; modernized smallholder agriculture in southern Mexico. The local seed supply was described through interviews and in situ seed collection. In spite of the dominance of commercial seed, the informal seed system was found to persist. True landraces were rare and most informal seed was derived from modern varieties (creolized). Seed lots were characterized for agronomical traits and molecular markers. We avoided the problem of non-consistent nomenclature by taking individual seed lots as the basis for diversity inference. We defined diversity as the weighted average distance between seed lots. Diversity was calculated for subsets of the seed supply to assess the impact of replacing traditional landraces with any of these subsets. Results were different for molecular markers, ear- and vegetative/flowering traits. Nonetheless, creolized varieties showed low diversity for all traits. These varieties were distinct from traditional landraces and little differentiated from their ancestral stocks. Although adoption of creolized maize into the informal seed system has lowered diversity as compared to traditional landraces, genetic erosion was moderated by the distinct features offered by modern varieties.     

Do seed transfer zones for ecological restoration reflect the spatial genetic variation of the common grassland species Lathyrus pratensis?

A common ecological restoration approach is the reestablishment of vegetation using seed mixtures. To preserve the natural genetic pattern of plant species local seed material should be used. Consequently, seed transfer zones (seed production areas and seed provenance regions) have been delineated for ecological restoration in Germany. Although it is assumed that these transfer zones represent genetic variation, there remains a lack of empirical data. In this study, we analyzed whether seed transfer zones reflect the genetic variation of the common grassland species Lathyrus pratensis. We sampled 706 individuals from 37 populations in Bavaria, Germany and analyzed genetic variation using amplified fragment length polymorphisms. In our study, we observed higher levels of genetic variation and fragment rarity in the southern Bavarian populations compared to northern populations. Our analyses revealed a strong genetic differentiation between southern and northern Bavarian populations delineated along the Danube River. However, seed production areas and seed provenance regions reflected genetic variation of L. pratensis only to a limited degree. Our study illustrates that the level of genetic variation within populations strongly depends on population history. Furthermore, the geomorphological and climatic attributes, which have been used to delineate seed provenance regions, do not reduce gene flow among populations. Seed collections for gene banks and seed production should comprise seeds from populations in southern and northern Bavaria representing the strong genetic variation between both regions, but prioritize southern populations due to higher levels of variation.     

Identification of Indian Landraces of Opium Poppy Papaver somniferum Resistant to Damping-off and Downy Mildew Fungal Diseases

A set of 32 landraces (traditional local cultivars) of poppy Papaver somniferum originating in the Indian states of Rajasthan, Madhya Pradesh, Uttar Pradesh and Tamilnadu, and four Indian commercial varieties were screened over four cropping seasons for their reaction to downy mildew disease caused by Peronospora arborescens and damping-off disease caused by Pythium dissotocum under both field and artificial inoculation conditions. The landrace 1018 was found to be resistant to damping-off disease and the landraces 1014 and N3 were resistant to downy mildew disease. A yield trial conducted over two seasons showed that the damping-off disease-resistant landrace 1018 was superior to all the commercial varieties in seed, morphine and/or codeine yield. The experiments provided further evidence that there is considerable genetic variability between the landraces.     

Keepers of maize in Chiapas,Mexico

This study concerns the knowledge and selection of biological diversity of maize (Zea mays) within its center of domestication in Mesoamerica. Maize farmers in central Chiapas of Southern México keep local varieties (landraces) belonging to six races and four race mixtures. Fifteen local varieties are recognized. In spite of widespread adoption of a modern, high yielding variety, maize farmers continue to select local varieties for specific soils and because of agronomic and use criteria. Farmers maintain maize varieties primarily through seed selection. Spatial and temporal separation do not seem sufficient to maintain varieties. The management of improved varieties can lead from a uniform population to a heterogeneous one as hybridization with local maize populations occurs.     

Waves of crown-of-thorns starfish outbreaks —where do they come from?

To explain the southward propagating waves of crown-of-thorns outbreaks on the Great Barrier Reef, it has been proposed that the northern region acts as a seed area for these waves. In this paper we study whether the highly variable current pattern of this region facilitates the start of local outbreaks, making the northern region the seed area or pace-maker of travelling waves of outbreaks. To this end we construct an artificial reef system, which resembles the Great Barrier Reef by having a northern area with a random current pattern, and a central and southern region with a (southward) biased current pattern. Travelling waves running from north to south are observed in the system both with and without a deviant current pattern in the northern area. This demonstrates that travelling waves are an emergent property of the system. The result indicates that the observed waves of crown-of-thorns outbreaks on the Great Barrier Reef do not necessarily imply that there is a seed area in the north.     

Phaseolin-protein Variability in Wild Forms and Landraces of the Common Bean(Phaseolus vulgaris): Evidence for Multiple Centers of Domestication

A sample of 106 wild forms and 99 landraces of common bean (Thaseolus vulgaris) from Middle America and the Andean region of South America were screened for variability in phaseolin seed protein using one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS/PAGE) and two-dimensional isoelectric focusing SDS/PAGE. The Middle American wild forms exhibited phaseolin patterns similar to the ‘S’ pattern described previously in cultivated forms, as well as a wide variety of additional banding patterns—‘M’ (Middle America) types—not encountered among common bean cultivars. The Andean wild forms showed only the ‘T’ phaseolin pattern, also described previously among cultivated forms. Landraces from Middle America showed ‘S’ or ‘S’-like patterns with the exception of 2 lines with ‘T’ phaseolin. In Andean South America, a majority of landraces had the ‘T’ phaseolin. Additional types represented in that region were (in decreasing order of frequency) the ‘S’ and ‘C’ types (already described among cultivated forms) as well as the ‘H’ (Huevo de huanchaco) and ‘A’ (Ayacucho), (new patterns previously undescribed among wild and cultivated beans). In each region—Middle America and Andean South America—the seeds of landraces with ‘T’ phaseolin were significantly larger than those of landraces with ‘S’ phaseolin. No significant differences in seed size were observed among landraces with ‘T,’ ‘C,’ ‘H,’ and ‘A’ phaseolin types of the Andean region. Our data favor 2 primary areas of domestication, one in Middle America leading to small-seeded cultivars with ‘S’ phaseolin patterns and the other in the Andes giving rise to large-seeded cultivars with ‘T’ (and possibly ‘C,’ ‘H,’ and ‘A’) phaseolin patterns.     

Evaluation of genetic variability of sorghum (Sorghum bicolor L. Moench) in northwestern Morocco by ISSR and RAPD markers

The study of the genetic variability of the Moroccan landraces of sorghum constitutes a necessary step that can be exploited in the programs of improvement and valorisation of this marginalized species. The aim of this investigation is to evaluate the variability of sorghum populations and to establish their phylogenetic relations using RAPD and ISSR markers. Sampling was taken in 33 fields of northern regions where this species is most cultivated. Individual plants (398) were collected in 13, 11, 5, and 4 fields of Larache, Tangier, Chefchaouen, and Tetouan, respectively. Thirty-eight RAPD primers and four ISSR primers were used. The percentage of polymorphic fragments revealed with ISSR (98%) is higher than the one revealed with RAPD (85%). The level of the variability obtained through the two techniques is very high. Nevertheless, ISSR markers revealed more diversity than RAPD (0.995+/-0.006 against 0.946+/-0.031). The classification based on Jaccard's similarity index distinguished the totality of fields. Data analysis revealed a genetic structure that is closely related to the micro-geographical repartition of the different fields.     

Swiss Mattenklee landraces,a distinct and diverse genetic resource of red clover (<Emphasis Type="Italic">Trifolium pratense</Emphasis> L.)

Genetic variability within and among 19 landraces and cultivars of red clover ( Trifolium pratense L.) was investigated by means of amplified fragment length polymorphism (AFLP) analysis in order to assess the potential value of Swiss Mattenklee landraces as genetic resources for plant breeding and the preservation of biodiversity. Populations were classified into three groups according to their origin and agronomic features: Mattenklee landraces (8), Mattenklee cultivars (8) and field clover cultivars (3). Analysis of molecular variance based on 276 polymorphic AFLP markers revealed 80% of total variability to be due to variability within populations while 12% were attributed to variability among groups. Stepwise discriminant analysis identified a subset of 126 AFLP markers which best separated individual plants into the three respective groups. Genetic distances between populations were considerably larger among groups than among populations within the same group, providing further evidence for the genetic distinction between Mattenklee landraces, Mattenklee cultivars and field clover cultivars. AFLP markers identified two landrace clusters, containing three and four populations respectively, which, together with one additional landrace, may sufficiently represent the genetic variability of all eight landraces investigated. The results of this study strongly suggest that Swiss Mattenklee landraces form a genetically distinct group of red clover. The data obtained provide criteria on how to efficiently manage, preserve and exploit Mattenklee germplasm.     

Genetic diversity, inter-gene pool introgression and nutritional quality of common beans (Phaseolus vulgaris L.) from Central Africa

The Great Lakes region of Central Africa is a major producer of common beans in Africa. The region is known for high population density and small average farm size. The common bean represents the most important legume crop of the region, grown on over a third of the cultivated land area, and the per capita consumption is among the highest in the world for the food crop. The objective of this study was to evaluate the genetic diversity in a collection of 365 genotypes from the Great Lakes region of Central Africa, including a large group of landraces from Rwanda as well as varieties from primary centers of diversity and from neighboring countries of Central Africa, such as the Democratic Republic of Congo and Uganda, using 30 fluorescently labeled microsatellite markers and automated allele detection. In addition, the landraces were evaluated for their seed iron and zinc concentration to determine if genetic diversity influenced nutritional quality. Principal coordinate and neighbor-joining analyses allowed the separation of the landraces into 132 Andean and 195 Mesoamerican (or Middle American) genotypes with 32 landraces and 6 varieties intermediate between the gene pools and representing inter-gene pool introgression in terms of seed characteristics and alleles. Genetic diversity and the number of alleles were high for the collection, reflecting the preference for a wide range of seed types in the region and no strong commercial class preference, although red, red mottled and brown seeded beans were common. Observed heterozygosity was also high and may be explained by the common practice of maintaining seed and plant mixtures, a coping strategy practiced by Central African farmers to reduce the effects of abiotic and biotic stresses. Finally, nutritional quality differed between the gene pools with respect to seed iron and zinc concentration, while genotypes from the intermediate group were notably high in both minerals. In conclusion, this study has shown that Central African varieties of common bean are a source of wide genetic diversity with variable nutritional quality that can be used in crop improvement programs for the region.     

Genetic variation among Saudi tomato (Solanum lycopersicum L.) landraces studied using SDS-PAGE and SRAP markers

Genetic diversity among seven Saudi tomato landraces collected from different regions of the country was assessed using SDS-PAGE and molecular (sequence-related amplified polymorphism- SRAP) markers. A total of 19 alternative protein bands with different mobility rates were identified within a molecular weight range of 9.584–225?KDa, with 53% polymorphism. Specific protein bands were observed in the “Hail 548” and “Qatif 565” landraces. Genetic similarity based on Jaccard’s coefficient ranged from 0.53 to 1.00, with an average of 0.72. For molecular evaluation, 143 amplicons (fragments) were generated using 27 SRAP primer pair combinations, of which 88 were polymorphic across all the landraces. The PIC values ranged from 0.46 to 0.90, with an average of 0.76. All landraces showed an average of 0.66 similarity coefficient value. The UPGMA dendrogram supported by principal coordinate analysis (PCoA) revealed clusters of the landraces that almost corresponded to their geographical origin. Thus, seed storage protein profiling based on SDS-PAGE and SRAP markers can efficiently be used to assess genetic variability among tomato germplasms. The information obtained in the analysis will be of great interest in the management of ex situ collections for utilization in breeding programs or for direct use in quality markets.     

Patterns of population structure in maize landraces from the Central Valleys of Oaxaca in Mexico

Assessing the impact of farmer management of maize landraces in the Central Valleys of Oaxaca, Mexico is crucial to an understanding of maize evolution, as it was first domesticated there. In this paper, we report on the impact of traditional farmer management of maize populations in this region in structuring molecular diversity and on the population dynamics of maize landraces. These populations, from a sample of local landraces cultivated by farmers in six villages, show little among-population differentiation (Fst=0.011). Most surprisingly, there is no isolation by distance and small among-village differentiation (Fst=0.003). For an outbreeding plant such as maize, one would expect populations to fit Hardy-Weinberg equilibrium, but significant homozygote excess (Fis=0.13) was found. This homozygote excess shows remarkable interpopulation and interlocus differences. We show that this pattern is related to variation in the mean anthesis-silking interval as well as to the flowering range or heterogeneity in flowering of a given population. A short anthesis-silking interval and high level of heterogeneity in flowering precocity will favor assortative mating. This leads to a locus-dependent population substructure giving an unusual case of Wahlund effect and inbreeding while high levels of seed exchange among farmers prevent population differentiation at both village and regional levels.     

Use of short tandem repeat sequences to study Mycobacterium leprae in leprosy patients in Malawi and India

Background

Inadequate understanding of the transmission of Mycobacterium leprae makes it difficult to predict the impact of leprosy control interventions. Genotypic tests that allow tracking of individual bacterial strains would strengthen epidemiological studies and contribute to our understanding of the disease.

Methodology/Principal Findings

Genotyping assays based on variation in the copy number of short tandem repeat sequences were applied to biopsies collected in population-based epidemiological studies of leprosy in northern Malawi, and from members of multi-case households in Hyderabad, India. In the Malawi series, considerable genotypic variability was observed between patients, and also within patients, when isolates were collected at different times or from different tissues. Less within-patient variability was observed when isolates were collected from similar tissues at the same time. Less genotypic variability was noted amongst the closely related Indian patients than in the Malawi series.

Conclusions/Significance

Lineages of M. leprae undergo changes in their pattern of short tandem repeat sequences over time. Genetic divergence is particularly likely between bacilli inhabiting different (e.g., skin and nerve) tissues. Such variability makes short tandem repeat sequences unsuitable as a general tool for population-based strain typing of M. leprae, or for distinguishing relapse from reinfection. Careful use of these markers may provide insights into the development of disease within individuals and for tracking of short transmission chains.     

Genetic diversity in bambara groundnut (Vigna subterranea (L.) Verdc) landraces revealed by AFLP markers.

Bambara groundnut (Vigna subterranea (L.) Verdc), an African indigenous legume, is popular in most parts of Africa. The present study was undertaken to establish genetic relationships among 16 cultivated bambara groundnut landraces using fluorescence-based amplified fragment length polymorphism (AFLP) markers. Seven selective primer combinations generated 504 amplification products, ranging from 50 to 400 bp. Several landrace-specific products were identified that could be effectively used to produce landrace-specific markers for identification purposes. On average, each primer combination generated 72 amplified products that were detectable by an ABI Prism 310 DNA sequencer. The polymorphisms obtained ranged from 68.0 to 98.0%, with an average of 84.0%. The primer pairs M-ACA + P-GCC and M-ACA + P-GGA produced more polymorphic fragments than any other primer pairs and were better at differentiating landraces. The dendrogram generated by the UPGMA (unweighted pair-group method with arithmetic averaging) grouped 16 landraces into 3 clusters, mainly according to their place of collection or geographic origin. DipC1995 and Malawi5 were the most genetically related landraces. AFLP analysis provided sufficient polymorphism to determine the amount of genetic diversity and to establish genetic relationships in bambara groundnut landraces. The results will help in the formulation of marker-assisted breeding in bambara groundnut.