Investigation of the population structure of barley landraces (Hordeum vulgare L.) from different eco-geographical environments in Syria

The population structure of accessions of barley landraces (BLR) (Hordeum vulgare L ssp. vulgare) from Syria was investigated using genetic markers. Barley landraces are old, diverse cultivars of barley which have evolved under cultivation without much directed selection. BLRs have been shown to outperform modern cultivars under low input conditions in Syria due to the level of local adaptation and population buffering (i.e. the ability to compensate the failure of a component by a genetically different component of the same population) based on a high level of diversity within landraces.The purpose of the present study was to identify suitable genetic markers, to use these to characterise the population structure and diversity of barley landraces, and to investigate how population structure is influenced by environmental conditions. Results were compared with those achieved for accessions of wild barley (Hordeumvulgare ssp. spontaneum C. Koch) and modern cultivars in order to investigate the influence of domestication and cultivation on mating system and population structure. Implications of the results for breeding strategies in low input agriculture and for conservation strategies were investigated.wo recent accessions of wild barley and 15 recent accessions of BLRs were available from Syria, where landraces are still under cultivation. Seven earlier accessions of the same landraces from Syria were available from gene banks. Modern cultivars and progeny of known pedigree were available from barley breeders. Genetic indices of accessions were analysed using three contrasting types of genetic markers, morphological, isoenzyme and molecular markers, respectively. Standard methods of population genetics were used to analyse the population structure of accessions. Environmental conditions of the sampling sites were analysed using the geographical information system ArcView.Results showed that BLRs are predominantly inbreeding populations with a low outcrossing rate of 1.7%. The same outcrossing rate has been reported for wild barley, so that it can be assumed that domestication has not influenced the outcrossing rate. Recently collected BLRs showed a high level of diversity and a regionally localised and geographically variable population structure. Harsh environmental conditions seem to increase diversity of BLRs. Genetic diversity may have been lost through the process of domestication. More diversity was found within populations of wild barley, while BLRs showed a higher proportion of diversity between accessions, for two of the three molecular markers used. Little diversity was found between modern cultivars, and no diversity within them. This may imply that modern breeding methods have led to a loss of diversity in the current gene pool. Gene flow between accessions within regions was high, but low between more distant regions, implying little seed exchange between farmers in different regions. However, it seemed that intensive extension work may lead to increased seed exchange over long distances and thus may decrease the level of local adaptations. Finally, a dramatic loss of genetic diversity of BLR accessions was found with increasing storage time in ex situ gene banks, suggesting the presence of genetic bottlenecks associated with the rejuvenation of ageing seeds accessions. Genetic diversity levels of recently collected BLRs support the implementation of in situ conservation strategies

A user-friendly database for Participatory Plant Breeding programs

In a decentralized and participatory plant breeding (PPB) program, in contrast to conventional plant breeding, farmers select from a large number of genotypes over a number of cycles in several locations. As selection is for location-specific adaptation a PPB program based on, for example, four stages of selection, generates large, unbalanced data sets. With common spreadsheet software it is not possible, or it is at least very cumbersome to extract all the information, particularly the one that is related to genotype x environment (GE) interactions. Therefore, there is a need for an information system that makes it as easy as possible to retrieve and compare data over all given factors in the PPB-program. Due to a lack of education and financial resources in developing countries, the use of existing databases was not an option because of their complexity and/or price. We have built a simple, free and user-friendly database that allows to store, retrieve and analyze the plant breeding data. The database is implemented using the Java based HyperSQL Database Engine (HSQLDB) in the package of Open Office with links to the input formats of Genstat and GGEbiPlot. The proposed database is capable of managing the following data in a PPBprogram for barley: (I) trial data for any trial or field design (II) field data for any given trait (III) results from statistical analyses (IV) farmers selection individually or in groups

Genetic variability among landraces of sesame in Ethiopia

Sesame ( Sesamum indicum d 46.4% for landraces and cultivars, respectively, indicates that both landraces and cultivars are line mixtures and segregants of past outcrossing results. A Neighbour-Joining dendrogram based on Modified Rogers' Distances (MRD) and a principal coordinate analysis based on a simple dissimilarity matrix, points towards some grouping based on geographical origin. The established SSR markers will be very useful for further diversity analyses among a large landrace collection of Ethiopian sesame and in the establishment of a core collection. Moreover, existence of great genetic variability between the landraces is a good starting point of sesame crop improvement programs in Ethiopia.La S\ue9same ( Sesamum indicum L.) est une culture \ue0 huile anciennement d\ue9nom\ue9e "Reine de graines ol\ue9agineuses"lus petite que la divergence g\ue9n\ue9tique parmi les populations. Un croisement h\ue9t\ue9rog\ue8ne \ue9lev\ue9 de 45 et 46.4 % pour les races locales et les cultivars, respectivement, indique que les races locales et les cultivars sont des lign\ue9es mixtes et s\ue9gr\ue9gants des r\ue9sultats des croisements h\ue9t\ue9rog\ue8nes pass\ue9s. Un dendogramme d\ue9velopp\ue9 sur base des Distances modifi\ue9es de Rogers (DMR) et l'analyse de principales coordonn\ue9es bas\ue9e sur une simple dissemblance matricielle montrent quelques groupements sur base de l'origine g\ue9ographique. Les marqueurs (SSR) \ue9tablis seront tr\ue8s utiles pour d'autres analyses de diversit\ue9 au sein d' une large collection de races locales de s\ue9sames ethiopiennes et dans l'\ue9tablissement d'une collection de base. En plus, l'existence d'une grande variabilit\ue9 g\ue9n\ue9tique entre les races locales est un bon point de d\ue9part pour des programmes d'am\ue9lioration de la cultutre de s\ue9same en Ethiopie

Patterns of molecular and phenotypic diversity in pearl millet [Pennisetum glaucum (L.) R. Br.] from West and Central Africa and their relation to geographical and environmental parameters

<p>Abstract</p> <p>Background</p> <p>The distribution area of pearl millet in West and Central Africa (WCA) harbours a wide range of climatic and environmental conditions as well as diverse farmer preferences and pearl millet utilization habits which have the potential to lead to local adaptation and thereby to population structure. The objectives of our research were to (i) assess the geographical distribution of genetic diversity in pearl millet inbreds derived from landraces, (ii) assess the population structure of pearl millet from WCA, and (iii) identify those geographical parameters and environmental factors from the location at which landraces were sampled, as well as those phenotypic traits that may have affected or led to this population structure. Our study was based on a set of 145 inbred lines derived from 122 different pearl millet landraces from WCA.</p> <p>Results</p> <p>Five sub-groups were detected within the entire germplasm set by STRUCTURE. We observed that the phenotypic traits flowering time, relative response to photoperiod, and panicle length were significantly associated with population structure but not the environmental factors which are expected to influence these traits in natural populations such as latitude, temperature, or precipitation.</p> <p>Conclusions</p> <p>Our results suggested that for pearl millet natural selection is compared to artificial selection less important in shaping populations.</p

Investigation of recent population bottlenecks in Kenyan wild sorghum populations (Sorghum bicolor (L.) Moench ssp. verticilliflorum (Steud.) De Wet) based on microsatellite diversity and genetic disequilibria

Identifying populations that have recently suffered a severe reduction in size is particularly important for their conservation as they are likely to suffer an increased risk of genetic erosion. We investigated the presence of recent bottlenecks in two wild sorghum populations from different eco-geographical conditions in Kenya employing 18 microsatellite markers. Microsatellite analysis showed high allelic diversity in the two populations, with a mean of 4.11 and 6.94 alleles per locus in the North-West wild sorghum population (NWWSP) and the South-East wild sorghum population (SEWSP), respectively. The mean observed heterozygosity was 0.34 and 0.56 in NWWSP and SEWSP, respectively. A large long-term effective populations size for both populations was observed assuming either an infinite allele model or a stepwise mutation model. There was no apparent loss of genetic variability for either of the populations. Test of heterozygosity excess indicated that a recent bottleneck in the two populations is highly unlikely. Furthermore, analysis of the allele frequency distribution revealed an L-shaped distribution which would not have been observed in case a recent bottleneck had reduced genetic variability in the two populations. The fact that most loci displayed a significant heterozygosity deficiency could be explained by population subdivision and the mixed mating system exhibited by wild sorghum populations. Furthermore, the possibility of a historical expansion of wild sorghum populations and presence of null alleles could not be ruled out

Getting the Most Out of Sorghum Low-Input Field Trials in West Africa Using Spatial Adjustment

Breeding sorghum for low-input conditions is hindered by soil heterogeneity. Spatial adjustment using mixed models can help account for this variation and increase precision of low-input field trials. Large small-scale spatial variation (CV 39.4 %) for plant available phosphorus was mapped in an intensely sampled low-input field. Spatial adjustments were shown to account for residual yield differences because of this and other growth factors. To investigate the potential of such models to increase the efficiency of low- and high-input field trials, 17 experiments with 70 sorghum genotypes conducted in Mali, West Africa, were analysed for grain yield using different mixed models including models with autoregressive spatial correlation terms. Spatial models (AR1, AR2) improved broad sense heritability estimates for grain yield, averaging gains of 10 and 6 % points relative to randomized complete block (RCB) and lattice models, respectively. The heritability estimate gains were even higher under low phosphorus conditions and in two-replicate analyses. No specific model was best for all environments. A single spatial model, AR1 × AR1, captured most of the gains for heritability and relative efficiency provided by the best model identified for each environment using Akaike's Information Criterion. Spatial modelling resulted in important changes in genotype ranking for grain yield. Thus, the use of spatial models was shown to have potentially important consequences for aiding effective sorghum selection in West Africa, particularly under low-input conditions and for trials with fewer replications. Thus, using spatial models can improve the resource allocation of a breeding program. Furthermore, our results show that good experimental design with optimal placement and orientation of blocks is essential for efficient statistical analysis with or without spatial adjustment

Impact of farmers’ practices and seed systems on the genetic structure of common sorghum varieties in Kenya and Sudan

To understand the effect of different farming systems on the dynamics of diversity of sorghum (Sorghum bicolor (L.) Moench) crop, genetic structure of widely used landraces and modern varieties collected from two contrasting agroecosystems, in eastern Sudan and western Kenya, were analysed with 16 polymorphic microsatellite markers. A total of 1104 accessions, grouped into 46 samples from individual farmers, were genotyped. Cluster analysis of the samples from the two countries displayed contrasting patterns. Most strikingly, differently named landraces from western Kenya formed widely overlapping clusters, indicating weak genetic differentiation, while those from eastern Sudan formed clearly distinguishable groups. Similarly, samples of the modern variety from Sudan displayed high homogeneity, whereas the most common modern variety from western Kenya was very heterogeneous. The high degree of fragmentation of farmlands of western Kenya, coupled with planting of different sorghum varieties in the same fields, increases the likelihood of inter-variety gene flow. This may explain the low genetic differentiation between the differently named landraces and heterogeneity of the modern variety from western Kenya. This study highlights the important role of farmers in shaping the genetic variation of their crops and provides population parameter estimates allowing forecasting of the fate of ‘modern’ germplasm (conventional or genetically modified) when introduced into subsistence farming systems

Genetic diversity and linkage disequilibrium of two homologous genes to maize D8: sorghum SbD8 and pearl millet PgD8

Yield and yield stability of sorghum [Sorghum bicolor (L.) Moench.] and pearl millet [Pennisetum glaucum (L.) R.Br.] are highly influenced by flowering time and photoperiodic sensitivity in the arid to semi-arid regions of West and Central Africa. Photoperiodic sensitivity is the key adaptation trait of local landraces because it assures flowering at the end of the rainy season, independent of variable dates of planting. Flowering time genes are mainly integrated into four pathways with close interaction among each other: Vernalization, autonomous, GA (gibberellic acid) and photoperiod. In the GA pathway, maize D8, wheat RHT1 and rice SLR have been identified as homologous genes to the Arabidopsis GAI, which is a negative regulator of GA response. We have identified two homologous genes to D8: Sorghum SbD8 and pearl millet PgD8. These genes were expressed in the root and leaves of sorghum and pearl millet as revealed by EST database search and reverse transcription PCR, respectively. The genetic diversity of SbD8 was considerably lower than that of PgD8. The extent of linkage disequilibrium in PgD8 is lower than that of maize D8. SbD8 and PgD8 polymorphisms might be appropriate for dissection of photoperiod sensitivity using association mapping approaches