Heiko K. Parzies

Estimating the outcrossing rate of barley landraces and wild barley populations collected from ecologically different regions of Jordan

The results of previous studies conducted at the University of Hohenheim and the International Center for Agricultural Research in the Dry Areas (ICARDA) indicated that the yielding ability and stability of barley (Hordeum vulgare L.) could be improved in environments with drought stress by increasing the level of heterozygosity. This would require increasing the outbreeding rate of locally adapted breeding materials. As a first step, we estimated the outcrossing rate of 12 barley landraces (Hordeum vulgare ssp. vulgare, in short H. vulgare) and 13 sympatrically occurring populations of its wild progenitor [Hordeum vulgare ssp. spontaneum (C. Koch), in short H. spontaneum] collected from semi-arid localities in Jordan during the 1999/2000 growing season. In each H. vulgare or H. spontaneum population 28–48 spikes were sampled, and up to six offspring (seeds) per spike (called a family) were used for PCR analyses. Collection sites covered high–low transects for rainfall and altitude in order to detect possible environmental effects on the outcrossing rate. Four microsatellite markers located on different chromosomes were used to genotype the samples for estimating the outcrossing rate. Low season-specific multilocus outcrossing rates (tm) were found in both cultivated and wild barley, ranging among populations from 0–1.8% with a mean of 0.34%. Outcrossing rates based on inbreeding equilibrium (te), indicating outcrossing averaged across years, were two- to threefold higher than the season-specific estimates. Under high rainfall conditions somewhat higher—though not significantly higher—outcrossing rates were observed in H. spontaneum than in H. vulgare. The season-specific outcrossing rate in H. spontaneum was positively correlated (r=0.67, P=0.01) with average annual precipitation and negatively correlated (r=0.59, P=0.05) with monthly average temperature during flowering. The results suggest that outcrossing may vary considerably among seasons and that high precipitation and cool temperatures during flowering tend to enhance outcrossing. The rather low levels of outcrossing detected indicate that increased vigour due to heterozygosity has not been a major fitness advantage in the evolution and domestication of H. spontaneum and H. vulgare, respectively. Stable seed production to secure survival under extreme heat and drought stress may have been more important. Cleistogamy may be considered as an effective mechanism to warrant pollination even in drought-stunted plants with non-extruding spikes.

Ecogeographical distribution of wild, weedy and cultivated Sorghum bicolor (L.) Moench in Kenya: implications for conservation and crop-to-wild gene flow

The potential gene flow between a crop and its wild relatives is largely determined by the overlaps in their ecological and geographical distributions. Ecogeographical databases are therefore indispensable tools for the sustainable management of genetic resources. In order to expand our knowledge of Sorghum bicolor distribution in Kenya, we conducted in situ collections of wild, weedy and cultivated sorghum. Qualitative and quantitative morphological traits were measured for each sampled wild sorghum plant. Farmers’ knowledge relating to the management of sorghum varieties and autecology of wild sorghum was also obtained. Cluster analysis supports the existence of several wild sorghum morphotypes that might correspond to at least three of the five ecotypes recognized in Africa. Intermediate forms between wild and cultivated sorghum belonging to the S. bicolor ssp. drummondii are frequently found in predominantly sorghum growing areas. Crop-wild gene flow in sorghum is likely to occur in many agroecosystems of Kenya.

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

BackgroundThe 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.ResultsFive 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.ConclusionsOur results suggested that for pearl millet natural selection is compared to artificial selection less important in shaping populations.

Inferring seed exchange between farmers from population genetic structure of barley landrace Arabi Aswad from Northern Syria

Apart from their significance in genetic conservation, barley landraces are still favoured by local farmers in low-input farming systems. They often perform more predictably under adverse conditions than modern cultivars due to local adaptation. Increased seed exchange between farmers may put adaptation of local populations of barley landraces at risk. Isozyme markers were used to investigate differentiation and infer gene flow between local populations of barley landrace Arabi Aswad in Northern Syria. Inferred gene flow decreased exponentially with geographic distance and may imply that seed exchange between farmers is limited to a regional scale and diminishes over longer distance. Gene flow seems to be a suitable index for estimating seed exchange in highly inbreeding crop species such as barley. In the future, improved mobility of farmers and extension work may facilitate seed exchange over longer distances, and consequently jeopardise preservation of locally adapted landraces in barley.

Wild sorghum from different eco-geographic regions of Kenya display a mixed mating system

Knowledge of mating systems is required in order to understand the genetic composition and evolutionary potential of plant populations. Outcrossing in a population may co-vary with the ecological and historical factors influencing it. However, literature on the outcrossing rate is limited in terms of wild sorghum species coverage and eco-geographic reference. This study investigated the outcrossing rates in wild sorghum populations from different ecological conditions of Kenya. Twelve wild sorghum populations were collected in four sorghum growing regions. Twenty-four individuals per population were genotyped using six polymorphic simple sequence repeat (SSR) markers to compute their indirect equilibrium estimates of outcrossing rate as well as population structure. In addition, the 12 populations were planted in a field in a randomised block design with five replications. Their progeny (250 individuals per population) were genotyped with the six SSR markers to estimate multi-locus outcrossing rates. Equilibrium estimates of outcrossing rates ranged from 7.0 to 75.0%, while multi-locus outcrossing rates (tm) ranged from 8.9 to 70.0% with a mean of 49.7%, indicating that wild sorghum exhibits a mixed mating system. The wide range of estimated outcrossing rates in wild sorghum populations indicate that environmental conditions may exist under which fitness is favoured by outcrossing and others under which selfing is more advantageous. The genetic structure of the populations studied is concordant with that expected for a species displaying mixed mating system.

Assessing genetic diversity, allelic richness and genetic relationship among races in ICRISAT foxtail millet core collection

Foxtail millet (Setaria italica (L.) P. Beauv.) is an ideal crop for changing climate and food habits of peoples due to its short duration, high photosynthetic efficiency, nutritional richness and fair resistance to pest and diseases. However, foxtail millet yields are low mainly due to the lack of effort for its improvement and the lack of proper utilization of existing genetic variability. To enhance the use of diverse germplasm in breeding programmes, a core collection in foxtail millet consisting of 155 accessions was established. Core collection accessions were fingerprinted using 84 markers (81 simple sequence repeats (SSRs) and three Expressed Sequence Tag (EST)-SSRs). Our results showed the presence of greater molecular diversity in the foxtail millet core collection. The 84 markers detected a total of 1356 alleles with an average of 16.14 alleles (4–35) per locus. Of these, 368 were rare alleles, 906 common alleles and 82 the most frequent alleles. Sixty-one unique alleles that were specific to a particular accession and useful for germplasm identification were also detected. In this study, the genetic diversity of foxtail millet was fairly correlated well with racial classification, and the race Indica showed a greater genetic distance from the races Maxima and Moharia. The pairwise estimate of dissimilarity was >0.50 except in 123 out of 11,935 pairs which indicated a greater genetic variability. Two hundred and fifty pairs of genetically most diverse accessions were identified. This large molecular variation observed in the core collection could be utilized effectively by breeders or researchers for the selection of diverse parents for breeding cultivars and the development of mapping populations.

Association analysis of photoperiodic flowering time genes in west and central African sorghum [Sorghum bicolor (L.) Moench].

BackgroundPhotoperiod-sensitive flowering is a key adaptive trait for sorghum (Sorghum bicolor) in West and Central Africa. In this study we performed an association analysis to investigate the effect of polymorphisms within the genes putatively related to variation in flowering time on photoperiod-sensitive flowering in sorghum. For this purpose a genetically characterized panel of 219 sorghum accessions from West and Central Africa was evaluated for their photoperiod response index (PRI) based on two sowing dates under field conditions.ResultsSorghum accessions used in our study were genotyped for single nucleotide polymorphisms (SNPs) in six genes putatively involved in the photoperiodic control of flowering time. Applying a mixed model approach and previously-determined population structure parameters to these candidate genes, we found significant associations between several SNPs with PRI for the genes CRYPTOCHROME 1 (CRY1-b1) and GIGANTEA (GI).ConclusionsThe negative values of Tajimas D, found for the genes of our study, suggested that purifying selection has acted on genes involved in photoperiodic control of flowering time in sorghum. The SNP markers of our study that showed significant associations with PRI can be used to create functional markers to serve as important tools for marker-assisted selection of photoperiod-sensitive cultivars in sorghum.

Population structure in sorghum accessions from West Africa differing in race and maturity class

Accounting for population structure to minimize spurious associations in association analyses is of crucial importance. With sorghum genomic sequence information being available, there is a growing interest in performing such association studies for a number of important agronomic traits using a candidate gene approach. The aims of our study were to conduct a systematic survey of molecular genetic diversity and analyze the population structure in cultivated sorghum [Sorghum bicolor (L.) Moench] accessions from West Africa. Our analysis included 219 West African cultivated sorghum accessions with differing maturity intended for a marker-trait association study. A total of 27 SSRs were used, which resulted in detection of 513 alleles. Genetic diversity estimates for the accessions were found to be high. The accessions were divided into two subgroups using a model-based approach. Our findings partly agree with previous studies in that the guinea race accessions could be distinguished clearly from other accessions included in the analysis. Race and geographical origin of the accessions may be responsible for the structure we observed in our material. The extent of linkage disequilibrium for all combinations of SSRs was in agreement with expectations based on the mating system.

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 of a Parasitic Weed, Striga hermonthica, on Sorghum and Pearl Millet in Mali

Eleven populations of witchweed, Striga hermonthica, were collected in four regions of Mali and investigated with 12 microsatellite markers. Extensive genetic diversity was observed, with most plants heterozygous for most markers. Allelic diversity was broadly distributed across populations with little genetic differentiation and large amounts of gene flow. Nearby fields of pearl millet and sorghum were found to have indistinguishable witchweed populations. Some population structure was apparent, but did not correlate with the local environment or host genotype, suggesting that seed transportation or other human-driven variables act to differentiate central Malian S. hermonthica populations from southern Malian populations.