AFLP-Based Analysis of Genetic Diversity, Population Structure, and Relationships with Agronomic Traits in Rice Germplasm from North Region of Iran and World Core Germplasm Set.

Analysis of the genetic diversity and population structure of crops is very important for use in breeding programs and for genetic resources conservation. We analyzed the genetic diversity and population structure of 47 rice genotypes from diverse origins using amplified fragment length polymorphism (AFLP) markers and morphological characters. The 47 genotypes, which were composed of four populations: Iranian native varieties, Iranian improved varieties, International Rice Research Institute (IRRI) rice varieties, and world rice collections, were analyzed using ten primer combinations. A total of 221 scorable bands were produced with an average of 22.1 alleles per pair of primers, of which 120 (54.30%) were polymorphic. The polymorphism information content (PIC) values varied from 0.32 to 0.41 with an average of 0.35. The high percentage of polymorphic bands (%PB) was found to be 64.71 and the resolving power (R p) collections were 63.36. UPGMA clustering based on numerical data from AFLP patterns clustered all 47 genotypes into three large groups. The genetic similarity between individuals ranged from 0.54 to 0.94 with an average of 0.74. Population genetic tree showed that Iranian native cultivars formed far distant cluster from the other populations, which may indicate that these varieties had minimal genetic change over time. Analysis of molecular variance (AMOVA) revealed that the largest proportion of the variation (84%) to be within populations showing the inbreeding nature of rice. Therefore, Iranian native varieties (landraces) may have unique genes, which can be used for future breeding programs and there is a need to conserve this unique diversity. Furthermore, crossing of Iranian genotypes with the genetically distant genotypes in the other three populations may result in useful combinations, which can be used as varieties and/or lines for future rice breeding programs.

Analysis of in situ diversity and population structure in Ethiopian cultivated Sorghum bicolor (L.) landraces using phenotypic traits and SSR markers.

Genetic diversity is a fundamental input for every plant breeding program, genetic resources conservation, and evolutionary studies. In situ diversity and population genetic structure of eight cultivated sorghum landrace populations were investigated in the center of origin, Ethiopia using seven phenotypic traits and 12 highly polymorphic sorghum SSR markers. In farmers' fields, DNA samples were collected using Whatman® plant saver card and quantitative phenotypic traits were measured from 160 individual plant samples belonging to the eight populations representing three diverse geographical regions. High diversity was observed among the various populations for the measured phenotypic traits. The 12 SSR loci produced a total of 123 alleles of which 78 (63.41%) were rare (frequency ≤0.05) with an average of 10.25 alleles per polymorphic locus. The polymorphism information content (PIC) was in the range 0.39-0.85 showing the good discriminatory power of the SSR loci used. Average observed heterozygosity and gene diversity across all populations and loci ranged 0.04-0.33 and 0.41-0.87, respectively. Neighbor-joining and STRUCTURE analyses grouped the 160 samples from the eight populations differently. AMOVA showed 54.44% of the variation to be within populations, 32.76% among populations within regions, and 12.8% among the regions of origin. There was high divergence in the total populations (FST = 0.40) indicating low level of gene flow (Nm = 0.38), but high gene flow was also observed in some adjacent populations. The populations from Wello displayed close relationship with remote Gibe and Metekel populations indicating that the variation followed human migration patterns. Implications of the results for sorghum improvement and germplasm conservation are discussed.

Ecotypic variation for seed dormancy, longevity and germination requirements in wild/weedy Sorghum bicolor in Ethiopia: implications for seed mediated transgene dispersal and persistence.

Seed dispersal is one of the vehicles of gene flow in plants. If a seed carrying transgene(s) is dispersed into the environment, the fate can be determined by its persistence in the soil bank, which can also vary in different ecotypes of a species and the physical environment of the soil including temperature and moisture. This study aimed at investigating ecotypic differences in wild sorghum for dormancy and longevity and their response to varying levels of temperature and moisture for seed germination to aid efforts to predict the potential risk of transgene flow via seeds and persistence in the soil. Wild sorghum seed was collected from different geographical regions in Ethiopia and buried for a maximum of 24 months in the soil. In a separate study, three levels of constant temperature and five levels of osmotic potential (Ψs) were used to investigate variation in wild sorghum ecotypes for seed germination. Viability of buried seeds declined over time, but the rate of decline differed among ecotypes. Better seed longevity was observed at 20 cm soil depth than 10 cm in two wild sorghum ecotypes. Crop seeds depleted within the first six months regardless of the burial depth whereas on the average 1.24% viability was observed in wild sorghum seed after 24 months of burial in the soil. Ecotypic differences were also evident in response to varying temperature and Ψs. Therefore, dispersed seeds carrying crop genes (including transgenes) could persist in the soil for considerable period of time, which may have implications for transgene flow and persistence.

Estimation of in situ mating systems in wild sorghum (Sorghum bicolor (L.) Moench) in Ethiopia using SSR-based progeny array data: implications for the spread of crop genes into the wild.

Because transgenic sorghum (Sorghum bicolor L.) is being developed for Africa, we investigated the potential for transgenes to spread to conspecific wild/weedy sorghum populations in Ethiopia, which is considered the centre of origin of cultivated sorghum. In the current study, the extent of outcrossing, and uniparental and biparental inbreeding were investigated in seven wild/weedy sorghum populations collected at elevations ranging from 631 to 1709 m. Based on allele frequency data of 1120 progenies and 140 maternal plants from five polymorphic microsatellite markers, outcrossing rates were estimated using standard procedures. The average multilocus outcrossing rate was 0.51, with a range of 0.31-0.65 among populations, and the family outcrossing rate was in the extreme range of 0 to 100%. The highest outcrossing (t(m) = 0.65) was recorded in a weedy population that was intermixed with an improved crop variety in Abuare (Wello region). It was also observed that the inbreeding coefficient of the progenies (F(p)) tend to be more than the inbreeding coefficient of both their maternal parents (F(m)) and the level of inbreeding expected at equilibrium (F(eq)), which is a characteristic of predominantly outbreeding species. Biparental inbreeding was evident in all populations and averaged 0.24 (range = 0.10-0.33). The high outcrossing rates of wild/weedy sorghum populations in Ethiopia indicate a high potential for crop genes (including transgenes) to spread within the wild pool. Therefore, effective risk management strategies may be needed if the introgression of transgenes or other crop genes from improved cultivars into wild or weedy populations is deemed to be undesirable.

Assessment of yield stability in sorghum using univariate and multivariate statistical approaches.

The experiment was carried out to estimate GEI in sorghum for grain yield using univariate and multivariate statistical approaches based on two sets of performance trials (T1 and T2). While T1 consisted of 15 genotypes and tested in 8 environments, T2 that consisted of 13 genotypes was carried out in 13 environments. Because the combined ANOVA of each trial revealed significant differences among the genotypes, among the environments and GEI, the five univariate stability estimates: CV(i), S(i)(2), W(i)(2), sigma(i)(2), b(i) and Sd(i)(2) were evaluated for ranking the genotypes. There was positive rank-correlation between CVi and S(i)(2) and among W(i)(2), sigma(i)(2), b(i). Sd(i)(2) had significant positive rank-correlation with sigma(i)(2) and bi in T1 but weak rank-correlation with the remaining parameters in both trials. The three types of univariate stability estimates and the only multivariate stability estimate, the AMMI analysis declared genotypes 2 and 5 to be the most stable in T1, but they gave quite unrelated ranking in T2. Because of the lack of correspondence among the tested stability estimates in the two trials, it was difficult to reach a conclusion on producing genotype recommendation based on the univariate statistical approach. However, as GEI has multivariate nature, the multivariate approach is believed to give more robust inference. Hence, some stable genotypes were suggested using the AMMI model for sorghum growing dry lowlands of the country.