A drought stress panel composed of diverse accessions selected from upland, aerobic, rainfed lowland and irrigated lowland environments, was assembled to serve as germplasm for aerobic adaptation breeding. Aerobic rice requires significant levels of tolerance to drought stress due to intermittent water deficit and high soil impedance caused by aerobic conditions. Genomic information may be utilized to investigate the nature of the panel to guide varietal improvement. Using 153 simple sequence repeat and 384 single nucleotide polymorphism markers, the aim of the study was to compare the allelic properties of the two marker types, infer population structure of the panel, and estimate kinship among the accessions. There was a general agreement between the results derived from the two marker types. Marker alleles were found to occur at low frequencies, as the panel was composed mostly of improved accessions with some landraces. The panel clustered into japonica (JA), aus (AU), upland-adapted indica (UL) and lowland-adapted indica (LL) subpopulations. The AU and JA subpopulations were more divergent from the rest of the subpopulations than were the LL and UL subpopulations. Average marker-based kinship for related accessions was less than 0.20, indicating a low degree of genetic relatedness in the panel. Within the LL and UL subpopulations, the low levels of kinship imply that there is still much genetic gain to be expected from utilizing the accessions in breeding. Thus, an understanding of the genetic variation in the panel suggests focusing on improving the mean in the short term, and tapping into the exotic alleles from the AU and JA subpopulations when genetic gain declines.

Local upland rice germplasm is an invaluable resource for farmers who grow rice on acidic soils without flooding that benefits wetland rice. In this study, we evaluated the adaptation to soil acidity in common local upland rice varieties from an area with acidic soil in Thailand. Tolerance to hydrogen and aluminium (Al) toxicity was determined by measuring root growth, plant dry weight and phosphorus (P) uptake in aerated solution culture without the supplementation of Al (0 mg/l) at pH 7 and 4 and with the supplementation of 10, 20 and 30 mg Al/l at pH 4. The root growth of upland rice plants grown from farmers' seed was depressed less by Al than that of common wetland rice varieties. Pure-line genotypes of upland rice varieties were differentiated into several classes of Al tolerance, with frequency distribution of the classes that sometimes differed between the accessions of the same varieties. The effect of Al tolerance on root length was closely correlated with depression by Al in root dry weight and whole-plant P content. A source for adaptation to soil acidity for exploitation in the genetic improvement of aerobic and rainfed rice is clearly found among local upland rice varieties grown on acidic soils. However, the variation in tolerance to soil acidity within and among the seed lots of the same varieties maintained by individual farmers as well as among the varieties needs to be taken into consideration.

Cultivated soybeans [Glycinemax (L.) Merr.] have various flower colours such as dark purple, purple, light purple, pink, magenta, near white and white. About one-third of the soybean accessions in the United States Department of Agriculture – Germplasm Resource Information Network (USDA-GRIN) Soybean Germplasm Collections have white flowers and are the second dominant accessions after the purple-flowered accessions. Earlier studies have shown that the w1 recessive allele of the W1 gene encoding flavonoid 3′,5′-hydroxylase produces white flowers. In the present study, we aimed to understand why the white-flowered accessions have become abundant among the cultivated soybeans and what their genetic and regional origin is. For this purpose, 99 landraces with white flowers and 39 landraces with purple flowers from eight Asian countries and Russia were analysed with regard to the nucleotide sequences of the W1 locus. We not only found that the w1 alleles of the 99 white-flowered landraces were identical to those of the white-flowered Williams 82, but also found that these w1 alleles displayed no polymorphism at all. By carrying out a phylogenetic analysis, we were able to identify a group with W1 alleles from which the w1 allele might have diverged.

Cultivars of Miscanthus used as bioenergy crops or tested in trials are largely clonally propagated, wild sourced genotypes or clonally propagated F1 hybrids. One of the most productive taxa is the sterile triploid M. × giganteus. Little domestication or breeding has been undertaken and there is huge potential to utilize the extensive genetic resources of the genus for crop improvement. The challenge is to generate new highly adapted genotypes suitable for a range of environments. Production on marginal land, not used for food crops, is particularly desirable, but presents many barriers to crop breeders, as these are largely unproductive and/or stressful environments. This article outlines progress made in characterizing natural genetic variation in Miscanthus including next-generation single-nucleotide polymorphism genotyping, quantitative trait locus analysis and association mapping. It also explains how this knowledge is being used to develop novel genotypes suited for growth in a broad range of agricultural and marginal lands by defining breeding pools, generating novel crosses, manipulating polyploidy and applying genomic selection approaches.

In Uruguay, onion (Allium cepa L.) germplasm is mainly derived from the genetic material introduced by several waves of European immigrants and subsequently multiplied by household farmers, resulting in a wealth of locally adapted populations. This study examined the genetic diversity in a collection of 27 local onion populations and two cultivars derived from them. A total of 843 onion plants were fingerprinted, and 83 inter-simple sequence repeat polymorphic bands were generated. Analysis of molecular variance showed high diversity within the populations (66% of the total variation). Some short-day populations from different geographical origins were grouped together by the unweighted pair-group method using arithmetic averages, principal coordinate analysis and cluster analysis, while the more extensively sampled long- and intermediate-day populations showed a widespread distribution, with no significant subgrouping among them. This weakly structured gene pool is probably the consequence of seed and bulb exchange between farmers and natural inter-pollination. Nevertheless, a Bayesian analysis allowed the distinction of four genetic backgrounds of alleles in the whole collection, and populations were predominately assigned to each genetic background. In addition, mitochondrial variants determining normal (N) pollen fertility or the sterile S or T types were analysed for the same set of plants using specific primers. Most accessions showed a proportion of male-sterile individuals. Cytoplasm type T was the most represented (26 out of 29 accessions), and cytoplasm type S was found in a low proportion of individuals in seven populations. Uruguayan onion germplasm maintains a low degree of genetic differentiation despite the small cultivated area and intense seed exchange, probably due in part to different market purposes based on the growing cycle.

The genebank at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India holds a collection of 542 accessions from the Caribbean and Central American (CCA) regions, of which 424 were evaluated for eight qualitative and 17 quantitative traits at ICRISAT farm. A hierarchical cluster analysis was performed using the scores of the first nine principal components that resulted in four clusters. The accessions of these four clusters exhibited the following good characteristics: cluster 1 had high pod-bearing length and high seed protein content; those of cluster 2 had high degree of branching, large number of pods per plant and high seed yield per plant; those of cluster 3 had long pods; and those of cluster 4 had larger seeds. In the whole collection of accessions, diversity was found to be maximum (H′ = 0.630+0.026) for plant height and minimum for tertiary branches per plant (H′ = 0.259+0.026). The highest correlation coefficient was observed between racemes per plant and pods per plant (r= 0.914) followed by between pods per plant and seed yield per plant (r= 0.744), and between shelling percentage and the harvest index (r= 0.703). In view of the poor representation of the world collection of pigeonpea (13,771 accessions) from the CCA regions, launching of collection missions in these countries has been suggested to fill gaps and increase the variability. Multi-location evaluation of the collections for agronomic traits at potential locations in the CCA regions and systematic evaluation for nutritional traits and resistance to biotic and abiotic stress could result in the identification of useful genotypes, particularly vegetable types, for use in breeding programmes to develop high-yielding cultivars as well as to release as varieties in these regions.

Understanding of genetic diversity and its distribution is essential for promoting the use of genetic resources. The development of core collections using molecular tools has been proposed as a strategy for increasing the economical use and conservation of genetic resources. In this study, we investigated the genetic variation among different geographical origins and potential entries that constituted a core collection of oil palm, using 29 microsatellite markers and by evaluating 788 oil palm accessions. Our results revealed important genetic diversity (HT= 0.759) between oil palm accessions from Angola and Cameroon, which exhibited a low coefficient of genetic differentiation between populations (GST= 0.022). However, the inclusion of oil palm accessions from Indonesia in the analysis resulted in a high coefficient of genetic differentiation between populations (GST= 0.251). We found that the combination of stratified sampling based on a sorting method and a heuristic algorithm was the most effective method for the development of an oil palm core collection set. Using this method, two core collections were identified. The first core collection, comprising 289 entries, contained 271 retained alleles in a sample representing 37% of the entire collection. The second one is a mini core collection, comprising 91 entries, that contained 271 retained alleles with a total He value of 0.72 in a sample representing 11% of the entire collection. The information reported in this study will be of great interest to oil palm researchers because new strategies for breeding programmes can be developed based on these advances.

The aim of the study was to develop the system of polymerase chain reaction (PCR)-based markers for the assessment of genetic diversity and population genetic studies of Gentiana lutea L. as well as to determine the utility of two indices of marker informativeness. The informativeness was determined for 40 PCR primers of different types (random amplified polymorphic DNA, inter simple sequence repeat, inter-retrotransposon amplified polymorphism, resistance gene analog polymorphism and conserved DNA-derived polymorphism markers) by evaluating discriminating power (DL) and resolving power (Rp) in a sample of 30 plants from two populations. Analysis of correlation between the index value and the number of differentiated pairs of genotypes in the given sample revealed that DL is more efficient than Rp; therefore, we selected primers based on the DL value. In total, 12 primers with the largest values of DL were chosen. Analysis of genetic relationship among 86 plants from six populations showed that the number of bands produced by the three of selected primers was sufficient to give average bootstrap support across six key nodes in the dendrogram higher than 85%, while using six of the primers resulted in average bootstrap value exceeding 99%. Thus, a minimal set of three to six selected primers are sufficient for a quick assessment of genetic diversity of G. lutea populations, depending on the sample size and degree of differentiation between populations, while the rest of the primers with DL values above 0.8 may be used for ecogenetic surveys. Preliminary results obtained with selected primers indicate the moderate level of genetic variation within the species and significant differentiation among individual populations.

Since the immediate wild relatives of Sorghum bicolor (L.) Moench are indigenous to Ethiopia, studying their population biology is timely for undertaking conservation measures. A study was conducted to investigate the occurrence of population bottlenecks and to estimate the long-term effective population size (Ne) in wild relatives of sorghum. For this, 40 samples of wild sorghum were collected from two remotely located populations that were allopatric to the cultivated sorghum. The presence of bottlenecks was investigated using heterozygosity excess/deficiency, mode shift and allelic diversity based on nine polymorphic simple sequence repeat (SSR) loci. We also estimated the Ne of the studied populations using two different methods employing SSR mutation models. The expected heterozygosity was found to be 0.41 and 0.71 and allelic richness was 3.0 and 4.9, in Awash and Gibe populations, respectively. Neither the heterozygosity excess nor the mode-shift methods detected signatures of bottlenecks in the studied populations. The effective size of the two wild sorghum populations studied also showed no risk of population reduction in these regions of Ethiopia. Therefore, these allopatric wild sorghum populations can survive by occupying patches by the roadsides and fences, areas within abandoned farm lands, forests, etc., which shows that their wild characteristics of adaptation have been adequate for them to survive from extinction despite extensive deforestation of their habitat for modern agriculture and frequent grazing by livestock. However, this does not guarantee the survival of these species for the future and ex situ conservation measures or policies could help maintain their diversity.

Core collections are the integral part of biotechnology-aided modern-day crop improvement programmes and utilized for a variety of applications including conventional plant breeding, association mapping, resequencing, among others. Since their advent, determination of core collection size has been based on the size of the whole collection. In this study, we precisely estimated the size of the core collection based on the diversity of the whole collection using the Similarity Elimination method. For each of the elimination cycle, allele retention and pairwise and mean genetic distances were calculated and used as the criteria for the precise estimation of the core collection size. We sampled a coconut core collection with 266 entries by retaining the diversity of the whole collection. During the elimination process, accessions with very rare alleles were eliminated first when compared with those having rare and common alleles. Therefore, our results support the hypothesis that the less frequent alleles seldom contribute to the genetic distance when compared with common alleles. In conclusion, presize can be efficiently utilized in any crop for the precise estimation of core collection size.

Microsatellite markers specific to Cheirostylis yunnanensis Rolfe were developed using an enriched genomic DNA library technique. The library was constructed using (AG)20 and (CAG)20 oligonucleotide repeats. A total of 48 primer pairs were designed and tested with 48 C. yunnanensis Rolfe samples, resulting in 11 polymorphic loci. The number of alleles per locus ranged from 2 to 12, with an average of six alleles. The observed and expected heterozygosity ranged from 0.0426 to 0.8085 and 0.0421 to 0.9078, respectively. Of the 11 polymorphic loci, three showed a significant deviation from Hardy–Weinberg equilibrium and one exhibited linkage disequilibrium. Cross-species amplification was tested with five samples of Cheirostylis of unknown species resulting in eight loci that could be amplified, with the number of alleles ranging from one to two. The microsatellite markers developed in this study will be useful for the genetic analysis of C. yunnanensis in order to differentiate species as well as to establish a conservation plan for this species.