Germplasm lines with resistance to the sugarbeet root maggot (SBRM) have been developed and released to the public, providing a means to generate hybrids with resistance against the most devastating insect pest of sugarbeet in North America. Effective use of this germplasm, however, requires knowledge of relative strengths of SBRM resistance between lines and knowledge of the diversity and genetic relationships between germplasm. Therefore, field studies comparing SBRM resistance of four released SBRM-resistant germplasm lines (F1015, F1016, F1024 and F1043), a SBRM-resistant parent (PI 179180) and an unreleased SBRM-resistant population (F1055) were performed, and genetic analysis of the diversity and relationships between SBRM-resistant germplasm and their available parents was conducted using simple sequence repeat (SSR) markers. Under natural SBRM infestations, resistant germplasm exhibited significantly less SBRM damage than a susceptible control, with similar, high levels of resistance in F1016, F1024, F1043, F1055 and PI 179180 and lower resistance in F1015. SSR analysis revealed genetic similarities between F1016, F1024 and F1055, while F1015 and F1043 were genetically distinct from these lines. Among resistant genotypes, F1015 and F1043 exhibited greatest and least within-line genetic diversity, indicating greater and lesser inbreeding for F1043 and F1015, respectively. Similarities in damage ratings and genetics for F1016, F1024 and F1055 indicate that these lines are likely to be equally effective at introducing SBRM resistance into elite populations and in combining ability. In contrast, F1043, with its unique parentage and genetic dissimilarity from other resistant lines, provides a genetically distinct, but similarly effective, source of SBRM resistance.

Shortawn foxtail (Alopecurus aequalis Sobol.) is an invasive and highly troublesome weed species originating from North America that has become widespread across China. Since its proliferation seriously threatens crop production worldwide, understanding its genetic diversity is critical for developing a forecasting system for integrated pest management plans. To accelerate the application of molecular markers in A. aequalis, this study aimed to develop a set of expressed sequence tag-simple sequence repeat (SSR) markers using previous high-throughput sequencing data. In this study, a total of 1411 SSR loci were identified from 95,479 unigenes. Tri-nucleotide repeat motifs were the most abundant type with a frequency of 66.27%, followed by di- (24.95%) and tetra-nucleotide (8.78%). Among the loci, 584 primer pairs were successfully designed for marker development. Subsequently, a subset of 36 primer pairs was randomly selected and synthesized, of which 12 (33.33%) pairs successfully revealed abundant allelic polymorphism. Additionally, to investigate their utility, the genotypes of 160 individuals from 20 natural populations representing diverse wild genotypes of A. aequalis were analysed by using these 12 polymorphic markers. These novel SSR markers developed here are reliable and useful for genetic analysis on this invasive plant and will greatly enrich its genetic resource.

Genome sequencing has greatly contributed to our understanding of parasitic protozoa. This is particularly the case for Cryptosporidium species (phylum Apicomplexa) which are difficult to propagate. Because of their polymorphic nature, simple sequence repeats have been used extensively as genotypic markers to differentiate between isolates, but no global analysis of amino acid repeats in Cryptosporidium genomes has been reported. Taking advantage of several newly sequenced Cryptosporidium genomes, a comparative analysis of single-amino-acid repeats (SAARs) in seven species was undertaken. This analysis revealed a striking difference between the SAAR profile of the gastric and intestinal species which infect mammals and one species which infects birds. In average, total SAAR length in gastric species is only 25% of the cumulative SAAR length in the genome of Cryptosporidium parvum, Cryptosporidium hominis and Cryptosporidium meleagridis, species infectious to humans. The SAAR profile in the avian parasite Cryptosporidium baileyi stands out due to the presence of long asparagine repeats. Cryptosporidium baileyi proteins with repeats ⩾20 residues are significantly enriched in regulatory functions. As postulated for the related apicomplexan species Plasmodium falciparum, these observations suggest that Cryptosporidium SAARs evolve in response to selective pressure. The putative selective mechanisms driving SAAR evolution in Cryptosporidium species are unknown.

Seed shape (SS) affects the yield and appearance of soybean seeds significantly. However, little detailed information has been reported about the quantitative trait loci (QTL) affecting SS, especially SS components such as seed length (SL), seed width (SW) and seed thickness (ST), and their mutual ratios of length-to-weight (SLW), length-to-thickness (SLT) and weight-to-thickness (SWT). The aim of the present study was to identify QTL underlying SS components using 129 recombinant inbred lines derived from a cross between Dongnong46 and L-100. Phenotypic data were collected from this population after it was grown across nine environments. A total of 213 simple sequence repeat markers were used to construct the genetic linkage map, which covered approximately 3623·39 cM, with an average distance of 17·01 cM between markers. Five QTL were identified as being associated with SL, five with SW, three with ST, four with SLW, two with SLT and three with SWT. These QTL could explain 1·46–22·16% of the phenotypic variation in SS component traits. Three QTL were identified in more than six tested environments three for SL, two for SW, one for ST, two for SLW and one for SLT. These QTL have great potential value for marker-assistant selection of SS in soybean seeds.

Red rice is a major weed in rice production in the southern United States. Red rice and rice intercross because they are the same species. Our objectives were to determine the genetic diversity represented by accessions of red rice and to identify DNA markers that might be useful in identifying hybrids between red and cultivated rice. Red rice accessions were collected from Arkansas and other rice-producing states. Seventy-nine red rice accessions, 10 known or putative hybrid derivatives of red rice and cultivated rice (RC hybrids), and seven rice cultivars were analyzed using microsatellite DNA markers developed for cultivated rice. Microsatellite markers differentiated awned and awnless red rice accessions, six of the seven rice cultivars, and all 10 RC hybrids tested. Thus, these markers were useful in identifying red rice types and RC hybrids.

Callosobruchus chinensis (Linnaeus) is one of the most destructive pests of leguminous seeds. Genetic differentiation and diversity analysis of 345 C. chinensis individuals from 23 geographic populations using 20 polymorphic simple sequence repeats revealed a total of 149 alleles with an average of 7.45 alleles per locus. The average Shannon's information index was 1.015. The gene flow and genetic differentiation rate values at the 20 loci ranged from 0.201 to 1.841 and 11.0–47.2%, with averages of 0.849 and 24.4%, respectively. In the 23 geographic populations, the effective number of alleles and observed heterozygosity ranged from 1.441 to 2.218 and 0.191–0.410, respectively. Shannon's information index ranged from 0.357 to 0.949, with the highest value in Hohhot and the lowest in Rudong. In all comparisons, the fixation index (FST) values ranged from 0.049 to 0.441 with a total FST value of 0.254 among the 23 C. chinensis populations, indicating a moderate level of genetic differentiation and gene flow among these populations. Analysis of molecular variance revealed that the genetic variation within populations accounted for 76.7% of the total genetic variation. The genetic similarity values between populations varied from 0.617 to 0.969, whereas genetic distances varied from 0.032 to 0.483. Using unweighted pair-group method using arithmetical averages cluster analysis, the 23 geographic collections were classified into four distinct genetic groups but most of them were clustered into a single group. The pattern of the three concentrated groups from polymerase chain reactions analysis showed a somewhat different result with cluster.

Understanding the genetic composition and population structure of plant species at a molecular level is essential for the development of adequate strategies aimed at enhancing the conservation and use of their genetic resources. In addition, such knowledge can help to plan ahead for a scenario under which wild and cultivated species come into contact with their genetically modified (GM) counterpart(s). Using ten simple sequence repeat markers, we genotyped 409 samples pertaining to the species in the Manihot genus known to occur in Colombia, i.e. cassava (Manihot esculenta) and its wild relatives Manihot brachyloba, Manihot carthaginensis and Manihot tristis. High genetic variation was observed in all the species (HE= 0.212–0.603), with cassava showing highest diversity. Most of the genetic variation was found within species populations. Our results suggest that outcrossing events among populations occur much more frequently in M. tristis and M. esculenta, and particularly so in the latter, where the exchange of varieties among local farmers plays a key role in maintaining and introducing new genetic diversity. The occurrence of gene flow within and among populations of Manihot species in Colombia becomes relevant in a biosafety context, where gene flow from GM cassava, if introduced to the country, might have detrimental effects on the structure and dynamics of populations of wild species. The baseline information on the genetic diversity and structure of the four Colombian species that we have presented here provides a first and indispensable step towards the development of targeted interventions necessary to preserve their genetic resources.

Simple sequence repeat markers have played an important role in elucidating the epidemiology of human and animal cryptosporidiosis. The drawback of sequence length polymorphisms is that nucleotide substitutions remain undetected. As some laboratories have opted for using length polymorphisms, while others have relied on sequencing, there is a need to compare both methods. We used a diversified set of unique length polymorphisms and matching nucleotide sequences to assess the ability of each genotyping protocol to discern clusters of related Cryptosporidium parvum isolates. We found a weak correlation between the two distance measures for individual markers. This analysis was extended to four-locus genotypes based on sequence length data or concatenated sequences from the same loci. We interrogated these data to assess whether one would reach the same conclusions regardless of the genotyping method. Clusters of isolates generated with the concatenated sequences were not observed with amplicon length, indicating that inferences on the structure of a Cryptosporidium population depend on the genotyping method. Moreover, isolate clusters derived from concatenated sequences were dependent on the algorithm used to calculate distances. These results emphasize the need for harmonizing genotyping tools, not only by selecting informative markers, but also by standardizing the entire genotyping method.

Chilli (Capsicum spp.) is an economically important vegetable and spice. The Tropical Vegetable Research and Development Center, Kasetsart University, Kamphaeng Saen Campus has collected more than 2500 chilli germplasm accessions since 1989. Investment to maintain and evaluate such a large germplasm collection is high. For efficient germplasm management and to reduce the cost of germplasm maintenance, a core collection needs to be established. Therefore, this study aimed to investigate the genetic diversity of chilli germplasm using microsatellites. A total of 230 chilli germplasm accessions were evaluated using ten anchored Capsicum microsatellite loci. These loci generated 42 alleles with a size ranging from 87 to 323 bp. The average polymorphic information content was 0.57, ranging from 0.414 to 0.681, and the probability of identity (PI) ranged from 0.17 to 0.49. The combined PI of the ten microsatellite loci was 2.30 × 10− 6. The similarity index ranged from 0.29 to 1.00. The 230 chilli accessions were divided into two major groups. Group I comprised mainly C. annuum, and group II comprised all four Capsicum species with the majority being C. frutescens, C. chinense and C. baccatum. The matrix comparison showed that a cophenetic correlation of 0.798 indicated the best fit of the obtained dendrogram. The PowerCore program selected 28 representative chilli accessions to form a core collection, which maintained a similar level of diversity to that of the overall 230 chilli accessions. The representative alleles in those 28 core accessions equalled all the alleles present in the entire collection.

The study of the genetic structure of cultivated plant populations maintained by farmers is of great importance for evolutionary and conservation biology. Such studies help understand the bases of crop evolution and conservation in relation to farmers' practices. In this study, we assessed the genetic structure underlying landrace diversity of dry-season sorghum. This crop constitutes a historical model of innovation developed by farmers to extend sorghum cultivation to the dry season. Two types of dry-season sorghum are cultivated. We aimed to assess the link between farmers' taxonomy and molecular genetic structure. We collected both types of dry-season sorghum in two villages of northern Cameroon which represented 20 landraces. These landraces were genotyped using eight polymorphic microsatellite markers. This study compared two clustering methods: a Bayesian method (STRUCTURE) which is based on explicit genetic assumptions and the discriminant analysis of principal component method. The latter, more recently proposed, is based on the combination of principal component analysis and discriminant analysis. We noticed a general congruence between these two methods. We also used both methods to infer the genetic structure of our sample. Our results showed strong genetic structuring of the landraces, with K= 14 genetic clusters. We then analysed the fit between farmers' taxonomy and genetic structure. The data suggested that each type and each landrace corresponds to a given genetic entity. This pattern was robust across both villages, despite differences in cultural practices.

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.

To assess genetic diversity in populations of the brown planthopper (Nilaparvata lugens Stål) (Homoptera: Delphacidae), we have developed and applied microsatellite, or simple sequence repeat (SSR), markers from expressed sequence tags (ESTs). We found that the brown planthopper clusters of ESTs were rich in SSRs with unique frequencies and distributions of SSR motifs. Three hundred and fifty-one EST-SSR markers were developed and yielded clear bands from samples of four brown planthopper populations. High cross-species transferability of these markers was detected in the closely related planthopper N. muiri. The newly developed EST-SSR markers provided sufficient resolution to distinguish within and among biotypes. Analyses based on SSR data revealed host resistance-based genetic differentiation among different brown planthopper populations; the genetic diversity of populations feeding on susceptible rice varieties was lower than that of populations feeding on resistant rice varieties. This is the first large-scale development of brown planthopper SSR markers, which will be useful for future molecular genetics and genomics studies of this serious agricultural pest.

The International Cocoa Genebank, Trinidad, is the largest field genebank collection of cacao (Theobroma cacao L.) in the public domain and the correct identity of each tree is crucial for germplasm movement, evaluation and phenotypic characterization. Nine microsatellite loci were used to assess the identity of 1477 trees from 486 cacao accessions representing approximately 16.9% of the trees and 29.2% of the accessions within the genebank. Heterogeneous plots (plots containing more than one genotype group) averaged 25.1% in The International Cocoa Genebank, Trinidad, with maximal admixture (32.6%) being recorded in Field 5B. The error rate did not differ significantly among different fields. Mislabeling error could be affected by accession grouping with an average error rate of 27.4% for accession groups in the genebank. Synonymous accessions were estimated to account for 14.4% of the field genebank. The results of the present study provide essential information for the management and utilization of the germplasm collection. Single-tree genotyping of every tree in this collection is strongly recommended.

Genetic diversity and phylogenetic relationships among 141 cowpea (Vigna unguiculata L. Walp.) accessions collected throughout the nine geographical regions of Ghana were evaluated using simple sequence repeat (SSR) molecular markers. Twenty-five primer combinations pre-selected by their ability to polymerase chain reaction amplify SSRs from a set of test cowpea germplasm were evaluated. Of these, 20 primer combinations gave reproducible polymorphisms among 97.2% of the cowpea accessions tested, with the remaining accessions being found to be genetically identical. The informative primer combinations revealed a total of 74 alleles at 20 loci with an average of 3.8 alleles detected per locus. Variation in heterozygosity among cowpea SSRs ranged from 0.01 to 0.84 with an average occurrence of 0.19. The polymorphism information content varied from 0.07 to 0.66 with an average of 0.38. The Ghanaian cowpea accessions clustered into five main branches, each of which was loosely associated with the geographical regions from which samples were obtained. Accession GH2288 was found to be the most divergent cowpea accession compared with all others including the outgroup IT84S-2049, a breeding line from Nigeria. Our results provide a framework for future studies aimed at the conservation and management of cultivated cowpea germplasm in Ghana, and a good starting point for the selection of parental lines for genetic improvement programmes.

The genus Limnanthes (Limnanthaceae), also known as meadowfoam, has attracted attention for industrial use due to the unique characteristics of its seed oil. Samples from wild populations showed variability in agronomically important traits involved in seed oil yield, warranting the establishment and continued development of a germplasm collection. The level of genetic diversity within the United States Department of Agriculture, Agriculture Research Service, National Plant Germplasm System (USDA-ARS-NPGS) Limnanthes collection was evaluated using 15 simple sequence repeat (SSR) markers across 62 accessions representing 7 species. Parsimony analysis separated the accessions into two main groups consistent with the traditional taxonomic sections Inflexae and Reflexae, but there was little resolution within groups. These two groups were confirmed using neighbour-joining analysis and principal coordinate analysis. SSR marker variation suggests that the Limnanthes germplasm collection is genetically diverse and the accessions within the species likely contain novel alleles, and therefore the collection contributes to the conservation of the wild Limnanthes gene pool.