A set of 68 simple sequence repeat (SSR) markers were selected from existing databases (including Medicago, soybean, cowpea and peanut) for the purpose of exploiting the transferability of SSRs across species and/or genera within the legume family. Primers were tested for cross-species and cross-genus fragment amplification with an array of 24 different legume accessions. Nearly one-third (30.78%) of the SSR primers screened generated reproducible and cross-genus amplicons. One hundred and seventeen cross-species polymorphic amplicons were identified and could be used as DNA markers. These polymorphic markers are now being used for characterization and evaluation of our collected and donated legume germ- plasm. The transferability of SSRs, mis-/multiple-primings, homologous/heterologous amplifications, single/multiple-amplicons and application of these amplicons as DNA markers are discussed. The transfer of SSR markers across species or across genera can be a very efficient approach for DNA marker development, especially for minor crops.

In order to enhance genetic potential of chickpea materials from the National University of Córdoba Breeding Programme and Germplasm collection (Argentina), a study for a comprehensive understanding of the amount and pattern of genetic variation within and between genotypes was carried out by applying a multivariate analysis form single simple repeats (SSR) and morphological data. Molecular data were also used to determine the discriminating power for genotype identification, and to find the optimal primer combination to ensure unambiguous identification. With the analysis of 15 SSR markers on 53 genotypes, a total of 58 alleles were detected with individual values ranging from one to nine alleles per locus. High values of discriminating power (Dj ⩾ 0.7, PIC ⩾ 0.7), and low values of confusion probability (Cj ⩽ 0.23) were obtained for at least four evaluated markers. The combination of TA113 + TA114 + H1B09 + TA106 primers was effective for discriminating the 53 chickpea genotypes with a cumulative confusion probability value (Ck) of 9.60 × 10−4. Except for some exceptions, individual chickpea genotypes within a cluster in the consensus tree were definitely more closely related with each other by the origin or pedigree. The results confirmed that both multivariate data analysis methods, ordination and clustering, were complementary. In most genotypes, discriminant principal component analysis classification was consistent with the original clusters defined by molecular data. Differences in results from molecular and morphological data indicate that they provide complementary and relevant information for establishing genetic relationships among chickpea materials and a better description and interpretation of the available variability in the germplasm collection.

Oaks are model species due to their importance in various ecosystems, worldwide distribution, high economic value and emerging genomic resources. As such, knowledge on population differentiation across their distribution range is of high importance for sustainable forest management. As in most angiosperms, chloroplasts are maternally (via seeds) inherited in oak species and acorns are dispersed over comparably short distances. Consequently, chloroplast markers reveal comparatively high differentiation between populations, making them highly viable for the analysis of historic migration patterns and the certification of reproductive material. Despite the existence of various white oak (section: Quercus) chloroplast markers, red oak (section: Lobatae) chloroplast markers remain limited. Northern red oak is one of the most important North American oak species and a widespread non-native plantation tree species in European forests. We took advantage of chloroplast genomes of Q. rubra L. and related oak chloroplast genomes to develop a set of robust and easy-to-use chloroplast microsatellite primers for northern red oak. Furthermore, we tested transferability of those novel red oak primer pairs to Q. robur L. and Q. petraea Matt. Liebl. The new set of fifteen polymorphic chloroplast microsatellite markers revealed three additional northern red oak haplotypes after screening 80 northern red oak individuals representing seven haplotypes, identified based on formerly available markers. Therefore, they provide a higher resolution of haplotypes as compared to currently available markers.

The fall armyworm (Spodoptera frugiperda), a destructive pest that originated in South and North America, spread to China in early 2019. Controlling this invasive pest requires an understanding of its population structure and migration patterns, yet the invasion genetics of Chinese S. frugiperda is not clear. Here, using the mitochondrial cytochrome oxidase subunit I (COI) gene, triose phosphate isomerase (Tpi) gene and eight microsatellite loci, we investigated genetic structure and genetic diversity of 16 S. frugiperda populations in China. The Tpi locus identified most S. frugiperda populations as the corn-strains, and a few were heterozygous strains. The microsatellite loci revealed that the genetic diversity of this pest in China was lower than that in South America. Furthermore, we found moderate differentiation among the populations, distinct genetic structures between adjacent populations and abundant genetic resources in the S. frugiperda populations from China sampled across 2 years. The survival rate of S. frugiperda was significantly higher when it was fed on corn leaves than on rice leaves, and the larval stage mortality rate was the highest under both treatments. Our results showed that S. frugiperda probably invaded China via multiple independent introductions and careful pesticide control, continuous monitoring and further studies will be needed to minimize its potential future outbreak.

Apricot is considered an ecologically and economically important tree species of the stone-fruit crops that is widely grown in temperate regions of the world. Very few studies on apricot genetic diversity assessment have been carried out from the regions of Kashmir and Ladakh. In this backdrop, the present study was carried out to analyse the genetic diversity and population structure of 120 apricot genotypes collected from both the regions using 21 SSR markers. A total of 52 alleles were amplified with average values of marker index (MI) = 0.7084, resolving power (RP) = 2.8690, polymorphism information content (PIC) = 0.3132, Na = 2.317, Ne = 1.720, I = 0.572, Ho = 0.284, He = 0.360 and an average polymorphism of 91.2% per assay indicating high level of genetic diversity. The neighbour-joining (NJ) dendrogram generated three main clusters among selected apricot genotypes independent of their geographical locations. Interestingly, the result of the dendrogram coincides with the results of structure analysis which showed that the 120 apricot genotypes could be assigned to three (K = 3) sub-populations and the grouping of genotypes did not follow their geographical location suggesting that they share the same genetic pool. Moreover, analysis of molecular variance showed that 73% of the variation was attributed to differences within the individuals, 25% among individuals while only 2% of the variation was observed among the populations. The present study represents the most comprehensive analysis of the genetic diversity and population structure of apricot genotypes in Kashmir and Ladakh regions of India.

Improving plant resistance against Fusarium wilt (FW) is key to sustaining chickpea production worldwide. Given this, the current study tested a set of 75 FW-responsive chickpea breeding lines including checks in a wilt-sick plot for two consecutive years (2016 and 2017). Genetic diversity analysis using 75 simple sequence repeats (SSRs) revealed a total of 267 alleles with an average of 3.56 alleles per marker. The entire set was divided into two major classes based on clustering method and factorial analysis. Similarly, STRUCTURE analysis placed the 75 genotypes into three distinct sub-groups (K = 3). Marker-trait association (MTA) analysis using the generalized linear model approach revealed nine and eight significant MTAs for FW resistance in the years 2016 and 2017, respectively. Three significant MTAs were obtained for FW resistance following the mixed linear model approach for both years. The SSR markers CESSR433, NCPGR21 and ICCM0284 could be potentially employed for targeted and accelerated improvement of FW resistance in chickpea. To the best of our knowledge, this is the first report on association mapping of the genomic loci controlling FW (Foc2) resistance in chickpea.

Bread wheat (Triticum aestivum) is one of the most important food crops in the world. Its physiological and morphological traits are closely related to yield. Therefore, it is generally important to discover the genomic region associated with these traits. In this research, associations between 21 simple sequence repeat (SSR) markers and 10 inter-simple sequence repeat (ISSR) markers with some traits related to root structure at the embryonic and seedling stages and also some agromorphological traits at the whole plant stage were evaluated on a set of 102 wheat genotypes. A highly significant coefficient of variation among different genotypes was observed in all measured traits. A high level of polymorphism with SSR and ISSR markers was obtained. Genetic structure analysis revealed two distinct subpopulations. Significant correlations were found between genomic markers and evaluated traits. A total of nine markers, including four SSR markers in 1A, 3A, 5A and 2B chromosomal regions and five different ISSR markers were related to the studied traits. Several molecular markers were significantly associated with more than one phenotypic trait, suggesting the possible presence of pleiotropic or indirect effects. The phenotypic variation justified by these alleles ranged from 4 to 15%. Obtained genetic information can be targeted for further validation and genetic analysis in the relevant populations or other breeding sets.

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.

Invasions can be genetically diverse, and that diversity may have implications for invasion management in terms of resistance or tolerance to control methods. We analyzed the population genetics of Russian-olive (Elaeagnus angustifolia L.), an ecologically important and common invasive tree found in many western U.S. riparian areas. We found three cpDNA haplotypes and, using 11 microsatellite loci, identified three genetic clusters in the 460 plants from 46 populations in the western United States. We found high levels of polymorphism in the microsatellites (5 to 15 alleles per locus; 106 alleles total). Our native-range sampling was limited, and we did not find a genetic match for the most common cpDNA invasive haplotype or a strong confirmation of origin for the most common microsatellite genetic cluster. We did not find geographic population structure (isolation by distance) across the U.S. invasion, but we did identify invasive populations that had the most diversity, and we suggest these as choices for initial biological control–release monitoring. Accessions from each genetic cluster, which coarsely represent the range of genetic diversity found in the invasion, are now included in potential classical biological control agent efficacy testing.

Low genetic diversity acts as a major bottleneck in garden pea breeding, and diverse parents are required to generate new genetic material. The diversity of parents utilized in hybridization programme was ascertained following simple sequence repeats (SSR) markers. Thirty-six homozygous F7 progenies were isolated from three intervarietal crosses through shuttle breeding programme over a period of 6 years (2009–2014). Two experiments were conducted for two consecutive years 2014/15 and 2015/16, for evaluating the agronomic performance of progenies along with four commercial control cultivars. Analysis of variance (ANOVA) revealed that genotype, growing year and their interaction had significant effects on most of the traits. Line ‘DPP-SP-6’ recorded significantly higher pod yield/plant in comparison to all other genotypes in 2014/15, 2015/16 and for pooled over years. In addition, ‘DPP-SP-22’, ‘DPP-SP-7’ and ‘DPP-SP-17’ also performed statistically at par with best-performing check ‘Pb-89’ during both the years. These superior lines, in general, showed better pod filling, green pod colour, high shelling, sweetness and resistance to powdery mildew disease. These superior progenies could act as an alternative to the popular check varieties after their exhaustive evaluation over environments.

Trait-specific characterization of rice landraces has significant potential for germplasm management, varietal identification and mining of novel gene/allele for various traits. In the current study, we have characterized 98 unique rice landraces collected from coastal regions of India, affected by submergence and salinity, based on Sub1 and Saltol quantitative trait loci (QTL) linked microsatellite markers. Among these genotypes, four genotypes (IC536558, IC536559, IC536604 and IC536604-1) collected from Kerala and two genotypes (AC34902 and IC324589) collected from West Bengal were identified with tolerance to submergence and salinity stress. A high level of genetic diversity of He = 0.349 and 0.529 at Sub1 and Saltol QTL region was detected by QTL-linked microsatellite markers, respectively. At Sub1 region one genotype, AC34902, was detected with maximum allelic similarity with FR13A, a known submergence tolerant variety. Besides, five genotypes (IC211188-1, IC536604-1, IC536604, IC536558 and IC536559) showed comparatively close genetic relationship with the salt tolerant variety FL478 for Saltol QTL and were clustered together in the neighbour joining dendrogram. Considering the haplotype structure, five genotypes (IC203801, IC203778, IC324584, IC413608 and IC413638) were identified which did not contain any common allele similar to FR13A but were still tolerant to submergence. These individuals need further characterization for identification of new alleles responsible for their tolerance.

Paphiopedilum hirsutissimum (Lindl. ex Hook. f.) Stein (Orchidaceae) is a valuable but endangered ornamental plant. In the present study, the microsatellites characteristics were analysed and 14 polymorphic simple sequence repeat (SSR) markers were developed based on the de novo transcriptome sequencing for P. hirsutissimum using Illumina pair-end sequencing technology. A total of 7406 SSRs were detected in 56,688 unigenes, with the occurrence frequency of 13.06% and an average density of one SSR per 5.42 kb; and 150 primer pairs randomly selected from 2090 pairs except mononucleotide repeats were synthesized for verification. These loci were validated in 32 individuals from the concentrated distribution centre, and were successfully amplified using 14 primer sets showing a high level of polymorphism. These SSR markers will be useful in future studies of genetic diversity, the population structure of P. hirsutissimum and make effective conservation strategy.

Athetis lepigone (Möschler) (Lepidoptera: Noctuidae) is a new outbreak pest in China. Consequently, it is unclear whether the emergence and spread of the outbreak of this pest are triggered by rapid in situ population size increases in each outbreak area, or by immigrants from a potential source area in China. In order to explore the outbreak process of this pest through a population genetics approach, we developed ten novel polymorphic expressed sequence tags (EST)-derived microsatellites. These new microsatellites had moderately high levels of polymorphism in the tested population. The number of alleles per locus ranged from 3 to 19, with an average of 8.6, and the expected heterozygosity ranged from 0.269 to 0.783. A preliminary population genetic analysis using these new microsatellites revealed a lack of population genetic structure in natural populations of A. lepigone. The estimates of recent migration rate revealed strong gene flow among populations. In conclusion, our study developed the first set of EST-microsatellite markers and shed a new light on the population genetic structure of this pest in China.

The Asian long-horned beetle (ALB), Anoplophora glabripennis (Motschulsky) (Coleoptera: Cerambycidae: Lamiinae), is a wood-borer and polyphagous xylophage that is native to Asia. It infests and seriously harms healthy trees, and therefore is a cause for considerable environmental concern. The analysis of population genetic structure of ALB and sibling species Anoplophora nobilis (Ganglbauer) will not only help to clarify the relationship between environmental variables and mechanisms of speciation, but also will enhance our understanding of evolutionary processes. However, the known genetic markers, particularly microsatellites, are limited for this species. SSRLocator software was used to analyze the distribution and frequencies of genomic simple sequence repeat (SSR), to infer the basic characteristics of repeat motifs, and to design primers. We developed SSR loci of 2–6 repeated units, including 10,650 perfect SSRs, and found 140 types of repeat motifs. A total of 2621 SSR markers were discovered in ALB whole-genome shotgun sequences. 48 pairs of SSR primers were randomly chosen from 2621 SSR markers, and half of these 48 pairs were polymorphic containing 4 di-, 7 tri-, 2 tetra-, and 11-hexamer SSRs. Four populations test the effectiveness of the primers. These results suggest that our method for whole-genome SSR screening is feasible and efficient, and the SSR markers developed in this study are suitable for further population genetics studies of ALB. Moreover, they may also be useful for the development of SSRs for other Coleoptera.

Recent advances in molecular methods and statistical analyses provide weed scientists with powerful tools for examining the genetic structure of weedy plant populations. The value of these studies depends on effective sampling protocols; however, there is little consensus on how to sample plant populations for genetic diversity analyses. In this review, we draw on published literature that incorporates sampling theory and spatial statistics in population genetic analyses to identify key factors to consider when designing a sampling strategy. We discuss how sampling design is affected by research objectives, biology of the study species, population structure, marker choice, and the genetic parameters to be investigated, and we offer suggestions on defining sampling units and developing sampling protocols.

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.

Medusahead is a close relative of bread wheat that is native to Eurasia but has become a noxious, invasive weed in North America. Intergeneric use of primers for bread wheat simple-sequence repeat (SSR) markers was tested in medusahead in order to expand the pool of available genetic resources for study of this plant. Forty-two primer pairs were screened in medusahead, of which 29 produced visible bands in agarose gels. Amplicons from eight of these markers were sequenced and analyzed for the presence of SSRs and single-nucleotide polymorphisms (SNPs) among medusahead individuals from six populations in the western Great Basin. Of the eight sequenced amplicons, two contained SSRs, both of which were polymorphic and shared by the original bread wheat marker. Six of the eight markers combined to detect 33 SNP loci. BLAST comparisons of the eight amplicons revealed variable numbers of matching sequences from wheat and other grass species ranging from 0 to > 200 matches. Using data from the polymorphic loci, population genetic analysis of the six invasive medusahead populations indicated that they arose from two separate introductions with two additional subclusters possible within the two principal clusters. Extrapolating from these results, it is reasonable to expect that between 170 and 830 of the approximately 1,200 publicly available bread wheat SSRs would produce useful marker loci in medusahead.

Technological advances in molecular biology have contributed substantially to our understanding of plant genetic diversity. Early studies of allozyme variation employing protein electrophoresis revealed that plant populations have high levels of genetic diversity, most of the variation at polymorphic loci is found within populations, and geographic range and breeding system explain the largest proportion of variation in genetic diversity. With the discovery of restriction endonucleases, the first DNA-based markers allowed the detection of variation in DNA sequences in plant population studies. More recently, techniques that utilize the polymerase chain reaction have allowed a more representative assessment of genetic variation in plants by screening multiple loci distributed throughout the genome. The analyses reveal sufficient polymorphism for the examination of fine-scale genetic differences among individuals. Information on plant genetic diversity is also emerging from studies of plant genome structure. Comparative genetic mapping studies of members of the Brassicaceae, Poaceae, and Solanaceae show that gene content is highly conserved between closely related species, although gene order on a chromosomal segment may differ between species. Comparative sequencing studies reveal higher degrees of diversity at the microstructural (less than 1 million base pairs) level than predicted at the genetic map level and suggest that genes are densely packed in gene-rich regions, rather than randomly distributed along chromosomes in species with large genomes. Sequencing of the entire genomes of rice and Arabidopsis thaliana will help identify genes controlling agronomically important traits, improve our understanding of genetic variation for fitness-related traits in wild plant populations including weed species, resolve evolutionary relationships among plant taxa, and potentially revolutionize current ideas on plant diversity and evolution.

Recent advances in sequencing technologies (next-generation sequencing) offer dramatically increased sequencing throughput at a lower cost than traditional Sanger sequencing. This technology is changing genomics research by allowing large scale sequencing experiments in nonmodel systems. Waterhemp is an important weed in the midwestern United States with characteristics that makes it an interesting ecological model. However, very few genomic resources are available for this species. One half of a 70 by 75 picotiter plate of 454-pyrosequencing was performed on total DNA isolated from waterhemp, generating 158,015 reads of an average length of 271 bp, or a total of nearly 43 Mbp of sequence. Included in this sequence was a nearly complete sequence of the chloroplast genome, sequences of several important herbicide resistance genes, leads for simple sequence repeat (SSR) markers, and a sampling of the repeated elements (e.g., transposons) present in this species. Here we present the waterhemp genomic data gleaned from this sequencing experiment and illustrate the value of next-generation sequencing technology to weed science research.

The oriental fruit moth (OFM) Grapholita molesta (Lepidoptera: Tortricidae) is an important economic pest of stone and pome fruits worldwide. We sequenced the OFM genome using next-generation sequencing and characterized the microsatellite distribution. In total, 56,674 microsatellites were identified, with 11,584 loci suitable for primer design. Twenty-seven polymorphic microsatellites, including 24 loci with trinucleotide repeat and three with pentanucleotide repeat, were validated in 95 individuals from four natural populations. The allele numbers ranged from 4 to 40, with an average value of 13.7 per locus. A high frequency of null alleles was observed in most loci developed for the OFM. Three marker panels, all of the loci, nine loci with the lowest null allele frequencies, and nine loci with the highest null allele frequencies, were established for population genetics analyses. The null allele influenced estimations of genetic diversity parameters but not the OFM's genetic structure. Both a STRUCTURE analysis and a discriminant analysis of principal components, using the three marker panels, divided the four natural populations into three groups. However, more individuals were incorrectly assigned by the STRUCTURE analysis when the marker panel with the highest null allele frequency was used compared with the other two panels. Our study provides empirical research on the effects of null alleles on population genetics analyses. The microsatellites developed will be valuable markers for genetic studies of the OFM.