Regulation of Arabidopsis defense responses against Spodoptera littoralis by CPK-mediated calcium signaling

Background

Genetic markers and linkage mapping are basic prerequisites for marker-assisted selection and map-based cloning. In the case of the key grassland species Lolium spp., numerous mapping populations have been developed and characterised for various traits. Although some genetic linkage maps of these populations have been aligned with each other using publicly available DNA markers, the number of common markers among genetic maps is still low, limiting the ability to compare candidate gene and QTL locations across germplasm.

Results

A set of 204 expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers has been assigned to map positions using eight different ryegrass mapping populations. Marker properties of a subset of 64 EST-SSRs were assessed in six to eight individuals of each mapping population and revealed 83% of the markers to be polymorphic in at least one population and an average number of alleles of 4.88. EST-SSR markers polymorphic in multiple populations served as anchor markers and allowed the construction of the first comprehensive consensus map for ryegrass. The integrated map was complemented with 97 SSRs from previously published linkage maps and finally contained 284 EST-derived and genomic SSR markers. The total map length was 742 centiMorgan (cM), ranging for individual chromosomes from 70 cM of linkage group (LG) 6 to 171 cM of LG 2.

Conclusions

The consensus linkage map for ryegrass based on eight mapping populations and constructed using a large set of publicly available Lolium EST-SSRs mapped for the first time together with previously mapped SSR markers will allow for consolidating existing mapping and QTL information in ryegrass. Map and markers presented here will prove to be an asset in the development for both molecular breeding of ryegrass as well as comparative genetics and genomics within grass species.     

Worldwide population differentiation at disease-associated SNPs

Background

Recent genome-wide association (GWA) studies have provided compelling evidence of association between genetic variants and common complex diseases. These studies have made use of cases and controls almost exclusively from populations of European ancestry and little is known about the frequency of risk alleles in other populations. The present study addresses the transferability of disease associations across human populations by examining levels of population differentiation at disease-associated single nucleotide polymorphisms (SNPs).

Methods

We genotyped ~1000 individuals from 53 populations worldwide at 25 SNPs which show robust association with 6 complex human diseases (Crohn's disease, type 1 diabetes, type 2 diabetes, rheumatoid arthritis, coronary artery disease and obesity). Allele frequency differences between populations for these SNPs were measured using Fst. The Fst values for the disease-associated SNPs were compared to Fst values from 2750 random SNPs typed in the same set of individuals.

Results

On average, disease SNPs are not significantly more differentiated between populations than random SNPs in the genome. Risk allele frequencies, however, do show substantial variation across human populations and may contribute to differences in disease prevalence between populations. We demonstrate that, in some cases, risk allele frequency differences are unusually high compared to random SNPs and may be due to the action of local (i.e. geographically-restricted) positive natural selection. Moreover, some risk alleles were absent or fixed in a population, which implies that risk alleles identified in one population do not necessarily account for disease prevalence in all human populations.

Conclusion

Although differences in risk allele frequencies between human populations are not unusually large and are thus likely not due to positive local selection, there is substantial variation in risk allele frequencies between populations which may account for differences in disease prevalence between human populations.     

Genetic diversity and association mapping of seed vigor in rice (Oryza sativa L.)

Key message

Twenty-seven QTLs were identified for rice seed vigor, in which 16 were novel QTLs. Fifteen elite parental combinations were designed for improving seed vigor in rice.

Abstract

Seed vigor is closely related to direct seeding in rice (Oryza sativa L.). Previous quantitative trait locus (QTL) studies for seed vigor were mainly derived from bi-parental segregating populations and no report from natural populations. In this study, association mapping for seed vigor was performed on a selected sample of 540 rice cultivars (419 from China and 121 from Vietnam). Population structure was estimated on the basis of 262 simple sequence repeat (SSR) markers. Seed vigor was evaluated by root length (RL), shoot length (SL) and shoot dry weight in 2011 and 2012. Abundant phenotypic and genetic diversities were found in the studied population. The population was divided into seven subpopulations, and the levels of linkage disequilibrium (LD) ranged from 10 to 80 cM. We identified 27 marker–trait associations involving 18 SSR markers for three traits. According to phenotypic effects for alleles of the detected QTLs, elite alleles were mined. These elite alleles could be used to design parental combinations and the expected results would be obtained by pyramiding or substituting the elite alleles per QTL (apart from possible epistatic effects). Our results demonstrate that association mapping can complement and enhance previous QTL information for marker-assisted selection and breeding by design.     

Resistance to stem rust Ug99 in six bread wheat cultivars maps to chromosome 6DS

Key message

Identified SSR markers ( Xcfd49 and Xbarc183 ) linked with stem rust resistance for efficient use in marker-assisted selection and stacking of resistance genes in wheat breeding programs.

Abstract

More than 80 % of the worldwide wheat (Triticum aestivum L.) area is currently sown with varieties susceptible to the Ug99 race group of stem rust fungus. However, wheat lines Niini, Tinkio, Coni, Pfunye, Blouk, and Ripper have demonstrated Ug99 resistance at the seedling and adult plant stages. We mapped stem rust resistance in populations derived from crosses of a susceptible parent with each of the resistant lines. The segregation of resistance in each population indicated the presence of a single gene. The resistance gene in Niini mapped to short arm of chromosome 6D and was flanked by SSR markers Xcfd49 at distances of 3.9 cM proximal and Xbarc183 8.4 cM distal, respectively. The chromosome location of this resistance was validated in three other populations: PBW343/Coni, PBW343/Tinkio, and Cacuke/Pfunye. Resistance initially postulated to be conferred by the SrTmp gene in Blouk and Ripper was also linked to Xcfd49 and Xbarc183 on 6DS, but it was mapped proximal to Xbarc183 at a similar position to previously mapped genes Sr42 and SrCad. Based on the variation in diagnostic marker alleles, it is possible that Niini and Pfunye may carry different resistance genes/alleles. Further studies are needed to determine the allelic relationships between various genes located on chromosome arm 6DS. Our results provide valuable molecular marker and genetic information for developing Ug99 resistant wheat varieties in diverse germplasm and using these markers to tag the resistance genes in wheat breeding.     

Mapping of the transcription start site (TSS) and identification of SNPs in the bovine neuropeptide Y (NPY) gene

Background

The domestic goat is one of the important livestock species of India. In the present study we assess genetic diversity of Indian goats using 17 microsatellite markers. Breeds were sampled from their natural habitat, covering different agroclimatic zones.

Results

The mean number of alleles per locus (NA) ranged from 8.1 in Barbari to 9.7 in Jakhrana goats. The mean expected heterozygosity (He) ranged from 0.739 in Barbari to 0.783 in Jakhrana goats. Deviations from Hardy-Weinberg Equilibrium (HWE) were statistically significant (P < 0.05) for 5 loci breed combinations. The D_A measure of genetic distance between pairs of breeds indicated that the lowest distance was between Marwari and Sirohi (0.135). The highest distance was between Pashmina and Black Bengal. An analysis of molecular variance indicated that 6.59% of variance exists among the Indian goat breeds. Both a phylogenetic tree and Principal Component Analysis showed the distribution of breeds in two major clusters with respect to their geographic distribution.

Conclusion

Our study concludes that Indian goat populations can be classified into distinct genetic groups or breeds based on the microsatellites as well as mtDNA information.     

Under the volcano: phylogeography and evolution of the cave-dwelling Palmorchestia hypogaea (Amphipoda, Crustacea) at La Palma (Canary Islands)

Background

The invasive garden ant, Lasius neglectus, is the most recently detected pest ant and the first known invasive ant able to become established and thrive in the temperate regions of Eurasia. In this study, we aim to reconstruct the invasion history of this ant in Europe analysing 14 populations with three complementary approaches: genetic microsatellite analysis, chemical analysis of cuticular hydrocarbon profiles and behavioural observations of aggression behaviour. We evaluate the relative informative power of the three methodological approaches and estimate both the number of independent introduction events from a yet unknown native range somewhere in the Black Sea area, and the invasive potential of the existing introduced populations.

Results

Three clusters of genetically similar populations were detected, and all but one population had a similar chemical profile. Aggression between populations could be predicted from their genetic and chemical distance, and two major clusters of non-aggressive groups of populations were found. However, populations of L. neglectus did not separate into clear supercolonial associations, as is typical for other invasive ants.

Conclusion

The three methodological approaches gave consistent and complementary results. All joint evidence supports the inference that the 14 introduced populations of L. neglectus in Europe likely arose from only very few independent introductions from the native range, and that new infestations were typically started through introductions from other invasive populations. This indicates that existing introduced populations have a very high invasive potential when the ants are inadvertently spread by human transport.     

Genetic variation in wild Prunus L. subgen. Cerasus germplasm from Iran characterized by nuclear and chloroplast SSR markers

Key message

The selected material of Cerasus subgen. will be useful for conservation and management and important for Prunus breeding programs.

Abstract

Knowledge of relationships among the cultivated and wild species of Cerasus is important for recognizing gene pools in germplasm and developing effective conservation and management strategies. In this study, genetic and phylogenetic relationships of wild Cerasus subgenus species naturally growing in Iran, including P. avium (mazzard), P. mahaleb, P. brachypetala, P. incana, P. yazdiana, P. microcarpa subsp. microcarpa, P. microcarpa subsp. diffusa and P. pseudoprostrata and three commercial species, sweet cherry (P. avium), sour cherry (P. cerasus) and duke cherry (P. x gondouinii) was investigated based on 16 nuclear SSR and five chloroplast SSR. Very high level of polymorphism was detected among the studied species based these molecular markers, indicating high inter and intraspecific genetic variation. Inter and intraspecific genetic similarity coefficients varied from 0.00 to 1.00, indicating high genetic variation in studied germplasm. These two molecular markers types could distinguish differences between all species so that accessions of each species were placed into a single group. Based on molecular markers, a close correlation was observed between intraspecific variation and geographical distribution. Furthermore, based on nuSSR primers, most wild species showed 2–4 alleles and may be tetraploid. In conclusion, the conservation of these highly diverse native populations of Iranian wild Cerasus germplasm is recommended for future breeding activity.     

Association between line per se and testcross performance for eight agronomic and quality traits in winter rye

Key message

We investigated associations between line per se and testcross performance in rye and suggested that selection for per se performance is valuable for several traits in multi-stage selection programs.

Abstract

Genotypic correlation between line per se and testcross performance is an important quantitative-genetic parameter for optimizing hybrid breeding programs. The main goal of this survey was to study the association of line per se and testcross performance at the phenotypic level. We used experimental data from the line per se and testcross performance of two segregating winter rye populations (A, B) with each of 220 progenies tested in six environments for eight agronomic and quality traits. Genotypic variances were considerably larger for per se than for testcross performance of all investigated traits resulting in higher heritabilities of the former in most instances. Genotypic correlations (r _g) between testcross and line per se performance decreased with increasing complexity of the trait as shown by the respective heritabilities. They were highest (r _g ≥ 0.7) for plant height and test weight in population B, and thousand-kernel weight, falling number and starch content in both populations. A selection of these traits for line per se performance in early generations will save field plots in further testing testcross performance and increase efficiency of hybrid breeding.     

Quantitative trait loci of stripe rust resistance in wheat

Key message

Over 140 QTLs for resistance to stripe rust in wheat have been published and through mapping flanking markers on consensus maps, 49 chromosomal regions are identified.

Abstract

Over thirty publications during the last 10 years have identified more than 140 QTLs for stripe rust resistance in wheat. It is likely that many of these QTLs are identical genes that have been spread through plant breeding into diverse backgrounds through phenotypic selection under stripe rust epidemics. Allelism testing can be used to differentiate genes in similar locations but in different genetic backgrounds; however, this is problematic for QTL studies where multiple loci segregate from any one parent. This review utilizes consensus maps to illustrate important genomic regions that have had effects against stripe rust in wheat, and although this methodology cannot distinguish alleles from closely linked genes, it does highlight the extent of genetic diversity for this trait and identifies the most valuable loci and the parents possessing them for utilization in breeding programs. With the advent of cheaper, high throughput genotyping technologies, it is envisioned that there will be many more publications in the near future describing ever more QTLs. This review sets the scene for the coming influx of data and will quickly enable researchers to identify new loci in their given populations.     

Gene duplications contribute to the overrepresentation of interactions between proteins of a similar age

Background

Disruptive selection has been documented in a growing number of natural populations. Yet, its prevalence within individual systems remains unclear. Furthermore, few studies have sought to identify the ecological factors that promote disruptive selection in the wild. To address these issues, we surveyed 15 populations of Mexican spadefoot toad tadpoles, Spea multiplicata, and measured the prevalence of disruptive selection acting on resource-use phenotypes. We also evaluated the relationship between the strength of disruptive selection and the intensity of intraspecific competition??an ecological agent hypothesized to be an important driver of disruptive selection.

Results

Disruptive selection was the predominant mode of quadratic selection across all populations. However, a directional component of selection favoring an extreme ecomorph??a distinctive carnivore morph??was also common. Disruptive selection was strongest in populations experiencing the most intense intraspecific competition, whereas stabilizing selection was only found in populations experiencing relatively weak intraspecific competition.

Conclusions

Disruptive selection can be common in natural populations. Intraspecific competition for resources may be a key driver of such selection.     

Long-term perspective of hybrid versus line breeding in wheat based on quantitative genetic theory

Key message

The predicted future yield potential of hybrids was competitive with lines in the near future, but on a long term the competitiveness of hybrids depends on a number of factors.

Abstract

The change from line to hybrid breeding in autogamous crops is a recent controversial discussion among scientists and breeders. Our objectives were to employ wheat as a model to: (1) deliver a theoretical framework for the comparison of the selection gain of hybrid versus line breeding; (2) elaborate key parameters affecting selection gain in this comparison; (3) and evaluate the potential to modify these parameters in applied breeding programs. We developed a prediction model for future yield potential in both breeding methods as the sum of the population mean and the expected selection gain. The expected selection gain was smaller in hybrid than in line breeding and depended strongly on the hybrid seed production costs and the genetic variance available in hybrid versus line breeding. Owing to heterosis, the predicted future yield potential of hybrids was competitive with lines in the near future. On a long term, however, the competitiveness of hybrid compared to line breeding is questionable and depends on a number of factors. However, market specifications and political reasons might justify the current high interest in hybrid wheat breeding.     

Fine mapping of the Rrs1 resistance locus against scald in two large populations derived from Spanish barley landraces

Key message

In two Spanish barley landraces with outstanding resistance to scald, the Rrs1 _Rh4 locus was fine mapped including all known markers used in previous studies and closely linked markers were developed.

Abstract

Scald, caused by Rhynchosporium commune, is one of the most prevalent barley diseases worldwide. A search for new resistance sources revealed that Spanish landrace-derived lines SBCC145 and SBCC154 showed outstanding resistance to scald. They were crossed to susceptible cultivar Beatrix to create large DH-mapping populations of 522 and 416 DH lines that were scored for disease resistance in the greenhouse using two R. commune isolates. To ascertain the pattern of resistance, parents and reference barley lines with known scald resistance were phenotyped with a panel of differential R. commune isolates. Subpopulations were genotyped with the Illumina GoldenGate 1,536 SNP Assay and a large QTL in the centromeric region of chromosome 3H, known to harbour several scald resistance genes and/or alleles, was found in both populations. Five SNP markers closest to the QTL were converted into CAPS markers. These CAPS markers, together with informative SSR markers used in other scald studies, confirmed the presence of the Rrs1 locus. The panel of differential scald isolates indicated that the allele carried by both donors was Rrs1 _Rh4 . The genetic distance between Rrs1 and its flanking markers was 1.2 cM (11_0010) proximally and 0.9 cM (11_0823) distally, which corresponds to a distance of just below 9 Mbp. The number and nature of scald resistance genes on chromosome 3H are discussed. The effective Rrs1 allele found and the closely linked markers developed are already useful tools for molecular breeding programs and provide a good step towards the identification of candidate genes.     

Molecular characterization of Nicaraguan Pinus tecunumanii Schw. ex Eguiluz et Perry populations for in situ conservation

Key message

We conducted molecular characterization of Nicaraguan Pinus tecunumanii populations using microsatellite markers. Populations possess considerable genetic variation but there are risks associated with inbreeding and population fragmentation.

Abstract

We carried out a molecular characterization of three natural populations of Pinus tecunumanii using nine microsatellite markers. All studied populations occur in Nicaragua, where the species has declined primarily due to human-influenced factors. The results showed that there is a high amount of genetic variation in populations (expected heterozygosities 0.775–0.841), populations do not show significant differentiation (mean F _ST 0.0073), apparently due to frequent gene flow or a more continuous distribution and homogenous genetic composition in the past, and inbreeding is common in all populations (F _IS 0.705–0.780). The Structure analysis revealed that there is no evident clustering pattern among P. tecunumanii individuals. Although all studied populations possess a considerable amount of genetic variation, risks associated with inbreeding and population fragmentation should be acknowledged and a conservation strategy developed to safeguard the genetic resources of P. tecunumanii.     

Whole-genome QTL analysis for MAGIC

Key message

An efficient whole genome method of QTL analysis is presented for Multi-parent advanced generation integrated crosses.

Abstract

Multi-parent advanced generation inter-cross (MAGIC) populations have been developed for mice and several plant species and are useful for the genetic dissection of complex traits. The analysis of quantitative trait loci (QTL) in these populations presents some additional challenges compared with traditional mapping approaches. In particular, pedigree and marker information need to be integrated and founder genetic data needs to be incorporated into the analysis. Here, we present a method for QTL analysis that utilizes the probability of inheriting founder alleles across the whole genome simultaneously, either for intervals or markers. The probabilities can be found using three-point or Hidden Markov Model (HMM) methods. This whole-genome approach is evaluated in a simulation study and it is shown to be a powerful method of analysis. The HMM probabilities lead to low rates of false positives and low bias of estimated QTL effect sizes. An implementation of the approach is available as an R package. In addition, we illustrate the approach using a bread wheat MAGIC population.     

Comparative QTL analysis of root lesion nematode resistance in barley

Key message

This study demonstrates for the first time that resistance to different root lesion nematodes ( P. neglectus and P. penetrans ) is controlled by a common QTL. A major resistance QTL ( Rlnnp6H ) has been mapped to chromosome 6H using two independent barley populations.

Abstract

Root lesion nematodes (Pratylenchus spp.) are important pests in cereal production worldwide. We selected two doubled haploid populations of barley (Igri × Franka and Uschi × HHOR 3073) and infected them with Pratylenchus penetrans and Pratylenchus neglectus. Nematode multiplication rates were measured 7 or 10 weeks after infection. In both populations, continuous phenotypic variations for nematode multiplication rates were detected indicating a quantitative inheritance of resistance. In the Igri × Franka population, four P. penetrans resistance QTLs were mapped with 857 molecular markers on four linkage groups (2H, 5H, 6H and 7H). In the Uschi × HHOR 3073 population, eleven resistance QTLs (P. penetrans and P. neglectus) were mapped with 646 molecular markers on linkage groups 1H, 3H, 4H, 5H, 6H and 7H. A major resistance QTL named Rlnnp6H (LOD score 6.42–11.19) with a large phenotypic effect (27.5–36.6 %) for both pests was mapped in both populations to chromosome 6H. Another resistance QTL for both pests was mapped on linkage group 5H (Igri × Franka population). These data provide first evidence for common resistance mechanisms against different root lesion nematode species. The molecular markers are a powerful tool for the selection of resistant barley lines among segregating populations because resistance tests are time consuming and laborious.     

Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians

Background

Hybridization receives attention because of the potential role that it may play in generating evolutionary novelty. An explanation for the emergence of novel phenotypes is given by transgressive segregation, which, if frequent, would imply an important evolutionary role for hybridization. This process is still rarely studied in natural populations as samples of recent hybrids and their parental populations are needed. Further, the detection of transgressive segregation requires phenotypes that can be easily quantified and analysed. We analyse variability in body shape of divergent populations of European sculpins (Cottus gobio complex) as well as natural hybrids among them.

Results

A distance-based method is developed to assign unknown specimens to known groups based on morphometric data. Apparently, body shape represents a highly informative set of characters that parallels the discriminatory power of microsatellite markers in our study system. Populations of sculpins are distinct and "unknown" specimens can be correctly assigned to their source population based on body shape. Recent hybrids are intermediate along the axes separating their parental groups but display additional differentiation that is unique and coupled with the hybrid genetic background.

Conclusion

There is a specific hybrid shape component in natural sculpin hybrids that can be best explained by transgressive segregation. This inference of how hybrids differ from their ancestors provides basic information for future evolutionary studies. Furthermore, our approach may serve to assign candidate specimens to their source populations based on morphometric data and help in the interpretation of population differentiation.     

Highly efficient genotyping of rice biparental populations by GoldenGate assays based on parental resequencing

Key message

A new time- and cost-effective strategy was developed for medium-density SNP genotyping of rice biparental populations, using GoldenGate assays based on parental resequencing.

Abstract

Since the advent of molecular markers, crop researchers and breeders have dedicated huge amounts of effort to detecting quantitative trait loci (QTL) in biparental populations for genetic analysis and marker-assisted selection (MAS). In this study, we developed a new time- and cost-effective strategy for genotyping a population of progeny from a rice cross using medium-density single nucleotide polymorphisms (SNPs). Using this strategy, 728,362 “high quality” SNPs were identified by resequencing Teqing and Lemont, the parents of the population. We selected 384 informative SNPs that were evenly distributed across the genome for genotyping the biparental population using the Illumina GoldenGate assay. 335 (87.2 %) validated SNPs were used for further genetic analyses. After removing segregation distortion markers, 321 SNPs were used for linkage map construction and QTL mapping. This strategy generated SNP markers distributed more evenly across the genome than previous SSR assays. Taking the GW5 gene that controls grain shape as an example, our strategy provided higher accuracy (0.8 Mb) and significance (LOD 5.5 and 10.1) in QTL mapping than SSR analysis. Our study thus provides a rapid and efficient strategy for genetic studies and QTL mapping using SNP genotyping assays.     

Wild peas vary in their cross-compatibility with cultivated pea (Pisum sativum subsp. sativum L.) depending on alleles of a nuclear–cytoplasmic incompatibility locus

Key message

Divergent wild and endemic peas differ in hybrid sterility in reciprocal crosses with cultivated pea depending on alleles of a nuclear ‘speciation gene’ involved in nuclear–cytoplasmic compatibility.

Background

In hybrids between cultivated and wild peas, nuclear–cytoplasmic conflict frequently occurs. One of the nuclear genes involved, Scs1, was earlier mapped on Linkage Group III.

Results

In reciprocal crosses of seven divergent pea accessions with cultivated P. sativum, some alleles of Scs1 manifested incompatibility with an alien cytoplasm as a decrease in pollen fertility to about 50 % in the heterozygotes and lack of some genotypic classes among F2 segregants. Earlier, we defined monophyletic evolutionary lineages A, B, C and D of pea according to allelic state of three markers, from nuclear, plastid and mitochondrial genomes. All tested representatives of wild peas from the lineages A and C exhibited incompatibility due to Scs1 deleterious effects in crosses with testerlines of P. sativum subsp. sativum (the common cultivated pea) at least in one direction. A wild pea from the lineage B and a cultivated pea from the lineage D were compatible with the testerline in both directions. The tested accession of cultivated P. abyssinicum (lineage A) was partially compatible in both directions. The Scs1 alleles of some pea accessions even originating from the same geographic area were remarkably different in their compatibility with cultivated Pisum sativum cytoplasm.

Conclusion

Variability of a gene involved in reproductive isolation is of important evolutionary role and nominate Scs1 as a speciation gene.     

Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees

Background

Ants typically distinguish nestmates from non-nestmates based on the perception of colony-specific chemicals, particularly cuticular hydrocarbons present on the surface of the ants' exoskeleton. These recognition cues are believed to play an important role in the formation of vast so-called supercolonies that have been described for some invasive ant species, but general conclusions about the role of these cues are hampered by only few species being studied. Here we use data on cuticular hydrocarbons, aggression and microsatellite genetic markers to investigate the interdependence of chemical recognition cues, genetic distance and nestmate discrimination in the pharaoh ant (Monomorium pharaonis), a widespread pest species, and ask whether introduced populations of this species are genetically differentiated and exhibit intraspecific aggression.

Results

Microsatellite analyses of a total of 35 colonies from four continents revealed extremely high levels of genetic differentiation between almost all colonies (F _ST = 0.751 ± 0.006 SE) and very low within-colony diversity. This implies that at least 34 and likely hundreds more independent lineages of this ant have spread worldwide. Aggression tests involving workers from 14 different colonies showed only low levels of aggression, even between colonies that were geographically and/or genetically very distant. Chemical analyses of groups of worker ants showed that all colonies had the same cuticular compounds, which varied only quantitatively among colonies. There was a positive correlation between geographical and genetic distance, but no other significant relationships were detected between aggression, chemical profile, genetic distance and geographical distance.

Conclusions

The pharaoh ant has a global invasion history of numerous independent introductions resulting in genetically highly differentiated colonies typically displaying surprisingly low levels of intraspecific aggression, a behaviour that may have evolved in the native range or by lineage selection in the introduced range.     

Genetic diversity and population structure in the US Upland cotton (Gossypium hirsutum L.)

Key message

Genetic diversity and population structure in the US Upland cotton was established and core sets of allelic richness were identified for developing association mapping populations in cotton.

Abstract

Elite plant breeding programs could likely benefit from the unexploited standing genetic variation of obsolete cultivars without the yield drag typically associated with wild accessions. A set of 381 accessions comprising 378 Upland (Gossypium hirsutum L.) and 3 G. barbadense L. accessions of the United States cotton belt were genotyped using 120 genome-wide SSR markers to establish the genetic diversity and population structure in tetraploid cotton. These accessions represent more than 100 years of Upland cotton breeding in the United States. Genetic diversity analysis identified a total of 546 alleles across 141 marker loci. Twenty-two percent of the alleles in Upland accessions were unique, specific to a single accession. Population structure analysis revealed extensive admixture and identified five subgroups corresponding to Southeastern, Midsouth, Southwest, and Western zones of cotton growing areas in the United States, with the three accessions of G. barbadense forming a separate cluster. Phylogenetic analysis supported the subgroups identified by STRUCTURE. Average genetic distance between G. hirsutum accessions was 0.195 indicating low levels of genetic diversity in Upland cotton germplasm pool. The results from both population structure and phylogenetic analysis were in agreement with pedigree information, although there were a few exceptions. Further, core sets of different sizes representing different levels of allelic richness in Upland cotton were identified. Establishment of genetic diversity, population structure, and identification of core sets from this study could be useful for genetic and genomic analysis and systematic utilization of the standing genetic variation in Upland cotton.