High Gene Diversity Research Articles

Human-Mediated Gene Flow Contributes to Metapopulation Genetic Structure of the Pathogenic Fungus Alternaria alternata from Potato.

Metapopulation structure generated by recurrent extinctions and recolonizations plays an important role in the evolution of species but is rarely considered in agricultural systems. In this study, generation and mechanism of metapopulation structure were investigated by microsatellite assaying 725 isolates of Alternaria alternata sampled from potato hosts at 16 locations across China. We found a single major cluster, no isolate-geography associations and no bottlenecks in the A. alternata isolates, suggesting a metapopulation genetic structure of the pathogen. We also found weak isolation-by-distance, lower among than within cropping region population differentiation, concordant moving directions of potato products and net gene flow and the highest gene diversity in the region with the most potato imports. These results indicate that in addition to natural dispersal, human-mediated gene flow also contributes to the generation and dynamics of the metapopulation genetic structure of A. alternata in China. Metapopulation structure increases the adaptive capacity of the plant pathogen as a result of enhanced genetic variation and reduced population fragmentation. Consequently, rigid quarantine regulations may be required to reduce population connectivity and the evolutionary potential of A. alternata and other pathogens with a similar population dynamics for a sustainable plant disease management.

Local epidemiology of the wood decay agent Laetiporus sulphureus in carob stands in Sicily

SummaryThe basidiomycete Laetiporus sulphureus (Bull) Murrill is a forest pathogen causing brown cubical heart rot in a broad range of host trees. Despite its wide distribution and importance, studies aimed at understanding the epidemiology of the fungus in specific areas or hosts are lacking. In this study, an incidence of L. sulphureus as high as 34% was determined through molecular analysis of wood samples collected from 70 carob (Ceratonia siliqua L.) trees in the South‐west of Sicily, Italy. A phylogenetic analysis of Internal Transcribed Spacer (ITS) sequences indicated that all carob isolates belonged to the cluster E of Laetiporus taxonomy. Ten molecular markers based on Single Sequence Repeats (SSRs) designed on the L. sulphureus genome were developed, and isolates were genotyped through High‐resolution Melting (HRM) analysis. High gene diversity (0.581), no correlation between fungal genotype and host tree species and significant correlation between spatial and genetic distance were observed, suggesting an important role of basidiospores in the epidemiology of the fungus and a risk of transmission from a host tree species to the others. Finally, from a prognostic perspective, significant differences among isolates in terms of mycelial growth suggest that in addition to an accurate identification, a phenotypic characterization of isolates affecting trees may also be important.

Autosomal Short Tandem Repeat (STR) Variation of 15 Loci in Muthanaa-Iraqi Population Revealed of New Alleles

Background:Today the Short Tandem Repeats STR” is used for personal identification widely over the world, while in Iraqi country this work field still need support to stand up really. Objectives: The study aims to estimate the allele frequency distributions and statistical forensic parameters of 15 STR and amelogenin locus, in Muthanaa Iraqi population MIP. Materials and Methods: A total of 102 buccal swab samples from healthy unrelated individuals were collected. An organic method was utilized to extract the Deoxyribonucleic acid DNA. The genotyping was carried out at 15 STR DNA markers, by Polymerase Chain Reaction using the AmpFISTR® Identifiler™ PCR Amplification Kit, the separation and detection of amplified products conducted by capillary electrophoresis in genetic analyzer. Upon the allelic frequencies, several statistical genetic and forensic parameters have been estimated using Powerstats Version 1.2 program. Results: The results revealed 17 novel alleles, shows high gene diversity, where 150 alleles were observed. The Power of Discrimination of STR markers was ranged from 0.846 of TPOX to 0.966 of D2S1338. The Combined Matching Probability CMP, Combined Power of Discrimination CPD and Combined Power of Exclusion CPE were 8.277523e-18, 0.9999and 0.9999 respectively. The comparison of PD for 10 tested loci compare

Genetic diversity analysis of the Mexican Lidia bovine breed population and its relation with the Spanish population by using a subset of SNPs under low gametic disequilibrium

Retaining features of the auroch (Bos taurus primigenius), the Lidia bovine is a primitive breed originated ~250 yr ago in the Iberian Peninsula, where is still distributed, along with France and several American countries. Selected upon a behavior, which enhances their aggressiveness; these bovines were raised to participate in popular festivities that nowadays reinforce the identity of regional cultures. Different festivities demanded diverse behavior patterns, prompting a fragmentation of the breed into small lineages. In Mexico, where these bovines reached high popularity, mainly two families of breeders imported Lidia bovines from Spain in the early XX century specializing their production either reproducing the new arrivals among them or realizing systematic crosses with local populations. Genetic diversity and structure of the Mexican and Spanish Lidia populations has been assessed with microsatellite data, but nowadays SNP molecular markers allows higher resolution level. Genetic diversity of the Mexican and Spanish Lidia populations and their relationship were assessed by using 573 SNPs with a low gametic disequilibrium (r2<0.01) from the 50K BeadChip on 468 individuals from both populations. In both populations, similar gene diversity values were observed. Significant FIS values in both populations means strong subdivision, higher FST genetic distances were observed in the Spanish than in the Mexican population. Genetic structure analysis showed similarity of three Spanish lineages with González family and some Llaguno breeders, but most Llaguno family clustered separated: genetic differentiation along with high gene diversity suggest an introgression of creole cattle in the constitution of the Mexican population.

Y-chromosome polymorphisms in the United Arab Emirates population

Y chromosome short tandem repeats (Y-STR) has been widely used in forensic DNA profiling and lineages analysis. The aim of this study is to establish a database of an extensive Y-STR profiles of the United Arab Emirates (UAE) population and to investigate the distribution of 17 Y-STR loci. Samples of 345 Emirati males using 17 Y-STR loci included in the AmpFLSTR® Y-filer® PCR Amplification kit (Life Technologies) (DYS456, DYS3891, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, GATA-H4, DYS437, DYS438 and DYS448). Statistical analysis of allele frequency, haplotype diversity and discrimination capacity were performed for the samples using Arlequin software version 3.5A total of 301 unique haplotypes were identified, 271 haplotypes were found to be unique and 22 haplotypes were shared between two individuals. In addition, there were four different haplotypes shared between more than two individuals. The haplotype diversity (HD) was found to be equal to 0.99885. The highest gene diversity was estimated to be 0.94142 for DYS385a/b whereas the lowest was estimated to be 0.4369 for DYS392. The discrimination capacity (DC) was calculated to be 90.03%

Using microsatellite markers to analyze genetic diversity in 14 sheep types in Iran

Abstract. Investigation of genetic relationship among populations has been traditionally based on the analysis of allele frequencies at different loci. The prime objective of this research was to measure the genetic polymorphism of five microsatellite markers (McMA2, BM6444, McMA26, HSC, and OarHH35) and study genetic diversity of 14 sheep types in Iran. Genomic DNA was extracted from blood samples of 565 individuals using an optimized salting-out DNA extraction procedure. The polymerase chain reaction (PCR) was successfully performed with the specific primers. Some locus–population combinations were not at Hardy–Weinberg equilibrium (P < 0. 05). The microsatellite analysis revealed high allelic and gene diversity in all 14 breeds. Pakistani and Arabi breeds showed the highest mean number of alleles (11.8 and 11 respectively), while the highest value for polymorphic information content was observed for the Arabi breed (0.88). A UPGMA (unweighted pair group method with arithmetic mean) dendrogram based on the Nei's standard genetic distance among studied breeds showed a separate cluster for Arabi and Pakistani breeds and another cluster for other breeds. The Shannon index (H0) for McMA2, BM6444, McMA26, HSC, and OarHH35 was 2.31, 2.17, 2.27, 2.04 and 2.18, respectively, and polymorphic information content (PIC) values were 0.88, 0.92, 0.87, 0.84, and 0.86 for McMA2, BM6444, McMA26, HSC, and OarHH35, respectively. The high degree of variability demonstrated within the studied sheep types implies that these populations are rich reservoirs of genetic diversity that must be preserved.

Genetic variability suggests that three populations of Ceratocystis fimbriata are responsible for the Ceratocystis wilt epidemic on kiwifruit in Brazil

Ceratocystis fimbriata is a native, soilborne pathogen in South America that causes a lethal wilt disease on a broad range of economically important plants. Ceratocystis wilt on kiwifruit (Actinidia spp.) was first recognized in 2010 in the state of Rio Grande do Sul, Brazil. The genetic variation among kiwifruit isolates was analized to determine if a single introduced strain of the pathogen was responsible for the epidemic or if there was substantial genetic variation in the population, suggesting that the fungus was soilborne and indigenous to the region. We used 14 microsatellite (simple sequence repeat, SSR) markers to identify 18 genotypes of C. fimbriata among 76 isolates from eight kiwifruit farms. The 18 genotypes clustered into three groups based on UPGMA analysis of the microsatellite alleles. The largest group comprised 60 isolates of 11 closely-related microsatellite genotypes obtained from seven of the eight farms. These genotypes appeared to have originated from a single farm that had supplied cuttings for grafting to the other farms. The population of the pathogen from the farm that supplied the cuttings had the highest level of genotypic diversity and relatively high gene diversity, suggesting that this source population represented an indigenous, soilborne population. Phylogenetic analyses of the DNA sequences of the mating type locus (including portions of MAT1-1-2 and MAT1-2-1) placed the isolates into three groups, corresponding to the three microsatellite groups. Most of the isolates, including all the tested isolates from the farm that supplied the cuttings, had mating type gene sequences that were distinct from other Brazilian populations of C. fimbriata. A second group comprised isolates from one farm that had mating type gene sequences typical of Mata Atlântica (Rio de Janeiro and Sao Paulo) populations of C. fimbriata on Colocasia esculenta and Mangifera indica. Three farms purchased kiwifruit plants or rootstocks from commercial nurseries in Brazil as well as scions from the source farm, and some of the isolates from these farms were genetically similar to Eucalyptus isolates of C. fimbriata from Bahia and Minas Gerais, Brazil. The kiwifruit epidemic in Rio Grande do Sul is the southern-most report of C. fimbriata in Brazil, and the primary pathogen population on kiwifruit appears to be indigenous and originated from a single farm that distributed the pathogen in grafting material. In addition, commercial nursery stock was also implicated as sources of C. fimbriata genotypes. The disease is a major limiting factor for kiwifruit production in southern Brazil, and the results suggest that clean planting stock will be important to successful production.

Unravelling wild carrot differentiation in Europe – preliminary data on a candidate gene approach

Carrot is an outcrossing species and levels of gene flow between populations, and even between wild and domesticated relatives, are expected to be high. Cases of natural hybridization and introgression of crops and wild relatives have been reported. Have these events diluted any putative habitat-adapted genotypes? In other words, can we still find a correlation between wild carrot genotypes and regional/local environment? We have chosen to start addressing this question using a member of the alternative oxidase (AOX) gene family. AOX genes seem to be linked to all kinds of abiotic and biotic stress reactions. Wild carrots were sampled in an environmental gradient across Western Europe. This gradient included sampling points with more deviating conditions, such as Sierra de Guadarrama or the central Pyrenees and the French Massif Central. Phylogenetic reconstruction on this molecular marker is to be combined with geographic, climatic, and ecological evidence. So far, the preliminary results suggest the existence of a biogeographical barrier at the Pyrenees, and higher gene diversity than initially expected. From an applied point of view, diversity of functional traits is much more relevant than species diversity. Gene transfer from wild to cultivated plants has contributed to the evolution of crop species. Providing that deterioration of genetic resources and biodiversity loss have not been drastic, gene transfer from wild plants has the potential to further contribute to a (targeted) improvement of cultivars.

Identification of genomic regions for grain yield and yield stability and their epistatic interactions

The task of identifying genomic regions conferring yield stability is challenging in any crop and requires large experimental data sets in conjunction with complex analytical approaches. We report findings of a first attempt to identify genomic regions with stable expression and their individual epistatic interactions for grain yield and yield stability in a large elite panel of wheat under multiple environments via a genome wide association mapping (GWAM) approach. Seven hundred and twenty lines were genotyped using genotyping-by-sequencing technology and phenotyped for grain yield and phenological traits. High gene diversity (0.250) and a moderate genetic structure (five groups) in the panel provided an excellent base for GWAM. The mixed linear model and multi-locus mixed model analyses identified key genomic regions on chromosomes 2B, 3A, 4A, 5B, 7A and 7B. Further, significant epistatic interactions were observed among loci with and without main effects that contributed to additional variation of up to 10%. Simple stepwise regression provided the most significant main effect and epistatic markers resulting in up to 20% variation for yield stability and up to 17% gain in yield with the best allelic combination.

Characterization of mitochondrial DNA polymorphisms in the Han population in Liaoning Province, Northeast China

This study characterized the genetic variations of mitochondrial DNA (mtDNA) to elucidate the maternal genetic structure of Liaoning Han Chinese. A total of 317 blood samples of unrelated individuals were collected for analysis in Liaoning Province. The mtDNA samples were analyzed using two distinct methods: sequencing of the hypervariable sequences I and II (HVSI and HVSII), and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the coding region. The results indicated a high gene diversity value (0.9997 ± 0.0003), a high polymorphism information content (0.99668) and a random match probability (0.00332). These samples were classified into 305 haplotypes, with 9 shared haplotypes. The most common haplogroup was D4 (12.93%). The principal component analysis map, the phylogenetic tree map, and the genetic distance matrix all indicated that the genetic distance of the Liaoning Han population from the Tibetan group was distant, whereas that from the Miao group was relatively close.

Forensic and population genetic analyses of the GlobalFiler STR loci in the Mongolian population

We have analyzed 24 loci including autosomal and Y-chromosomal short tandem repeats (STRs), Y-indel, and sex-determining marker in a sample of 267 unrelated individuals from the Mongolian population using the GlobalFiler™ PCR Amplification Kit to provide an expanded and more reliable forensic database. Khalkh among 15 Mongolian minor-groups accounts for about 80% of the entire Mongolian population. A total of 267 different DNA profiles were found in this work. The highest gene diversity was observed in the SE33 (0.9376) locus, and the lowest value was found in the TPOX (0.6142) locus. Although individual power of discrimination estimates varied at the studied loci, combined probability of match from the 21 STR loci was estimated to be 1.139 × 10−24, which is highly informative. Based on the results of pairwise F ST genetic distances and multi-dimensional scaling plot showed that Mongolians were clustered into Europeans and Asians, although Mongolia is geographically located in Northeastern Asia. Thus, the present survey of the Mongolian population may help establish a comprehensive reference database for forensic and population genetic analyses.

Relationship among Heterosis, Combining Ability and SSR Based Genetic Distance in Single Cross Hybrids of Maize (Zea Mays L)

Relationship among Heterosis, Combining Ability and SSR Based Genetic Distance in Single Cross Hybrids of Maize (Zea Mays L) Combining ability and heterosis for different morphological and quality traits were studied under three environments using 10 inbred lines, 45 single cross hybrids and three commercial hybrids as checks at SHIATS, Allahabad, India during monsoon, 2014. Ten simple sequence markers (SSR) were used to quantify genetic distance, which was further used to analyse relationship with combining ability and heterosis in single cross hybrids. Pearson’s correlation and linear regression were analysed to identify the important factors determining heterosis and per se performance of hybrids. Variances due to general combining ability (GCA) and specific combining ability (SCA) were found to be significant for all but their interaction with environments were significant only for morphological traits. SSR marker bnlg 1523 was found as a potential marker for discriminating maize inbred lines at molecular level as it has high PIC (0.71) and gene diversity (0.74). Significant positive association were recorded for per se performance with mid parent heterosis (MPH) and best parent heterosis (BPH) along with high coefficient of determination for days to 50% tasseling, days to 50% silking, days to 50% maturity, seed fill duration, number of grain rows/cob, number of grains/row, 100 seed weight, grain yield/plant, starch, protein and oil content. Moreover, F1’s grain yield showed significant positive relationship with varying degree to MPH, BPH and SCA of hybrids in all environments. Correlation of SSR based genetic distance with heterosis and combining ability was significant positive for oil content but non-significant positive or negative for other traits indicating the significant role of SSR based genetic distance for determining heterosis and combining ability of oil content. Besides, SCA was found as a key determinant for heterosis and mean performance of all morphological and quality traits...

Fertility variation among individuals in natural stands of Acacia leucophloea

Abstract Growth characteristics and fertility variations were evaluated at four natural stands of tropical arid zone species, A. leucophloea in southern India. Three stands (TNL 1, TNL 2 and PDM) were situated in dry upland regions while one stand (RKP) was at waterlogged site. The tree height and girth at breast height did not vary between stands in two years. Fertility variation (sibling coefficient, ψ) was estimated based on flowering abundance and fruit set collected for two consecutive years. Fruit production per tree was generally lower in the RKP stand than the other three stands. No year-to-year variation was observed on fruit set in all stands. Growth and flower production showed a weak-positive correlation in both years (R2 = 0.39 to 0.1). The correlation to check if the larger inflorescence size, the higher number of fruit production was also failed. Male fertility variation did not vary much among stands (ψm = 1.28 ~ 1.62). Female fertility variation was low (ψf = 1.71 ~ 2.02) in the three stands situated in dry upland regions than the RKP stand (ψf = 4.09 ~ 4.16). The cumulative contribution of trees to the overall fertility was deviated from the ideal situation (equal contribution) in all stands, especially the RKP stand showed a skewed distribution (R2 ≤ 6.5). The effective population size was low in the RKP predicting a high genetic drift when compared with other sites. Similarly high group coancestry and low gene diversity were observed in the stand RKP. The implications of fertility variation on gene diversity of the species and future management of the natural stands were also discussed.

Genetic diversity of high-molecular-weight glutenin subunit compositions in bread wheat landraces originated from Turkey

AbstractFocusing on 116 bread wheat landraces, this study investigated high molecular weight glutenin allele polymorphism, gene diversity, genetic variation and linkage disequilibrium (LD) inGlu-1loci. To identify gluten alleles, sodium dodesyl sulphate-polyacrylamide, gel electrophoresis was used and for statistical analyses POPGENE software was employed. The results indicated that average genetic variation (h) was the highest inGlu-B1(0.6421) and the lowest inGlu-A1locus (0.4548); genetic similarity ratio (I) was the highest inGlu-B1(1.4170); the highest average genetic diversity (Ht) was observed inGlu-B1(0.6575) and the lowest diversity was observed inGlu-A1(0.4558). It was also observed that genetic diversity inGlu-1locus was largely due to intra-population variations. Inter-population gene flow was also calculated as 4.0051. Marmara and Southeastern Anatolia regions, the results further indicated, had the highest (2.8691) and lowest (0.1694) heterozygosity. Genetic erosion risk for Turkish bread wheat landraces was also seen to be high. Considering the mutual analyses of subunits of nationwide wheat landraces, it is possible to speculate about a limited migration between the landraces. LD of the landraces was largely because of this limited migration and/or epistatic natural selection. Since Turkey is known as the gene centre for major cereals including wheat, barley, rye and oat, where they diversified and spread throughout the world, studying the gluten allele diversity of Turkish bread wheat landraces is important. In addition, this study has revealed the applicability of LD, and neutrality tests to gluten protein diversity for the first time.

A Reassessment of the Impact of European Contact on the Structure of Native American Genetic Diversity.

Our current understanding of pre-Columbian history in the Americas rests in part on several trends identified in recent genetic studies. The goal of this study is to reexamine these trends in light of the impact of post-Columbian admixture and the methods used to study admixture. The previously-published data consist of 645 autosomal microsatellite genotypes from 1046 individuals in 63 populations. We used STRUCTURE to estimate ancestry proportions and tested the sensitivity of these estimates to the choice of the number of clusters, K. We used partial correlation analyses to examine the relationship between gene diversity and geographic distance from Beringia, controlling for non-Native American ancestry (from Africa, Europe and East Asia), and taking into account alternative paths of migration. Principal component analysis and multidimensional scaling were used to investigate the relationships between Andean and non-Andean populations and to explore gene-language correspondence. We found that 1) European and East Asian ancestry estimates decline as K increases, especially in Native Canadian populations, 2) a north-south decline in gene diversity is driven by low diversity in Amazonian and Paraguayan populations, not serial founder effects from Beringia, 3) controlling for non-Native American ancestry, populations in the Andes and Mesoamerica have higher gene diversity than populations in other regions, and 4) patterns of genetic and linguistic diversity are poorly correlated. We conclude that patterns of diversity previously attributed to pre-Columbian processes may in part reflect post-Columbian admixture and the choice of K in STRUCTURE analyses. Accounting for admixture, the pattern of diversity is inconsistent with a north-south founder effect process, though the genetic similarities between Mesoamerican and Andean populations are consistent with rapid dispersal along the western coast of the Americas. Further, even setting aside the disruptive effects of European contact, gene-language congruence is unlikely to have ever existed at the geographic scale analyzed here.

The Evolution of Innate Immune Genes: Purifying and Balancing Selection on β-Defensins in Waterfowl.

In disease dynamics, high immune gene diversity can confer a selective advantage to hosts in the face of a rapidly evolving and diverse pathogen fauna. This is supported empirically for genes involved in pathogen recognition and signalling. In contrast, effector genes involved in pathogen clearance may be more constrained. β-Defensins are innate immune effector genes; their main mode of action is via disruption of microbial membranes. Here, five β-defensin genes were characterized in mallards (Anas platyrhynchos) and other waterfowl; key reservoir species for many zoonotic diseases. All five genes showed remarkably low diversity at the individual-, population-, and species-level. Furthermore, there was widespread sharing of identical alleles across species divides. Thus, specific β-defensin alleles were maintained not only spatially but also over long temporal scales, with many amino acid residues being fixed across all species investigated. Purifying selection to maintain individual, highly efficacious alleles was the primary evolutionary driver of these genes in waterfowl. However, we also found evidence for balancing selection acting on the most recently duplicated β-defensin gene (AvBD3b). For this gene, we found that amino acid replacements were more likely to be radical changes, suggesting that duplication of β-defensin genes allows exploration of wider functional space. Structural conservation to maintain function appears to be crucial for avian β-defensin effector molecules, resulting in low tolerance for new allelic variants. This contrasts with other types of innate immune genes, such as receptor and signalling molecules, where balancing selection to maintain allelic diversity has been shown to be a strong evolutionary force.

Assessment of genetic diversity in natural European hophornbeam (Ostrya carpinifolia Scop.) populations in Turkey

ABSTRACTGenetic diversity is a crucial component for plant survivability and fitness in terms of adaptation, genetic stability and variability. In this study, a total of 160 genotypes were investigated using 12 random amplified polymorphic DNA (RAPD) primers to understand the genetic structure and diversity of nine naturally distributed Ostrya carpinifolia populations in Turkey. Twelve RAPD primers yielded 111 clearly identifiable DNA bands, of which 71 bands were found to be polymorphic (64%). Observed number of alleles (Na), effective number of alleles (Ne) and Nei's gene diversity (h) were found as 2, 1.53 and 0.32, respectively. Total genetic variation (HT), within-population genetic variation (HS) and Nei's genetic differentiation coefficient (GST) were found as 0.32, 0.09 and 0.70, respectively. Genetic diversity analysis (AMOVA) revealed highly significant (P < 0.001) genetic variations among and within populations. 69.94% of total variation was observed among populations while 26.69% was within populations. Gene flow value was calculated as 0.21 (Nm < 0.5), which could homogenize the genetic structure of a population. Two geographically isolated populations demonstrated high gene diversity and polymorphic loci ratio, indicating a relationship between geographic distribution of populations and eco-geographic factors. The findings of this study will pave the way for understanding the genetic diversity between inter- and intra-populations of O. carpinifolia species, as well as they would provide valuable information for management, conservation and utilization of in situ and ex situ Ostrya germplasms.

Characterization of Three Rice Multiparent Advanced Generation Intercross (MAGIC) Populations for Quantitative Trait Loci Identification.

Three new rice ( L.) multiparent advanced generation intercross (MAGIC) populations were developed using eight elite rice varieties from different breeding programs. These three populations were two recombinant inbred line (RIL) populations derived from two 4-way crosses, DC1 and DC2, and one RIL population derived from an 8-way cross. These populations were genotyped using an Illumina Infinium rice 6K SNP chip. The potential of the three MAGIC populations in identifying marker-trait associations was demonstrated using the plant height (PH) and heading date (HD) measured in 2014. A population of 248 IRRI breeding lines and a population of 323 Chinese breeding lines were also included to compare genetic diversity and linkage disequilibrium (LD) pattern. Our study discovered that (i) the 8-way population had a higher gene diversity than the DC1, DC2, and IRRI populations; (ii) all three MAGIC populations showed no clear population structure; (iii) LD decayed to < 0.2 at about 2.5, 2.5, 1.25, 1.75, and 4.0 Mb for the DC1, DC2, 8-way, IRRI, and Chinese populations, respectively; and (iv) the 8-way population was more powerful than the DC1, DC2, and IRRI populations on QTL identification. The association analysis identified two and three QTL for PH and HD, respectively. Four of the five QTL had peak markers close to known genes. A novel QTL for PH was identified on chromosome 12 using the 8-way population. Therefore, our study suggests that the three new MAGIC populations are valuable resources for QTL identification.

Comparative population structure and trichothecene mycotoxin profiling of Fusarium graminearum from corn and wheat in Ontario, central Canada

Fusarium graminearum causes fusarium head blight (FHB) of wheat and gibberella ear rot (GER) of corn in Canada and also contaminates grains with trichothecene mycotoxins. Very little is known about trichothecene diversity and population structure of the fungus from corn in Ontario, central Canada. Trichothecene genotypes of F. graminearum isolated from corn (n = 452) and wheat (n = 110) from 2010 to 2012 were identified. All the isolates were deoxynivalenol (DON) type. About 96% of corn isolates and 98% of wheat isolates were 15‐acetyl deoxynivalenol (15ADON) type. The fungal population structures from corn (n = 313) and wheat (n = 73) were compared using 10 variable number tandem repeat (VNTR) markers. The fungal populations and subpopulations categorized based on host, cultivar groups, years and geography showed high gene (H = 0.818–0.928) and genotypic (GD = 0.999–1.00) diversity. Gene flow was also high between corn and wheat population pairs (Nm = 8.212), and subpopulation pairs within corn (Nm = 7.13–23.614) or wheat (Nm = 19.483) populations. Phylogenetic analysis revealed that isolates from both hosts were F. graminearum clade 7. These findings provide baseline data on 3‐acetyl deoxynivalenol (3ADON) and 15ADON profiles of F. graminearum isolates from corn in Canada and are useful in evaluating mycotoxin contamination risks in corn and wheat grains. Understanding the fungal genetic structure will assist evaluation and development of resistant cultivars/germplasm for FHB on wheat and GER on corn.

Population Structuring of Land and Coastal Ducks (&lt;i&gt;Anas platyrhynchos&lt;/i&gt;) Using Microsatellite Markers

Twenty-four polymorphic and ubiquitously distributed microsatellite loci were utilized to genotype four populations of indigenous Mallard ducks in India using Khaki campbell as an out-group. The data was used to establish population parameters and genetic relationship among the populations. All the selected loci exhibited high polymorphic information content and gene diversity. F -statistics revealed population structure in four indigenous duck populations. There was not much differentiation among the duck populations along coastline, while land birds were found to be distinct from coastline ducks. The data presented here will be useful for undertaking duck improvement programmes in future.