Haplotype Patterns Research Articles

Repeated hybridization of two closely related gazelle species (Gazella bennettii and Gazella subgutturosa) in central Iran.

Interspecific hybridization increasingly occurs in the course of anthropogenic actions, such as species translocations and introductions, and habitat modifications or occurs in sympatric species due to the shortage of conspecific mates. Compared with anthropogenically caused hybridization, natural hybridization is more difficult to prove, but both play an important role in conservation. In this study, we detected hybridization of two gazelle sister species, Gazella bennettii (adapted to dry areas) and Gazella subgutturosa (adapted to open plains), in five habitat areas, where G. bennettii naturally occur in central Iran. The hybrids have a nuclear genomic identity (based on two introns), habitat preference, and phenotype of G. bennettii, but the mitochondrial identity (based on cyt b) of G. subgutturosa. We suggest that natural hybridization of female G. subgutturosa and male G. bennettii happened twice in central Iran in prehistoric times, based on the haplotype pattern that we found. However, we found indications of recent hybridization between both species under special circumstances, for example, in breeding centers, due to translocations, or in areas of sympatry due to the shortage of conspecific mates. Therefore, these two species must be kept separately in the breeding centers, and introduction of one of them into the habitat of the other must be strictly avoided.

Differences in local population history at the finest level: the case of the Estonian population

Several recent studies detected fine-scale genetic structure in human populations. Hence, groups conventionally treated as single populations harbour significant variation in terms of allele frequencies and patterns of haplotype sharing. It has been shown that these findings should be considered when performing studies of genetic associations and natural selection, especially when dealing with polygenic phenotypes. However, there is little understanding of the practical effects of such genetic structure on demography reconstructions and selection scans when focusing on recent population history. Here we tested the impact of population structure on such inferences using high-coverage (~30×) genome sequences of 2305 Estonians. We show that different regions of Estonia differ in both effective population size dynamics and signatures of natural selection. By analyzing identity-by-descent segments we also reveal that some Estonian regions exhibit evidence of a bottleneck 10–15 generations ago reflecting sequential episodes of wars, plague and famine, although this signal is virtually undetected when treating Estonia as a single population. Besides that, we provide a framework for relating effective population size estimated from genetic data to actual census size and validate it on the Estonian population. This approach may be widely used both to cross-check estimates based on historical sources as well as to get insight into times and/or regions with no other information available. Our results suggest that the history of human populations within the last few millennia can be highly region specific and cannot be properly studied without taking local genetic structure into account.

Evolutionary relationship and population structure of domestic Bovidae animals based on MHC-linked and neutral autosomal microsatellite markers

Major histocompatibility complex (MHC) genes are critical for disease resistance or susceptibility responsible for host-pathogen interactions determined mainly by extensive polymorphisms in the MHC genes. Here, we examined the diversity and phylogenetic pattern of MHC haplotypes reconstructed using three MHC-linked microsatellite markers in 55 populations of five Bovidae species and compared them with those based on neutral autosomal microsatellite markers (NAMs). Three-hundred-and-forty MHC haplotypes were identified in 1453 Bovidae individuals, suggesting significantly higher polymorphism and heterozygosity compared with those based on NAMs. The ambitious boundaries in population differentiation (phylogenetic network, pairwise FST and STRUCTURE analyses) within and between species assessed using the MHC haplotypes were different from those revealed by NAMs associated closely with speciation, geographical distribution, domestication and management histories. In addition, the mean FST was significantly correlated negatively with the number of observed alleles (NA), observed (HO) and expected (HE) heterozygosity and polymorphism information content (PIC) (P < 0.05) in the MHC haplotype dataset while there was no correction of the mean FST estimates (P> 0.05) between the MHC haplotype and NAMs datasets. Analysis of molecular variance (AMOVA) revealed a lower percentage of total variance (PTV) between species/groups based on the MHC-linked microsatellites than NAMs. Therefore, it was inferred that individuals within populations accumulated as many MHC variants as possible to increase their heterozygosity and thus the survival rate of their affiliated populations and species, which eventually reduced population differentiation and thereby complicated their classification and phylogenetic relationship inference. In summary, host-pathogen coevolution and heterozygote advantage, rather than demographic history, act as key driving forces shaping the MHC diversity within the populations and determining the interspecific MHC diversity.

Fc-gamma IIIa-V158F receptor polymorphism contributes to the severity of Guillain-Barré syndrome.

ObjectiveGuillain‐Barré syndrome (GBS) is a rare, life‐threatening disorder of the peripheral nervous system. Immunoglobulin G Fc‐gamma receptors (FcγRs) mediate and regulate diverse effector functions and are involved in the pathogenesis of GBS. We investigated whether the FcγR polymorphisms FcγRIIa H/R131 (rs1801274), FcγRIIIa V/F158 (rs396991), and FcγRIIIb NA1/NA2, and their haplotype patterns affect the affinity of IgG‐FcγR interactivity and influence GBS susceptibility and severity.MethodsWe determined FcγR polymorphisms in 303 patients with GBS and 302 ethnically matched healthy individuals from Bangladesh by allele‐specific polymerase chain reaction. Pairwise linkage disequilibrium and haplotype patterns were analyzed based on D ´statistics and the genotype package of R statistics, respectively. Logistic regression analysis and Fisher’s exact test with corrected P (Pc) values were employed for statistical comparisons.ResultsFcγRIIIa‐V158F was associated with the severe form of GBS compared to the mild form (P = 0.005, OR = 2.24, 95% CI = 1.28–3.91; Pc = 0.015); however, FcγR genotypes and haplotype patterns did not show any association with GBS susceptibility compared to healthy controls. FcγRIIIa‐V/V158 and FcγRIIIb‐NA2/2 were associated with recent Campylobacter jejuni infection (P ≤ 0.001, OR = 0.36, 95% CI = 0.23–0.56; Pc ≤ 0.003 and P = 0.004, OR = 1.70, 95% CI = 1.18–2.44; Pc ≤ 0.012, respectively). Haplotype 1 (FcγRIIa‐H131R‐ FcγRIIIa‐V158F‐ FcγRIIIb‐NA1/2) and the FcγRIIIb‐NA2/2 genotype were more prevalent among anti‐GM1 antibody‐positive patients (P = 0.031, OR = 9.61, 95% CI = 1.24–74.77, Pc = 0.279; P = 0.027, OR = 1.62, 95% CI = 1.06–2.5, Pc = 0.081, respectively).InterpretationFcγR polymorphisms and haplotypes are not associated with susceptibility to GBS, though the FcγRIIIa‐V158F genotype is associated with the severity of GBS.

New insights into the haplotype diversity of the cosmopolitan cat flea Ctenocephalides felis (Siphonaptera: Pulicidae)

The present study investigated the genetic profile of the cosmopolitan cat flea, Ctenocephalides felis (Siphonaptera: Pulicidae) from Malaysia and the reference data available in the National Center for Biotechnology Information (NCBI) GenBank. A set of sequences of 100 Malaysian samples aligned as 550 characters of the cytochrome c oxidase subunit I (cox1) and 706 characters of the II (cox2) genes revealed ten haplotypes (A1–A10) and eight haplotypes (B1–B8), respectively. The concatenated sequences of cox1 and cox2 genes with a total of 1256 characters revealed 15 haplotypes (AB1–AB15). Analyses indicated that haplotype AB1 was the most frequent and the most widespread haplotype in Malaysia. Overall haplotype and nucleotide diversities of the concatenated sequences were 0.52909 and 0.00424, respectively, with moderate genetic differentiation (FST = 0.17522) and high gene flow (Nm = 1.18). The western population presented the highest genetic diversity (Hd = 0.78333, Pi = 0.01269, Nh = 9), whereas the southern population demonstrated the lowest diversity (Hd = 0.15667, Pi = 0.00019, Nh = 3). The concatenated sequences showed genetic distances ranged from 0.08 % to 4.39 %. There were three aberrant haplotypes in cox2 sequences that highly divergent, suggesting the presence of cryptic species or occurrence of introgression. In the global point of view, the aligned sequences of C. felis revealed 65 haplotypes (AA1–AA65) by the cox1 gene (n = 586), and 27 haplotypes (BB1–BB27) by the cox2 gene (n = 204). Mapping of the haplotype network showed that Malaysian C. felis possesses seven unique haplotypes in both genes with the common haplotypes demonstrated genetic affinity with C. felis from Southeast Asia for cox1 and South America for cox2. The topologies of cox1 and cox2 phylogenetic trees were concordant with relevant grouping pattern of haplotypes in the network but revealed two major lineages by which Malaysian haplotypes were closely related with haplotypes from the tropical region.

Genetic diversity of Tulipa suaveolens (Liliaceae) and its evolutionary relationship with early cultivars of T. gesneriana

Polychromatic Tulipa suaveolens occurs over a vast territory ranging from the Crimea to eastern Kazakhstan. Its phylogenetic relationship to cultivated T. gesneriana is still under discussion. We used sequences from the psbE–petL region of chloroplast DNA and the complete internal transcribed spacer of nuclear ribosomal DNA to examine the genetic variability of T. suaveolens specimens from European Russia and the adjoining regions. Our data set also included 8 varieties of cultivated T. gesneriana. The research on biogeographic patterns of plastid haplotype and nuclear ribotype distribution provides evidence that their origin and dispersal over the Lower and Middle Volga Region are linked to the Khazar or Early Khvalynian transgression of the Caspian Sea and subsequent events. In the Crimea and the adjacent regions, the pattern of haplotypes’ distribution indicates that their origin and expansion may be linked to the Karangat transgression of the Black Sea and the subsequent New Euxinian regression. Based on our results, we propose that T. suaveolens is the likeliest wild ancestor of early T. gesneriana.

Phylogeography of the Siberian weasel (Mustela sibirica), based on a mitochondrial DNA analysis

AbstractWe investigated the genetic diversity and distribution pattern of mitochondrial DNA control-region haplotypes across the distributional range of the Siberian weasel (Mustela sibirica) in Eastern Eurasia. We identified 23 haplotypes from 65 individuals sampled from 21 localities. Our analyses showed two major phylogeographical groups: group I comprised continental Russia, Tsushima and Korea, and group II comprised China, Taiwan and Korea. Two novel haplotypes found in the Amur area and one from Gansu Province were closely related to the Tsushima and Taiwan clades, respectively. Phylogeographical and demographic analyses indicated a recent population expansion for group I, whereas no clear evidence for expansion was obtained for group II. The recent expansion of group I is also supported by historical records. Closely related haplotypes were found between the continental populations and the insular populations on Tsushima and Taiwan, suggesting that the ancestors of the insular populations immigrated from the continent via land bridges. The two groups could have evolved allopatrically in parts of eastern Asia differing in climate and vegetation.

A haplotype-specific linkage disequilibrium pattern of monoamine oxidase A gene associated with regular smoking in women.

Cigarette smoking in women is raising a public health problem. The X-linked monoamine oxidase A (MAOA) was considered as a susceptibility gene to substance abuse of tobacco, but the evolutionary effect of MAOA may lead to a positive or negative association between genetic variations and smoking development among study regions. Based on linkage disequilibrium (LD), we performed a haplotype-based association to explore the effect of MAOA gene on women's smoking risk in a case-control study. Genotyped single nucleotide polymorphisms (SNPs) of MAOA gene, rs5953210G>A, rs2283725A>G and rs1137070T>C, were significantly associated with current smoking risk in women, and the increased level of plasma MAO-A activity was raised with per copy increment of risk allele in current smokers (P < .01). The haplotype patterns with minor haplotype frequency >.05 were constructed using the Expectation-Maximization algorithm, and the haplotype-specific A-G-C pattern raised the 2-fold risk to develop regular smoking (P = .0005). In the diplotype analysis based on X-inactivation mechanism relative to no and full dosage compensation, we showed that A-G-C haplotype not only increased regular smoking risk in a dose-dependent manner (Ptrend = .0011) but also contributed to smoking risk in the dosage compensation mechanism. Compared to non-smokers, the effect of A-G-C haplotype on random X-activation was associated with the raised MAO-A activity in women smokers (P < .05) although the lifetime cigarette consumption showed a difference that was not statistically significant. This study provides information on MAOA LD-based haplotype and diplotype patterns in women smoking.

Designation of flyways and genetic structure of Woodpigeon Columba palumbus in Europe and Morocco

The Woodpigeon Columba palumbus is an abundant and widespread Palearctic species that uses multiple flyways in Europe. The designation of the main flyways of Woodpigeon in Europe and the study of the genetic structure of the populations are necessary for the sustainable management of this species. Both ringing recovery data of Woodpigeons and mtDNA D-loop sequences from 606 individuals sampled across Europe and in Morocco were used in this study. In total, 763 direct recoveries of birds ringed during the breeding season in 1908–2016 were analysed, while D-loop sequences were analysed from 416 birds sampled in 2014–2018 and 190 individuals that had been sampled in 2004–2009 for a preliminary investigation. In the median-joining network of D-loop haplotypes, six haplogroups were identified in Woodpigeons from various biogeographical populations. Certain differences in the frequency of haplogroups were found between resident Woodpigeons of the Iberian Peninsula and migratory birds from Eastern and Northern Europe. Relatively low genetic variability within the D-loop was observed in samples of resident birds from the Balearic Islands and the Iberian Peninsula. No genetic variation was found in resident Woodpigeons breeding in Morocco. The analysis of ringing recovery data and distribution patterns of different haplotypes confirmed that Woodpigeons from the north and east of Europe use the Eastern Atlantic flyway, while birds breeding in Hungary use the Mediterranean flyway. It is likely that Woodpigeons from south-eastern Russia, eastern Ukraine and birds breeding further east use the Black Sea flyway. It was also confirmed that the majority of Woodpigeons breeding in Belgium are resident or short-distance migrants. Due to the variability identified in the genetic make-up of different populations of Woodpigeons in Europe, we remark the management implications regarding the species that are relevant in various regions of the continent.

Genetic variability in Iranian limb-girdle muscular dystrophy type 2B patients: An evidence of a founder effect.

BackgroundDysferlinopathies are a group of autosomal recessive limb‐girdle muscular dystrophies (LGMDs) caused by mutations in DYSF (#603,009). This gene encodes a transmembrane protein called dysferlin. Since there are few reports on Iranian dysferlinopathy patients, we tried to identify the DYSF mutations in affected individuals of Iran.MethodsEight unrelated Iranian families have been selected for this study. Sanger sequencing followed by haplotype analysis was performed to identify individual variations in DYSF sequence. Identified variants were analyzed, and their pathogenicity was interpreted according to the recommendations of the American College of Medical Genetics and Genomics.ResultsWe identified two new mutations in DYSF, the first one is a nonsense mutation c.2419C > T (p.Gln807*), which eliminates downstream part of the protein. Another novel mutation is c. (1,053 + 1_1,054‐1)_(1,397 + 1_1,398‐1)del, which causes deletion of the DNA segment from exon 12 to exon 15.ConclusionTwo of the other six families are from the same ethnicity and share the same mutation and haplotype patterns, suggesting a founder mutation. Genetic analysis of dysferlinopathy can prevent a wrong diagnosis of myositis for these patients.

Interspecific Gene Exchange Introduces High Genetic Variability in Crop Pathogen.

Genome analyses have revealed a profound role of hybridization and introgression in the evolution of many eukaryote lineages, including fungi. The impact of recurrent introgression on fungal evolution however remains elusive. Here, we analyzed signatures of introgression along the genome of the fungal wheat pathogen Zymoseptoria tritici. We applied a comparative population genomics approach, including genome data from five Zymoseptoria species, to characterize the distribution and composition of introgressed regions representing segments with an exceptional haplotype pattern. These regions are found throughout the genome, comprising 5% of the total genome and overlapping with > 1,000 predicted genes. We performed window-based phylogenetic analyses along the genome to distinguish regions which have a monophyletic or nonmonophyletic origin with Z. tritici sequences. A majority of nonmonophyletic windows overlap with the highly variable regions suggesting that these originate from introgression. We verified that incongruent gene genealogies do not result from incomplete lineage sorting by comparing the observed and expected length distribution of haplotype blocks resulting from incomplete lineage sorting. Although protein-coding genes are not enriched in these regions, we identify 18 that encode putative virulence determinants. Moreover, we find an enrichment of transposable elements in these regions implying that hybridization may contribute to the horizontal spread of transposable elements. We detected a similar pattern in the closely related species Zymoseptoria ardabiliae, suggesting that hybridization is widespread among these closely related grass pathogens. Overall, our results demonstrate a significant impact of recurrent hybridization on overall genome evolution of this important wheat pathogen.

Human leukocyte antigen‐DQB1 polymorphisms and haplotype patterns in Guillain‐Barré syndrome

ObjectiveThe etiology of Guillain‐Barré syndrome (GBS) remains enigmatic, although genetic and environmental factors are speculated to be associated with this autoimmune condition. We investigated whether polymorphisms and the haplotype structures of the human leukocyte antigen (HLA)‐DQB1 gene relate to the autoimmune response to infection and affect the development of GBS.Methods HLA‐DQB1 polymorphic alleles (*0201, *030x, *0401, *050x, *060x) were determined for 151 Bangladeshi patients with GBS and 151 ethnically matched healthy controls using sequence‐specific polymerase chain reaction. Pairwise linkage disequilibrium (LD) and haplotype patterns were analyzed based on D ´statistics and the genotype package in R statistics, respectively. Association studies were conducted using Fisher's exact test and logistic regression analysis. The Bonferroni method was applied to correct for multiple comparisons, whereby the P‐value was multiplied with the number of comparisons and denoted as Pc (Pc, P corrected).ResultsNo associations were observed between HLA‐DQB1 alleles and susceptibility to disease in the comparison between GBS patients and healthy subjects. Haplotype 9 (DQB1*0303‐*0601) tended to be less frequent among patients with GBS than healthy controls (P = 0.006, OR = 0.49, 95% CI = 0.30–0.82; Pc = 0.06). Haplotype 5 (DQB1*0501‐*0602) and the DQB1*0201 alleles were more frequent in the Campylobacter jejuni‐triggered axonal variant of GBS (P = 0.024, OR = 4.06, 95% CI = 1.25–13.18; Pc = 0.24) and demyelinating subtype (P = 0.027, OR = 2.68, 95% CI = 1.17–6.17; Pc = 0.35), though these associations were not significant after Bonferroni correction.InterpretationThis study indicates that HLA‐DQB1 polymorphisms are not associated with susceptibility to GBS. In addition, these genetic markers did not influence the clinical features or serological subgroup in patients with C. jejuni‐triggered axonal variant of GBS.

Relationship between T-cell receptor α gene polymorphisms and symptomatic differences in patients with narcolepsy type 1.

Recent genome-wide association studies have identified an important role of T-cell receptor α (TRA) gene in the development of narcolepsy type 1. However, the role of TRA haplotype polymorphisms in the symptomatic diversity of narcolepsy remains unclear. This study aimed to investigate whether TRA polymorphisms can influence the symptomatic diversity of narcolepsy. Totally, 903 patients with narcolepsy type 1 were included in the study. Patients were divided into different groups according to their symptoms. First, 13 genotyped single nucleotide polymorphisms in the TRA were assessed for their association with symptoms of narcolepsy. We used the Chi-square test to determine differences in genotype frequencies in patients with narcolepsy. Further, we identified the haplotypes and variations of the TRA and tested their association with the symptoms of narcolepsy using a logistic regression model. According to the results of the logistic regression, TRA haplotypes TG and CT were significantly associated with auditory hallucination, with odds ratios of 1.235 (95% confidence interval [CI], 1.012-1.507) and 1.236 (95% CI, 1.012-1.511), respectively (P < 0.05). The patterns of haplotype in TRA (haplotypes TG and CT) are associated with hypnagogic auditory hallucination in patients with narcolepsy type 1. However, further studies are needed to confirm our results and explore the underlying mechanisms.

Episodic but ample sporophyte production in the moss Drepanocladus turgescens (Bryophyta: Amblystegiaceae) in SE Sweden

Abstract In the Baltic area, the long-lived dioicous wetland moss Drepanocladus turgescens (T.Jensen) Broth. produces sporophytes rarely and at irregular intervals. Based on surveys of sporophyte occurrences at 13 sites in two regions in northern Gotland (Sweden) during three to five years, we ask: (1) Is sporophyte formation associated with precipitation and a precipitation index that considers the dry periods during July-August of the preceding year, when gametangia are formed and fertilization occurs? (2) Does the estimated spore output suffice for the species’ long-term persistence of the (Northern) European population species? In one of the study regions, where D. turgescens occurs in depressions, sporophyte formation was associated with the two precipitation parameters. In the other study region, with relatively higher precipitation and exposed occurrences on a slightly sloping bedrock with very little accumulated soil, no such association existed. We suggest that this lack of weather effects results from that the exposed rock habitat requires longer continuously wet periods than the depression habitat to allow for gametangia initiation and development, and fertilisation. Average spore production for six spore capsules, from three Gotland localities was 181,000. Based on the sporophyte counts during the survey years, we estimated the total reproductive output as 411.5 million spores in 2013, and 42.5 million in 2015, in the two respective study regions. Taken together with data on haplotype patterns and considering observations on recent colonisations, we argue that such a relatively low and episodic regional spore production is sufficient to maintain global populations of long-lived species, even if these occur in specialized and geographically restricted habitats.

Examining population structure of a bertha armyworm, Mamestra configurata (Lepidoptera: Noctuidae), outbreak in western North America: Implications for gene flow and dispersal.

The bertha armyworm (BAW), Mamestra configurata, is a significant pest of canola (Brassica napus L. and B. rapa L.) in western North America that undergoes cyclical outbreaks every 6–8 years. During peak outbreaks millions of dollars are spent on insecticidal control and, even with control efforts, subsequent damage can result in losses worth millions of dollars. Despite the importance of this pest insect, information is lacking on the dispersal ability of BAW and the genetic variation of populations from across its geographic range which may underlie potential differences in their susceptibility to insecticides or pathogens. Here, we examined the genetic diversity of BAW populations during an outbreak across its geographic range in western North America. First, mitochondrial cytochrome oxidase 1 (CO1) barcode sequences were used to confirm species identification of insects captured in a network of pheromone traps across the range, followed by haplotype analyses. We then sequenced the BAW genome and used double-digest restriction site associated DNA sequencing, mapped to the genome, to identify 1000s of single nucleotide polymorphisms (SNP) markers. CO1 haplotype analysis identified 9 haplotypes distributed across 28 sample locations and three laboratory-reared colonies. Analysis of genotypic data from both the CO1 and SNP markers revealed little population structure across BAW’s vast range. The CO1 haplotype pattern showed a star-like phylogeny which is often associated with species whose population abundance and range has recently expanded and combined with pheromone trap data, indicates the outbreak may have originated from a single focal point in central Saskatchewan. The relatively recent introduction of canola and rapid expansion of the canola growing region across western North America, combined with the cyclical outbreaks of BAW caused by precipitous population crashes, has likely selected for a genetically homogenous BAW population adapted to this crop.

Early non-invasive detection of stage Ia lung cancer using circulating tumor DNA methylation haplotypes (ctmDNA) in plasma.

e13159 Background: Lung cancer is one of the most common forms of cancer and is responsible for approximately 1.8 million deaths per year worldwide. The current 5-year survival rate for lung cancer is only 18%; however, this improves to 56% if the cancer is detected early. While low-dose CT scans have shown promise as an early detection method, only 16% of lung cancer is currently detected at an early stage. We therefore set out to develop a non-invasive blood-based screening assay to identify lung cancer at an early stage using ctmDNA (circulating tumor methylated DNA haplotypes). Methods: Blood samples were prospectively collected from two partner hospitals from 325 healthy individuals and 116 individuals diagnosed with lung nodules by low-dose CT scan in EDTA or Streck BCT tubes and immediately separated into plasma. Patients with lung nodules that appeared cancerous then underwent surgical resection, and cancer diagnosis was confirmed via pathology. Patients were matched between healthy and cancer groups by age, sex, and smoking status. Plasma samples were processed using the Singlera Genomics LUNA assay, a targeted bisulfite sequencing method which identifies methylation haplotype patterns related to early-stage lung cancer. 241 samples were used to train a classification model based on pathology results, and 200 samples were used as a test set to validate the model. Results: In the independent test set, the LUNA assay was able to show a sensitivity of 91.9% to detect early-stage lung cancer with a specificity of 93.3% in healthy patients. Even patients with stage Ia lung cancer were readily detected by the LUNA assay (sensitivity of 91.7%). Conclusions: We have shown that ctmDNA can be utilized to non-invasively screen for early-stage lung cancer with high sensitivity and specificity, paving the way for a blood-based lung cancer early screening assay.

Phylogenetic analysis of exotic invasive species of the brine shrimp Artemia Leach, 1819 (Branchiopoda, Anostraca) in Al Wathba Wetland Reserve (U.A.E.; Abu Dhabi)

Abstract The taxonomic identity of an unknown Artemia population inhabiting the Al Wathba Wetland Reserve in Abu Dhabi, U.A.E., was determined using phylogenetic analysis of the mitochondrial marker Cytochrome Oxidase Subunit 1 (COI). The results showed that the examined population belongs to an exotic invasive species, Artemia franciscana. Based on the distribution pattern of haplotypes, the studied population could possibly have originated from that inhabiting the Great Salt Lake (Utah, U.S.A.).

Identification of spontaneous mutation for broad-spectrum brown planthopper resistance in a large, long-term fast neutron mutagenized rice population

BackgroundThe development of rice varieties with broad-spectrum resistance to insect pests is the most promising approach for controlling a fast evolving insect pest such as the brown planthopper (BPH). To cope with rapid evolution, discovering new sources of broad-spectrum resistance genes is the ultimate goal.ResultsWe used a forward genetics approach to identify BPH resistance genes in rice (Oryza sativa L.) using double digest restriction site-associated DNA sequencing (ddRADseq) for quantitative trait loci (QTL)-seq of the backcross inbred lines (BILs) derived from a cross between the BPH-susceptible cultivar KDML105 and BPH-resistant cultivar Rathu Heenati (RH). Two major genomic regions, located between 5.78–7.78 Mb (QBPH4.1) and 15.22–17.22 Mb (QBPH4.2) on rice chromosome 4, showed association with BPH resistance in both pooled BILs and individual highly resistant and susceptible BILs. The two most significant candidate resistance genes located within the QBPH4.1 and QBPH4.2 windows were lectin receptor kinase 3 (OsLecRK3) and sesquiterpene synthase 2 (OsSTPS2), respectively. Functional markers identified in these two genes were used for reverse screening 9323 lines of the fast neutron (FN)-mutagenized population developed from the BPH-susceptible, purple-pigmented, indica cultivar Jao Hom Nin (JHN). Nineteen FN-mutagenized lines (0.24%) carried mutations in the OsLecRK3 and/or OsSTPS2 gene. Among these mutant lines, only one highly resistant line (JHN4) and three moderately resistant lines (JHN09962, JHN12005, and JHN19525) were identified using three active, local BPH populations. The 19 mutant lines together with three randomly selected mutant lines, which did not harbor mutations in the two target genes, were screened further for mutations in six known BPH resistance genes including BPH9, BPH14, BPH18, BPH26, BPH29, and BPH32. Multiple single nucleotide polymorphisms (SNPs) and insertion-deletion (Indel) mutations were identified, which formed gene-specific haplotype patterns (HPs) essential for broad-spectrum resistance to BPH in both BILs and JHN mutant populations.ConclusionOn the one hand, HPs of OsLekRK2–3, OsSTPS2, and BPH32 determined broad-spectrum resistance to BPH among RH-derived BILs. On the other hand, in the JHN mutant population, BPH9 together with seven significant genes on chromosome 4 played a crucial role in BPH resistance.

Genome-wide haplotype analysis improves trait predictions in Brassica napus hybrids

Combining ability is crucial for parent selection in crop hybrid breeding. Many studies have attempted to provide reliable and quick methods to identify genome regions in parental lines correlating with improved hybrid performance. The local haplotype patterns surrounding densely spaced DNA markers include a large amount of genetic information, and analysis of the relationships between haplotypes and hybrid performance can provide insight into the underlying genome regions which might contribute to enhancing combining ability. Here, we generated 24,403 single-copy, genome-wide SNP loci and calculated the general combining ability (GCA) of 950 hybrids from a diverse panel of 475 pollinators of spring-type canola inbred lines crossed with two testers for days to flowering (DTF) and seed glucosinolate content (GSL). We performed a genome-wide analysis of the haplotypes and detected eight and seven haplotype regions that were significantly associated with the GCA values for DTF and seed GSL, respectively. Additionally, two haplotype blocks containing orthologs of flowering time genes FLOWERING LOCUS T (FT) and FLOWERING LOCUS C (FLC) on chromosome A02 showed additive epistatic interactions influencing flowering time. Moreover, two homoeologous haplotype regions on chromosomes A02 and C02 corresponded to major quantitative trait loci (QTL) for GSL which showed additive effects related to reduction of seed GSL in F1 hybrids. Our study showed that haplotype analysis has the potential to substantially improve the efficiency of hybrid breeding programs.

Haplotype and biometric patterns in loggerhead turtles from the Adriatic foraging ground

The Adriatic Sea is an important foraging area for the loggerhead turtle Caretta caretta. Due to the increase of anthropogenic impacts, a growing number of individuals are captured as by-catch, found stranded or drifting at sea. Turtles mortality within the Adriatic Sea can affect Mediterranean populations, increasing the risk of losing genetic diversity. Biometric data on 93 loggerheads from three Adriatic areas (northwestern, northeastern and southern Adriatic) and patterns of sequence polymorphism of the mtDNA Control Region long fragment were used to investigate the sizes/age distribution of the collected individuals and to assess their geographic origins by using a Bayesian Mixed Stock Analysis (MSA). The biometric data revealed that collected turtles belonged to a wide range of sizes, although juveniles and subadults were the most abundant classes. Five haplotypes were detected. Two are endemic of Mediterranean rookeries and one is a rare haplotype found once in a Floridian rookery and in two Mediterranean nests. The other two haplotypes were found both in Atlantic and Mediterranean populations. The Mixed Stock Analysis revealed the presence of individuals from Greek and Turkish rookeries, this latter group was found in the southern Adriatic. Individuals from Libya and Cyprus rookeries were also found in the Adriatic stock. Current patterns, juvenile natal homing and imprinting of ontogenetic habitats could be potential drivers of the stock composition in the three Adriatic areas. Variations of turtle migration patterns, recruitment and mortality may drive differential contributions of rookeries to the foraging grounds. In this study, a substructuring within the Adriatic basin is hypothesized, consisting of differential distribution of stocks among three areas. However, these results might be biased by the uneven sample size among areas. Further studies with consistent sample sizes are recommended to quantify potential genetic differentiation within the Adriatic Sea. Nevertheless, present results recommend preservation action to be taken both at the nesting sites and in the foraging grounds were genetically isolated Caretta caretta populations, originating from different Mediterranean rookeries, mix together.