Parallel formation of hybrid swarms of ground beetles in the genus Carabus (Coleoptera: Carabidae) in adjacent river basins

Populations of forms intermediate between Carabus (Ohomopterus) insulicola and Carabus (Ohomopterus) arrowianus occur at the boundaries between the two species in the Kiso Valley, Nagano Prefecture, central Honshu, Japan. Morphological and mitochondrial DNA analyses revealed that these populations are derived from a hybrid swarm established as a result of secondary contact between the two species. A similar hybrid swarm has been reported in the Ina Valley, an adjacent river basin separated by the Kiso Mountain Range, where the two species are distributed parapatrically. The hybrid swarm individuals in the two valleys show parallelism in the morphological evolution of the male genitalia upon secondary contact and subsequent formation of hybrid swarms between the two Carabus species.     

Sensilla on the aedeagus of the ground beetle Carabus (Ohomopterus) arrowianus arrowianus (Breuning) (Coleoptera: Carabidae)

Sensilla on the aedeagus of the ground beetle Carabus (Ohomopterus) arrowianus arrowianus (Breuning) were investigated by scanning electron microscopy. On the aedeagus, a total of six types of sensillum were confirmed: five basiconic and one coeloconic. The external features and distributional patterns of the sensilla are described.     

Microsatellite DNA markers for two endemic ground beetles: Carabus punctatoauratus and C. solieri

We isolated and characterized nine and five polymorphic microsatellite loci in the respective ground beetles Carabus punctatoauratus and C. solieri. We tested cross‐species amplification of all these loci plus six isolated in C. solieri and for which primers sequences were soon published. From these combined analyses, we obtained 14 and 17 polymorphic markers, respectively, for C. punctatoauratus and C. solieri.     

Analysis of ROH patterns in the Noriker horse breed reveals signatures of selection for coat color and body size

Overlapping runs of homozygosity (ROH islands) shared by the majority of a population are hypothesized to be the result of selection around a target locus. In this study we investigated the impact of selection for coat color within the Noriker horse on autozygosity and ROH patterns. We analyzed overlapping homozygous regions (ROH islands) for gene content in fragments shared by more than 50% of horses. Long‐term assortative mating of chestnut horses and the small effective population size of leopard spotted and tobiano horses resulted in higher mean genome‐wide ROH coverage (S_ROH) within the range of 237.4–284.2 Mb, whereas for bay, black and roan horses, where rotation mating is commonly applied, lower autozygosity (S_ROH from 176.4–180.0 Mb) was determined. We identified seven common ROH islands considering all Noriker horses from our dataset. Specific islands were documented for chestnut, leopard spotted, roan and bay horses. The ROH islands contained, among others, genes associated with body size (ZFAT, LASP1 and LCORL/NCAPG), coat color (MC1R in chestnut and the factor PATN1 in leopard spotted horses) and morphogenesis (HOXB cluster in all color strains except leopard spotted horses). This study demonstrates that within a closed population sharing the same founders and ancestors, selection on a single phenotypic trait, in this case coat color, can result in genetic fragmentation affecting levels of autozygosity and distribution of ROH islands and enclosed gene content.     

GENITAL LOCK-AND-KEY AS A SELECTIVE AGENT AGAINST HYBRIDIZATION

We demonstrate experimentally that differences in genital characters impose a direct cost of interspecific copulation on two closely related carabid species, Carabus (Ohomopterus) maiyasanus and C. (O.) iwawakianus, that share a narrow hybrid zone. Males of both species attempted copulation indiscriminately between conspecific and heterospecific females. Females experiencing heterospecific mating often suffered mortality due to rupture of their vaginal membranes. Those without fatal injury laid eggs which developed into F₁ adults, but the fertilization rate was much lower than for intraspecific pairs. Males of C. maiyasanus, but not C. iwawakianus, often had broken genital parts (copulatory pieces) following interspecific copulations, which may prevent normal copulation in subsequent matings. Because of female mortality and low fertilization rate, the estimated fitness cost of interspecific mating was very large in terms of the reduction in the number of offspring (hatching larvae) for both sexes and both species. Thus, genital lock-and-key appears to exert significant selection against hybridization in the hybrid zone of these carabid beetles.     

Genome‐wide association studies reveal genetic loci associated with plasma cholinesterase activity in ducks

Plasma cholinesterase (PCHE) activity is an important auxiliary test in human clinical medicine. It can distinguish liver diseases from non‐liver diseases and help detect organophosphorus poisoning. Animal experiments have confirmed that PCHE activity is associated with obesity and hypertension and changes with physiological changes in an animal's body. The objective of this study was to locate the genetic loci responsible for PCHE activity variation in ducks. PCHE activity of Pekin duck × mallard F2 ducks at 3 and 8 weeks of age were analyzed, and genome‐wide association studies were conducted. A region of about 1.5 Mb (21.8–23.3 Mb) on duck chromosome 9 was found to be associated with PCHE activity at both 3 and 8 weeks of age. The top SNP, g.22643979C>T in the butyrylcholinesterase (BCHE) gene, was most highly associated with PCHE activity at 3 weeks (?logP = 21.45) and 8 weeks (?logP = 27.60) of age. For the top SNP, the strong associations of CC and CT genotypes with low PCHE activity and the TT genotype with high PCHE activity indicates the dominant inheritance of low PCHE activity. Problems with block inheritance or linkage exist in this region. This study supports that BCHE is a functional gene for determining PCHE levels in ducks and that the genetic variations around this gene can cause phenotypic variations of PCHE activity.     

Genetic markers that influence feed efficiency phenotypes also affect cattle temperament as measured by flight speed

Flight speed is a predictive indicator of cattle temperament and is associated with feed efficiency phenotypes. Genetic markers associated with both traits may assist with selection of calmer animals with improved economic value. A preliminary genome‐wide association study determined chromosomal regions on BTA9, and 17 were associated with flight speed. The genes quaking (QKI), glutamate receptor, ionotropic, AMPA 2 (GRIA2) and glycine receptor β (GLRB) were identified in these regions as potential functional candidates. Beef steers (n = 1057) were genotyped with SNPs located within and flanking these genes. One SNP located near QKI and one near GRIA2 were nominally associated with flight speed (P ≤ 0.05) although neither was significant after Bonferroni correction. Several studies have shown a correlation between flight speed and feed intake or gain; therefore, we also analyzed SNPs on BTA6:38–39 Mb known to be associated with average daily gain (ADG) and average daily feed intake (ADFI) for association with flight speed. Several SNPs on BTA6 were associated with flight speed (P ≤ 0.005), and three were significant after Bonferroni correction. These results suggest that the genes tested are unlikely to contribute to flight speed variation for our cattle population, but SNPs on BTA6 associated with ADG and ADFI may influence temperament. Use of these markers to select for economically important feed efficiency phenotypes may produce cattle with more desirable temperaments.     

A genome‐wide association study for gestation length in swine

Selection for increased litter size in swine has potentially resulted in a correlated increase in preweaning mortality. Additional selection criteria should be considered when selecting for increased litter size to account for associated decreases in piglet quality, specifically piglet survival, initial weight and growth. Traits such as gestation length (GL), which have been associated with piglet performance, could be utilized to improve piglet development and survivability. The objective of this study was to conduct a genome‐wide association study to identify genomic regions associated with GL in differing parities in swine (n = 831) from the University of Nebraska–Lincoln reproductive longevity project. Gestation length was calculated as the number of days between last insemination administered and farrowing. Sows were genotyped with the Illumina SNP60 BeadArray, and the data were analyzed using Bayesian mixture models for GL at parity 1, 2, 3 and 4 (GL1, GL2, GL3 and GL4 respectively). Means (SD) for GL1–GL4 were 113 (1.4), 114 (1.2), 114 (1.3) and 115 (1.2) respectively. Posterior mean heritability estimates (PSD) for GL1, GL2, GL3 and GL4 were 0.33 (0.06), 0.34 (0.07), 0.32 (0.08) and 0.20 (0.08) respectively. Rank correlations between genomic estimated breeding values between GL1 and GL2, GL3 and GL4 respectively were moderate: 0.67, 0.65 and 0.60. The top SNP (ASGA0017859, SSC4, 7.8 Mb), located in the top common genomic region associated with GL1, GL2 and GL3, was associated with a difference of 1.1 days in GL1 between homozygote genotypes (P < 0.0001). The results of this study suggest that GL is a largely polygenic trait with relatively minor contributions from multiple genomic regions.     

Validation of genetic polymorphisms on BTA14 associated with carcass trait in a commercial Hanwoo population

The objective of this study was to validate the association of significant SNPs identified from a previous genome‐wide association study with carcass weight (CWT) in a commercial Hanwoo population. We genotyped 13 SNPs located on BTA14 in 867 steers from Korea Hanwoo feedlot bulls. Of these 13 SNPs, five SNPs, namely rs29021868, rs110061498, rs109546980, rs42404006 and rs42303720, were found to be significantly associated (P < 0.001) with CWT. These five significant markers spanned the 24.3 to 29.4 Mb region of BTA14. The most significant marker (rs29021868) for CWT in this study had a 13.07 kg allele substitution effect and accounted for 2.4% of the additive genetic variance in the commercial Hanwoo population. The SNP marker rs109546980 was found to be significantly associated with both CWT (P < 0.001) and eye muscle area (P < 0.001) and could potentially be exploited for marker‐assisted selection in Hanwoo cattle. We also genotyped the ss319607402 variation, which maps to intron2 of PLAG1 gene and which is already reported to be associated with height, to identify any significant association with carcass weight; however, no such association was observed in this Hanwoo commercial population.     

The Ficus erecta genome aids Ceratocystis canker resistance breeding in common fig (F. carica)

Ficus erecta, a wild relative of the common fig (F. carica), is a donor of Ceratocystis canker resistance in fig breeding programmes. Interspecific hybridization followed by recurrent backcrossing is an effective method to transfer the resistance trait from wild to cultivated fig. However, this process is time consuming and labour intensive for trees, especially for gynodioecious plants such as fig. In this study, genome resources were developed for F. erecta to facilitate fig breeding programmes. The genome sequence of F. erecta was determined using single‐molecule real‐time sequencing technology. The resultant assembly spanned 331.6 Mb with 538 contigs and an N50 length of 1.9 Mb, from which 51 806 high‐confidence genes were predicted. Pseudomolecule sequences corresponding to the chromosomes of F. erecta were established with a genetic map based on single nucleotide polymorphisms from double‐digest restriction‐site‐associated DNA sequencing. Subsequent linkage analysis and whole‐genome resequencing identified a candidate gene for the Ceratocystis canker resistance trait. Genome‐wide genotyping analysis enabled the selection of female lines that possessed resistance and effective elimination of the donor genome from the progeny. The genome resources provided in this study will accelerate and enhance disease‐resistance breeding programmes in fig.     

Development of the gregarious ectoparasitoid Nasonia vitripennis using five species of necrophagous flies as hosts and at various developmental temperatures

The utility of five species of necrophagous flies (Diptera) as pupal hosts for Nasonia vitripennis (Walker) (Hymenoptera: Pteromalidae) was examined by comparing incidences of parasitism, fecundity, and several features of wasp development at three rearing temperatures. Species differences in host suitability were evident in all life history features examined, with the highest incidences of parasitism, largest clutches and adult body sizes, and shortest periods of development occurring when the sarcophagid Sarcophaga bullata Parker served as hosts, regardless of temperature in which the wasps developed. Puparia of the calliphorids Lucilia illustris Meigen, Phormia regina Meigen, and Protophormia terraenovae Robineau‐Desvoidy were also accepted as hosts by the female parasitoids, albeit not equally so, and each yielded large, female‐biased broods. By contrast, pupae of the calliphorid Chrysomya rufifacies (Macquart) were not well suited to serve as an oviposition site or support the development of N. vitripennis. When successful parasitism did occur on any host species, duration of parasitoid development increased, adult body sizes were truncated, male‐biased sex ratios were produced, and mortality from egg hatch to adult emergence elevated with increasing rearing temperature. Unlike with the four other fly species, C. rufifacies did not yield any adult parasitoids when the rearing temperature was 35 °C. The results argue that developmental data determined for this wasp derived from a single host species is not sufficient for applying to all scenarios in which wasp development is necessary to estimate a postmortem interval or periods of insect activity.     

Late‐onset progressive retinal atrophy in the Gordon and Irish Setter breeds is associated with a frameshift mutation in C2orf71

Progressive retinal atrophy (PRA) in dogs is characterised by the degeneration of the photoreceptor cells of the retina, resulting in vision loss and eventually complete blindness. The condition affects more than 100 dog breeds and is known to be genetically heterogeneous between breeds. Around 14 mutations have now been identified that are associated with PRA in around 49 breeds, but for the majority of breeds the mutation(s) responsible have yet to be identified. Using genome‐wide association with 16 Gordon Setter PRA cases and 22 controls, we identified a novel PRA locus, termed rod–cone degeneration 4 (rcd4), on CFA17 (P_raw = 2.22 × 10^?8, P_genome = 2.00 × 10^?5), where a 3.2‐Mb region was homozygous within cases. A frameshift mutation was identified in C2orf71, a gene located within this region. This variant was homozygous in 19 of 21 PRA cases and was at a frequency of approximately 0.37 in the Gordon Setter population. Approximately 10% of cases in our study (2 of 21) are not associated with this C2orf71 mutation, indicating that PRA in this breed is genetically heterogeneous and caused by at least two mutations. This variant is also present in a number of Irish Setter dogs with PRA and has an estimated allele frequency of 0.26 in the breed. The function of C2orf71 remains unknown, but it is important for retinal development and function and has previously been associated with autosomal recessive retinitis pigmentosa in humans.     

SNPs in SNCA,MCCC1, DLG2, GBF1 and MBNL2 are associated with Parkinson's disease in southern Chinese population

Numerous single nucleotide polymorphisms (SNPs), which have been identified as susceptibility factors for Parkinson's disease (PD) as per genome‐wide association studies, have not been fully characterized for PD patients in China. This study aimed to replicate the relationship between 12 novel SNPs of 12 genes and PD risk in southern Chinese population. Twelve SNPs of 12 genes were detected in 231 PD patients and 249 controls, using the SNaPshot technique. Meta‐analysis was used to assess heterogeneity of effect sizes between this study and published data. The impact of SNPs on gene expression was investigated by analysing the SNP‐gene association in the expression quantitative trait loci (eQTL) data sets. rs8180209 of SNCA (allele model: P = .047, OR = 0.77; additive model: P = .047, OR = 0.77), rs2270968 of MCCC1 (dominant model: P = .024, OR = 1.52), rs7479949 of DLG2 (recessive model; P = .019, OR = 1.52), rs10748818 of GBF1 (additive model: P < .001, OR = 0.37), and rs4771268 of MBNL2 (recessive model: P = .003, OR = 0.48) were replicated to be significantly associated with the increased risk of PD. Noteworthy, a meta‐analysis of previous studies suggested rs8180209, rs2270968, rs7479949 and rs4771268 were in line with those of our cohort. Our study replicated five novel functional SNPs in SNCA, MCCC1, DLG2, GBF1 and MBNL2 could be associated with increased risk of PD in southern Chinese population.     

Comparative study of development parameters of four Ooencyrtus spp. (Hymenoptera: Encyrtidae) on natural and factitious hosts

Biological control approaches such as seeding and augmentation releases of populations of natural enemies mostly rely on the indoor production of predator or parasitoid species, often with the use of alternative prey/host species. In this study, we investigated several development parameters of four egg parasitoid species: Ooencyrtus fecundus, O. near fecundus, O. pityocampae and O. telenomicida, and compared their performance on their natural host, the variegated caper bug (CB) Stenozygum coloratum, and on an alternative, factitious host, the silk moth (SM) Bombyx mori. Survival was higher and development duration shorter in CB eggs, making the CB a better host for these congeners. However, adult longevity was generally longer for individuals that developed in SM eggs. Moreover, O. fecundus and O. pityocampae females that had developed in SM eggs displayed higher fecundity than all other female/host combinations. Survival also varied according to the age of the SM eggs: parasitoid survival rates were significantly higher in 9‐ to 12‐month‐old (post‐diapausing) eggs than in young (about 1 month old) ones. These results were probably influenced by differences among the egg sizes of the studied hosts. The number of non‐laying females and self‐superparasitism rates were exceptionally high in O. near fecundus. These findings suggest that SM eggs, and especially those which are being utilized after a long storage, could serve for mass rearing of the studied Ooencyrtus spp.     

Chromosome‐scale pseudomolecules refined by optical,physical and genetic maps in flax

Genomes of varying sizes have been sequenced with next‐generation sequencing platforms. However, most reference sequences include draft unordered scaffolds containing chimeras caused by mis‐scaffolding. A BioNano genome (BNG) optical map was constructed to improve the previously sequenced flax genome (Linum usitatissimum L., 2n = 30, about 373 Mb), which consisted of 3852 scaffolds larger than 1 kb and totalling 300.6 Mb. The high‐resolution BNG map of cv. CDC Bethune totalled 317 Mb and consisted of 251 BNG contigs with an N50 of 2.15 Mb. A total of 622 scaffolds (286.6 Mb, 94.9%) aligned to 211 BNG contigs (298.6 Mb, 94.2%). Of those, 99 scaffolds, diagnosed to contain assembly errors, were refined into 225 new scaffolds. Using the newly refined scaffold sequences and the validated bacterial artificial chromosome‐based physical map of CDC Bethune, the 211 BNG contigs were scaffolded into 94 super‐BNG contigs (N50 of 6.64 Mb) that were further assigned to the 15 flax chromosomes using the genetic map. The pseudomolecules total about 316 Mb, with individual chromosomes of 15.6 to 29.4 Mb, and cover 97% of the annotated genes. Evidence from the chromosome‐scale pseudomolecules suggests that flax has undergone palaeopolyploidization and mesopolyploidization events, followed by rearrangements and deletions or fusion of chromosome arms from an ancient progenitor with a haploid chromosome number of eight.     

The genome of the marine medaka Oryzias melastigma

Marine medaka (Oryzias melastigma) is considered to be a useful fish model for marine and estuarine ecotoxicology studies and has good potential for field‐based population genomics because of its geographical distribution in Asian estuarine and coastal areas. In this study, we present the first whole‐genome draft of O. melastigma. The genome assembly consists of 8,602 scaffolds (N50 = 23.737 Mb) and a total genome length of 779.4 Mb. A total of 23,528 genes were predicted, and 12,670 gene families shared with three teleost species (Japanese medaka, mangrove killifish and zebrafish) were identified. Genome analyses revealed that the O. melastigma genome is highly heterozygous and contains a large number of repeat sequences. This assembly represents a useful genomic resource for fish scientists.     

A genome‐wide association study for a proxy of intermuscular fat level in the Italian Large White breed identifies genomic regions affecting an important quality parameter for dry‐cured hams

Intermuscular fat content in protected designations of origin dry‐cured hams is a very important meat quality trait that affects the acceptability of the product by the consumers. An excess in intermuscular fat (defined as the level of fat deposition between leg muscles) is a defect that depreciates the final product. In this study we carried out a genome‐wide association study for visible intermuscular fat (VIF) of hams in the Italian Large White pig breed. This trait was evaluated on the exposed muscles of green legs in 1122 performance‐tested gilts by trained personnel, according to a classification scale useful for routine and cheap evaluation. All animals were genotyped with the Illumina PorcineSNP60 BeadChip. The genome‐wide association study identified three QTL regions on porcine chromosome 1 (SSC1; accounting for ~79% of the SNPs below the 5.0E?04 threshold) and SSC2, two on SSC7 and one each on SSC3, SSC6, SSC9, SSC11, SSC13, SSC15, SSC16 and SSC17. The most significant SNP (ALGA0004143 on SSC1 at 77.3 Mb; P_FDR < 0.05), included in the largest QTL region which spanned about 6.8 Mb on SSC1, is located within the glutamate ionotropic receptor kainate type subunit 2 (GRIK2) gene. Functional annotation of all genes included in QTL regions for VIF suggested that intermuscular fat in the Italian Large White breed is a complex trait apparently influenced by complex biological mechanisms also involving obesity‐related processes. These QTL target mainly chromosome regions different from those affecting subcutaneous and intramuscular fat deposition.