Differential Response of a Local Population of Entomopathogenic Nematodes to Non-Native Herbivore Induced Plant Volatiles (HIPV) in the Laboratory and Field

Recent work has shown the potential for enhanced efficacy of entomopathogenic nematodes (EPN) through their attraction to herbivore induced plant volatiles. However, there has been little investigation into the utilization of these attractants in systems other than in those in which they were identified. We compared (E)-β-caryophyllene and pregeijerene in the highbush blueberry (Vaccinium corymbosum) agroecosystem in their ability to enhance the attraction of EPN to and efficacy against the system’s herbivore, oriental beetle (Anomala orientalis). The relative attractiveness of (E)-β-caryophyllene and pregeijerene to a local isolate of the EPN species Steinernema glaseri was tested in a six-arm olfactometer in the laboratory to gather baseline values of attraction to the chemicals alone in sand substrate before field tests. A similar arrangement was used in a V. corymbosum field by placing six cages with assigned treatments and insect larvae with and without compound into the soil around the base of 10 plants. The cages were removed after 72 h, and insect baits were retrieved and assessed for EPN infection. The lab results indicate that in sand alone (E)-β-caryophyllene is significantly more attractive than pregeijerene to the local S. glaseri isolate Conversely, there was no difference in attractiveness in the field study, but rather, native S. glaseri were more attracted to cages with G. mellonella larvae, no larvae, and cages with the blank control and G. mellonella larvae.     

Populations of the Gall Midge Dasineura oxycoccana on Cranberry and Blueberry Produce and Respond to Different Sex Pheromones

We identified and field-tested the sex pheromones of Dasineura oxycoccana (Johnson) (Diptera: Cecidomyiidae) midges collected from cranberry, Vaccinium macrocarpon Aiton, and from highbush blueberry, Vaccinium corymbosum L., commonly named cranberry tipworm (CTW) and blueberry gall midge (BGM), respectively. Coupled gas chromatographic-electroantennographic detection (GC-EAD) analyses of pheromone gland extract from the ovipositor of calling CTW females revealed one component (<10 pg per ovipositor/pheromone gland) that elicited antennal responses from CTW males. Stepwise identification was based on its mass spectrum in a concentrated sample with 300 pheromone gland equivalents, retention indices (RI) on three GC columns (DB-5, DB-23, and DB 210), RI inter-column differentials, and RIs and double bond positions of other midge pheromones. These analyses indicated that (8Z)-2,14-diacetoxy-8-heptadecene (2,14-8Z-17) was the candidate pheromone of the CTW. GC-EAD analysis of pheromone gland extract from calling BGM females revealed two components that elicited antennal responses from BGM males. Retention times on the three GC columns were consistent with 2,14-8Z-17 and 2,14-17, indicating that these were candidate pheromone components of the BGM. The four stereoisomers of 2,14-8Z-17 were stereoselectively synthesized and field-tested in cranberry. Delta-type traps baited with SS-2,14-8Z-17 captured significantly more CTW males than did traps baited with any other single stereoisomer or with all four stereoisomers combined. In blueberry, delta-type traps baited with RR-2,14-8Z-17 captured significantly more BGM males than did traps baited with any other single stereoisomer or with all four stereoisomers combined. Subsequent field experiments demonstrated that RR-2,14-17 is the major pheromone component of BGM, and that RR-2,14-8Z-17 is a pheromone component that does not enhance attractiveness of RR-2,14-17. The BGM pheromone RR-2,14-17 has no antagonistic effect on the CTW pheromone SS-2,14-8Z-17 and vice versa. Our results substantiate the conclusion that populations of D. oxycoccana on cranberry and blueberry represent two cryptic species.     

Varietal difference in lipid content and fatty acid composition of highbush blueberries

Lipids from five cultivars of highbush blueberries (Vaccinium corymbosum L.) were extracted and fractionated into neutral lipids (60–66%), glycolipids (20–22%) and phospholipids (14–18%). The major fatty acids in all fractions were palmitic (16∶0), oleic (18∶1), linoleic (18∶2), and linolenic (18∶3) acids. All lipid classes had a large concentration of C₁₈ polyunsaturated acids (84–92%), indicating that blueberries are a rich source of linoleic and linolenic acids. Changes in the fatty acid composition of neutral lipids and phospholipids were not significantly different among the five cultivars, but significant differences were noted in the ratios of linoleic and linolenic acids in the glycolipids fraction.     

Intraspecific Variation in Aphid Resistance and Constitutive Phenolics Exhibited by the Wild Blueberry <Emphasis Type="Italic">Vaccinium darrowi</Emphasis>

Illinoia pepperi (MacGillivray) infests cultivated highbush blueberries, Vaccinium corymbosum L., in the Northeastern United States. Allopatric resistance to I. pepperi was examined in Vaccinium darrowi Camp, which evolved in the absence of I. pepperi in the Southeastern U.S. V. corymbosum cv. “Elliott”, was used as a susceptible control. Between population variability in I. pepperi resistance was assessed by measuring length of the prereproductive period, fecundity, and survivorship on 14 V. darrowi accessions representing 11 discrete wild populations. Length of I. pepperi’s prereproductive period and survivorship were not significantly affected. However, differences were detected in fecundity and the intrinsic rate of increase (r _m ). Within population variability in resistance was measured by confining first instars to 24 accessions from a single wild population of V. darrowi (NJ88-06). Significant differences in the mean total number of aphids occurring after 20 d were only detected between 2 of the 24 V. darrowi accessions. A greater degree of diversity in I. pepperi resistance exists between populations of V. darrowi compared to within a population. Constitutive leaf and stem polyphenolics were identified by HPLC-MS and quantified from 14 of the V. darrowi accessions. The accessions varied in concentrations of five phenolic acids and seven flavonol glycosides, but a correlation was not found between individual or total phenolics and aphid performance. Overall, screening within and between populations of V. darrowi identified promising sources of aphid resistance, but phenolic acid and flavonol glycoside profiles did not predict resistance levels. The mechanism of resistance remains to be identified.     

Genome-Wide SNP Markers for Genotypic and Phenotypic Differentiation of Melon (Cucumis melo L.) Varieties Using Genotyping-by-Sequencing

Melon (Cucumis melo L.) is an economically important horticultural crop with abundant morphological and genetic variability. Complex genetic variations exist even among melon varieties and remain unclear to date. Therefore, unraveling the genetic variability among the three different melon varieties, muskmelon (C. melo subsp. melo), makuwa (C. melo L. var. makuwa), and cantaloupes (C. melo subsp. melo var. cantalupensis), could provide a basis for evolutionary research. In this study, we attempted a systematic approach with genotyping-by-sequencing (GBS)-derived single nucleotide polymorphisms (SNPs) to reveal the genetic structure and diversity, haplotype differences, and marker-based varieties differentiation. A total of 6406 GBS-derived SNPs were selected for the diversity analysis, in which the muskmelon varieties showed higher heterozygote SNPs. Linkage disequilibrium (LD) decay varied significantly among the three melon varieties, in which more rapid LD decay was observed in muskmelon (r² = 0.25) varieties. The Bayesian phylogenetic tree provided the intraspecific relationships among the three melon varieties that formed, as expected, individual clusters exhibiting the greatest genetic distance based on the posterior probability. The haplotype analysis also supported the phylogeny result by generating three major networks for 48 haplotypes. Further investigation for varieties discrimination allowed us to detect a total of 52 SNP markers that discriminated muskmelon from makuwa varieties, of which two SNPs were converted into cleaved amplified polymorphic sequence markers for practical use. In addition to these markers, the genome-wide association study identified two SNPs located in the genes on chromosome 6, which were significantly associated with the phenotypic traits of melon seed. This study demonstrated that a systematic approach using GBS-derived SNPs could serve to efficiently classify and manage the melon varieties in the genebank.     

Differences among sibling speciesRhagoletis mendax andR. pomonella (diptera: ephritidae) in their antennal sensitivity to host fruit compounds

Prior electrophoretic and morphological studies have identified two closely related, economically important tephritid flies,R. mendax (Curran) andR. pomonella (Walsh), which infest the fruits of ericaceous and rosaceous plants, respectively. Further studies also have shown consistent differences among these species in their ovipositional preferences for apples and highbush blueberries and have determined that their ovipositional behavior is elicited by extracts obtained from these fruits. In this paper we report the results of an experiment that tested whether these species show distinct electroantennogram (EAG) responses to a large array of compounds present in gas chromatograph-fractionated pentane extracts of apples and highbush blueberries.R. mendax andR. pomonella flies were found to have significant differences in their antennal sensitivity to 11 blueberry and nine apple extract peaks, which correspond to 24.4% of all blueberry and 25.0% of all apple peaks that elicited a measurable EAG response from either species. Interspecific differences in peripheral sensitivity were more pronounced for blueberry than apple extract;R. pomonella flies were most sensitive to blueberry compounds with low retention times, whereasR. mendax flies responded to blueberry compounds with a broader range of retention times. Both species were most sensitive to apple peaks with high retention times. The retention times of most apple and blueberry peaks that elicited EAG responses fromR. mendax andR. pomonella flies were different from the retention times of seven attractant fruit esters that were previously identified by Fein et al. (1982). The identification of these unknown apple and blueberry compounds could lead to the discovery of new chemical cues that mediate the host-plant preferences of these sibling species.     

Nanopore Sequencing for De Novo Bacterial Genome Assembly and Search for Single-Nucleotide Polymorphism

Nanopore sequencing (ONT) is a new and rapidly developing method for determining nucleotide sequences in DNA and RNA. It serves the ability to obtain long reads of thousands of nucleotides without assembly and amplification during sequencing compared to next-generation sequencing. Nanopore sequencing can help for determination of genetic changes leading to antibiotics resistance. This study presents the application of ONT technology in the assembly of an E. coli genome characterized by a deletion of the tolC gene and known single-nucleotide variations leading to antibiotic resistance, in the absence of a reference genome. We performed benchmark studies to determine minimum coverage depth to obtain a complete genome, depending on the quality of the ONT data. A comparison of existing programs was carried out. It was shown that the Flye program demonstrates plausible assembly results relative to others (Shasta, Canu, and Necat). The required coverage depth for successful assembly strongly depends on the size of reads. When using high-quality samples with an average read length of 8 Kbp or more, the coverage depth of 30× is sufficient to assemble the complete genome de novo and reliably determine single-nucleotide variations in it. For samples with shorter reads with mean lengths of 2 Kbp, a higher coverage depth of 50× is required. Avoiding of mechanical mixing is obligatory for samples preparation. Nanopore sequencing can be used alone to determine antibiotics-resistant genetic features of bacterial strains.     

Lingonberry (Vaccinium vitis-idaea L.) Fruit as a Source of Bioactive Compounds with Health-Promoting Effects—A Review

Berries, especially members of the Ericaceae family, are among the best dietary sources of bioactive compounds with beneficial health effects. The most popular berries are in the genus Vaccinium, such as bilberry (Vaccinium myrtillus), cranberry (Vaccinium macrocarpon, V. oxycoccos), and blueberry (Vaccinium corymbosum). Lingonberry (Vaccinium vitis-idaea) is less prevalent in the daily human diet because they are collected from the wild, and plant breeding of lingonberry is still on a small scale. Lingonberries are classed as “superfruits” with the highest content of antioxidants among berries and a broad range of health-promoting effects. Many studies showed various beneficial effects of lingonberries, such as anti-inflammatory, antioxidant, and anticancer activities. Lingonberries have been shown to prevent low-grade inflammation and diet-induced obesity in diabetic animals. Moreover, lingonberry intake has been associated with a beneficial effect on preventing and treating brain aging and neurodegenerative disorders. The consumption of berries and their health-promoting activity is a subject receiving a great deal of attention. Many studies investigated the natural compounds found in berries to combat diseases and promote healthy aging. This article’s scope is to indicate the potential beneficial effect of lingonberry consumption on health, to promote well-being and longevity.     

A Long-Read Sequencing Approach for Direct Haplotype Phasing in Clinical Settings

The reconstruction of individual haplotypes can facilitate the interpretation of disease risks; however, high costs and technical challenges still hinder their assessment in clinical settings. Second-generation sequencing is the gold standard for variant discovery but, due to the production of short reads covering small genomic regions, allows only indirect haplotyping based on statistical methods. In contrast, third-generation methods such as the nanopore sequencing platform developed by Oxford Nanopore Technologies (ONT) generate long reads that can be used for direct haplotyping, with fewer drawbacks. However, robust standards for variant phasing in ONT-based target resequencing efforts are not yet available. In this study, we presented a streamlined proof-of-concept workflow for variant calling and phasing based on ONT data in a clinically relevant 12-kb region of the APOE locus, a hotspot for variants and haplotypes associated with aging-related diseases and longevity. Starting with sequencing data from simple amplicons of the target locus, we demonstrated that ONT data allow for reliable single-nucleotide variant (SNV) calling and phasing from as little as 60 reads, although the recognition of indels is less efficient. Even so, we identified the best combination of ONT read sets (600) and software (BWA/Minimap2 and HapCUT2) that enables full haplotype reconstruction when both SNVs and indels have been identified previously using a highly-accurate sequencing platform. In conclusion, we established a rapid and inexpensive workflow for variant phasing based on ONT long reads. This allowed for the analysis of multiple samples in parallel and can easily be implemented in routine clinical practice, including diagnostic testing.     

Impact of Ozonation Process on the Microbiological Contamination and Antioxidant Capacity of Highbush Blueberry (Vaccinum corymbosum L.) Fruit during Cold Storage

In the studies conducted, the impact of the innovative ozonation procedure on the microbial state and antioxidant potential of highbush blueberry (Vaccinum corymbosum L.) stored under cold storage conditions was assessed. Microbiological analysis was carried out to determine the total number of mesophilic aerobic bacteria and the total number of fungi during the storage experiment. In addition, changes in the flavonoid, anthocyanins, and vitamin C content and the total antioxidant capacity were monitored during the storage. The degree of fruit infection with gray mold and anthracnose was determined. It was found that daily ozonation of fruits with a dose of 15 ppm for 30 min, every 12 h, for 28 days effectively reduced the development of aerobic mesophilic bacteria and fungi. On the last day of storage, symptoms of the infection by gray mold were observed in 27.5% of the control fruit, while the absence of symptoms was observed in case of the ozonated fruit. On the other hand, ozone was ineffective in case of inhibiting the infection by anthracnose. Nevertheless, the ozonation process allowed maintaining a high antioxidant potential of the fruit and substantially reduced losses of flavonoids, anthocyanins, and vitamin C. The utilized procedure has proved to be effective, providing the possibility of extensive use of ozone as a factor allowing sustaining a high commercial and consumption value of the fruit over extended time.     

A Longitudinal Study of the Association between the LEPR Polymorphism and Treatment Response in Patients with Bipolar Disorder

Patients with bipolar disorder (BD) exhibit individual variability in the treatment outcome, and genetic background could contribute to BD itself and the treatment outcome. Leptin levels significantly change in BD patients treated with valproate (VPA), but whether LEPR polymorphisms are associated with treatment response is still unknown. This longitudinal study aimed to investigate the associations between LEPR polymorphisms and VPA treatment response in BD patients who were drug naïve at their first diagnosis of BD. The single-nucleotide polymorphisms (SNPs) of LEPR (rs1137101, rs1137100, rs8179183, and rs12145690) were assayed, and the LEPR polymorphism frequencies of alleles and genotypes were not significantly different between the controls (n = 77) and BD patients (n = 130). In addition, after the 12-week course of VPA treatment in BD patients, the LEPR polymorphisms showed significant effects on changes in disease severity. Moreover, considering the effect of the LEPR haplotype, the frequency of the CAGG haplotype in BD patients was higher than that in the controls (9.3 vs. 2.9%, p = 0.016), and the LEPR CAGG haplotype was associated with a better treatment response than the other haplotypes in BD patients receiving VPA treatment. Therefore, LEPR polymorphisms might serve as mediators involved in the therapeutic action of VPA treatment.     

Computer Vision for Real-Time Measurements of Shrinkage and Color Changes in Blueberry Convective Drying

The effect of temperature on blueberry drying rate, shrinkage, and color changes was evaluated from drying experiments for both high bush (Vaccinium corymbosum L.) and wild (Vaccinium angustifolium) blueberries. Drying temperature significantly affected texture and color of both varieties. Temperatures above 55°C caused a significant color change (ΔE > 25) within 30 min of the beginning of drying, followed by a significant drop in density from 1.02 to 0.38 g/cm³. In contrast, drying at temperatures below 50°C resulted in nonsignificant color changes and an eventual density increase to 1.26 g/cm³. It follows that blueberry color could be used as an early stage indicator of quality degradation in the process of drying.     

Genome-Wide Association Study Identifies a Rice Panicle Blast Resistance Gene Pb3 Encoding NLR Protein

Rice blast is a worldwide fungal disease that seriously affects the yield and quality of rice. Identification of resistance genes against rice blast disease is one of the effective ways to control this disease. However, panicle blast resistance genes, which are useful in the fields, have rarely been studied due to the difficulty in phenotypic identification and the environmental influences. Here, panicle blast resistance-3 (Pb3) was identified by a genome-wide association study (GWAS) based on the panicle blast resistance phenotypes of 230 Rice Diversity Panel I (RDP-I) accessions with 700,000 single-nucleotide polymorphism (SNP) markers. A total of 16 panicle blast resistance loci (PBRLs) within three years including one repeated locus PBRL3 located in chromosome 11 were identified. In addition, 7 genes in PBRL3 were identified as candidate genes by haplotype analysis, which showed significant differences between resistant and susceptible varieties. Among them, one nucleotide-binding domain and Leucine-rich Repeat (NLR) gene Pb3 was highly conserved in multiple resistant rice cultivars, and its expression was significantly induced after rice blast inoculation. Evolutionary analysis showed that Pb3 was a typical disease resistance gene containing coiled-coil, NB-ARC, and LRR domains. T-DNA insertion mutants and CRISPR lines of Pb3 showed significantly reduced panicle blast resistance. These results indicate that Pb3 is a panicle blast resistance gene and GWAS is a rapid method for identifying panicle blast resistance in rice.     

Virus Elimination from Naturally Infected Field Cultivars of Potato (Solanum tuberosum) by Transgenic RNA Interference

Tissue culture methods enable virus elimination from vegetatively propagated crop plants but cannot prevent new infections. Here we used a tissue culture transgenic approach for curing field cultivars of Solanum tuberosum through the stimulation of RNA interference (RNAi)-based antiviral defenses. Expression cassettes carrying inverted repeats of potato virus S (PVS, genus Carlavirus) movement or coat protein sequences were used for the transformation of potato cultivars naturally infected with PVS and/or a related carlavirus potato virus M (PVM), without or with potato virus Y (PVY, genus Potyvirus). A high proportion of transformants PCR-positive for transgenes were cured from both carlaviruses and PVY. After 3-year field trials, 22 transgenic lines representing seven cultivars remained free of any virus or became infected only with PVY. Vegetative progenies of the transgenic lines of cultivar Zeren (initially coinfected with PVS, PVM, and PVY), sampled after in vitro propagation or field trials, and other field cultivars accumulated transgene-derived 21, 22, and 24 nt small interfering (si)RNAs almost exclusively from the PVS inverted repeats. Additionally, some field progenies accumulated 21–22 nt siRNAs from the entire PVY genome, confirming PVY infection. Taken together, transgenic RNAi is effective for virus elimination from naturally infected potato cultivars and their sequence-specific immunization against new infections.     

Genome-Wide Association Studies Reveal Novel Loci for Herbivore Resistance in Wild Soybean (Glycine soja)

The production of soybean [Glycine max (L.) Merr.] is seriously threatened by various leaf-feeding insects, and wild soybean [Glycine soja Sieb. & Zucc.] has a greater resistance capacity and genetic diversity. In this study, a natural population consisting of 121 wild soybean accessions was used for detecting insect resistance genes. The larval weight (LW) of the common cutworm (CCW), the resistance level (RL) and the index of damaged leaf (IDL) were evaluated as resistance indicators to herbivores. An association synonymous SNP AX-94083016 located in the coding region of the respiratory burst oxidase gene GsRbohA1 was identified by genome-wide association study (GWAS) analyses. The overexpression of GsRbohA1 in soybean hairy roots enhanced resistance to CCW. One SNP in the promoter region cosegregated with AX-94083016 contributing to soybean resistance to CCW by altering GsRbohA1 gene expression and reactive oxygen species (ROS) accumulation. Two major haplotypes, GsRbohA1^A and GsRbohA1^G, were identified based on the SNP. The resistant haplotype GsRbohA1^A predominates in wild soybeans, although it has been gradually lost in landraces and cultivars. The nucleotide diversity around GsRbohA1 is much lower in landraces and cultivars than in its ancestors. In conclusion, a new resistant haplotype, GsRbohA1^A, was identified in wild soybean, which will be a valuable gene resource for soybean insect resistance breeding through introducing into improvement lines, and it offers a strategy for exploring resistance gene resources from its wild relatives.     

Genome-Wide Association Study Identifies a Rice Panicle Blast Resistance Gene,Pb2, Encoding NLR Protein

Rice blast is one of the main diseases in rice and can occur in different rice growth stages. Due to the complicated procedure of panicle blast identification and instability of panicle blast infection influenced by the environment, most cloned rice resistance genes are associated with leaf blast. In this study, a rice panicle blast resistance gene, Pb2, was identified by genome-wide association mapping based on the panicle blast resistance phenotypes of 230 Rice Diversity Panel 1 (RDP1) accessions with 700,000 single-nucleotide polymorphism (SNP) markers. A genome-wide association study identified 18 panicle blast resistance loci (PBRL) within two years, including 9 reported loci and 2 repeated loci (PBRL2 and PBRL13, PBRL10 and PBRL18). Among them, the repeated locus (PBRL10 and PBRL18) was located in chromosome 11. By haplotype and expression analysis, one of the Nucleotide-binding domain and Leucine-rich Repeat (NLR) Pb2 genes was highly conserved in multiple resistant rice cultivars, and its expression was significantly upregulated after rice blast infection. Pb2 encodes a typical NBS-LRR protein with NB-ARC domain and LRR domain. Compared with wild type plants, the transgenic rice of Pb2 showed enhanced resistance to panicle and leaf blast with reduced lesion number. Subcellular localization of Pb2 showed that it is located on plasma membrane, and GUS tissue-staining observation found that Pb2 is highly expressed in grains, leaf tips and stem nodes. The Pb2 transgenic plants showed no difference in agronomic traits with wild type plants. It indicated that Pb2 could be useful for breeding of rice blast resistance.     

Application of Novel Polymorphic Microsatellite Loci Identified in the Korean Pacific Abalone (Haliotis diversicolor supertexta (Haliotidae)) in the Genetic Characterization of Wild and Released Populations

The small abalone, Haliotis diversicolor supertexta, of the family Haliotidae, is one of the most important species of marine shellfish in eastern Asia. Over the past few decades, this species has drastically declined in Korea. Thus, hatchery-bred seeds have been released into natural coastal areas to compensate for the reduced fishery resources. However, information on the genetic background of the small abalone is scarce. In this study, 20 polymorphic microsatellite DNA markers were identified using next-generation sequencing techniques and used to compare allelic variation between wild and released abalone populations in Korea. Using high-throughput genomic sequencing, a total of 1516 (2.26%; average length of 385 bp) reads containing simple sequence repeats were obtained from 86,011 raw reads. Among the 99 loci screened, 28 amplified successfully, and 20 were polymorphic. When comparing allelic variation between wild and released abalone populations, a total of 243 different alleles were observed, with 18.7 alleles per locus. High genetic diversity (mean heterozygosity = 0.81; mean allelic number = 15.5) was observed in both populations. A statistical analysis of the fixation index (F_ST) and analysis of molecular variance (AMOVA) indicated limited genetic differences between the two populations (F_ST = 0.002, p > 0.05). Although no significant reductions in the genetic diversity were found in the released population compared with the wild population (p > 0.05), the genetic diversity parameters revealed that the seeds released for stock abundance had a different genetic composition. These differences are likely a result of hatchery selection and inbreeding. Additionally, all the primer pair sets were effectively amplified in another congeneric species, H. diversicolor diversicolor, indicating that these primers are useful for both abalone species. These microsatellite loci may be valuable for future aquaculture and population genetic studies aimed at developing conservation and management plans for these two abalone species.     

Genome-Wide Association Mapping Identifies New Candidate Genes for Cold Stress and Chilling Acclimation at Seedling Stage in Rice (Oryza sativa L.)

Rice (Oryza sativa L.) is a chilling-sensitive staple food crop, and thus, low temperature significantly affects rice growth and yield. Many studies have focused on the cold shock of rice although chilling acclimation is more likely to happen in the field. In this paper, a genome-wide association study (GWAS) was used to identify the genes that participated in cold stress and chilling accumulation. A total of 235 significantly associated single-nucleotide polymorphisms (SNPs) were identified. Among them, we detected 120 and 88 SNPs for the relative shoot fresh weight under cold stress and chilling acclimation, respectively. Furthermore, 11 and 12 quantitative trait loci (QTLs) were identified for cold stress and chilling acclimation, respectively, by integrating the co-localized SNPs. Interestingly, we identified 10 and 15 candidate genes in 11 and 12 QTLs involved in cold stress and chilling acclimation, respectively, and two new candidate genes (LOC_Os01g62410, LOC_Os12g24490) were obviously up-regulated under chilling acclimation. Furthermore, OsMYB3R-2 (LOC_Os01g62410) that encodes a R1R2R3 MYB gene was associated with cold tolerance, while a new C3HC4-type zinc finger protein-encoding gene LOC_Os12g24490 was found to function as a putative E3 ubiquitin-protein ligase in rice. Moreover, haplotype, distribution, and Wright’s fixation index (FST) of both genes showed that haplotype 3 of LOC_Os12g24490 is more stable in chilling acclimation, and the SNP (A > T) showed a difference in latitudinal distribution. FST analysis of SNPs in OsMYB3R-2 (LOC_Os01g62410) and LOC_Os12g24490 indicated that several SNPs were under selection in rice indica and japonica subspecies. This study provided new candidate genes in genetic improvement of chilling acclimation response in rice.     

Phylogeography and Genetic Differentiation among Populations of the Moon Turban Snail Lunella granulata Gmelin, 1791 (Gastropoda: Turbinidae)

We examined the genetic variation and phylogeographic relationships among 10 populations of Lunella granulata from mainland China, Penghu Archipelago, Taiwan Island, and Japan using mitochondrial COI and 16S markers. A total of 45 haplotypes were obtained in 112 specimens, and relatively high levels of haplotype diversity (h = 0.903) and low levels of nucleotide diversity (π = 0.0046) were detected. Four major phylogenetic lineage clusters were revealed and were concordant with their geographic distribution, agreeing with the haplotype network. These results suggested that geographic barrier isolating effects were occurring among the populations. This hypothesis was also supported by a significant genetic differentiation index (F_ST = 0.709) and by a spatial analysis of molecular variance (SAMOVA) analysis. A mismatch distribution analysis, neutrality tests and Bayesian skyline plots found a single significant population expansion. This expansion occurred on the coast of mainland China before 20–17 ka. Consequently, although the dispersal ability of the planktonic stage and the circulation of ocean currents generally promote genetic exchanges among populations, L. granulata has tended to maintain distinct genetic groups that reflect the respective geographic origins of the constituent lineages. Although the circulation of ocean currents, in principle, may still play a role in determining the genetic composition of populations, long-distance migration between regions is difficult even at the planktonic stage.