Bidirectional backcrosses between wild and cultivated lettuce identify loci involved in nonhost resistance to downy mildew

Key message

The nonhost resistance of wild lettuce to lettuce downy mildew seems explained by four components of a putative set of epistatic genes.

Abstract

The commonplace observation that plants are immune to most potential pathogens is known as nonhost resistance (NHR). The genetic basis of NHR is poorly understood. Inheritance studies of NHR require crosses of nonhost species with a host, but these crosses are usually unsuccessful. The plant-pathosystem of lettuce and downy mildew, Bremia lactucae, provides a rare opportunity to study the inheritance of NHR, because the nonhost wild lettuce species Lactuca saligna is sufficiently cross-compatible with the cultivated host Lactuca sativa. Our previous studies on NHR in one L. saligna accession led to the hypothesis that multi-locus epistatic interactions might explain NHR. Here, we studied NHR at the species level in nine accessions. Besides the commonly used approach of studying a target trait from a wild donor species in a cultivar genetic background, we also explored the opposite, complementary approach of cultivar introgression in a wild species background. This bidirectional approach encompassed (1) nonhost into host introgression: identification of L. saligna derived chromosome regions that were overrepresented in highly resistant BC1 plants (F1?×?L. sativa), (2) host into nonhost introgression: identification of L. sativa derived chromosome regions that were overrepresented in BC1 inbred lines (F1?×?L. saligna) with relatively high infection levels. We demonstrated that NHR is based on resistance factors from L. saligna and the genetic dose for NHR differs between accessions. NHR seemed explained by combinations of epistatic genes on three or four chromosome segments, of which one chromosome segment was validated by the host into nonhost approach.

     

Inheritance pattern and genetic correlations among growth and wood quality traits in Para rubber tree (<Emphasis Type="Italic">Hevea brasiliensis</Emphasis>) and implications for breeding

Inheritance pattern of wood traits viz. specific gravity, fibre dimensions and fibre-derived biometrical indices and their interactions among themselves and with that of growth are reported in Hevea brasiliensis. Girth (h² =???0.02?±?0.44 to h² =?0.35?±?0.24) showed moderate genetic control. Among wood traits, specific gravity (h²?=?0.15?±?0.31 to h² =?0.33?±?0.28) was found to be under moderate genetic control. Fibre traits viz., fibre length (h² =???0.26?±?0.30 to h² =?0.50?±?0.34), fibre diameter (h² =?0.19?±?0.49 to h² =?0.70?±?0.11), fibre lumen diameter (h² =???0.18?±?0.35 to h² =?0.56?±?0.47) and fibre wall thickness (h² =???5.17?±?5.26 to h² =?0.50?±?0.50) were under moderate to strong genetic control. Among fibre-derived indices, flexibility coefficient (h² =?0.48?±?0.21 to h² =?0.89?±?0.29) showed moderate to very strong genetic control. The Runkel ratio (h² =???0.40?±?0.27 to h² =?0.42?±?0.29) and slenderness ratio (h² =???0.36?±?0.29 to h² =?0.43?±?0.28) showed moderate genetic control. Girth showed very strong positive genetic correlation with fibre wall thickness and strong positive correlation with fibre width indicating scope of indirect selection potential for these traits. Wood specific gravity was not correlated with either girth or fibre traits. Hence, it would be possible to concomitantly improve growth and fibre traits without adversely affecting wood specific gravity. Moderate to very high estimates of heritability for fibre traits, girth and specific gravity indicated that considerable genetic gain can be realised for these traits. Implications of the above findings in genetic improvement of wood in Hevea are discussed.     

Mapping QTLs for physiological and biochemical traits related to grain yield under control and terminal heat stress conditions in bread wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.)

In order to detect genomic regions with different effects for some of the physiological and biochemical traits of wheat, four experiments were conducted at Research Farm of Agricultural and Natural Resources Research Center of Zabol in 2015–2016 and 2016–2017 growing seasons. The experiments were carried out using four alpha lattice designs with two replications under non-stress and terminal heat stress conditions. Plant materials used in this study included 167 recombinant inbred lines and their parents (‘SeriM82’ and ‘Babax’). Six traits including grain yield (GY), proline content (PRO), water soluble carbohydrates (WSC), maximum efficiency of photosystem II (Fv/Fm), cytoplasmic membrane stability (CMS) and chlorophyll content (CHL) were evaluated. Genetic linkage map consisted of 211 AFLP marker, 120 SSR marker and 144 DArT markers with 1864 cm length and 4.4 cm mean distance. QTL analysis was carried out using a mixed-model-based composite interval mapping (MCIM) method. By the combined analysis of normal phenotypic values, 27 additive QTLs and five pairs of epistatic effects were identified for studied traits, among which two additive and one epistatic QTL showed significant QTL?×?environment interactions. By the combined analysis of stress phenotypic values, a total of 26 QTLs with additive effects and 5 epistatic QTLs were detected, among which one additive and one epistatic QTL showed QTL?×?environment interactions. Six QTLs with major effects (QGY-2B, QGY-2D, QPro-5B, QWSC-4A, QFv/Fm-6A and QCMS-4B), which were common between two conditions could be useful for marker-assisted selection (MAS) in order to develop heat tolerant and high-performance wheat varieties.     

Gas exchange,carbon balance and stomatal traits in wild and cultivated rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) genotypes

Carbon balancing within the plant species is an important feature for climatic adaptability. Photosynthesis and respiration traits are directly linked with carbon balance. These features were studied in 20 wild rice accessions Oryza spp., and cultivars. Wide variation was observed within the wild rice accessions for photosynthetic oxygen evolution or photosynthetic rate (A), dark (R _d), and light induced respiration (LIR) rates, as well as stomatal density and number. The mean rate of A varied from 10.49 μmol O₂ m^?2 s^?1 in cultivated species and 13.09 μmol O₂ m^?2 s^?1 in wild spp., The mean R _d is 2.09 μmol O₂ m^?2 s^?1 and 2.31 μmol O₂ m^?2 s^?1 in cultivated and wild spp., respectively. Light induced Respiration (LIR) was found to be almost twice in wild rice spp., (16.75 μmol O₂ m^?2 s^?1) compared to cultivated Oryza spp., Among the various parameters, this study reveals LIR and A as the key factors for positive carbon balance. Stomatal contribution towards carbon balance appears to be more dependent on abaxial surface where several number of stomata are situated. Correlation analysis indicates that R _d and LIR increase with the increase in A. In this study, O. nivara (CR 100100, CR 100097), O. rufipogon (IR 103404) and O. glumaepatula (IR104387) were identified as potential donors which could be used in rice breeding program. Co-ordination between gas exchange and patchiness in stomatal behaviour appears to be important for carbon balance and environmental adaptation of wild rice accessions, therefore, survival under harsh environment.     

Diversity and symbiotic divergence of endophytic and non-endophytic rhizobia of <Emphasis Type="Italic">Medicago sativa</Emphasis>

Knowledge of rhizobium diversity is helping to enable the utilization of rhizobial resources. To analyze the phenotypic and genetic diversity and the symbiotic divergence of rhizobia of Medicago sativa, 30 endophytic and non-endophytic isolates were collected from different parts of five alfalfa varieties in three geographic locations in Gansu, China. Numerical analyses based on 72 phenotypic properties and restriction fragment length polymorphism (RFLP) fingerprinting indicated the abundant phenotypic and genetic diversity of the tested strains. According to the phylogenetic analysis of 16S RNA, atpD, glnII, and recA gene sequences, Rhizobium and Ensifer were further classified into four different genotypes: Rhizobium radiobacter, Rhizobium sp., Rhizobium rosettiformans, and Ensifer meliloti. The differences in architecture and functioning of the rhizobial genomes and, to a lesser extent, environment diversification helped explain the diversity of tested strains. The tested strains exhibited similar symbiotic feature when inoculated onto M. sativa cvs. Gannong Nos. 3 and 9 and Qingshui plants for the clustering feature of their parameter values. An obvious symbiotic divergence of rhizobial strains was observed in M. sativa cvs. Longzhong and WL168HQ plants because of the scattered parameter values. Their symbiotic divergence differed according to alfalfa varieties, which indicated that the sensitivity of different alfalfa varieties to rhizobial strains may differ. Most of the tested strains exhibited plant growth-promoting traits including phosphate solubilization and production of indole-3-acetic acid (IAA) when colonizing plant tissues and soil.     

Estimates of Heritability for Growth and Shell Color Traits and Their Genetic Correlations in the Black Shell Strain of Pacific Oyster <Emphasis Type="Italic">Crassostrea gigas</Emphasis>

The Pacific oyster Crassostrea gigas has been introduced widely and massively and became an economically important aquaculture species on a global scale. We estimated heritabilities of growth and shell color traits and their genetic correlations in black shell strain of C. gigas. Analyses were performed on 22 full-sib families in a nested mating design including 410 individuals at harvest (24 months of age). The parentage assignment was inferred based on four panels of multiplex PCR markers including 10 microsatellite loci and 94.9% of the offspring were unambiguously assigned to single parent pairs. The Spearman correlation test (r = ? 0.992, P < 0.001) demonstrated the high consistency of the shell pigmentation (SP) and L* and their same efficacy in shell color measurements. The narrow-sense heritability estimated under the animal model analysis was 0.18 ± 0.12 for shell height, 0.25 ± 0.16 for shell length, 0.10 ± 0.09 for shell width, 0.42 ± 0.20 for total weight, 0.32 ± 0.18 for shell weight, and 0.68 ± 0.16 for L*, 0.69 ± 0.16 for shell pigmentation, respectively. The considerable additive genetic variation in growth and shell color traits will make it feasible to produce genetic improvements for these traits in selective breeding program. High genetic and phenotypic correlations were found among growth traits and among shell color traits. To optimize a selection strategy for both fast growth and pure dark shell strain of C. gigas, it is proposed to take both total weight and black shell as joint objective traits in selective breeding program. Our study offers an important reference in the process of selective breeding in black shell color stain of C. gigas and will facilitate to develop favorable breeding strategies of genetic improvements for this economically important strain.     

Quantitative trait loci mapping of yield and related traits using a high-density genetic map of maize

Improving grain yield is the ultimate goal of the maize-breeding programs. In this study, analyses of conditional and unconditional quantitative trait locus (QTL) and epistatic interactions were used to elucidate the genetic architecture of yield and its related traits. A total of 15 traits of a recombinant inbred line population, including yield per plant (YPP), seven ear-related traits, and seven kernel-related traits, were measured in six different environments. Based on the genetic linkage map constructed using 2091 bins as markers, 56 main-effect QTLs for these traits were identified. These QTLs were distributed across eight genomic regions (bin 1.06, bin 4.02/4.05/4.08, bin 5.04, bin 7.04, bin 8.08, and bin 9.04), within the marker intervals of 85.45–6260.66 kb, and the phenotypic variance explained ranging from 5.69 to 11.56 %. One gene (GRMZM2G168229) encoding SBP-box domain protein was located in the small interval of qKRN4-3 and may be involved in patterning of kernel row number. Seventeen conditional QTLs identified for YPP were conditioned on its related traits and explained 6.18–23.15 % of the phenotypic variance. Conditional mapping analysis revealed that qYPP4-1, qYPP6-1, and qYPP8-1 are partially influenced by YPP-related traits at the individual QTL level. Digenic epistatic analysis identified 12 digenic interactions involving 22 loci across the whole genome. In addition, conditional digenic epistatic analysis identified 14 digenic interactions involving 21 loci. This study provides valuable information for understanding the genetic relationship between YPP and related traits and constitutes the first step toward the cloning of the relevant genes.     

Interaction between checkpoint genes <Emphasis Type="Italic">RAD9, RAD17, RAD24</Emphasis>, and <Emphasis Type="Italic">RAD53</Emphasis> involved in the determination of yeast <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> sensitivity to ionizing radiation

Mechanisms for genetic control of cell division cycle (checkpoint control) have been studied in most detail in yeast Saccharomyces cerevisiae. To clarify the role of checkpoint genes RAD9, RAD17, RAD24, and RAD53 in cell radioresistance, double mutants were analyzed for cell sensitivity to ionizing radiation. Double mutants carrying mutations in combination with mutation rad9Δ were shown to manifest the epistatic type of interaction. Our results suggest that checkpoint genes RAD9, RAD17, RAD24, and RAD53 belong to a single epistatic group designated RAD9 and govern the same pathway. Genes RAD9 and RAD53 have a positive effect on sensitivity to γ-radiation, whereas RAD17 and RAD24 have a negative effect. Interactions between mutations may differ when considering their sensitivity to γ-radiation and UV light; mutations rad9Δ and rad24Δ were shown to manifest the additive effect in the first case and epistatic effect in the second.     

Association analysis of the SNP (rs345476947) in the <Emphasis Type="Italic">FUT2</Emphasis> gene with the production and reproductive traits in pigs

The FUT2 gene was considered as an important candidate for pathogenic infections, while the potential associations between this gene and the production and reproductive traits of pigs have not been explored. In this study, we detected the genetic variants of porcine FUT2 gene and analyzed the associations of the polymorphisms with FUT2 mRNA expression and production and reproductive traits (age at 100 kg, backfat thickness at 100 kg, eye muscle thickness, the number of newborn piglets, the number of weaned piglets, and birth weight) in 100 Large White sows. One single nucleotide polymorphism (SNP) (rs345476947, C→T) in the intron of FUT2 and three genotypes (TT, CT and CC) were determined. Association analysis revealed significant associations between this SNP with the number of newborn piglets and weaned piglets. Furthermore, individuals with the TT genotype had significantly higher numbers of newborn piglets and weaned piglets than those with the CC genotype (P?<?0.05). Quantitative PCR analysis showed that FUT2 expression in individuals with CC genotype was significantly higher than those with TT and CT genotypes in the liver and lymph gland (P?<?0.05) and higher than that of CT in the spleen, kidney, and duodenum (P?<?0.05). These findings indicated that the TT genotype may be a favorable genotype for the reproductive traits of pigs. Our study revealed the genetic variants of the FUT2 gene and identified a promising candidate SNP (rs345476947) associated with the reproductive traits, which has the potential to be applied in selective breeding of pigs.     

Development of species diagnostic SNP markers for quality control genotyping in four rice (<Emphasis Type="Italic">Oryza</Emphasis> L.) species

Species misclassification (misidentification) and handling errors have been frequently reported in various plant species conserved at diverse gene banks, which could restrict use of germplasm for correct purpose. The objectives of the present study were to (i) determine the extent of genotyping error (reproducibility) on DArTseq-based single-nucleotide polymorphisms (SNPs); (ii) determine the proportion of misclassified accessions across 3134 samples representing three African rice species complex (Oryza glaberrima, O. barthii, and O. longistaminata) and an Asian rice (O. sativa), which are conserved at the AfricaRice gene bank; and (iii) develop species- and sub-species (ecotype)-specific diagnostic SNP markers for rapid and low-cost quality control (QC) analysis. Genotyping error estimated from 15 accessions, each replicated from 2 to 16 times, varied from 0.2 to 3.1%, with an overall average of 0.8%. Using a total of 3134 accessions genotyped with 31,739 SNPs, the proportion of misclassified samples was 3.1% (97 of the 3134 accessions). Excluding the 97 misclassified accessions, we identified a total of 332 diagnostic SNPs that clearly discriminated the three indigenous African species complex from Asian rice (156 SNPs), O. longistaminata accessions from both O. barthii and O. glaberrima (131 SNPs), and O. sativa spp. indica from O. sativa spp. japonica (45 SNPs). Using chromosomal position, minor allele frequency, and polymorphic information content as selection criteria, we recommended a subset of 24 to 36 of the 332 diagnostic SNPs for routine QC genotyping, which would be highly useful in determining the genetic identity of each species and correct human errors during routine gene bank operations.     

Comparison of molecular genetic utilities of TD,AFLP, and MSAP among the accessions of <Emphasis Type="Italic">japonica,indica</Emphasis>, and <Emphasis Type="Italic">Tongil</Emphasis> of <Emphasis Type="Italic">Oryza sativa</Emphasis> L.

Rice is one of the most important food crops in the world. Genetic diversity is essential for cultivar improvement programs. We compared genetic diversity derived from insertion–deletion (in–del) or base substitutions by amplified fragment length polymorphism (AFLP), from transposon transposition mutations by transposon display (TD), and from cytosine methylation by methylation-sensitive amplified polymorphism (MSAP) in japonica, indica, and Tongil type varieties of Oryza sativa L. Polymorphic profiles from the three marker systems allowed us to clearly distinguish the three types of varieties. The indica type varieties showed the highest genetic diversity followed by the Tongil and japonica type varieties. Of the three marker systems, TD produced the highest marker indices, and AFLP and MSAP produced similar marker indices. Pair-wise comparisons of the three marker systems showed that the correlation between the two genetic markers systems (AFLP and TD, r = 0.959) was higher than the correlations between the genetic and epigenetic marker systems (AFLP and MSAP, r = 0.52; TD and MSAP, r = 0.505). Both genetic marker systems had similar levels of gene differentiation (G _ST ) and gene flow (N _m ), which differed in the epigenetic marker system. Although the G _ST of the epigenetic marker system was lower than the genetic marker systems, the N _m of the epigenetic marker system was higher than in the genetic marker systems, indicating that epigenetic variations have a greater influence than genetic variations among the O. sativa L. types.     

Chromosomes A07 and A05 associated with stable and major QTLs for pod weight and size in cultivated peanut (<Emphasis Type="Italic">Arachis hypogaea</Emphasis> L.)

Key message

Co-localized intervals and candidate genes were identified for major and stable QTLs controlling pod weight and size on chromosomes A07 and A05 in an RIL population across four environments.

Abstract

Cultivated peanut (Arachis hypogaea L.) is an important legume crops grown in > 100 countries. Hundred-pod weight (HPW) is an important yield trait in peanut, but its underlying genetic mechanism was not well studied. In this study, a mapping population (Xuhua 13 × Zhonghua 6) with 187 recombinant inbred lines (RILs) was developed to map quantitative trait loci (QTLs) for HPW together with pod length (PL) and pod width (PW) by both unconditional and conditional QTL analyses. A genetic map covering 1756.48 cM was constructed with 817 markers. Additive effects, epistatic interactions, and genotype-by-environment interactions were analyzed using the phenotyping data generated across four environments. Twelve additive QTLs were identified on chromosomes A05, A07, and A08 by unconditional analysis, and five of them (qPLA07, qPLA05.1, qPWA07, qHPWA07.1, and qHPWA05.2) showed major and stable expressions in all environments. Conditional QTL mapping found that PL had stronger influences on HPW than PW. Notably, qHPWA07.1, qPLA07, and qPWA07 that explained 17.93–43.63% of the phenotypic variations of the three traits were co-localized in a 5 cM interval (1.48 Mb in physical map) on chromosome A07 with 147 candidate genes related to catalytic activity and metabolic process. In addition, qHPWA05.2 and qPLA05.1 were co-localized with minor QTL qPWA05.2 to a 1.3 cM genetic interval (280 kb in physical map) on chromosome A05 with 12 candidate genes. This study provides a comprehensive characterization of the genetic components controlling pod weight and size as well as candidate QTLs and genes for improving pod yield in future peanut breeding.

     

A PCR-based analysis of plant DNA reveals the feeding preferences of <Emphasis Type="Italic">Apolygus lucorum</Emphasis> (Heteroptera: Miridae)

The mirid bug Apolygus lucorum (Meyer-Dür) (Heteroptera: Miridae) is a severe pest of cotton and other crops in China. The feeding preferences of this pest are unclear due to its frequent movement among different host plants and the inconspicuous signs of its feeding. Here, we present results of a field trial that used direct observation of bug densities and a PCR-based molecular detection assay to detect plant DNA in bugs to explore relationships between A. lucorum population abundance and its feeding preference between two host plants, Humulus scandens (Loureiro) Merrill and Medicago sativa L. The field-plot samples showed that A. lucorum adults generally prefer flowering host plants. Its density was significantly higher on flowering H. scandens than on seedlings of M. sativa, and a similarly higher bug density was observed on flowering M. sativa than on seedlings of H. scandens. In the laboratory, we designed two pairs of species-specific primers targeting the trnL-F region for H. scandens and M. sativa, respectively. The detectability of plant DNA generally decreased with time post-feeding, and the half-life of plant DNA detection (DS₅₀) in the gut was estimated as 6.26 h for H. scandens and 3.79 h for M. sativa with significant differences between each other. In mirid bugs exposed to seedlings of H. scandens and flowering M. sativa, the detection rate of M. sativa DNA was significantly higher than that of H. scandens. Meanwhile, in mirid bugs exposed to seedlings of M. sativa and flowering H. scandens, a significantly higher detection rate of H. scandens DNA was found. We developed a useful tool to detect the remaining plant food species specifically from the gut of A. lucorum in the current study. We provided direct evidence of its feeding preference between H. scandens and M. sativa at different growth stages, which strongly supported a positive correlation between population abundance and feeding preference of A. lucorum on different plants under field conditions. The findings provide new insights into the understanding of A. lucorum’s feeding preference, and are helpful for developing the strategies to control this pest.     

Conjugative plasmid transfer from <Emphasis Type="Italic">Escherichia coli</Emphasis> is a versatile approach for genetic transformation of thermophilic <Emphasis Type="Italic">Bacillus</Emphasis> and <Emphasis Type="Italic">Geobacillus</Emphasis> species

We previously demonstrated efficient transformation of the thermophile Geobacillus kaustophilus HTA426 using conjugative plasmid transfer from Escherichia coli BR408. To evaluate the versatility of this approach to thermophile transformation, this study examined genetic transformation of various thermophilic Bacillus and Geobacillus spp. using conjugative plasmid transfer from E. coli strains. E. coli BR408 successfully transferred the E. coli–Geobacillus shuttle plasmid pUCG18T to 16 of 18 thermophiles with transformation efficiencies between 4.1 × 10^?7 and 3.8 × 10^?2/recipient. Other E. coli strains that are different from E. coli BR408 in intracellular DNA methylation also generated transformants from 9 to 15 of the 18 thermophiles, including one that E. coli BR408 could not transform, although the transformation efficiencies of these strains were generally lower than those of E. coli BR408. The conjugation was performed by simple incubation of an E. coli donor and a thermophile recipient without optimization of experimental conditions. Moreover, thermophile transformants were distinguished from abundant E. coli donor only by high temperature incubation. These observations suggest that conjugative plasmid transfer, particularly using E. coli BR408, is a facile and versatile approach for plasmid introduction into thermophilic Bacillus and Geobacillus spp., and potentially a variety of other thermophiles.     

Diversity and enzymatic potentialities of <Emphasis Type="Italic">Bacillus</Emphasis> sp. strains isolated from a polluted freshwater ecosystem in Cuba

Genotypic and phenotypic characterization of Bacillus spp. from polluted freshwater has been poorly addressed. The objective of this research was to determine the diversity and enzymatic potentialities of Bacillus spp. strains isolated from the Almendares River. Bacilli strains from a polluted river were characterized by considering the production of extracellular enzymes using API ZYM. 14 strains were selected and identified using 16S rRNA, gyrB and aroE genes. Genotypic diversity of the Bacillus spp. strains was evaluated using pulsed field gel electrophoresis. Furthermore, the presence of genetic determinants of potential virulence toxins of the Bacillus cereus group and proteinaceous crystal inclusions of Bacillus thuringiensis was determined. 10 strains were identified as B. thuringiensis, two as Bacillus megaterium, one as Bacillus pumilus and one as Bacillus subtilis. Most strains produced proteases, amylases, phosphatases, esterases, aminopeptidases and glucanases, which reflect the abundance of biopolymeric matter in Almendares River. Comparison of the typing results revealed a spatio-temporal distribution among B. thuringiensis strains along the river. The results of the present study highlight the genotypic and phenotypic diversity of Bacillus spp. strains from a polluted river, which contributes to the knowledge of genetic diversity of Bacilli from tropical polluted freshwater ecosystems.     

Detection of Insertions/Deletions Within <Emphasis Type="Italic">SIRT1</Emphasis>, <Emphasis Type="Italic">SIRT2</Emphasis> and <Emphasis Type="Italic">SIRT3</Emphasis> Genes and Their Associations with Body Measurement Traits in Cattle

Growth traits are complex quantitative traits controlled by numerous candidate genes, and they can be well-evaluated using body measurement traits. As the members of the nicotinamide adenine dinucleotide-dependent family of histone deacetylases, class I sirtuin genes (including SIRT1, SIRT2 and SIRT3) play crucial roles in regulating lipid metabolism, cellular growth and metabolism, suggesting that they are potential candidate genes affecting body measurement traits in animals. Hence, the objective of this work aimed to detect novel insertions/deletions (indels) of SIRT1, SIRT2 and SIRT3 genes in 955 cattle belonging to five breeds, as well as to evaluate their effects on body measurement traits. Herein, the novel 12-bp indel of SIRT1 gene, the 7-bp indel of SIRT2 gene and the 26-bp indel of SIRT3 gene were firstly reported, respectively. The association analysis indicated that the indels within SIRT1 and SIRT2 genes were significantly associated with body measurement traits such as body weight, chest circumference, height at hip cross, hip width, body height, etc. (P?<?0.05 or P?<?0.01). Therefore, based on these findings, the two novel indel variants within bovine SIRT1 and SIRT2 genes could be considered as potential molecular markers for growth traits in cattle selection practices and breeding.     

Susceptibility of germinating cruciferous seeds to <Emphasis Type="Italic">Bagrada hilaris</Emphasis> (Hemiptera: Pentatomidae) feeding injury

Bagrada hilaris (Burmeister) (Hemiptera: Pentatomidae) is a serious pest that attacks both germinating and seedling stages of a variety of cruciferous crops grown in the Central Coast of California. B. hilaris feeding on germinating seeds can cause severe stunting and plant mortality, and little is known about the feeding preference of B. hilaris for germinating seeds of major cruciferous hosts and varieties of hosts. No-choice and choice experiments were conducted in which germinating seeds in soilless and soil settings were exposed to B. hilaris adults for 7 days. Susceptibility scores were developed using B. hilaris feeding injury sites, distorted leaves, and deformed and dead plants to determine the overall B. hilaris preference for germinating host seeds. Based on the scores, the order of preference was arugula (Eruca sativa L.)?>?turnip (B. rapa L. var. rapa)?>?mizuna (B. rapa L. nipposinica)?>?kale (B. oleracea L. acephala)?>?choi (Brassica rapa L. var. chinensis)?>?broccoli (B. oleracea var. italica Plenck)?>?cauliflower (B. oleracea L. var. botrytis)?>?lettuce (Lactuca sativa L.)?>?sweet alyssum (Lobularia maritima [L.] Desv.). The lowest feeding injury was recorded on germinating lettuce and sweet alyssum seeds. Furthermore, no-choice and choice experiments were conducted with four varieties each of arugula and mizuna, twelve varieties each of kale and choi, and nine varieties/types of leafy Asian greens. The arugula varieties ‘Wild Rocket’ and ‘Spirit’ were more damaged by B. hilaris than other varieties tested. Among mizuna varieties, ‘Beira F1’ was more attractive to B. hilaris than ‘Scarlet’ or ‘Starbor F1.’ The choi varieties ‘Tokyo Bekana,’ ‘Feng Qing Choi F1,’ ‘Joi Choi F1,’ and ‘Win-Win Choi F1’ were more attractive than ‘Rosie F1.’ The leafy Asian greens variety ‘Carlton F1’ was more attractive to B. hilaris than ‘Yukina Savon,’ ‘Tatsoi OG,’ ‘Komatsuna Summerfest F1,’ ‘Red Rain F1,’ and ‘Shungiku.’ Therefore, the results suggest that not all varieties were equally susceptible to B. hilaris feeding and possibly be utilized for further field evaluation as a trap crop or developing more resistant varieties to B. hilaris.     

Molecular genetic diversity of <Emphasis Type="Italic">Gongylonema neoplasticum</Emphasis> (Fibiger &amp; Ditlevsen, 1914) (Spirurida: Gongylonematidae) from rodents in Southeast Asia

More than a dozen Gongylonema spp. (Spirurida: Spiruroidea: Gongylonematidae) have been described from a variety of rodent hosts worldwide. Gongylonema neoplasticum (Fibiger & Ditlevsen, 1914), which dwells in the gastric mucosa of rats such as Rattus norvegicus (Berkenhout) and Rattus rattus (Linnaeus), is currently regarded as a cosmopolitan nematode in accordance with global dispersion of its definitive hosts beyond Asia. To facilitate the reliable specific differentiation of local rodent Gongylonema spp. from the cosmopolitan congener, the genetic characterisation of G. neoplasticum from Asian Rattus spp. in the original endemic area should be considered since the morphological identification of Gongylonema spp. is often difficult due to variations of critical phenotypical characters, e.g. spicule lengths and numbers of caudal papillae. In the present study, morphologically identified G. neoplasticum from 114 rats of seven species from Southeast Asia were selected from archived survey materials from almost 4,500 rodents: Thailand (58 rats), Cambodia (52 rats), Laos (three rats) and Philippines (one rat). In addition, several specimens from four rats in Indonesia were used in the study. Nucleotide sequences of the ribosomal RNA gene (rDNA) (5,649 bp) and the cytochrome c oxidase subunit 1 gene (cox1) (818 bp) were characterised. The rDNA showed little nucleotide variation, including the internal transcribed spacer (ITS) regions. The cox1 showed 24 haplotypes, with up to 15 (1.83%) nucleotide substitutions regardless of parasite origin. Considering that Rattus spp. have been shown to originate from the southern region of Asia and G. neoplasticum is their endogenous parasite, it is reasonable to propose that the present study covers a wide spectrum of the genetic diversity of G. neoplasticum, useful for both the molecular genetic speculation of the species and the molecular genetic differentiation of other local rodent Gongylonema spp. from the cosmopolitan congener.