Markers For Disease Resistance Research Articles

Polymorphisms in major histocompatibility complex genes and its associations with milk quality in Murrah buffaloes

Animal breeding programs have used molecular genetic tools as an auxiliary method to identify and select animals with superior genetic merit for milk production and milk quality traits as well as disease resistance. Genes of the major histocompatibility complex (MHC) are important molecular markers for disease resistance that could be applied for genetic selection. The aim of this study was to identify single nucleotide polymorphisms (SNPs) and haplotypes in DRB2, DRB3, DMA, and DMB genes in Murrah breed and to analyze the association between molecular markers and milk, fat, protein and mozzarella production, fat and protein percentage, and somatic cell count. Two hundred DNA samples from Murrah buffaloes were used. The target regions of candidate genes were amplified by polymerase chain reaction (PCR) followed by sequencing and identification of polymorphisms. Allele and genotype frequencies, as well as linkage disequilibrium between SNPs, were calculated. Genotypes were used in association analyses with milk production and quality traits. Except for the DMA gene, identified as monomorphic, the other genes presented several polymorphisms. The DMB, DRB2, and DRB3 genes presented two, six, and seven SNPs, respectively. Fifty-seven haplotype blocks were constructed from 15 SNPs identified, which was used in association analyses. All the studied traits had at least one associated haplotype. In conclusion, it is suggested that the haplotypes found herein can be associated with important traits related to milk production and quality.

Identifying Verticillium dahliae Resistance in Strawberry Through Disease Screening of Multiple Populations and Image Based Phenotyping.

Verticillium dahliae is a highly detrimental pathogen of soil cultivated strawberry (Fragaria x ananassa). Breeding of Verticillium wilt resistance into commercially viable strawberry cultivars can help mitigate the impact of the disease. In this study we describe novel sources of resistance identified in multiple strawberry populations, creating a wealth of data for breeders to exploit. Pathogen-informed experiments have allowed the differentiation of subclade-specific resistance responses, through studying V. dahliae subclade II-1 specific resistance in the cultivar “Redgauntlet” and subclade II-2 specific resistance in “Fenella” and “Chandler.” A large-scale low-cost phenotyping platform was developed utilizing automated unmanned vehicles and near infrared imaging cameras to assess field-based disease trials. The images were used to calculate disease susceptibility for infected plants through the normalized difference vegetation index score. The automated disease scores showed a strong correlation with the manual scores. A co-dominant resistant QTL; FaRVd3D, present in both “Redgauntlet” and “Hapil” cultivars exhibited a major effect of 18.3% when the two resistance alleles were combined. Another allele, FaRVd5D, identified in the “Emily” cultivar was associated with an increase in Verticillium wilt susceptibility of 17.2%, though whether this allele truly represents a susceptibility factor requires further research, due to the nature of the F1 mapping population. Markers identified in populations were validated across a set of 92 accessions to determine whether they remained closely linked to resistance genes in the wider germplasm. The resistant markers FaRVd2B from “Redgauntlet” and FaRVd6D from “Chandler” were associated with resistance across the wider germplasm. Furthermore, comparison of imaging versus manual phenotyping revealed the automated platform could identify three out of four disease resistance markers. As such, this automated wilt disease phenotyping platform is considered to be a good, time saving, substitute for manual assessment.

Genome-Wide Association Studies Identified Resistance Loci to Orange Rust and Yellow Leaf Virus Diseases in Sugarcane (Saccharum spp.).

Sugarcane (Saccharum spp.) supplies globally ∼80% of table sugar and 60% of bioethanol. Sugarcane orange rust and Sugarcane yellow leaf virus (SCYLV) are major sugarcane diseases, causing up to 50 and 40% yield losses, respectively. Sugarcane cultivars resistant to these diseases are needed to sustain sugarcane production in several regions. Dissecting DNA sequence variants controlling disease resistance provides a valuable tool for fulfilling a breeding strategy to develop resistant cultivars. In this study, we evaluated disease reactions to orange rust and SCYLV of a sugarcane diversity panel in repeated trials. We conducted a genome-wide association study between high-density markers and disease resistance reactions. We identified 91 putative DNA markers and 82 candidate genes significantly associated with resistance to one of the two diseases. These provide an important genetic resource for finding genes and molecular markers for disease resistance. Our results emphasized the importance of utilizing a wide germplasm collection for breeding resistant sugarcane cultivars.

Genome-wide Association Studies and Candidate Gene Identification for Leaf Scald and Net Blotch in Barley (Hordeum vulgare L.).

We report genomic regions that significantly control resistance to scald, net form (NFNB) and spot form net blotch (SFNB) in barley. Barley genotypes from Ethiopia, ICARDA, and the United States were evaluated in Ethiopia and North Dakota State University (NDSU). Genome-wide association studies (GWAS) were conducted using 23,549 single nucleotide polymorphism (SNP) markers for disease resistance in five environments in Ethiopia. For NFNB and SFNB, we assessed seedling resistance in a glasshouse at NDSU. A large proportion of the Ethiopian landraces and breeding genotypes were resistant to scald and NFNB. Most of genotypes resistant to SFNB were from NDSU. We identified 17, 26, 7, and 1 marker-trait associations (MTAs) for field-scored scald, field-scored net blotch, greenhouse-scored NFNB, and greenhouse-scored SFNB diseases, respectively. Using the genome sequence and the existing literature, we compared the MTAs with previously reported loci and genes for these diseases. For leaf scald, only a few of our MTAs overlap with previous reports. However, the MTAs found for field-scored net blotch as well as NFNB and SFNB mostly overlap with previous reports. We scanned the barley genome for identification of candidate genes within 250 kb of the MTAs, resulting in the identification of 307 barley genes for the 51 MTAs. Some of these genes are related to plant defense responses such as subtilisin-like protease, chalcone synthase, lipoxygenase, and defensin-like proteins.

Comparative assessment of genetic diversity in Albanian olive (Olea europaea L.) using SSRs from anonymous and transcribed genomic regions

A total of 560,578 sequencing reads obtained from the de novo NGS transcriptome sequencing of Olea europaea were searched for the presence of tri- and tetra-nucleotide repeat motifs, which resulted in 375 tri-nucleotide microsatellites and 252 tetra-nucleotides. Twelve expressed sequence tags (EST)-derived SSRs that gave a reproducible pattern, enabling easy scoring and allele size determination, were further tested for polymorphism on 165 cultivars O. europaea subsp. sativa and on 18 oleasters (O. europaea subsp. sylvestris). The main diversity parameters of EST-SSRs were compared to the genomic SSRs that have been most frequently used so far in olive genotyping and mapping studies. Diversity parameters were also compared for different lengths of repeat motifs (di-nucleotide, tri-nucleotide, and tetra-nucleotide microsatellites). The occurrence of null alleles was only observed in anonymous SSRs, while their frequencies were negative for all EST-SSR loci. Eight out of 12 EST-SSRs were classified as highly informative, indicating their applicability in assessing molecular diversity and genetic relatedness in olive. The 12 novel EST-SSR markers selected as a subset of all identified loci containing SSR motifs showed their suitability for evaluation of genetic diversity and population structure and for genetic mapping. They were also linked to genes and, as shown by annotation analysis, four of them have potential for interpretation of allelic variability related to disease resistance and can be evaluated as a potential diagnostic marker for disease resistance. The development of new EST-SSRs provides a valuable tool in molecular breeding programs for both cultivated and wild olives.

Development of user-friendly markers for disease resistance to black root rot of tobacco through genotyping by sequencing

Black root rot (BRR), a disease caused by the hemibiotrophic fungus Thielaviopsis basicola, seriously compromises yield and leaf quality in tobacco (Nicotiana tabacum). Full resistance to black root rot, conferred by the resistance to BRR 1 (RBRR1) locus from Nicotiana debneyi Domin, was transferred to a burley tobacco cultivar through interspecific hybridization. Some undesirable traits potentially caused by linkage drag restrict wider application of RBRR1 in flue-cured tobacco. Therefore, user-friendly molecular markers are needed to assist selection for resistance to black root rot and to break the unfavorable linkage. Genotyping by sequencing (GBS) is a rapid and robust approach for reduced representation sequencing of multiplexed genomic DNA samples that combines genome-wide molecular marker discovery with genotyping. In the present study, we used GBS to identify single-nucleotide polymorphisms (SNPs) linked to the RBRR1 locus, and PCR-based assays for detection of these SNPs were also developed. Sequence analysis of the SNP markers suggested that RBRR1 is located on chromosome 17, providing a basis for map-based cloning of this valuable gene. Co-dominant CAPS markers that co-segregate with the disease-resistant phenotype offer user-friendly tools for tobacco breeding and variety improvement. Furthermore, tested with diverse N. tabacum germplasm, SS192650 displayed 100% selection accuracy for resistance to BRR, suggesting that this marker can be used in diverse tobacco populations.

Screening of Pig (Sus scrofa) Bactericidal Permeability-Increasing Protein (BPI) Gene as Marker for Disease Resistance

ABSTRACTSalmonella infection can cause septicemia, acute or chronic enteritis and wasting in weaned pigs, but may occur in other age groups. The bactericidal/permeability-increasing protein (BPI) gene plays an important role in the natural defense of the host and is found to be associated with resistance/susceptibility to Salmonella infection and identified as a candidate gene for disease resistance breeding in pig. This study was conducted to screen the resistance and/or susceptibility of pigs to Salmonella infection, to determine the genotype and evaluate presence of resistant allele of the BPI gene in population of pigs, and to establish genetic data for pig breeders for the improvement of Philippine pig industry. In this study, 389 blood samples from different pig breeds were collected from pig breeder farms in the Philippines. Genomic DNA was extracted from these samples and genotyping was done by PCR-RFLP analysis using AvaII restriction enzyme. Out of 389 pigs, the genotypic frequency showed that 98.4, 1.3, and 0.3% pigs are resistant (GG), heterozygous type (AG), and susceptible (AA), respectively. The application of BPI gene as marker for disease resistance will provide information to the pig industry to implement strategies for the identification of Salmonella infection-resistant pigs.

Linkage disequilibrium analysis of rice sheath blight resistance markers of rice grown in the cold region of Northeast China

A total of 192 native rice germplasm lines from the cold region of Northeast China were analyzed for rice sheath blight resistance at the late tillering stage using the toothpick embedding method. Disease rating, absolute disease lesion height, relative lesion length and lesion length served as indicators of sheath blight resistance. Germplasm resources were then subjected to population structure analysis and linkage disequilibrium analysis in order to identify disease resistance markers for use in marker-assisted breeding for sheath blight resistance. The germplasm resources were segregated into three main groups .Notably, a total of nine markers were significantly associated with rice sheath blight resistance; eight of these markers(OSR23, RM270, RM339, RM470, RM536, RM569,RM1022, RM1163) were associated with disease rating. The additional marker RM283 was associated with both relative lesion length and lesion length and made a high contribution to the rate of phenotypic variation. Ultimately, the sheath blight resistance markers described in this study could be useful for rice marker-assisted selection of sheath blight resistant cultivars breeding.

Germplasm evaluation and molecular selection of potato (Solanum tuberosum L.) cultivars with disease resistance in China

Foreground and background selections are two important aspects that need to be carefully considered by plant breeders during field selection. In this article, we used 7 disease resistance markers, including four late blight and three potato virus disease resistance gene markers, and 12 microsatellite markers to evaluate the disease resistance and genetic diversity of 76 potato cultivars in total which were collected from 15 provinces of China. The foreground selection results showed that a number of materials, clustered separately, contained more than two late blight resistance markers or pyramided late blight and virus disease resistance gene markers together. A lot of them were collected from the southwest of China. Additionally, the genetic backgrounds of all cultivars were relatively narrow and a limited number of cultivars (15.8%) contained both potato late blight and potato virus Y resistance markers. Also, only two accessions (Yunshu 103 and Lishu 7) contained both late blight and potato virus X resistance markers. In conclusion, this comprehensive evaluation of genetic resources will shed the light on potato disease resistance breeding in the future.

Early molecular signatures of responses of wheat to Zymoseptoria tritici in compatible and incompatible interactions.

Zymoseptoria tritici, the causal agent of septoria tritici blotch, a serious foliar disease of wheat, is a necrotrophic pathogen that undergoes a long latent period. Emergence of insensitivity to fungicides, and pesticide reduction policies, mean there is a pressing need to understand septoria and control it through greater varietal resistance. Stb6 and Stb15, the most common qualitative resistance genes in modern wheat cultivars, determine specific resistance to avirulent fungal genotypes following a gene‐for‐gene relationship. This study investigated compatible and incompatible interactions of wheat with Z. tritici using eight combinations of cultivars and isolates, with the aim of identifying molecular responses that could be used as markers for disease resistance during the early, symptomless phase of colonization. The accumulation of TaMPK3 was estimated using western blotting, and the expression of genes implicated in gene‐for‐gene interactions of plants with a wide range of other pathogens was measured by qRT‐PCR during the presymptomatic stages of infection. Production of TaMPK3 and expression of most of the genes responded to inoculation with Z. tritici but varied considerably between experimental replicates. However, there was no significant difference between compatible and incompatible interactions in any of the responses tested. These results demonstrate that the molecular biology of the gene‐for‐gene interaction between wheat and Zymoseptoria is unlike that in many other plant diseases, indicate that environmental conditions may strongly influence early responses of wheat to infection by Z. tritici, and emphasize the importance of including both compatible and incompatible interactions when investigating the biology of this complex pathosystem.

Peripheral blood blast clearance is an independent prognostic factor for survival and response to acute myeloid leukemia induction chemotherapy.

In patients with acute myeloid leukemia (AML), rapid reduction of circulating blasts with induction chemotherapy may serve as an in vivo marker of chemosensitivity. We performed a retrospective analysis of 363 patients with untreated AML who received induction chemotherapy in order to determine the relationship between day of blast disappearance (DOBD) and complete remission (CR) rates, event-free survival (EFS), and overall survival (OS). DOBD ≤ 5 vs. >5 was identified as the most discriminating cutoff for OS. DOBD > 5 was observed in 35 patients (9.6%). The CR rate for patients with DOBD ≤ 5 vs. >5 was 74.0 and 28.6%, median EFS was 9.4 and 1.8 months, and median OS was 17.1 and 5.8 months, respectively (P < 0.001 for all). DOBD > 5 was independently associated with a lower CR rate and shorter EFS and OS (P < 0.001 for all). DOBD > 5 retained prognostic significance for EFS and OS when patients were stratified by cytogenetic risk group, de novo vs. secondary or therapy-related AML, European LeukemiaNet-based risk groups, and whether CR was achieved. We propose DOBD > 5 as a simple and early marker of disease resistance that identifies patients with poor prognosis who otherwise may not be identified with existing risk stratification systems. Am. J. Hematol. 91:1221-1226, 2016. © 2016 Wiley Periodicals, Inc.

Development and identification of Verticillium wilt-resistant upland cotton accessions by pyramiding QTL related to resistance

Cotton Verticillium wilt is a serious soil-borne disease that leads to significant losses in fiber yield and quality worldwide. Currently, the most effective way to increase Verticillium wilt resistance is to develop new resistant cotton varieties. Lines 5026 and 60182 are two Verticillium wilt-resistant upland cotton accessions. We previously identified a total of 25 quantitative trait loci (QTLs) related to Verticillium wilt resistance from 5026 and 60182 by assembling segregating populations from hybridization with susceptible parents. In the current study, using 13 microsatellite markers flanking QTLs related to Verticillium wilt resistance, we developed 155 cotton inbred lines by pyramiding different QTLs related to Verticillium wilt resistance from a filial generation produced by crossing 5026 and 60182. By examining each allele's effect and performing multiple comparison analysis, we detected four elite QTLs/alleles (q-5/NAU905-2, q-6/NAU2754-2, q-8/NAU3053-1 and q-13/NAU6598-1) significant for Verticillium wilt resistance, pyramiding these elite alleles increased the disease resistance of inbred lines. Furthermore, we selected 34 elite inbred lines, including five lines simultaneously performing elite fiber quality, high yield and resistance to V. dahliae, 14 lines with elite fiber quality and disease resistance, three lines with high yield and disease resistance, and 12 lines with resistance to V. dahliae. No correlation between Verticillium wilt resistance and fiber quality traits/yield and its components was detected in the 155 developed inbred lines. Our results provide candidate markers for disease resistance for use in marker-assisted breeding (MAS), as well as elite germplasms for improving important agronomic traits via modern cotton breeding.

Biotechnology and apple breeding in Japan.

Apple is a fruit crop of significant economic importance, and breeders world wide continue to develop novel cultivars with improved characteristics. The lengthy juvenile period and the large field space required to grow apple populations have imposed major limitations on breeding. Various molecular biological techniques have been employed to make apple breeding easier. Transgenic technology has facilitated the development of apples with resistance to fungal or bacterial diseases, improved fruit quality, or root stocks with better rooting or dwarfing ability. DNA markers for disease resistance (scab, powdery mildew, fire-blight, Alternaria blotch) and fruit skin color have also been developed, and marker-assisted selection (MAS) has been employed in breeding programs. In the last decade, genomic sequences and chromosome maps of various cultivars have become available, allowing the development of large SNP arrays, enabling efficient QTL mapping and genomic selection (GS). In recent years, new technologies for genetic improvement, such as trans-grafting, virus vectors, and genome-editing, have emerged. Using these techniques, no foreign genes are present in the final product, and some of them show considerable promise for application to apple breeding.

Omics approaches to probe markers of disease resistance in animal sciences.

Omics technologies have been developed in recent decades and used in different thematics. More advancements were done in human and plant thematics. Omics is the conjugation of different techniques, studying all biological molecules (DNA, RNA, proteins, metabolites, etc.). Omics is then able to study entire pathways, elucidating phenotypes and their control. Thus, thanks to Omics, it is possible to have a broad overview of the linkage between genotypes and phenotypes. Disease phenotypes (tolerance or resistance) are important to understand in both production and health. Nowadays a plethora of research articles are presenting results in the field of natural disease resistance of animals using Omics technologies. Moreover, thanks to advanced high throughput technologies novel modes of infections (infection pathways) are coming to the surface. Such pathways are complex (hundreds to thousands of molecules implied, with complicated control mechanisms), and Omics can generate useful knowledge to understand those pathways. Here we aim to review several angles of Omics used to probe markers of disease resistance with recent publications and data on the field, and present perspectives and its utilization for a better understanding of diseases.

Effectiveness of beneficial bacteria to promote systemic resistance of grapevine to gray mold as related to phytoalexin production in vineyards

The rhizospheric Bacillus subtilis PTA-271 (271) and endophytic Pseudomonas fluorescens PTA-CT2 (CT2) and Pantoea agglomerans PTA-AF2 (AF2) bacteria are able to induce systemic resistance (ISR) in grapevine against B. cinerea, but ISR markers and their costs remained unknown in vineyards. In this study, we investigated the relationship between the effectiveness of single and binary combinations of selected bacteria to induce ISR and their ability to trigger phytoalexin accumulation, as a potential marker for disease resistance, in leaves and berries, as well as their impact on grape yield in vineyards. Grapevine plants were treated during 2006 in two vineyards by drenching soil with single or binary mixtures of bacteria. Induced resistance against B. cinerea was evaluated and stilbenic phytoalexins were analyzed by HPLC in both leaves and berries. Grape yield was also assessed as number and weight of clusters at ripening. Both single and mixtures of bacteria were effective in reducing gray mold severity in the leaves and berries in vineyards. Disease control was accompanied by a significant accumulation of stilbenic phytoalexins, trans-resveratrol and e-viniferin, in both leaves and berries in the bacterized plants. δ-Viniferin also accumulated, but only in berries of the treated plants. Reduction of disease symptoms and accumulation of resveratrol and viniferins were higher in the plants treated with single CT2 compared to AF2 and 271. Treatment of grapevine plants with binary mixtures of these isolates resulted in a significant performance of CT2+AF2 in leaves and CT2+271 in berries. On the other hand, bacterial treatments did not show any negative effect on grape yield. These results revealed the efficacy of CT2 alone or in combination with AF2 or with 271 in triggering grapevine resistance against B. cinerea and enhancing systemic accumulation of resveratrol and viniferins, without compromising grape yield.

Association of Mx1 gene polymorphism with some economic traits in Meishan pigs

This study was conducted to determine the association of polymorphisms in exon 14 of the Mx1 gene with significant economic traits in Meishan pigs, with the aim of identifying genetic markers of disease resistance. PCR-RFLP analysis of exon 14 of the Mx1 gene was conducted and associations with some cytokine levels (IFN-$\alpha$, IFN-$\gamma$, IL-2, IL-6, IL-10, and IL-12), early body weight (birth weight, 20-day weight, and 40-day weight), and reproductive performance within different parities (total number born, number born alive, number in live weaning litter, birth weight, and weaning weight) were analyzed. The results showed that there were AA, AB, and BB genotypes defined, while a G36T mutation was identified in BB genotype individuals of Meishan pigs. Correlation analysis indicated that the IFN-$\gamma$ levels were significantly higher in the AA genotype than the AB genotype (P < 0.05). However, there were no significant differences in the levels of other cytokines, early body weight, and reproductive performance among the three genotypes. These data indicated that selective molecular breeding practices may enhance the antiviral capability of Meishan pigs without detrimental influences on early body weight, development, and reproductive performance.

Association between the MUC4 g.243A &gt; G polymorphism and immune andproduction traits in Large White pigs

PCR-RFLP analysis of intron 17 of the MUC4 gene was conducted in Large White pigs and associations with cytokine levels (IFN-?, IL-1AŸ, IL-4, IL-6, IL-8, IL-10, TGF-AŸ, and TNF-?), production traits (100-kg-weight day age, back-fat depth, and eye muscle depth), and reproductive performance within different litters (total number born, number born alive, number in live weaning litter) were analyzed with the aim of identifying genetic markers of disease resistance. The results revealed AA, AG, and GG genotypes, with an A243G mutation identified in the GG genotype. Correlation analysis indicated that IL-8 and IL-10 levels and 100-kg-weight day age were significantly higher in the GG genotype compared with AA and AG genotypes (P 0.05). These data indicate that MUC4 g.243A>G may enhance the antidisease capability and affect the growth rate of groups in the fattening period of Large White pigs without detrimental influences on resistance to disease, other production traits, and reproductive performance.

Identification of potential general markers of disease resistance in American oysters, Crassostrea virginica through gene expression studies

Several diseases have a significant impact on American oyster populations in the Atlantic coasts of North America. Knowledge about the responses of oysters to pathogenic challenge could help in identifying potential markers of disease resistance and biomarkers of the health status of an oyster population. A previous analysis of the transcriptome of resistant and susceptible American oysters in response to challenge with the bacterial pathogen Roseovarius crassostreae, as well as sequencing of suppression subtractive hybridization libraries from oysters challenged with the protozoan parasite Perkinsus marinus, provided a list of genes potentially involved in disease resistance or susceptibility. We investigated the patterns of inducible gene expression of several of these genes in response to experimental challenge with the oyster pathogens R. crassostreae, Vibrio tubiashii, and P. marinus. Oysters showing differential susceptibility to R. crassostreae demonstrated differential patterns of expression of genes coding for immune (serine protease inhibitor-1, SPI1) and stress-related (heat shock protein 70, HSP70; arginine kinase) proteins 30 days after challenge with this bacterial pathogen. Differential patterns of expression of immune (spi1, galectin and a matrix metalloproteinase) and stress-related (hsp70, histone H4, and arginine kinase) genes was observed in hemocytes from adult oysters challenged with P. marinus, but not with V. tubiashii. While levels of spi1 expression in hemocytes collected 8 and 21 days after P. marinus challenge were negatively correlated with parasite load in oysters tissues at the end of the challenge (62 days), levels of expression of hsp70 in hemocytes collected 1-day after challenge were positively correlated with oyster parasite load at 62 days. Our results confirm previous research on the role of serine protease inhibitor-1 in immunity and disease resistance in oysters. They also suggest that HSP70 and histone H4 could be used as a markers of health status or disease susceptibility in oysters.

Differential regulation of microRNA transcriptome in chicken lines resistant and susceptible to necrotic enteritis disease

Necrotic enteritis (NE) is a re-emerging disease as a result of increased restriction on the use of antibiotics in poultry. However, the molecular mechanisms underlying the pathogenesis of NE are unclear. Small RNA transcriptome analysis was performed using spleen and intestinal intraepithelial lymphocytes (IEL) from 2 inbred chicken lines selected for resistance or susceptibility to Marek's disease (MD) in an experimentally induced model of avian NE to investigate whether microRNA (miRNA) control the expression of genes associated with host response to pathogen challenge. Unique miRNA represented only 0.02 to 0.04% of the total number of sequences obtained, of which 544 were unambiguously identified. Hierarchical clustering revealed that most of miRNA in IEL were highly expressed in the MD-susceptible line 7.2 compared with MD-resistant line 6.3. Reduced CXCL14 gene expression was correlated with differential expression of several unique miRNA in MD-resistant chickens, whereas TGFβR2 gene expression was correlated with altered gga-miR-216 miRNA levels in MD-susceptible animals. In conclusion, miRNA profiling and deep sequencing of small RNA in experimental models of infectious diseases may be useful for further understanding of host-pathogen interactions, and for providing insights into genetic markers of disease resistance.

QTL for white spot syndrome virus resistance and the sex-determining locus in the Indian black tiger shrimp (Penaeus monodon).

BackgroundShrimp culture is a fast growing aquaculture sector, but in recent years there has been a shift away from tiger shrimp Penaeus monodon to other species. This is largely due to the susceptibility of P. monodon to white spot syndrome virus disease (Whispovirus sp.) which has impacted production around the world. As female penaeid shrimp grow more rapidly than males, mono-sex production would be advantageous, however little is known about genes controlling or markers associated with sex determination in shrimp. In this study, a mapped set of 3959 transcribed single nucleotide polymorphisms were used to scan the P. monodon genome for loci associated with resistance to white-spot syndrome virus and sex in seven full-sibling tiger shrimp families challenged with white spot syndrome virus.ResultsLinkage groups 2, 3, 5, 6, 17, 18, 19, 22, 27 and 43 were found to contain quantitative trait loci significantly associated with hours of survival after white spot syndrome virus infection (P < 0.05 after Bonferroni correction). Nine QTL were significantly associated with hours of survival. Of the SNPs mapping to these and other regions with suggestive associations, many were found to occur in transcripts showing homology to genes with putative immune functions of interest, including genes affecting the action of the ubiquitin-proteasome pathway, lymphocyte-cell function, heat shock proteins, the TOLL pathway, protein kinase signal transduction pathways, mRNA binding proteins, lectins and genes affecting the development and differentiation of the immune system (eg. RUNT protein 1A). Several SNPs significantly associated with sex were mapped to linkage group 30, the strongest associations (P < 0.001 after Bonferroni correction) for 3 SNPs located in a 0.8 cM stretch between positions 43.5 and 44.3 cM where the feminisation gene (FEM-1, affecting sexual differentiation in Caenorhabditis elegans) mapped.ConclusionsThe markers for disease resistance and sexual differentiation identified by this study could be useful for marker assisted selection to improve resistance to WSSV and for identifying homogametic female individuals for mono-sex (all female) production. The genes with putative functions affecting immunity and sexual differentiation that were found to closely map to these loci provide leads about the mechanisms affecting these important economic traits in shrimp.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-731) contains supplementary material, which is available to authorized users.