Phenotypic Variance For Resistance Research Articles

Resistance of juvenile Nile tilapia Oreochromis niloticus from Brazilian populations to Streptococcus agalactiae (serotype Ib and ST-NT)

Nile tilapia is the main farmed fish in Brazilian aquaculture. Streptococcus agalactiae (GBS) is responsible for high mortality rates in fish farms. Genetic improvement is considered an effective alternative for producing resistant animals in aquaculture. The objective of this study was to estimate genetic parameters for resistance to GBS infection in a breeding population of Nile tilapia from Brazil, based on disease challenge using a circulating serotype (Ib and ST-NT). Furthermore, genetic correlations between resistance to GBS and average daily gain (ADG) were estimated to determine whether these traits can be included in selective breeding programs. Survival (SS) and time until death (TD) were the evaluated traits. The survival of the most resistant families was approximately 30%, indicating high phenotypic variation in resistance to the infection. Low to moderate heritability values for resistance traits in the Nile tilapia population were estimated, ranging from 0.14 to 0.27. Heritability for ADG was moderate to high (0.40) based on a growth trial involving 43 families (735 animals). Phenotypic correlations between the resistance traits (SS and TD) and ADG were positive and low, ranging from 0.09 to 0.18, whereas genetic correlations were close to zero. Phenotypic and genetic correlations between SS and TD were considered high and positive, ranging from 0.38 to 0.72. The results suggest that selection for resistance against GBS does not negatively affect juvenile weight gain in Nile tilapia.

Genomic Insights Into Sclerotinia Basal Stalk Rot Resistance Introgressed From Wild Helianthus praecox Into Cultivated Sunflower (Helianthus annuus L.).

Crop wild relatives of the cultivated sunflower (Helianthus annuus L.) are a valuable resource for its sustainable production. Helianthus praecox ssp. runyonii is a wild sunflower known for its resistance against diseases caused by the fungus, Sclerotinia sclerotiorum (Lib.) de Bary, which infects over 400 broadleaf hosts including many important food crops. The objective of this research was to dissect the Sclerotinia basal stalk rot (BSR) resistance introgressed from H. praecox ssp. runyonii into cultivated sunflower. An advanced backcross quantitative trait loci (AB-QTL) mapping population was developed from the cross of a H. praecox accession with cultivated sunflower lines. The AB-QTL population was evaluated for BSR resistance in the field during the summers of 2017–2018 and in the greenhouse in the spring of 2018. Highly significant genetic variations (p < 0.001) were observed for the BSR disease in the field and greenhouse with a moderately high broad-sense heritability (H2) ranging from 0.66 to 0.73. Genotyping-by-sequencing approach was used to genotype the parents and the progeny lines of the AB-QTL population. A genetic linkage map spanning 1,802.95 cM was constructed using 1,755 single nucleotide polymorphism (SNP) markers mapped on 17 sunflower chromosomes. A total of 19 BSR resistance QTL were detected on nine sunflower chromosomes, each explaining 2.21%–16.99% of the phenotypic variance for resistance in the AB-QTL population. Sixteen of the 19 QTL had alleles conferring increased BSR resistance derived from the H. praecox parent. SNP markers flanking the identified QTL will facilitate marker-assisted breeding to combat the disease in sunflower.

Genomic regions and candidate genes linked with Phytophthora capsici root rot resistance in chile pepper (Capsicum annuum L.)

BackgroundPhytophthora root rot, caused by Phytophthora capsici, is a major disease affecting Capsicum production worldwide. A recombinant inbred line (RIL) population derived from the hybridization between ‘Criollo de Morellos-334’ (CM-334), a resistant landrace from Mexico, and ‘Early Jalapeno’, a susceptible cultivar was genotyped using genotyping-by-sequencing (GBS)-derived single nucleotide polymorphism (SNP) markers. A GBS-SNP based genetic linkage map for the RIL population was constructed. Quantitative trait loci (QTL) mapping dissected the genetic architecture of P. capsici resistance and candidate genes linked to resistance for this important disease were identified.ResultsDevelopment of a genetic linkage map using 1,973 GBS-derived polymorphic SNP markers identified 12 linkage groups corresponding to the 12 chromosomes of chile pepper, with a total length of 1,277.7 cM and a marker density of 1.5 SNP/cM. The maximum gaps between consecutive SNP markers ranged between 1.9 (LG7) and 13.5 cM (LG5). Collinearity between genetic and physical positions of markers reached a maximum of 0.92 for LG8. QTL mapping identified genomic regions associated with P. capsici resistance in chromosomes P5, P8, and P9 that explained between 19.7 and 30.4% of phenotypic variation for resistance. Additive interactions between QTL in chromosomes P5 and P8 were observed. The role of chromosome P5 as major genomic region containing P. capsici resistance QTL was established. Through candidate gene analysis, biological functions associated with response to pathogen infections, regulation of cyclin-dependent protein serine/threonine kinase activity, and epigenetic mechanisms such as DNA methylation were identified.ConclusionsResults support the genetic complexity of the P. capsici–Capsicum pathosystem and the possible role of epigenetics in conferring resistance to Phytophthora root rot. Significant genomic regions and candidate genes associated with disease response and gene regulatory activity were identified which allows for a deeper understanding of the genomic landscape of Phytophthora root rot resistance in chile pepper.

Identification of Two New Loci for Adult Plant Resistance to Leaf Rust and Stripe Rust in the Chinese Wheat Variety 'Neimai 836'.

The characterization of leaf rust (caused by Puccinia triticina) and stripe rust (caused by Puccinia striiformis f. sp. tritici) resistance genes is the basis for breeding resistant wheat varieties and managing epidemics of these diseases in wheat. A cross between the susceptible wheat variety 'Apav#1' and resistant variety 'Neimai 836' was used to develop a mapping population containing 148 F5 recombinant inbred lines (RILs). Leaf rust phenotyping was done in field trials at Ciudad Obregón, Mexico, in 2017 and 2018, and stripe rust data were generated at Toluca, Mexico, in 2017 and in Mianyang, Ezhou, and Gansu, China, in 2019. Inclusive complete interval mapping (ICIM) was used to create a genetic map and identify significant resistance quantitative trait loci (QTL) with 2,350 polymorphic markers from a 15K wheat single-nucleotide polymorphism (SNP) array and simple-sequence repeats (SSRs). The pleiotropic multipathogen resistance gene Lr46/Yr29 and four QTL were identified, including two new loci, QLr.hzau-3BL and QYr.hzau-5AL, which explained 3 to 16% of the phenotypic variation in resistance to leaf rust and 7 to 14% of that to stripe rust. The flanking SNP markers for the two loci were converted to Kompetitive Allele-Specific PCR (KASP) markers and used to genotype a collection of 153 wheat lines, indicating the Chinese origin of the loci. Our results suggest that Neimai 836, which has been used as a parent for many wheat varieties in China, could be a useful source of high-level resistance to both leaf rust and stripe rust.

Genotype-Specific Expression and NLR Repertoire Contribute to Phenotypic Resistance Diversity in Plantago lanceolata.

High levels of phenotypic variation in resistance appears to be nearly ubiquitous across natural host populations. Molecular processes contributing to this variation in nature are still poorly known, although theory predicts resistance to evolve at specific loci driven by pathogen-imposed selection. Nucleotide-binding leucine-rich repeat (NLR) genes play an important role in pathogen recognition, downstream defense responses and defense signaling. Identifying the natural variation in NLRs has the potential to increase our understanding of how NLR diversity is generated and maintained, and how to manage disease resistance. Here, we sequenced the transcriptomes of five different Plantago lanceolata genotypes when inoculated by the same strain of obligate fungal pathogen Podosphaera plantaginis. A de novo transcriptome assembly of RNA-sequencing data yielded 24,332 gene models with N50 value of 1,329 base pairs and gene space completeness of 66.5%. The gene expression data showed highly varying responses where each plant genotype demonstrated a unique expression profile in response to the pathogen, regardless of the resistance phenotype. Analysis on the conserved NB-ARC domain demonstrated a diverse NLR repertoire in P. lanceolata consistent with the high phenotypic resistance diversity in this species. We find evidence of selection generating diversity at some of the NLR loci. Jointly, our results demonstrate that phenotypic resistance diversity results from a crosstalk between different defense mechanisms. In conclusion, characterizing the architecture of resistance in natural host populations may shed unprecedented light on the potential of evolution to generate variation.

Estimation of genetic parameters for resistance to Vibrio alginolyticus infection in the Pacific oyster (Crassostrea gigas)

The Pacific oyster (Crassostrea gigas) is one of the most important aquaculture species in the world, while its industry has been hampered by mass summer mortality caused by pathogenic factors including Vibrio bacteria. Selective breeding of oyster strains with high resistance to Vibrio bacteria would be an effective and sustainable approach to prevent massive economic loss. Estimation of genetic parameters for disease resistance is the critical step toward selective breeding. In this study, we constructed 52 full-sib families using the C. gigas with diverse genetic backgrounds, and performed an artificial infection experiment to assess disease resistance among families and estimate genetic parameters for resistance to Vibrio alginolyticus infection. The survival rate of the 52 families ranged from 0% to 56.25%, suggesting high levels of phenotypic variation in resistance to V. alginolyticus infection. Genetic parameters for resistance to V. alginolyticus infection estimated using six different models revealed low to moderate heritability, ranging from 0.133 to 0.257. The Pearson and Spearman correlation coefficients among family estimated breeding values (EBVs) were high (correlation coefficients ≥0.989), indicating that the predictive ability of different models for family EBVs was consistent. The genetic and phenotypic correlation between resistance to V. alginolyticus and growth traits were low, suggesting the feasibility of simultaneous genetic improvement of both growth and resistance traits. This work reported the first estimation of genetic parameters for resistance to V. alginolyticus and provided valuable information toward genetic improvement of resistance to V. alginolyticus using traditional selection or genomic selection breeding approach.

Phenotypic Variation of Tobramycin and Ofloxacin Resistance of Pseudomonas aeruginosa by Repeated Exhibition

Pseudomonas aeruginosa has the ability to resist almost all available antibiotics by rapidly accumulating multiple resistance mechanisms and thus lead to a therapeutic impasse and higher mortality in infected patients.&#x0D; The objective of this study was to assess the phenotypic variation in resistance to tobramycin and ofloxacin from Pseudomonas aeruginosa by repeated exhibition after determination of the minimum inhibitory concentration.&#x0D; This is a prospective and descriptive study carried out in the Laboratory of Microbiology of Fundamental and Applied Biochemistry (Faculty of Sciences, Antananarivo) during the month of January 2020. The strains studied were the virulent wild strain of Pseudomonas aeruginosa PAO1 supplied by the Laboratory and two clinical strains of Pseudomonas aeruginosa from the Microbiology Laboratory of the Joseph Ravoahangy Andrianavalona University Hospital Center, Antananarivo.&#x0D; The strains of P. aeruginosa were cultured in the liquid culture medium (which is Luria Bertani, added with a buffer system of 3- (N-morpholino) propanesulfonic acid (LB-MOPS) which will stabilize the pH and a solid culture medium which is Columbia agar. Repeated exhibition to Tobramycin and Ofloxacin from these strains have been made. The MIC is determined by a visual evaluation of the turbidity of the various wells of the microplate.&#x0D; The MIC value of Pseudomonas aeruginosa with tobramycin and ofloxacin is very variable for the initial MIC until the 5th generation after repeated exhibition. More Pseudomonas aeruginosa is exposed to an antibiotic many times, the more it develops resistance to this antibiotic, even being sensitive at the start. That is to say, clinically, the dose prescribed for the antibiotic has been greatly exceeded if Pseudomonas aeruginosa is repeatedly exposed to the same antibiotic.

QNCLB7.02, a novel QTL for resistance to northern corn leaf blight in maize

Northern corn leaf blight (NCLB), which is caused by the hemibiotrophic fungal pathogen Setosphaeria turcica, is a devastating foliar disease that results in considerable maize yield losses. In the present study, quantitative trait locus (QTL) analysis was conducted across two environments using an ultra-high-density bin map constructed using recombinant inbred lines (RILs) derived from a cross between Ye478 and Qi319. A total of 11 QTLs, located on chromosomes 1, 4, 5, 6, 7, 8, 9, and 10, were detected that confer resistance to physiological race 0 of NCLB. Each QTL could explain 3.53–15.29% of the total phenotypic variation in disease resistance after artificial inoculation in two environments. Among these QTL, qNCLB7.02, which is located on chromosome 7, had the largest effect, accounting for 10.11 and 15.29% of the phenotypic variation in resistance in two field trials and BLUP. The common confidence interval (CI) for qNCLB7.02 was 1.4 Mb, according to the B73 RefGen_v3 sequence. The resistance effect of qNCLB7.02 was validated in 2016 by using chromosome segment substitution lines (CSSLs) derived from Qi319 as the donor in the genetic background of Ye478. The type 6 CSSL, which harbors introgressed qNCLB7.02, was found to be significantly associated with resistance to NCLB by linked marker bnlg1808 and exhibited greater resistance than the other CSSLs that did not carry this QTL (P = 0.0008). The combination of linkage mapping in RILs and validation in CSSLs is a powerful approach for the dissection of QTL for disease resistance in maize.

Molecular mapping of four blast resistance genes using recombinant inbred lines of 93-11 and nipponbare

Molecular mapping of new blast resistance genes is important for developing resistant rice cultivars using marker-assisted selection. In this study, 259 recombinant inbred lines (RILs) were developed from a cross between Nipponbare and 93-11, and were used to construct a 1165.8-cM linkage map with 131 polymorphic simple sequence repeat (SSR) markers. Four major quantitative trait loci (QTLs) for resistance to six isolates of Magnaporthe oryzae were identified: qPi93-1, qPi93-2, qPi93-3, and qPiN-1. For the three genes identified in 93-11, qPi93-1 is linked with SSR marker RM116 on the short arm of chromosome 11 and explains 33% of the phenotypic variation in resistance to isolate CHE86. qPi93-2 is linked with SSR marker RM224 on the long arm of chromosome 11 and accounts for 31% and 25% of the phenotypic variation in resistance to isolates 162-8B and ARB50, respectively. qPi93-3 is linked with SSR marker RM7102 on chromosome 12 and explains 16%, 53%, and 28% of the phenotypic variation in resistance to isolates CHE86, ARB52, and ARB94, respectively. QTL qPiN-1 from Nipponbare is associated with SSR marker RM302 on chromosome 1 and accounts for 34% of the phenotypic variation in resistance to isolate PO6-6. These new genes can be used to develop new varieties with blast resistance via marker-aided selection and to explore the molecular mechanism of rice blast resistance.

Resistance to Phytophthora nicotianae in Tobacco Breeding Lines Derived from Variety Beinhart 1000.

Black shank, caused by Phytophthora nicotianae, is managed primarily by host resistance. The rapid emergence of race 1 eliminated the usefulness of available complete resistance, leading breeders to search for new sources of resistance. Cigar tobacco 'Beinhart 1000' (BH) is highly resistant to all races of P. nicotianae. Doubled-haploid (DH) lines from a cross of BH and the susceptible 'Hicks' were evaluated for black shank resistance, and quantitative trait loci (QTL) on linkage groups (LGs) 4 and 8 accounted for >43% of the phenotypic variation in resistance. Forty-three DH lines and parents were evaluated, and genotypes with one or both QTL from BH on LGs 4 and 8 had increased incubation periods and decreased root rot but higher final inoculum levels than genotypes with neither QTL. A low level of stem resistance was observed in BH and DH lines with the QTL from BH on LG 4 but not LG 8. Low levels of leaf resistance were seen for Hicks, BH, and DH lines with both QTL from BH on LG 4 and 8. The partial resistance from BH has not been used commercially and may provide an increase in level of partial resistance in future tobacco varieties.

Mapping of QTLs in tomato line FLA456 associated with resistance to a virus causing tomato yellow leaf curl disease

Tomato (yellow) leaf curl disease (TYLCD) is a serious threat to tomato production in the tropics and subtropics. The genetics of resistance to Tomato yellow leaf curl Thailand virus Taiwan strain (TYLCTHV-[TW]) in a highly resistant tomato line FLA456 was studied through quantitative trait loci (QTL) analysis. Four QTLs named qTy4.1, qTy6.1, qTy10.1 and qTy11.1 were detected on chromosomes 4, 6, 10, and 11, respectively, through evaluation of an F6 recombinant inbred line (RIL) population derived from a cross between FLA456 (resistant) and CLN1621L (susceptible). Gene action of all QTLs was recessive based on disease reaction of the F1. The markers SINAC1 and SLM4-34 flanked qTy4.1 on chromosome 4, and SLM11-12 and SLM11-17 defined qTy11.1, which co-located with the previously identified Ty-5 and Ty-2 loci, respectively. qTy6.1 was flanked by the markers SLM6-55 and TES-0014, and qTy10.1 by the markers SLM10-80-SLM10-46 on chromosomes 6 and 10. The LOD values of the putative QTLs ranged from 2.79 to 13.76. The phenotypic variance explained by each QTL ranged from 7.1 to 31.9 %. The four QTLs collectively contributed about 60.5 % of the phenotypic variation in resistance against TYLCTHV-[TW]. Group mean severity scores of those RILs possessing three or four qTy were generally lower than RIL groups with only one or no qTy. Given the diversity of begomoviruses that cause TYLCD across the regions, the new QTLs from FLA456 would be valuable in tomato breeding for developing varieties with durable resistance. Two QTL intervals (qTy4.1 and qTy10.1) contained virus resistance candidate genes such as CTV.22 and eukaryotic translation initiation factor 4E.

Identification of Pm8 Suppressor at the Pm3 Locus in Soft Red Winter Wheat

ABSTRACTThe 1BL.1RS wheat (Triticum aestivum L.)–rye (Secale cereale L.) translocation possesses genes Pm8, Yr9, Lr26, and Sr31 for resistance to several major fungal pathogens of small grain cereals. However, not all wheat cultivars with the 1RS translocation are resistant to Pm8‐avirulent isolates of Blumeria graminis f. sp. tritici (Bgt), the causal pathogen of wheat powdery mildew. A suppressor is postulated to limit the function of Pm8 in certain genetic backgrounds, such as ‘AGS 2000’. To illustrate the genetic basis of the suppressor in AGS 2000, a 178 recombinant inbred line (RIL) population was used by crossing AGS 2000 with another 1BL.1RS cultivar Pioneer 26R61 (Pm8 effective). A single Bgt isolate, Ken‐2‐5, avirulent to Pm8 and virulent to Pm3a was chosen to inoculate the entire RIL population at the seedling stage. One major quantitative trait locus (QTL), QSuPm.uga‐1AS, was stably detected as having an inhibiting effect on Pm8 in AGS 2000, and the QTL was postulated to be Pm3a based on its location. Further evidence of the Pm8‐suppressing nature of Pm3a was obtained when eight lines from the 2010 Gulf Atlantic Wheat Nursery were inoculated with Ken‐2‐5. The eight lines all have Pm8 (1BL.1RS) but were susceptible, as they also have Pm3a. In addition, a functional locus, QPm.uga‐7AL, was identified in Pioneer 26R61, where it accounted for up to 41% of phenotypic variation in resistance to isolate Ken‐2‐5. QPm.uga‐7AL was flanked by simple sequence repeat (SSR) markers Xcfa2257 and Xwmc525 on 7AL, and its relationship with other known Pm loci on this chromosome arm remains uncertain.

Copy Number Variation and Transposable Elements Feature in Recent, Ongoing Adaptation at the Cyp6g1 Locus

The increased transcription of the Cyp6g1 gene of Drosophila melanogaster, and consequent resistance to insecticides such as DDT, is a widely cited example of adaptation mediated by cis-regulatory change. A fragment of an Accord transposable element inserted upstream of the Cyp6g1 gene is causally associated with resistance and has spread to high frequencies in populations around the world since the 1940s. Here we report the existence of a natural allelic series at this locus of D. melanogaster, involving copy number variation of Cyp6g1, and two additional transposable element insertions (a P and an HMS-Beagle). We provide evidence that this genetic variation underpins phenotypic variation, as the more derived the allele, the greater the level of DDT resistance. Tracking the spatial and temporal patterns of allele frequency changes indicates that the multiple steps of the allelic series are adaptive. Further, a DDT association study shows that the most resistant allele, Cyp6g1-[BP], is greatly enriched in the top 5% of the phenotypic distribution and accounts for ∼16% of the underlying phenotypic variation in resistance to DDT. In contrast, copy number variation for another candidate resistance gene, Cyp12d1, is not associated with resistance. Thus the Cyp6g1 locus is a major contributor to DDT resistance in field populations, and evolution at this locus features multiple adaptive steps occurring in rapid succession.

Heritability of resistance to oxidative stress in early life

Oxidative stress has recently been suggested to play an important role in life-history evolution, but little is known about natural variation and heritability of this physiological trait. Here, we explore phenotypic variation in resistance to oxidative stress of cross-fostered yellow-legged gull (Larus cachinnans) chicks. Resistance to oxidative stress was not related to plasma antioxidants at hatching, which are mostly derived from maternal investment into eggs. Common environmental effects on phenotypic variation in resistance to oxidative stress were not significant. Heritability was relatively low and nonsignificant in hatchlings, but interestingly, the chicks of age 8 days showed high and significant heritability (h(2) = 0.59). Our results suggest that resistance to oxidative stress is determined mainly by the genotype as chicks grow. Further work is required to explore the genetic role of oxidative stress in life-history evolution.

A quantitative approach detects three QTLs involved in powdery mildew resistance at the seedling stage in the winter wheat line RE714

Powdery mildew (Blumeria graminis f. sp. tritici) is one of the major diseases of wheat (Triticum aestivum). The objective of the present study was to describe the quantitative resistance to powdery mildew of the winter wheat line RE714 at the seedling stage and to identify microsatellite markers tightly linked to the RE714 resistance QTL, which could be used in marker-assisted selection. A population of 160 recombinant inbred lines obtained from the cross between RE714 (resistant) and Hardi (susceptible) was genotyped with microsatellite and AFLP markers. Fifteen powdery mildew isolates were used to test the resistance of these lines at the seedling stage. QTL analysis enabled us to identify three major QTLs controlling powdery mildew resistance in RE714: a QTL located on chromosome 2A, corresponding to the Pm4b gene, explaining 76–93% of the phenotypic variance for resistance to six isolates; two QTLs located on chromosomes 5D and 6A, each explaining 20–67% of the phenotypic variance for resistance to five isolates. A minor QTL for resistance to four of the six isolates revealing Pm4b was detected in the same region as the 5D QTL. Other minor QTLs were detected on chromosomes 2A and 6B, explaining, respectively, 10.9 and 11.5% of the phenotypic variance for resistance to isolate 96-27. The maps around the three major QTLs were enriched with microsatellite markers that could be used in marker-assisted selection of these QTLs.

Mapping of a quantitative trait locus for resistance against infectious salmon anaemia in Atlantic salmon (Salmo Salar): comparing survival analysis with analysis on affected/resistant data

BackgroundInfectious Salmon Anaemia (ISA) is a viral disease affecting farmed Atlantic salmon (Salmo salar) worldwide. The identification of Quantitative Trait Loci (QTL) affecting resistance to the disease could improve our understanding of the genetics underlying the trait and provide a means for Marker-Assisted Selection. We previously performed a genome scan on commercial Atlantic salmon families challenge tested for ISA resistance, identifying several putative QTL. In the present study, we set out to validate the strongest of these QTL in a larger family material coming from the same challenge test, and to determine the position of the QTL by interval mapping. We also wanted to explore different ways of performing QTL analysis within a survival analysis framework (i.e. using time-to-event data), and to compare results using survival analysis with results from analysis on the dichotomous trait 'affected/resistant'.ResultsThe QTL, located on Atlantic salmon linkage group 8 (following SALMAP notation), was confirmed in the new data set. Its most likely position was at a marker cluster containing markers BHMS130, BHMS170 and BHMS553. Significant segregation distortion was observed in the same region, but was shown to be unrelated to the QTL. A maximum likelihood procedure for identifying QTL, based on the Cox proportional hazard model, was developed. QTL mapping was also done using the Haley-Knott method (affected/resistant data), and within a variance-component framework (affected/resistant data and time-to-event data). In all cases, analysis using affected/resistant data gave stronger evidence for a QTL than did analysis using time-to-event data.ConclusionA QTL for resistance to Infectious Salmon Anaemia in Atlantic salmon was validated in this study, and its more precise location on linkage group eight was determined. The QTL explained 6% of the phenotypic variation in resistance to the disease. The linkage group also displayed significant segregation distortion. Survival models proved in this case not to be more suitable than models based on the dichotomous trait 'affected/resistant' for analysing the data.

Genetic Variation in Drosophila melanogaster Resistance to Infection: A Comparison Across Bacteria

Insects use a generalized immune response to combat bacterial infection. We have previously noted that natural populations of D. melanogaster harbor substantial genetic variation for antibacterial immunocompetence and that much of this variation can be mapped to genes that are known to play direct roles in immunity. It was not known, however, whether the phenotypic effects of variation in these genes are general across the range of potentially infectious bacteria. To address this question, we have reinfected the same set of D. melanogaster lines with Serratia marcescens, the bacterium used in the previous study, and with three additional bacteria that were isolated from the hemolymph of wild-caught D. melanogaster. Two of the new bacteria, Enterococcus faecalis and Lactococcus lactis, are gram positive. The third, Providencia burhodogranaria, is gram negative like S. marcescens. Drosophila genotypes vary highly significantly in bacterial load sustained after infection with each of the four bacteria, but mean loads are largely uncorrelated across bacteria. We have tested statistical associations between immunity phenotypes and nucleotide polymorphism in 21 candidate immunity genes. We find that molecular variation in some genes, such as Tehao, contributes to phenotypic variation in the suppression of only a subset of the pathogens. Variation in SR-CII and 18-wheeler, however, has effects that are more general. Although markers in SR-CII and 18-wheeler explain >20% of the phenotypic variation in resistance to L. lactis and E. faecalis, respectively, most of the molecular polymorphisms tested explain <10% of the total variance in bacterial load sustained after infection.

Mapping QTLs for Witches' Broom (Crinipellis Perniciosa) Resistance in Cacao (Theobroma Cacao L.)

Molecular markers (RAPD, AFLP and microsatellites) were used to generate a linkage map and to identify QTLs associated to witches' broom (Crinipellis perniciosa) resistance in cacao (Theobroma cacao), using 82 individuals of an F2 population derived from the clones ICS-1 (susceptible) and Scavina-6 (resistant). Fifteen evaluations of the number of brooms have been carried out in six years (1997–2002). In order to increase the precision and accuracy in the measures of resistance, each F2 plant was cloned in three replications in a randomized block design with single-tree plots and evaluated over 2 years. Three hundred and forty-two markers were obtained, being 33 microsatellites, 77 AFLPs and 232 RAPDs. The distribution of the number of brooms in the F2 population was skewed to resistance, suggesting the involvement of major genes controlling resistance and the repeatability estimated for resistance was 44%. A strong putative QTL was detected as being related to witches' broom resistance. Associated to this QTL, the microsatellite mTcCIR35 explained 35.5% of the phenotypic variation in resistance. This marker is being used for marker-assisted selection in Scavina-6 progenies, including those selected in private plantations, as an auxiliary tool to the phenotypic selection.

Linkage disequilibrium mapping of a Verticillium dahliae resistance quantitative trait locus in tetraploid potato ( Solanum tuberosum) through a candidate gene approach.

We have used the linkage disequilibrium mapping method to test for an association between a candidate gene marker and resistance to Verticillium dahliae in tetraploid potato. A probe derived from the tomato Verticillium resistance gene ( Ve1) identified homologous sequences ( StVe1) in potato, which in a diploid population map to chromosome 9, in a position analogous to that of the tomato resistance gene. When a molecular marker closely linked (1.5 cM) to the homologues was used as a candidate gene marker on 137 tetraploid potato genotypes (mostly North American cultivars), the association between the marker and resistance was confirmed ( P<0.001). The amount of phenotypic variation in resistance explained by the allele of the STM1051 marker was greater than 10% and 25% in two subpopulations that were inferred from coancestry data matrix. Cloning of homologues from the highly resistant potato cv. Reddale indicates that the resistance quantitative trait locus (QTL) comprises at least an eleven-member family, encoding plant-specific leucine-rich repeat proteins highly similar to the tomato Ve genes. The sequence analysis shows that all homologues are uninterrupted open reading frames and thus represent putative functional resistance genes. This is the first time that the linkage disequilibrium method has been used to find an association between a resistance gene and a candidate gene marker in tetraploid potato. We have shown that it is possible to map QTL directly on already available potato cultivars, without developing a new mapping population.

Resistance of Coffea arabica cv. Ruiru 11 tested with different isolates of Colletotrichum kahawae, the causal agent of coffee berry disease

Seven single conidia isolates of Colletotrichum kahawae varying in pathogenicity were used to inoculate hybrid progenies from 66 crosses ofCoffea arabica cv. Ruiru 11. The objective of this study was to investigate the effect of pathogen variation on resistance of the Ruiru 11 cultivar. The main effects of crosses and isolates were significant (p ≤0.05) while their interaction effects were non-significant. Partitioning variance components indicated that the proportion of phenotypic variance for resistance that is due to genetic effects was low. It was concluded that variation for resistance among hybrid progenies of the Ruiru 11 cultivar was probably due to differences in aggressiveness of the pathogen as reflected by the significant main effects of crosses and isolates in combination with other environmental factors which influence disease epidemics. The coffee berry disease pathogen is unlikely to have adapted to the cultivar because of the non-significant crosses × isolates interaction effects.