Application of Genomic and Quantitative Genetic Tools to Identify Candidate Resistance Genes for Brown Rot Resistance in Peach

The availability of a complete peach genome assembly and three different peach genome sequences created by our group provide new opportunities for application of genomic data and can improve the power of the classical Quantitative Trait Loci (QTL) approaches to identify candidate genes for peach disease resistance. Brown rot caused by Monilinia spp., is the most important fungal disease of stone fruits worldwide. Improved levels of peach fruit rot resistance have been identified in some cultivars and advanced selections developed in the UC Davis and USDA breeding programs. Whole genome sequencing of the Pop-DF parents lead to discovery of high-quality SNP markers for QTL genome scanning in this experimental population. Pop-DF created by crossing a brown rot moderately resistant cultivar ‘Dr. Davis’ and a brown rot resistant introgression line, ‘F8,1–42’, derived from an initial almond × peach interspecific hybrid, was evaluated for brown rot resistance in fruit of harvest maturity over three seasons. Using the SNP linkage map of Pop-DF and phenotypic data collected with inoculated fruit, a genome scan for QTL identified several SNP markers associated with brown rot resistance. Two of these QTLs were placed on linkage group 1, covering a large (physical) region on chromosome 1. The genome scan for QTL and SNP effects predicted several candidate genes associated with disease resistance responses in other host-pathogen systems. Two potential candidate genes, ppa011763m and ppa026453m, may be the genes primarily responsible for M. fructicola recognition in peach, activating both PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI) responses. Our results provide a foundation for further genetic dissection, marker assisted breeding for brown rot resistance, and development of peach cultivars resistant to brown rot.     

Genome-wide association mapping of Fusarium head blight resistance in contemporary barley breeding germplasm

Utilization of quantitative trait loci (QTL) identified in bi-parental mapping populations has had limited success for improving complex quantitative traits with low to moderate heritability. Association mapping in contemporary breeding germplasm may lead to more effective marker strategies for crop improvement. To test this approach, we conducted association mapping of two complex traits with moderate heritability; Fusarium head blight (FHB) severity and the grain concentration of mycotoxin associated with disease, deoxynivalenol (DON). To map FHB resistance in barley, 768 breeding lines were evaluated in 2006 and 2007 in four locations. All lines were genotyped with 1,536 SNP markers and QTL were mapped using a mixed model that accounts for relatedness among lines. Average linkage disequilibrium within the breeding germplasm extended beyond 4 cM. Four QTL were identified for FHB severity and eight QTL were identified for the DON concentration in two independent sets of breeding lines. The QTL effects were small, explaining 1–3% of the phenotypic variation, as might be expected for complex polygenic traits. We show that using breeding germplasm to map QTL can complement bi-parental mapping studies by providing independent validation, mapping QTL with more precision, resolving questions of linkage and pleiotropy, and identifying genetic markers that can be applied immediately in crop improvement.     

QTL analysis of ergot resistance in sorghum

Sorghum ergot, caused predominantly by Claviceps africana Frederickson, Mantle, de Milliano, is a significant threat to the sorghum industry worldwide. The objectives of this study were firstly, to identify molecular markers linked to ergot resistance and to two pollen traits, pollen quantity (PQ) and pollen viability (PV), and secondly, to assess the relationship between the two pollen traits and ergot resistance in sorghum. A genetic linkage map of sorghum RIL population R931945-2-2 x IS 8525 (resistance source) was constructed using 303 markers including 36 SSR, 117 AFLPtrade mark, 148 DArTtrade mark and two morphological trait loci. Composite interval mapping identified nine, five, and four QTL linked to molecular markers for percentage ergot infection (PCERGOT), PQ and PV, respectively, at a LOD >2.0. Co-location/linkage of QTL were identified on four chromosomes while other QTL for the three traits mapped independently, indicating that both pollen and non pollen-based mechanisms of ergot resistance were operating in this sorghum population. Of the nine QTL identified for PCERGOT, five were identified using the overall data set while four were specific to the group data sets defined by temperature and humidity. QTL identified on SBI-02 and SBI-06 were further validated in additional populations. This is the first report of QTL associated with ergot resistance in sorghum. The markers reported herein could be used for marker-assisted selection for this important disease of sorghum.     

Bayesian QTL mapping using genome-wide SSR markers and segregating population derived from a cross of two commercial F<Subscript>1</Subscript> hybrids of tomato

Key message

Using newly developed euchromatin-derived genomic SSR markers and a flexible Bayesian mapping method, 13 significant agricultural QTLs were identified in a segregating population derived from a four-way cross of tomato.

Abstract

So far, many QTL mapping studies in tomato have been performed for progeny obtained from crosses between two genetically distant parents, e.g., domesticated tomatoes and wild relatives. However, QTL information of quantitative traits related to yield (e.g., flower or fruit number, and total or average weight of fruits) in such intercross populations would be of limited use for breeding commercial tomato cultivars because individuals in the populations have specific genetic backgrounds underlying extremely different phenotypes between the parents such as large fruit in domesticated tomatoes and small fruit in wild relatives, which may not be reflective of the genetic variation in tomato breeding populations. In this study, we constructed F₂ population derived from a cross between two commercial F₁ cultivars in tomato to extract QTL information practical for tomato breeding. This cross corresponded to a four-way cross, because the four parental lines of the two F₁ cultivars were considered to be the founders. We developed 2510 new expressed sequence tag (EST)-based (euchromatin-derived) genomic SSR markers and selected 262 markers from these new SSR markers and publicly available SSR markers to construct a linkage map. QTL analysis for ten agricultural traits of tomato was performed based on the phenotypes and marker genotypes of F₂ plants using a flexible Bayesian method. As results, 13 QTL regions were detected for six traits by the Bayesian method developed in this study.

     

QTL mapping of resistance to Fusarium ear rot using a RIL population in maize

Fusarium ear rot is a prevalent disease in maize, reducing grain yields and quality. Resistance breeding is an efficient way to minimize losses caused by the disease. In this study, 187 lines from a RIL population along with the resistant (87-1) and susceptible (Zong 3) parents were planted in Zhengzhou and Beijing with three replications in years 2004 and 2006. Each line was artificially inoculated using the nail-punch method. Significant genotypic variation in response to Fusarium ear rot was detected in both years. Based on a genetic map containing 246 polymorphic SSR markers with average genetic distances of 9.1 cM, the ear-rot resistance QTL were firstly analyzed by composite interval mapping (CIM). Three QTL were detected in both Zhengzhou and Beijing in 2004; and three and four QTL, respectively, were identified in 2006. The resistant parent contributed all resistance QTL. By using composite interval mapping and a mixed model (MCIM), significant epistatic effects on Fusarium ear rot as well as interactions between mapped loci and environments were observed across environments. Two QTL on chromosome 3 (3.04 bin) were consistently identified across all environments by the two methods. The major resistant QTL with the largest effect was flanked by markers umc1025 and umc1742 on chromosome 3 (3.04 bin), explaining 13–22% of the phenotypic variation. The SSR markers closely flanking the major resistance QTL will facilitate marker-assisted selection (MAS) of resistance to Fusarium ear rot in maize breeding programs.     

Uncovering QTL for resistance and survival time to Philasterides dicentrarchi in turbot (Scophthalmus maximus)

Disease resistance‐related traits have received increasing importance in aquaculture breeding programs worldwide. Currently, genomic information offers new possibilities in breeding to address the improvement of this kind of traits. The turbot is one of the most promising European aquaculture species, and Philasterides dicentrarchi is a scuticociliate parasite causing fatal disease in farmed turbot. An appealing approach to fight against disease is to achieve a more robust broodstock, which could prevent or diminish the devastating effects of scuticociliatosis on farmed individuals. In the present study, a genome scan for quantitative trait loci (QTL) affecting resistance and survival time to P. dicentrarchi in four turbot families was carried out. The objectives were to identify QTL using different statistical approaches [linear regression (LR) and maximum likelihood (ML)] and to locate significantly associated markers for their application in genetic breeding strategies. Several genomic regions controlling resistance and survival time to P. dicentrarchi were detected. When analyzing each family separately, significant QTL for resistance were identified by the LR method in two linkage groups (LG1 and LG9) and for survival time in LG1, while the ML methodology identified QTL for resistance in LG9 and LG23 and for survival time in LG6 and LG23. The analysis of the total data set identified an additional significant QTL for resistance and survival time in LG3 with the LR method. Significant association between disease resistance‐related traits and genotypes was detected for several markers, a single one explaining up to 22% of the phenotypic variance. Obtained results will be essential to identify candidate genes for resistance and to apply them in marker‐assisted selection programs to improve turbot production.     

Dissecting the genetic architecture of agronomic traits in multiple segregating populations in rapeseed (<Emphasis Type="Italic">Brassica napus</Emphasis> L.)

Detection of QTL in multiple segregating populations is of high interest as it includes more alleles than mapping in a single biparental population. In addition, such populations are routinely generated in applied plant breeding programs and can thus be used to identify QTL which are of direct relevance for a marker-assisted improvement of elite germplasm. Multiple-line cross QTL mapping and joint linkage association mapping were used for QTL detection. We empirically compared these two different biometrical approaches with regard to QTL detection for important agronomic traits in nine segregating populations of elite rapeseed lines. The plants were intensively phenotyped in multi-location field trials and genotyped with 253 SNP markers. Both approaches detected several additive QTL for diverse traits, including flowering time, plant height, protein content, oil content, glucosinolate content, and grain yield. In addition, we identified one epistatic QTL for flowering time. Consequently, both approaches appear suited for QTL detection in multiple segregating populations.     

Comparative genetic analysis of quantitative traits in sunflower (Helianthus annuus L.)

One hundred and fifty F₂–F₃ families from a cross between two inbred sunflower lines FU and PAZ2 were used to map quantitative trait loci (QTL) for resistance to white rot (Sclerotinia sclerotiorum) attacks of terminal buds and capitula, and black stem (Phoma macdonaldii). A genetic linkage map of 18 linkage groups with 216 molecular markers spanning 1,937 cM was constructed. Disease resistances were measured in field experiments for S. sclerotiorum and under controlled conditions for P. macdonaldii. For resistance to S. sclerotiorum terminal bud attack, seven QTL were identified, each explaining less than 10% of phenotypic variance. For capitulum attack by this parasite, there were four QTL (each explaining up to 20% of variation) and for P. macdonaldii resistance, four QTL were identified, each having effects of up to 16%. The S. sclerotiorum capitulum resistance QTL were compared with those reported previously and it was concluded that resistance to this disease is governed by a considerable number of QTL, located on almost all the sunflower linkage groups.     

Discovery and validation of genomic regions associated with resistance to maize lethal necrosis in four biparental populations

In sub-Saharan Africa, maize is the key determinant of food security for smallholder farmers. The sudden outbreak of maize lethal necrosis (MLN) disease is seriously threatening the maize production in the region. Understanding the genetic basis of MLN resistance is crucial. In this study, we used four biparental populations applied linkage mapping and joint linkage mapping approaches to identify and validate the MLN resistance-associated genomic regions. All populations were genotyped with low to high density markers and phenotyped in multiple environments against MLN under artificial inoculation. Phenotypic variation for MLN resistance was significant and heritability was moderate to high in all four populations for both early and late stages of disease infection. Linkage mapping revealed three major quantitative trait loci (QTL) on chromosomes 3, 6, and 9 that were consistently detected in at least two of the four populations. Phenotypic variance explained by a single QTL in each population ranged from 3.9% in population 1 to 43.8% in population 2. Joint linkage association mapping across three populations with three biometric models together revealed 16 and 10 main effect QTL for MLN-early and MLN-late, respectively. The QTL identified on chromosomes 3, 5, 6, and 9 were consistent with the QTL identified by linkage mapping. Ridge regression best linear unbiased prediction with five-fold cross-validation revealed high accuracy for prediction across populations for both MLN-early and MLN-late. Overall, the study discovered and validated the presence of major effect QTL on chromosomes 3, 6, and 9 which can be potential candidates for marker-assisted breeding to improve the MLN resistance.     

Identification and validation of QTL for Sclerotinia midstalk rot resistance in sunflower by selective genotyping

Midstalk rot, caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important cause of yield loss in sunflower (Helianthus annuus L.). Objectives of this study were to: (1) estimate the number, genomic positions and genetic effects of quantitative trait loci (QTL) for resistance to midstalk rot in line TUB-5-3234, derived from an interspecific cross; (2) determine congruency of QTL between this line and other sources of resistance; and (3) make inferences about the efficiency of selective genotyping (SG) in detecting QTL conferring midstalk rot resistance in sunflower. Phenotypic data for three resistance (stem lesion, leaf lesion and speed of fungal growth) and two morphological (leaf length and leaf length with petiole) traits were obtained from 434 F₃ families from cross CM625 (susceptible) × TUB-5-3234 (resistant) under artificial infection in field experiments across two environments. The SG was applied by choosing the 60 most resistant and the 60 most susceptible F₃ families for stem lesion. For genotyping of the respective F₂ plants, 78 simple sequence repeat markers were used. Genotypic variances were highly significant for all traits. Heritabilities and genotypic correlations between resistance traits were moderate to high. Three to four putative QTL were detected for each resistance trait explaining between 40.8% and 72.7% of the genotypic variance ( ). Two QTL for stem lesion showed large genetic effects and corroborated earlier findings from the cross NDBLOS_sel (resistant) × CM625 (susceptible). Our results suggest that SG can be efficiently used for QTL detection and the analysis of congruency for resistance genes across populations.     

A consensus ‘Honeycrisp’ apple (Malus × domestica) genetic linkage map from three full-sib progeny populations

The apple cultivar Honeycrisp is emerging in North American markets due to its outstanding eating quality. A set of three ‘Honeycrisp’ progeny populations from the University of Minnesota apple breeding program were utilized to construct parental and consensus ‘Honeycrisp’ linkage maps to enable marker-assisted breeding. Two populations were segregated for fruit texture traits and a third was of interest in examining disease resistance. All available individuals were genotyped with the International RosBREED SNP Consortium (IRSC) apple 8K SNP array v1, for a total of 318 progeny individuals. Three unique ‘Honeycrisp’ parental maps (‘Honeycrisp’ × ‘Monark,’ ‘Honeycrisp’ × ‘Gala,’ and ‘Honeycrisp’ × MN1764) were developed, consisting of 1,018, 1,042, and 1,041 single-nucleotide polymorphism (SNP) markers, respectively. Among all three ‘Honeycrisp’ parental maps, 951 SNP markers were in common. Combining these maps with the MergeMap tool, a consensus ‘Honeycrisp’ linkage map with 1,091 SNP markers was developed with an average distance of 1.36 cM between consecutive markers. The ‘Honeycrisp’ consensus map was largely in agreement with the physical position of markers in the ‘Golden Delicious’ reference genome sequence (v1.0, as of February 2013). The consensus linkage map is informative for an elite cultivar that is being utilized in breeding programs worldwide for its superb fruit quality traits.     

Identification of quantitative trait loci (QTL) for fruit-quality traits and number of weeks of flowering in the cultivated strawberry

Fruit quality and repeat flowering are two major foci of several strawberry breeding programs. The identification of quantitative trait loci (QTL) and molecular markers linked to these traits could improve breeding efficiency. In this work, an F₁ population derived from the cross ‘Delmarvel’ × ‘Selva’ was used to develop a genetic linkage map for QTL analyses of fruit-quality traits and number of weeks of flowering. Some QTL for fruit-quality traits were identified on the same homoeologous groups found in previous studies, supporting trait association in multiple genetic backgrounds and utility in multiple breeding programs. None of the QTL for soluble solids colocated with a QTL for titratable acids, and, although the total soluble solid contents were significantly and positively correlated with titratable acids, the correlation coefficient value of 0.2452 and independence of QTL indicate that selection for high soluble solids can be practiced independently of selection for low acidity. One genomic region associated with the total number of weeks of flowering was identified quantitatively on LG IV-S-1. The most significant marker, FxaACAO2I8C-145S, explained 43.3 % of the phenotypic variation. The repeat-flowering trait, scored qualitatively, mapped to the same region as the QTL. Dominance of the repeat-flowering allele was demonstrated by the determination that the repeat-flowering parent was heterozygous. This genomic region appears to be the same region identified in multiple mapping populations and testing environments. Markers linked in multiple populations and testing environments to fruit-quality traits and repeat flowering should be tested widely for use in marker-assisted breeding.     

Mapping of quantitative trait loci (QTLs) for oil yield using SSRs and gene-based markers in African oil palm (<Emphasis Type="Italic">Elaeis guineensis</Emphasis> Jacq.)

The identification of quantitative trait loci (QTLs) based on anchor markers, especially candidate genes that control a trait of interest, has been noted to increase the power of QTL detection. Since these markers can be scored as co-dominant data, they are also valuable for comparing and integrating the QTL linkage maps from diverse mapping populations. To estimate the position and effects of QTLs linked to oil yield traits in African oil palm, co-dominant microsatellites (SSR) and candidate gene-based sequence polymorphisms were applied to construct a linkage map for a progeny showing large differences in oil yield components. The progeny was genotyped for 97 SSR markers, 93 gene-linked markers, and 12 non-gene-linked SNP markers. From these, 190 segregating loci could be arranged into 31 linkage groups while 12 markers remained unmapped. Using the single marker linkage, interval mapping and multiple QTL methods, 16 putative QTLs on seven linkage groups affecting important oil yield related traits such as fresh fruit bunch yield (FFB), ratio of oil per fruit (OF), oil per bunch (OB), fruit per bunch (FB) and wet mesocarp per fruit (WMF) could be identified in the segregating population with estimated values for explained variance ranging from 12.4 % to 54.5 %. Markers designed from some candidate genes involved in lipid biosynthesis were found to be mapped near significant QTLs for various economic yield traits. Associations between QTLs and potential candidate genes are discussed.     

QTL mapping of yield and fiber traits based on a four-way cross population in <Emphasis Type="Italic">Gossypium hirsutum</Emphasis> L.

Four-way cross (4WC) involving four different inbred lines frequently appears in the cotton breeding programs. However, linkage analysis and quantitative trait loci (QTL) mapping with molecular markers in cotton has largely been applied to populations derived from a cross between two inbred lines, and few results of QTL dissection were conducted in a 4WC population. In this study, an attempt was made to construct a linkage map and identify QTL for yield and fiber quality traits in 4WC derived from four different inbred lines in Gossypium hirsutum L. A linkage map was constructed with 285 SSR loci and one morphological locus, covering 2113.3 cM, approximately 42% of the total recombination length of the cotton genome. A total of 31 QTL with 5.1–25.8% of the total phenotypic variance explained were detected. Twenty-four common QTL across environments showed high stability, and six QTL were environment-specific. Several genomic segments affecting multiple traits were identified. The advantage of QTL mapping using a 4WC were discussed. This study presents the first example of QTL mapping using a 4WC population in upland cotton. The results presented here will enhance the understanding of the genetic basis of yield and fiber quality traits and enable further marker-assisted selection in cultivar populations in upland cotton.     

Identification and stability of QTLs for fruit quality traits in apple

Breeding for fruit quality traits is complex due to the polygenic (quantitative) nature of the genetic control of these traits. Therefore, to improve the speed and efficiency of genotype selection, attention in recent years has focused on the identification of quantitative trait loci (QTLs) and molecular markers associated with these QTLs. However, despite the huge potential of molecular markers in breeding programmes, their implementation in practice has been limited by the lack of information on the stability of QTLs across different environments and within different genetic backgrounds. Here, we present the results from a comprehensive analysis of the inheritance of fruit quality traits within a population derived from a cross between the apple cultivars ‘Telamon’ and ‘Braeburn’ over two successive seasons. A total of 74 different QTLs were identified for all the major fruit physiological traits including fruit height, diameter, weight and stiffness, flesh firmness, rate of flesh browning, acidity, the oBrix content and harvest date. Seventeen of these QTLs were ‘major’ QTLs, accounting for over 20% of the observed population variance of the trait. However, only one third (26) of the identified QTLs were stable over both harvest years, and of these year-stable QTLs only one was a major QTL. A direct comparison with published QTL results obtained using other populations (King et al., Theor Appl Genet 102:1227–1235, 2001; Liebhard et al., Plant Mol Biol 52:511–526, 2003) is difficult because the linkage maps do not share a sufficient number of common markers and due to differences in the trait evaluation protocols. Nonetheless, our results suggest that for the six fruit quality traits which were measured in all populations, nine out of a total of 45 QTLs were common or stable across all population × environments combinations. These results are discussed in the framework of the development and application of molecular markers for fruit quality trait improvement.     

QTL mapping reveals the genetic architecture of loci affecting pre- and post-zygotic isolating barriers in Louisiana Iris

ABSTRACT: BACKGROUND: Hybridization among Louisiana Irises has been well established and the genetic architecture of reproductive isolation is known to affect the potential for and the directionality of introgression between taxa. Here we use co-dominant markers to identify regions where QTL are located both within and between backcross maps to compare the genetic architecture of reproductive isolation and fitness traits across treatments and years. RESULTS: QTL mapping was used to elucidate the genetic architecture of reproductive isolation between Iris fulva and Iris brevicaulis. Homologous co-dominant EST-SSR markers scored in two backcross populations between I. fulva and I. brevicaulis were used to generate genetic linkage maps. These were used as the framework for mapping QTL associated with variation in 11 phenotypic traits likely responsible for reproductive isolation and fitness. QTL were dispersed throughout the genome, with the exception of one region of a single linkage group (LG) where QTL for flowering time, sterility, and fruit production clustered. In most cases, homologous QTL were not identified in both backcross populations, however, homologous QTL for flowering time, number of growth points per rhizome, number of nodes per inflorescence, and number of flowers per node were identified on several linkage groups. CONCLUSION: Two different traits affecting reproductive isolation, flowering time and sterility, exhibit different genetic architectures, with numerous QTL across the Iris genome controlling flowering time and fewer, less distributed QTL affecting sterility. QTL for traits affecting fitness are largely distributed across the genome with occasional overlap, especially on LG 4, where several QTL increasing fitness and decreasing sterility cluster. Given the distribution and effect direction of QTL affecting reproductive isolation and fitness, we have predicted genomic regions where introgression may be more likely to occur (those regions associated with an increase in fitness and unlinked to loci controlling reproductive isolation) and those that are less likely to exhibit introgression (those regions linked to traits decreasing fitness and reproductive isolation).     

Association mapping for phenological, morphological, and quality traits in canola quality winter rapeseed (Brassica napus L.)

QTL mapping by association analysis has recently gained interest in plant breeding research as an alternative to QTL mapping in segregating populations from biparental crosses. In a first experiment on whole-genome association analysis in rapeseed, 684 mapped AFLP markers were tested for association with 14 traits in a set of 84 canola quality winter rapeseed cultivars. For association analysis a general linear model was used. By testing significance of marker-trait associations against a false discovery rate of 0.2, between 1 and 34 associated markers were found for 10 of the 14 traits. Taking into account linkage disequilibrium between the significant markers, these markers represent between 1 and 22 putative QTL for the respective traits. The minimum phenotypic variance explained by the QTL for the different traits ranged from 15% to 53%. A subset of 27 markers were significantly associated with two or more traits. These markers were predominantly shared between traits that were significantly correlated at the phenotypic level. The results show clearly that in rapeseed, QTL mapping by association analysis is a viable alternative to QTL mapping in segregating populations.     

The first genetic map of the American cranberry: exploration of synteny conservation and quantitative trait loci

The first genetic map of cranberry (Vaccinium macrocarpon) has been constructed, comprising 14 linkage groups totaling 879.9 cM with an estimated coverage of 82.2 %. This map, based on four mapping populations segregating for field fruit-rot resistance, contains 136 distinct loci. Mapped markers include blueberry-derived simple sequence repeat (SSR) and cranberry-derived sequence-characterized amplified region markers previously used for fingerprinting cranberry cultivars. In addition, SSR markers were developed near cranberry sequences resembling genes involved in flavonoid biosynthesis or defense against necrotrophic pathogens, or conserved orthologous set (COS) sequences. The cranberry SSRs were developed from next-generation cranberry genomic sequence assemblies; thus, the positions of these SSRs on the genomic map provide information about the genomic location of the sequence scaffold from which they were derived. The use of SSR markers near COS and other functional sequences, plus 33 SSR markers from blueberry, facilitates comparisons of this map with maps of other plant species. Regions of the cranberry map were identified that showed conservation of synteny with Vitis vinifera and Arabidopsis thaliana. Positioned on this map are quantitative trait loci (QTL) for field fruit-rot resistance (FFRR), fruit weight, titratable acidity, and sound fruit yield (SFY). The SFY QTL is adjacent to one of the fruit weight QTL and may reflect pleiotropy. Two of the FFRR QTL are in regions of conserved synteny with grape and span defense gene markers, and the third FFRR QTL spans a flavonoid biosynthetic gene.     

Genetic mapping of rust resistance loci in biomass willow

Rust diseases caused by Melampsora spp. represent a major threat to the productivity of short rotation coppice (SRC) willows grown for biomass, causing yield losses of up to 40%. The routine use of fungicide in SRC plantations is not a viable option because of economic and environmental considerations; thus, breeding for rust resistance is a major target for willow breeding programmes. To characterise the genetic basis of rust resistance in willow and provide targets for use in future marker-assisted selections, quantitative trait analyses were performed using a large full-sib mapping population (K8) which segregates for rust resistance and several other important agronomic traits. Rust resistance in field conditions was assessed in three consecutive years. For a more detailed genetic dissection, laboratory inoculation tests using isolates of two distinct and prevalent pathotypes (LET1 and LET5) were also performed. For field-based resistance, a major quantitative resistance locus, designated SRR1 (Salix Rust Resistance 1), was detected in addition to several quantitative trait loci (QTL) of more modest effect. Inoculation test data also supported an important role for SRR1. Specific interactions between particular rust isolates and different QTL were detected, and QTL that only influenced resistance in field conditions were identified. The QTL reported here represent an important basis for the future development of markers for use in willow breeding programmes. As the linkage map for the K8 population is anchored to the Populus trichocarpa genome sequence, a more efficient marker development for future fine-scale mapping and candidate gene identification is possible.     

Identification,characterisation and mapping of simple sequence repeat (SSR) markers from raspberry root and bud ESTs

Raspberry breeding is a long, slow process in this highly heterozygous out-breeder. Selections for complex traits like fruit quality are broad-based and few simple methodologies and resources are available for glasshouse and field screening for key pest and disease resistances. Additionally, the timescale for selection of favourable agronomic traits requires data from different seasons and environmental locations before any breeder selection can proceed to finished cultivar. Genetic linkage mapping offers the possibility of a more knowledge-based approach to breeding through linking favourable traits to markers and candidate genes on genetic linkage maps. To further increase the usefulness of existing maps, a set of 25 polymorphic SSRs derived from expressed sequences (EST-SSRs) have been developed in red raspberry (Rubus idaeus). Two different types of expressed sequences were targeted. One type was derived from a root cDNA library as a first step in assessing sequences which may be involved in root vigour and root rot disease resistance and the second type were ESTs from a gene discovery project examining bud dormancy release and seasonality. The SSRs detect between 2 and 4 alleles per locus and were assigned to linkage groups on the existing ‘Glen Moy’ × ‘Latham’ map following genotyping of 188 progeny and examined for association with previously mapped QTL. The loci were also tested on a diverse range of Rubus species to determine transferability and usefulness for germplasm diversity studies and the introgression of favourable alleles.