Parental Maps Research Articles

Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing.

Although numerous linkage maps have been constructed in the genus Populus, they are typically sparse and thus have limited applications due to low throughput of traditional molecular markers. Restriction-site associated DNA sequencing (RADSeq) technology allows us to identify a large number of single nucleotide polymorphisms (SNP) across genomes of many individuals in a fast and cost-effective way, and makes it possible to construct high-density genetic linkage maps. We performed RADSeq for 299 progeny and their two parents in an F1 hybrid population generated by crossing the female Populus deltoides ‘I-69’ and male Populus simonii ‘L3’. A total of 2,545 high quality SNP markers were obtained and two parent-specific linkage maps were constructed. The female genetic map contained 1601 SNPs and 20 linkage groups, spanning 4,249.12 cM of the genome with an average distance of 2.69 cM between adjacent markers, while the male map consisted of 940 SNPs and also 20 linkage groups with a total length of 3,816.24 cM and an average marker interval distance of 4.15 cM. Finally, our analysis revealed that synteny and collinearity are highly conserved between the parental linkage maps and the reference genome of P. trichocarpa. We demonstrated that RAD sequencing is a powerful technique capable of rapidly generating a large number of SNPs for constructing genetic maps in outbred forest trees. The high-quality linkage maps constructed here provided reliable genetic resources to facilitate locating quantitative trait loci (QTLs) that control growth and wood quality traits in the hybrid population.

A first generation microsatellite-based linkage map of the Chinese mitten crab Eriocheir sinensis and its application in quantitative trait loci (QTL) detection

Genetic linkage maps provide excellent tools for detecting quantitative trait loci (QTL) and understanding genome organization and evolution. By taking advantage of a large number of microsatellite markers isolated from the genome of the Chinese mitten crab Eriocheir sinensis in our previous study, here we constructed a first generation genetic linkage map for this species using 1300 microsatellite markers that genotyped a F1 full-sib family from an intercross between northern and southern populations in China. A total of 674 markers (52%) were informative and grouped on the two parental maps. The number of linkage groups is quite close to the actual number of the crab haploid chromosomes (n=73). The female linkage map contained 466 markers which mapped to 71 linkage groups, spanning a total genetic distance of 2430.9cM with an average marker space of 6.2cmd The male map contained 457 markers which mapped to 70 linkage groups, spanning 2658.4cM with an average marker space of 6.9cmd The crab genome length was estimated to be 3390.0cM, covering 71.7% of genome for the female map, and 3678.8cM covering 72.3% of genome for the male map. Furthermore, the linkage maps were used for preliminary detection of QTL. Nine growth-related QTL for body length, width and weight were mapped to seven linkage groups. Additionally, two QTL were identified to be associated with sexual precocity. The linkage maps and the identified QTL will be valuable for marker-assisted selection breeding programs of the mitten crab. Statement of relevanceA first generation genetic linkage map of the Chinese mitten crab was created using 1300 microsatellite markers. Nine growth-related QTL and two sexual precocity-related QTL were identified, which will be valuable for further studies of the genetic mechanisms of development and sexual precocity, and marker-assisted selection breeding programs for this species.

Identification of stable QTLs for vegetative and reproductive traits in the microvine (Vitis vinifera L.) using the 18 K Infinium chip

BackgroundThe increasing temperature associated with climate change impacts grapevine phenology and development with critical effects on grape yield and composition. Plant breeding has the potential to deliver new cultivars with stable yield and quality under warmer climate conditions, but this requires the identification of stable genetic determinants. This study tested the potentialities of the microvine to boost genetics in grapevine. A mapping population of 129 microvines derived from Picovine x Ugni Blanc flb, was genotyped with the Illumina® 18 K SNP (Single Nucleotide Polymorphism) chip. Forty-three vegetative and reproductive traits were phenotyped outdoors over four cropping cycles, and a subset of 22 traits over two cropping cycles in growth rooms with two contrasted temperatures, in order to map stable QTLs (Quantitative Trait Loci).ResultsTen stable QTLs for berry development and quality or leaf area were identified on the parental maps. A new major QTL explaining up to 44 % of total variance of berry weight was identified on chromosome 7 in Ugni Blanc flb, and co-localized with QTLs for seed number (up to 76 % total variance), major berry acids at green lag phase (up to 35 %), and other yield components (up to 25 %). In addition, a minor QTL for leaf area was found on chromosome 4 of the same parent. In contrast, only minor QTLs for berry acidity and leaf area could be found as moderately stable in Picovine. None of the transporters recently identified as mutated in low acidity apples or Cucurbits were included in the several hundreds of candidate genes underlying the above berry QTLs, which could be reduced to a few dozen candidate genes when a priori pertinent biological functions and organ specific expression were considered.ConclusionsThis study combining the use of microvine and a high throughput genotyping technology was innovative for grapevine genetics. It allowed the identification of 10 stable QTLs, including the first berry acidity QTLs reported so far in a Vitis vinifera intra-specific cross. Robustness of a set of QTLs was assessed with respect to temperature variation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0588-0) contains supplementary material, which is available to authorized users.

Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine.

Genotyping by sequencing (GBS) provides opportunities to generate high-resolution genetic maps at a low genotyping cost, but for highly heterozygous species, missing data and heterozygote undercalling complicate the creation of GBS genetic maps. To overcome these issues, we developed a publicly available, modular approach called HetMappS, which functions independently of parental genotypes and corrects for genotyping errors associated with heterozygosity. For linkage group formation, HetMappS includes both a reference-guided synteny pipeline and a reference-independent de novo pipeline. The de novo pipeline can be utilized for under-characterized or high diversity families that lack an appropriate reference. We applied both HetMappS pipelines in five half-sib F1 families involving genetically diverse Vitis spp. Starting with at least 116,466 putative SNPs per family, the HetMappS pipelines identified 10,440 to 17,267 phased pseudo-testcross (Pt) markers and generated high-confidence maps. Pt marker density exceeded crossover resolution in all cases; up to 5,560 non-redundant markers were used to generate parental maps ranging from 1,047 cM to 1,696 cM. The number of markers used was strongly correlated with family size in both de novo and synteny maps (r = 0.92 and 0.91, respectively). Comparisons between allele and tag frequencies suggested that many markers were in tandem repeats and mapped as single loci, while markers in regions of more than two repeats were removed during map curation. Both pipelines generated similar genetic maps, and genetic order was strongly correlated with the reference genome physical order in all cases. Independently created genetic maps from shared parents exhibited nearly identical results. Flower sex was mapped in three families and correctly localized to the known sex locus in all cases. The HetMappS pipeline could have wide application for genetic mapping in highly heterozygous species, and its modularity provides opportunities to adapt portions of the pipeline to other family types, genotyping technologies or applications.

High‐density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe

AbstractMiscanthus is a perennial C4 grass that has recently become an important bioenergy crop. The efficiency of breeding improved Miscanthus biomass cultivars could be greatly increased by marker‐assisted selection. Thus, a high‐density genetic map is critical to Miscanthus improvement. In this study, a mapping population of 261 F1 progeny was developed from a cross between two diploid M. sinensis cultivars, ‘Strictus’ and ‘Kaskade’. High‐density genetic maps for the two parents were produced with 3044 newly developed single nucleotide polymorphisms (SNPs) obtained from restriction site‐associated DNA sequencing, and 138 previously mapped GoldenGate SNPs. The female parent (‘Strictus’) map spanned 1599 cM, with 1989 SNPs on 19 linkage groups, and an average intermarker spacing of 0.8 cM. The length of the male parent (‘Kaskade’) map was 1612 cM, with 1821 SNPs, and an average intermarker spacing of 0.9 cM. The utility of the map was confirmed by locating quantitative trait loci (QTL) for the zebra‐striped trait, which was segregating in this population. Three QTL for zebra‐striped presence/absence (zb1, zb2 on LG 7, and zb3 on LG 10) and three for zebra‐striped intensity (zbi1, zbi2, zbi3 on LGs 7, 10, 3) were identified. Each allele that caused striping was recessive. Incomplete penetrance was observed for each zb QTL, but penetrance was greatest when two or more zb QTL were homozygous for the causative alleles. Similarly, the intensity of striping was greatest when two or more zbi QTL were homozygous for alleles that conferred the trait. Comparative mapping indicated putative correspondence between zb3 and/or zbi2 on LG 10 to previously sequenced genes conferring zebra stripe in maize and rice. These results demonstrate that the new map is useful for identifying marker–trait associations. The mapped markers will become a valuable community resource, facilitating comparisons among studies and the breeding of Miscanthus.

The inheritance of bract pigmentation and fleshy thorns on the globe artichoke capitulum

The bracts of the globe artichoke inflorescence vary in their pigmentation and the extent of fleshy thorn development. Here, a genetic analysis of these two traits is presented, based on a pre-existing and well-characterized mapping population derived from a cross between a globe artichoke variety and a cultivated cardoon. While both traits appeared to be simply inherited when the number of trait classes was limited to three (pigmentation) or two (thorniness), extending the classification to a larger number of states generated continuous distributions appropriate for a quantitative trait locus (QTL) analysis. The seven QTL identified by this means, mapping to five different linkage groups, were all expressed across two growing seasons. The largest effect QTL mapped onto homologues linkage group in each parental maps, and explained up to 69 and 73 % of the phenotypic variance respectively for bracts pigmentation and thorniness.

Generation of silver stained TE-AFLP markers in tea (Camellia sinensis) and their assessment in filling gaps with construction of a genetic linkage map

Silver stained TE-AFLP markers were generated in tea (Camellia sinensis). Thirty six primer combinations were screened leading to identification of five primer combinations which showed high polymorphism (average 43.75%) among 17 tea accessions studied. The efficacy of these five primer combinations was evaluated using four parameters, namely Polymorphic Information Content, Effective Multiplex Ratio, Marker Index and Resolving Power. The selected five primer combinations were employed for further study on construction of preliminary linkage maps based on a two-way pseudo-testcross strategy in a F1 population of bi-clonal seed stock TS463 (TV1 and TV19 clones) of tea. A total of 153 markers were detected of which 100 markers segregated in a 1:1 ratio. TV1 parent map consisted of 36 loci, spread over 10 linkage groups spanning a total length of 388.9cM while in TV19 map, 30 loci were distributed in 11 linkage groups spanning over 410.7cM. The observed genome coverage was determined, i.e., 50.76% and 45.91% for TV1 and TV19, respectively. Furthermore, sequences of the TE-AFLP fragments were subjected to BLAST analysis. Many of the sequences showed positive hit with the database of whole genome shot gun contigs of tea (Camellia sinensis var. sinensis). The identification of markers in these linkage maps may be an important resource for further research and would be helpful for marker-assisted selection breeding programmes in tea.

Construction of High Density Sweet Cherry (Prunus avium L.) Linkage Maps Using Microsatellite Markers and SNPs Detected by Genotyping-by-Sequencing (GBS).

Linkage maps are valuable tools in genetic and genomic studies. For sweet cherry, linkage maps have been constructed using mainly microsatellite markers (SSRs) and, recently, using single nucleotide polymorphism markers (SNPs) from a cherry 6K SNP array. Genotyping-by-sequencing (GBS), a new methodology based on high-throughput sequencing, holds great promise for identification of high number of SNPs and construction of high density linkage maps. In this study, GBS was used to identify SNPs from an intra-specific sweet cherry cross. A total of 8,476 high quality SNPs were selected for mapping. The physical position for each SNP was determined using the peach genome, Peach v1.0, as reference, and a homogeneous distribution of markers along the eight peach scaffolds was obtained. On average, 65.6% of the SNPs were present in genic regions and 49.8% were located in exonic regions. In addition to the SNPs, a group of SSRs was also used for construction of linkage maps. Parental and consensus high density maps were constructed by genotyping 166 siblings from a ‘Rainier’ x ‘Rivedel’ (Ra x Ri) cross. Using Ra x Ri population, 462, 489 and 985 markers were mapped into eight linkage groups in ‘Rainier’, ‘Rivedel’ and the Ra x Ri map, respectively, with 80% of mapped SNPs located in genic regions. Obtained maps spanned 549.5, 582.6 and 731.3 cM for ‘Rainier’, ‘Rivedel’ and consensus maps, respectively, with an average distance of 1.2 cM between adjacent markers for both ‘Rainier’ and ‘Rivedel’ maps and of 0.7 cM for Ra x Ri map. High synteny and co-linearity was observed between obtained maps and with Peach v1.0. These new high density linkage maps provide valuable information on the sweet cherry genome, and serve as the basis for identification of QTLs and genes relevant for the breeding of the species.

Exploring potential of pearl millet germplasm association panel for association mapping of drought tolerance traits.

A pearl millet inbred germplasm association panel (PMiGAP) comprising 250 inbred lines, representative of cultivated germplasm from Africa and Asia, elite improved open-pollinated cultivars, hybrid parental inbreds and inbred mapping population parents, was recently established. This study presents the first report of genetic diversity in PMiGAP and its exploitation for association mapping of drought tolerance traits. For diversity and genetic structure analysis, PMiGAP was genotyped with 37 SSR and CISP markers representing all seven linkage groups. For association analysis, it was phenotyped for yield and yield components and morpho-physiological traits under both well-watered and drought conditions, and genotyped with SNPs and InDels from seventeen genes underlying a major validated drought tolerance (DT) QTL. The average gene diversity in PMiGAP was 0.54. The STRUCTURE analysis revealed six subpopulations within PMiGAP. Significant associations were obtained for 22 SNPs and 3 InDels from 13 genes under different treatments. Seven SNPs associations from 5 genes were common under irrigated and one of the drought stress treatments. Most significantly, an important SNP in putative acetyl CoA carboxylase gene showed constitutive association with grain yield, grain harvest index and panicle yield under all treatments. An InDel in putative chlorophyll a/b binding protein gene was significantly associated with both stay-green and grain yield traits under drought stress. This can be used as a functional marker for selecting high yielding genotypes with ‘stay green’ phenotype under drought stress. The present study identified useful marker-trait associations of important agronomics traits under irrigated and drought stress conditions with genes underlying a major validated DT-QTL in pearl millet. Results suggest that PMiGAP is a useful panel for association mapping. Expression patterns of genes also shed light on some physiological mechanisms underlying pearl millet drought tolerance.

Filling gaps with construction of a genetic linkage map in tetraploid roses.

Rose (Rosa sp.) is one of the most economically important ornamental crops worldwide. The present work contains a genetic linkage map for tetraploid roses that was constructed from an F1 segregation population using AFLPs and SSRs on 189 individuals. The preliminary ‘Yunzheng Xiawei’ and ‘Sun City’ maps consisted of 298 and 255 markers arranged into 26 and 32 linkage groups, respectively. The recombined parental maps covered 737 and 752 cM of the genome, respectively. The integrated linkage map was composed of 295 polymorphic markers that spanned 874 cM, and it had a mean intermarker distance of 2.9 cM. In addition, a set of newly developed EST-SSRs that are distributed evenly throughout the mapping population were released. The work identified 67 anchoring points that came from 43 common SSRs. The results that were produced from a large number of individuals (189) and polymorphic SSRs (242) will enhance the ability to construct higher density consensus maps with the available diploid level rose maps, and they will definitely serve as a tool for accurate QTL detection and marker assisted selection.

COMPARATIVE GENETIC MAPPING BETWEEN CLEMENTINE, PUMMELO AND SWEET ORANGE AND THE INTERSPECICIC STRUCTURE OF THE CLEMENTINE GENOME

The availability of a saturated genetic map of Clementine was identified by the International Citrus Genome Consortium as an essential prerequisite to assist the assembly of the reference whole genome sequence based on a Clementine derived haploid. The primary goals of the present study were to establish a Clementine reference map, and to perform comparative mapping with pummelo and sweet orange. Five parental genetic maps were established with SNPs, SSRs and InDels. A medium density reference map (961 markers for 1084.1 cM) of Clementine was established and used by the ICGC to facilitate the chromosome assembly of the haploid genome sequence. Comparative mapping with pummelo and sweet orange revealed that the linear order of markers was highly conserved. Reasonable inferences of most citrus genomes should be obtained by mapping next-generation sequencing data against the haploid reference genome sequence. Skewed segregations were frequent and higher in the male than female Clementine potentially leading to false interpretation of the genetic determinism of phenotypic traits. The mapping data confirmed that Clementine arose from hybridization between 'Mediterranean' mandarin and sweet orange and identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome. Introgression of pummelo genome fragments were identified in heterozygosity in each chromosome. Moreover, it appeared that the genome of the haploid Clementine used to establish the citrus reference genome sequence was inherited primarily from the 'Mediterranean' mandarin. The usefulness of this genetic map, anchored in the reference whole genome sequence, is discussed. (Resume d'auteur)

Quantitative genetic analysis of berry firmness in table grape (Vitis vinifera L.)

Berry texture is a determinant quality trait in the breeding of new table grape varieties. We present the first mapping quantitative trait loci (QTL) results for berry firmness in table grape. Two segregating progenies, Muscat Hamburg × Sugraone (153 offspring) and Ruby Seedless × Moscatuel (78 offspring), were evaluated for this trait during two and four productive seasons, respectively. Firmness was scored at harvest as the force (newtons) required for a 20 % deformation of the berries. Parental and consensus genetic maps were built for each population. QTL analyses revealed a complex genetic control of firmness. Significant QTLs at genome-wide level were detected in seven genomic regions on linkage groups (LGs) 1, 4, 5, 9, 10, 13, and 18, individually explaining up to 19.8 % of the total phenotypic variance. The combined effect of all the QTLs detected in one season explained up to 44.5 % of the total phenotypic variance. Some annotated genes colocating with the LOD-1 support intervals of those QTLs are proposed as putative candidate genes that might be responsible for the QTLs that affect berry firmness.

Multiple QTLs Linked to Agro-Morphological and Physiological Traits Related to Drought Tolerance in Potato

Dissection of the genetic architecture of adaptation and abiotic stress-related traits is highly desirable for developing drought-tolerant potatoes and enhancing the resilience of existing cultivars, particularly as agricultural production in rain-fed areas may be reduced by up to 50 % by 2020. The “DMDD” potato progeny was developed at International Potato Center (CIP) by crossing the sequenced double monoploid line DM and a diploid cultivar of the Solanum tuberosum diploid Andigenum Goniocalyx group. Recently, a high-density integrated genetic map based on single nucleotide polymorphism (SNP), diversity array technology (DArT), simple sequence repeats (SSRs), and amplified fragment length polymorphism (AFLP) markers was also made available for this population. Two trials were conducted, in greenhouse and field, for drought tolerance with two treatments each, well-watered and terminal drought, in which watering was suspended 60 days after planting. The DMDD population was evaluated for agro-morphological and physiological traits before and after initiation of stress, at multiple time points. Two dense parental genetic maps were constructed using published genotypic data, and quantitative trait locus (QTL) analysis identified 45 genomic regions associated with nine traits in well-watered and terminal drought treatments and 26 potentially associated with drought stress. In this study, the strong influence of environmental factors besides water shortage on the expression of traits and QTLs reflects the multigenic control of traits related to drought tolerance. This is the first study to our knowledge in potato identifying QTLs for drought-related traits in field and greenhouse trials, giving new insights into genetic architecture of drought-related traits. Many of the QTLs identified have the potential to be used in potato breeding programs for enhanced drought tolerance.

A transactional model of spoken vocabulary variation in toddlers with intellectual disabilities.

The authors examined (a) whether dose frequency of milieu communication teaching (MCT) affects children's canonical syllabic communication and (b) whether the relation between early canonical syllabic communication and later spoken vocabulary is mediated by parental linguistic mapping in children with intellectual disabilities (ID). The authors drew on extant data from a recent differential treatment intensity study in which 63 toddlers with ID were randomly assigned to receive either five 1-hr MCT sessions per week (i.e., daily treatment) or one 1-hr MCT session per week (i.e., weekly treatment) for 9 months. Children's early canonical syllabic communication was measured after 3 months of treatment, and later spoken vocabulary was measured at posttreatment. Midpoint parental linguistic mapping was measured after 6 months of treatment. A moderate-sized effect in favor of daily treatment was observed on canonical syllabic communication. The significant relation between canonical syllabic communication and spoken vocabulary was partially mediated by linguistic mapping. These results suggest that canonical syllabic communication may elicit parental linguistic mapping, which may in turn support spoken vocabulary development in children with ID. More frequent early intervention boosted canonical syllabic communication, which may jump-start this transactional language-learning mechanism. Implications for theory, research, and practice are discussed.

QTL analysis and candidate gene mapping for the polyphenol content in cider apple.

Polyphenols have favorable antioxidant potential on human health suggesting that their high content is responsible for the beneficial effects of apple consumption. They control the quality of ciders as they predominantly account for astringency, bitterness, color and aroma. In this study, we identified QTLs controlling phenolic compound concentrations and the average polymerization degree of flavanols in a cider apple progeny. Thirty-two compounds belonging to five groups of phenolic compounds were identified and quantified by reversed phase liquid chromatography on both fruit extract and juice, over three years. The average polymerization degree of flavanols was estimated in fruit by phloroglucinolysis coupled to HPLC. Parental maps were built using SSR and SNP markers and used for the QTL analysis. Sixty-nine and 72 QTLs were detected on 14 and 11 linkage groups of the female and male maps, respectively. A majority of the QTLs identified in this study are specific to this population, while others are consistent with previous studies. This study presents for the first time in apple, QTLs for the mean polymerization degree of procyanidins, for which the mechanisms involved remains unknown to this day. Identification of candidate genes underlying major QTLs was then performed in silico and permitted the identification of 18 enzymes of the polyphenol pathway and six transcription factors involved in the apple anthocyanin regulation. New markers were designed from sequences of the most interesting candidate genes in order to confirm their co-localization with underlying QTLs by genetic mapping. Finally, the potential use of these QTLs in breeding programs is discussed.

Quantitative Trait Loci Associated with Drought Tolerance in Creeping Bentgrass

ABSTRACTImprovement in the drought tolerance of the cool‐season perennial grass species creeping bentgrass (Agrostis stolonifera L.) has significant value within the turfgrass industry. Understanding genomic regions associated with quantitative trait loci (QTL) such as drought tolerance will allow for advancement of breeding strategies to identify creeping bentgrass germplasm with improved abiotic stress tolerance. A multiyear and multienvironment study was performed to identify QTL in a mapping population of creeping bentgrass segregating for phenotypic traits associated with drought tolerance. Phenotypic data was collected during two growth chamber studies and 2 yr of a field trial. The phenotypic traits that were measured included turf quality (TQ), relative water content (RWC), canopy temperature depression (CTD), osmotic adjustment (OA), electrolyte leakage (EL), chlorophyll content (CHL), water use efficiency (WUE), and the normalized difference vegetative index (NDVI). Quantitative trait loci were identified for all traits on both parental maps except for OA and EL. Quantitative trait loci were found within all linkage groups except for group 2 in both parents. The linkage group areas that had QTL with a significant amount of overlapping for multiple traits and trials included linkage group 5.2, 7.1, and 7.2 on the drought tolerant parent ‘L‐93’ and groups 4.2 and 7.2 on the drought sensitive parent 7418–3. These and other QTL identified in this study have potential to be used in future studies that aim to more closely identify the genes associated with these QTL areas and for further investigation of their potential for use in marker‐assisted selection practices.

Genetic mapping of polygenic scab (Venturia pirina) resistance in an interspecific pear family

The need for chemical control of scab (Venturia pirina, V. nashicola) is the main barrier preventing sustainable pear production. As cultivars with durable resistance are not available yet commercially, the development of molecular markers for early selection is desirable to enhance the efficiency of breeding such cultivars. Interspecific pear progeny PEAR1 × PEAR2 derived from European (Pyrus communis) and Asian (P. pyrifolia and P. ussuriensis) pears was infected with three single-spore isolates of V. pirina using the droplet inoculation technique. Illumina Infinium® HD Assay technology was employed to genotype the progeny with single nucleotide polymorphism markers for map construction. With one linkage group missing in each parent, the parental maps covered 17 linkage groups in total, 1,132.3 and 1,136.8 centimorgan for the female and male parents, respectively. Resistance mapping resulted in the identification of seven quantitative trait loci (QTLs) by Kruskal–Wallis analysis. Parent PEAR1 contributed a QTL on linkage group (LG) 17 that was effective against all three scab isolates, while PEAR2 contributed one on LG7 that was effective against two isolates. The other five QTLs, on LG2 and LG5 of PEAR2, and LG7 and LG10 of PEAR1, displayed differential interactions, with each QTL being paired with a single incompatible isolate. Additive effects of combined resistance loci displayed a higher level of resistance than single loci, and the role of nonhost resistance is discussed.

Multi-Dimensional Scaling and MODELLER-Based Evolutionary Algorithms for Protein Model Refinement.

Protein structure prediction, i.e., computationally predicting the three-dimensional structure of a protein from its primary sequence, is one of the most important and challenging problems in bioinformatics. Model refinement is a key step in the prediction process, where improved structures are constructed based on a pool of initially generated models. Since the refinement category was added to the biennial Critical Assessment of Structure Prediction (CASP) in 2008, CASP results show that it is a challenge for existing model refinement methods to improve model quality consistently. This paper presents three evolutionary algorithms for protein model refinement, in which multidimensional scaling(MDS), the MODELLER software, and a hybrid of both are used as crossover operators, respectively. The MDS-based method takes a purely geometrical approach and generates a child model by combining the contact maps of multiple parents. The MODELLER-based method takes a statistical and energy minimization approach, and uses the remodeling module in MODELLER program to generate new models from multiple parents. The hybrid method first generates models using the MDS-based method and then run them through the MODELLER-based method, aiming at combining the strength of both. Promising results have been obtained in experiments using CASP datasets. The MDS-based method improved the best of a pool of predicted models in terms of the global distance test score (GDT-TS) in 9 out of 16test targets.

QTL Analysis Coupled with PTR-ToF-MS and Candidate Gene-Based Association Mapping Validate the Role of Md-AAT1 as a Major Gene in the Control of Flavor in Apple Fruit

Volatile organic compounds (VOCs) are fundamental elements of flavor, one of the most important fruit-quality traits. Despite its importance, this aspect is still poorly considered in assisted breeding programs, due to the lack of suitable and fast detection systems as well as validated functional markers. In this work, a full-sib parental mapping population (‘Fuji × Delearly’) was initially employed to perform a comprehensive quantitative trait locus (QTL) survey, to assess the VOC segregation detected by a novel proton-transfer-reaction time-of-flight mass spectrometry (PTR-ToF-MS) on fruit collected after a 2-month period of postharvest storage. Among this set of genomic regions, on chromosome 2 was also verified the coincident location between a group of QTLs, mainly associated to esters and alcohols, with a functional marker designed for Md-AAT1, a gene involved in the last step of the ester biosynthetic pathway. The allelic effect of this marker (here named Md-AAT1SSR) was further validated by candidate gene association mapping approach in a collection of 124 apple accessions. In this case, the volatile profiling was performed on peeled fruit flesh, as an important fraction of the aromatic blend of apple is released only after cutting. This work proposed a new and fast method for aroma phenotyping as well as a novel marker for an easy and widely applicable apple fruit quality advanced selection.

Genetic Linkage Mapping and Transmission Ratio Distortion in a Three-Generation Four-Founder Population ofPanicum virgatum(L.)

Switchgrass (Panicum virgatum L.), a warm season, C4, perennial grass, is one of the predominant grass species of the North American tall grass prairies. It is viewed as a high-potential bioenergy feedstock species because it can produce large amounts of lignocellulosic material with relatively few inputs. The objectives of this project were to develop an advanced switchgrass population and use it for the construction of genetic linkage maps and trait characterization. A three-generation, four-founder population was created and a total of 182 progeny of this advanced population were genotyped, including a mixture of self-pollinated and hybrid individuals. The female map integrated both subpopulations and covered 1629 cM of the switchgrass genome, with an average map length of 91 cM per linkage group. The male map of the hybrid progeny covered 1462 cM, with an average map length of 81 cM per linkage group. Average marker density of the female and male maps was 3.9 and 3.5 cM per marker interval, respectively. Based on the parental maps, the genome length of switchgrass was estimated to be 1776 cM and 1596 cM for the female map and male map, respectively. The proportion of the genome within 5 cM of a mapped locus was estimated to be 92% and 93% for the female map and male map, respectively. Thus, the linkage maps have covered most of the switchgrass genome. The assessment of marker transmission ratio distortion found that 26% of the genotyped markers were distorted from either 1:1 or 3:1 ratios expected for segregation of single dose markers in one or both parents, respectively. Several regions affected by transmission ratio distortion were found, with linkage groups Ib-m and VIIIa-f most affected.