Awais Khan

Background

Tuber appearance is highly variable in the Andean cultivated potato germplasm. The diploid backcross mapping population ‘DMDD’ derived from the recently sequenced genome ‘DM’ represents a sample of the allelic variation for tuber shape and eye depth present in the Andean landraces. Here we evaluate the utility of morphological descriptors for tuber shape for identification of genetic loci responsible for the shape and eye depth variation.
Results

Subjective morphological descriptors and objective tuber length and width measurements were used for assessment of variation in tuber shape and eye depth. Phenotypic data obtained from three trials and male–female based genetic maps were used for quantitative trait locus (QTL) identification. Seven morphological tuber shapes were identified within the population. A continuous distribution of phenotypes was found using the ratio of tuber length to tuber width and a QTL was identified in the paternal map on chromosome 10. Using toPt-437059, the marker at the peak of this QTL, the seven tuber shapes were classified into two groups: cylindrical and non-cylindrical. In the first group, shapes classified as ‘compressed’, ‘round’, ‘oblong’, and ‘long-oblong’ mainly carried a marker allele originating from the male parent. The tubers in this group had deeper eyes, for which a strong QTL was found at the same location on chromosome 10 of the paternal map. The non-cylindrical tubers classified as ‘obovoid’, ‘elliptic’, and ‘elongated’ were in the second group, mostly lacking the marker allele originating from the male parent. The main QTL for shape and eye depth were located in the same genomic region as the previously mapped dominant genes for round tuber shape and eye depth. A number of candidate genes underlying the significant QTL markers for tuber shape and eye depth were identified.
Conclusions

Utilization of a molecular marker at the shape and eye depth QTL enabled the reclassification of the variation in general tuber shape to two main groups. Quantitative measurement of the length and width at different parts of the tuber is recommended to accompany the morphological descriptor classification to correctly capture the shape variation.

Drought is one of the major abiotic factors that affect potato production in the tropics and sub-tropics. Molecular plant breeding offers promising opportunities for developing drought tolerant cultivars, but genetic gains to be achieved through breeding depends strongly on the genetic variance and heritability of traits used in the selection process. In the present study, genetic variance and heritability of tuber yield and its components were estimated in the native potato cultivar group Andigenum, expected to include promising drought tolerant progenitors. Twenty-seven full sib families obtained from crossing 18 parents arranged in 3 mating sets were grown under irrigated and terminal drought conditions. Heritability for tuber yield, estimated from female to male variance components was 0.68 and 0.41, respectively, in the irrigated treatment, and only 0.18 and 0.06 under drought conditions. Tuber number was highly significantly correlated to tuber yield but the heritability of this trait (estimated both from female to male variance) was lower than yield heritability and its non-additive genetic variance was higher than its additive genetic variance, particularly when estimated from the female variance component. Heritability of average weight per tuber estimated for male variance component was very high under both irrigated and drought conditions. Its additive genetic variance was much higher than its non-additive genetic variance. However, average weight per tuber correlated to tuber yield within parents but not within families. These results indicate that selection for increased tuber yield under drought conditions in the Andigenum cultivar group may be slow due to its low heritability and high value of non-additive genetic variance. They also suggest that yield components may not be useful as indirect selection criterion for yield, because of their low heritability and/or poor association with yield. The identification of drought tolerance related traits with high heritability and closely associated to tuber yield under drought is consequently required to improve adaptation of potato to drought-prone conditions and efficient utilization of Andigenum potatoes for this purpose.

The impacts of water restriction and high temperatures on potato production will increase over the next decades, due to climate change and the extension of cultivation in drought and heat prone areas. We review recent achievements and describe new avenues in the evaluation of tolerance to these abiotic stresses in potato, focusing on the definition of target populations of environments, choice and characterization of the managed stress environment, stress monitoring, and secondary traits measurement.

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.

An efficient in vitro system for early generation selection of heat-tolerant potato breeding materials was tested and validated in field conditions. At the family level, family groups expected to be heat tolerant due to their genetic background were identified as heat tolerant. In the in vitro assay, LTVR × LTVR, an advanced heat-tolerant breeding population developed at CIP, had 100 % of plants with tubers at 18 °C, 73 % at 25 °C and 2 % at 32 °C in the dark. The results from true seed family level in vitro screening at 25 °C and tuber family evaluation under field conditions in Tacna, an arid sub-tropical environment in Southern Peru, were positively correlated (r = 0.57). There was low to moderate correlation between percentage of plants with tubers under 27 °C in vitro temperature treatment and harvest index in the in vivo conditions in Majes–Arequipa, San Ramon, and La Molina that followed increasing temperature ranges between the sites. This indicates that the methodology can predict putative heat tolerant clones with a low level of confidence. Low correlation is possibly due to differential responses of the clones to characteristics of the growing environment, such as soil versus media, which were not represented in the in vitro assay, as well as the fact that in the field, day–night temperatures vary during tuberization and tuber filling, and throughout the season, while in vitro temperature and the dark period were kept constant, and conditions were controlled specifically to assess tuberization (tuber induction) at high night temperatures. The ability of the in vitro seedling screening assay to identify families tolerant to high temperatures in an inexpensive and less time consuming way without need of transplanting experimental material to the field will facilitate evaluation of significant samples of genetic resources and improved populations in breeding programs attempting to improve potato for adaptation to new environments and climate change.

Fire blight, incited by the enterobacterium Erwinia amylovora, is a destructive disease of Rosaceae, particularly of apples and pears. There are reports on the molecular mechanisms underlying E. amylovora pathogenesis and how the host activates its resistance mechanism. The host's resistance mechanism is quantitatively controlled, although some major genes might also be involved. Thus far, quantitative trait loci (QTL) mapping and differential expression studies have been used to elucidate those genes and/or genomic regions underlying quantitative resistance present in the apple genome. In this study, an effort is undertaken to dissect the genetic basis of fire blight resistance in apple using both QTL and genome-wide association mapping. Based on an F1 pedigree of ‘Coop 16’ × ‘Coop 17’ and a genome wide association study (GWAS) mapping population of Malus accessions (species, old and new cultivars and selections), new QTLs and associations have been identified. A total of three QTLs for resistance to fire blight, with above 95% significant LOD threshold value of 2.5, have been identified on linkage groups (LGs) 02, 06, and 15 of the apple genome with phenotypic variation explained (PVE) values of 14.7, 20.1, and 17.4, respectively. Although elevated p-values with signals for marker-trait associations are observed for some linkage groups, these are not found to be significant. However, a total of 34 significant associations, with p-values ≥0.02, have been detected including eight for lesion length at 7 days following inoculation (PL1), 14 for lesion length at 14 days following inoculation (PL2), and 12 for shoot length.

Genetic maps serve as frameworks for determining the genetic architecture of quantitative traits, assessing structure of a genome, as well as aid in pursuing association mapping and comparative genetic studies. In this study, a dense genetic map was constructed using a high-throughput 1,536 EST-derived SNP GoldenGate genotyping platform and a global consensus map established by combining the new genetic map with four existing reliable genetic maps of apple. The consensus map identified markers with both major and minor conflicts in positioning across all five maps. These major inconsistencies among marker positions were attributed either to structural variations within the apple genome, or among mapping populations, or genotyping technical errors. These also highlighted problems in assembly and anchorage of the reference draft apple genome sequence in regions with known segmental duplications. Markers common across all five apple genetic maps resulted in successful positioning of 2875 markers, consisting of 2033 SNPs and 843 SSRs as well as other specific markers, on the global consensus map. These markers were distributed across all 17 linkage groups, with an average of 169±33 marker per linkage group and with an average distance of 0.70±0.14 cM between markers. The total length of the consensus map was 1991.38 cM with an average length of 117.14±24.43 cM per linkage group. A total of 569 SNPs were mapped onto the genetic map, consisting of 140 recombinant individuals, from our recently developed apple Oligonucleotide pool assays (OPA). The new functional SNPs, along with the dense consensus genetic map, will be useful for high resolution QTL mapping of important traits in apple and for pursuing comparative genetic studies in Rosaceae.

The draft genome of the pear (Pyrus bretschneideri) using a combination of BAC-by-BAC and next-generation sequencing is reported. A 512.0-Mb sequence corresponding to 97.1% of the estimated genome size of this highly heterozygous species is assembled with 194× coverage. High-density genetic maps comprising 2005 SNP markers anchored 75.5% of the sequence to all 17 chromosomes. The pear genome encodes 42,812 protein-coding genes, and of these, ∼28.5% encode multiple isoforms. Repetitive sequences of 271.9 Mb in length, accounting for 53.1% of the pear genome, are identified. Simulation of eudicots to the ancestor of Rosaceae has reconstructed nine ancestral chromosomes. Pear and apple diverged from each other ∼5.4–21.5 million years ago, and a recent whole-genome duplication (WGD) event must have occurred 30–45 MYA prior to their divergence, but following divergence from strawberry. When compared with the apple genome sequence, size differences between the apple and pear genomes are confirmed mainly due to the presence of repetitive sequences predominantly contributed by transposable elements (TEs), while genic regions are similar in both species. Genes critical for self-incompatibility, lignified stone cells (a unique feature of pear fruit), sorbitol metabolism, and volatile compounds of fruit have also been identified. Multiple candidate SFB genes appear as tandem repeats in the S-locus region of pear; while lignin synthesis-related gene family expansion and highly expressed gene families of HCT, C3′H, and CCOMT contribute to high accumulation of both G-lignin and S-lignin. Moreover, alpha-linolenic acid metabolism is a key pathway for aroma in pear fruit.

The breakdown of self-incompatibility, which could result from the accumulation of non-functional S-haplotypes or competitive interaction between two different functional S-haplotypes, has been studied extensively at the molecular level in tetraploid Rosaceae species. In this study, two tetraploid Chinese cherry (Prunus pseudocerasus) cultivars and one diploid sweet cherry (Prunus avium) cultivar were used to investigate the ploidy of pollen grains and inheritance of pollen-S alleles. Genetic analysis of the S-genotypes of two intercross-pollinated progenies showed that the pollen grains derived from Chinese cherry cultivars were hetero-diploid, and that the two S-haplotypes were made up of every combination of two of the four possible S-haplotypes. Moreover, the distributions of single S-haplotypes expressed in self- and intercross-pollinated progenies were in disequilibrium. The number of individuals of the two different S-haplotypes was unequal in two self-pollinated and two intercross-pollinated progenies. Notably, the number of individuals containing two different S-haplotypes (S1- and S5-, S5- and S8-, S1- and S4-haplotype) was larger than that of other individuals in the two self-pollinated progenies, indicating that some of these hetero-diploid pollen grains may have the capability to inactivate stylar S-RNase inside the pollen tube and grow better into the ovaries.

Fruit skin color is an important parameter of outer quality and plays an important role in attracting customers. In many plants, it is the result of coordinative regulation of anthocyanin pathway genes. In our study, the differential expression of cDNA library in a pair of pear mutant with red and green color was investigated to find candidate genes which might regulate the anthocyanin biosynthesis and control the coloration of pear. We constructed a cDNA library using the cDNA-amplified fragment length polymorphism approach to analyze the transcriptional differences between the original cultivar “Early red Doyenne du Comice” with high anthocyanin content in the peel and its green color mutant with comparatively low anthocyanin content. Altogether, 47 transcript-derived fragments, putatively involved in anthocyanin biosynthesis, primary metabolism, stress, and defense responses, were identified. The relationships of differentially expressed genes and coloration were investigated by quantitative real-time PCR with fruit skin samples at different developmental stages. A gene putatively involved in anthocyanin biosynthesis was found and named as PyMADS18. Its sequence is similar to genes reported in the literature as regulators of anthocyanin biosynthesis. The expression results indicate that PyMADS18 is likely to be involved in anthocyanin accumulation and regulation of anthocyanin synthesis in early fruit development of pear.

Association mapping (AM), also known as linkage disequilibrium (LD) mapping, is a viable approach to overcome limitations of pedigree-based quantitative trait loci (QTL) mapping. In AM, genotypic and phenotypic correlations are investigated in unrelated individuals. Unlike QTL mapping, AM takes advantage of both LD and historical recombination present within the gene pool of an organism, thus utilizing a broader reference population. In plants, AM has been used in model species with available genomic resources. Pursuing AM in tree species requires both genotyping and phenotyping of large populations with unique architectures. Recently, genome sequences and genomic resources for forest and fruit crops have become available. Due to abundance of single nucleotide polymorphisms (SNPs) within a genome, along with availability of high-throughput resequencing methods, SNPs can be effectively used for genotyping trees. In addition to DNA polymorphisms, copy number variations (CNVs) in the form of deletions, duplications, and insertions also play major roles in control of expression of phenotypic traits. Thus, CNVs could provide yet another valuable resource, beyond those of microsatellite and SNP variations, for pursuing genomic studies. As genome-wide SNP data are generated from high-throughput sequencing efforts, these could be readily reanalysed to identify CNVs, and subsequently used for AM studies. However, forest and fruit crops possess unique architectural and biological features that ought to be taken into consideration when collecting genotyping and phenotyping data, as these will also dictate which AM strategies should be pursued. These unique features as well as their impact on undertaking AM studies are outlined and discussed.

EST data generated from 14 apple genotypes were downloaded from NCBI and mapped against a reference EST assembly to identify Single Nucleotide Polymorphisms (SNPs). Mapping of these SNPs was undertaken using 90% of sequence similarity and minimum coverage of four reads at each SNP position. In total, 37,807 SNPs were identified with an average of one SNP every 187 bp from a total of 6888 unique EST contigs. Identified SNPs were checked for flanking sequences of ≥ 60 bp along both sides of SNP alleles for reliable design of a custom high-throughput genotyping assay. A total of 12,299 SNPs, representing 6525 contigs, fit the selected criterion of ≥ 60 bp sequences flanking a SNP position. Of these, 1411 SNPs were validated using four apple genotypes. Based on genotyping assays, it was estimated that 60% of SNPs were valid SNPs, while 26% of SNPs might be derived from paralogous regions.

Starch is one of the major components of cereals, tubers, and fruits. Genes encoding granule-bound starch synthase (GBSS), which is responsible for amylose synthesis, have
been extensively studied in cereals but little is known about them in fruits. Due to their low copy gene number, GBSS genes have been used to study plant phylogenetic and evolutionary relationships. In this study, GBSS genes have been isolated and characterized in three fruit trees, including apple, peach, and orange. Moreover, a comprehensive

Artemisinin is a plant natural product produced by Artemisia annua and the active ingredient in the most effective treatment for malaria. Efforts to eradicate malaria are increasing demand for an affordable, high-quality, robust supply of artemisinin. We performed deep sequencing on the transcriptome of A. annua to identify genes and markers for fast-track breeding. Extensive genetic variation enabled us to build a detailed genetic map with nine linkage groups. Replicated field trials resulted in a quantitative trait loci (QTL) map that accounts for a significant amount of the variation in key traits controlling artemisinin yield. Enrichment for positive QTLs in parents of new high-yielding hybrids confirms that the knowledge and tools to convert A. annua into a robust crop are now available.

Fire blight, caused by the necrogenic Gram-negative bacterium Erwinia amylovora, is one of the most destructive bacterial diseases of apple (Malus × domestica) and pear (Pyrus communis), among other members of the Rosaceae family. This disease poses a major economic threat to pome production as there are no available effective control measures. Genetic enhancement of fire blight resistance in apples is the best alternative for averting disease damage, loss of crop, and loss of whole trees. In this review, current knowledge of the molecular mechanisms of E. amylovora pathogenesis will be presented, especially those of effector proteins during bacterial–host interactions, as well as assessment of current understanding of the molecular controls of plant host resistance. Recent studies are elucidating how type III effectors modulate plant susceptibility and promote growth and dissemination of the pathogen. The large multidomain protein DspE is essential for E. amylovora pathogenesis and plays an additional role(s) in inhibiting salicylic acid-mediated innate immunity. On the other hand, the apple host defends itself against E. amylovora invasion by relying on quantitative resistance genes that likely respond to and/or complex with E. amylovora effectors. Thus far, a total of 27 quantitative trait loci (QTL) linked to fire blight resistance have been identified in different apple genetic backgrounds and in response to different E. amylovora strains. In addition to quantitative genetic approaches, microarray analysis of E. amylovora-challenged apple genotypes identified differential transcriptional expression in susceptible and resistant apples. Mechanisms of bacterial pathogenicity and plant host resistance offer intriguing scenarios as to how effector proteins in E. amylovora interact with groups of genes for resistance in the apple host, particularly when considering that these quantitative genes have small effects in plant defense against the invading bacterial pathogen. This collective knowledge will provide insights into bacterial pathogenesis and plant host resistance, as well as highlight implications and opportunities for developing fire blight-resistant apple cultivars.

A total of 355 simple sequence repeat (SSR) markers were developed, based on expressed sequence tag (EST) and bacterial artificial chromosome (BAC)-end sequence databases, and successfully used to construct an SSR-based genetic linkage map of the apple. The consensus linkage map spanned 1143 cM, with an average density of 2.5 cM per marker. Newly developed SSR markers along with 279 SSR markers previously published by the HiDRAS project were further used to integrate physical and genetic maps of the apple using a PCR-based BAC library screening approach. A total of 470 contigs were unambiguously anchored onto all 17 linkage groups of the apple genome, and 158 contigs contained two or more molecular markers. The genetically mapped contigs spanned ∼421 Mb in cumulative physical length, representing 60.0% of the genome. The sizes of anchored contigs ranged from 97 kb to 4.0 Mb, with an average of 995 kb. The average physical length of anchored contigs on each linkage group was ∼24.8 Mb, ranging from 17.0 Mb to 37.73 Mb. Using BAC DNA as templates, PCR screening of the BAC library amplified fragments of highly homologous sequences from homoeologous chromosomes. Upon integrating physical and genetic maps of the apple, the presence of not only homoeologous chromosome pairs, but also of multiple locus markers mapped to adjacent sites on the same chromosome was detected. These findings demonstrated the presence of both genome-wide and segmental duplications in the apple genome and provided further insights into the complex polyploid ancestral origin of the apple.

This study identified eight S-haplotype-specific F-box genes (SFB alleles) and one S-haplotype-specific F-box-like gene (SFB-like gene) from genomic DNA by PCR combined with cleaved amplified polymorphic sequence markers in Prunus pseudocerasus and Prunus speciosa. The unknown sequences of C-termini were obtained by thermal asymmetric interlaced PCR. The whole nucleotide sequences of these genes were submitted to the EMBL/GenBank database. The SFBs shared typical structural features with SFBs from other Prunus species exhibiting gametophytic self-incompatibility. The deduced amino acid identity ranged from 77.1% to 82.4% among the four PpsSFBs and from 70.4% to 80.2% among the four PspeSFBs. The typical structural features were also detected in the PpsFB, but the sequence polymorphism was lower. The nucleotide identities ranged from 71.3% to 90.3% among the eight introns of the SFBs, the length of these introns varied from 95 to 121 bp and showed few polymorphisms. The distance between these SFBs and the corresponding S-RNases (S-ribonucleases) varied from 33 to 956 bp. Moreover, sequence analysis showed that interspecific amino acid identities in comparison with some other Prunus species were often higher than intraspecific identities, similar to S-RNase alleles. In addition, a similarity comparison found that the deduced amino acid identities among SFB alleles were higher than among S-RNase alleles, and the similarity data showed that the relationships among SFB alleles differed among S-RNase alleles, suggesting that the S-RNase and SFB alleles were separated but correlated during the coevolutionary process.

Jatropha curcas L. has been promoted as an oilseed crop for use to meet the increased world demand for vegetable oil production, and in particular, as a feedstock for biodiesel production. Seed meal is a protein-rich by-product of vegetable oil extraction, which can either be used as an organic fertilizer, or converted to animal feed. However, conversion of J. curcas seed meal into animal feed is complicated by the presence of toxins, though plants producing “edible” or “non-toxic” seeds occur in Mexico. Toxins present in the seeds of J. curcas include phorbol esters and a type-I ribosome inactivating protein (curcin). Although the edible seeds of J. curcas are known to lack phorbol esters, the curcin content of these seeds has not previously been studied. We analyzed the phorbol ester and curcin content of J. curcas seeds obtained from Mexico and Madagascar, and conclude that while phorbol esters are lacking in edible seeds, both types contain curcin. We also analyzed spatial distribution of these toxins in seeds. Phorbol-esters were most concentrated in the tegmen. Curcin was found in both the endosperm and tegmen. We conclude that seed toxicity in J. curcas is likely to be due to a monogenic trait, which may be under maternal control. We also conducted AFLP analysis and conclude that genetic diversity is very limited in the Madagascan collection compared to the Mexican collection.

Simple sequence repeats (SSRs) were used to assess genetic diversity and study genetic relatedness in a large collection of Malus germplasm. A total of 164 accessions from the Malus core collection, maintained at the University of Illinois, were genotyped using apple SSR markers. Each of the accessions was genotyped using a single robust SSR marker from each of the 17 different linkage groups in Malus. Data were subjected to principal component analysis, and a dendrogram was constructed to establish genetic relatedness. As expected, this diverse core collection showed high allelic diversity; moreover, this allelic diversity was higher than that previously reported. Cluster analysis revealed the presence of four distinct clusters of accessions in this collection.

Fire blight, a devastating disease of apple, pear, and many Rosaceae species worldwide is caused by enterobacterium Erwinia amylovora. At present, disease control mainly relies on antibiotics, prevention, and eradication-based strategies. Prevention and eradication is expensive, while resistance development for antibiotics can reduce their efficacy over time. Apple varieties do, however, exhibit a wide range of relative tolerance to fire blight. As part of our long-term strategy to design sustainable fire blight controls, we have initiated a breeding project to identify quantitative trait loci (QTLs) and markers linked to them. F1 segregating progeny plants of ‘Fiesta’ × ‘Discovery’ were inoculated with a strain of Erwinia amylovora and studied under quarantine conditions to identify QTLs (Quantitative Trait Loci) for fire blight resistance. Progress of disease was measured at different time intervals as percent shoot lesion length (PLL) and used for QTL analysis. One significant QTL (P < 0.05) was identified on the linkage group 7 of ‘Fiesta’ (F7), which explained about 37.5 to 38.6% of the phenotypic variation. Two RAPD markers bracketing the QTL have been transformed into SCAR markers and a SSR marker specific for the region was developed. Stability of the effect of this QTL allele in different backgrounds and different cultivars was tested. Plants that amplified both flanking markers were significantly more resistant than those that did not amplify both markers, indicating high stability of the F7 QTL allele in different backgrounds, which makes it promising for use in marker-assisted selection (MAS). Work is currently ongoing to identify additional QTLs linked to fire blight in apple using a different cross ‘Florina’ × ‘Novaeasygro’.

Fire blight is a devastating bacterial disease of rosaceous plants. Its damage to apple production is a major concern, since no existing control option has proven to be completely effective. Some commercial apple varieties, such as `Florina' and `Nova Easygro', exhibit a consistent level of resistance to fire blight. In this study, we used an F1 progeny of `Florina' × `Nova Easygro' to build parental genetic maps and identify quantitative trait loci (QTLs) related to fire blight resistance. Linkage maps were constructed using a set of microsatellites and enriched with amplified fragment length polymorphism (AFLP) markers. In parallel, progeny plants were artificially inoculated with Erwinia amylovora strain CFBP 1430 in a quarantine glasshouse. Shoot length measured 7 days after inoculation (DAI) and lesion length measured 7 and 14 DAI were used to calculate the lesion length as a percentage of the shoot length (PLL1 and PLL2, respectively). Percent lesion length data were log10-transformed (log10(PLL)) and used to perform the Kruskal-Wallis test, interval mapping (IM), and multiple QTL mapping (MQM). Two significant fire blight resistance QTLs were detected in `Florina'. One QTL was mapped on linkage group 10 by IM and MQM; it explained 17.9% and 15.3% of the phenotypic variation by MQM with log10(PLL1) and log10(PLL2) data, respectively. A second QTL was identified on linkage group 5 by MQM with log10(PLL2) data; it explained 10.1% of the phenotypic variation. Genotyping the plants of `Florina' pedigree with the microsatellites flanking the QTLs showed that the QTLs on linkage groups 5 and 10 were inherited from `Jonathan' and `Starking' (a `Red Delicious' sport mutation), respectively. Other putative QTLs (defined as QTLs with LOD scores above the chromosomal threshold and below the genome-wide threshold) were detected by IM on linkage groups 5 and 9 of `Nova Easygro'.

Patterns of geographical diversity, and the relationship between agro-morphological traits and fatty acid composition were assessed for 193 safflower (Carthamus tinctorius) accessions representing forty countries. Accessions were assigned to eight groups based on geographical proximity. Cluster and Principal Component analyses were performed to assess patterns of diversity among the accessions and to select the most distant accessions from each of eight groups for analysis of randomly amplified polymorphic DNA (RAPD) markers. There was a large amount of diversity for agro-morphological traits, fatty acid composition, and RAPD markers. Most correlations among different traits were rather low. Plant height showed a positive correlation with days to flowering (r = 0.63**). Palmitic acid was positively correlated with stearic acid and oleic acid values, and negatively correlated with linoleic acid (P < 0.01). Oleic acid and linoleic acid showed a strong negative correlation (r = −0.89**). The first three principal components together explained 59% of the variation, however, neither principal component analysis (PCA) nor marker analysis revealed a clear relationship between diversity pattern and geographical origin. Accessions from some geographical regions tended to group together, such as accessions from South Western Asia, Central Western Europe, and the Mediterranean region. The correlation between the morphological matrix and the genetic matrix based on RAPD markers was not significant (r = 0.027). Wide diversity in safflower germplasm indicates a considerable potential for improving this crop for both agronomic and quality traits.

A fire blight resistance QTL explaining 34.3%-46.6% of the phenotypic variation was recently identified on linkage group 7 of apple cultivar `Fiesta' (F7). However, markers flanking this QTL were AFLP and RAPD markers unsuitable for marker-assisted selection (MAS). Two RAPD markers bracketing the QTL have been transformed into SCAR (sequence-characterized amplified region) markers, and an SSR marker specific for the region was developed. Pedigree analysis of `Fiesta' with these markers enabled tracking of the F7 QTL allele back to `Cox's Orange Pippin'. Stability of the effect of this QTL allele in different backgrounds was analyzed by inoculating progeny plants of a cross between `Milwa', a susceptible cultivar, and `1217', a moderately resistant cultivar, and a set of cultivars that carry or lack the allele conferring increased fire blight resistance. Progenies and cultivars that carried both markers were significantly more resistant than those that did not carry both markers, indicating high stability of the F7 QTL allele in different backgrounds. This stability and the availability of reproducible markers bracketing the QTL make this locus promising for use in MAS.

Fire blight caused by the bacterium Erwinia amylovora is a severe threat to apple and pear orchards worldwide. Apple varieties exhibit a wide range of relative susceptibility/tolerance to fire blight. Although, no monogenic resistance against fire blight has been identified yet, recent evidence indicates the existence of quantitative resistance. Potential sources of fire blight resistance include several wild Malus species and some apple cultivars. F1 progenies of ‘Fiesta’בDiscovery’ were inoculated with the Swiss strain Ea 610 and studied under controlled conditions to identify quantitative trait loci (QTLs) for fire blight resistance. Disease was evaluated at four time points after inoculation. Shoot lesion length and the area under disease progress curve (AUDPC) values were used for QTL analysis. One significant (LOD score of 7.5–8.1, p<0.001) QTL was identified on the linkage group 7 of ‘Fiesta’ (F7). The F7 QTL explained about 37.5–38.6% of the phenotypic variation.

Agave tequilana is native to Mexico and is famous for its use in the production of the alcoholic beverage tequila. The crop is extremely prone to insects and diseases, and a breeding programme for selection and conservation is required. Moreover, poorly understood classification of agave varieties and the limited availability of molecular data represent a big hurdle in its genetic research and improvement. Retrotransposons are mobile genetic elements that can occupy large proportions of plant genomes and play a vital role in their organisation and evolution. They can be used as genetic tools to address the challenges faced by A. tequilana. Ty1-Copia retrotransposons were isolated and characterised, and their copy number in the genome of A. tequilana was estimated. The phylogenetic analysis of isolated reverse transcriptase sequences showed that A. tequilana contains a large population of Ty1-Copia retrotransposons. They occur in the form of groups of closely related heterogeneous elements. The copy number estimates revealed that they are extremely abundant in A. tequilana. The characterisation of the Ty1-Copia population suggests that they are a major component of the agave genome and might have played a vital role in its genome organisation and evolution.