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Most Japanese chestnuts have difficult-peeling pellicles, which make it time-consuming and costly to remove the pellicle from the nut during processing. Therefore, an easy-peeling pellicle has been an important goal of Japanese chestnut breeding programs. In previous studies, we identified the peeling locus, which controls peelability in Japanese chestnut. Homozygous recessive plants (p/p) have an easy-peeling pellicle. Here, we developed a novel simple sequence repeat (SSR) marker, CmSca06716, which is suitable for the selection of pellicle peelability in Japanese chestnut. We also constructed a fine map of Tsukuba-43 and localized the peeling locus within a 1.1-cM region between SSR markers CmSca05637 (or CmSca01731) and CmSca03291. The CmSca06716 marker co-segregated with the peeling locus in all F1 plantlets of a 'Porotan' × Tsukuba-43 cross. The peeling region was located within a 1.5-Mb region of chromosome 1 in two Chinese chestnut genome assemblies. The 394-bp allele of CmSca06716 was linked in the coupling phase to the recessive easy-peeling allele (p) possessed by 'Porotan', 'Porosuke', and 'Yakko', which are easy to peel, and in their relatives. We also identified three new cultivars that were heterozygous for the 394-bp allele at the CmSca06716 locus and the p allele at the peeling locus. Furthermore, we developed a cost-efficient and rapid marker-assisted selection system and applied it to our breeding program for Japanese chestnut. This information will lead to a better understanding of the genetic control and physiological mechanisms underlying pellicle peelability in Japanese chestnut. [ABSTRACT FROM AUTHOR]

Japanese chestnut (Castanea crenata Sieb. et Zucc.), unlike other Castanea species, is resistant to most diseases and wasps. However, genomic data of Japanese chestnut that could be used to determine its biotic stress resistance mechanisms have not been reported to date. In this study, we employed long-read sequencing and genetic mapping to generate genome sequences of Japanese chestnut at the chromosome level. Long reads (47.7 Gb; 71.6× genome coverage) were assembled into 781 contigs, with a total length of 721.2 Mb and a contig N50 length of 1.6 Mb. Genome sequences were anchored to the chestnut genetic map, comprising 14,973 single nucleotide polymorphisms (SNPs) and covering 1,807.8 cM map distance, to establish a chromosome-level genome assembly (683.8 Mb), with 69,980 potential protein-encoding genes and 425.5 Mb repetitive sequences. Furthermore, comparative genome structure analysis revealed that Japanese chestnut shares conserved chromosomal segments with woody plants, but not with herbaceous plants, of rosids. Overall, the genome sequence data of Japanese chestnut generated in this study is expected to enhance not only its genetics and genomics but also the evolutionary genomics of woody rosids. [ABSTRACT FROM AUTHOR]

Background: Understanding mechanisms of sugar accumulation and composition is essential to determining fruit quality and maintaining a desirable balance of sugars in plant storage organs. The major sugars in mature Rosaceae fruits are sucrose, fructose, glucose, and sorbitol. Among these, sucrose and fructose have high sweetness, whereas glucose and sorbitol have low sweetness. Japanese pear has extensive variation in individual sugar contents in mature fruit. Increasing total sugar content and that of individual high-sweetness sugars is a major target of breeding programs. The objective of this study was to identify quantitative trait loci (QTLs) associated with fruit traits including individual sugar accumulation, to infer the candidate genes underlying the QTLs, and to assess the potential of genomic selection for breeding pear fruit traits. Results: We evaluated 10 fruit traits and conducted genome-wide association studies (GWAS) for 106 cultivars and 17 breeding populations (1112 F1 individuals) using 3484 tag single-nucleotide polymorphisms (SNPs). By implementing a mixed linear model and a Bayesian multiple-QTL model in GWAS, 56 SNPs associated with fruit traits were identified. In particular, a SNP located close to acid invertase gene PPAIV3 on chromosome 7 and a newly identified SNP on chromosome 11 had quite large effects on accumulation of sucrose and glucose, respectively. We used 'Golden Delicious' doubled haploid 13 (GDDH13), an apple reference genome, to infer the candidate genes for the identified SNPs. In the region flanking the SNP on chromosome 11, there is a tandem repeat of early responsive to dehydration (ERD6)-like sugar transporter genes that might play a role in the phenotypes observed. Conclusions: SNPs associated with individual sugar accumulation were newly identified at several loci, and candidate genes underlying QTLs were inferred using advanced apple genome information. The candidate genes for the QTLs are conserved across Pyrinae genomes, which will be useful for further fruit quality studies in Rosaceae. The accuracies of genomic selection for sucrose, fructose, and glucose with genomic best linear unbiased prediction (GBLUP) were relatively high (0.67–0.75), suggesting that it would be possible to select individuals having high-sweetness fruit with high sucrose and fructose contents and low glucose content. [ABSTRACT FROM AUTHOR]

Trees with weeping traits have been prized for centuries because of their unique shape. Weeping trees of various species have been selected and propagated for their ornamental appeal as landscape plants, but there is limited information on the genes that control weeping. The genetic control of weeping in Japanese chestnut (Castanea crenata Sieb. et Zucc.) is reported to involve a dominant or recessive gene depending on the genetic background. In every case examined to date, weeping is controlled by a single gene of unknown location. Here, we identified the exact position of the dominant gene controlling the weeping trait in the Japanese chestnut. Using the genome scanning approach, which can cost-effectively screen for markers linked to traits, we first mapped this gene, referred to here as Weep, to the middle of linkage group L. Then, we developed new simple sequence repeat (SSR) markers using the genomic resources to enrich the target region. Using these markers and previously reported markers, we constructed the linkage group covering most of the chromosome (60.9 cM) with an average marker density of 4.7 cM per marker. Weep was located within a 3.0-cM genome region. SSR marker CmSca01437 co-segregated with Weep in all 138 F1 plantlets of a Tsukuba-38 × 668-6 cross. Our identification of the exact locus of the dominant weeping gene in Japanese chestnut, in conjunction with previous studies of recessive weeping genes in this and other tree species, furthers our understanding of the genetic mechanism of the weeping trait. [ABSTRACT FROM AUTHOR]

Haplotypes provide useful information for genomics-based approaches, genomic prediction, and genome-wide association study. As a small number of superior founders have contributed largely to the breeding history of fruit trees, the information of founder haplotypes may be relevant for performing the genomics-based approaches in these plants. In this study, we proposed a method to estimate 14 haplotypes from 7 founders and automatically trace the haplotypes forward to apple parental (185 varieties) and breeding (659 F1 individuals from 16 full-sib families) populations based on 11,786 single-nucleotide polymorphisms, by combining multiple algorithms. Overall, 92% of the single-nucleotide polymorphisms information in the parental and breeding populations was characterized by the 14 founder haplotypes. The use of founder haplotype information improved the accuracy of genomic prediction in 7 traits and the resolution of genome-wide association study in 13 out of 27 fruit quality traits analyzed in this study. We also visualized the significant propagation of the founder haplotype with the largest genetic effect in genome-wide association study over the pedigree tree of the parental population. These results suggest that the information of founder haplotypes can be useful for not only genetic improvement of fruit quality traits in apples but also for understanding the selection history of founder haplotypes in the breeding program of Japanese apple varieties. [ABSTRACT FROM AUTHOR]

Fruit skin type is one of the most important components of fruit appearance. Pears have three types of fruit skin—russet, intermediate, and smooth—depending on the extent of the cork layer on the epicarp. Russet type is controlled by a dominant genetic factor, R, and a quantitative trait locus (QTL) associated with fruit skin type has been identified on chromosome 8. Although some markers have been developed, the relationship between their alleles and fruit skin type has not been established across multiple cultivars; thus, the effectiveness of these markers in marker-assisted selection (MAS) has not been demonstrated. In this study, haplotypes of 93 accessions estimated by Beagle 4.0 were classified into the major haplotypes HAP1–HAP8 using new simple sequence repeat (SSR) markers Psc07, Psc34, and Psc03. Out of the eight haplotypes, HAP1–HAP7 were found in Japanese pear, whereas HAP8 was specific to Chinese pear. By comparing the haplotypes and phenotypes of accessions and F1 populations, we found that HAP1–HAP3 and HAP7 had dominant effects and promoted cork layer formation, whereas HAP4–HAP6 and HAP8 were recessive and did not contribute to russeting. All eight haplotypes can be distinguished completely by Psc07 and Psc03, which would be useful for MAS. This information on haplotype structure of accessions and molecular markers associated with fruit skin type will be useful for future pear breeding programs. [ABSTRACT FROM AUTHOR]

Japanese chestnut (Castanea crenata Sieb. et Zucc.), the only fruit tree species domesticated in Japan, has been cultivated alongside natural stands since prehistorical times. Understanding the genetic diversity of this species and the relationships between cultivated and wild chestnut is important for clarifying its breeding history and determining conservation strategies. We assessed 3 chestnut cultivar populations and 29 wild chestnut populations (618 accessions). Genetic distance analysis revealed that wild populations in the Kyushu region are genetically distant from other populations, whereas other wild and cultivar populations are comparatively similar. Assignment tests suggested that cultivars were relatively similar to populations from central to western Honshu. Bayesian structure analyses showed that wild individuals were roughly classified according to geographical distribution along the Japanese archipelago, except that some wild individuals carried the genetic cluster prevalent in cultivars. Parentage analyses between cultivars and wild individuals identified 26 wild individuals presumed to have a parent–offspring relationship with a cultivar. These results suggested that the genetic structure of some wild individuals in natural stands was influenced by gene flow from cultivars. To conserve wild individuals carrying true "wild" genetic clusters, these individuals should be collected and preserved by ex situ conservation programs. [ABSTRACT FROM AUTHOR]

The Chinese chestnut (Castanea mollissima Bl.) was introduced into Japan about 100 years ago. Since then, a number of Chinese chestnut cultivars and Japanese–Chinese hybrid cultivars have been selected by farmers and plant breeders, but little information has been available about their origins and genetic relationships. A classification based on simple sequence repeat markers was conducted using 230 cultivars including Japanese chestnut (Castanea crenata Sieb. et Zucc.) cultivars originated in Japan, Japanese–Chinese hybrid cultivars, and Chinese chestnut cultivars originated in both Japan and China. First, a search for synonyms (cultivars with identical genotypes) revealed 23 synonym groups among the Chinese chestnut cultivars, and all but one cultivar from each synonym group was omitted from further analyses. Second, genetic structure analysis showed a clear division between Japanese and Chinese chestnut, and most of the Japanese and Chinese cultivars had a simple genetic structure corresponding to the expected species. On the other hand, most Japanese–Chinese hybrid cultivars had admixed genetic structure. Through a combination of parentage and chloroplast haplotype analyses, 16 of the 18 hybrid cultivars in this study were inferred to have parent–offspring relationships with other cultivars originated in Japan. Finally, Bayesian clustering and chloroplast haplotype analysis showed that the 116 Chinese chestnut cultivars could be divided into two groups: one originated in the Hebei region of China and the other originated in the Jiangsu and Anhui regions of China. The Chinese chestnut cultivars selected in Japan showed various patterns of genetic structure including Hebei origin, Jiangsu or Anhui origin, and admixed. The chestnut cultivar genetic classifications obtained in this study will be useful for both Japanese and Chinese chestnut breeding programs. [ABSTRACT FROM AUTHOR]

Sweetness is the most important trait for fruit breeding and is fundamentally determined by both total and individual sugar contents. We analyzed the contents of sucrose, fructose, glucose, and sorbitol in mature fruit in an F1 population derived from crossing modern Japanese pear cultivar ‘Akizuki’ and breeding line ‘373-55’. A genetic linkage map was constructed using simple sequence repeats (SSRs) and single-nucleotide polymorphisms (SNP). We identified two regions associated with individual sugar contents on linkage group (LG) 1 and LG 7. The percentages of the variance in sucrose, fructose, and glucose explained by the quantitative trait loci (QTLs) were 26.6, 15.9, and 18.5%, respectively, for the region on LG 1, and 22.2, 20.0, and 9.5%, respectively, for the region on LG 7. In both regions, genotypes associated with increases in sucrose were associated with decreases in both fructose and glucose. The 1.5-LOD support intervals of the QTLs on LGs 1 and 7 include SSRs within the regions flanking acid invertase genes PPAIV3 and PPAIV1, respectively. Because acid invertase is a key enzyme in the conversion of sucrose to hexose, these are promising candidates for genes underlying those QTLs and controlling individual sugar contents. We also found one region on LG 11 that explained 21.4% of the variation in total sugar content but was not significantly associated with variation for individual sugars. The information obtained in this study will accelerate research and breeding programs to improve fruit sweetness. [ABSTRACT FROM AUTHOR]

Retrotransposons are major components of eukaryotic genomes and are present in high copy numbers. We developed retrotransposon-based insertion polymorphism (RBIP) markers based on long terminal repeat (LTR) sequences and flanking genome regions by using shotgun genome sequence data of mango ( Mangifera indica L.). Three novel LTR sequences were identified based on two LTR retrotransposon structural features; a 5′ LTR located upstream of the primer binding site and a 3′ LTR showing high sequence similarity to the 5′ LTR. Starting with 377 unique sequences containing both 3′ LTR and downstream genome region sequences, we developed 82 RBIP markers that were applied to DNA fingerprinting of 16 mango accession. Five RBIP markers were enough to distinguish all 16 accessions. Our result showed that LTR identification from shotgun genome sequences was effective for development of retrotransposon-based DNA markers without whole-genome sequence information. We discuss application of the developed RBIP markers for identification of genetic diversity and construction of a genetic linkage map. [ABSTRACT FROM AUTHOR]

Determining the molecular mechanism of fruit tree architecture is important for tree management and fruit production. An apple mutant 'McIntosh Wijcik', which was discovered as a bud mutation from 'McIntosh', exhibits a columnar growth phenotype that is controlled by a single dominant gene, Co. In this study, the mutation and the Co gene were analyzed. Fine mapping narrowed the Co region to a 101 kb region. Sequence analysis of the Co region and the original wild-type co region identified an insertion mutation of an 8202 bp long terminal repeat (LTR) retroposon in the Co region. Segregation analysis using a DNA marker based on the insertion polymorphism showed that the LTR retroposon was closely associated with the columnar growth phenotype. RNA-seq and RT-PCR analysis identified a promising Co candidate gene (91071-gene) within the Co region that is specifically expressed in 'McIntosh Wijcik' but not in 'McIntosh'. The 91071-gene was located approximately 16 kb downstream of the insertion mutation and is predicted to encode a 2-oxoglutarate-dependent dioxygenase involved in an unknown reaction. Overexpression of the 91071-gene in transgenic tobaccos and apples resulted in phenotypes with short internodes, like columnar apples. These data suggested that the 8202 bp retroposon insertion in 'McIntosh Wijcik' is associated with the short internodes of the columnar growth phenotype via upregulated expression of the adjacent 91071-gene. Furthermore, the DNA marker based on the insertion polymorphism could be useful for the marker-assisted selection of columnar apples. [ABSTRACT FROM AUTHOR]

The degree of inbreeding should ideally be determined across the entire genome, but is instead widely measured using the pedigree-based coefficients of kinship ( f) for pairs of individuals and of inbreeding ( F) for individuals. For fruit trees, this biases the estimates for pairs of cross-parents and crossbred accessions, because f and F do not account for any latent kinship among the parents, particularly when these are local cultivars. Local cultivars are often important genetic resources but usually have an unknown pedigree. Several estimators have been developed for estimating kinship and inbreeding from DNA marker data. Among these, we selected the kinship estimator of Wang (Genet Res 89: 135; ) and the inbreeding estimator of Leutenegger et al. (Am J Hum Genet 73: 516; ), using 207 simple sequence repeat markers in 73 Japanese pear ( Pyrus pyrifolia Nakai) and 3 Chinese pear ( Pyrus ussuriensis Maxim.) accessions with high potential as cross-parents in breeding of Japanese pear. Pedigree-based coefficients calculated from accessions with all known great-grandparents were used to compare the performance (measured by root mean square errors and correlations) of the estimators. Most marker kinship estimates matched the expected values for parent-offspring and full-sibling pairs, and indicated latent inbreeding, especially among accessions with f = 0, including local cultivars. Marker estimators highlighted latent inbreeding early in the breeding program. The data presented here will help breeders identify the degree of inbreeding in breeding populations and avoid inbreeding during crossbreeding of Japanese pear. [ABSTRACT FROM AUTHOR]

The Japanese chestnut ( Castanea crenata Siebold et Zucc.) is naturally distributed throughout Japan and is cultivated for its fruit (nuts) throughout the country. Many native cultivars have cultivation records going back more than 100 years. Researchers have speculated that native cultivars that originated in the Tanba region, the most important region of cultivation, were spread throughout Japan. To clarify the breeding history and spreading pattern of Japanese chestnut cultivars, we estimated the population structure of a set of 60 native chestnut cultivars via hierarchical clustering and Bayesian model-based clustering. Both analyses gave similar results. The cultivars were divided into two main clusters: one with cultivars from the Tanba region, the other with cultivars from other areas of Japan. However, there were some exceptions to this pattern, suggesting that propagation of clones and seeds by humans was a part of the spreading process. Additionally, parent-offspring relationships were estimated from the data obtained for 175 simple sequence repeat markers. Out of the 60 genotypes, nine putative parent-offspring pairs and eight putative parent-offspring trios were identified. These results suggest that native cultivars are likely to have been selected from crosses of older native cultivars. In particular, some native cultivars from outside the Tanba region had parent-offspring relationships with cultivars from the Tanba region. This result suggests that cultivars from outside the Tanba region had been crossed with cultivars from the Tanba region and then selected as a means of introducing favorable traits from the Tanba cultivars. [ABSTRACT FROM AUTHOR]

The development of single nucleotide polymorphism (SNP) markers in Japanese pear ( Pyrus pyrifolia Nakai) offers the opportunity to use DNA markers for marker-assisted selection in breeding programs because of their high abundance, codominant inheritance, and potential for automated high-throughput analysis. We developed a 1,536-SNP bead array without a reference genome sequence from more than 44,000 base changes on the basis of a large-scale expressed sequence tag (EST) analysis combined with 454 genome sequencing data of Japanese pear 'Housui'. Among the 1,536 SNPs on the array, 756 SNPs were genotyped, and 609 SNP loci were mapped to linkage groups on a genetic linkage map of 'Housui', based on progeny of an interspecific cross between European pear ( Pyrus communis L.) 'Bartlett' and 'Housui'. The newly constructed genetic linkage map consists of 951 loci, comprising 609 new SNPs, 110 pear genomic simple sequence repeats (SSRs), 25 pear EST-SSRs, 127 apple SSRs, 61 pear SNPs identified by the 'potential intron polymorphism' method, and 19 other loci. The map covers 22 linkage groups spanning 1341.9 cM with an average distance of 1.41 cM between markers and is anchored to reference genetic linkage maps of European pears and apples. A total of 514 contigs containing mapped SNP loci showed significant similarity to known proteins by functional annotation analysis. [ABSTRACT FROM AUTHOR]

Loquat canker disease, caused by Pseudomonas syringae pv. eriobotryae, is one of the most harmful diseases of commercial cultivars of loquat ( Eriobotrya japonica). To introgress resistance to loquat canker, we identified the linkage group and position of the resistance locus derived from the related wild species bronze loquat ( Eriobotrya deflexa). The segregation of resistance and susceptibility fit the expected ratio of 1:1 in 96 individuals from a three-way cross involving bronze loquat (heterozygous for resistance) and two cultivars of loquat (susceptible). The genomic region containing Pse-a was identified by using a genome scanning approach, and the loquat canker resistance locus was mapped at the top of linkage group 10 by applying novel simple sequence repeat (SSR) markers designed on the basis of the 'Golden Delicious' apple genome sequence. The constructed linkage group spans 69.4 cM and has an average marker density of 2.6 cM per marker. The developed molecular markers tightly linked to the loquat canker resistance locus will be useful for marker-assisted selection and for introgression of resistance into loquat in breeding programs. [ABSTRACT FROM AUTHOR]

The Japanese chestnut ( Castanea crenata Sieb. et Zucc.) has a pellicle that is difficult to peel, which increases the labor and cost for removing the pellicle from the nut during processing. Thus, a pellicle that is easier to peel has been an important objective of Japanese chestnut breeding programs. A newly released cultivar ('Porotan') exhibits a unique, easily peeled pellicle. A previous study indicated that this trait is controlled by recessive gene p, and that several of the ancestors of Porotan (e.g., 'Tanzawa' and 550-40) were P/p heterozygotes. Two F populations from intra-specific crosses of Japanese chestnut, Tanzawa ( P/p) × Porotan ( p/p) and 550-40 ( P/p) × Tanzawa ( P/p), were used for genetic mapping of the gene that controls this characteristic. A total of 11 simple sequence repeat (SSR) markers were obtained that showed significant linkages to the p gene, and genetic linkage maps for the region around the p gene were established. Pedigree analysis was conducted for eight ancestors of Porotan around the pellicle-peeling locus using graphical genotypes based on the 11 SSR loci. The two recessive p alleles and surrounding haplotypes of Porotan were inherited through different intermediate cultivars: one allele was derived from 'Otomune' ( P/p) via Tanzawa and the other was derived from Otomune via Tanzawa, 'Kunimi' ( P/p), and breeding line 550-40. A recombination event was found in the flanking region close to the p gene in Kunimi. Molecular identification of the easy peel pellicle trait will lead to marker-assisted selection and will greatly improve Japanese chestnut breeding. [ABSTRACT FROM AUTHOR]

With 3 figures and 2 tables Abstract In a previous study, a QTL analysis was conducted on a pear F1 progeny derived from a cross 'Passe Crassane' (PC) × 'Harrow Sweet' (HS). Four genomic regions associated with fire blight resistance were identified, including two main QTL located on linkage groups (LGs), 2A and 4 of 'Harrow Sweet' (HS02A and HS04). In the present study, we report the combination of LGs HS02A and HS02B into a single LG by mapping additional SSR loci from Malus or Pyrus spp. We could thereby precisely identify a single major QTL on LG HS02. We also confirm a putative QTL on LG HS04 by including new SSR markers to the pre-existing LG HS04. Based on SSR marker analysis of 'Harrow Sweet' pedigree, the major HS02 QTL is presumed to originate from the cultivar 'Early Sweet', while the HS04 QTL was traced from 'Harrow Sweet' back to 'Bartlett'. We also describe the validation of the major HS02 QTL for the fire blight severity trait in a second F1 progeny derived from a cross 'Angelys' × 'Harrow Sweet'. [ABSTRACT FROM AUTHOR]

The chloroplast genome of Pyrus was found to be 159,922 bp in length which included a pair of inverted repeats (IRs) of 26,392 bp, separated by a small single-copy region of 19,237 bp and a large single-copy region (LSC) of 87,901 bp. A total of 130 predicted genes (113 unique genes and 17 genes, which were duplicated in the IR) including 79 protein-coding genes, four ribosomal RNA genes and 30 tRNA genes were identified based on similarity to homologs from the chloroplast genome of Nicotiana tabacum. Genome organization was very similar to the inferred ancestral angiosperm chloroplast genome. Comparisons between Pyrus, Malus, and Prunus in Rosaceae revealed 220 indels (≥10 bp). Excluding ycf1 and ycf2, which contained deletions in the coding region, all of these were detected in the spacer or intron regions. Three insertions and 13 deletions were detected in Pyrus compared to the same loci in Malus and Prunus. After comparing 89 noncoding chloroplast DNA regions in Pyrus and Malus, highly variable regions such as ndhC-trnV and trnR-atpA were identified. In Pyrus and Malus, the IR/LSC borders were 62 bp shorter than those of Prunus. In addition, there were length mutations at the IRa/LSC junction and in trnH. A total of 67 simple sequence repeats (more than 10 repeated motifs) were identified in the Pyrus chloroplast genome. The indels and simple sequence repeats will be useful evolutionary tools at both intra- and interspecific levels. Phylogenetic analysis demonstrated a close relationship between Pyrus and Prunus in the Rosaceae. [ABSTRACT FROM AUTHOR]

Identification of markers associated with genes of interest and quantitative trait loci (QTLs), combined with high-density genetic linkage maps, can help reduce labor and costs by enabling marker-assisted selection (MAS). In this study, a dwarfing apple rootstock cultivar 'JM7' ( Malus prunifolia × Malus pumila 'Malling 9') and wild apple Malus sieboldii 'Sanashi 63' (section Sorbomalus) were used for constructing genetic linkage maps. Here, a species from section Sorbomalus was used for the first time as a target species in a genome-wide mapping study. We also developed and mapped 137 novel-expressed sequence tag-simple sequence repeat (EST-SSR) markers. The genetic linkage maps of 'JM7' and 'Sanashi 63' consisted of 415 and 310 loci and spanned 998.0 and 981.8 cM, respectively, comparable to the reference map of Malus × domestica 'Discovery'. A BLASTN search revealed that all of the EST-SSR sequences used in this study exhibited very high homology to one or more previously characterized apple genome contigs. Although the most homologous contigs of 89 EST-SSRs were located within the same linkage groups (LGs) identified by mapping analysis, the other 48 EST-SSRs were aligned into contigs positioned in different LGs than those identified by mapping. When search criteria were expanded to include the five most homologous contigs of each EST-SSR, at least one of the top five contigs for 15 of these 48 EST-SSRs corresponded to the LG obtained by mapping. The maps of 'JM7' and 'Sanashi 63' may be useful for analyzing important rootstock characteristics and identifying markers for MAS. [ABSTRACT FROM AUTHOR]

Retrotransposons are present in all plant genomes and play important roles in genome size, genome structure remodeling, gene function, and genome evolution. Eight novel long terminal repeat retrotransposons were identified from a bacterial artificial chromosome library of Japanese pear ( Pyrus pyrifolia). On the basis of the order of gene arrangement within the gag and pol domains (protease, integrase, reverse transcriptase, and RNase H), these newly identified retrotransposons appear to be closely related to Ty1- copia retrotransposons. They were designated Ppcrt1-8 and classified into two groups based on the presence or absence of a 142-amino-acid deletion within the group-specific antigen DNA-binding domain. Ppcrt1-8 were grouped with the copia-like retrotransposons RIRE1 and BARE-1 by phylogenetic analysis based on the amino acid sequences encoded by the gag and pol domains. Fluorescence in situ hybridization analysis showed that sequences homologous to Ppcrt4 were dispersed throughout more than half of the pear chromosomes. Southern blot analysis suggested that many copies of Ppcrt retrotransposons exist in the pear genome. Sequence information from these eight retrotransposons should be useful for the development of retrotransposon-based molecular marker systems in Japanese pear. [ABSTRACT FROM AUTHOR]

Background: The mechanism underlying the interaction between host plant and host-selective toxin (HST)-producing Alternaria alternata during infection is of particular interest for sustainable crop production. Alternaria blotch of apple (Malus × domestica Borkh.) caused by A. alternata apple pathotype is a major disease particularly in East Asia, which is the largest producer of apples globally. A single dominant gene, Alt, controls the susceptibility of the apple cultivar 'Delicious' to Alternaria blotch. In this study, we fine mapped the Alt locus and characterized three potential candidate genes. Results: We used 797 F1 individuals derived from 15 crosses between apple accessions susceptible (Alt/alt) and resistant (alt/alt) to Alternaria blotch to construct physical and genetic maps of the Alt locus located on the top of chromosome 11. Susceptible accessions were derived from 'Delicious.' To fine map the Alt locus, we constructed a BAC library of 'Starking Delicious,' a sport of 'Delicious,' and used graphical genotyping to delimit the Alt locus to a region of 43 kb. Three genes predicted within the candidate Alt region were potentially involved in plant defense response, among which the gene encoding a coiled coil-nucleotide binding-leucine rich repeat (CC-NB-LRR) type disease resistance protein was the most promising. Moreover, a 12-bp insertion was uniquely identified in the 5′ untranslated region of the Alt-associated allele of this gene, the presence or absence of which co-segregated with the susceptibility or resistance to A. alternata apple pathotype, respectively, among 43 tested cultivars including old ones and founders of modern apple breeding. Conclusion: A disease resistance protein has been suggested as a determinant of susceptibility/resistance to HST-producing A. alternata for the first time. Our finding provides new insight into the mechanism of HST-mediated disease control used by A. alternata against host plants. [ABSTRACT FROM AUTHOR]

Japanese chestnut (Castanea crenata Sieb. et Zucc.) has a long juvenile phase, so breeders have to wait many years to evaluate nut traits. Molecular markers associated with genes of interest would accelerate selection in chestnut breeding programs. We evaluated five nut traits (nut harvest date, nut weight, pericarp splitting, insect infestation, and specific gravity) in 99 Japanese chestnut cultivars and selections. A wide range of phenotypic variation was observed for each of the traits, suggesting that the collection harbored sufficient genetic diversity for breeding. A Bayesian genome-wide association study was conducted using 162 simple sequence repeat markers and 741 single nucleotide polymorphism markers. To evaluate the potential of marker-assisted selection, we examined 12 molecular markers found to be associated with nut traits: 4 for nut harvest date, 4 for nut weight, 1 for pericarp splitting, and 3 for insect infestation. The percentages of phenotypic variance explained ranged from 4.8 to 37.1%. Although insect infestation showed only medium heritability (0.672), we obtained two quantitative trait loci (QTLs) with extremely high posterior probabilities (0.93 and 1.00). Out of the 12 molecular markers, 3 of the 4 markers for nut harvest time could be validated in a breeding population. Accuracies of genomic selection were extremely high for nut harvest date (0.841) and moderate for insect infestation (0.604), suggesting that genomic selection based on Bayesian regression would reduce the cost of phenotypic evaluation of these traits and possibly others. [ABSTRACT FROM AUTHOR]