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• Pear scab resistance in the Chinese pear 'Hong Li' was controlled by a single dominant gene. • The novel scab resistance gene, Rvn4 , was mapped at the top of linkage group 7. • New SSR marker Pbr.chr07.20 had a significant linkage to Rvn4 , with a genetic distance of 1.3 cM. • DNA markers linked to the novel resistance gene can allow efficient marker-assisted selection and the pyramiding of multiple resistance genes. Pear scab, caused by Venturia nashicola , is one of the most harmful diseases of pears, especially of Japanese and Chinese pears. The breeding of new cultivars resistant to pear scab has long been an aim of the Asian pear breeding programs. Although loci for pear scab disease resistance have been identified in Japanese and European pears, information on the genes controlling scab resistance in Chinese pears is limited. Genetic control of scab resistance in Chinese pear is reported to involve a single dominant gene. Here, we reaffirmed the scab resistance in the Chinese pear 'Hong Li' controls a single dominant gene and identified the exact location of a scab resistance gene, Rvn4. We first mapped Rvn4 at the top of linkage group (LG) 7 and then used public genome sequences to develop novel simple sequence repeat (SSR) markers to enrich the target region. Using these novel SSRs and the previously published SSR markers, we constructed a LG 7 of 'Hong Li' with an average marker density of 1.4 cM per marker. The novel SSR marker Pbr.chr07.20 had a significant linkage to Rvn4 , with a genetic distance of 1.3 cM. The identification of the precise locus of Rvn4 in Chinese pear, together with previous studies in Japanese and European pear, will enhance our understanding of the mechanisms of pear scab resistance. DNA markers linked to the novel gene may also allow efficient selection of scab-resistant seedlings in pear breeding programs and the pyramiding of multiple resistance genes. [ABSTRACT FROM AUTHOR]

We developed retrotransposon-based insertional polymorphism (RBIP) markers based on the long terminal repeat (LTR) sequences of copia-like retrotransposon Ppcrt4 and flanking genome sequences, which were derived from 454 sequencing data from Japanese pear (Pyrus pyrifolia) 'Hosui'. Out of 40 sequences including both LTR and flanking genome regions, we developed 22 RBIP markers and used them for DNA profiling of 80 pear cultivars: 64 Japanese, 10 Chinese (Pyrus ussuriensis) and 6 European (Pyrus communis). Three RBIP markers were enough to differentiate 'Hosui' from the other Japanese pear cultivars. The 22 RBIP markers could also distinguish 61 of the 64 Japanese pear cultivars. European pears showed almost no amplification of the 22 RBIP markers, which might suggest that retrotransposons had transposed during Asian pear evolution or reflect the genetic relationship between Asian and European pears. Sixteen of the RBIP markers could be positioned on a genetic linkage map of 'Hosui'. The RBIP loci were distributed in 10 linkage groups, and some loci were very closely located within the same linkage group. The information obtained will be applicable to developing cultivar-specific RBIP marker sets in plants. [ABSTRACT FROM AUTHOR]

We developed 73 novel expressed sequence tag (EST)--simple sequence repeat (SSR) markers based on ESTs derived from 11 different cDNA libraries of the Japanese pear (Pyrus pyrifolia Nakai) cultivar 'Housui', comprising 30, 36, two, one, and four SSRs with repeat motifs of di-, tri-, tetra-, penta-, and hexa-nucleotides, respectively. Forty-eight EST sequences showed significant homology to Arabidopsis thaliana genes. The linkage groups and positions of 57 loci generated from 53 SSR markers covering all 17 linkage groups, were identified. These EST-SSRs will be useful for high-throughput genotyping of marker-assisted selection. The numbers of alleles and the observed and expected heterozygosities at single-locus EST-SSR markers in ten Japanese and ten European pears suggest high polymorphism and heterozygosity of the EST-SSRs. Di-nucleotide EST-SSRs showed two to three times the polymorphism and heterozygosity of tri-nucleotide EST-SSRs. Some of the EST-SSRs proved transferable to other species in the Rosaceae, paying the way for the development of markers for the same phenotypic traits among species of the Rosaceae. [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.), 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]

• A non-host-resistance gene against Venturia nashicola of 'La France' is a single dominant gene. • We constructed a genetic map and narrowed the candidate region of the gene on Chr2. • These new DNA markers can be used to select resistant individuals without inoculation tests and to pyramid multiple resistance genes. Pear scab disease caused by Venturia nashicola is one of the most serious diseases of Asian pears. To facilitate the breeding of scab-resistant cultivars, we mapped and developed markers for a resistance gene from the European pear (Pyrus communis) cultivar 'La France'. By using a pseudo-backcross strategy to introduce genes from 'La France' into Japanese pear (P. pyrifolia) cultivars, we developed a mapping population from a cross between Japanese pear 'Akiakari' and interspecific hybrid progeny line 537–14. The individuals in the mapping population were evaluated for resistance by inoculation testing in 2020 and 2021. The segregation ratio of resistant to susceptible individuals was 1:1, indicating that resistance is inherited as a single dominant gene, which we named Vnlf. A genetic linkage map was constructed using single-nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers. On the basis of the genetic map of 537–14, we narrowed down the putative region carrying Vnlf to 959 kb on chromosome 2 between SNPs Chr2_20220913 and Chr2_21180341. To facilitate marker-assisted selection in Japanese pear breeding programs, we developed SSRs closely linked to Vnlf , one of which (LFA02a09) showed complete linkage to the resistance phenotype in an inoculation test of 175 individuals. These linked markers will enable introgression of Vnlf into breeding materials without the need for inoculation tests and will facilitate pyramiding Vnlf with other scab resistance loci. [ABSTRACT FROM AUTHOR]

Highlights • We constructed a database of 48 Japanese chestnut cultivars genotyped with 20 SSRs. • Pollen dispersal was studied by seed paternity analysis using the SSR database. • The percentage of seeds sired by a given pollinizer was highest in the closest rows. • Bur set and yield per tree decreased as distance from the pollinizer row increased. • Planting different cultivars in adjacent rows maximizes cross-pollination. Abstract Chestnut (Castanea spp.) is mainly self-sterile, so interplanting of different cultivars in orchards is recommended. However, effective pollen dispersal distances for cross-pollination in chestnut orchards have not been determined. We examined pollen dispersal in three chestnut fields by tracking the movement of cultivar-specific pollen through paternity analysis based on simple sequence repeat (SSR) markers. We genotyped 48 major cultivars with 20 SSRs and constructed a reference database, from which we inferred the pollen parent of each seed. In Field A, which consisted of a single row of pollinizer 'Riheiguri' and four rows of 'Porotan' at distances of 4, 8, 12, and 16 m from the pollinizer row, the percentage of seeds sired by the pollinizer pollen was higher at 4 and 8 m from the pollinizer trees (65.3% and 61.1%, respectively) than at 12 and 16 m (37.5% and 43.1%, respectively). The percentages of bur set and yield per tree decreased as the distance from the pollinizer row increased (66.2%, 42.4%, 33.7%, and 24.8%; 7.0, 2.5, 1.6, and 1.1 kg: 4, 8, 12, and 16 m, respectively). In analyses of two other fields, which contained interplanted rows of different cultivars, the percentages of seeds sired by pollen from cultivars planted in adjacent rows were much higher than from cultivars planted in more distant rows. These results suggest that it is important to plant different cultivars in adjacent rows. [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]

Loquat canker disease, caused by Pseudomonas syringae pv. eriobotryae , is one of the most serious diseases of loquat ( Eriobotrya japonica (Thunb.) Lindl.). We identified the linkage group and position of the resistance gene pse-c , which confers resistance to Group C of the pathogen, by using 141 seedlings derived from self-pollinated ‘Nagasakiwase’ ( Pse-c/pse-c ). Bulked segregant analysis revealed two RAPD markers, RAPD-OPY-03 and RAPD-OPA-18, with significant linkages to pse-c . The nucleotide sequences of these markers showed high similarity to the genome sequence of chromosomes 3 and 11 of ‘Golden Delicious’ apple. Of 448 SSR markers based on those genome sequences, five had significant linkages to pse-c . A linkage group including the pse-c gene, the two RAPD markers, and the five SSR markers spanned 37.9 cM with an average interval of 5.4 cM, and corresponded to the top of chromosome 3 of apple. The 170-bp allele of marker Chr3-ssr85 and the 184-bp allele of Chr3-ssr91 showed tight linkages with pse-c . The development of molecular markers linked to loquat canker resistance genes would be an effective way to establish marker-assisted selection and to pyramid several resistance genes in loquat breeding programs. [ABSTRACT FROM AUTHOR]

Although the potential of marker-assisted selection (MAS) in fruit tree breeding has been reported, biparental QTL mapping before MAS has hindered the introduction of MAS to fruit tree breeding programs. Genome-wide association studies (GWAS) are an alternative to bi-parental QTL mapping in long-lived perennials. Selection based on genomic predictions of breeding values (genomic selection: GS) is another alternative for MAS. This study examined the potential of GWAS and GS in pear breeding with 76 Japanese pear cultivars to detect significant associations of 162 markers with nine agronomic traits. We applied multilocus Bayesian models accounting for ordinal categorical phenotypes for GWAS and GS model training. Significant associations were detected at harvest time, black spot resistance and the number of spurs and two of the associations were closely linked to known loci. Genome-wide predictions for GS were accurate at the highest level (0.75) in harvest time, at medium levels (0.38-0.61) in resistance to black spot, firmness of flesh, fruit shape in longitudinal section, fruit size, acid content and number of spurs and at low levels (<0.2) in all soluble solid content and vigor of tree. Results suggest the potential of GWAS and GS for use in future breeding programs in Japanese pear. [ABSTRACT FROM AUTHOR]

Abstract: A total of 366 novel simple sequence repeat (SSR) markers were developed in Japanese chestnut (Castanea crenata), comprising 220 genomic SSRs derived from enriched genomic libraries and 146 expressed sequence tag (EST)–SSRs obtained from large-scale EST sequencing analysis. Thirty accessions, comprising Japanese, Chinese (C. mollissima), European (Castanea sativa), and American chestnuts (Castanea dentata), were used for evaluation of SSR polymorphism and transferability across species. The EST–SSRs showed less polymorphism than the genomic SSRs and were more transferable. The mean observed heterozygosity (H O) and the mean expected heterozygosity (H E) of genomic SSRs in the Japanese chestnuts were 0.63 and 0.68, respectively; those of EST-SSRs were each 0.47. Although about 80% of the genomic SSRs were amplified in all 4 species, more than 95% of the EST–SSRs were transferable across all 4 species. The many novel SSRs developed in this study will be applicable for the construction of genetic linkage maps, QTL analysis of phenotypic traits, high-throughput genotyping of marker-assisted selection, and association genetics. [Copyright &y& Elsevier]

The history of chestnut utilization in Japan is very long. Many cultivars have been preserved without being sufficiently organized and studied with respect to genetic variation. We developed 12 new SSR (simple sequence repeat) markers from Japanese chestnut (Castanea crenata) by using SSR-enriched genomic libraries. All 12 primer pairs selected for SSR analysis successfully amplified fragments in 6 Castanea species. The genetic diversity and relationships among 216 chestnut accessions were assessed by SSR markers, including 142 Japanese chestnuts, 38 Chinese chestnuts (C. mollissima), 2 European chestnuts (C. sativa), 9 American chestnuts (C. dentata), and 23 Japanese-Chinese hybrids. Among the 216 accessions, we identified 21 synonym groups (including 1 bud sport group), and 189 different genotypes. The mean values of observed heterozygosity (HO) and the expected heterozygosity (HE) in the Japanese chestnuts were 0.65 and 0.65, respectively. A phenogram of the 189 genotypes revealed 3 major groups, corresponding to Japanese, Chinese and American chestnuts. Japanese-Chinese hybrid cultivars were mainly included in the Chinese chestnut group. In the present study, genetic backgrounds could be identified for native and cultivated Japanese chestnuts and Japanese-Chinese hybrid cultivars, and many synonyms showing identical SSR genotypes were found. Genetic and geographical relationships of unique characteristics such as "Shidareguri" (weeping) and "Togenashi" (spineless) were also discussed. These results will improve the efficiency of cultivar identification and of chestnut breeding programs. [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]

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]

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 distribution of phenotypic values of peelability in Japanese chestnut populations preselected for a major peelability gene was biased toward maximum values. • Use of rank-based inverse normal transformation and categorization of peelability phenotypes was applied for GWAS to further identify QTLs associated with peelability. • A single QTL for peelability was identified at CCR1.0F_56177061 on chromosome F. Peelability is one of the most important traits in Japanese chestnut (Castanea crenata Sieb. et Zucc.) breeding. Previous studies revealed that the peelability of Japanese chestnut is controlled by a major recessive peeling gene (MRPG). This locus has been used effectively for marker-assisted selection in chestnut breeding programs, but there are also likely to be minor loci that would further improve the efficiency of breeding for peelability. We conducted a genome-wide association study (GWAS) based on a variational approximation version of BayesB using 27 cultivars and MRPG-preselected populations consisting of 520 F 1 seedlings from 22 families. Using double-digest restriction site-associated DNA sequencing (ddRAD-Seq), we obtained 9164 tag single-nucleotide polymorphisms. Because the phenotypic values of peelability were distributed very asymmetrically, with a peak at the high end due to the preselection for MRPG, we converted the original data set to both inverse normal transformed values and categorical scores, and we analyzed both sets of converted data by GWAS. In both analyses, a quantitative trait locus (QTL) for peelability at CCR1.0F_56177061 was identified with posterior probability values of 0.68 and 1.00, respectively. The average values of genotypes at CCR1.0F_56177061 for cultivars and seedlings in this study were 60.4% (peelability rate) for CC, 63.7% for CT, and 86.5% for TT. This analysis reveals a significant association between CCR1.0F_56177061 genotype and peelability, indicating that this newly identified QTL will be useful for improving peelability in chestnut breeding programs. [ABSTRACT FROM AUTHOR]

• The distribution of phenotypic values of peelability in Japanese chestnut populations preselected for a major peelability gene was biased toward maximum values. • Use of rank-based inverse normal transformation and categorization of peelability phenotypes was applied for GWAS to further identify QTLs associated with peelability. • A single QTL for peelability was identified at CCR1.0F_56177061 on chromosome F. Peelability is one of the most important traits in Japanese chestnut (Castanea crenata Sieb. et Zucc.) breeding. Previous studies revealed that the peelability of Japanese chestnut is controlled by a major recessive peeling gene (MRPG). This locus has been used effectively for marker-assisted selection in chestnut breeding programs, but there are also likely to be minor loci that would further improve the efficiency of breeding for peelability. We conducted a genome-wide association study (GWAS) based on a variational approximation version of BayesB using 27 cultivars and MRPG-preselected populations consisting of 520 F 1 seedlings from 22 families. Using double-digest restriction site-associated DNA sequencing (ddRAD-Seq), we obtained 9164 tag single-nucleotide polymorphisms. Because the phenotypic values of peelability were distributed very asymmetrically, with a peak at the high end due to the preselection for MRPG, we converted the original data set to both inverse normal transformed values and categorical scores, and we analyzed both sets of converted data by GWAS. In both analyses, a quantitative trait locus (QTL) for peelability at CCR1.0F_56177061 was identified with posterior probability values of 0.68 and 1.00, respectively. The average values of genotypes at CCR1.0F_56177061 for cultivars and seedlings in this study were 60.4% (peelability rate) for CC, 63.7% for CT, and 86.5% for TT. This analysis reveals a significant association between CCR1.0F_56177061 genotype and peelability, indicating that this newly identified QTL will be useful for improving peelability in chestnut breeding programs. [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]

We developed 18 polymorphic simple sequence repeat (SSR) markers in pineapple (Ananas comosus) by us-ing genomic libraries enriched for GA and CA motifs. The markers were used to genotype 31 pineapple ac-cessions, including seven cultivars and 11 breeding lines from Okinawa Prefecture, 12 foreign accessions and one from a related species. These SSR loci were highly polymorphic: the 31 accessions contained three to seven alleles per locus, with an average of 4.1. The values of expected heterozygosity ranged from 0.09 to 0.76, with an average of 0.52. All 31 accessions could be successfully differentiated by the 18 SSR mark-ers, with the exception of 'N67-10' and 'Hawaiian Smooth Cayenne'. A single combination of three markers TsuAC004, TsuACOlO and TsuAC041, was enough to distinguish all accessions with one exception. A pheno-gram based on the SSR genotypes did not show any distinct groups, but it suggested that pineapples bred in Japan are genetically diversed. We reconfirmed the parentage of 14 pineapple accessions by comparing the SSR alleles at 17 SSR loci in each accession and its reported parents. The obtained information will contrib-ute substantially to protecting plant breeders' rights. [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]

Abstract: Parthenocarpy—the production of seedless fruits without fertilization—is very useful for fruit cultivation, especially in self-incompatible species such as pears. To search for parthenocarpic genetic resources in pear, 31 pear accessions [20 Chinese pears (13 Pyrus bretschneideri, seven Pyrus ussuriensis), five European pears (Pyrus communis), two Japanese pears (Pyrus pyrifolia), and four interspecific hybrids] were subjected to flower emasculation and left unpollinated, and then the fruit-set ratio and fruit enlargement were investigated. All European pears examined had a stable and high degree of fruit set, and ‘La France’ had high fruit enlargement. The possibility of stenospermocarpy was ruled out, because the emasculated flowers were left unpollinated in paper bags and the absence of seed was confirmed in the enlarged fruits. Neither Chinese nor Japanese pears treated with emasculation and no pollination showed consistently stable fruit set and fruit enlargement. An analysis of parthenocarpy in the offspring of ‘La France’ suggested that both high fruit set and fruit enlargement were inherited and that it should be possible to introduce parthenocarpy into Japanese pears. Although parthenocarpic ‘La France’ fruits weighed slightly less than those from cross-pollinated flowers, their cortex enlargement compared favorably with that seen with cross-pollinated ones. By using a customized pear cDNA microarray, we compared the gene expression profiles of highly and weakly parthenocarpic cultivars before flowering. Expression of several phenylpropanoid-related genes and photosystem-related genes differed significantly between the two groups. Some of these genes were putatively encoded in the chloroplast genome. These genes might be candidates of DNA markers for achievement of parthenocarpy in Japanese pear breeding. [Copyright &y& Elsevier]

Abstract: A custom oligoarray of Japanese pear (Pyrus pyrifolia) based on 9812 independent ESTs from different tissues (fruits at various growth stages, vegetative and flower tissues) was designed and used for comprehensive investigation of gene expression before and during ripening (105–147 days after full bloom). Results of one-way ANOVA test indicated that the expression of about 30% of the genes (corresponding to 3062 independent ESTs) showed a significant difference between 105 (before ripening) and 147 (ripened) days after full bloom. Classification of expression pattern of those 3062 ESTs showed 11 sets, five of them contain 545 up-regulated ESTs and the other six sets contain 1920 down-regulated ones. Among them, 16 genes showed remarkable increase of more than 100 fold from 105 to 147 days after full bloom. The largest increase (more than 9000 fold) was exhibited by the glutathione S-transferase gene. The major functional group of remarkably up-regulated genes was in a glycosyl hydrolase family such as polygalacturonase. Genes participating in ethylene metabolism and sulfate transport were also identified. On the contrary, 18 genes were down-regulated to less than 1% during the same period. Glycosyl hydrolase family genes, invertase/pectin methylesterase inhibitor genes, and genes involved in secondary metabolism were the major groups identified. In addition, putative regulatory genes such as bHLH transcription factor also showed remarkable decreasing in expression. The cDNA oligoarray analysis efficiently provided individual gene expression profiles and new insights for elucidating the biological mechanisms responsible for fruit ripening in Japanese pear. [Copyright &y& Elsevier]

• Watercore is a disorder characterized by watery translucent areas in Japanese pear fruit flesh. • Use of F1 sibs helped to solve its poor reproducibility problem. • F1 sibs enabled differential transcriptome analysis before symptoms become visible. • Susceptible sibs highly expressed metallothionein, invertase and hormone-related genes. • Our data provide new insights into the mechanisms of watercore development. Watercore is a physiological disorder of Japanese pear fruits, in which a watery translucent area appears in the flesh of fruits on the tree. The disorder leads to the loss of commercial value, and resistance to watercore is one of the most important features to be studied in the breeding of Japanese pear. Even in susceptible cultivars such as 'Hosui' (syn. 'Housui'), the degree of watercore development varies markedly from year to year, which makes it difficult to analyze the characteristics of this phenomenon prior to visible watercore development. We used two F1 sib pairs from 'Hosui' × 'Hougetsu' and 'Akiakari' × 'Taihaku' crosses. Each pair contains a susceptible sib and a resistant sib. In these pairs, susceptible sibs developed severe watercore in all the fruits examined in each year, whereas no watercore was found even in overmature fruits of resistant sibs. To search for genes related to watercore, we used a custom pear microarray and studied differential gene expression in susceptible and resistant sibs prior to visible watercore development. We identified 115 differentially expressed genes including sugar metabolism–, hormone–, and cell wall–related genes. Some of these genes were differentially expressed only in immature fruits prior to watercore development. These genes would be useful as molecular markers to predict watercore at early developmental stages or in pear breeding programs. [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]