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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]

Japanese chestnuts ( Castanea crenata Sieb. et Zucc.) generally have difficult-peeling pellicles even after heating, making easy-peeling pellicle (EPP) an important breeding target. Recently, EPP cultivars ‘Porotan’ and ‘Porosuke’ were released by a government-funded breeding program. However, very few genotypes carry the major recessive gene responsible for the EPP trait, resulting in inbreeding within a narrow gene pool. To discover other genetic materials having the potential for EPP breeding, we evaluated the pellicle peelability of 59 accessions (51 Japanese local cultivars and 8 wild individuals) by using the high-temperature oil peeling method. We discovered that ‘Yakko’ had an exceptionally high pellicle peelability score (87%), close to that of ‘Porotan’ (94%). The results of segregation ratio analysis of pellicle peelability and genotype prediction by simple sequence repeat (SSR) markers among F 1 seedlings suggested that the EPP alleles of ‘Porotan’ and ‘Yakko’ are at the same locus. However, a haplotype structure analysis of the EPP genome region with SSR markers revealed that both haplotypes of ‘Yakko’ differed from those of ‘Porotan’, suggesting that the EPP gene of ‘Yakko’ had a different origin from that of ‘Porotan’ or was inherited from a common ancestor many generations ago. [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]

Self-compatible mutants of self-incompatible crops have been extensively studied for research and agricultural purposes. Until now, the only known pollen-part self-compatible mutants in Rosaceae subtribe Pyrinae, which contains many important fruit trees, were polyploid. This study revealed that the pollen-part self-compatibility of breeding selection 415-1, a recently discovered mutant of Japanese pear ( Pyrus pyrifolia) derived from γ-irradiated pollen, is caused by a duplication of an S-haplotype. In the progeny of 415-1, some plants had three S-haplotypes, two of which were from the pollen parent. Thus, 415-1 was able to produce pollen with two S-haplotypes, even though it was found to be diploid: the relative nuclear DNA content measured by flow cytometry showed no significant difference from that of a diploid cultivar. Inheritance patterns of simple sequence repeat (SSR) alleles in the same linkage group as the S-locus (LG 17) showed that some SSRs closely linked to S-haplotypes were duplicated in progeny containing the duplicated S-haplotype. These results indicate that the pollen-part self-compatibility of 415-1 is not caused by a mutation of pollen S factors in either one of the S-haplotypes, but by a segmental duplication encompassing the S-haplotype. Consequently, 415-1 can produce S-heteroallelic pollen grains that are capable of breaking down self-incompatibility (SI) by competitive interaction between the two different S factors in the pollen grain. 415-1 is the first diploid pollen-part self-compatible mutant with a duplicated S-haplotype to be discovered in the Pyrinae. The fact that 415-1 is not polyploid makes it particularly valuable for further studies of SI mechanisms. [ABSTRACT FROM AUTHOR]

'Porotan' is a Japanese chestnut cultivar (Castanea crenata Sieb. et Zucc.) that was selected from offspring of the cross 550-40 x 'Tanzawa' and released in 2006. Its nut is distinguished by a pellicle that is easy to peel after roasting; previously, all Japanese chestnut cultivars were thought to have a pellicle that was difficult to peel. Both 550-40 and 'Tanzawa' are Japanese chestnuts, and 550-40 is a selection descended from 'Tanzawa'. Both 550-40 and 'Tanzawa' have a pellicle that is difficult to peel. Among 59 offspring of a cross of 550-40 x 'Tanzawa', 12 had an easy-peeling pellicle and 47 had a difficult-peeling pellicle; this ratio is not significantly different from the 1:3 expected ratio for monogenic inheritance based on a chi-square test at P= 0.05. A haif-diallel cross without selfings was made among 'Porotan', 'Tanzawa', and 'Tsukuba'. All the offspring from 'Tanzawa' x 'Tsukuba' and from 'Tsukuba' x 'Porotan' had a difficult-peeling pellicle; in contrast, 39 offspring from 'Tanzawa' x 'Porotan' segregated in a ratio of 19 difficult-peeling pellicle to 20 easy-peeling pellicle, which is not significantly different from the expected I:1 ratio for monogenic segregation based on a chi-square test at P = 0.05. These results suggest that the easy-peeling pellicle trait of 'Porotan' is controlled by a major recessive gene at a single locus. We designated the pellicle peelability locus as P/p. According to this model, the 'Tsukuba' genotype is homozygous-dominant (PP), the 'Tanzawa' genotype is heterozygous (Pp), and the 'Porotan' genotype is homozygous-recessive (pp). [ABSTRACT FROM AUTHOR]

Abstract: Plant height, a vigor trait, in 1-year-old seedlings made from Japanese pear (Pyrus pyrifolia) cultivars/selections was measured using 994 individuals from 29 families. The family mean of plant height was negatively correlated (r =−0.72**) to the inbreeding coefficients (F). The regression of the family mean (Fm) on the F value (Fm=130−104F) showed that inbreeding depressions were 8%, 20%, and 40% for F =0.1, 0.25, and 0.5, respectively. According to the regression, the family mean at F =0 was estimated at 130cm. These results showed that the vigor was greatly influenced by inbreeding in Japanese pear. Within-family variances, the genetic segregation of offspring in a family, differed according to family. The proportions of offspring with plant height above 130cm (estimated Fm for F =0) were extremely low, i.e., 0–17% for 0.5≤ F <0.60 and 0–8% for F =0.75. [Copyright &y& Elsevier]

• 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]

• 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 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]