Assessment of Genetic Diversity of Chinese Sand Pear Landraces (Pyrus pyrifolia Nakai) Using Simple Sequence Repeat Markers

Jiang, Zhengwang; Tang, Feiyan; Huang, Hongwen; Hu, Hongju; Chen, Qiliang

doi:10.21273/hortsci.44.3.619

Cited by 17 publications

(9 citation statements)

References 28 publications

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“…The AMOVA carried out with all loci showed that most of the existing variability was within groups (97%) rather than among groups (Table S8 ), which is in agreement with many outbreeding species and similar studies in pear (Jiang et al, 2009 ; Miranda et al, 2010 ; Wolko et al, 2015 ; Wuyun et al, 2015 ). Nonetheless, differences among the 4 groups (CV, LV, RS, and UA) were found in terms of the effective number of alleles and levels of heterozygosity.…”

Section: Resultssupporting

confidence: 86%

Characterization and Phylogenetic Analysis of Ancient Italian Landraces of Pear

et al. 2017

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Pear is one of the oldest fruit tree crops and the third most important temperate fruit species. Its domestication took place independently in the Far East (China) and in the Caucasus region. While the origin of Eastern Asian cultivars is clear, that of European cultivars is still in doubt. Italy has a wealth of local varieties and genetic resources safeguarded by several public and private collections to face the erosion caused by the introduction of improved varieties in specialized orchards. The objectives of the present study were: (i) to characterize the existing germplasm through nuclear (SSR) and (ii) to clarify the genetic divergence between local and cultivated populations through chloroplast DNA (cpDNA) markers in order to provide insights into phylogenetic relationships of Pyrus spp. For this reason, 95 entries from five different germplasm collections, including nine European, Mediterranean and Eastern Asian species, were analyzed, and the intergenic accD-psaI sequences were compared to the worldwide distributed dataset encompassing a total of 298 sequences from 26 different Pyrus species. The nine nuclear SSRs were able to identify a total of 179 alleles, with a loci polymorphism P = 0.89. Most of the variation (97%) was found within groups. Five accessions from different sources were confirmed to be the same. Eight out of 20 accessions of unknown origin were identified, and six synonyms were detected. Locus NH030a was found to be monomorphic in all the cultivated accessions and in reference species interfertile with P. communis, leading to hypothesize selection pressures for adaptation to cultivation. The cpDNA sequences of the 95 accessions were represented by 14 haplotypes, six of which (derived from P. communis, P. cossonii and P. ussuriensis) are recorded here for the first time and may suggest the ancient origin of some local varieties. The network analysis of the 298 cpDNA sequences allowed two different haplogroups, Eastern and Western Eurasia, to be defined, supporting recent views of a clear division between Occidental and Oriental species. By combining the results from nuclear and uniparental markers, it was possible to better define many unknown accessions.

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Section: Resultssupporting

confidence: 86%

Characterization and Phylogenetic Analysis of Ancient Italian Landraces of Pear

et al. 2017

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“…The history of pear breeding before the early modern period in Japan is still unclear, but some local cultivars may have been domesticated from Chinese materials. Jiang et al [ 42 ] suggested that there were opportunities for ancient cultivar exchange between Japan and eastern China. Thus, the “yellow” genetic background might have been introduced by genetic exchange with Chinese cultivars.…”

Section: Discussionmentioning

confidence: 99%

Estimation of loss of genetic diversity in modern Japanese cultivars by comparison of diverse genetic resources in Asian pear (Pyrus spp.)

et al. 2016

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BackgroundPears (Pyrus spp.) are one of the most important fruit crops in temperate regions. Japanese pear breeding has been carried out for over 100 years, working to release new cultivars that have good fruit quality and other desirable traits. Local cultivar ‘Nijisseiki’ and its relatives, which have excellent fruit texture, have been repeatedly used as parents in the breeding program. This strategy has led to inbreeding within recent cultivars and selections. To avoid inbreeding depression, we need to clarify the degree of inbreeding among crossbred cultivars and to introgress genetic resources that are genetically different from modern cultivars and selections. The objective of the present study was to clarify the genetic relatedness between modern Japanese pear cultivars and diverse Asian pear genetic resources.ResultsWe genotyped 207 diverse accessions by using 19 simple sequence repeat (SSR) markers. The heterozygosity and allelic richness of modern cultivars was obviously decreased compared with that of wild individuals, Chinese pear cultivars, and local cultivars. In analyses using Structure software, the 207 accessions were classified into four clusters (K = 4): one consisting primarily of wild individuals, one of Chinese pear cultivars, one of local cultivars from outside the Kanto region, and one containing both local cultivars from the Kanto region and crossbred cultivars. The results of principal coordinate analysis (PCoA) were similar to those from the Structure analysis. Wild individuals and Chinese pears appeared to be distinct from other groups, and crossbred cultivars became closer to ‘Nijisseiki’ as the year of release became more recent.ConclusionsBoth Structure and PCoA results suggest that the modern Japanese pear cultivars are genetically close to local cultivars that originated in the Kanto region, and that the genotypes of the modern cultivars were markedly biased toward ‘Nijisseiki’. Introgression of germplasm from Chinese pear and wild individuals that are genetically different from modern cultivars seems to be key to broadening the genetic diversity of Japanese pear. The information obtained in this study will be useful for pear breeders and other fruit breeders who have observed inbreeding depression.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0380-7) contains supplementary material, which is available to authorized users.

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“…Among the three species, P. pyrifolia is presumed to have been introduced into Japan prehistorically and became the major species in Japan [5]. Previous reports suggested that there were opportunities for ancient cultivar exchange between Japan and eastern China [6,7], but the varieties currently cultivated in Japan and China are genetically different from each other, suggesting that they have different breeding histories. In Japan, local cultivar 'Nijisseiki' has been one of the leading cultivars, and 'Nijisseiki' and its relatives have been repeatedly used as parents in breeding programs, suggesting that recent cultivars are de cient in genetic diversity [7].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide Association Study of Individual Sugar Content and Sugar Conversion in Fruit of Japanese Pear (Pyrus spp.)

Nishio

Hayashi

Shirasawa

et al. 2021

Preprint

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Background: Sweetness is one of the most important traits determining fruit quality. Sweetness is controlled not only by the total sugar content but also by the contents of individual sugars. The major sugars in mature Rosaceae fruits are sucrose, fructose, glucose, and sorbitol, which have different levels of sweetness. Among these, sucrose and fructose have high sweetness, whereas glucose and sorbitol have low sweetness. The objective of this study was to identify the quantitative trait loci (QTLs) associated with fruit traits including individual sugar accumulation and conversion, 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) genotyped by double-digest restriction-site associated DNA sequencing (ddRAD-Seq). By implementing a mixed linear model and a Bayesian multiple-QTL model in GWAS, 56 SNPs associated with fruit traits were identified. Four loci were presumed to be associated with sugar conversion because the SNPs were significant for more than one individual sugar and the individual sugar contents associated with each SNP genotype were negatively correlated. 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 sugar conversion. We used ‘Golden Delicious’ doubled haploid (GDDH) 13, 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 which might play a role in the phenotypes observed.Conclusions: SNPs associated with sugar accumulation and conversion were newly identified at several loci, and candidate genes underlying QTLs were inferred using advanced apple genome information. Several QTLs showed clear effects with more than 10% of phenotypic variance explained by those SNPs in the breeding populations. By combining the effects of multiple QTLs, breeders would be able to select seedlings that will later bear fruit with high sucrose and fructose content.

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Assessment of Genetic Diversity of Chinese Sand Pear Landraces (Pyrus pyrifolia Nakai) Using Simple Sequence Repeat Markers

Cited by 17 publications

References 28 publications

Characterization and Phylogenetic Analysis of Ancient Italian Landraces of Pear

Characterization and Phylogenetic Analysis of Ancient Italian Landraces of Pear

Estimation of loss of genetic diversity in modern Japanese cultivars by comparison of diverse genetic resources in Asian pear (Pyrus spp.)

Genome-wide Association Study of Individual Sugar Content and Sugar Conversion in Fruit of Japanese Pear (Pyrus spp.)

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