Dataset Information

Marker-trait associations and genomic predictions of interspecific pear (Pyrus) fruit characteristics.

ABSTRACT: Interspecific pear (Pyrus spp.) hybrid populations are often used to develop novel cultivars. Pear cultivar breeding is a lengthy process because of long juvenility and the subsequent time required for reliable fruit phenotyping. Molecular techniques such as genome-wide association (GWA) and genomic selection (GS) provide an opportunity to fast-forward the development of high-value cultivars. We evaluated the genetic architecture of 10 pear fruit phenotypes (including sensory traits) and the potential of GS using genotyping-by-sequencing of 550 hybrid seedlings from nine interrelated full-sib families. Results from GWA suggested a complex polygenic nature of all 10 traits as the maximum variance explained by each marker was less than 4% of the phenotypic variance. The effect-size of SNPs for each trait suggested many genes of small effect and few of moderate effect. Some genomic regions associated with pear sensory traits were similar to those reported for apple - possibly a result of high synteny between the apple and pear genomes. The average (across nine families) GS accuracy varied from 0.32 (for crispness) to 0.62 (for sweetness), with an across-trait average of 0.42. Further efforts are needed to develop larger genotype-phenotype datasets in order to predict fruit phenotypes of untested seedlings with sufficient efficiency.

SUBMITTER: Kumar S

PROVIDER: S-EPMC6588632 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

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Marker-trait associations and genomic predictions of interspecific pear (Pyrus) fruit characteristics.

Kumar Satish S Kirk Chris C Deng Cecilia Hong CH Shirtliff Angela A Wiedow Claudia C Qin Mengfan M Wu Jun J Brewer Lester L

Scientific reports 20190621 1

Interspecific pear (Pyrus spp.) hybrid populations are often used to develop novel cultivars. Pear cultivar breeding is a lengthy process because of long juvenility and the subsequent time required for reliable fruit phenotyping. Molecular techniques such as genome-wide association (GWA) and genomic selection (GS) provide an opportunity to fast-forward the development of high-value cultivars. We evaluated the genetic architecture of 10 pear fruit phenotypes (including sensory traits) and the pot ...[more]

PMID: 31227781

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Project description:Although pear is an important edible fruit species, the current available genomic information is limited. Combining the Solexa/ Illumina RNA-seq high-throughput sequencing approach with Digital Gene Expression (DGE) analysis results in a powerful transcriptomic study. This publication reports the transcriptome profiling analysis of Pyrus bretschneideri Rehd. using RNA-seq and DGE in order to better understand the molecular mechanisms underlying biological aspects of pear, especially fruit development and maturation.Using high-throughput Illumina RNA-seq combined with a tag-based Digital Gene Expression (DGE) system, de novo transcriptome assembly and gene expression analysis of P. bretschneideri were performed at an unprecedented depth (5.47 gigabase pairs). Approximately 60.77 million reads were obtained, trimmed, and assembled into 90,227 unigenes. The unigenes comprised 17,619 contig clusters and 72,608 singletons and were an average length of 508 bp and had an N50 of 635 bp. Sequence similarity analyses against six public databases (Uniprot, NR and COGs at NCBI, Pfam, InterPro and KEGG) found 61,636 unigenes that could be annotated with gene descriptions, conserved protein domains, or gene ontology terms. 34.6% of the unigenes (31,215) were annotated against KEGG into 121 known metabolic or signaling pathways. DGE libraries of five different developmental fruit stages were constructed and analyzed, and the gene expression variations between two consecutive stages were compared. Thousands of genes showed significantly different expression levels based on the various comparisons. Extensive transcriptome and DGE profiling data have been obtained from the deep sequencing of the Chinese white pear, which can serve as an important public information platform for gene expression, genomic, and functional genomic studies in P. bretschneideri and which provides comprehensive gene expression information at the transcriptional level that could facilitate understanding of the molecular mechanisms in fruit development and maturation.

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Project description:BackgroundUnderstanding 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.ResultsWe 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.ConclusionsSNPs 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.

Dataset Information

Marker-trait associations and genomic predictions of interspecific pear (Pyrus) fruit characteristics.

Publications

Marker-trait associations and genomic predictions of interspecific pear (Pyrus) fruit characteristics.

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