Dataset Information

Homozygosity Mapping Reveals Population History and Trait Architecture in Self-Incompatible Pear (Pyrus spp.).

ABSTRACT: Runs of homozygosity (ROH) have been widely used to study population history and trait architecture in humans and livestock species, but their application in self-incompatible plants has not been reported. The distributions of ROH in 199 accessions representing Asian pears (45), European pears (109), and interspecific hybrids (45) were investigated using genotyping-by-sequencing in this study. Fruit phenotypes including fruit weight, firmness, Brix, titratable acidity, and flavor volatiles were measured for genotype-phenotype analyses. The average number of ROH and the average total genomic length of ROH were 6 and 11 Mb, respectively, in Asian accessions, and 13 and 30 Mb, respectively, in European accessions. Significant associations between genomic inbreeding coefficients (F_ROH) and phenotypes were observed for 23 out of 32 traits analyzed. An overlap between ROH islands and significant markers from genome-wide association analyses was observed. Previously published quantitative trait loci for fruit traits and disease resistances also overlapped with some of the ROH islands. A prominent ROH island at the bottom of linkage group 17 overlapped with a recombination-supressed genomic region harboring the self-incompatibility locus. The observed ROH patterns suggested that systematic breeding of European pears would have started earlier than of Asian pears. Our research suggest that F_ROH would serve as a novel tool for managing inbreeding in gene-banks of self-incompatible plant species. ROH mapping provides a complementary strategy to unravel the genetic architecture of complex traits, and to evaluate differential selection in outbred plants. This seminal work would provide foundation for the ROH research in self-incompatible plants.

SUBMITTER: Kumar S

PROVIDER: S-EPMC7813798 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Homozygosity Mapping Reveals Population History and Trait Architecture in Self-Incompatible Pear (<i>Pyrus</i> spp.).

Kumar Satish S Deng Cecilia Hong CH Hunt Martin M Kirk Chris C Wiedow Claudia C Rowan Daryl D Wu Jun J Brewer Lester L

Frontiers in plant science 20210105

Runs of homozygosity (ROH) have been widely used to study population history and trait architecture in humans and livestock species, but their application in self-incompatible plants has not been reported. The distributions of ROH in 199 accessions representing Asian pears (45), European pears (109), and interspecific hybrids (45) were investigated using genotyping-by-sequencing in this study. Fruit phenotypes including fruit weight, firmness, Brix, titratable acidity, and flavor volatiles were ...[more]

PMID: 33469460

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Project description:The fruit skin types of pear (Pyrus spp.) are divided into russet, smooth, and intermediate. One of the important traits in pear breeding programs is russet on pear fruit skin because it affects the commercial value. In the present study, a high-density genetic linkage map of 'Whangkeumbae' (smooth) × 'Minibae' (russet) was constructed. In addition, quantitative trait loci (QTL) analysis was performed to identify russet related QTL and develop a cleaved amplified polymorphism sequence (CAPS) marker. Together with SNPs derived from Axiom Pear 70K Genotyping Array and genotyping-by-sequencing derived SNPs and SSRs generated in previous study, an integrated genetic linkage map of 'Whangkeumbae' × 'Minibae' was constructed. A total of 1263 markers were anchored in 17 linkage groups (LGs) with a total genetic distance of 1894.02 cM and an average marker density of 1.48 cM. The chromosome coverage of 'Whangkeumbae' × 'Minibae' map was improved because the SNPs derived from Axiom Pear 70K Genotyping Array were anchored. QTL analysis was performed using previous russet phenotype data evaluated with russet coverage and Hunter a. As a result of QTL analysis, russet coverage- and Hunter a-related QTLs were identified in LG8 of the 'Whangkeumbae' × 'Minibae' map, and SNPs located in the QTL region were heterozygous in the 'Minibae'. Although the russet coverage- and Hunter a-related QTLs were commonly detected in LG8, the logarithm of odds values of SNPs in the QTL region were higher in QTL related to russet coverage than to Hunter a. The CAPS marker (CBp08ca01) was developed using an array SNP located in the russet coverage related QTL, and the genotype of CBp08ca01 showed a 1:1 ratio in 'Whangkeumbae' × 'Minibae' (χ2 = 0.65, p > 0.05). 'Whangkeumbae' and 'Minibae' were thought to have rr and Rr genotypes, respectively, and the genetic factors controlling the russet formation might be located in chromosome 8. The CBp08ca01 was able to select F1 individuals with less than 30% russet coverage. Thus, it will be a useful tool for marker-assisted selection in pears.

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.

Project description:BackgroundGenomic analysis technologies can promote efficient fruit tree breeding. Genotyping by sequencing (GBS) enables generating efficient data for high-quality genetic map construction and QTL analysis in a relatively accessible way. Furthermore, High-resolution genetic map construction and accurate QTL detection can significantly narrow down the putative candidate genes associated with important plant traits.ResultsWe genotyped 162 offspring in the F1 'Spadona' x 'Harrow Sweet' pear population using GBS. An additional 21 pear accessions, including the F1 population's parents, from our germplasm collection were subjected to GBS to examine diverse genetic backgrounds that are associated to agriculturally relevant traits and to enhance the power of SNP calling. A standard SNP calling pipeline identified 206,971 SNPs with Asian pear ('Suli') as the reference genome and 148,622 SNPs with the European genome ('Bartlett'). These results enabled constructing a genetic map, after further stringent SNP filtering, consisting of 2036 markers on 17 linkage groups with a length of 1433 cM and an average marker interval of 0.7 cM. We aligned 1030 scaffolds covering a total size of 165.5 Mbp (29%) of the European pear genome to the 17 linkage groups. For high-resolution QTL analysis covering the whole genome, we used phenotyping for vegetative budbreak time in the F1 population. New QTLs associated to vegetative budbreak time were detected on linkage groups 5, 13 and 15. A major QTL on linkage group 8 and an additional QTL on linkage group 9 were confirmed. Due to the significant genotype-by-environment (GxE) effect, we were able to identify novel interaction QTLs on linkage groups 5, 8, 9 and 17. Phenotype-genotype association analysis in the pear accessions for main genotype effect was conducted to support the QTLs detected in the F1 population. Significant markers were detected on every linkage group to which main genotype effect QTLs were mapped.ConclusionsThis is the first vegetative budbreak study of European pear that makes use of high-resolution genetic mapping. These results provide tools for marker-assisted selection and accurate QTL analysis in pear, and specifically at vegetative budbreak, considering the significant GxE and phenotype-plasticity effects.

Dataset Information

Homozygosity Mapping Reveals Population History and Trait Architecture in Self-Incompatible Pear (Pyrus spp.).

Publications

Homozygosity Mapping Reveals Population History and Trait Architecture in Self-Incompatible Pear (<i>Pyrus</i> spp.).

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