| Pear(Pyrus;2n=34),the third most important temperate fruit crop,hold a wide germplasm resource and widely distribution.Pear mainly includes wild accessions,landrace accessions,and improved accessions from Asian and European pear.Currently,most of cultivars belong to landrace accessions,and has serious quality defects,such as high stone cell content,bad flavor,weak aroma,heavy diseases and insect peats,short maturity,and big difference of fruit size.Therefore,it is urgent to improve and breed new excellent cultivars.Recently,the release of pear genome,re-sequencing,and multiple OMICS data make the molecular assisted breeding based on the big data possible in pear.Here,we explored the genetic basis of pear domestication and improvement in the transcriptome level,and identified candidate genes associated with important agronomic traits.This work laid a solid foundation for molecular breeding and improvement of pear.Meanwhile,based on the re-sequencing,we developed a pear 200K SNP genotyping array to apply for quickly and accurately genotyping of Pyrus species,thus promote the process of molecular breeding in pear.The main results were as follows:1.We compared representative sets of 14 wild accessions,12 landrace accessions,and 15 improved accessions of pear(P.pyrifolia)to gain insight into domestication and improvement with RNA-seq.Results showed that a close population relationships and similar nucleotide diversity level was observed between the wild and landrace groups,whereas the improved group had substantially reduced nucleotide diversity.Based on two comparisons of wild vs.landrace accessions(domestication process)and landrace and improved accessions(improvement process),a total of 11.13 Mb of genome sequence was identified to bear the signature of selective sweeps that occurred during pear domestication,while a distinct and smaller set of genomic regions(4.04 Mb)were identified as being associated with subsequent improvement efforts.The expression diversity of genes from the selective sweep regions exhibited a 20.89%reduction from the wild group to the landrace group,but a 23.13%recovery was observed from the landrace to the improved group,showing distinct different pattern with variation of sequence diversity.Further,a transcriptomic analysis of three key developmental stages of pear fruit was performed.Approximately 2,900 genes were differentially expressed between wild and cultivated pears during fruit development.These genes were inputted into module-trait association analysis to identify candidate genes associated with important fruit quality traits.Results showed that a total of 16 distinct coexpression modules were identified,and 6 modules were highly associated with important fruit traits.The candidate trait-linked differentially expressed genes(DEGs)associated with stone cells,fruit size,and sugar content were identified in the selected regions,and many of these could also be mapped to the previously reported quantitative trait loci(QTL).Thus,our study reveals the specific pattern of domestication and improvement of perennial trees at the transcriptome level,and provides valuable genes source of fruit trait contribute to pear breeding and improvement.2.We performed a whole genome-wide identification,structure and evolution analyses for MYB and ERF gene families,and predicted gene functions in each group from phylogenetic tree.In our study,a total of 231 MYB and 155 ERF candidate genes were captured.Compared with MYB and ERF genes identified from Arabidopsis.which hold known functions,all MYB and ERF genes were grouped and predicted their functions in pear.In MYB gene family,we used transcriptome of different developmental stages of pear fruit and qRT-PCR experiment to doubly verify genes in the C1 group,which was predicted to involve in lignin synthesis.Results strongly supported our hypothesis of C1 group involved in lignin synthesis,thus,it also further verify the reliability of function predictions in other groups.Similarly,we used transcriptome of wild and cultivated pear fruit,transcriptome data of pear seedlings subjected to dehydration treatment,and qRT-PCR experiment to multiply validate 7 genes in the Ⅲ group,which was predicted to respond stresses.Results strongly supported our hypothesis that 4 of the 7 genes responded to drought conditions.3.We present here 200K AXIOM(?)PyrSNP,a large-scale single nucleotide polymorphism(SNP)genotyping array to facilitate genotyping of Pyrus species.A diverse panel of 113 re-sequenced pear genotypes was used to discover SNPs to promote increased adoption of the array.A set of 188 diverse accessions and an F1 population of 98 individuals from ’Cuiguan’ × ’Starkrimson’ were genotyped with the array to assess its effectiveness.A large majority of SNPs(166,335 or 83%)are of high quality.The high density and uniform distribution of the array SNPs facilitated prediction of centromeric regions on 17 pear chromosomes,and significantly improved the genome assembly from 75.5%to 81.4%based on genetic mapping.Identification of a gene associated with flowering time and candidate genes linked to size of fruit core via GWAS showed the usefulness of the array in pear genetic research.The newly developed high-density SNP array presents an important tool for rapid and high-throughput genotyping in pear for genetic map construction,QTL identification and genomic selection. |
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