Xiongwei Li

Whole-Genome Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm.

Peach was domesticated in China more than four millennia ago and from there it spread world-wide. Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collection of parental lines (founders). This is one reason for the observed low levels of variability of the commercial gene pool, implying that knowledge of the extent and distribution of genetic variability in peach is critical to allow the choice of adequate parents to confer enhanced productivity, adaptation and quality to improved varieties. With this aim we genotyped 1,580 peach accessions (including a few closely related Prunus species) maintained and phenotyped in five germplasm collections (four European and one Chinese) with the International Peach SNP Consortium 9K SNP peach array. The study of population structure revealed the subdivision of the panel in three main populations, one mainly made up of Occidental varieties from breeding programs (POP1OCB), one of Occidental landraces (POP2OCT) and the third of Oriental accessions (POP3OR). Analysis of linkage disequilibrium (LD) identified differential patterns of genome-wide LD blocks in each of the populations. Phenotypic data for seven monogenic traits were integrated in a genome-wide association study (GWAS). The significantly associated SNPs were always in the regions predicted by linkage analysis, forming haplotypes of markers. These diagnostic haplotypes could be used for marker-assisted selection (MAS) in modern breeding programs.

Development of simple sequence repeat (SSR) markers from a genome survey of Chinese bayberry (Myrica rubra).

BackgroundChinese bayberry (Myrica rubra Sieb. and Zucc.) is a subtropical evergreen tree originating in China. It has been cultivated in southern China for several thousand years, and annual production has reached 1.1 million tons. The taste and high level of health promoting characters identified in the fruit in recent years has stimulated its extension in China and introduction to Australia. A limited number of co-dominant markers have been developed and applied in genetic diversity and identity studies. Here we report, for the first time, a survey of whole genome shotgun data to develop a large number of simple sequence repeat (SSR) markers to analyse the genetic diversity of the common cultivated Chinese bayberry and the relationship with three other Myrica species.ResultsThe whole genome shotgun survey of Chinese bayberry produced 9.01Gb of sequence data, about 26x coverage of the estimated genome size of 323 Mb. The genome sequences were highly heterozygous, but with little duplication. From the initial assembled scaffold covering 255 Mb sequence data, 28,602 SSRs (≥5 repeats) were identified. Dinucleotide was the most common repeat motif with a frequency of 84.73%, followed by 13.78% trinucleotide, 1.34% tetranucleotide, 0.12% pentanucleotide and 0.04% hexanucleotide. From 600 primer pairs, 186 polymorphic SSRs were developed. Of these, 158 were used to screen 29 Chinese bayberry accessions and three other Myrica species: 91.14%, 89.87% and 46.84% SSRs could be used in Myrica adenophora, Myrica nana and Myrica cerifera, respectively. The UPGMA dendrogram tree showed that cultivated Myrica rubra is closely related to Myrica adenophora and Myrica nana, originating in southwest China, and very distantly related to Myrica cerifera, originating in America. These markers can be used in the construction of a linkage map and for genetic diversity studies in Myrica species.ConclusionMyrica rubra has a small genome of about 323 Mb with a high level of heterozygosity. A large number of SSRs were identified, and 158 polymorphic SSR markers developed, 91% of which can be transferred to other Myrica species.

Identification of volatile and softening-related genes using digital gene expression profiles in melting peach

To reveal the comprehensive mechanism which is associated with the biosynthesis of volatile compounds and the accompanying texture change, RNA-seq was employed to survey the differentially expressed genes (DEGs), at the transcriptional level, of one cultivar at three stages of ripening and of four melting peach cultivars at harvest stage. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that highly ranked genes are involved in “Ribosome” and “Plant-pathogen interaction,” “Flavonoid biosynthesis,” “Linoleic acid metabolism,” and “Flavone and flavonol biosynthesis” during the fruit-ripening process. The quantitative real-time PCR (qRT-PCR) validation with 15 aroma and softening-related genes showed high correlation with the RNA-seq results. Transcripts of a nonspecific lipid transfer protein (nsLTP, ppa013554) and an ATP-binding cassette transporter (ABC, ppa002351) increased from the early ripening stage to the commercial harvest stage and then declined in the fully ripening stage. The highest transcript abundance was in the aroma-enriched cv. “Hu Jing Mi Lu” (HJ) and lowest in the cv. “Zhong Hua Shou Tao” with slight aroma. Fifty gene families related to the formation of aroma compounds were found. For peach lactone biosynthesis, we inferred that ppa002510 and ppa002282 may be the two important acyl-CoA oxidase genes correlating with the difference in γ-decalactone concentrations among the four cultivars. The expression of one 3-hydroxyacyl-CoA dehydrogenase gene (HCAD, ppa008854) was upregulated during ripening. Thirteen gene families were associated to fruit softening. Four aquaporin (AQP) genes showed cultivar-specificity for HJ, and one of them, ppa009506, reached maximum accumulation of transcripts at harvest stage. The batch of novel genes (nsLTP, ACX, AOC, ABC, HCAD, AQP) found here facilitates understanding of the molecular mechanism of melting peach aroma biosynthesis and fruit softening.

The PpLTP1 Primary Allergen Gene is Highly Conserved in Peach and Has Small Variations in Other Prunus Species

Peach lipid transfer protein (LTP1), Pru p 3.01, is a major allergen causing severe systemic reactions in peach allergic patients in Mediterranean countries and China. Significant expression variability has been reported among peach cultivars at both transcript and protein level. In this study, the allele diversity of the LTP1-encoding gene was assessed in a large set of peach cultivars by direct sequencing of the gene and its upstream region. Evolution of the LTP1-encoding genes in peach (Prunus persica) and three other Prunus species (Prunus kansuensis, Prunus mira, and Prunus davidiana) were also inferred. Sequence analysis revealed that LTP1-encoding genes are highly conserved among peach cultivars and wild peach. Three different allele sequences were obtained from 50 Prunus accessions on the basis of the upstream region of the LTP1-encoding gene and three allele specific markers were derived according to the polymorphic sites. These markers were used to test 316 peach cultivars, most of which clustered within the three main subpopulations of peach, ‘Yu Lu’, ‘Hakuho’ and landraces. The genotypic frequencies and allele frequencies in the oriental peach cultivars in these subpopulations except for ‘Yu Lu’ were found to be in Hardy-Weinberg equilibrium (P < 0.05). The dominant alleles were upLTP1-a in the ‘Yu Lu’ subpopulation and upLTP1-c in the ‘Hakuho’ subpopulation, allele upLTP1-b and allele upLTP1-c had the highest rates in the landraces, and the dominant allele in the three peach wild relatives was allele upLTP1-b. Furthermore, we found many light-responsive elements in the upstream region. Most of the polymorphic sites in Prunus species are located in the intron region. Phylogenetic analysis suggests that Prunus kansuensis KC311794 and Prunus mira KC311791 are related more closely to Prunus persica KC311795 than to Prunus davidiana KC311792 and KC311793. The allele sequences we derived on the basis of this variability were distributed unevenly, indicating the need to study allergenicity in different subpopulations and the association between allele sequences and allergenicity.