Gengrui Zhu

Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops

BackgroundRecently, many studies utilizing next generation sequencing have investigated plant evolution and domestication in annual crops. Peach, Prunus persica, is a typical perennial fruit crop that has ornamental and edible varieties. Unlike other fruit crops, cultivated peach includes a large number of phenotypes but few polymorphisms. In this study, we explore the genetic basis of domestication in peach and the influence of humans on its evolution.ResultsWe perform large-scale resequencing of 10 wild and 74 cultivated peach varieties, including 9 ornamental, 23 breeding, and 42 landrace lines. We identify 4.6 million SNPs, a large number of which could explain the phenotypic variation in cultivated peach. Population analysis shows a single domestication event, the speciation of P. persica from wild peach. Ornamental and edible peach both belong to P. persica, along with another geographically separated subgroup, Prunus ferganensis.We identify 147 and 262 genes under edible and ornamental selection, respectively. Some of these genes are associated with important biological features. We perform a population heterozygosity analysis in different plants that indicates that free recombination effects could affect domestication history. By applying artificial selection during the domestication of the peach and facilitating its asexual propagation, humans have caused a sharp decline of the heterozygote ratio of SNPs.ConclusionsOur analyses enhance our knowledge of the domestication history of perennial fruit crops, and the dataset we generated could be useful for future research on comparative population genomics.

Genome-wide association study of 12 agronomic traits in peach

Peach (Prunus persica L.) is a highly valuable crop species and is recognized by molecular researchers as a model fruit for the Rosaceae family. Using whole-genome sequencing data generated from 129 peach accessions, here we perform a comprehensive genome-wide association study for 12 key agronomic traits. We show that among the 10 qualitative traits investigated, nine exhibit consistent and more precise association signals than previously identified by linkage analysis. For two of the qualitative traits, we describe candidate genes, one potentially involved in cell death and another predicted to encode an auxin-efflux carrier, that are highly associated with fruit shape and non-acidity, respectively. Furthermore, we find that several genomic regions harbouring association signals for fruit weight and soluble solid content overlapped with predicted selective sweeps that occurred during peach domestication and improvement. Our findings contribute to the large-scale characterization of genes controlling agronomic traits in peach.

Comparative Transcriptome and Microscopy Analyses Provide Insights into Flat Shape Formation in Peach (Prunus persica)

Fruit shape is an important external characteristic that consumers use to select preferred fruit cultivars. In peach, the flat fruit cultivars have become more and more popular worldwide. Genetic markers closely linking to the flat fruit trait have been identified and are useful for marker-assisted breeding. However, the cellular and genetic mechanisms underpinning flat fruit formation are still poorly understood. In this study, we have revealed the differences in fruit cell number, cell size, and in gene expression pattern between the traditional round fruit and modern flat fruit cultivars. Flat peach cultivars possessed significantly lower number of cells in the vertical axis because cell division in the vertical direction stopped early in the flat fruit cultivars at 15 DAFB (day after full bloom) than in round fruit cultivars at 35 DAFB. This resulted in the reduction in vertical development in the flat fruit. Significant linear relationship was observed between fruit vertical diameter and cell number in vertical axis for the four examined peach cultivars (R2 = 0.9964) at maturation stage, and was also observed between fruit vertical diameter and fruit weight (R2 = 0.9605), which indicated that cell number in vertical direction contributed to the flat shape formation. Furthermore, in RNA-seq analysis, 4165 differentially expressed genes (DEGs) were detected by comparing RNA-seq data between flat and round peach cultivars at different fruit development stages. In contrast to previous studies, we discovered 28 candidate genes potentially responsible for the flat shape formation, including 19 located in the mapping site and 9 downstream genes. Our study indicates that flat and round fruit shape in peach is primarily determined by the regulation of cell production in the vertical direction during early fruit development.

Accumulated chilling hours during endodormancy impact blooming and fruit shape development in peach （Prunus persica L.）

Winter chill is essential for the growth and development of deciduous species. To understand the relationship between accumulated chilling hours during endodormancy and blooming and fruit shape development, we controlled chilling hours and investigated their effects on blooming date and fruit shape of peaches. The results showed that the number of days to full bloom date and the heat requirement for blooming were negatively correlated with accumulated chilling hours. Accumulated chilling hours were significantly negatively correlated with fruit shape index and fruit tip lengths, suggesting that the number of chilling hours affect the fruit shape development. Fewer accumulated chilling hours may be the major reason for longer fruit shape and protruding fruit tips. In conclusion, our results indicate specifically that decreased winter chilling hours can delay the bloom date and may lead to aberrant fruit shape development in peaches. Our study provides preliminary insights into the response of temperate fruit species to global climate change.

The Evaluation Criteria of Some Botanical Quantitative Characters of Peach Genetic Resources

There were two peach descriptors systems: one from IPRGI in 1980 and the other from China in 1990. The former had only reference cultivars without quantity grades; the latter had only a list of some characteristics. This makes it difficult sharing of genetic resource information for breeders. To describe the main quantitative characteristics, a new system was established. Ten characteristics of 346-476 peach cultivars were investigated from 1986 to 2002 in the National Peach Genetic Collection in Zhengzhou City, China. These characteristics and their coefficients of variation were as follows: flower diameter 19.55%, vertical diameter of fruit 14.24%, cheek diameter of fruit 10.36%, suture diameter of fruit 11.44%, stone length 19.04%, stone width 10.86%, stone thickness 11.19%, leaf length 7.9%, leaf width 10.55%, and leaf stalk length 19.03%, respectively. Grade index and reference cultivars were given by statistical data for peach description. These grade indexes were recorded on 1-5 grades, and the third grade as a middle one occupied 39% or more of the distribution. In general, two reference cultivars for each grade were chosen, one is USA cultivar and the other is Chinese cultivar. This paper tried to use them as the reference cultivars, which are planted or used widely by Chinese breeders.