RNA-Seq analysis unveils gene regulation of fruit size cooperatively determined by velocity and duration of fruit swelling in peach.

Fruit swelling determines fruit size and usually occurs in two distinct time periods in peach. However, little is known about the gene regulation of fruit swelling. In this study, measurements of longitudinal and transverse diameters in developing and ripening peach fruits unveiled two periods of fruit swelling: the first swelling ends at approximately 65 days after flower blooming (DAFB) and the second swelling starts at approximately 75 DAFB. Comparisons of diameters sizes and development periods among cultivars and accessions revealed a cooperative regulation of swelling velocity and swelling duration, which leads to final determination of fruit size. Furthermore, RNA-sequencing was conducted for fruits at the initial swelling, non-swelling interval between the two swellings (hereafter, 'the interval'), second swelling and ripening stages. A total of 110 and 128 differentially expressed genes were screened from fruits in the first and second swelling, respectively. Besides, the nine most differentially expressed genes located within the reported quantitative trait locations (QTLs) of fruit size in peach were detected in both the first and second swelling stages. Those genes have been reported to be involved in mediating cell size, which indicates the occurrence of both cell proliferation and cell expansion in each of the two major periods of fruit swelling. In addition, a potential gene regulation network is proposed herein and could be used to elucidate the molecular mechanism of peach fruit swellings mediated by multiple key genes.

Peach genetic resources: diversity, population structure and linkage disequilibrium.

BACKGROUND: Peach (Prunus persica (L.) Batsch) is one of the most important model fruits in the Rosaceae family. Native to the west of China, where peach has been domesticated for more than 4,000 years, its cultivation spread from China to Persia, Mediterranean countries and to America. Chinese peach has had a major impact on international peach breeding programs due to its high genetic diversity. In this research, we used 48 highly polymorphic SSRs, distributed over the peach genome, to investigate the difference in genetic diversity, and linkage disequilibrium (LD) among Chinese cultivars, and North American and European cultivars, and the evolution of current peach cultivars. RESULTS: In total, 588 alleles were obtained with 48 SSRs on 653 peach accessions, giving an average of 12.25 alleles per locus. In general, the average value of observed heterozygosity (0.47) was lower than the expected heterozygosity (0.60). The separate analysis of groups of accessions according to their origin or reproductive strategies showed greater variability in Oriental cultivars, mainly due to the high level of heterozygosity in Chinese landraces. Genetic distance analysis clustered the cultivars into two main groups: one included four wild related Prunus, and the other included most of the Oriental and Occidental landraces and breeding cultivars. STRUCTURE analysis assigned 469 accessions to three subpopulations: Oriental (234), Occidental (174), and Landraces (61). Nested STRUCTURE analysis divided the Oriental subpopulation into two different subpopulations: 'Yu Lu' and 'Hakuho'. The Occidental breeding subpopulation was also subdivided into nectarine and peach subpopulations. Linkage disequilibrium (LD) analysis in each of these subpopulations showed that the percentage of linked (r2 > 0.1) intra-chromosome comparisons ranged between 14% and 47%. LD decayed faster in Oriental (1,196 Kbp) than in Occidental (2,687 Kbp) samples. In the 'Yu Lu' subpopulation there was considerable LD extension while no variation of LD with physical distance was observed in the landraces. From the first STRUCTURE result, LG1 had the greatest proportion of alleles in LD within all three subpopulations. CONCLUSIONS: Our study demonstrates a high level of genetic diversity and relatively fast decay of LD in the Oriental peach breeding program. Inclusion of Chinese landraces will have a greater effect on increasing genetic diversity in Occidental breeding programs. Fingerprinting with genotype data for all 658 cultivars will be used for accession management in different germplasms. A higher density of markers are needed for association mapping in Oriental germplasm due to the low extension of LD. Population structure and evaluation of LD provides valuable information for GWAS experiment design in peach.

Safety profile evaluation of different herbicides used on peach rootstock seedlings.

To screen out suitable herbicides for peach nurseries, we treated the potted seedlings of the peach rootstock 'Nemaguard' with eleven herbicides under recommended doses to investigate the changes of physiological indices and comprehensively evaluate the safety of different herbicides using principal component analysis (PCA). The results showed that soil application of quizalofop-p exhibited no detectable phytotoxicity on rootstock seedlings, while the remaining herbicides generated multiple symptoms, including green loss, wilting, spot, and withering. Starane caused rapid wilting and death, with a 100.0% phytotoxicity index (PI). Soil application of n-(phosphonomethyl)glycine, glufosinate-ammonium, acetochlor, and MCPA-Na showed a PI＞65.0%. As compared with the control, all herbicides inhibited leaf area growth to varying degrees, with a 10.0%-56.2% and 5.8%-44.4% reduction in young leaf area and mature leaf area, respectively. All herbicides, except quizalofop-p, increased the electrolyte permeability of leaf and root tip cells by 21.2%-145.0% and 36.9%-291.4%, respectively, and significantly inhibited root growth. The total root length, root surface area, root volume, and the number of root tips significantly decreased by 37.3%-75.3%, 35.7%-83.0%, 44.3%-89.9%, and 42.6%-73.7%, respectively. Although net photosynthetic rate (Pn) and transpiration rate (Tr) of leaves were not significantly affected by quizalofop-p, mesotrione-atrazine, MCPA-Na·bentazone, bensulfuron-methyl·quinclorac, and bensulfuron-methyl·acetochlor, there was significant reduction of 29.6%, 28.9%, 28.4% and 27.9% in Pn and 21.9%, 29.2%, 26.4%, and 19.7% in Tr post soil application of n-(phosphonomethyl)glycine, glufosinate-ammonium, acetochlor, and MCPA-Na. The overall safety ranking of the 11 examined herbicides is as follows: quizalofop-p>bensulfuron-methyl·acetochlor>bensulfuron-methyl·quinclorac>esotrione·atrazine> auizalofop-p·fluoroglycofen>acetochlor>MCPA-Na·bentazone>MCPA-Na>n-(phosphonomethyl)glycine>glufosinate-ammonium>sterane.

Gene regulation of anthocyanin biosynthesis in two blood-flesh peach (Prunus persica (L.) Batsch) cultivars during fruit development.

The blood-flesh peach has become popular in China due to its attractive anthocyanin-induced pigmentation and antioxidant properties. In this study, we investigated the molecular mechanisms underlying anthocyanin accumulation by examining the expression of nine genes of the anthocyanin biosynthesis pathway found in the peach mesocarp. Expression was measured at six developmental stages in fruit of two blood-flesh and one white-flesh peach cultivars, using quantitative reverse transcription polymerase chain reaction (qRT-PCR). Results show that the expression of the chalcone synthase (CHS) gene was closely related to anthocyanin accumulation in both of the blood-flesh peaches. In the white-flesh peach, we found that the transcription level of phenylalanine ammonia-lyase (PAL) during fruit development was much lower than that in the blood-flesh peach, even though all other genes of the anthocyanin biosynthesis pathway were highly expressed, suggesting that the PAL gene may be limiting in anthocyanin production in the white-flesh peach. Moreover, the transcription levels of the CHS and UDP-glucose-flavonoid 3-O-glucosyltransferase (UFGT) genes were markedly up-regulated at three days after bag removal (DABR) in the blood-flesh peach, suggesting that CHS and UFGT are the key genes in the process of anthocyanin biosynthesis for both of the blood-flesh peaches. The present study will be of great help in improving understanding of the molecular mechanisms involved in anthocyanin accumulation in blood-flesh peaches.