Isolation and expression analysis of four HD-ZIP III family genes targeted by microRNA166 in peach.

MicroRNA166 (miR166) is known to have highly conserved targets that encode proteins of the class III homeodomain-leucine zipper (HD-ZIP III) family, in a broad range of plant species. To further understand the relationship between HD-ZIP III genes and miR166, four HD-ZIP III family genes (PpHB14, PpHB15, PpHB8, and PpREV) were isolated from peach (Prunus persica) tissue and characterized. Spatio-temporal expression profiles of the genes were analyzed. Genes of the peach HD-ZIP III family were predicted to encode five conserved domains. Deduced amino acid sequences and tertiary structures of the four peach HD-ZIP III genes were highly conserved, with corresponding genes in Arabidopsis thaliana. The expression level of four targets displayed the opposite trend to that of miR166 throughout fruit development, with the exception of PpHB14 from 35 to 55 days after full bloom (DAFB). This finding indicates that miR166 may negatively regulate its four targets throughout fruit development. As for leaf and phloem, the same trend in expression level was observed between four targets and miR166 from 75 to 105 DAFB. However, the opposite trend was observed for the transcript level between four targets and miR166 from 35 to 55 DAFB. miRNA166 may negatively regulate four targets in some but not all developmental stages for a given tissue. The four genes studied were observed to have, exactly or generally, the same change tendency as individual tissue development, a finding that suggests genes of the HD-ZIP III family in peach may have complementary or cooperative functions in various tissues.

Potassium contributes to zinc stress tolerance in peach (Prunus persica) seedlings by enhancing photosynthesis and the antioxidant defense system.

Zinc (Zn) is considered to be a major industrial pollutant because excessive amounts can impair plant growth. In this paper, we found that peach 'Yoshihime' seedlings are promising Zn tolerant plants. However, heavy Zn toxicity (2 mM) damaged plant performance by disrupting biochemical processes, including photosynthesis, proline production, and K(+) nutrition. Notably, elevated external K(+) supply (10 mM) alleviated peach seedlings from Zn toxicity, evidenced by enhanced photosynthesis, antioxidant defense systems, and plant K(+) nutritional status. Moreover, the transcript levels of KUP (K(+) uptake) genes involved in K(+) acquisition, transport, and homeostasis were significantly upregulated following supply of sufficient K(+) upon Zn toxicity. In general, K(+) favorably contributes to improvements in internal K(+) homeostasis, via the help of K(+) transporters, further protecting plant photosynthesis and the antioxidative defense system. Our findings further benefit the study of the mechanisms underpinning heavy metal tolerance in woody plants.

Diversity, population structure, and evolution of local peach cultivars in China identified by simple sequence repeats.

The fruit peach originated in China and has a history of domestication of more than 4000 years. Numerous local cultivars were selected during the long course of cultivation, and a great morphological diversity exists. To study the diversity and genetic background of local peach cultivars in China, a set of 158 accessions from different ecological regions, together with 27 modern varieties and 10 wild accessions, were evaluated using 49 simple sequence repeats (SSRs) covering the peach genome. Broad diversity was also observed in local cultivars at the SSR level. A total of 648 alleles were amplified with an average of 13.22 observed alleles per locus. The number of genotypes detected ranged from 9 (UDP96015) to 58 (BPPCT008) with an average of 27.00 genotypes per marker. Eight subpopulations divided by STRUCTURE basically coincided with the dendrogram of genetic relationships and could be explained by the traditional groups. The 8 subpopulations were juicy honey peach, southwestern peach I, wild peach, Buddha peach + southwestern peach II, northern peach, southern crisp peach, ornamental peach, and Prunus davidiana + P. kansuensis. Most modern varieties carried the genetic backgrounds of juicy honey peach and southwestern peach I, while others carried diverse genetic backgrounds, indicating that local cultivars were partly used in modern breeding programs. Based on the traditional evolution pathway, a modified pathway for the development of local peach cultivars in China was proposed using the genetic background of subpopulations that were identified by SSRs. Current status and prospects of utilization of Chinese local peach cultivars were also discussed according to the SSR information.

Genome-wide analysis and identification of KT/HAK/KUP potassium transporter gene family in peach (Prunus persica).

The KT/HAK/KUP family members encoding high-affinity potassium (K(+)) transporters mediate K(+) transport across the plasma membranes of plant cells to maintain plant normal growth and metabolic activities. In this paper, we identified 16 potassium transporter genes in the peach (Prunus persica) using the Hidden Markov model scanning strategy and searching the peach genome database. Utilizing the Arabidopsis KT/HAK/KUP family as a reference, phylogenetic analysis indicates that the KT/HAK/KUP family in the peach can be classified into 3 groups. Genomic localization indicated that 16 KT/HAK/KUP family genes were well distributed on 7 scaffolds. Gene structure analysis showed that the KT/HAK/KUP family genes have 6-9 introns. In addition, all of the KT/HAK/KUP family members were hydrophobic proteins; they exhibited similar secondary structure patterns and homologous tertiary structures. Putative cis-elements involved in abiotic stress adaption, Ca(2+) response, light and circadian rhythm regulation, and seed development were observed in the promoters of the KT/HAK/KUP family genes. Subcellular localization prediction indicated that the KT/HAK/KUP members were mainly located in the plasma membrane. Expression levels of the KT/HAK/ KUP family genes were much higher in the fruit and flower than those in the other 7 tissues examined, indicating that the KT/HAK/KUP family genes may have important roles in K(+) uptake and transport, which mainly contribute to flower formation and fruit development in the peach.

Genome-wide analysis of the homeodomain-leucine zipper (HD-ZIP) gene family in peach (Prunus persica).

In this study, 33 homeodomain-leucine zipper (HD-ZIP) genes were identified in peach using the HD-ZIP amino acid sequences of Arabidopsis thaliana as a probe. Based on the phylogenetic analysis and the individual gene or protein characteristics, the HD-ZIP gene family in peach can be classified into 4 subfamilies, HD-ZIP I, II, III, and IV, containing 14, 7, 4, and 8 members, respectively. The most closely related peach HD-ZIP members within the same subfamilies shared very similar gene structure in terms of either intron/exon numbers or lengths. Almost all members of the same subfamily shared common motif compositions, thereby implying that the HD-ZIP proteins within the same subfamily may have functional similarity. The 33 peach HD-ZIP genes were distributed across scaffolds 1 to 7. Although the primary structure varied among HD-ZIP family proteins, their tertiary structures were similar. The results from this study will be useful in selecting candidate genes from specific subfamilies for functional analysis.

Efficient identification of ornamental peach cultivars using RAPD markers with a manual cultivar identification diagram strategy.

One of the most important uses of DNA markers is cultivar identification. However, no DNA fingerprint analysis strategy is available for making DNA markers helpful in practical plant cultivar identification, especially for the identification of a large number of cultivars. We developed a manual cultivar identification diagram strategy for efficient identification of plant cultivars, from which a cultivar identification diagram (CID) of genotyped plant individuals can be constructed manually. This CID could be used as a reference for quick identification of plant cultivars of interest. We used 11-mer RAPD primers to amplify DNA samples of 32 ornamental peach genotypes; all the cultivars were well distinguished by fingerprints from 6 primers. The utility of this CID was verified by identification of three randomly chosen groups of cultivars among the 32 ones that we selected. This CID generated will be useful for the identification of commercially important ornamental peach cultivars.

Genome-wide analysis of the AP2/ERF superfamily in peach (Prunus persica).

We identified 131 AP2/ERF (APETALA2/ethylene-responsive factor) genes in material from peach using the gene sequences of AP2/ERF amino acids of Arabidopsis thaliana (Brassicaceae) as probes. Based on the number of AP2/ERF domains and individual gene characteristics, the AP2/ERF superfamily gene in peach can be classified broadly into three families, ERF (ethylene-responsive factor), RAV (related to ABI3/VP1), and AP2 (APETALA2), containing 104, 5, and 21 members, respectively, along with a solo gene (ppa005376m). The 104 genes in the ERF family were further divided into 11 groups based on the group classification made for Arabidopsis. The scaffold localizations of the AP2/ERF genes indicated that 129 AP2/ERF genes were all located on scaffolds 1 to 8, except for two genes, which were on scaffolds 17 and 10. Although the primary structure varied among AP2/ERF superfamily proteins, their tertiary structures were similar. Most ERF family genes have no introns, while members of the AP2 family have more introns than genes in the ERF and RAV families. All sequences of AP2 family genes were disrupted by introns into several segments of varying sizes. The expression of the AP2/ERF superfamily genes was highest in the mesocarp; it was far higher than in the other seven tissues that we examined, implying that AP2/ERF superfamily genes play an important role in fruit growth and development in the peach. These results will be useful for selecting candidate genes from specific subgroups for functional analysis.

An improved strategy based on RAPD markers efficiently identified 95 peach cultivars.

DNA markers have useful applications in cultivar identification. A novel analysis approach called cultivar identification diagram (CID) was developed using DNA markers in the separation of plant individuals. This new strategy is less time- and cost-consuming, has reliable results, and was constructed for fingerprinting. Ten 11-mer primers were used to amplify the genotypes; all 95 peach genotypes (from the National Peach Germplasm Repository, in Nanjing, China) were distinguished by a combination of 54 primers. The utilization of the CID among these 95 peach cultivars was also verified by the identification of three randomly chosen groups of cultivars. This identification showed some advantages including the use of fewer primers and easy separation of all cultivars by the corresponding primers marked in the right position on the CID. This peach CID could provide the information to separate any peach cultivars of these 95, which may be of help to the peach industry in China and for the utilization of DNA markers to identify other plant species.