Marker-assisted selection (MAS) in stone fruit (Prunus species) breeding is currently difficult to achieve due to the polygenic nature of the most relevant agronomic traits linked to fruit quality. Genotyping by sequencing (GBS), however, provides a large quantity of useful data suitable for fine mapping using Single Nucleotide Polymorphisms (SNPs) from a reference genome. In this study, GBS was used to genotype 272 seedlings of three F1 Japanese plum (P. salicina Lindl) progenies derived from crossing ‘98-99’ (as a common female parent) with ‘Angeleno’, ‘September King’ and ‘September Queen’ as male parents. Raw sequences were aligned to the Peach genome v1, and 42,909 filtered SNPs were obtained after sequence alignment. In addition, 153 seedlings from the ‘98-99’ × ‘Angeleno’ cross were used to develop a genetic map for each parent. A total of 981 SNPs were mapped (479 for ’98-99’ and 502 for ‘Angeleno’), covering a genetic distance of 688.8 cM and 647.03 cM, respectively. Fifty five seedlings from this progeny were phenotyped for different fruit quality traits including ripening time, fruit weight, fruit shape, chlorophyll index, skin color, flesh color, over color, firmness and soluble solids content in the years 2015 and 2016. Linkage-based QTL analysis allowed the identification of genomic regions significantly associated with ripening time (LG4 of both parents and both phenotyping years), fruit skin color (LG3 and LG4 of both parents and both years), chlorophyll degradation index (LG3 of both parents in 2015) and fruit weight (LG7 of both parents in 2016). These results represent a promising situation for GBS in the identification of SNP variants associated to fruit quality traits, potentially applicable in breeding programs through MAS, in a highly heterozygous crop species such as Japanese plum.

Alstroemeriais a genus native to South America from which many varieties of ornamental plants have been developed and introduced into the market. Interspecific hybridization followed by embryo rescue has been one of the most common breeding techniques to obtain new varieties. This study was aimed at obtaining alstroemeria hybrids through interspecific crosses using novel scented parental lines and assessing these hybrids. A total of 3669 embryos were rescued, from which 18 flowering plants were morphologically evaluated. Flower stem length ranged from 25 (14E07) to 83 cm (14A11) and most of the flowers showed pink/white colors with stripes over the inner tepals. Only 3 hybrids were perceived as scented and one of them (14E08) was evaluated through GC-MS analysis, detecting 9 VOCs, all of them monoterpenes. Molecular analysis using RAPD markers clustered two main groups: (A) hybrids withA. pelegrinaas parental line and (B) hybrids coming from the crossing UC05 × C3 and its reciprocal. Moreover through this analysis was possible to subcluster hybrids coming from different seasons. A protocol for obtaining alstroemeria hybrids was successfully developed for this species using molecular and phenotypic evaluation to provide information about their pedigree and to spot those traits which are attractive for the ornamental plant market.

The physiology of Prunus fruit ripening is a complex and not completely understood process. To improve this knowledge, postharvest behavior during the shelf-life period at the transcriptomic level has been studied using high-throughput sequencing analysis (RNA-Seq). Monitoring of fruits has been analyzed after different ethylene regulator treatments, including 1-MCP (ethylene-inhibitor) and Ethrel (ethylene-precursor) in two contrasting selected apricot (Prunus armeniaca L.) and Japanese plum (P. salicina L.) cultivars, ‘Goldrich’ and ‘Santa Rosa’. KEEG and protein–protein interaction network analysis unveiled that the most significant metabolic pathways involved in the ripening process were photosynthesis and plant hormone signal transduction. In addition, previously discovered genes linked to fruit ripening, such as pectinesterase or auxin-responsive protein, have been confirmed as the main genes involved in this process. Genes encoding pectinesterase in the pentose and glucuronate interconversions pathway were the most overexpressed in both species, being upregulated by Ethrel. On the other hand, auxin-responsive protein IAA and aquaporin PIP were both upregulated by 1-MCP in ‘Goldrich’ and ‘Santa Rosa’, respectively. Results also showed the upregulation of chitinase and glutaredoxin 3 after Ethrel treatment in ‘Goldrich’ and ‘Santa Rosa’, respectively, while photosystem I subunit V psaG (photosynthesis) was upregulated after 1-MCP in both species. Furthermore, the overexpression of genes encoding GDP-L-galactose and ferredoxin in the ascorbate and aldarate metabolism and photosynthesis pathways caused by 1-MCP favored antioxidant activity and therefore slowed down the fruit senescence process.

Kiwifruit (Actinidia chinensis var. deliciosa (A Chev) Liang et Ferguson) is a sub-tropical vine species from the Actinidiaceae family native to China. This species has an allohexaploid genome (from diploid and autotetraploid parents), contained in 174 chromosomes producing a climacteric and fleshy fruit called kiwifruit. Currently, only a small body of transcriptomic and proteomic data are available for A. chinensis var. deliciosa. In this low molecular knowledge context, the main goal of this study is to construct a tissue-specific de novo transcriptome assembly, generating differential expression analysis among these specific tissues, to obtain new useful transcriptomic information for a better knowledge of vegetative, floral and fruit growth in this species. In this study, we have analyzed different whole transcriptomes from shoot, leaf, flower bud, flower and fruit at four development stages (7, 50, 120 and 160 days after flowering; DAF) in kiwifruit obtained through RNA-seq sequencing. The first version of the developed A. chinensis var. deliciosa de novo transcriptome contained 142,025 contigs ($\overline{\mathrm{x}}$ = 1044 bp, N50 = 1133 bp). Annotation was performed with BLASTX against the TAIR10 protein database, and we found an annotation proportion of 35.6% (50,508), leaving 64.4% (91,517) of the contigs without annotation. These results represent a reference transcriptome for allohexaploid kiwifruit generating a database of A. chinensis var. deliciosa genes related to leaf, flower and fruit development. These results provided highly valuable information identifying over 20,000 exclusive genes including all tissue comparisons, which were associated with the proteins involved in different biological processes and molecular functions.