Population Structure and Association Mapping for Agronomical and Biochemical Traits of a Large Spanish Apple Germplasm

A basic knowledge of linkage disequilibrium and population structure is necessary in order to determine the genetic control and identify significant associations with agronomical and phytochemical compounds in apple (Malus × domestica Borkh). In this study, 186 apple accessions (Pop1), representing both Spanish native accessions (94) and non-Spanish cultivars (92) from the EEAD-CSIC apple core collection, were assessed using 23 SSRs markers. Four populations were considered: Pop1, Pop2, Pop3, and Pop4. The initial Pop1 was divided into 150 diploid (Pop2) and 36 triploid accessions (Pop3), while for the inter-chromosomal linkage disequilibrium and the association mapping analysis, 118 phenotype diploid accessions were considered Pop4. Thus, the average number of alleles per locus and observed heterozygosity for the overall sample set (Pop1) were 15.65 and 0.75, respectively. The population structure analysis identified two subpopulations in the diploid accessions (Pop2 and Pop4) and four in the triploids (Pop3). Regarding the Pop4, the population structure with K = 2 subpopulations segregation was in agreement with the UPGMA cluster analysis according to the genetic pairwise distances. Moreover, the accessions seemed to be segregated by their origin (Spanish/non-Spanish) in the clustering analysis. One of the two subpopulations encountered was quite-exclusively formed by non-Spanish accessions (30 out of 33). Furthermore, agronomical and basic fruit quality parameters, antioxidant traits, individual sugars, and organic acids were assessed for the association mapping analysis. A high level of biodiversity was exhibited in the phenotypic characterization of Pop4, and a total of 126 significant associations were found between the 23 SSR markers and the 21 phenotypic traits evaluated. This study also identified many new marker-locus trait associations for the first time, such as in the antioxidant traits or in sugars and organic acids, which may be useful for predictions and for a better understanding of the apple genome.

Genetic architecture and genomic predictive ability of apple quantitative traits across environments

Implementation of genomic tools is desirable to increase the efficiency of apple breeding. Recently, the multi-environment apple reference population (apple REFPOP) proved useful for rediscovering loci, estimating genomic predictive ability, and studying genotype by environment interactions (G × E). So far, only two phenological traits were investigated using the apple REFPOP, although the population may be valuable when dissecting genetic architecture and reporting predictive abilities for additional key traits in apple breeding. Here we show contrasting genetic architecture and genomic predictive abilities for 30 quantitative traits across up to six European locations using the apple REFPOP. A total of 59 stable and 277 location-specific associations were found using GWAS, 69.2% of which are novel when compared with 41 reviewed publications. Average genomic predictive abilities of 0.18-0.88 were estimated using main-effect univariate, main-effect multivariate, multi-environment univariate, and multi-environment multivariate models. The G × E accounted for up to 24% of the phenotypic variability. This most comprehensive genomic study in apple in terms of trait-environment combinations provided knowledge of trait biology and prediction models that can be readily applied for marker-assisted or genomic selection, thus facilitating increased breeding efficiency.

Biochemical Characterization and Differential Expression of PAL Genes Associated With "Translocated" Peach/Plum Graft-Incompatibility

Grafting is an ancient plant propagation technique widely used in horticultural crops, particularly in fruit trees. However, the involvement of two different species in grafting may lead to lack of affinity and severe disorders between the graft components, known as graft-incompatibility. This complex agronomic trait is traditionally classified into two categories: "localized" (weak graft unions with breaks in cambial and vascular continuity at the graft interface and absence of visual symptoms in scion leaves and shoots) and "translocated" (degeneration of the sieve tubes and phloem companion cells at the graft interface causing translocation problems in neighboring tissues, and reddening/yellowing of scion leaves). Over the decades, more attention has been given to the different mechanisms underlying the "localized" type of graft-incompatibility; whereas the phenylpropanoid-derived compounds and the differential gene expression associated with the "translocated" graft-incompatibility remain unstudied. Therefore, the aim of this study was to shed light on the biochemical and molecular mechanisms involved in the typical "translocated" graft-incompatibility of peach/plum graft-combinations. In this study, the "Summergrand" (SG) nectarine cultivar was budded on two plum rootstocks: "Adara" and "Damas GF 1869". "Translocated" symptoms of incompatibility were shown and biochemically characterized in the case of "SG/Damas GF 1869" graft-combination, 3 years after grafting. Non-structural carbohydrates (soluble sugars and starch), phenolic compounds and antioxidant activity, were significantly enhanced in the incompatible graft-combination scion. Similarly, the enzymatic activities of the antioxidant enzyme peroxidase, the phenylalanine ammonia-lyase (PAL) and polyphenol oxidase involved in the phenylpropanoid pathway were significantly affected by the incompatible rootstock "Damas GF 1869", inducing higher activities in the scion than those induced by the compatible rootstock "Adara". In addition, a positive and strong correlation was obtained between total phenol content, antioxidant capacity and the expression of the key genes involved in the phenylpropanoid pathway, PAL1 and PAL2. Regarding the "SG/Adara" graft-combination, there were neither external symptoms of "translocated" incompatibility nor significant differences in the biochemical and molecular parameters between scion and rootstock, proving it to be a compatible combination. The differential expression of PAL genes together with the biochemical factors cited above could be good markers for the "translocated" peach/plum graft-incompatibility.

Association Mapping Analysis for Fruit Quality Traits in Prunus persica Using SNP Markers

The identification of genes involved in variation of peach fruit quality would assist breeders to create new cultivars with improved fruit quality. Peach is a genetic and genomic model within the Rosaceae. A large quantity of useful data suitable for fine mapping using Single Nucleotide Polymorphisms (SNPs) from the peach genome sequence was used in this study. A set of 94 individuals from a peach germplasm collection was phenotyped and genotyped, including local Spanish and modern cultivars maintained at the Experimental Station of Aula Dei, Spain. Phenotypic evaluation based on agronomical, pomological and fruit quality traits was performed at least 3 years. A set of 4,558 out of a total of 8,144 SNPs markers developed by the Illumina Infinium BeadArray (v1.0) technology platform, covering the peach genome, were analyzed for population structure analysis and genome-wide association studies (GWAS). Population structure analysis identified two subpopulations, with admixture within them. While one subpopulation contains only modern cultivars, the other one is formed by local Spanish and several modern cultivars from international breeding programs. To test the marker trait associations between markers and phenotypic traits, four models comprising both general linear model (GLM) and mixed linear model (MLM) were selected. The MLM approach using co-ancestry values from population structure and kinship estimates (K model) identified a maximum of 347 significant associations between markers and traits. The associations found appeared to map within the interval where many candidate genes involved in different pathways are predicted in the peach genome. These results represent a promising situation for GWAS in the identification of SNP variants associated to fruit quality traits, potentially applicable in peach breeding programs.

Identification of Genetic Loci Associated with Quality Traits in Almond via Association Mapping

To design an appropriate association study, we need to understand population structure and the structure of linkage disequilibrium within and among populations as well as in different regions of the genome in an organism. In this study, we have used a total of 98 almond accessions, from five continents located and maintained at the Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA; Spain), and 40 microsatellite markers. Population structure analysis performed in 'Structure' grouped the accessions into two principal groups; the Mediterranean (Western-Europe) and the non-Mediterranean, with K = 3, being the best fit for our data. There was a strong subpopulation structure with linkage disequilibrium decaying with increasing genetic distance resulting in lower levels of linkage disequilibrium between more distant markers. A significant impact of population structure on linkage disequilibrium in the almond cultivar groups was observed. The mean r2 value for all intra-chromosomal loci pairs was 0.040, whereas, the r2 for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits, five models comprising both general linear models and mixed linear models were selected to test the marker trait associations. The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 16 significant associations for chemical traits and 12 for physical traits. This study reports for the first time the use of association mapping for determining marker-locus trait associations in a world-wide almond germplasm collection. It is likely that association mapping will have the most immediate and largest impact on the tier of crops such as almond with the greatest economic value.

Discovery of non-climacteric and suppressed climacteric bud sport mutations originating from a climacteric Japanese plum cultivar (Prunus salicina Lindl.)

Japanese plums are classified as climacteric; however, some economically important cultivars selected in California produce very little ethylene and require long ripening both "on" and "off" the tree to reach eating-ripe firmness. To unravel the ripening behavior of different Japanese plum cultivars, ripening was examined in the absence (air) or in the presence of ethylene or propylene (an ethylene analog) following a treatment or not with 1-methylcyclopropene (1-MCP, an ethylene action inhibitor). Detailed physiological studies revealed for the first time three distinct ripening types in plum fruit: climacteric, suppressed-climacteric, and non-climacteric. Responding to exogenous ethylene or propylene, the slow-softening supressed-climacteric cultivars produced detectable amounts of ethylene, in contrast to the novel non-climacteric cultivar that produced no ethylene and softened extremely slowly. Genetic analysis using microsatellite markers produced identical DNA profiles for the climacteric cultivars "Santa Rosa" and "July Santa Rosa," the suppressed-climacteric cultivars "Late Santa Rosa," "Casselman," and "Roysum" and the novel non-climacteric "Sweet Miriam," as expected since historic records present most of these cultivars as bud-sport mutations derived initially from "Santa Rosa." This present study provides a novel fruit system to address the molecular basis of ripening and to develop markers that assist breeders in providing high-quality stone fruit cultivars that can remain "on-tree," increasing fruit flavor, saving harvesting costs, and potentially reducing the need for low-temperature storage during postharvest handling.

Association mapping for kernel phytosterol content in almond

Almond kernels are a rich source of phytosterols, which are important compounds for human nutrition. The genetic control of phytosterol content has not yet been documented in almond. Association mapping (AM), also known as linkage disequilibrium (LD), was applied to an almond germplasm collection in order to provide new insight into the genetic control of total and individual sterol contents in kernels. Population structure analysis grouped the accessions into two principal groups, the Mediterranean and the non-Mediterranean. There was a strong subpopulation structure with LD decaying with increasing genetic distance, resulting in lower levels of LD between more distant markers. A significant impact of population structure on LD in the almond cultivar groups was observed. The mean r(2) -value for all intra-chromosomal loci pairs was 0.040, whereas, the r(2) for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits five models were tested. The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 13 significant associations. Most of the associations found appeared to map within the interval where many candidate genes involved in the sterol biosynthesis pathway are predicted in the peach genome. These findings provide a valuable foundation for quality gene identification and molecular marker assisted breeding in almond.

Agronomical parameters, sugar profile and antioxidant compounds of "Catherine" peach cultivar influenced by different plum rootstocks

The influence of seven plum rootstocks (Adesoto, Monpol, Montizo, Puebla de Soto 67 AD, PM 105 AD, St. Julien GF 655/2 and Constantí 1) on individual and total sugars, as well as on antioxidant content in fruit flesh of "Catherine" peaches, was evaluated for three years. Agronomical and basic fruit quality parameters were also determined. At twelve years after budding, significant differences were found between rootstocks for the different agronomic and fruit quality traits evaluated. The Pollizo plum rootstocks Adesoto and PM 105 AD seem to induce higher sweetness to peach fruits, based on soluble solids content, individual (sucrose, fructose and sorbitol) and total sugars. A clear tendency was also observed with the rootstock Adesoto, inducing the highest content of phenolics, flavonoids, vitamin C and relative antioxidant capacity (RAC). Thus, the results of this study demonstrate the significant effect of rootstock on the sugar profile and phytochemical characteristics of peach fruits. In addition, this work shows the importance of the sugar profile, because specific sugars play an important role in peach flavour quality, as well as the studied phytochemical compounds when looking for high quality peaches with enhanced health properties.

Mapping quantitative trait loci for kernel composition in almond

BACKGROUND

Almond breeding is increasingly taking into account kernel quality as a breeding objective. Information on the parameters to be considered in evaluating almond quality, such as protein and oil content, as well as oleic acid and tocopherol concentration, has been recently compiled. The genetic control of these traits has not yet been studied in almond, although this information would improve the efficiency of almond breeding programs.

RESULTS

A map with 56 simple sequence repeat or microsatellite (SSR) markers was constructed for an almond population showing a wide range of variability for the chemical components of the almond kernel. A total of 12 putative quantitative trait loci (QTL) controlling these chemical traits have been detected in this analysis, corresponding to seven genomic regions of the eight almond linkage groups (LG). Some QTL were clustered in the same region or shared the same molecular markers, according to the correlations already found between the chemical traits. The logarithm of the odds (LOD) values for any given trait ranged from 2.12 to 4.87, explaining from 11.0 to 33.1 % of the phenotypic variance of the trait.

CONCLUSIONS

The results produced in the study offer the opportunity to include the new genetic information in almond breeding programs. Increases in the positive traits of kernel quality may be looked for simultaneously whenever they are genetically independent, even if they are negatively correlated. We have provided the first genetic framework for the chemical components of the almond kernel, with twelve QTL in agreement with the large number of genes controlling their metabolism.

Genetic diversity and relatedness of sweet cherry (prunus avium L.) cultivars based on single nucleotide polymorphic markers

Most previous studies on genetic fingerprinting and cultivar relatedness in sweet cherry were based on isoenzyme, RAPD, and simple sequence repeat (SSR) markers. This study was carried out to assess the utility of single nucleotide polymorphism (SNP) markers generated from 3' untranslated regions (UTR) for genetic fingerprinting in sweet cherry. A total of 114 sweet cherry germplasm representing advanced selections, commercial cultivars, and old cultivars imported from different parts of the world were screened with seven SSR markers developed from other Prunus species and with 40 SNPs obtained from 3' UTR sequences of Rainier and Bing sweet cherry cultivars. Both types of marker study had 99 accessions in common. The SSR data was used to validate the SNP results. Results showed that the average number of alleles per locus, mean observed heterozygosity, expected heterozygosity, and polymorphic information content values were higher in SSRs than in SNPs although both set of markers were similar in their grouping of the sweet cherry accessions as shown in the dendrogram. SNPs were able to distinguish sport mutants from their wild type germplasm. For example, "Stella" was separated from "Compact Stella." This demonstrates the greater power of SNPs for discriminating mutants from their original parents than SSRs. In addition, SNP markers confirmed parentage and also determined relationships of the accessions in a manner consistent with their pedigree relationships. We would recommend the use of 3' UTR SNPs for genetic fingerprinting, parentage verification, gene mapping, and study of genetic diversity in sweet cherry.