Nnadozie Oraguzie

Association mapping in plants

An Overview of Association Mapping.- Linkage Disequilibrium.- What Are SNPs?.- Single Nucleotide Polymorphism Discovery.- Single Nucleotide Polymorphism Genotyping in Plants.- SNP Applications in Plants.- Linkage Disequilibrium Mapping Concepts.- Statistical Analysis and Experimental Design.- Linkage Disequilibrium-Based Association Mapping in Forage Species.- Gene-Assisted Selection Applications of Association Genetics for Forest Tree Breeding.- Prospects of Association Mapping in Perennial Horticultural Crops.

Genetic identity and relationships of Iranian apple (Malus × domestica Borkh.) cultivars and landraces, wild Malus species and representative old apple cultivars based on simple sequence repeat (SSR) marker analysis

In order to shed light on the role of Iran in apple evolution and domestication, we chose to investigate the relationships of a collection of 159 accessions of wild and domesticated apples including Iranian indigenous apple cultivars and landraces, selected wild species, and old apple scion and rootstock cultivars from different parts of the world. The majority of the wild species belonged to M. sieversii, which is widely believed to be the main maternal wild ancestor of domestic apples, from Kazakhstan and M. orientalis, which is one of the probable minor ancestors of domestic apples, from Turkey and Russia located on the east and west of Iran, respectively. The accessions were assigned into six arbitrary populations for the purpose of generating information on genetic parameters. Nine simple sequence repeat (SSR) loci selected from previous studies in apple were screened over DNA extracted from all the accessions. Results showed that all SSR loci displayed a very high degree of polymorphism with 11–25 alleles per locus. In total, there were 153 alleles across all loci with an average of 17 alleles per locus. The SSR allelic data were then used for estimation of population genetic parameters, including genetic variation statistics, F-statistics, gene flow, genetic identity, genetic distance and then cluster analysis using POPGENE 1.32 software. The F-statistics and gene flow in particular, showed that there was more intra-population than between population variation. The genetic identity and genetic distance estimates, and the dendrogram generated from the un-weighted pair group arithmetic average (UPGMA) method of cluster analysis showed that the Iranian cultivars and landraces were more closely related to M. sieversii from Central Asia (east of Iran) and M. orientalis native to Turkey and Russia than to other accessions of Malus species. Also, the old apple cultivars from different parts of the world have a closer genetic relationship to M. sieversii, M. orientalis and the Iranian apples, than to other wild species. Based on these results, we suggest that the Iranian apples may occupy an intermediate position between the domesticated varieties and wild species. We propose that Iran could be one of the major players in apples’ domestication and transfer from Central Asia to the western countries.

Estimation of genetic parameters in a recurrent selection program in Apple

Combining ability was estimated for 8 tree and 11 agronomic traits in a multi-location apple genetics population to select individuals for the next cycle of selections. Families more than three standard errors away from the general mean were identified for each trait and extreme individuals (with regard to that trait) from those families were selected. On the whole, 148 individuals were chosen based upon individual traits and, in a few cases a combination of traits, in a way that maintains the original diversity within the population. Narrow-sense heritability estimated separately for each site for fruit ribbing, fruit russet, fruit overcolour amount and fruit weight ranged from 0.0–0.13, 0.05–0.58, 0.34–0.40 and 0.27–0.90 respectively. Phenotypic correlation and additive genetic correlation were small and from small to moderately high respectively, between pairs of traits. The implication of these genetic parameter estimates in apple breeding is discussed.

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.

Phenolic compounds in Rosaceae fruit and nut crops.

The demand for new fruit cultivars with high levels of phytochemicals, in particular phenolic compounds, has received increasing attention from biochemists, pharmaceutical companies, plant breeders, and the general public due to their health benefits. This review focuses on the economically important Rosaceae, which contains varying proportions and concentrations of these compounds. The paper discusses the common phenolics in the Rosaceae including phenolic acids, flavonols, flavanols, anthocyanins, and dihydrochalcones. The nonextractable phenolics are also presented but not discussed in detail. The metabolism and bioavailability of phenolics, as well as human and environmental factors that affect their concentration and composition, are highlighted. Furthermore, the paper presents different approaches for biofortification and posits that breeding may be the most viable and sustainable option as it improves other fruit quality traits simultaneously and increases confidence in adoption of new cultivars with enhanced consumer appeal.

Uniform standards for genome databases in forest and fruit trees

TreeGenes and tree fruit Genome Database Resources serve the international forestry and fruit tree genomics research communities, respectively. These databases hold similar sequence data and provide resources for the submission and recovery of this information in order to enable comparative genomics research. Large-scale genotype and phenotype projects have recently spawned the development of independent tools and interfaces within these repositories to deliver information to both geneticists and breeders. The increase in next generation sequencing projects has increased the amount of data as well as the scale of analysis that can be performed. These two repositories are now working towards a similar goal of archiving the diverse, independent data sets generated from genotype/phenotype experiments. This is achieved through focused development on data input standards (templates), pipelines for the storage and automated curation, and consistent annotation efforts through the application of widely accepted ontologies to improve the extraction and exchange of the data for comparative analysis. Efforts towards standardization are not limited to genotype/phenotype experiments but are also being applied to other data types to improve gene prediction and annotation for de novo sequencing projects. The resources developed towards these goals represent the first large-scale coordinated effort in plant databases to add informatics value to diverse genotype/phenotype experiments.

Prospects of Association Mapping in Perennial Horticultural Crops

Many horticultural crops share several characteristics that complicate genetic analysis including long generation intervals, protracted evaluation times, high costs of breeding inputs, slow maturation, and polyploidy. Partly as a result of the limited economic impact of individual species new technologies have been incorporated into breeding strategies in horticultural crops at a relatively slow pace. As outlined in previous sections, association mapping has only recently begun to be applied to plants and there is no published data yet on horticultural crops. We outline here the characteristics of perennial horticultural species that impinge on the application of association mapping, assess the potential impact of this technology and propose some guidelines for incorporating association mapping into conventional horticultural breeding programs. For the sake of simplicity, we will illustrate many of the points in the discussion with examples from the Rosaceae, a family of plants that has a diverse range of uses and ranks third in economic importance in the USA and temperate regions throughout the world. The most valuable fruit producing crops in this family include apple (Malus), pear

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.

A review of genetic resources of pome fruits in Iran

Iran is very rich in plant genetic resources, due largely to the diversity in the agro-ecological landscape. Protection, preservation and utilization of genetic resources would facilitate development of premium varieties and biotech products that can potentially lead to a change in the food, agricultural, pharmaceutical and chemical industries in Iran. This paper discusses the distribution, ethnobotany, diversity and utilization of wild and domestic genetic resources of pome fruit species in Iran including apple (Malus spp.), pear (Pyrus spp.), quince (Cydoniaoblonga Mill.), hawthorn (Crataegus spp.), medlar (Mespilus germanica L.) and loquat (Eriobotryajaponica Lindl.), all of which are members of the Rosaceae family. The goal of this paper is to highlight the importance of Iran as a contributor to the diversity of pome fruit genetic resources in the world.

A DNA test for routine prediction in breeding of sweet cherry fruit color, Pav-Rf-SSR

Sweet cherry fruit color is a market class-defining trait. The two main market classes in the USA are mahogany, consisting fruit with red skin and flesh, and blush, consisting clear-fleshed fruit with yellow skin and a red overcolor on less than the entire skin surface. Fruit color is a major consideration in sweet cherry breeding as resources and selection thresholds are often differentially applied to each market class. The use of DNA-based information could improve breeding efficiency and accuracy for fruit color, but a predictive DNA test is required. The objective of this study was to develop a reliable, simple DNA test for the prediction of sweet cherry color-based market classes, targeting the major locus, termed here as Rf, associated with fruit color variation. Haplotypes were developed based on 14 SNP markers from the RosBREED cherry 6K SNP array v1 that were associated with the two market classes. To convert the multiple SNP markers to a single, simple PCR-based assay, 11 PCR-based assays targeting microsatellite motifs were designed, using the peach reference genome sequence, and used to screen 20 individuals representing the most common SNP haplotypes. One assay, subsequently named Pav-Rf-SSR, was used to screen 221 phenotyped individuals of the RosBREED sweet cherry reference germplasm set and accurately differentiated individuals with mahogany and blush fruits. Pav-Rf-SSR can be used in DNA-informed breeding schemes to efficiently and accurately predict genetic potential for fruit color and is one of the first DNA tests publicly available for a sweet cherry fruit quality trait.