Association mapping for kernel phytosterol content in almond

An overview on lipids in nuts and oily fruits: oil content, lipid composition, health effects, lipidomic fingerprinting and new biotechnological applications of their by-products

Tree nuts and oily fruits are used as a diet complement and are highly consumed worldwide. The production and consumption of these foods have been increasing, and an enormous global market value is forecasted for 2023. Besides their high nutritional value and lipid content, they provide health benefits to fat metabolism, heart, skin, and brain. The industrial by-products of these oily foods represent promising raw materials for many industries. However, the lipidomic analysis of nuts and oily fruits is still in its early stages. State-of-the-art analytical approaches for the lipid profiling and fingerprinting of nuts and oily fruits have been developed using high-performance liquid chromatography and high-resolution mass spectrometry for the accurate identification and structural characterization at the molecular species level. It is expected to bring a new understanding of these everyday foods' nutritional and functional value. This review comprises the oil content and lipid composition of various nuts and oily fruits, particularly those mostly consumed worldwide and having recognized beneficial health effects, biological activities associated with the lipids from different oily foodstuffs, analytical methodologies to analyze lipids in nuts and oily fruits, and the potential biotechnological applications of their industrial by-products for a lipid-based commercial valorization.

Molecular Characterization of Prunus Cultivars from Romania by Microsatellite Markers

In Romania, Prunus species have great economic and social importance. With the introduction of new cultivars arises the need to preserve and characterize the local Prunus germplasm. Thus, a set of 24 polymorphic SSRs were selected for the overall characterization, including 10 peach, 11 apricot and 5 nectarine cultivars. The average number of alleles per locus (Na = 1.958), in addition to overall observed (Ho = 0.299) and expected heterozygosity (He = 0.286) were lower or comparable to those reported in similar studies, probably explained by the smaller number of analyzed cultivars restricted to a smaller geographic area. Among 26 genotypes a total of 101 alleles were identified, of which 46 alleles were in peach, 55 in apricot and 40 in nectarine, respectively. Six alleles from six loci (CPPCT-030, Pchgms-003, Pchgms-004, Pchgms-010, UDP97-401, UDP98-405) were common to all taxonomic groups. The most informative loci were BPPCT-025, Pchgms-021 and UDP96-001 in peach; BPPCT-025, BPPCT-001 and UDP96-001 in nectarine; and BPPCT-002, BPPCT-025, Pchgms-004, Pchgms-020 and Pchgms-021 in apricot. Clustering and genetic similarity analysis indicated that the degree of interspecific divergence in peach and nectarine cultivars was less than that in peach and apricot. These results will be useful to prevent confusion between cultivars, to improve breeding strategies and to benefit the management of Prunus cultivars bred in Romania.

Almond oil: A comprehensive review of chemical composition, extraction methods, preservation conditions, potential health benefits, and safety

Almond oil, a rich source of macronutrients and micronutrients, is extracted for food flavorings and the cosmetics industry. In recent years, the need for high-quality and high-quantity production of almond oil for human consumption has been increased. The present review examines the chemical composition of almond oil, storage conditions, and clinical evidence supporting the health benefits of almond oil. From the reviewed studies, it appears that almond oil contains a significant proportion of poly and monounsaturated fatty acids, with oleic acid as the main compound, and an important amount of tocopherol and phytosterol content. Some variations in almond oil composition can be found depending on the kernel's origin and the extraction system used. Some new technologies such as ultrasonic-assisted extraction, supercritical fluid extraction, subcritical fluid extraction, and salt-assisted aqueous extraction have emerged as the most promising extraction techniques that allow eco-friendly and effective recovery of almond oil. This safe oil was reported by several clinical studies to have potential roles in cardiovascular risk management, glucose homeostasis, oxidative stress reduction, neuroprotection, and many dermatologic and cosmetic applications. However, the anticarcinogenic and fertility benefits of almond oil have yet to be experimentally verified.

Genetic characterization of an almond germplasm collection and volatilome profiling of raw and roasted kernels

Almond is appreciated for its nutraceutical value and for the aromatic profile of the kernels. In this work, an almond collection composed of 96 Sicilian accessions complemented with 10 widely cultivated cultivars was phenotyped for the production of volatile organic compounds using a proton-transfer time-of-flight mass spectrometer and genotyped using the Illumina Infinium^®18 K Peach SNP array. The profiling of the aroma was carried out on fresh and roasted kernels enabling the detection of 150 mass peaks. Sixty eight, for the most related with sulfur compounds, furan containing compounds, and aldehydes formed by Strecker degradation, significantly increased during roasting, while the concentration of fifty-four mass peaks, for the most belonging to alcohols and terpenes, significantly decreased. Four hundred and seventy-one robust SNPs were selected and employed for population genetic studies. Structure analysis detected three subpopulations with the Sicilian accessions characterized by a different genetic stratification compared to those collected in Apulia (South Italy) and the International cultivars. The linkage-disequilibrium (LD) decay across the genome was equal to r² = 0.083. Furthermore, a high level of collinearity (r² = 0.96) between almond and peach was registered confirming the high synteny between the two genomes. A preliminary application of a genome-wide association analysis allowed the detection of significant marker-trait associations for 31 fresh and 33 roasted almond mass peaks respectively. An accurate genetic and phenotypic characterization of novel germplasm can represent a valuable tool for the set-up of marker-assisted selection of novel cultivars with an enhanced aromatic profile.

Genome wide association study of 5 agronomic traits in olive (Olea europaea L.)

Olive (Olea europaea L.) is one of the most economically and historically important fruit crops worldwide. Genetic progress for valuable agronomic traits has been slow in olive despite its importance and benefits. Advances in next generation sequencing technologies provide inexpensive and highly reproducible genotyping approaches such as Genotyping by Sequencing, enabling genome wide association study (GWAS). Here we present the first comprehensive GWAS study on olive using GBS. A total of 183 accessions (FULL panel) were genotyped using GBS, 94 from the Turkish Olive GenBank Resource (TOGR panel) and 89 from the USDA-ARS National Clonal Germplasm Repository (NCGR panel) in the USA. After filtering low quality and redundant markers, GWAS was conducted using 24,977 SNPs in FULL, TOGR and NCGR panels. In total, 52 significant associations were detected for leaf length, fruit weight, stone weight and fruit flesh to pit ratio using the MLM_K. Significant GWAS hits were mapped to their positions and 19 candidate genes were identified within a 10-kb distance of the most significant SNP. Our findings provide a framework for the development of markers and identification of candidate genes that could be used in olive breeding programs.

Identification of genetic loci associated with crude protein and mineral concentrations in alfalfa (Medicago sativa) using association mapping

BACKGROUND

Alfalfa (Medicago sativa) is one of the most important legume forage species in China and many other countries of the world. It provides a quality source of proteins and minerals to animals. Genetic underpinnings for these important traits, however, are elusive. An alfalfa (M. sativa) association mapping study for six traits, namely crude protein (CP), rumen undegraded protein (RUP), and four mineral elements (Ca, K, Mg and P), was conducted in three consecutive years using a large collection encompassing 336 genotypes genotyped with 85 simple sequence repeat (SSR) markers.

RESULTS

All the traits were significantly influenced by genotype, environment, and genotype × environment interaction. Eight-five significant associations (P < 0.005) were identified. Among these, five associations with Ca were repeatedly observed and six co-localized associations were identified.

CONCLUSIONS

The identified marker alleles significantly associated with the traits provided important information for understanding genetic controls of alfalfa quality. The markers could be used in assisting selection for the individual traits in breeding populations for developing new alfalfa cultivars.

Genetic diversity, population structure and association analysis in linseed (Linum usitatissimum L.)

The present investigation aimed to explore the level of genetic diversity, determine the population structure in a larger set of germplasm of linseed using microsatellite marker and identify linked markers through association mapping. A total of 168 accessions of linseed were evaluated for major agro-economic traits and SSRs markers deployed for diversity assessment. A total of 337 alleles were amplified by 50 SSRs ranging from 2 to 13 with an average of 6.74 ± 2.8 alleles per loci. The neighbor joining based clustering grouped all the accessions into three major clusters that were also confirmed by scatter plot of PCoA. While model based clustering determined four sub-populations (K = 4). Further, analysis of molecular variance analysis considering three population showed that maximum variation (79%) was within the population. We identified one putative SSR marker (Lu_3043) linked with days to 50% flowering through both GLM and MLM analysis of association mapping. The results of this preliminary study revealed genetic diversity, population structure in linseed and linked marker which could be utilized in future breeding program.

Genetic variation and association mapping of waterlogging tolerance in chrysanthemum

Forty-five molecular markers were detected significantly associated with chrysanthemum' waterlogging tolerance, and four favorable parental lines were identified as potential donors for improving waterlogging tolerance in chrysanthemum. The productivity of chrysanthemum is downgraded by waterlogging soils, which has driven a search for germplasm showing an enhanced level of waterlogging tolerance (WT). As yet little is known regarding the mode of inheritance of WT in chrysanthemum. The study set out to characterize the extent of genetic variation for WT represented in a collection of one hundred chrysanthemum accessions by testing them under both greenhouse and field conditions. A membership function value of waterlogging (MFVW), which integrated a wilting index, a chlorosis score and the proportion of dead leaf in waterlogged plants, was used as a measure of WT. The variation for MFVW among plants grown in the greenhouse (two experiments) was generally higher than that generated in field-grown (one experiment) plants. The MFVW broad sense heritability was 0.82, and the phenotypic coefficient of variation (31.8 %) was larger than the genetic one (28.8 %). Association mapping (AM) identified 45 markers related to WT: 25 by applying the general linear model (GLM) + principal component (PC) model, 16 by applying the mixed linear model (MLM), 31 by applying the MLM + Q matrix model and 12 by applying the MLM + PC model. Of the associated markers, eight and two were predictive in two and three experiments within all models, respectively; the proportion of the phenotypic variance explained by the eight associations ranged from 6.3 to 16.4 %. On the basis of their harboring all four of the leading markers E2M16-2, SSR150-6, E19M16-1 and E10M10-12, the varieties 'Nannong Xuefeng', 'Qx097', 'Nannong Xunzhang' and 'Finch' were identified as potential donors for future improvement of WT in chrysanthemum.

Application of Genomic Technologies to the Breeding of Trees

The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure. Dissection of complex traits became possible through the availability of genome sequences along with phenotypic variation data, which allow to elucidate the causative genetic differences that give rise to observed phenotypic variation. Association mapping facilitates the association between genetic markers and phenotype in unstructured and complex populations, identifying molecular markers for assisted selection and breeding. Also, genomic data provide in silico identification and characterization of genes and gene families related to important traits, enabling new tools for molecular marker assisted selection in tree breeding. Deep sequencing of transcriptomes is also a powerful tool for the analysis of precise expression levels of each gene in a sample. It consists in quantifying short cDNA reads, obtained by NGS technologies, in order to compare the entire transcriptomes between genotypes and environmental conditions. The miRNAs are non-coding short RNAs involved in the regulation of different physiological processes, which can be identified by high-throughput sequencing of RNA libraries obtained by reverse transcription of purified short RNAs, and by in silico comparison with known miRNAs from other species. All together, NGS techniques and their applications have increased the resources for plant breeding in tree species, closing the former gap of genetic tools between trees and annual species.

A review of the impact of processing on nutrient bioaccessibility and digestion of almonds

Almond kernels contain phytochemicals and nutrients that potentially have positive health benefits in relation to heart disease, diabetes and obesity. One important mechanism associated with these benefits is an imposed limit on bioaccessibility (release) of nutrients, such as lipids, from almond tissue during mastication and digestion. Recent studies have demonstrated the importance of food structure during the digestion of plant foods. In particular, in the almond kernel, depending on its structure and degree of processing, the amount of lipid released from the almond tissue matrix and the fatty acids produced from lipolysis has been found to vary substantially. This review aims at discussing the commercial methods of almond processing and the different almond forms produced for human consumption, mainly with respect to their impact on nutrient composition, digestion and metabolism.

Identification and Characterization of Microsatellite Loci in Maqui (Aristotelia chilensis [Molina] Stunz) Using Next-Generation Sequencing (NGS)

Maqui (Aristotelia chilensis [Molina] Stunz) is a small dioecious tree native to South America with edible fruit characterized by very high antioxidant capacity and anthocyanin content. To preserve maqui as a genetic resource it is essential to study its genetic diversity. However, the complete genome is unknown and only a few gene sequences are available in databases. Simple sequence repeats (SSR) markers, which are neutral, co-dominant, reproducible and highly variable, are desirable to support genetic studies in maqui populations. By means of identification and characterization of microsatellite loci from a maqui genotype, using 454 sequencing technology, we develop a set of SSR for this species. Obtaining a total of 165,043 shotgun genome sequences, with an average read length of 387 bases, we covered 64 Mb of the maqui genome. Reads were assembled into 4,832 contigs, while 98,546 reads remained as singletons, generating a total of 103,378 consensus genomic sequences. A total of 24,494 SSR maqui markers were identified. Of them, 15,950 SSR maqui markers were classified as perfects. The most common SSR motifs were dinucleotide (31%), followed by tetranucleotide (26%) and trinucleotide motifs (24%). The motif AG/CT (28.4%) was the most abundant, while the motif AC (89 bp) was the largest. Eleven polymorphic SSRs were selected and used to analyze a population of 40 maqui genotypes. Polymorphism information content (PIC) ranged from 0.117 to 0.82, with an average of 0.58. Non-significant groups were observed in the maqui population, showing a panmictic genetic structure. In addition, we also predicted 11150 putative genes and 3 microRNAs (miRNAs) in maqui sequences. This results, including partial sequences of genes, some miRNAs and SSR markers from high throughput next generation sequencing (NGS) of maqui genomic DNA, constitute the first platform to undertake genetic and molecular studies of this important species.

Association Mapping for Fiber-Related Traits and Digestibility in Alfalfa (Medicago sativa)

Association mapping is a powerful approach for exploring the molecular genetic basis of complex quantitative traits. An alfalfa (Medicago sativa) association panel comprised of 336 genotypes from 75 alfalfa accessions represented by four to eight genotypes for each accession. Each genotype was genotyped using 85 simple sequence repeat (SSR) markers and phenotyped for five fiber-related traits in four different environments. A model-based structure analysis was used to group all genotypes into two groups. Most of the genotypes have a low relative kinship (<0.3), suggesting population stratification not be an issue for association analysis. Generally, the Q + K model exhibited the best performance to eliminate the false associated positives. In total, 124 marker-trait associations were predicted (p < 0.005). Among these, eight associations were predicted in two environments repeatedly and 20 markers were predicted to be associated with multiple traits. These trait-associated markers will greatly help marker-assisted breeding programs to improve fiber-related quality traits in alfalfa.

Genome-Wide Association Analysis of the Anthocyanin and Carotenoid Contents of Rose Petals

Petal color is one of the key characteristics determining the attractiveness and therefore the commercial value of an ornamental crop. Here, we present the first genome-wide association study for the important ornamental crop rose, focusing on the anthocyanin and carotenoid contents in petals of 96 diverse tetraploid garden rose genotypes. Cultivated roses display a vast phenotypic and genetic diversity and are therefore ideal targets for association genetics. For marker analysis, we used a recently designed Axiom SNP chip comprising 68,000 SNPs with additionally 281 SSRs, 400 AFLPs and 246 markers from candidate genes. An analysis of the structure of the rose population revealed three subpopulations with most of the genetic variation between individual genotypes rather than between clusters and with a high average proportion of heterozygous loci. The mapping of markers significantly associated with anthocyanin and carotenoid content to the related Fragaria and Prunus genomes revealed clusters of associated markers indicating five genomic regions associated with the total anthocyanin content and two large clusters associated with the carotenoid content. Among the marker clusters associated with the phenotypes, we found several candidate genes with known functions in either the anthocyanin or the carotenoid biosynthesis pathways. Among others, we identified a glutathione-S-transferase, 4CL, an auxin response factor and F3'H as candidate genes affecting anthocyanin concentration, and CCD4 and Zeaxanthine epoxidase as candidates affecting the concentration of carotenoids. These markers are starting points for future validation experiments in independent populations as well as for functional genomic studies to identify the causal factors for the observed color phenotypes. Furthermore, validated markers may be interesting tools for marker-assisted selection in commercial breeding programmes in that they provide the tools to identify superior parental combinations that combine several associated markers in higher dosages.