Perspectives and recent progress of genome-wide association studies (GWAS) in fruits

Comprehensive insights on association mapping in perennial fruit crops breeding - Its implications, current status and future perspectives

In order to provide food and nutritional security for the world's rapidly expanding population, fruit crop researchers have identified two critical priorities: increasing production and preserving fruit quality during the pre- and post-harvest periods. The genetic basis of these complex, commercially important fruit traits which are uniquely regulated by polygenes or multi-allelic genes that interact with one another and the environment can be analyzed with the aid of trait mapping tools. The most interesting trait mapping approach that offers the genetic level investigation for marker-trait associations (MTAs) for these complex fruit traits, without the development of mapping population, is association mapping. This approach was used during the genetic improvement program, emphasizing the obstacles (breeding strategies adopted, generation interval, and their genomic status) pertaining to perennial fruit crops. This method of studying population diversity and linkage disequilibrium in perennial fruit crops has been made possible by recent developments in genotyping, phenotyping, and statistical analysis. Thus, the purpose of this review is to provide an overview of different trait mapping techniques, with a focus on association mapping (method, essential components, viability, constraints, and future perspective) and its advantages, disadvantages, and possibilities for breeding perennial fruit crops.

Genetic mosaic of the Mediterranean fig: comprehensive genomic insights from a gene bank collection

High-depth whole-genome resequencing of 53 diverse fig tree genotypes yielded a rich dataset of genetic variants. We successfully identified 5,501,460 single-nucleotide polymorphisms (SNPs) and 1,228,537 insertions and deletions (InDels), providing a high-density and excellent-quality genetic map of the fig tree. We also performed a detailed population structure analysis, dividing the 53 genotypes into three geographical groups and assessing their genetic diversity and divergence. Analysis of structural variants (SVs) and copy number variations (CNVs) revealed their potential functional impact, particularly in plant-pathogen interaction and secondary metabolism. Metabolomic fingerprinting of fig genotypes uncovered extensive variation in primary metabolites and polyphenolic compounds, highlighting the influence of genotype on fruit quality traits such as nutritional content and bioactive compound composition. The genome-wide association study (GWAS) identified critical SNPs associated with fruit quality and morphological features. The discovery of significant candidate genes, such as AGL62, GDSL, and COBRA-like protein 4 genes, offers promising targets for marker-assisted selection and genome editing approaches to improve fig fruit morphological and quality traits. This extensive genomic analysis of fig trees enhances our understanding of the genetic basis of important agronomic traits and provides a rich resource for future research in this economically and nutritionally significant fruit.

Genome-wide association study to identify novel loci and genes for Fusarium root rot resistance in sweet potato using genotyping-by-sequencing

Fusarium root rot, caused by Fusarium solani, is a major post-harvest disease in sweet potatoes (Ipomoea batatas (L.) Lam.). An effective strategy for controlling this disease is the development of resistant varieties. In this study, a genome-wide association study (GWAS) was conducted on 96 sweet potato genotypes to identify novel candidate loci and dissect the genetic basis of Fusarium root rot resistance. Genotyping was performed using genotyping-by-sequencing (GBS), and 44,255 SNPs were identified after filtering. The genotypes (n = 96) were evaluated through resistance tests in 2021 and 2022, separately and combined. The GWAS identified two significant SNP markers (LG3_22903756 and LG4_2449919) on chromosomes 3 and 4 associated with Fusarium root rot resistance, respectively. Lesion length showed significant differences between homozygous A and G alleles of LG3_22903756, which can potentially be used to develop molecular markers for selecting accessions resistant to Fusarium root rot. Expression analysis of 11 putative genes flanking the significant SNPs revealed the alteration in the expression of nine genes, indicating their possible involvement in Fusarium root rot resistance. The results of this study will aid in the marker-assisted selection and functional analysis of candidate genes for Fusarium root rot resistance in sweet potatoes.

Construction and genetic characterization of an interspecific raspberry hybrids panel aiming resistance to late leaf rust and adaptation to tropical regions

Raspberries (Rubus spp) are temperate climate fruits with profitable high returns and have the potential for diversification of fruit growing in mid to low-latitude regions. However, there are still no cultivars adapted to climatic conditions and high pressure of diseases that occurs in tropical areas. In this context, our objective was to evaluate the genetic diversity from a 116 raspberry genotypes panel obtained from interspecific crosses in a testcross scheme with four cultivars already introduced in Brazil. The panel was genotyped via genotyping-by-sequencing. 28,373 and 27,281 SNPs were obtained, using the species R. occidentalis and R. idaeus genomes as references, respectively. A third marker dataset was constructed consisting of 41,292 non-coincident markers. Overall, there were no differences in the results when using the different marker sets for the subsequent analyses. The mean heterozygosity was 0.54. The average effective population size was 174, indicating great genetic variability. The other analyses revealed that the half-sibling families were structured in three groups. It is concluded that the studied panel has great potential for breeding and further genetic studies. Moreover, only one of the three marker matrices is sufficient for diversity studies.

Genome-wide association studies: an intuitive solution for SNP identification and gene mapping in trees

Analysis of natural diversity in wild/cultivated plants can be used to understand the genetic basis for plant breeding programs. Recent advancements in DNA sequencing have expanded the possibilities for genetically altering essential features. There have been several recently disclosed statistical genetic methods for discovering the genes impacting target qualities. One of these useful methods is the genome-wide association study (GWAS), which effectively identifies candidate genes for a variety of plant properties by examining the relationship between a molecular marker (such as SNP) and a target trait. Conventional QTL mapping with highly structured populations has major limitations. The limited number of recombination events results in poor resolution for quantitative traits. Only two alleles at any given locus can be studied simultaneously. Conventional mapping approach fails to work in perennial plants and vegetatively propagated crops. These limitations are sidestepped by association mapping or GWAS. The flexibility of GWAS comes from the fact that the individuals being examined need not be linked to one another, allowing for the use of all meiotic and recombination events to increase resolution. Phenotyping, genotyping, population structure analysis, kinship analysis, and marker-trait association analysis are the fundamental phases of GWAS. With the rapid development of sequencing technologies and computational methods, GWAS is becoming a potent tool for identifying the natural variations that underlie complex characteristics in crops. The use of high-throughput sequencing technologies along with genotyping approaches like genotyping-by-sequencing (GBS) and restriction site associated DNA (RAD) sequencing may be highly useful in fast-forward mapping approach like GWAS. Breeders may use GWAS to quickly unravel the genomes through QTL and association mapping by taking advantage of natural variances. The drawbacks of conventional linkage mapping can be successfully overcome with the use of high-resolution mapping and the inclusion of multiple alleles in GWAS.

Genetic analysis of protein content and oil content in soybean by genome-wide association study

Soybean seed protein content (PC) and oil content (OC) have important economic value. Detecting the loci/gene related to PC and OC is important for the marker-assisted selection (MAS) breeding of soybean. To detect the stable and new loci for PC and OC, a total of 320 soybean accessions collected from the major soybean-growing countries were used to conduct a genome-wide association study (GWAS) by resequencing. The PC ranged from 37.8% to 46.5% with an average of 41.1% and the OC ranged from 16.7% to 22.6% with an average of 21.0%. In total, 23 and 29 loci were identified, explaining 3.4%-15.4% and 5.1%-16.3% of the phenotypic variations for PC and OC, respectively. Of these, eight and five loci for PC and OC, respectively, overlapped previously reported loci and the other 15 and 24 loci were newly identified. In addition, nine candidate genes were identified, which are known to be involved in protein and oil biosynthesis/metabolism, including lipid transport and metabolism, signal transduction, and plant development pathway. These results uncover the genetic basis of soybean protein and oil biosynthesis and could be used to accelerate the progress in enhancing soybean PC and OC.

Identification of Genetic Markers and Genes Putatively Involved in Determining Olive Fruit Weight

The fruit size of a cultivated olive tree is consistently larger than its corresponding wild relatives because fruit size is one of the main traits associated with olive tree domestication. Additionally, large fruit size is one of the main objectives of modern olive breeding programs. However, as the long juvenile period is one main hindrance in classic breeding approaches, obtaining genetic markers associated with this trait is a highly desirable tool. For this reason, GWAS analysis of both genetic markers and the genes associated with fruit size determination, measured as fruit weight, was herein carried out in 50 genotypes, of which 40 corresponded to cultivated and 10 to wild olive trees. As a result, 113 genetic markers were identified, which showed a very high statistically significant correlation with fruit weight variability, p < 10−10. These genetic markers corresponded to 39 clusters of genes in linkage disequilibrium. The analysis of a segregating progeny of the cross of “Frantoio” and “Picual” cultivars allowed us to confirm 10 of the 18 analyzed clusters. The annotation of the genes in each cluster and the expression pattern of the samples taken throughout fruit development by RNAseq enabled us to suggest that some studied genes are involved in olive fruit weight determination.

Genome-Wide SNP Markers Accelerate Perennial Forest Tree Breeding Rate for Disease Resistance through Marker-Assisted and Genome-Wide Selection

The ecological and economic importance of forest trees is evident and their survival is necessary to provide the raw materials needed for wood and paper industries, to preserve the diversity of associated animal and plant species, to protect water and soil, and to regulate climate. Forest trees are threatened by anthropogenic factors and biotic and abiotic stresses. Various diseases, including those caused by fungal pathogens, are one of the main threats to forest trees that lead to their dieback. Genomics and transcriptomics studies using next-generation sequencing (NGS) methods can help reveal the architecture of resistance to various diseases and exploit natural genetic diversity to select elite genotypes with high resistance to diseases. In the last two decades, QTL mapping studies led to the identification of QTLs related to disease resistance traits and gene families and transcription factors involved in them, including NB-LRR, WRKY, bZIP and MYB. On the other hand, due to the limitation of recombination events in traditional QTL mapping in families derived from bi-parental crosses, genome-wide association studies (GWAS) that are based on linkage disequilibrium (LD) in unstructured populations overcame these limitations and were able to narrow down QTLs to single genes through genotyping of many individuals using high-throughput markers. Association and QTL mapping studies, by identifying markers closely linked to the target trait, are the prerequisite for marker-assisted selection (MAS) and reduce the breeding period in perennial forest trees. The genomic selection (GS) method uses the information on all markers across the whole genome, regardless of their significance for development of a predictive model for the performance of individuals in relation to a specific trait. GS studies also increase gain per unit of time and dramatically increase the speed of breeding programs. This review article is focused on the progress achieved in the field of dissecting forest tree disease resistance architecture through GWAS and QTL mapping studies. Finally, the merit of methods such as GS in accelerating forest tree breeding programs is also discussed.

Recent status of Genotyping by Sequencing (GBS) Technology in cucumber (Cucumis sativus L.): a review

Current and advanced breeding tools are being used to improve economically important horticultural crops to meet the consumers' needs and preferences. Genotyping-by-sequencing (GBS) is an extremely useful tool in the investigation and analysis of the genetic diversity of different cultivars. Based on a broad range of genetic backgrounds like single nucleotide polymorphism (SNPs), GBS is known as a novel technique to facilitate the detection of quantitative trait loci (QTL) regions robustly linked with interested traits compared to genome-wide association study (GWAS) and QTL. GBS has gained popularity among breeders in recent years and it is also employed in cucumber breeding programs. Cucumbers (C. sativus L.) are monoecious, gynoecious and some of them are parthenocarpic species. Cucumber is one of the most economical and essential crops in the Cucurbitaceae family. For time immemorial, cucumber has been produced and consumed all over the world like other cucurbits. To a large extent, cultivated cucurbits are beneficial to human health for providing necessary minerals and fibers.Therefore, this review portrays the current status of advances made by using GBS and its combination with other tools in various studies of cucumber such as the use of GBS and single nucleotide polymorphism (SNP) markers, GBS and GWAS, also with QTL and marker-assisted selection (MAS) are applied to display and detect explicit genetic architecture complex traits in crops and chromosome rearrangements.Cucumber breeding programs have undoubtedly benefited from genotyping-by-sequencing. Using the GBS method, research discovered lots of new candidate genes that control various traits including spine color, fruit stalk-end color, and disease resistance in cucumber lines.