Single Nucleotide Polymorphism Detection for Peach Gummosis Disease Resistance by Genome-Wide Association Study

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.

Transcriptomic and sugar metabolic analysis reveals molecular mechanisms of peach gummosis in response to Neofusicoccum parvum infection

Peach gummosis, a devastating disease caused by Neofusicoccum parvum, significantly shortens peach tree lifespan and reduces the yield of peach trees. Despite its impact, the molecular mechanism underlying this disease remains largely unexplored. In this study, we used RNA-seq, sugar metabolism measurements, and an integrated transcriptional and metabolomic analysis to uncover the molecular events driving peach gummosis. Our results revealed that N. parvum infection drastically altered the transcripts of cell wall degradation-related genes, the log2Fold change in the transcript level of Prupe.1G088900 encoding xyloglucan endotransglycosylase decreased 2.6-fold, while Prupe.6G075100 encoding expansin increased by 2.58-fold at 12 hpi under N. parvum stress. Additionally, sugar content analysis revealed an increase in maltose, sucrose, L-rhamnose, and inositol levels in the early stages of infection, while D-galactose, D-glucose, D-fructose consistently declined as gummosis progressed. Key genes related to cell wall degradation and starch degradation, as well as UDP-sugar biosynthesis, were significantly upregulated in response to N. parvum. These findings suggest that N. parvum manipulates cell wall degradation and UDP-sugar-related genes to invade peach shoot cells, ultimately triggering gum secretion. Furthermore, weighted gene co-expression network analysis (WGCNA) identified two transcription factors, ERF027 and bZIP9, as central regulators in the downregulated and upregulated modules, respectively. Overall, this study enhances our understanding of the physiological and molecular responses of peach trees to N. parvum infection and provide valuable insights into the mechanisms of peach defense against biotic stresses.

Origins and Genetic Characteristics of Egyptian Peach

Peach (Prunus persica), a significant economic fruit tree in the Rosaceae family, is extensively cultivated in temperate and subtropical regions due to its abundant genetic diversity, robust adaptability, and high nutritional value. Originating from China over 4000 years ago, peaches were introduced to Persia through the Silk Road during the Han Dynasty and gradually spread to India, Greece, Rome, Egypt, Europe, and America. Currently grown in more than 80 countries worldwide, the expansion of peach cultivation in Egypt is mainly due to the development and utilization of peach varieties with low chilling requirements. These varieties exhibit unique phenotypic characteristics such as early maturity, reduced need for winter cold temperatures, low water requirements, and high economic value. In this study, a systematic analysis was conducted on the genetic characteristics and kinship relationships of peaches with low chilling requirements in Egypt. We conducted a comprehensive evolutionary and Identity-by-Descent (IBD) analysis on over 300 peach core germplasm resources, including Egyptian cultivars with low chilling requirements, to investigate their origin and genetic characteristics. The evolutionary analysis revealed that 'Bitter almond' is closely related to China's wild relative species Prunus tangutica Batal, while 'Early grand' shares one branch with Chinese ornamental peach cultivars, and 'Nemaguard' clusters with some ancient local varieties from China. The IBD analysis also indicated similar genetic backgrounds, suggesting a plausible origin from China. Similarly, the analysis suggested that 'Swelling' may have originated from the Czech Republic while 'Met ghamr' has connections to South Africa. 'Desert red', 'Early swelling', and 'Florida prince' are likely derived from Brazil. These findings provide valuable insights into the genetic characteristics of Egyptian peach cultivars. They offer a significant foundation for investigating the origin and spread of cultivated peaches worldwide and serve as a valuable genetic resource for breeding low chilling requirement cultivars, which is of considerable significance for the advancement of peach cultivation in Egypt.

Multiple-statistical genome-wide association analysis and genomic prediction of fruit aroma and agronomic traits in peaches

'Chinese Cling' is an important founder in peach breeding history due to the pleasant flavor. Genome-wide association studies (GWAS) combined with genomic selection are promising tools in fruit tree breeding, as there is a considerable time lapse between crossing and release of a cultivar. In this study, 242 peaches from Shanghai germplasm were genotyped with 145 456 single-nucleotide polymorphisms (SNPs). The six agronomic traits of fruit flesh color, fruit shape, fruit hairiness, flower type, pollen sterility, and soluble solids content, along with 14 key volatile odor compounds (VOCs), were recorded for multiple-statistical GWAS. Except the reported candidate genes, six novel genes were identified as associated with these traits. Thirty-nine significant SNPs were associated with eight VOCs. The putative candidate genes were confirmed for VOCs by RNA-seq, including three genes in the biosynthesis pathway found to be associated with linalool, soluble solids content, and cis-3-hexenyl acetate. Multiple-trait genomic prediction enhanced the predictive ability for γ-decalactone to 0.7415 compared with the single-trait model value of 0.1017. One PTS1-SSR marker was designed to predict the linalool content, and the favorable genotype 187/187 was confirmed, mainly existing in the 'Shanghai Shuimi' landrace. Overall, our findings will be helpful in determining peach accessions with the ideal phenotype and show the potential of multiple-trait genomic prediction to improve accuracy for highly correlated genetic traits. The diagnostic marker will be valuable for the breeder to bridge the gap between quantitative trait loci and marker-assisted selection for developing strong-aroma cultivars.

Two decades of association mapping: Insights on disease resistance in major crops

Climate change across the globe has an impact on the occurrence, prevalence, and severity of plant diseases. About 30% of yield losses in major crops are due to plant diseases; emerging diseases are likely to worsen the sustainable production in the coming years. Plant diseases have led to increased hunger and mass migration of human populations in the past, thus a serious threat to global food security. Equipping the modern varieties/hybrids with enhanced genetic resistance is the most economic, sustainable and environmentally friendly solution. Plant geneticists have done tremendous work in identifying stable resistance in primary genepools and many times other than primary genepools to breed resistant varieties in different major crops. Over the last two decades, the availability of crop and pathogen genomes due to advances in next generation sequencing technologies improved our understanding of trait genetics using different approaches. Genome-wide association studies have been effectively used to identify candidate genes and map loci associated with different diseases in crop plants. In this review, we highlight successful examples for the discovery of resistance genes to many important diseases. In addition, major developments in association studies, statistical models and bioinformatic tools that improve the power, resolution and the efficiency of identifying marker-trait associations. Overall this review provides comprehensive insights into the two decades of advances in GWAS studies and discusses the challenges and opportunities this research area provides for breeding resistant varieties.