Genome-wide association studies in apple reveal loci of large effect controlling apple polyphenols

McClure, Kendra A.; Gong, YuiHui; Song, Jun; Vinqvist‐Tymchuk, Melinda; Palmer, Leslie Campbell; Fan, Lihua; Burgher-MacLellan, Karen; Zhang, Zhaoqi; Celton, Jean‐Marc; Forney, Charles F.; Migicovsky, Zoë; Myles, Sean

doi:10.1038/s41438-019-0190-y

Cited by 56 publications

(39 citation statements)

References 61 publications

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“…Three of these studies were based on bi-parental mapping populations (Chagné et al, 2012;Khan et al, 2012;Verdu et al, 2014). A strong but non-significant signal was detected for chlorogenic acid in a breeding-relevant population using mG-WAS (McClure et al, 2019). The stronger mQTL signal we observed could be due to the specific breeding-relevant germplasm used for this study.…”

Section: Previous Studies Have Identified An Mqtl On the Bottom Ofmentioning

confidence: 89%

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Integrating genomics and multi-platform metabolomics enables metabolite QTL detection in breeding-relevant apple germplasm

Bilbrey

Williamson

Hatzakis

et al. 2021

Preprint

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Research Conducted: Apple (Malus x domestica) has commercial and nutritional value, but breeding constraints of tree crops limit varietal improvement. Marker-assisted selection minimizes these drawbacks, but breeders lack applications for targeting fruit phytochemicals. To understand genotype-phytochemical associations in apples, we have developed a high-throughput integration strategy for genomic and multi-platform metabolomics data. Methods: 124 apple genotypes, including members of three pedigree-connected breeding families alongside diverse cultivars and wild selections, were genotyped and phenotyped. Metabolite genome-wide association studies (mGWAS) were conducted with ~10,000 single nucleotide polymorphisms and phenotypic data acquired via LC-MS and 1H NMR untargeted metabolomics. Putative metabolite quantitative trait loci (mQTL) were then validated via pedigree-based analyses (PBA). Key Results: Using our developed method, 519, 726, and 177 putative mQTL were detected in LC-MS positive and negative ionization modes and NMR, respectively. mQTL were indicated on each chromosome, with hotspots on linkage groups 16 and 17. A chlorogenic acid mQTL was discovered on chromosome 17 via mGWAS and validated with a two-step PBA, enabling discovery of novel candidate gene-metabolite relationships. Main Conclusion: Complementary data from three metabolomics approaches and dual genomics analyses increased confidence in validity of compound annotation and mQTL detection. Our platform demonstrates the utility of multi-omics integration to advance data-driven, phytochemical-based plant breeding.

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Section: Previous Studies Have Identified An Mqtl On the Bottom Ofmentioning

confidence: 89%

“…LG 17 for chlorogenic acid (Chagné et al, 2012;Khan et al, 2012;Verdu et al, 2014;McClure et al, 2019). Three of these studies were based on bi-parental mapping populations (Chagné et al, 2012;Khan et al, 2012;Verdu et al, 2014).…”

Section: Previous Studies Have Identified An Mqtl On the Bottom Ofmentioning

confidence: 99%

Integrating genomics and multi-platform metabolomics enables metabolite QTL detection in breeding-relevant apple germplasm

Bilbrey

Williamson

Hatzakis

et al. 2021

Preprint

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“…QTL mapping was undertaken using the seedling families, while a GWAS performed on 233 accessions produced detailed information on associations between allelic configurations and associated traits. A set of 172 apple accessions from the Nova Scotia Fruit Growers’ Association Cultivar Education Trial, Kentville, Canada were genotyped with GBS-derived SNPs and phenotyped during two years for fruit quality traits and resistance/susceptibility to apple scab ( Venturia ineaqualis (Cooke) G.Winter) [ 180 ] and for content of phenolic compounds [ 181 ]. GWAS revealed several known loci for skin color, harvest date, and firmness at harvest.…”

Section: Phenotypic Traitsmentioning

confidence: 99%

Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops

Nybom

Lācis

2021

Plants

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Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit and berries, potatoes and woody ornamentals. The primary goal is usually to identify true-to-type plant material, detect possible synonyms, and investigate genetic diversity and relatedness among accessions. A secondary goal may be to create sustainable databases that can be utilized in research and breeding for several years ahead. Commonly applied DNA markers (like microsatellite DNA and SNPs) and next-generation sequencing each have their pros and cons for these purposes. Methods for large-scale phenotyping have lagged behind, which is unfortunate since many commercially important traits (yield, growth habit, storability, and disease resistance) are difficult to score. Nevertheless, the analysis of gene action and development of robust DNA markers depends on environmentally controlled screening of very large sets of plant material. Although more time-consuming, co-operative projects with broad-scale data collection are likely to produce more reliable results. In this review, we will describe some of the approaches taken in genotyping and/or phenotyping projects concerning a wide variety of vegetatively propagated crops.

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“…functional groups [13][14][15] . They are classified into the following groups: phenolic acids, flavonoids, lignans, curcuminoids, stilbenes, and tannins 16 .…”

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confidence: 99%

Stability and anti-proliferative properties of biologically active compounds extracted from Cistus L. after sterilization treatments

Ammendola

Haponska

Balik

et al. 2020

Sci Rep

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The growing interest of oncologists in natural compounds such as polyphenols and flavonoids is encouraging the development of innovative and efficient carriers for the delivery of those drugs. This study examines carboxymethyl chitosan-based microcapsules created by spray drying as a method for delivering biologically active compounds isolated from the Cistus herb. Effects of sterilization and encapsulation on the polyphenol and flavonoid content of Cistus extract were investigated to optimize the production process. Furthermore, in vitro studies were carried out to examine the anticancer properties of sterilized polyphenols and flavonoids on glioblastoma cells isolated from oncological patients. Acquired results show high anticancer potential towards glioblastoma as well as low cytotoxicity towards non-cancer cell lines by the substances in question. Steam sterilization is shown to affect the content of biologically active compounds the least. We demonstrate that the investigated form of drug encapsulation is both efficient and potentially possible to scale up from the viewpoint of the pharmaceutical industry. According to apress statement launched by the International Agency for Research on Cancer from the World Health Organization (WHO), in 2018the global cancer burdenaffected 18.1 million new cases and 9.6 million of people passed away. Ten in 50 men and one in 60 women worldwide suffer from cancer during their life, and ten in 80 men and eleven in 110 women posse awaydue to thisillness. Moreover, cancer is a most frequent causeof children death. Worldwide, every year, approximately 300.000 of children are diagnosed by oncologists with a cancer disease 1,2. Furthermore, according to the published statistic data, the total number of people who are alive within 5 years of a cancer diagnosis, called the 5-year prevalence, is arround 43.8 million 3. As stated in the WHO report,the frequent types of cancer in men are cancer of lung, prostate, colorectal, stomach and liver, while in case on women, the most common type of cancer are: breast, colorectal, lung, cervix and thyroid cancer. The uncontrollable growth of tumor cells is the most fundamental aspect of cancer 4. Even if available therapies such as surgery, immunotherapy, chemotherapy, targeted therapy, hormone therapy and radiation therapy play a significant role in cancer treatment, drug resistance and toxicity remain main problems and challenges to cure cancer patients 5. Oncologists have called for basic investigationsand new upstream technologieswhich insustainably, efficiently and safely way will meet the current and future patients' needs 6,7. Additionally, during the last years the "integrative" oncology society has demanded advancesfrom scientists on the development of natural medicals 8,9. Indeed, the anticancer effects of biologically active compounds, such as natural polyphenols synthesized by fruits, vegetables, teas, apples, cocoa and other plants, have become a hot topic in many laboratories 10-12 .

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Genome-wide association studies in apple reveal loci of large effect controlling apple polyphenols

Cited by 56 publications

References 61 publications

Integrating genomics and multi-platform metabolomics enables metabolite QTL detection in breeding-relevant apple germplasm

Integrating genomics and multi-platform metabolomics enables metabolite QTL detection in breeding-relevant apple germplasm

Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops

Stability and anti-proliferative properties of biologically active compounds extracted from Cistus L. after sterilization treatments

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