Biology subjects

Bulut, M.

Publications and source records attributed to Bulut, M..

4 recordsLinked to original sources

bioRxiv2026

Multi-omic analysis reveals the genetic architecture of water-deficit stress in Phaseolus vulgaris

Common bean (Phaseolus vulgaris L.) is one of the most important grain legumes for direct human consumption. Currently, 60% of its production is estimated to be at risk due to drought. However, the genetic basis of common beans drought resistance is poorly understood. To this end, we assessed the genetic architecture of drought-responsive changes in a whole genome-sequenced population of 218 common bean accessions. Using multi-omics-based trait evaluation, including lipidomics, photosynthetic and agronomic traits, followed by multi-omics genome-wide association studies (moGWAS), yielded in the detection of a myriad of moQTL for photosynthesis and yield, as well as the levels of various lipids. QTL associated with glycolipids, which are integral to photosynthesis, since they constitute the major membrane components of chloroplasts, were identified. In addition, we molecularly validated several lipid-related candidate genes via P. vulgaris hairy root transformation as well as transient expression in tobacco. In particular, a lipoxygenase and an allene oxide synthase were identified as explaining the variation in triacylglycerol by oxylipin production. These data provide a blueprint for multi-omics-assisted improvement of crop water stress resilience.

plant biology↗

bioRxiv2024

Genetic architecture of the tomato fruit lipidome; new insights link lipid and volatile compounds

Tomato (Solanum lycopersicum L.) fruit flavor is determined by a combination of multiple volatile compounds, including several derived from lipids and fatty acids. Although fruit flavor has been intensively studied, the linkage between lipid metabolism and flavor remains largely undefined. Here, we performed a genome-wide association study (GWAS) and QTL mapping for the fruit lipid content from 550 tomato accessions and 107 backcross inbred lines (BILs) in two consecutive seasons. Over 130 lipid compounds were identified and mapped, allowing for the identification of over 600 metabolic QTL (mQTL). We further described and validated candidate genes associated with lipid content. Among them is a lipase-like protein (TomLLP) whose function was validated in vivo using overexpression lines in tomato and knockout mutants in Arabidopsis. We also identified functions for three enzymes: a class III lipase (Sl-LIP8), a cyclopropane-fatty-acyl-phospholipid synthase (CFAPS1), and Lipoxygenase C (TomLoxC). By utilizing knockout lines for CFAPS1 and CRISPR-Cas9 loss-of-function lines for Sl-LIP8 and TomLoxC, we demonstrated the functional importance of these enzymes in fruit lipid metabolism. Our study provides a comprehensive analysis of the tomato fruit lipidome and insights into key genes that shaped the natural variation in tomato lipid content and their links to flavor-associated volatile compounds.

molecular biology↗

bioRxiv2023

The genetic architecture of the pepper metabolome provides insights into the regulation of capsianoside biosynthesis

Capsicum (pepper) is among the most economically important species worldwide, the fruit accumulates specialized metabolites with essential roles in plant environmental interaction and potential health benefits. However, the underlying genetic basis of their biosynthesis remains largely unknown. In this study, we developed and assessed both wild genetic variance and a bespoke mapping population to determine the genetic architecture of the pepper metabolome. The genetic analysis provided over 30 metabolic quantitative trait loci (mQTL) for over 1100 metabolites. We identified 92 candidate genes involved in various mQTL. Among the identified loci, we described and validated by transient overexpression a domestication gene cluster of eleven UDP-glycosyltransferases involved in monomeric capsianoside biosynthesis. We additionally constructed the biosynthetic reactions and annotated the genes involved in capsianoside biosynthesis in pepper. Given that differential glycosylation of acyclic diterpenoid glycosides contributes to plant resistance and acts as anticancer agents in humans, our data provide new insight, and resources for better understanding the biosynthesis of beneficial natural compounds to improve human health.

genetics↗

bioRxiv2020

Apple peel and flesh contain pro-neurogenic compounds

As mammals evolved exposed to particular diets, naturally abundant compounds may have become part of the set of environmental co-determinants that shaped brain structure and function. Here we investigated whether bioactive factors found in apples directly affect hippocampal neural stem cells and promote neurogenesis in the adult mouse. Whereas the consumption of apple juice per se neither altered adult hippocampal neurogenesis nor improved learning and memory, we did find specific direct effects of apple-derived factors on neural stem cell survival and differentiation. Our results revealed that quercetin, the most abundant flavanol in apple peel, was anti-proliferative at high concentrations but acted pro-neurogenically at low concentrations. This was confirmed in vivo, with intraperitoneally-delivered quercetin promoting survival and neuronal differentiation, without affecting proliferation, likely via the PI3 kinase-Akt and Nrf2-Keap1 pathways, respectively. Using a bio-assay-guided fractionation approach with high-resolution collision induced dissociation mass spectroscopy, we also identified additional pro-neurogenic compounds in apple flesh that were not related to flavonoids. In particular, we found that 3,5-dihydroxybenzoic acid, a weak agonist to the lactate receptor, significantly increased both in vitro and in vivo neural precursor cell proliferation and neurogenesis. Altogether, this work shows that both flavonoids and 3,5-dihydroxybenzoic acid are pro-neurogenic, not only by activating precursor cell proliferation but also through promoting cell cycle exit, cellular survival, and neuronal differentiation.

neuroscience↗