Biology subjects

Amaya, I.

Publications and source records attributed to Amaya, I..

6 recordsLinked to original sources

bioRxiv2025

Novel substrate affinity of FaCCR1 and FaCCR1/FaOCT4 expression control the content of medium-chain esters in strawberry fruit

Fruit flavor and aroma are influenced by the sugars-to-acid ratio and most importantly by the specific profile and abundance of volatile organic compounds (VOCs). While over 550 VOCs have been identified in strawberry fruit, fewer than 20 are believed to be key for aroma, being esters the major components. A major and stable quantitative trait locus (QTL) explaining a large percentage (40%) of phenotypic variation for several medium-chain esters (MCE) was mapped at about 19 Mb in chromosome 6A using both a biparental population and genome-wide association studies (GWAS). Using a combination of genetic mapping, global transcriptomic studies of bulked contrasting lines, and in vivo and in silico functional analyses, we identified the cinnamoyl Co-A reductase FaCCR1(6A) and the organic cation/carnitine transporter FaOCT4(6A) as underlying genes. Subcellular localization experiments indicated that FaCCR1(6A) and FaOCT4(6A) localize at the cytosol and tonoplast membrane respectively. Transient overexpression of FaCCR1(6A) and FaOCT4(6A) in fruits resulted in a significant increase in MCE content. Despite the well-described function of CCRs in the biosynthesis of monolignols, in vitro enzymatic assays and molecular docking revealed that FaCCR1(6A) also presents high affinity for MCE precursors, indicating a previously unidentified function of this protein in volatile biosynthesis. Based in our findings, we have developed a predictive KASP assay in FaOCT4(6A) for selecting superior cultivars with enhanced fruit aroma.

plant biology↗

bioRxiv2024

Differential expression ofCCD4(4B) drives natural variation in fruit carotenoidcontent in strawberry ( Fragaria spp.)

Pigments, mainly anthocyanins and carotenoids, are important contributors to fruits visual appearance and nutritional properties. In strawberry (Fragaria spp.), the genetic and molecular mechanisms regulating fruit carotenoid biosynthesis and its natural variation remain largely unexplored. In this study, we sought to identify genomic loci contributing to variation in yellow flesh pigmentation. A major QTL, qYellow Flesh-4B, accounting for 82% of the total phenotypic variation was identified on F. x ananassa chromosome 4B. Following a candidate gene approach, we determined that CCD4(4B), a carotenoid cleavage dioxygenase (CCD), was the underlying gene. Specific polymorphisms on CCD4(4B) promoter region were associated with the yellow flesh phenotype and with differential regulation of CCD4(4B) expression during fruit ripening. Furthermore, CCD4(4B) expression levels were negatively correlated with violaxanthin, lutein, zeaxanthin, {beta}-carotene and total carotenoid content. The role of CCD4(4B) in carotenoid turnover was confirmed by transient overexpression in F. x ananassa fruits, which led to a decrease in carotenoid accumulation. Notably, a -35 C>T SNP identified in CCD4(4B) promoter was found to be predictive for CCD4(4B) expression, and carotenoid content in fruits of a diverse germplasm collection, which included different octoploid Fragaria species. Taken together, these results provide important genetic insights into the natural variation of carotenoid content in strawberry. The High-Resolution Melting (HRM) DNA test here developed offers a fast and reliable method to predict high fruit carotenoid content, representing a useful tool for breeding projects aiming to enhance the nutritional value of this crop.

plant biology↗

bioRxiv2024

Genome-wide association studies in a diverse strawberry collection unveil loci controlling agronomic and fruit quality traits

Strawberries are cherished for their organoleptic properties and nutritional value. However, breeding new cultivars involves the simultaneous selection of many agronomical and fruit quality traits. The strawberry germplasm collection here studied exhibited extensive phenotypic variation in 26 agronomic and fruit quality traits across three consecutive seasons. Phenotypic correlations and Principal Component Analysis (PCA) revealed relationships among traits and accessions, emphasizing the impact of plant breeding. Genetic diversity analysis on 124 accessions using 44,408 markers denoted a population structure divided into six subpopulations that still retain considerable diversity. Genome-wide association studies (GWAS) for the 26 traits unveiled 121 significant marker-trait associations distributed across 95 quantitative trait loci (QTL). Multiple associations were detected for fruit firmness, a key breeding target, including a prominent locus on chromosome 6A. The candidate gene FaPG1, controlling fruit softening, was identified within this QTL region. Differential expression of FaPG1 confirmed its role as the main contributor to natural variation in fruit firmness. A Kompetitive Allele-Specific PCR (KASP) assay based on SNP AX-184242253, associated with the 6A QTL, predicts a substantial increase in fruit firmness, validating its utility for Marker-Assisted Selection (MAS). In essence, this comprehensive study provides insights into the phenotypic and genetic landscape of the strawberry collection and lays a robust foundation for propelling the development of superior strawberry cultivars through precision breeding. HighlightSeveral QTL controlling agronomic and fruit quality traits detected by genome wide association studies. Natural variation on FaPG1 expression is associated with a mayor and stable QTL for fruit firmness.

plant biology↗

bioRxiv2023

Strawberry phenotypic plasticity in flowering time is driven by interaction between genetic loci and temperature

The flowering time, which determines when the fruits or seeds can be harvested, is known to be sensitive to plasticity, i.e. the ability of a genotype to display different phenotypes in response to environmental variations. In the context of climate change, strawberry breeding can take advantage of phenotypic plasticity to create high-performing varieties adapted either to local conditions or to a wide range of climates. To decipher how the environment affects the genetic architecture of flowering time in cultivated strawberry (Fragaria xananassa) and modify its QTL effects, we used a bi-parental segregating population grown for two years at widely divergent latitudes (5 European countries) and combined climatic variables with genomic data (Affymetrix(R) SNP array). We detected 10 unique flowering time QTL and demonstrated that temperature modulates the effect of plasticity-related QTL. We propose candidate genes for the three main plasticity QTL, including FaTFL1 which is the most relevant candidate in the interval of the major temperature-sensitive QTL (6D_M). We further designed and validated a genetic marker for the 6D_M QTL which offers great potential for breeding programs, for example for selecting of early-flowering strawberry varieties well adapted to different environmental conditions. HighlightsA GXE study of a segregating strawberry population in Europe showed that temperature is the main driver of flowering time plasticity. A genetic marker was designed for the main QTL.

genetics↗

bioRxiv2023

A genome-wide overexpression screen reveals Mycobacterium smegmatis growth inhibitors encoded by mycobacteriophage Hammy

During infection, bacteriophages produce diverse gene products to overcome bacterial anti-phage defenses, to outcompete other phages, and take over cellular processes. Even in the best-studied model phages, the roles of most phage-encoded gene products are unknown, and the phage population represents a largely untapped reservoir of novel gene functions. Considering the sheer size of this population, experimental screening methods are needed to sort through the enormous collection of available sequences and identify gene products that can modulate bacterial behavior for downstream functional characterization. Here, we describe the construction of a plasmid-based overexpression library of 94 genes encoded by Hammy, a Cluster K mycobacteriophage closely related to those infecting clinically important mycobacteria. The arrayed library was systematically screened in a plate-based cytotoxicity assay, identifying a diverse set of 24 gene products (representing 25% of the Hammy genome) capable of inhibiting growth of the host bacterium Mycobacterium smegmatis. Half of these are related to growth inhibitors previously identified in related phage Waterfoul, supporting their functional conservation; the other genes represent novel additions to the list of known anti-mycobacterial growth inhibitors. This work, conducted as part of the HHMI-supported Science Education Alliance Gene-function Elucidation by a Network of Emerging Scientists (SEA-GENES) project, highlights the value of parallel, comprehensive overexpression screens in exploring genome-wide patterns of phage gene function and novel interactions between phages and their hosts.

microbiology↗

bioRxiv2020

Allelic Variation of MYB10 is the Major Force Controlling Natural Variation of Skin and Flesh Color in Strawberry (Fragaria spp.) fruit

Anthocyanins are the principal color-producing compounds synthesized in developing fruits of strawberry (Fragaria spp.). Substantial natural variation in color have been observed in fruits of diploid and octoploid accessions, resulting from distinct accumulation and distribution of anthocyanins in fruits. Anthocyanin biosynthesis is controlled by a clade of R2R3 MYB transcription factors, among which MYB10 has been shown as the main activator in strawberry fruit. Here, we show that MYB10 mutations cause most of the anthocyanin variation observed in diploid woodland strawberry (F. vesca) and octoploid cultivated strawberry (F. xananassa). Using a mapping-by-sequencing approach, we identified a gypsy-transposon insertion in MYB10 that truncates the protein and knocks out anthocyanin biosynthesis in a white-fruited F. vesca ecotype. Two additional loss-of-function MYB10 mutations were identified among geographically diverse white-fruited F. vesca ecotypes. Genetic and transcriptomic analyses in octoploid Fragaria spp. revealed that FaMYB10-2, one of three MYB10 homoeologs identified, residing in the F. iinumae-derived subgenome, regulates the biosynthesis of anthocyanins in developing fruit. Furthermore, independent mutations in MYB10-2 are the underlying cause of natural variation in fruit skin and flesh color in octoploid strawberry. We identified a CACTA-like transposon (FaEnSpm-2) insertion in the MYB10-2 promoter of red-fleshed accessions that was associated with enhanced expression and anthocyanin accumulation. Our findings suggest that putative cis regulatory elements provided by FaEnSpm-2 are required for high and ectopic MYB10-2 expression and induction of anthocyanin biosynthesis in fruit flesh. We developed MYB10-2 (sub-genome) specific DNA markers for marker-assisted selection that accurately predicted anthocyanin phenotypes in octoploid segregating populations.

plant biology↗