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A phased genome of the highly heterozygous ‘Texas’ almond uncovers patterns of allele-specific expression linked to heterozygous structural variants
(Oxford University Press, 2024-04-09)
The vast majority of traditional almond varieties are self-incompatible, and the level of variability of the species is very high, resulting in a high-heterozygosity genome. Therefore, information on ...
An efficient CRISPR-Cas9 enrichment sequencing strategy for characterizing complex and highly duplicated genomic regions. A case study in the Prunus salicina LG3-MYB10 genes cluster
(BMC, 2022-08-27)
Background: Genome complexity is largely linked to diversifcation and crop innovation. Examples of regions with duplicated genes with relevant roles in agricultural traits are found in many crops. In ...
Exploring large-scale gene coexpression networks in peach (Prunus persica L.): a new tool for predicting gene function
(Oxford University Press, 2024-01-02)
Peach is a model for Prunus genetics and genomics, however, identifying and validating genes associated to peach breeding traits is a
complex task. A gene coexpression network (GCN) capable of capturing ...
Exploring deep learning for complex trait genomic prediction in polyploid outcrossing species
(Frontiers Media, 2020-02-06)
Genomic prediction (GP) is the procedure whereby the genetic merits of untested candidates are predicted using genome wide marker information. Although numerous examples of GP exist in plants and animals, ...
Almond population genomics and non-additive GWAS reveal new insights into almond dissemination history and candidate genes for nut traits and blooming time
(Oxford University Press, 2023-09-25)
Domestication drastically changed crop genomes, fixing alleles of interest and creating different genetic populations. Genome-wide
association studies (GWASs) are a powerful tool to detect these alleles ...
An improved melon reference genome with single-molecule sequencing uncovers a recent burst of transposable elements with potential impact on genes
(Frontiers Media, 2020-01-31)
The published melon (Cucumis melo L.) reference genome assembly (v3.6.1) has still 41.6 Mb (Megabases) of sequences unassigned to pseudo-chromosomes and about 57 Mb of gaps. Although different approaches ...
The ethylene-responsive transcription factor ERF024 is a novel regulator of climacteric fruit ripening in melon
(Wiley, 2024-06-20)
Fruit ripening is an essential developmental stage in Angiosperms triggered by hormonal signals such as
ethylene, a major player in climacteric ripening. Melon is a unique crop showing both climacteric ...
Effect of root colonization by arbuscular mycorrhizal fungi on growth, Productivity and blast resistance in rice
(SpringerOpen, 2020-06-22)
Background
Arbuscular mycorrhizal (AM) fungi form symbiotic associations with roots in most land plants. AM symbiosis provides benefits to host plants by improving nutrition and fitness. AM symbiosis ...
Copy Number Variation on ABCC2-DNMBP Loci Affects the Diversity and Composition of the Fecal Microbiota in Pigs
(American Society for Microbiology, 2023-05-31)
Genetic variation in the pig genome partially modulates the composition of porcine gut microbial communities. Previous studies have been focused on the association between single nucleotide polymorphisms ...
An improved assembly and annotation of the melon (Cucumis melo L.) reference genome
(Nature Research, 2018-05-24)
We report an improved assembly (v3.6.1) of the melon (Cucumis melo L.) genome and a new genome annotation (v4.0). The optical mapping approach allowed correcting the order and the orientation of 21 ...