Biology subjects

Castanera, R.

Publications and source records attributed to Castanera, R..

3 recordsLinked to original sources

bioRxiv2024

Evaluation of Deep Learning for predicting rice traits using structural and single-nucleotide genomic variants

Structural variants (SVs) such as deletions, inversions, duplications, and Transposable Element (TE) Insertion Polymorphisms (TIPs) are prevalent in plant genomes and have played an important role in evolution and domestication, as they constitute a significant source of genomic and phenotypic variability. Nevertheless, most methods in quantitative genetics focusing on crop improvement, such as genomic prediction, consider Single Nucleotide Polymorphisms (SNPs) as the only type of genetic marker. Here, we used rice to investigate whether combining the structural and nucleotide genome-wide variation can improve prediction ability of traits when compared to using only SNPs. Moreover, we also examine the potential advantage of Deep Learning (DL) networks over Bayesian Linear models, which have been widely applied in genomic prediction. Specifically, the performance of BayesC and a Bayesian Reproducible Kernel Hilbert space regressions were compared to two different DL architectures, the Multilayer Perceptron, and the Convolution Neural Network. We further explore their prediction ability by using various marker input strategies and found that exploiting structural and nucleotide variation improves prediction ability on complex traits in rice. Also, DL models outperformed Bayesian models in 75% of the studied cases. Finally, DL systematically improved prediction ability of binary traits against the Bayesian models.

genomics↗

bioRxiv2020

The replicative amplification of MITEs and their impact on rice trait variability

Transposable elements (TEs) are a rich source of genetic variability. Among TEs, Miniature Inverted- repeat Transposable Elements (MITEs) are of particular interest as they are present in high copy numbers in plant genomes and are closely associated with genes. MITEs are deletion derivatives of class II transposons, and can be mobilized by the transposases encoded by the latters through a typical cut-and-paste mechanism. However, this mechanism cannot account for the high copy number MITEs attain in plant genomes, and the mechanism by which MITEs amplify remains elusive. We present here an analysis of 103,109 Transposon Insertion Polymorphisms (TIPs) in 1,059 O. sativa genomes representing the main rice population groups. We show that an important fraction of MITE insertions has been fixed in rice concomitantly with rice domestication. However, another fraction of MITE insertions is present at low frequencies. We performed MITE TIP-GWAS to study the impact of these elements on agronomically important traits and found that these elements uncover more trait associations than SNPs on important phenotypes such as grain width. Finally, using SNP-GWAS and TIP-GWAS we provide evidences of the replicative amplification of MITEs, suggesting a mechanism of amplification uncoupled from the typical cut-and-paste mechanism of class II transposons.

molecular biology↗

bioRxiv2019

Transposons played a major role in the diversification between the closely related almond (Prunus dulcis) and peach (P. persica) genomes: Results from the almond genome sequence

Combining both short and long-read sequencing, we have estimated the almond Prunus dulcis cv. Texas genome size in 235 Mbp and assembled 227.6 Mb of its sequence. The highly heterozygous compact genome of Texas comprises eight chromosomes, to which we have anchored over 91% of the assembly. We annotated 27,042 protein-coding genes and 6,800 non-coding transcripts. High levels of genetic variability were characterized after resequencing a collection of ten almond accessions. Phylogenomic comparison with the genomes of 16 other close and distant species allowed estimating that almond and peach diverged around 5.88 Mya. Comparison between peach and almond genomes confirmed the high synteny between these close relatives, but also revealed high numbers of presence-absence variants, many attributable to the movement of transposable elements (TEs). The number and distribution of TEs between peach and almond was similar, but the history of TE movement was distinct, with peach having a larger proportion of recent transpositions and almond preserving a higher level of polymorphism in the older TEs. When focusing on specific genes involved in key characters such as the bitter vs. sweet kernel taste and the formation of a fleshy mesocarp, we found that for one gene associated with the biosynthesis of amygdalin that confers the bitter kernel taste, several TEs were inserted in its vicinity only in sweet almond cultivars but not in bitter cultivars and Prunus bitter kernel relatives, including P. webbii, P. mume, and other species like peach and cherry. TE insertions likely to produce affects in the expression of six more genes involved in the formation of the fleshy mesocarp were also identified. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond with respect to peach.

genomics↗