Biology subjects

Rubio-Cabetas, M. J.

Publications and source records attributed to Rubio-Cabetas, M. J..

3 recordsLinked to original sources

bioRxiv2021

Polymorphisms and gene expression in the almond IGT family are not correlated to variability in growth habit in major commercial almond cultivars

Almond breeding programs aimed at selecting cultivars adapted to intensive orchards have recently focused on the optimization of tree architecture. This multifactorial trait is defined by numerous components controlled by processes such as hormonal responses, gravitropism and light perception. Gravitropism sensing is crucial to control the branch angle and therefore, the tree habit. A gene family, denominated IGT family after a share conserved domain, has been described as involved in the regulation of branch angle in several species, including rice and Arabidopsis, and even in fruit trees like peach. Here we identified six members of this family in almond: LAZY1, LAZY2, TAC1, DRO1, DRO2, IGT-like. After analyzing their protein sequences in forty-one almond cultivars and wild species, little variability was found, pointing a high degree of conservation in this family. Gene expression was analyzed in fourteen cultivars of agronomical interest comprising diverse tree habit phenotypes. Only LAZY1, LAZY2 and TAC1 were expressed in almond shoot tips during the growing season. No relation was established between the expression profile of these genes and the tree habit. However, some insight has been gained in how LAZY1 and LAZY2 are regulated, identifying the IPA1 almond homologues and other transcription factors involved in hormonal responses as regulators of their expression. Besides, we have found various polymorphisms that could not be discarded as involved in a potential polygenic origin of regulation of architectural phenotypes. Therefore, we have established that unlike many species, IGT family genes do not play a critical role in the control of tree habit in currently commercialized almond cultivars, with other gene families contributing to the variability of these traits.

plant biology↗

bioRxiv2020

PEDIGREE ANALYSIS OF 222 ALMOND GENOTYPES REVEALS TWO WORLD MAINSTREAM BREEDING LINES BASED ON ONLY THREE DIFFERENT CULTIVARS

Loss of genetic variability is a steadily increasing challenge in tree breeding programs due to the repeated use of a reduced number of founder genotypes. High-quality pedigree data of 222 almond [Prunus dulcis (Miller) D.A. Webb, syn. P. amygdalus (L) Batsch] cultivars and breeding selections were used to study global genetic variability in modern breeding programs from Argentina, Australia, France, Greece, Israel, Italy, Russia, Spain and the USA. Inbreeding coefficients, pairwise relatedness and genetic contribution were calculated for these genotypes. The results reveal two mainstream breeding lines based on three cultivars from two different geographical regions: Tuono- Cristomorto (local landraces from Puglia, Italy) and Nonpareil (chance seedling selected in California, USA, from French original stock). Direct descendants from Tuono or Cristomorto number 75 (sharing 30 descendants), while Nonpareil has 72 direct descendants. The mean inbreeding coefficient of the analyzed genotypes was 0.036, with 13 genotypes presenting a high inbreeding coefficient, over 0.250. Breeding programs from the USA, France and Spain showed inbreeding coefficients of 0.067, 0.050 and 0.034, respectively. According to their genetic contribution, modern cultivars from Israel, France, the USA, Spain and Australia, trace back to six, five, four, four and two main founding genotypes respectively. Among the group of 65 genotypes carrying the Sf allele for self-compatibility, the mean relatedness coefficient was 0.133, with Tuono as the main founding genotype (23.75% of total genetic contribution). Increasing as well as preserving current genetic variability is required in almond breeding programs worldwide to assure genetic gain and continuing breeding progress. Breeding objectives, apart from high and efficient productivity, should include disease resistance and adaptation to climate change. Ultimately, any new commercial almond cultivar has to be economically viable and breeders play a critical role in achieving this goal.

genetics↗

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↗