Application of genomic technologies to the breeding of trees

The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure. Dissection of complex traits became possible through the availability of genome sequences along with phenotypic variation data, which allow to elucidate the causative genetic differences that give rise to observed phenotypic variation. Association mapping facilitates the association between genetic markers and phenotype in unstructured and complex populations, identifying molecular markers for assisted selection and breeding. Also, genomic data provide in silico identification and characterization of genes and gene families related to important traits, enabling new tools for molecular marker assisted selection in tree breeding. Deep sequencing of transcriptomes is also a powerful tool for the analysis of precise expression levels of each gene in a sample. It consists in quantifying short cDNA reads, obtained by NGS technologies, in order to compare the entire transcriptomes between genotypes and environmental conditions. The miRNAs are non-coding short RNAs involved in the regulation of different physiological processes, which can be identified by high-throughput sequencing of RNA libraries obtained by reverse transcription of purified short RNAs, and by in silico comparison with known miRNAs from other species. All together, NGS techniques and their applications have increased the resources for plant breeding in tree species, closing the former gap of genetic tools between trees and annual species

Gene expression analysis in cold stress conditions reveals BBX20 and CLO as potential biomarkers for cold tolerance in almond

Late spring frosts can become one of the limiting factors for the expansion of cultivation area towards a harsher climate for the almond [Prunus amygdalus Batsch syn P. dulcis (Mill.) D.A. Webb] crop as spring frost can damage up to 90% of the harvest. In order to identify key genes favoring cold tolerance in almonds, branches from three late-blooming genotypes: ‘Guara’, ‘Soleta’ and ‘Belona’ were exposed at -4¿C during 24 h in a constant climate chamber. Phenotype analysis showed that ‘Guara’ and ‘Soleta’ had a greater acclimation capacity to cold than ‘Belona’. The qRT-PCR BioMark System technology was used to monitor the relative expression of 30 candidate genes with a potential relation to cold response, which are either involved in the ICE-CBF-COR pathway or the independent CBF pathway, and also genes not yet characterized or with unknown function in almond genome. Differences in the gene expression profiles were found among the three studied genotypes and the three time-points of cold exposure (0, 2 and 24 h). BBX20 and CLO genes behaved as differentiator genes between tolerant and susceptible genotypes in cold stress response in almond pistils. In addition, the differences of expression among the tolerant genotypes suggested the intervention of different mechanisms responding to cold stress in almonds. © 2021 by the authors. Licensee MDPI, Basel, Switzerland

Caracterización de la respuesta adaptativa a sequía de dos cultivares de melocotonero en condiciones de aridez

Se evaluó la respuesta a sequía de dos cultivares de melocotonero con distinta época de maduración, 'Ufo-3' y 'Fergold', injertados sobre el patrón híbrido almendro × melocotonero, 'Garnem', en los veranos de 2015 y 2016 en Murcia, España. En poscosecha, los árboles se sometieron a 5 días sin riego y, posteriormente, a 5 días de recuperación de riego. Se evaluó el estado hídrico del árbol, el intercambio gaseoso, así como el contenido en ácido abscísico (ABA) foliar. Se comprobó un descenso del contenido hídrico del suelo (CHS), que ocasionó la reducción del potencial hídrico foliar (PHF) y el cierre estomático. Reiniciado el riego, el estado hídrico de los árboles estresados fue recuperado. Se observó una correlación negativa entre el PHF y el uso eficiente del agua intrínseco (UEAi) en 2015, indicando una posible estrategia de tolerancia mediante la cual se conservase la capacidad fotosintética, a pesar de los bajos valores de conductancia estomática (gs) y PHF. Por otra parte, la regulación del cierre estomático observada en los árboles estresados no fue provocada por la acumulación de ABA. Esta evaluación agronómica permitirá una mayor comprensión del posible efecto del patrón 'Garnem' en la adaptación fisiológica y bioquímica a la sequía y su comportamiento en recuperación bajo condiciones de campo áridas de los cultivares de melocotonero injertados

Pedigree analysis of 220 almond genotypes reveals two world mainstream breeding lines based on only three different cultivars

Loss of genetic variability is an increasing challenge in tree breeding programs due to the repeated use of a reduced number of founder genotypes. However, in almond, little is known about the genetic variability in current breeding stocks, although several cases of inbreeding depression have been reported. To gain insights into the genetic structure in modern breeding programs worldwide, marker-verified pedigree data of 220 almond cultivars and breeding selections were analyzed. Inbreeding coefficients, pairwise relatedness, and genetic contribution were calculated for these genotypes. The results reveal two mainstream breeding lines based on three cultivars: “Tuono”, “Cristomorto”, and “Nonpareil”. Descendants from “Tuono” or “Cristomorto” number 76 (sharing 34 descendants), while “Nonpareil” has 71 descendants. The mean inbreeding coefficient of the analyzed genotypes was 0.041, with 14 genotypes presenting a high inbreeding coefficient, over 0.250. Breeding programs from France, the USA, and Spain showed inbreeding coefficients of 0.075, 0.070, and 0.037, respectively. According to their genetic contribution, modern cultivars from Israel, France, the USA, Spain, and Australia trace back to a maximum of six main founding genotypes. Among the group of 65 genotypes carrying the Sf allele for self-compatibility, the mean relatedness coefficient was 0.125, with “Tuono” as the main founding genotype (24.7% of total genetic contribution). The results broaden our understanding about the tendencies followed in almond breeding over the last 50 years and will have a large impact into breeding decision-making process worldwide. Increasing current genetic variability is required in almond breeding programs to assure genetic gain and continuing breeding progress

Interaction of root-knot nematodes (RKN) and the bacterium Agrobacterium tumefaciens in roots of Prunus cerasifera : evidence of the protective effect of the Ma RKN resistance genes against expression of crown gall symptoms

International audienc

Patrones de Prunus cerasifera resistentes a los nematodos agalladores (Meloydogine spp.) previenen del ataque de la bacteria Agrobacterium tumefaciens

Especial Produccion integra IIIInternational audienc

Detection of molecular markers for resistance to root-knot nematodes (RKN) in myrobalan plum (Prunus cerasifera)

International audienc

Evidence of a new gene for high resistance to Meloidogyne spp. in Myrobalan plum, Prunus cerasifera

International audienc

Characterization and selection of Prunus rootstocks resistant to abiotic stresses: waterrlogging, water deficit and iron chlorosis

Stone fruits (Prunus spp.) are mainly grown in Mediterranean climates. The objective of a rootstock breeding program is to obtain a new 2 and 3-way rootstock generation, not only resistant to RKN nematodes, but also better adapted to Mediterranean environments that exhibit abiotic stresses (drought, chlorosis and waterlogging). This was done by the characterization of new interspecific material between nematode resistant Myrobalan plums, P. cerasifera (P.2980 and P.2175) and the peach (P. persica) × almond (P. amygdalus) hybrids: GN 15 (‘Garnem’) and GN 22 (‘Felinem’). The first data on the characterization of this plant material has revealed that tolerance to waterlogging and propagation ability, characteristics of the Myrobalan parent, have been inherited to a satisfactory level. Characterization for drought and chlorosis tolerance has also shown a satisfactory level of inheritance from the almond parent and from the almond × peach hybrids GxN. The plant material already characterized is the basis for new approaches to better understand the mechanism of tolerance to abiotic stresses

RAPD and SCAR markers linked to the Ma1 root-knot nematode resistance gene in Myrobalan plum (Prunus cerasifera Ehr.)

International audienc