Almond diversity and homozygosity define structure, kinship, inbreeding, and linkage disequilibrium in cultivated germplasm, and reveal genomic associations with nut and seed weight

Almond[Prunus dulcis Miller(D.A.Webb)]is the main tree nut species worldwide.Here,genotyping-by-sequencing(GBS)was applied to 149 almond cultivars from the ex situ collections of the Italian Council for Agricultural Research(CREA)and the Spanish National Research Council(CSIC),leading to the detection of 93,119 single-nucleotide polymorphisms(SNPs).The study of population structure outlined four distinct genetic groups and highlighted diversification between the Mediterranean and Californian gene pools.Data on SNP diversity and runs of homozygosity(ROHs)allowed the definition of kinship,inbreeding,and linkage disequilibrium(LD)decay in almond cultivated germplasm.Four-year phenotypic observations,gathered on 98 cultivars of the CREA collection,were used to perform a genome-wide association study(GWAS)and,for the first time in a crop species,homozygosity mapping(HM),resulting in the identification of genomic associations with nut,shell,and seed weight.Both GWAS and HM suggested that loci controlling nut and seed weight are mostly independent.Overall,this study provides insights on the almond cultivation history and delivers information of major interest for almond genetics and breeding.In a broader perspective,our results encourage the use of ROHs in crop science to estimate inbreeding,choose parental combinations minimizing the risk of inbreeding depression,and identify genomic footprints of selection for specific traits.

Transcriptome reprogramming,epigenetic modifications and alternative splicing orchestrate the tomato root response to the beneficial fungus Trichoderma harzianum

Beneficial interactions of rhizosphere microorganisms are widely exploited for plant biofertilization and mitigation of biotic and abiotic constraints.To provide new insights into the onset of the roots–beneficial microorganisms interplay,we characterised the transcriptomes expressed in tomato roots at 24,48 and 72 h post inoculation with the beneficial fungus Trichoderma harzianum T22 and analysed the epigenetic and post-trascriptional regulation mechanisms.We detected 1243 tomato transcripts that were differentially expressed between Trichoderma-interacting and control roots and 83 T.harzianum transcripts that were differentially expressed between the three experimental time points.Interaction with Trichoderma triggered a transcriptional response mainly ascribable to signal recognition and transduction,stress response,transcriptional regulation and transport.In tomato roots,salicylic acid,and not jasmonate,appears to have a prominent role in orchestrating the interplay with this beneficial strain.Differential regulation of many nutrient transporter genes indicated a strong effect on plant nutrition processes,which,together with the possible modifications in root architecture triggered by ethylene/indole-3-acetic acid signalling at 72 h post inoculation may concur to the well-described growth-promotion ability of this strain.Alongside,T.harzianum-induced defence priming and stress tolerance may be mediated by the induction of reactive oxygen species,detoxification and defence genes.A deeper insight into gene expression and regulation control provided first evidences for the involvement of cytosine methylation and alternative splicing mechanisms in the plant–Trichoderma interaction.A model is proposed that integrates the plant transcriptomic responses in the roots,where interaction between the plant and beneficial rhizosphere microorganisms occurs.