Identification of genes associated with kernel size in almond [Prunus dulcis (Mill.) D.A. Webb] using RNA-Seq

• Published in: Plant growth regulation 2022-06, Vol.97 (2), p.357-373
• Main Authors: Jafari, Marjan, Shiran, Behrouz, Rabiei, Gholamreza, Ravash, Rudabeh, Sayed Tabatabaei, Badraldin Ebrahim, Martínez-García, Pedro J., Martínez-Gómez, Pedro
• Format: Article
• Language: English
• Subjects: ABC transporter; Agriculture; Annotations; Biomedical and Life Sciences; Cell interactions; Crops; Cultivars; Cytochrome P450; Cytochromes P450; Dioxygenase; Fruits; Genes; Genetic control; Genotypes; Gibberellic acid; Gibberellins; Kernels; Life Sciences; Metabolites; Nutritive value; Original Paper; Plant Anatomy/Development; Plant Physiology; Plant reproduction; Plant Sciences; Pollen; Pollination; Proteins; Prunus dulcis; Regulatory mechanisms (biology); Ribonucleic acid; RNA; Rosaceae; Seeds; Sucrose; Sucrose synthase
• ISSN: 0167-6903; 1573-5087
• DOI: 10.1007/s10725-022-00801-4

Almond is a stone fruit crop belonging to the Rosaceae family, cultivated in the temperate region of the world for its high nutritive valued fruits. In today’s marketplace, the grower profit is directly related to input traits such as large fruit size. To elucidate the genetic control of seed size in almonds, we use the xenia phenomenon. For this purpose, in this study, almond cultivars ‘Sefid’ and ‘Mamaee Pooya’ were pollinated with pollen from almond cultivars ‘Mamaee’ (large seeds) and a genotype ‘Orientalis’ (small seeds). The seed quantitative traits showed pollination with ‘Mamaee’ increased these traits of each female parent compared to pollination with ‘Orientalis’. Comparative profiling demonstrated 258 differentially expressed genes (DEGs) between the two assayed RNA-Seq samples (one sample containing a pool of seeds of ‘Sefid’ × ‘Mamaee’ and the other a pool of seeds of ‘Sefid’ × ‘Orientalis’). Which among them 150 were up-regulated and 108 were down-regulated. Gene ontology (GO) annotation analysis revealed that DEGs were associated with hormone signaling, metabolite synthesis and cell communication. KEGG pathway analysis on 256 DEGs showed that many genes are engaged in the control of kernel size. Also, analysis of protein–protein interaction network displayed that several genes such as PduBEN1 (Protein BRI1-5 ENHANCED 1), PduSUS2 (Sucrose synthase 2), PduGA2OX2 (Gibberellin 2-beta-dioxygenase 2), PduABCG25 (ABC transporter G family member 25), PduGASA1 (gibberellic acid-stimulated Arabidopsis) and PduCYP72C1 (cytochrome p450 72c1) had a remarkable impact on kernel size. This study has provided considerable insights into the complicated regulatory mechanism underlying the kernel size trait in almonds.