A Genome-Wide Analysis of the Pentatricopeptide Repeat (PPR) Gene Family and PPR-Derived Markers for Flesh Color in Watermelon (Citrullus lanatus)

Abstract

Watermelon (Citrullus lanatus) is an economically important fruit crop grown for consumption of its large edible fruit flesh. Pentatricopeptide-repeat (PPR) encoding genes, one of the large gene families in plants, are important RNA-binding proteins involved in the regulation of plant growth and development by influencing the expression of organellar mRNA transcripts. However, systematic information regarding the PPR gene family in watermelon remains largely unknown. In this comprehensive study, we identified and characterized a total of 422 C. lanatus PPR (ClaPPR) genes in the watermelon genome. Most ClaPPRs were intronless and were mapped across 12 chromosomes. Phylogenetic analysis showed that ClaPPR proteins could be divided into P and PLS subfamilies. Gene duplication analysis suggested that 11 pairs of segmentally duplicated genes existed. In-silico expression pattern analysis demonstrated that ClaPPRs may participate in the regulation of fruit development and ripening processes. Genotyping of 70 lines using 4 single nucleotide polymorphisms (SNPs) from 4 ClaPPRs resulted in match rates of over 0.87 for each validated SNPs in correlation with the unique phenotypes of flesh color, and could be used in differentiating red, yellow, or orange watermelons in breeding programs. Our results provide significant insights for a comprehensive understanding of PPR genes and recommend further studies on their roles in watermelon fruit growth and ripening, which could be utilized for cultivar development of watermelon.

High-resolution genome-wide association study of a large Czech collection of sweet cherry (Prunus avium L.) on fruit maturity and quality traits

“…Matsum. & Nakai), ClaPPR140 cosegregates perfectly with red flesh colour [ 48 ]. In woodland strawberry ( Fragaria vesca L.) accessions with white fruits, PPRs are among the genes significantly downregulated, compared with accessions with red fruits [ 49 ].…”

Cucurbitaceae: Multi-omics, functional analysis, and molecular breeding

“…For example, the MADS-box transcription factor (TF) RIPENING INHIBITOR (RIN), STAY-GREEN 1 (SGR1), AP2/ethylene response factor-type TF (RAP2.2), and phytochrome interacting factor 1 (PIF1) regulate the accumulation of carotenoids in tomato fruits by interacting with the SlPSY1 promoter . In watermelon, four PPR family genes, which are important RNAbinding proteins in plants, were correlated with flesh color (Subburaj et al, 2020). In the present study, several transcriptional regulators were identified in the candidate region for Clwf2, such as the PPR protein (Cla97C06G121830), the TPR protein (Cla97C06G121890), and AP2/ERF (Cla97C06G121910) (Supplementary Table S5).…”

“…In Arabidopsis, ARR4 transcription factor acts as a signaling module in the light signal transduction pathway (Haberer and Kieber, 2002). A study using GBSbased BSA-seq analysis in pepper identified a candidate gene CaPRR2 related to plastid development and pigment biosynthesis, affecting the levels of chlorophyll a and chlorophyll b and controlling the color of fruit (Lee et al, 2020).…”

Research Progress of PPR Proteins in RNA Editing, Stress Response, Plant Growth and Development

“…It was shown that genotyping 70 lines utilizing four SNPs from four ClaPPRs resulted in match rates above 0.87 for each validated SNP in association with the distinct phenotypes of skin colour. These findings contribute to a better knowledge of PPR genes and their functions in watermelon fruit growth and ripening, which may be useful in watermelon cultivar improvement (Subburaj et al, 2020). GhImA, which encodes a PPR protein, is involved in mitochondrial nad7 splicing, respiratory metabolism, and cotton fibre formation via ATP supply and ROS balancing (Zhang et al, 2021).…”