Santos Marlene, Gila-Navarro Alberto, Weiss Julia, Gonçalves Berta, Matos Manuela, Egea-Cortines Marcos
Centre for Research and Technology of Agro-Environmental and Biological Sciences , CITAB, Inov4Agro, University of Trás-os-Montes and Alto Douro, UTAD, Quinta de Prados, 5000-801, Vila Real, Portugal.
Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena Campus Muralla del Mar, Cartagena, 30202, Spain.
Sci Rep. 2025 Jul 22;15(1):26619. doi: 10.1038/s41598-025-11006-w.
Fruit cracking is a developmental defect depending on genetic and environmental conditions. Fruit cracking has a negative impact on quality and production. Fruits with cracking cannot be commercialized and enhance pathogen contaminations. Identifying genes as markers may help in breeding and post-harvest treatments. We compared qPCR and dPCR methods using a set of 16 genes that appear to be differentially expressed in the cherry varieties Sweatheart with low cracking and Burlat with high cracking indexes. Differences in absolute transcripts spanned across nearly three orders of magnitude. Overall qPCR and dPCR show a highly significant negative correlation of -0.90. The equation allowed converting Ct values to dPCR copy number. However, copy number in dPCR allow a direct comparison across experiments and transcriptomic analysis. The combination of PaCER1, PaXTH, PaEXP1, PaEXP2, PaKCS6, PaWINA, PaWINB and PaCER3 as an expression bitmap can separate cherry fruits with low and high cracking phenotypes based on gene expression. Our results highlight the importance of the wax biosynthesis and cell wall metabolic pathways in susceptibility to fruit cracking. Furthermore, the newly identified bitmap may be useful to test in other locations and with different varieties.
果实开裂是一种取决于遗传和环境条件的发育缺陷。果实开裂对果实品质和产量有负面影响。开裂的果实无法商业化销售，还会增加病原体污染。鉴定作为标记的基因可能有助于育种和采后处理。我们使用一组16个基因比较了定量聚合酶链反应（qPCR）和数字聚合酶链反应（dPCR）方法，这些基因在裂果率低的“甜心”樱桃品种和裂果率高的“伯拉特”樱桃品种中似乎存在差异表达。绝对转录本的差异跨越了近三个数量级。总体而言，qPCR和dPCR显示出高度显著的负相关，相关系数为-0.90。该方程可将Ct值转换为dPCR拷贝数。然而，dPCR中的拷贝数允许在不同实验和转录组分析之间进行直接比较。将PaCER1、PaXTH、PaEXP1、PaEXP2、PaKCS6、PaWINA、PaWINB和PaCER3组合作为一个表达位图，可以根据基因表达区分裂果表型低和高的樱桃果实。我们的结果突出了蜡生物合成和细胞壁代谢途径在果实开裂易感性中的重要性。此外，新鉴定的位图可能有助于在其他地点和不同品种上进行测试。
