Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India.
Planta. 2024 Aug 17;260(3):74. doi: 10.1007/s00425-024-04507-x.
Transcriptome analysis in potato varieties revealed genes associated with tuber yield-related traits and developed gene expression markers. This study aimed to identify genes involved in high tuber yield and its component traits in test potato varieties (Kufri Frysona, Kufri Khyati, and Kufri Mohan) compared to control (Kufri Sutlej). The aeroponic evaluation showed significant differences in yield-related traits in the varieties. Total RNA sequencing was performed using tuber and leaf tissues on the Illumina platform. The high-quality reads (QV > 25) mapping with the reference potato genomes revealed statistically significant (P < 0.05) differentially expressed genes (DEGs) into two categories: up-regulated (> 2 Log fold change) and down-regulated (< -2 Log fold change). DEGs were characterized by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Collectively, we identified genes participating in sugar metabolism, stress response, transcription factors, phytohormones, kinase proteins, and other genes greatly affecting tuber yield and its related traits. A few selected genes were UDP-glucose glucosyltransferase, glutathion S-transferase, GDSL esterase/lipase, transcription factors (MYB, WRKY, bHLH63, and BURP), phytohormones (auxin-induced protein X10A, and GA20 oxidase), kinase proteins (Kunitz-type tuber invertase inhibitor, BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1) and laccase. Based on the selected 17 peptide sequences representing 13 genes, a phylogeny tree and motifs were analyzed. Real time-quantitative polymerase chain reaction (RT-qPCR) analysis was used to validate the RNA-seq results. RT-qPCR based gene expression markers were developed for the genes such as 101 kDa heat shock protein, catechol oxidase B chloroplastic, cysteine protease inhibitor 1, Kunitz-type tuber invertase inhibitor, and laccase to identify high yielding potato genotypes. Thus, our study paved the path for potential genes associated with tuber yield traits in potato under aeroponics.
马铃薯品种的转录组分析揭示了与块茎产量相关性状相关的基因，并开发了基因表达标记物。本研究旨在鉴定与对照（Kufri Sutlej）相比，测试马铃薯品种（Kufri Frysona、Kufri Khyati 和 Kufri Mohan）中高块茎产量及其组成性状相关的基因。气培评价显示品种间产量相关性状存在显著差异。使用 Illumina 平台对块茎和叶片组织进行了全转录组测序。将高质量读数（QV>25）与马铃薯参考基因组进行映射，发现统计上显著（P<0.05）差异表达基因（DEGs）分为两类：上调（>2 Log 倍变化）和下调（<-2 Log 倍变化）。通过基因本体论（GO）和京都基因与基因组百科全书（KEGG）途径对 DEGs 进行了表征。总的来说，我们鉴定了参与糖代谢、应激反应、转录因子、植物激素、激酶蛋白和其他对块茎产量及其相关性状有重大影响的基因。一些选定的基因是 UDP-葡萄糖葡萄糖基转移酶、谷胱甘肽 S-转移酶、GDSL 酯酶/脂肪酶、转录因子（MYB、WRKY、bHLH63 和 BURP）、植物激素（生长素诱导蛋白 X10A 和 GA20 氧化酶）、激酶蛋白（Kunitz 型块茎转化酶抑制剂、BRASSINOSTEROID INSENSITIVE 1 相关受体激酶 1）和漆酶。基于代表 13 个基因的 17 个肽序列，分析了系统发育树和基序。实时定量聚合酶链反应（RT-qPCR）分析用于验证 RNA-seq 结果。为 101 kDa 热休克蛋白、儿茶酚氧化酶 B 质体、半胱氨酸蛋白酶抑制剂 1、Kunitz 型块茎转化酶抑制剂和漆酶等基因开发了实时定量 PCR 基因表达标记物，以鉴定高产量马铃薯基因型。因此，我们的研究为气培条件下马铃薯与块茎产量性状相关的潜在基因铺平了道路。
