Comparative analysis of developing grain transcriptome reveals candidate genes and pathways improving GPC in wheat lines
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PLANT GENETICS • ORIGINAL PAPER
Comparative analysis of developing grain transcriptome reveals candidate genes and pathways improving GPC in wheat lines derived from wild emmer Fangyi Gong 1 & Lin Huang 1 & Tiangang Qi 1 & Guan Tang 1 & Jia Liu 1 & Lan Xiang 1 & Jingshu He 1 & Youliang Zheng 1,2 & Dengcai Liu 1,2 & Bihua Wu 1,2 Received: 20 July 2020 / Revised: 18 September 2020 / Accepted: 30 September 2020 # Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2020
Abstract The grain protein content (GPC) in modern wheat is inherently low. Wild emmer wheat (Triticum turgidum ssp. dicoccoides, 2n = 4x = 28, AABB) gene pool harbors wide genotypic variations in GPC. However, the characterization of candidate genes associated with high GPC is a challenge due to the complex characteristic of this trait. In the current study, we performed RNAseq analysis on developing grains of wild emmer genotype D1, common wheat CN16, and their hexaploid wide hybrid BAd1074 with contrasting GPC. We have found a total of 39,795 expressed genes on chromosomes A and B, of which 24,152 were shared between D1, CN16, and BAd107-4. From 1744 differentially expressed genes (DEGs), 1203 were downregulated and 541 were upregulated in the high GPC (D1+BAd107-4) compared with low GPC (CN16) groups. The majority of DEGs were associated with protein processing in endoplasmic reticulum, starch and sucrose metabolism, galactose metabolism, and protein export pathways. Expression levels of nine randomly selected genes were verified by qRT-PCR, which was consistent with the transcriptome data. The present database will help us to understand the potential regulation networks underlying wheat grain protein accumulation and provide the foundation for simultaneous improvement of grain protein content and yield in wheat breeding programs. Keywords Wild emmer wheat . Common wheat . Wide hybridization . GPC . RNA-seq . Differentially expressed genes
Introduction
Fangyi Gong and Lin Huang contributed equally to this work. Communicated by: Izabela Pawłowicz Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13353-020-00588-y) contains supplementary material, which is available to authorized users. * Lin Huang [email protected] * Bihua Wu [email protected] 1
State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
2
Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
Wheat provides approximately 20% of the calories and 25% of proteins in the human diet and is also an important source of micronutrients. While the protein and micronutrients levels in modern wheat grains are inherently low (Chen et al. 2017), cereal-based diet is short of providing sufficient protein and micronutrients, leading to increased world’s population suffering from micronutrient deficiencies (Cakmak 2008) and pr
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