Data_Sheet_1_Transcriptional Regulation of Quinoa Seed Quality: Identification of Novel Candidate Genetic Markers for Increased Protein Content.zip

Quinoa (Chenopodium quinoa Willd.) is a crop that has great potential for increased cultivation in diverse climate regions. The seed protein quality obtained from this crop is high concerning the requirements to meet human nutritional needs, but the seed protein content is relatively low if compared to crops such as grain legumes. Increased seed protein content is desirable for increasing the economic viability of this crop in order for it to be used as a protein crop. In this study, we characterized three genotypes of quinoa with different levels of seed protein content. By performing RNA sequencing of developing seeds, we determined the genotype differences in gene expression and identified genetic polymorphisms that could be associated with increased protein content. Storage nutrient analyses of seeds of three quinoa genotypes (Titicaca, Pasankalla, and Regalona) from different ecoregions grown under controlled climate conditions showed that Pasankalla had the highest protein content (20%) and the lowest starch content (46%). Our seed transcriptome analyses revealed highly differentially expressed transcripts (DETs) in Pasankalla as compared to the other genotypes. These DETs encoded functions in sugar transport, starch and protein synthesis, genes regulating embryo size, and seed transcription factors. We selected 60 genes that encode functions in the central carbon metabolism and transcription factors as potential targets for the development of high-precision markers. Genetic polymorphisms, such as single nucleotide polymorphisms (SNPs) and base insertions and deletions (InDels), were found in 19 of the 60 selected genes, which can be further evaluated for the development of genetic markers for high seed protein content in quinoa. Increased cultivation of quinoa can contribute to a more diversified agriculture and support the plant protein diet shift. The identification of quinoa genotypes with contrasting seed quality can help establish a model system that can be used for the identification of precise breeding targets to improve the seed quality of quinoa. The data presented in this study based on nutrient and transcriptome analyses contribute to an enhanced understanding of the genetic regulation of seed quality traits in quinoa and suggest high-precision candidate markers for such traits.

藜麦（Chenopodium quinoa Willd.）是一种在多种气候区域具有显著增种潜力的作物。该作物所获得的种子蛋白质质量，在满足人类营养需求方面表现出色，然而，与谷物豆类等作物相比，其种子蛋白质含量相对较低。提高种子蛋白质含量对于提升该作物的经济可行性至关重要，以便将其作为蛋白质作物利用。在本研究中，我们对三种不同种子蛋白质含量水平的藜麦基因型进行了特征化分析。通过发育种子的RNA测序，我们确定了基因型在基因表达上的差异，并识别出可能与蛋白质含量增加相关的遗传多态性。对来自不同生态区域、在可控气候条件下种植的三种藜麦基因型（蒂蒂卡卡、帕桑卡拉和雷加洛纳）的种子储存营养分析显示，帕桑卡拉具有最高的蛋白质含量（20%）和最低的淀粉含量（46%）。我们的种子转录组分析揭示了与其它基因型相比，帕桑卡拉存在高度差异表达的转录本（DETs），这些转录本编码糖转运、淀粉和蛋白质合成、调节胚胎大小和种子转录因子的功能。我们选取了60个编码中央碳代谢和转录因子的基因作为开发高精度标记的潜在靶标。在60个选取的基因中，发现了19个存在遗传多态性，如单核苷酸多态性（SNPs）和碱基插入与缺失（InDels），这些可以进一步评估以开发藜麦高种子蛋白质含量遗传标记。藜麦的增种有助于农业多样化，并支持植物蛋白饮食的转变。识别具有对比性种子质量的藜麦基因型，有助于建立一个模型系统，用于确定精确的育种目标，以改善藜麦的种子质量。本研究基于营养和转录组分析所提供的数据，有助于加深对藜麦种子质量性状遗传调控的理解，并提出了高精度候选标记。