Transcriptional Regulation of Quinoa Seed Quality: Identification of Novel Candidate Genetic Markers for Increased Protein Content

Abstract

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.

A comprehensive characterization of agronomic and end-use quality phenotypes across a quinoa world core collection

“…Among these traits, crude protein, total amino acid content, and ash content had strong positive correlations with one another, while crude protein had a moderate positive correlation with crude fat content. In a study of Pasankalla, Titicaca, and Regalona, Grimberg et al. (2022) found Pasankalla to have the highest protein and oil content.…”

“…Storage proteins increase significantly in quinoa during maturation, in addition to oil accumulation, which provides evidence of a possible tradeoff between maturation and seed composition ( Shen et al., 2022 ). For instance, Grimberg et al. (2022) found Pasankalla matured 13 days after Titicaca and Regalona under controlled conditions (12-hour days) and had significantly higher protein and oil content.…”

Genomic basis of seed colour in quinoa inferred from variant patterns using extreme gradient boosting

“…In total, 21 of the 41 genes were annotated with functions and GO terms, with 40% of them directly related to reproduction or seed development (Table S6 ). We used publicly available shotgun proteomics (Poza‐Viejo et al ., 2023 ) and transcriptomics (Grimberg et al ., 2022 ) data from quinoa seeds to assess the expression of the 41 candidate genes. Our results showed that 27 of the 41 candidates could be detected in the proteome and 39 of the 41 candidate genes could be detected in the transcriptome.…”

Agro‐morphological and nutritional assessment of chenopod and quinoa germplasm—Highly adaptable potential crops

“…They suggested high-precision candidate markers for nutritional traits in quinoa (Grimberg et al, 2022). Previous studies also showed the value of Chenopodium leaves as a vegetable supplement; such studies might be considered in C. album for future studies (Bhargava et al, 2019).…”