Background: Soil salinity is one of the major abiotic stress factors that affect crop growth and yield, which seriously restricts the sustainable development of agriculture. Quinoa is considered as one of the most promising crops in the future for its high nutrition value and strong adaptability to extreme weather and soil conditions. However, the molecular mechanisms underlying the adaptive response to salinity stress of quinoa remain poorly understood. To identify candidate genes related to salt tolerance, we performed reference-guided assembly and compared the gene expression in roots treated with 300 mM NaCl for 0, 0.5, 2, and 24 h of two contrasting quinoa genotypes differing in salt tolerance. Results: The salt-tolerant (ST) genotype displayed higher seed germination rate and plant survival rate, and stronger seedling growth potential as well than the salt-sensitive (SS) genotype under salt stress. An average of 38,510,203 high-quality clean reads were generated. Significant Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified to deeper understand the differential response. Transcriptome analysis indicated that salt-responsive genes in quinoa were mainly related to biosynthesis of secondary metabolites, alpha-Linolenic acid metabolism, plant hormone signal transduction, and metabolic pathways. Moreover, several pathways were significantly enriched amongst the differentially expressed genes (DEGs) in ST genotypes, such as phenylpropanoid biosynthesis, plant-pathogen interaction, isoquinoline alkaloid biosynthesis, and tyrosine metabolism. One hundred seventeen DEGs were common to various stages of both genotypes, identified as core salt-responsive genes, including some transcription factor members, like MYB, WRKY and NAC, and some plant hormone signal transduction related genes, like PYL, PP2C and TIFY10A, which play an important role in the adaptation to salt conditions of this species. The expression patterns of 21 DEGs were detected by quantitative real-time PCR (qRT-PCR) and confirmed the reliability of the RNA-Seq results. Conclusions: We identified candidate genes involved in salt tolerance in quinoa, as well as some DEGs exclusively expressed in ST genotype. The DEGs common to both genotypes under salt stress may be the key genes for quinoa to adapt to salinity environment. These candidate genes regulate salt tolerance primarily by participating in reactive oxygen species (ROS) scavenging system, protein kinases biosynthesis, plant hormone signal transduction and other important biological processes. These findings provide theoretical basis for further understanding the regulation mechanism underlying salt tolerance network of quinoa, as well establish foundation for improving its tolerance to salinity in future breeding programs.

Quinoa (Chenopodium quinoa Willd.) is a balanced nutritional crop, but its breeding improvement has been limited by the lack of information on its genetics and genomics. Therefore, it is necessary to obtain knowledge on genomic variation, population structure, and genetic diversity and to develop novel Insertion/Deletion (InDel) markers for quinoa by whole-genome re-sequencing. We re-sequenced 11 quinoa accessions and obtained a coverage depth between approximately 7× to 23× the quinoa genome. Based on the 1453-megabase (Mb) assembly from the reference accession Riobamba, 8,441,022 filtered bi-allelic single nucleotide polymorphisms (SNPs) and 842,783 filtered InDels were identified, with an estimated SNP and InDel density of 5.81 and 0.58 per kilobase (kb). From the genomic InDel variations, 85 dimorphic InDel markers were newly developed and validated. Together with the 62 simple sequence repeat (SSR) markers reported, a total of 147 markers were used for genotyping the 129 quinoa accessions. Molecular grouping analysis showed classification into two major groups, the Andean highland (composed of the northern and southern highland subgroups) and Chilean coastal, based on combined STRUCTURE, phylogenetic tree and PCA (Principle Component Analysis) analyses. Further analysis of the genetic diversity exhibited a decreasing tendency from the Chilean coast group to the Andean highland group, and the gene flow between subgroups was more frequent than that between the two subgroups and the Chilean coastal group. The majority of the variations (approximately 70%) were found through an analysis of molecular variation (AMOVA) due to the diversity between the groups. This was congruent with the observation of a highly significant FST value (0.705) between the groups, demonstrating significant genetic differentiation between the Andean highland type of quinoa and the Chilean coastal type. Moreover, a core set of 16 quinoa germplasms that capture all 362 alleles was selected using a simulated annealing method. The large number of SNPs and InDels identified in this study demonstrated that the quinoa genome is enriched with genomic variations. Genetic population structure, genetic core germplasms and dimorphic InDel markers are useful resources for genetic analysis and quinoa breeding.

Quinoa is a resilient crop known for its adaptability to diverse environmental conditions. This study examined the agronomic performance and ecological adaptability of quinoa across four distinct altitudes in the northwestern regions of China. Six quinoa genotypes were assessed for agronomic traits, phenology and yield performances, and nutritional quality characteristics in Yining city, Nilka County, Tekes County and Zhaosu County under varied environmental conditions. Our findings demonstrate significant variations in all measured traits including agronomic and nutritional quality traits across the various altitudes and genotypes. In Yining City, a warmer and lower altitude area, genotypes exhibit superior traits for fodder production, including increased branches, longer panicles, robust stems, and high seed protein content. Genotypes Jinli 1 and Beijing 2 achieve yields exceeding 3 tons per hectare (T/ha), highlighting the region’s productivity. Nilka and Tekes counties boasted the shortest quinoa crop cycles, with Jinli 1 yielding 4.05 T/ha seeds in Tekes County, exhibiting high protein and fat content alongside low saponins, making it prime location for yield production. Zhaosu County, with its cooler climate and fertile chernozem soil, elicited high 1000 seed weight and more robust protein response than Nilka and Tekes counties, illustrating the impact of soil fertility on nutritional composition. Correlation analyses further elucidated that the plants characterized by shorter flowering times, crop cycles, compact inflorescence, and taller heights exhibited superior seed yields. Our study contributes significant insights into the ecological adaptability and nutritional dynamics of quinoa, with implications for sustainable crop production and food security in diverse agroecosystems.

The homeodomain-leucine zipper (HD-Zip) proteins are important transcription factors in the regulation of plant growth and development and abiotic stress responses. However, our understanding of the HD-Zip family is still limited in quinoa. In this study, 41 CqHD-Zip genes were identified in the quinoa genome and then phylogenetically classified into four subfamilies. Their characterizations, chromosomal locations, gene structures, conserved motifs, and phylogenetic relationships were comprehensively analyzed through genome-wide bioinformatics methods. Our RNA-Seq data showed that a subset of the 41 HD-Zip genes exhibited expression changes under salt stress, among which CqHDZ5, CqHDZ12, CqHDZ13, CqHDZ18, CqHDZ19, and CqHDZ21 responded positively to salt stress, and the results were confirmed by qRT-PCR analysis. Tissue expression revealed that CqHDZ5, CqHDZ13, CqHDZ18, and CqHDZ21 were significantly expressed in developing seeds, and CqHDZ12 and CqHDZ19 were highly expressed in roots. Additionally, the transcript levels of these six genes were significantly up-regulated in response to osmotic and low-temperature stress, indicating that they may participate in stress resistance against salt, osmosis, and low temperature. It is shown that HD-Zip is a multifunctional gene family, and the results will provide valuable information for further analysis of the potential role of HD-Zip genes in abiotic stress responses and genetic improvement of quinoa.

Background: Soil salinity is one of the major abiotic stress factors that affect crop growth and yield, which seriously restricts the sustainable development of agriculture. Quinoa is considered as one of the most promising crops in the future for its high nutrition value and strong adaptability to extreme weather and soil conditions. However, the molecular mechanisms underlying the adaptive response to salinity stress of quinoa remain poorly understood. To identify candidate genes related to salt tolerance, we performed reference-guided assembly and compared the gene expression in roots treated with 300 mM NaCl for 0, 0.5, 2, and 24 h of two contrasting quinoa genotypes differing in salt tolerance.Results: The salt-tolerant (ST) genotype displayed higher seed germination rate and plant survival rate, and stronger seedling growth potential as well than the salt-sensitive (SS) genotype under salt stress. An average of 38,510,203 high-quality clean reads were generated. Significant Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified to deeper understand the differential response. Transcriptome analysis indicated that salt-responsive genes in quinoa were mainly related to biosynthesis of secondary metabolites, alpha-Linolenic acid metabolism, plant hormone signal transduction, and metabolic pathways. Moreover, several pathways were significantly enriched amongst the differentially expressed genes (DEGs) in ST genotypes, such as phenylpropanoid biosynthesis, plant-pathogen interaction, isoquinoline alkaloid biosynthesis, and tyrosine metabolism. 117 DEGs were common to various stages of both genotypes, identified as core salt-responsive genes, including some transcription factor members, like MYB, WRKY and NAC, and some plant hormone signal transduction related genes, like PYL, PP2C and TIFY10A, which play an important role in the adaptation to salt conditions of this species. The expression patterns of 21 DEGs were detected by quantitative real-time PCR (qRT-PCR) and confirmed the reliability of the RNA-Seq results. Conclusions: We identified candidate genes involved in salt tolerance in quinoa, as well as some DEGs exclusively expressed in ST genotype. The DEGs common to both genotypes under salt stress may be the key genes for quinoa to adapt to salinity environment. These candidate genes regulate salt tolerance primarily by participating in reactive oxygen species (ROS) scavenging system, protein kinases biosynthesis, plant hormone signal transduction and other important biological processes. These findings provide theoretical basis for further understanding the regulation mechanism underlying salt tolerance network of quinoa, as well establish foundation for improving its tolerance to salinity in future breeding programs.