BackgroundQuinoa (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.ResultsWe 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4093-8) contains supplementary material, which is available to authorized users.

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.

Cynanchum auriculatum is a traditional herbal medicine in China and can grow in saline soils. However, little is known in relation to the underlying molecular mechanisms. In the present study, C. auriculatum seedlings were exposed to 3.75‰ and 7.5‰ salinity. Next, transcriptome profiles of leaves were compared. Transcriptome sequencing showed 35,593 and 58,046 differentially expressed genes (DEGs) in treatments with 3.75‰ and 7.5‰, compared with the control, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of these DEGs enriched various defense-related biological pathways, including ROS scavenging, ion transportation, lipid metabolism and plant hormone signaling. further analyses suggested that C. auriculatum up-regulated Na + /H + exchanger and V-type proton Atpase to avoid accumulation of na + . The flavonoid and phenylpropanoids biosynthesis pathways were activated, which might increase antioxidant capacity in response to saline stress. The auxin and ethylene signaling pathways were upregulated in response to saline treatments, both of which are important plant hormones. Overall, these results raised new insights to further investigate molecular mechanisms underlying resistance of C. auriculatum to saline stress.www.nature.com/scientificreports www.nature.com/scientificreports/ and V-type proton ATPase, the flavonoid and phenylpropanoids biosynthesis pathways, the auxin and ethylene signaling pathways were upregulated to improve the antioxidant capacity of C. auriculatum in response to saline treatments. These changes might facilitate resistance of C. auriculatum to saline stress. Flavonoid and phenylpropanoids appear to play roles in resistance to salt tolerance in C. auriculatum, possibly due to its pharmacodynamics.

Aim: To explore the potential of whole-plant quinoa (WPQ) as a high-protein source for livestock feed, this study evaluated the effects of additives on the fermentation quality and bacterial community of high-moisture WPQ silage. Methods and Results:High-moisture WPQ was ensiled with one of the following additives: untreated control (C), fibrolytic enzyme (E), molasses (M), LAB inoculant (L), a combination of fibrolytic enzyme and LAB inoculant (EL) and a combination of molasses and LAB inoculant (ML). The fermentation quality and bacterial community after 60 days of ensiling were analysed. Naturally fermented WPQ exhibited acetic acid-type fermentation dominated by enterobacteria, with low lactic acid content (37.0 g/kg DM), and high pH value (5.65), acetic acid (70.8 g/kg DM) and NH 3 -N production (229 g/kg TN). Adding molasses alone or combined with LAB inoculant shifted the fermentation pattern towards increased intensity of lactic acid fermentation, lowering the pH value (<4.56), contents of acetic acid (<46.7 g/kg DM) and NH 3 -N (<140 g/kg TN) and total abundance of enterobacteria (<16.0%), and increasing the lactic acid content (>60.5 g/kg DM), lactic/acetic acid ratio (>1.40) and the relative abundance of Lactobacillus (>83.0%). Conclusions:The results suggested that the lack of fermentable sugar could be the main factor of restricting extensive lactic acid fermentation in WPQ silage.Supplementing fermentable sugar or co-ensiling with materials with high WSC content and low moisture content are expected to be beneficial strategies for producing high-quality WPQ silage.Significance and Impact of Study: High biomass production and high protein content make WPQ to be an ideal forage source for livestock feed. Results of this study revealed the restricting factor for extensive lactic acid fermentation in WPQ silage, which could be helpful in producing high-quality WPQ silage.

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.