Table 3.

Molecular advances in pseudocereals.

Pseudocereals	Marker development	Studies on genetic variation and population analysis	Gene expression profiling	Quantitative trait loci (QTL) analysis and gene discovery	Whole-genome sequencing	References
Amaranth	Plant material from six Amaranthus species were gathered from eight geographic regions of Indo-Gangetic plains, and unique SCAR markers were developed (A. caudatus, A. cruentus, A. gangeticus, A. hypochondriacus, A. paniculatus, and A. viridis)	Genetic analysis revealed that A. hypochondriacus and A. caudatus are closely related, as 313 accessions with 0.75% genomic overlap, and were grouped into two distinct genetic lineages Gene-specific primers for SSSI and GBSSI genes were employed to distinguish A. caudatus and A. hypochondriacus; 22 detected alleles showed an average of 0.657 polymorphism information content, reflecting diversity. A. powellii and A. retroflexus exhibited the highest SNPs, while A. quitensis and A. caudatus displayed very close genetic relationships. Genetic diversity was observed between edible and wild amaranth species	Identified 8,260 homologous sequences with A. tuberculatus and 1,971 stress-responsive genes. Revealed differentially expressed proteins and transcripts involved in stress defense and signaling pathways. Upregulated transcription factors like DOF1 and MIF1 were associated with stress adaptation and growth regulation. Downregulated genes were linked to cell differentiation and secondary metabolism	Identified AhDODA-1, AhDODA-2, AhcDOPA5-GT, and AhB5-GT genes for betanin biosynthesis. AhNF-YC: Linked with stress resistance and growth. Ah24: A newly identified stress-responsive gene from Amaranthus cruentus roots has been associated with reactions to salt stress, herbivore attack, and exposure to methyl jasmonate. In addition, ERF and Dof transcription factors linked to stress were found to play roles in the plant’s response to salt, drought, and signaling molecules like jasmonic acid, salicylic acid, and abscisic acid (ABA)	The transcriptome of A. hypochondriacus revealed independent C4 evolution. The grain amaranth genome (377 Mb, 3,518 scaffolds) included 23,059 protein-coding genes, with 48% consisting of repeat sequences. A chromosome-scale assembly (403.9 Mb) constructed with Hi-C chromatin contact maps and PacBio long reads scaffolded 98% of the genome into 16 chromosomes Domestication studies identified a MYB-like transcription factor as a potential regulator of seed coat color variation. Three independent domestication events from a single wild ancestor were observed, with the conversion of dark to white seed coats linked to this process	Wu and Blair, 2017; Casique-Arroyo et al., 2014; Palmeros-Suárez et al., 2015, Julio et al., 2015, 2016; Sunil et al., 2014; Clouse et al., 2016; Lightfoot et al., 2017; Stetter et al., 2020
Buckwheat	AFLP and pooled DNA mapping approaches identified genetic markers associated with Sht1 allelic site in a cross between non-brittle and brittle buckwheat lines. Microsatellite variability in common buckwheat. SSR marker development in Tartary buckwheat	Identified high levels of genetic variation within cultivars and populations along with 3 RAPD markers. 19 Japanese varieties using 5 microsatellite loci. Reported 86.5% polymorphism in 79 Tartary buckwheat accessions using AFLP markers. Analyzed 179 common buckwheat accessions with SSR markers. GBS in buckwheat revealed more nucleotide diversity (0.0065). RAPD and AFLP markers explored genetic relationships among wild and domesticated varieties	RNA-seq of filling stage seeds. Key genes in storage proteins, flavonoid biosynthesis, transcription factors identified. RNA-seq revealed aluminum-responsive genes involved in cell wall defense and oxidative stress. Identified numerous drought-responsive genes through transcriptomic data analysis	Two dominant genes are identified for seed shattering. QTLs identified for photoperiod sensitivity. High expression of genes for flavonoid and rutin biosynthesis identified. FtGBSSI gene in Tartary buckwheat, crucial for amylose synthesis isolated and characterized. Identified AI-responsive genes, abiotic stress genes, auxin-signaling genes. Isolated FaesAP3, a MADS-box gene, identified 65 MADS-box genes, Identified FePG1 associated with heteromorphic self-incompatibility	Produced a draft assembly with 387,594 scaffolds using next-generation sequencing. Combined multiple sequencing approaches, including Illumina short reads, SMRT long reads, Hi-C sequencing, and BioNano genome maps. Annotated 33,366 protein-coding genes, offering a comprehensive resource for functional genomics and breeding programs	Hou et al., 2016; Shi et al., 2017; Mizuno and Yasui, 2019; Gao et al., 2017; Yao et al., 2017; Zhu et al., 2015; Wu et al., 2019; Thiyagarajan et al., 2016; Wang et al., 2014; Yokosho et al., 2014; He et al., 2019; Liu et al., 2018; Fang et al., 2014; Liu et al., 2019; Takeshima et al., 2019; Yasui et al., 2016; Zhang et al., 2017
Quinoa	A linkage map was constructed for a recombinant inbred line (RIL) using 216 polymorphic SSR markers. Morphological characteristic variations together with chloroplast rbcL and matK gene sequences were assessed across 19 Chenopodium accessions. Also, the first C. quinoa-specific SNP primer, R1RQ-AFR, was identified based on rbcL sequences	Studied 19 accessions of Chenopodium using 33 RAPD primers, characterized Chilean and South American quinoa accessions with SSR markers, developed 511 SNP assays and InDels, racked quinoa diversity over 18 centuries with SSR markers, analyzed 121 quinoa accessions, used RAPD and ISSR markers	Identified 20,337 unique transcripts and 462 putative drought- and abiotic-stress-related gene products. Used RNA-Seq to study Groundnut Chlorotic Fan-spot Tospo virus-infected leaves. Performed RNA-Seq across six inflorescence developmental stages	Characterized homologous loci in salt tolerance and found differential expression of genes in shoots and roots under salt stress. Identified 90 NAC transcription factors. Provided two 11S genes with cDNA and genomic sequences. Isolated Ty3-retrotransposon and Ty1-copia retrotransposons. Identified unique specific genes (459) expressed in flowers, meristems and CqAmaSy1 (quinoa amaranthin synthetase 1) gene	Published a draft genome sequence of quinoa, consisting of 25k scaffolds, totaling 1 Gbp genomic size N50 contig length of 86 kbp. Superior quality genome draft was generated, comprising 64.5% repeated sequences including 54,438 genes for protein-coding and 192 microRNA genes	Devi and Chrungoo, 2017; Maughan et al., 2012; Zhang et al., 2017; Winkel et al., 2018; Saad-Allah and Youssef, 2018; Raney et al., 2014; Chou et al., 2017; Wu et al., 2019; Ruiz-Carrasco et al., 2011; Li et al., 2019; Kolano et al., 2013; Golicz et al., 2019; Imamura et al., 2019; Yasui et al., 2016; Zou et al., 2017; Jarvis et al., 2017

Plant databases provide open access to genomic resources for breeders and researchers. The availability of extensive data from genetic markers, complete genetic sequences, GWAS studies, different types of ionome, metabolomics, and transcriptomics studies of millets and other crops like pseudocereals could serve as a valuable insight to researchers that can greatly support efforts to improve medicinal properties, disease resistance, climatic resilience, food innovations, precision breeding, and agriculture sustainability.