Grain Amaranth is the most promising C₄ dicotyledonous pseudocereal and is distributed globally. It has an excellent nutritional profile and adaptability against a broad range of environmental factors. These traits have renewed the interest of researchers and breeders in exploring this underutilized orphan crop. The present study aimed to validate the genome-wide SSR to assess the genetic diversity among 94 Amaranthus hypochondriacus accessions using 57 genomic SSR (g-SSR) markers developed in-house. A total of 36 g-SSRs were recorded as polymorphic and amplified 138 alleles, with an average of 3.83 alleles per locus. Major allele frequency ranged from 0.29 to 0.98, with an average of 0.63 per marker. The expected heterozygosity ranged from 0.03 to 0.81, with an average of 0.46 per locus. Polymorphism information content (PIC) ranged from 0.03 to 0.79, with an average of 0.40, indicating a high level of polymorphism across amaranth accessions. Population structure analysis resulted into two major genetic clusters irrespective of their geographical origin, which suggests there may be sharing of common genomic regions across the accessions. High allelic frequency and heterozygosity levels indicate significant genetic variability in the germplasm, which can be further used in future breeding programs.

Amaranthus is a genus of C4 dicotyledonous herbaceous plant species that are widely distributed in Asia, Africa, Australia, and Europe and are used as grain, vegetables, forages, and ornamental plants. Amaranth species have gained significant attention nowadays as potential sources of nutritious food and industrial products. In this study, we performed a comparative genome analysis of five amaranth species, namely, Amaranthus hypochondriacus, Amaranthus tuberculatus, Amaranthus hybridus, Amaranthus palmeri, and Amaranthus cruentus. The estimated repeat content ranged from 54.49% to 63.26% and was not correlated with the genome sizes. Out of the predicted repeat classes, the majority of repetitive sequences were Long Terminal Repeat (LTR) elements, which account for about 13.91% to 24.89% of all amaranth genomes. Phylogenetic analysis based on 406 single-copy orthologous genes revealed that A. hypochondriacus is most closely linked to A. hybridus and distantly related to A. cruentus. However, dioecious amaranth species, such as A. tuberculatus and A. palmeri, which belong to the subgenera Amaranthus Acnida, have formed their distinct clade. The comparative analysis of genomic data of amaranth species will be useful to identify and characterize agronomically important genes and their mechanisms of action. This will facilitate genomics-based, evolutionary studies, and breeding strategies to design faster, more precise, and predictable crop improvement programs.

Sesame, one of the ancient oil crops, is an important oilseed due to its nutritionally rich seeds with high protein content. Genomic scale information for sesame has become available in the public databases in recent years. The genes and their families involved in oil biosynthesis in sesame are less studied than in other oilseed crops. Therefore, we retrieved a total of 69 genes and their translated amino acid sequences, associated with gene families linked to the oil biosynthetic pathway. Genome-wide in silico mining helped identify key regulatory genes for oil biosynthesis, though the findings require functional validation. Comparing sequences of the SiSAD (stearoyl-acyl carrier protein (ACP)-desaturase) coding genes with known SADs helped identify two SiSAD family members that may be palmitoyl-ACP-specific. Based on homology with lysophosphatidic acid acyltransferase (LPAAT) sequences, an uncharacterized gene has been identified as SiLPAAT1. Identified key regulatory genes associated with high oil content were also validated using publicly available transcriptome datasets of genotypes contrasting for oil content at different developmental stages. Our study provides evidence that a longer duration of active oil biosynthesis is crucial for high oil accumulation during seed development. This underscores the importance of early onset of oil biosynthesis in developing seeds. Up-regulating, identified key regulatory genes of oil biosynthesis during early onset of seed development, should help increase oil yields.

Cryopreservation approaches have been implemented in gene banks as a strategy to back up plant genetic resource collections that are vegetatively propagated. Different strategies have been employed to effectively cryopreserve plant tissue. There is little information on the cellular processes and molecular adjustments that confer resilience to the multiple stresses imposed during a cryoprotocol. In the present work, the cryobionomics of banana (Musa sp.), a non-model species, was investigated through the transcriptomic approach using RNA-Seq. Proliferating meristems of in vitro explants (Musa AAA cv ‘Borjahaji’) were cryopreserved using the droplet-vitrification technique. Transcriptome profiling analysis of eight cDNA libraries including the bio-replicates for T0 (stock cultures (control tissue), T1 (high sucrose pre-cultured), T2 (vitrification solution-treated) and T3 (liquid nitrogen-treated) meristem tissues was carried out. The raw reads obtained were mapped with a Musa acuminata reference genome sequence. A total of 70 differentially expressed genes (DEGs) comprising 34 upregulated and 36 downregulated were identified in all three phases as compared to control (T0). Among the significant DEGs (>log FC 2.0), during sequential steps, 79 in T1, 3 in T2 and the 4 in T3 were upregulated and 122 in T1, 5 in T2 and 9 in T3 were downregulated. Gene ontology (GO) enrichment analysis showed that these significant DEGs were involved in the upregulation of biological process (BP-170), cellular component (CC-10) and molecular function (MF-94) and downregulation of biological process (BP-61), cellular component (CC-3) and molecular function (MF-56). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEGs were involved in the biosynthesis of secondary metabolites, glycolysis/gluconeogenesis, MAPK signaling, EIN 3-lke 1 protein, 3-ketoacy-CoA synthase 6-like, and fatty acid elongation during cryopreservation. For the first time, a comprehensive transcript profiling during four stages of cryopreservation in banana were carried out, which will pave the way for devising an effective cryopreservation protocol.

Genetic resources are the fundamental source of diversity available to plant breeders for the improvement of desired traits. However, a large germplasm set is difficult to preserve and use as a working collection in genetic studies. Hence, the present study evaluates the genetic diversity of 3115 safflower accessions from the Indian National Gene Bank, including Indian cultivars, to develop a manageable set of accessions, with similar genetic variations of germplasm studied. A total of 18 polymorphic SSR markers were used. The genetic diversity analysis revealed that germplasm accessions were highly diverse and there is no correlation between genetic diversity and the geographical collection of germplasm or sourcing of germplasm. A core set was developed using a core hunter software with different levels of composition, and it was found that 10% of the accessions showed maximum gene diversity and represented an equal number of alleles and major allele frequency in the germplasm studied. The developed core consisted of 351 accessions, including Indian cultivars, and they were validated with various genetic parameters to ascertain that they were a true core set for the studied accessions of safflower germplasm.