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Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a 'poor man's crop', finger millet has regained attention over the past decade for its climate resilience and the nutritional qualities of its grain. To bring finger millet breeding into the 21st century, here we present the assembly and annotation of a chromosome-scale reference genome. We show that this ~1.3 million years old allotetraploid has a high level of homoeologous gene retention and lacks subgenome dominance. Population structure is mainly driven by the differential presence of large wild segments in the pericentromeric regions of several chromosomes. Trait mapping, followed by variant analysis of gene candidates, reveals that loss of purple coloration of anthers and stigma is associated with loss-of-function mutations in the finger millet orthologs of the maize R1/B1 and Arabidopsis GL3/EGL3 anthocyanin regulatory genes. Proanthocyanidin production in seed is not affected by these gene knockouts.

Lack of genomic resources in sunn hemp (Crotalaria juncea L.), a leguminous bast fiber crop, is one of the major constraints for germplasm characterization and genetic analysis. We identified non-redundant sets of a variety of molecular markers from the de novo flower-bud transcriptome of sunn hemp. These molecular markers included 1683 simple sequence repeats, 4759 intron length polymorphism markers primarily from protein-coding genes, and 3309 single nucleotide polymorphism allele-specific markers. All of these marker resources have been integrated into a simple database for easy access. To evaluate marker efficiency and polymorphism information content of the sampled primers, a subset of SSR and intron length polymorphism markers were validated in sunn hemp germplasm accessions to obtain average PIC values of 0.26–0.32. The SSR genotyping profiles also aided in the genetic distance matrix-based clustering of sunn hemp germplasm accessions. The ability of these molecular markers to successfully amplify in cross-genera bast fiber crops further demonstrated their effectiveness in genotyping. Thus, the current study describes the identification of previously undisclosed endogen)ous molecular markers in sunn hemp, which have potential applications in genetic studies and breeding in sunn hemp for bast fiber improvement. [ABSTRACT FROM AUTHOR]

Fungal blast disease is one of the major constraints in finger millet production. Breeding for disease resistance in finger millet, needs characterization of genetic polymorphism among and between the resistant and susceptible genotypes. In total, 67 finger millet genotypes, which are resistant or susceptible to fungal blast disease, were analysed using sequence-related amplified polymorphism (SRAP) and simple sequence repeat (SSR) markers to assess genetic variations and select diverse parents. Twelve each of SRAP and SSR primers produced 95.1 and 93.1% polymorphic bands and grouped them into unweighted pair-group method with arithmetic average clusters. Two of the finger millet genotypes, IE 4709 (blast resistant) and INDAF 7 (susceptible) were distinguished as most diverse genotypes as parents. Several genotype-specific bands observed with SSR primers are potential in developing genotype-specific markers. A high genetic diversity within the resistant and susceptible genotypes, rather than between them, was revealed through Nei's gene diversity (h) index and analysis of molecular variance. The finding helps us to understand the extent of genetic polymorphism between blast disease resistant and susceptible finger millet genotypes to exploit in resistance breeding programs. [ABSTRACT FROM AUTHOR]

A T-DNA based promoter trapped mutant has led to the identification of a novel lateral organ junction specific promoter upstream of the pentatricopeptide repeat (PPR) protein coding gene LOJ in Arabidopsis thaliana by our laboratory. Various in silico based prediction tools are employed to characterize the upstream sequence of the LOJ gene. Out of numerous cis-elements detected in the LOJ promoter a few are considered important based on the expression pattern of the LOJ gene. These elements would provide a basis for designing experiments for more accurate promoter function annotation. A comparative search for conserved elements in the 5'-upstream region of few genes involved in lateral organ development and meristem related expression reveals few common relevant regulatory motifs. The coding region of the LOJ gene is intron-less and contains 19 PPR units. Based on in silico analysis, LOJ protein is predicted to be hydrophobic in nature and targeted to mitochondria. A partial 3D model of the LOJ protein has been suggested using a homology-based modeling program. [ABSTRACT FROM AUTHOR]