Comparative Analysis of Coding and Non-Coding Features within Insect Tolerance Loci in Wheat with Their Homologs in Cereal Genomes

Food insecurity and malnutrition have reached critical levels with increased human population, climate fluctuations, water shortage; therefore, higher-yielding crops are in the spotlight of numerous studies. Abiotic factors affect the yield of staple food crops; among all, wheat stem sawfly (Cephus cinctus Norton) and orange wheat blossom midge (Sitodiplosis mosellana) are two of the most economically and agronomically harmful insect pests which cause yield loss in cereals, especially in wheat in North America. There is no effective strategy for suppressing this pest damage yet, and only the plants with intrinsic tolerance mechanisms such as solid stem phenotypes for WSS and antixenosis and/or antibiosis mechanisms for OWBM can limit damage. A major QTL and a causal gene for WSS resistance were previously identified in wheat, and 3 major QTLs and a causal gene for OWBM resistance. Here, we present a comparative analysis of coding and non-coding features of these loci of wheat across important cereal crops, barley, rye, oat, and rice. This research paves the way for our cloning and editing of additional WSS and OWBM tolerance gene(s), proteins, and metabolites.

Characterization of Little millet (Panicum sumatrense) varieties using Morphological descriptors and SSR based DNA fingerprinting

Little millet varieties are generally distinguished by morphological descriptors which are being used for seed certification and DUS characterization [1]. But in practical terms, these key differentiation descriptors between varieties of little millet are very fewer and hence difficult to differentiate germplasm accessions. Germplasm registration in NBPGR needs DNA fingerprint to show the uniqueness of germplasm in comparison to existing varieties. DNA fingerprinting is a better option to identify unique markers to differentiate the varieties. Available genomic resources are scarce since little millet is still considered to be an orphan crop. Therefore markers from other cereal genomes such as maize, pearl millet and barnyard millet that are been utilized for DNA fingerprinting purpose with a clue of cereal synteny relationship. Twenty-one morphological descriptors studies revealed that the variety ATL 1 is different from the other varieties for more than 16 morphological characters studied. DNA fingerprinting is attempted in five genotypes of little millets such as BL6, ATL 1, TNPsu 176, Co (Samai) 4, Paiyur 2 using cereal SSR markers. Among the 25 maize SSR markers used two markers viz., phi213984 and phi295450 scored polymorphism by the amplicon size of 310bp and 600bp respectively. From the 25 Pearl millet SSR markers used only one SSR marker found polymorphic at 305bp allele size for ATL 1 and Hence, SSR based DNA fingerprinting helped to differentiate ATL1, the newly released high yielding variety from other genotypes of little millets which can be used for varietal identification purpose.

Parallelism and convergence in post-domestication adaptation in cereal grasses

The selection of desirable traits in crops during domestication has been well studied. Many crops share a suite of modified phenotypic characteristics collectively known as the domestication syndrome. In this sense, crops have convergently evolved. Previous work has demonstrated that, at least in some instances, convergence for domestication traits has been achieved through parallel molecular means. However, both demography and selection during domestication may have placed limits on evolutionary potential and reduced opportunities for convergent adaptation during post-domestication migration to new environments. Here we review current knowledge regarding trait convergence in the cereal grasses and consider whether the complexity and dynamism of cereal genomes (e.g., transposable elements, polyploidy, genome size) helped these species overcome potential limitations owing to domestication and achieve broad subsequent adaptation, in many cases through parallel means. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.

The Dark Matter of Large Cereal Genomes: Long Tandem Repeats

Reference genomes of important cereals, including barley, emmer wheat and bread wheat, were released recently. Their comparison with genome size estimates obtained by flow cytometry indicated that the assemblies represent not more than 88–98% of the complete genome. This work is aimed at identifying the missing parts in two cereal genomes and proposing techniques to make the assemblies more complete. We focused on tandemly organised repetitive sequences, known to be underrepresented in genome assemblies generated from short-read sequence data. Our study found arrays of three tandem repeats with unit sizes of 1242 to 2726 bp present in the bread wheat reference genome generated from short reads. However, this and another wheat genome assembly employing long PacBio reads failed in integrating correctly the 2726-bp repeat in the pseudomolecule context. This suggests that tandem repeats of this size, frequently incorporated in unassigned scaffolds, may contribute to shrinking of pseudomolecules without reducing size of the entire assembly. We demonstrate how this missing information may be added to the pseudomolecules with the aid of nanopore sequencing of individual BAC clones and optical mapping. Using the latter technique, we identified and localised a 470-kb long array of 45S ribosomal DNA absent from the reference genome of barley.