Molecular organization and comparative analysis of chromosome 5B of the wild wheat ancestor Triticum dicoccoides

Abstract

Wild emmer wheat, Triticum turgidum ssp. dicoccoides is the wild relative of Triticum turgidum, the progenitor of durum and bread wheat, and maintains a rich allelic diversity among its wild populations. The lack of adequate genetic and genomic resources, however, restricts its exploitation in wheat improvement. Here, we report next-generation sequencing of the flow-sorted chromosome 5B of T. dicoccoides to shed light into its genome structure, function and organization by exploring the repetitive elements, protein-encoding genes and putative microRNA and tRNA coding sequences. Comparative analyses with its counterparts in modern and wild wheats suggest clues into the B-genome evolution. Syntenic relationships of chromosome 5B with the model grasses can facilitate further efforts for fine-mapping of traits of interest. Mapping of 5B sequences onto the root transcriptomes of two additional T. dicoccoides genotypes, with contrasting drought tolerances, revealed several thousands of single nucleotide polymorphisms, of which 584 shared polymorphisms on 228 transcripts were specific to the drought-tolerant genotype. To our knowledge, this study presents the largest genomics resource currently available for T. dicoccoides, which, we believe, will encourage the exploitation of its genetic and genomic potential for wheat improvement to meet the increasing demand to feed the world.

Mapping QTLs conferring salt tolerance and micronutrient concentrations at seedling stage in wheat

“…tauschii and T . urartu , reflecting their close ancestral relationships with bread wheat 37 . Another top species from BLAST comparisons was H .…”

“…Only 84 polymorphic markers were assigned to the D genome as compared to 342 and 562 markers assigned to A and B genome. This has been linked to lower nucleotide diversity of the D genome due to its relatively recent evolutionary origin 37 , 38 . Our genetic map has a total length of 2317.88 cM in comparison to 3739.23 cM for the published wheat consensus map 19 , largely due to the lack of diversity/segregation in the D genome under salinity.…”

Complete chloroplast genome sequence and comparative analysis of loblolly pine (Pinus taeda L.) with related species

“…The advent of high-throughput next-generation sequencing technologies from Illumina, Pacific Biosciences, Life Technologies, and Roche, among others, have rapidly improved genomic studies [ 45 , 46 ]. In addition to draft or whole genomes of microbes and animals, genomic studies were performed to determine the chromosomal structures and molecular organization of wheat [ 47 , 48 ] and maize [ 49 ]. In addition, these technologies have been extensively used to evaluate organelles, particularly chloroplast.…”

Dissecting miRNAs in Wheat D Genome Progenitor, Aegilops tauschii

“…Several of the above mentioned in silico methods have utilized the NGS data, accumulated by the latest breakthrough in sequencing technologies ( Vitulo et al, 2011 ; Hernandez et al, 2012 ; Kantar et al, 2012 ; Lucas and Budak, 2012 ; Kurtoglu et al, 2014 ; Akpinar et al, 2015b ). miRNA identification at the subgenomic level has also taken advantage of the recently developed chromosome flow sorting technique, which reduces the complex and repetitive genomes to a manageable size ( Vrána et al, 2000 , 2012 ; Kubaláková et al, 2002 ).…”