ABSTRACT Advancements in plant genome sequencing and assembly have enabled the production of increasingly accurate and contiguous genome sequences. Here, we present the chromosome‐level assembly of the durum wheat ( Triticum turgidum L. ssp. durum, cv. Svevo) reference genome produced using accurate long‐reads, optical mapping and Hi‐C. The new assembly (Svevo Rel.2.0) comprises 263 hybrid scaffolds with an N50 value of 112.3 Mb, arranged into 14 contiguous pseudomolecules spanning 10.4 Gb. The Svevo Rel.2.0 genome assembly was annotated using extensive short‐ and long‐read RNA sequencing data obtained from 60 tissue/treatment combinations. The resulting annotation comprises 68 154 high‐confidence protein‐coding genes, which have been integrated into a comprehensive transcriptome atlas accessible through an eFP browser. Annotation was manually curated for storage protein gene families and for Leucine‐Rich Repeat‐Containing Receptor genes yielding 3763 LRR‐CR loci. The genome assembly's accuracy and completeness were demonstrated by the correct reconstruction of the physical map of Tg1‐B (Tenacious glumes 1), a locus controlling the free threshing trait located on chromosome 2B that was not assembled in the previous genome release (Svevo Rel.1.0). A wealth of 6621 QTLs/MTAs from the literature were mapped onto Svevo Rel.2.0 to identify QTL hotspots and trait‐specific candidate genes. The ancestry of the durum genome to representative wild emmer populations from North‐Eastern and Southern‐Levant Fertile Crescent assessed by tracing haplotype transmission patterns revealed a clear mosaic pattern. This new durum reference genome, enhanced with advanced annotation and an expression atlas linked to QTLome data, is the most comprehensive tool available for durum wheat genomics.
E. Mazzucotelli, C. Forestan, Gina Zastrow-Hayes et al.· Plant Biotechnology Journal· 0 citations
Germplasm characterization and gene identification are essential first steps in developing drought-resilient cultivars. Evaluation of diverse tetraploid wheat accessions representing cultivated and wild species under severe drought stress using an
in-house
protocol identified three extremely tolerant genotypes including the CIMMYT-bred durum (
Triticum turgidum
ssp.
durum
) variety Altar 84 and the two wild emmer (
T. turgidum
ssp.
dicoccoides
) accessions PI 478742 and PI 481521. Chromosome substitution lines involving individual pairs of chromosomes from PI 478742 and PI 481521 substituted for homologous pairs of chromosomes in drought sensitive durum variety Langdon 16 were evaluated to identify chromosome(s) carrying loci controlling drought tolerance. The 11 chromosome substitution lines available for PI 478742 (2A, 3A, and 3B substitution lines were not available) were all sensitive to drought suggesting tolerance may be conferred by a locus on one of the chromosomes not evaluated. All 14 possible chromosome substitution lines were available for PI 481521, and among these, 13 were drought sensitive. The substitution line involving chromosome 3A (LDN-DIC 3A(521)) was tolerant to drought. QTL mapping in a durum inter-varietal population of 138 recombinant inbred lines (RILs) derived by crossing Altar 84 and Langdon 16 identified a major QTL on the short arm of chromosome 4B explaining 26% of phenotypic variation (PVE). This QTL spans large physical region of approximately 265.52 Mb in the Svevo RefSeq v1.0 genome. Sequence analysis of
TRITD4Bv1G024340
, an orthologue of drought tolerance gene (
TaWD40-4B.1
) cloned and previously reported from same genomic region in hexaploid wheat, suggested that QTL identified in this study in Altar 84 is governed by a different genomic region. Additionally, two drought tolerance regions identified (on chromosome 3A and 4BS) in this study are two independent QTLs originated from different sources, and hence they might have different genetic tolerance mechanism. Drought tolerant lines and the genomic regions identified in this study serve as valuable resources for developing drought-resilient durum wheat varieties.
Santosh Gudi, Jatinder Singh, Justin D. Faris et al.· BMC Genomics· 0 citations
