Genome-Wide Genetic Diversity and Population Structure of Tunisian Durum Wheat Landraces Based on DArTseq Technology

Abstract

Tunisia, being part of the secondary center of diversity for durum wheat, has rich unexploited landraces that are being continuously lost and replaced by high yielding modern cultivars. This study aimed to investigate the genetic diversity and population structure of 196 durum wheat lines issued from landraces collected from Tunisia using Diversity Array Technology sequencing (DArTseq) and to understand possible ways of introduction in comparing them to landraces from surrounding countries. A total of 16,148 polymorphic DArTseq markers covering equally the A and B genomes were effective to assess the genetic diversity and to classify the accessions. Cluster analysis and discriminant analysis of principal components (DAPC) allowed us to distinguish five distinct groups that matched well with the farmer’s variety nomenclature. Interestingly, Mahmoudi and Biskri landraces constitute the same gene pool while Jenah Zarzoura constitutes a completely different group. Analysis of molecular variance (AMOVA) showed that the genetic variation was among rather than within the landraces. DAPC analysis of the Tunisian, Mediterranean and West Asian landraces confirmed our previous population structure and showed a genetic similarity between the Tunisian and the North African landraces with the exception of Jenah Zarzoura being the most distant. The genomic characterization of the Tunisian collection will enhance their conservation and sustainable use.

Whole Genome Scan Reveals Molecular Signatures of Divergence and Selection Related to Important Traits in Durum Wheat Germplasm

“…Italian landraces were characterized by a moderate level of genetic diversity (He = 0.26), which is comparable with that of Mediterranean (He = 0.24) or Tunisian and Iranian (He = 0.25) landraces, as revealed by the analysis of patterns of genetic diversity using AFLP (Moragues et al, 2007;Nazco et al, 2012) and DArT markers (Fayaz et al, 2018;Robbana et al, 2019), respectively. Relatively small differences in Nei and Shannon indices were observed moving from LR to MC, while we observed that a weak genetic bottleneck (i.e., loss of rare alleles) has been imposed by breeding programs on the old Italian durum wheat ( H = −0.09), suggesting that the overall molecular diversity of durum wheat has undergone moderate fluctuations during the 20th century (Maccaferri et al, 2005;Martos et al, 2005;Laidò et al, 2013).…”

Genomic Analysis Of Spanish Wheat Landraces Reveals Their Variability And Potential For Breeding

“…The assessment of genome-wide diversity by GBS provides robust estimates of diversity and has been increasingly adopted as a fast, high-throughput cost-effective tool for whole-genome genetic diversity analysis in large germplasm sets (16). The DArTseq (Diversity Array Technology sequence) markers, based on GBS (17), efficiently target low-copy-number sequences via a complexity reduction method and have been successfully applied for genetic diversity studies in different species (18)(19)(20)(21).…”

Morphological Characterization and Genetic Diversity Analysis of a Tunisian Durum Wheat (Triticum Turgidum Var. Durum) Collection

“…However, lower genetic diversity was observed in 33 Anatolian, 136 south Italian and 40 North-West African durum wheat landraces using 14, 44 and 29 SSR markers, respectively [2,12,23]. Low genetic diversity (PIC=0.1; He=0.25) was also observed in 196 Tunisian durum wheat accessions by Robbana et al [18], due i) to the use of biallelic DArTseq markers with lower informativeness level than multi-allelic SSR markers and ii) to a germplasm collection limited to 5 landraces. This variability between results suggests that capturing the maximum genetic diversity would depend essentially on the type of deployed markers, the number of landraces, the origin and geographical distribution (genetic backgrounds) of the studied collection.…”

“…In our study, grain size didn't signi cantly differ between C1 and C2 suggesting that both clusters have indeed western Mediteranean origin. Moreover, Robbana et al [18] mentioned that most of Tunisian landraces were introduced from the early Carthage trade maritime activity in the Mediterranean Sea, through pathways from Lebanon, Greece and Italy.…”

“…The levels of genetic diversity of Tunisian durum wheat germplasm were assessed by Medini et al [7] using AFLP and SSR markers which reveals an important polymorphism within cultivars. More recently, Robbana et al [18] investigated the genetic diversity and population structure of 196 durum wheat landrace accessions (including Tunisian and North African accessions) using DArTseq markers. Their results showed that genetic variation was higher among landraces than within them, with a remarkable genetic similarity between the Tunisian and the North African landraces.…”