The Global Durum Wheat Panel (GDP): An International Platform to Identify and Exchange Beneficial Alleles

Abstract

Representative, broad and diverse collections are a primary resource to dissect genetic diversity and meet pre-breeding and breeding goals through the identification of beneficial alleles for target traits. From 2,500 tetraploid wheat accessions obtained through an international collaborative effort, a Global Durum wheat Panel (GDP) of 1,011 genotypes was assembled that captured 94–97% of the original diversity. The GDP consists of a wide representation of Triticum turgidum ssp. durum modern germplasm and landraces, along with a selection of emmer and primitive tetraploid wheats to maximize diversity. GDP accessions were genotyped using the wheat iSelect 90K SNP array. Among modern durum accessions, breeding programs from Italy, France and Central Asia provided the highest level of genetic diversity, with only a moderate decrease in genetic diversity observed across nearly 50 years of breeding (1970–2018). Further, the breeding programs from Europe had the largest sets of unique alleles. LD was lower in the landraces (0.4 Mbp) than in modern germplasm (1.8 Mbp) at r2 = 0.5. ADMIXTURE analysis of modern germplasm defined a minimum of 13 distinct genetic clusters (k), which could be traced to the breeding program of origin. Chromosome regions putatively subjected to strong selection pressure were identified from fixation index (Fst) and diversity reduction index (DRI) metrics in pairwise comparisons among decades of release and breeding programs. Clusters of putative selection sweeps (PSW) were identified as co-localized with major loci controlling phenology (Ppd and Vrn), plant height (Rht) and quality (gliadins and glutenins), underlining the role of the corresponding genes as driving elements in modern breeding. Public seed availability and deep genetic characterization of the GDP make this collection a unique and ideal resource to identify and map useful genetic diversity at loci of interest to any breeding program.

Agronomic, Physiological and Genetic Changes Associated With Evolution, Migration and Modern Breeding in Durum Wheat

“…The large differences between the agronomic performance of durum wheat landraces and modern cultivars identified in the current study agree with the contrasting genetic background of both germplasm types reported in previous studies (Soriano et al, 2016 ; Mazzucotelli et al, 2020 ). Group mean analysis, observation of frequency distributions for each group and the multivariate analysis (PCA for traits) indicated that the significant yield advantage of modern cultivars was associated with greater number of grains per spike and a drastically improved harvest index but not with any difference in kernel weight, confirming results from previous studies (Gale and Youssefian, 1985 ; De Vita et al, 2007 ; Royo et al, 2007 , 2008 ; Fayaz et al, 2013 ).…”

Importance of Landraces in Cereal Breeding for Stress Tolerance

“…Recently, the Expert Working Group on Durum Wheat Genomics and Breeding, in the frame of the Wheat Initiative, and the International Durum Wheat Genome Sequencing Consortium developed two large germplasm collections: The Global Durum Wheat Panel (GDP) and the Tetraploid wheat Germplasm Collection (TGC), respectively [ 34 , 35 ]. Both collections are suitable for identifying beneficial alleles for traits of agronomic importance to be used in breeding and pre-breeding programs.…”

“…If focusing on specific geographic areas has the advantage of exploring within a range of genotypes well adapted to that environment, examining wider collections opens the possibility of investigating the genetic relationship across landraces spread around the world, and having a more precise estimation of the genetic diversity within the group of landraces and with respect to advanced breeding lines or modern cultivars. To quote some examples, studies carried out on panels of hundreds of landraces have been considered in durum and common wheat [ 35 , 59 , 60 ], barley [ 61 , 62 ] and rye [ 63 ]. In general, a higher genetic diversity has been observed in the group of landraces compared to the groups of advanced breeding lines and modern cultivars, indicating landraces as a useful source of variation for breeding.…”

“…In more recent times, high-throughput methods have been developed, such as those based on fixed markers arrays, which include Diversity Array Technology (DArT) markers and SNP arrays. These methods have been shown to be suitable for genetic studies on cereal landraces and can assess a large number of entries, as in the case of panels with several hundreds of durum wheat landraces from Spain, assessed with DArT markers, or from Ethiopia and different countries worldwide, tested with SNP arrays [ 35 , 39 ]. An important aspect is that a certain ascertainment bias should be considered, as these platforms were mainly developed starting from cultivars [ 34 ].…”

“…The use of high-throughput markers allowed, in particular, the collection of more precise information on decay of linkage disequilibrium in landrace panels, which showed a higher resolution compared to commercial cultivars, for their use in association mapping analysis [ 51 , 73 ]. Moreover, the availability of a large number of markers with a good coverage of the genome is important to identify rare and private alleles, which are present only in a defined group of genotypes [ 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 ]. This kind of knowledge is very important for breeding, as landraces can be chosen not only based on their diversity per se, but also for specific alleles of interest in a particular breeding program.…”