Phenotypic evaluation of landraces is important to identify sources of useful loci for traits of interest in breeding and pre-breeding programs, in relation to traits with a simple genetic basis as the resistance to diseases, but also to complex traits such as grain yield (reviewed by Dwiwedi et al.
[30]). Nevertheless, a clearer picture, in terms of genetic diversity, can be achieved using molecular markers. Markers based on polymorphisms at the level of seed storage proteins have been used in different cereal species such as Ethiopian emmer accessions
[13], durum wheat and barley landraces
[29][31][29,31]. Molecular markers based on DNA have been developed, both at the chromosome and the DNA sequence level. Polymorphisms were identified at the level of chromosome banding, through cytofluorometry
[32][33][32,33]. The analysis of 58 varieties and landraces demonstrated a remarkable reproducibility and sensitivity of flow cytometry for the detection of numerical and structural chromosome changes
[34]. In this regard, the dissection of complex genomes by flow cytometric sorting into the individual chromosomes reduces its complexity in a lossless manner, having a significant impact in many areas of research and giving a strong impulse to the sequencing of complex plant genomes
[35][36][37][35,36,37]. At sequence level, DNA-based molecular markers have become the most suitable tool in this kind of study, thanks to their informativeness and to the great reduction in time processing and costs observed in the last few years. Random Amplified Polymorphic DNA (RAPD) markers were initially used for assessing genetic diversity in cereal landraces
[13], but they were characterized by a low reproducibility, therefore Simple Sequence Repeat (SSR) markers became the method of choice thanks to their reproducibility and informativeness with a high number of alleles detected per locus. As an example, 8.1 alleles per locus were detected in a panel of 66 barley landraces from Tunisia
[14], and 14.6 alleles per locus were identified in a collection including 36 oat commercial varieties and 141 landraces from Spain
[17]. 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
[23][3][3,23]. An important aspect is that a certain ascertainment bias should be considered, as these platforms were mainly developed starting from cultivars
[38]. For this reason, methods based on Genotyping by sequencing, including DArTseq, are also used in this kind of study
[10][39][10,39]. 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
[15][40][15,40]. 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
[23][41][1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][24][25][1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,41]. 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.