Abstract
The first breeding program in the world for durum wheat was conceived in Italy in the early 1900s. Over the decades, pressure exerted by natural and artificial selection could have progressively reduced the genetic diversity of the durum wheat germplasm. In the present study, a large panel of Italian durum wheat accessions that includes landraces, old and modern cultivars was subjected to genotyping using the Illumina iSelect 15K wheat SNP array. The aim was to assess the impact that selection has in shaping Italian durum wheat genetic diversity and to exploit the patterns of genetic diversity between populations to identify molecular signatures of divergence and selection. Relatively small differences in genetic diversity have been observed among accessions, which have been selected and cultivated in Italy over the past 150 years. Indeed, directional selection combined with that operated by farmers/breeders resulted in the increase of linkage disequilibrium (LD) and in changes of the allelic frequencies in DNA regions that control important agronomic traits. Results from this study also show that major well-known genes and/or QTLs affecting plant height (RHT), earliness (VRN, PPD) and grain quality (GLU, PSY, PSD, LYC, PPO, LOX3) co-localized with outlier SNP loci. Interestingly, many of these SNPs fall in genomic regions where genes involved in nitrogen metabolism are. This finding highlights the key role these genes have played in the transition from landraces to modern cultivars. Finally, our study remarks on the need to fully exploit the genetic diversity of Italian landraces by intense pre-breeding activities aimed at introducing a new source of adaptability and resistance in the genetic background of modern cultivars, to contrast the effect of climate change. The list of divergent loci and loci under selection associated with useful agronomic traits represents an invaluable resource to detect new allelic variants for target genes and for guiding new genomic selection programs in durum wheat.
Highlights
Durum wheat [Triticum turgidum subsp. durum (Desf.) Husn] is one of the most important staple crops and it is primarily cultivated in the Mediterranean regions, Southern Europe, and North Africa
Indices of genetic diversity were computed to describe the variability within the 259 durum wheat accessions included in the whole collection and among subpopulations (i.e., LR, old cultivars (OC), modern cultivars (MC), MC1, MC2, and MC3) (Table 1)
The number of P and parsimony informative sites (PIS) sites slightly decreased moving from LR (P = 3,059 and PIS = 2,819) to OC (P = 2,897 and PIS = 2,495), while it increased again up to P = 3,084 and PIS = 2,689 in MC
Summary
Durum wheat [Triticum turgidum subsp. durum (Desf.) Husn] is one of the most important staple crops and it is primarily cultivated in the Mediterranean regions, Southern Europe, and North Africa. Its domestication took place about 10,000 years ago in the Fertile Crescent, as a result of selection and domestication of wild and domesticated emmer (Zohary et al, 2012). As it happened with most crops, the wheat domestication process occurs in four stages (Meyer and Purugganan, 2013; Gaut et al, 2018), during which phenotypic traits changed due to variations in genetic diversity patterns. Differentiation between wild and domesticated populations is affected by artificial (intentional and/or unconscious) and natural selection that contributes to the adaptation of crops to particular climates and diverse environments (McKey et al, 2012) Artificial selection favors traits identified as valuable by the breeders within wild populations, which are characterized by a wide genetic diversity due to demographic factors, including population size and a variation in recombination rate (Jordan et al, 2015).
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