The domestication of wild emmer wheat led to the selection of modern durum wheat, grown mainly for pasta production. We describe the 10.45 gigabase (Gb) assembly of the genome of durum wheat cultivar Svevo. The assembly enabled genome-wide genetic diversity analyses revealing the changes imposed by thousands of years of empirical selection and breeding. Regions exhibiting strong signatures of genetic divergence associated with domestication and breeding were widespread in the genome with several major diversity losses in the pericentromeric regions. A locus on chromosome 5B carries a gene encoding a metal transporter (TdHMA3-B1) with a non-functional variant causing high accumulation of cadmium in grain. The high-cadmium allele, widespread among durum cultivars but undetected in wild emmer accessions, increased in frequency from domesticated emmer to modern durum wheat. The rapid cloning of TdHMA3-B1 rescues a wild beneficial allele and demonstrates the practical use of the Svevo genome for wheat improvement.

Pigments are essential to the life of all living organisms. Animals and plants have been the subjects of basic and applied research with the aim of determining the basis of the accumulation and physiological roles of pigments. In crop species, the edible organs show large variations in colour. In durum wheat grain, which is a staple food for humans, the colour is mainly due to two natural classes of pigment: carotenoids and anthocyanins. The carotenoids provide the yellow pigmentation of the durum wheat endosperm, and consequently of the semolina, which has important implications for the marketing of end products based on durum wheat. Anthocyanins accumulate in the aleurone or pericarp of durum wheat and provide the blue, purple and red colours of the grain. Both the carotenoids and the anthocyanins are known to provide benefits for human health, in terms of decreased risks of certain diseases. Therefore, accumulation of these pigments in the grain represents an important trait in breeding programs aimed at improving the nutritional value of durum wheat grain and its end products. This review focuses on the biochemical and genetic bases of pigment accumulation in durum wheat grain, and on the breeding strategies aimed at modifying grain colour.