Vol.:(0123456789) 1 3 Theoretical and Applied Genetics https://doi.org/10.1007/s00122-018-3080-z ORIGINAL ARTICLE Simultaneous improvement of grain yield and protein content in durum wheat by diferent phenotypic indices and genomic selection M. Rapp 1  · V. Lein 2  · F. Lacoudre 5  · J. Laferty 6  · E. Müller 7  · G. Vida 8  · V. Bozhanova 3  · A. Ibraliu 4  · P. Thorwarth 1  · H. P. Piepho 9  · W. L. Leiser 1  · T. Würschum 1  · C. F. H. Longin 1 Received: 24 November 2017 / Accepted: 24 February 2018 © Springer-Verlag GmbH Germany, part of Springer Nature 2018 Abstract Key message Simultaneous improvement of protein content and grain yield by index selection is possible but its efficiency largely depends on the weighting of the single traits. The genetic architecture of these indices is similar to that of the primary traits. Abstract Grain yield and protein content are of major importance in durum wheat breeding, but their negative correlation has hampered their simultaneous improvement. To account for this in wheat breeding, the grain protein deviation (GPD) and the protein yield were proposed as targets for selection. The aim of this work was to investigate the potential of diferent indices to simultaneously improve grain yield and protein content in durum wheat and to evaluate their genetic architecture towards genomics-assisted breeding. To this end, we investigated two diferent durum wheat panels comprising 159 and 189 genotypes, which were tested in multiple feld locations across Europe and genotyped by a genotyping-by-sequencing approach. The phenotypic analyses revealed signifcant genetic variances for all traits and heritabilities of the phenotypic indices that were in a similar range as those of grain yield and protein content. The GPD showed a high and positive correla- tion with protein content, whereas protein yield was highly and positively correlated with grain yield. Thus, selecting for a high GPD would mainly increase the protein content whereas a selection based on protein yield would mainly improve grain yield, but a combination of both indices allows to balance this selection. The genome-wide association mapping revealed a complex genetic architecture for all traits with most QTL having small efects and being detected only in one germplasm set, thus limiting the potential of marker-assisted selection for trait improvement. By contrast, genome-wide prediction appeared promising but its performance strongly depends on the relatedness between training and prediction sets. Introduction Durum wheat (Triticum turgidum ssp. durum) is mainly used for human consumption and modern durum varieties need to combine high grain yield and a number of grain qual- ity parameters demanded by pasta producers. The protein Communicated by Xianchun Xia. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00122-018-3080-z) contains supplementary material, which is available to authorized users. * C. F. H. Longin friedrich.longin@uni-hohenheim.de 1 State Plant Breeding Institute, University of Hohenheim, 70599 Stuttgart, Germany 2 Rémy, France 3 Field Crops Institute, 6200 Chirpan, Bulgaria 4 Department of Plant Science and Technology, Agricultural University of Tirana, 1029 Tirana, Albania 5 Limagrain Europe, 11492 Castelnaudary Cedex, France 6 Saatzucht Donau, 2301 Probstdorf, Austria 7 Südwestdeutsche Saatzucht GmbH & Co. KG, Im Rheinfeld 1-13, 76437 Rastatt, Germany 8 Centre for Agricultural Research, Hungarian Academy of Sciences, 2462 Martonvásár, Hungary 9 Biostatistics Unit, University of Hohenheim, 70593 Stuttgart, Germany