Genetic Diversity and Association Mapping for Agromorphological and Grain Quality Traits of a Structured Collection of Durum Wheat Landraces Including subsp. durum, turgidum and diccocon

Abstract

Association mapping was performed for 18 agromorphological and grain quality traits in a set of 183 Spanish landraces, including subspecies durum, turgidum and dicoccon, genotyped with 749 DArT (Diversity Array Technology) markers. Large genetic and phenotypic variability was detected, being the level of diversity among the chromosomes and genomes heterogeneous, and sometimes complementary, among subspecies. Overall, 356 were monomorphic in at least one subspecies, mainly in dicoccon, and some of them coincidental between subspecies, especially between turgidum and dicoccon. Several of those fixed markers were associated to plant responses to environmental stresses or linked to genes subjected to selection during tetraploid wheat domestication process. A total of 85 stable MTAs (marker–trait associations) have been identified for the agromorphological and quality parameters, some of them common among subspecies and others subspecies-specific. For all the traits, we have found MTAs explaining more than 10% of the phenotypic variation in any of the three subspecies. The number of MTAs on the B genome exceeded that on the A genome in subsp. durum, equalled in turgidum and was below in dicoccon. The validation of several adaptive and quality trait MTAs by combining the association mapping with an analysis of the signature of selection, identifying the putative gene function of the marker, or by coincidences with previous reports, showed that our approach was successful for the detection of MTAs and the high potential of the collection to identify marker–trait associations. Novel MTAs not previously reported, some of them subspecies specific, have been described and provide new information about the genetic control of complex traits.

SNP-based association study of kernel architecture in a worldwide collection of durum wheat germplasm

“…In previous studies of kernel traits in durum, only kernel weight-related QTLs have been identified using traditional linkage mapping and genome-wide association mapping [38][39][40][41][42][43][44][45][46][47][48][49][50][51][52][53][54]. After searching QTL identified here with previously reported QTL in durum wheat genome, most of the SNPs identified from kernel-related traits in this study were close to or overlapped with the positions of kernel weight-related QTL reported in previous studies.…”

Genetic Diversity within a Global Panel of Durum Wheat (Triticum durum) Landraces and Modern Germplasm Reveals the History of Alleles Exchange

“…However, the setting of k is highly dependent on the scope of the research and here the preference was given to capturing similarities rather than divergences. A large portion of admixture among landraces remained unfixed with the set value of k , and this could justify the difference in the number of clusters between our work and that of Ruiz et al (2012). The ability to distinguish following waves of dispersion among landraces was one of our scopes and this was achieved by finding separation between the two main centers of origin/diversity (Middle East and Ethiopia) and other landraces.…”

“…In previous research, a panel of 190 Spanish durum wheat landraces was attributed to nine sub-populations (Ruiz et al, 2012), while a similar set of the germplasm collection used here, comprising 134 modern durum cultivars, was assigned to six sub-populations by Maccaferri et al (2003). In our research, the number of clusters used for stratification could have been increased, to allocate four additional sub-populations among landraces of Cluster 4.…”

Genome-Wide Association Mapping of Prostrate/Erect Growth Habit in Winter Durum Wheat

“…More recently, a genomic wide association study (GWAS) has been conducted for seedling habit, together with other important agronomic traits, and significant marker-trait associations (MTAs) have been found for this trait on chromosomes 3B, 4A and 6B [21]. Significant MTAs for the prostrate/erect trait have also been identified in durum wheat: Giraldo et al [22] found two chromosome regions on 3A and 3BL, significantly associated to plant juvenile growth habit in tetraploid wheats (T. durum and T. dicoccum). In the case of barley, the close association existing between the semi-dwarfing sdw1/denso gene regulating plant height and the prostrate growth habit could be explained by the pleiotropic effect of sdw1/denso gene on tiller angle [23].…”