Training set optimization under population structure in genomic selection.

KEY MESSAGE: Population structure must be evaluated before optimization of the training set population. Maximizing the phenotypic variance captured by the training set is important for optimal performance. The optimization of the training set (TRS) in genomic selection has received much interest in both animal and plant breeding, because it is critical to the accuracy of the prediction models. In this study, five different TRS sampling algorithms, stratified sampling, mean of the coefficient of determination (CDmean), mean of predictor error variance (PEVmean), stratified CDmean (StratCDmean) and random sampling, were evaluated for prediction accuracy in the presence of different levels of population structure. In the presence of population structure, the most phenotypic variation captured by a sampling method in the TRS is desirable. The wheat dataset showed mild population structure, and CDmean and stratified CDmean methods showed the highest accuracies for all the traits except for test weight and heading date. The rice dataset had strong population structure and the approach based on stratified sampling showed the highest accuracies for all traits. In general, CDmean minimized the relationship between genotypes in the TRS, maximizing the relationship between TRS and the test set. This makes it suitable as an optimization criterion for long-term selection. Our results indicated that the best selection criterion used to optimize the TRS seems to depend on the interaction of trait architecture and population structure.

Quantitative genetic analysis and mapping of leaf angle in durum wheat.

The leaf erectness profile has been used to optimize plant architecture since erect leaves can enhance photosynthesis and dry matter production by greater sunlight capture. Brassinosteroid is a recent class of phytohormones that has been related to a more erect profile. There are no reports in the literature of the genetic variability of leaf angle in doubled haploid durum wheat populations; most studies on leaf angle have focused on the inheritance. Our aim was to study the genetic variation in flag and penultimate leaf angle in a durum wheat doubled haploid mapping population, identifying and mapping quantitative trait loci influencing leaf angle. An F(1)-derived doubled haploid population of 89 lines from the cross Strongfield/Blackbird was used to construct a genetic map using 423 molecular marker loci. Two greenhouse experiments and one field test were conducted using an alpha lattice in a randomized complete block design with three replicates. The leaf angle was measured on flag and penultimate leaf with a protractor at three different growth stages. The results indicated poor to moderate correlations between the position of the leaf angle and the growth stage. Transgressive segregation beyond Strongfield and Blackbird of leaf angle was observed for all environments. Putative trait loci were identified on chromosomes 2A, 2B, 3A, 3B, 4B, 5B and 7A. This work helps to understand the genetics of leaf angle in durum wheat.

Brassinosteroid leaf unrolling QTL mapping in durum wheat.

Brassinosteroids are a newly reported class of plant growth phytohormones found in plants throughout the plant kingdom. Functioning at very low concentrations, they play an essential role in improving biomass yield and stress tolerance. There are no reports in the literature of the genetic variability of responsiveness of brassinosteroids in wheat; most studies on brassinosteroids have focused on the physiological effects of exogenous addition of brassinosteroids. Our aim was to study the genetic variation in the responsiveness of a doubled haploid durum wheat population to three brassinosteroid concentrations using the leaf unrolling test, which is a simple bioassay to test brassinosteroid activity. An F(1)-derived doubled haploid population of 77 individuals from the cross Strongfield/Blackbird was used to construct a genetic map of 427 molecular marker loci. The leaf unrolling test was performed on the parents and doubled haploid genotypes of the population using 0.2, 2 and 20 nM brassinosteroid concentrations. The results indicated significant differences in leaf unrolling between the two parents, doubled haploid genotypes, treatments and genotype-by-treatment combinations. Transgressive segregation beyond Strongfield of leaf unrolling was observed for all concentrations, with the strongest response at 20 nM. Putative quantitative trait loci were revealed in the intervals Xgwm2-Xbarc45 on chromosome 3A and Xwmc643a-Xwmc625a on chromosome 3B. Additional quantitative trait loci were associated with markers Xwmc48a, Xwmc511, Xwmc89a and Xgwmc692 on chromosome 4B, and Xwmc17 on chromosome 7A. This work should enhance the understanding of the relationship between stress tolerance and productivity, and responsiveness to brassinosteroids.

Changes in duration of developmental phases of durum wheat caused by breeding in Spain and Italy during the 20th century and its impact on yield.

BACKGROUND AND AIMS: Although the apical development of wheat has been widely described, studies analysing how genetic breeding over the 20th century influenced the developmental phases and its consequences on yield generation are lacking, especially for durum wheat under field conditions in Mediterranean environments. The aims of this study were to analyse the effects of breeding in Spain and Italy on crop development during the last century, to determine whether or not breeding significantly altered the developmental phases between sowing and maturity, and to evaluate the importance of each phase in determining the number of grains per spike of durum wheat (Triticum durum) cultivars representing the germplasm grown throughout the 20th century in Spain and Italy. METHODS: Eight field experiments were carried out during 4 years in two contrasting latitudes (Lleida and Granada, Spain). Plant material consisted of 24 durum wheat cultivars (12 Italian and 12 Spanish) grown throughout the 20th century in Spain and Italy. KEY RESULTS: In Spanish materials, breeding reduced the duration of the period from sowing to anthesis, placing the grain-filling period in better conditions. In those cultivars, the sub-phase sowing-terminal spikelet formation was reduced while the duration of the period from booting to anthesis was increased. The number of grains per spike increased by 23 % from old to modern cultivars, by changes in the number of grains per spikelet in both Spanish and Italian cultivars. Floral abortion from booting to anthesis diminished by 24 % from old to modern cultivars, and grain setting increased by 13 %. CONCLUSIONS: The results suggest that breeding reduced not only plant height, but also the time to anthesis. By extending the duration of the phase from booting to anthesis, which was associated with an increase in spike dry weight and grains per spike, it suggests that future increases in spike fertility could be achieved by enlarging that phase.