Extensive genomic characterization of a set of near-isogenic lines for heterotic QTL in maize (Zea mays L.)

Background Despite the crucial role that heterosis has played in crop improvement, its genetic and molecular bases are still elusive. Several types of structured populations were used to discover the genetic architecture underlying complex phenotypes, and several QTL related to heterosis were detected. However, such analyses generally lacked the statistical power required for the detailed characterization of individual QTL. Currently, QTL introgression into near-isogenic materials is considered the most effective strategy to this end, despite such materials inevitably contain a variable, unknown and undesired proportion of non-isogenic genome. An introgression program based on residual heterozygous lines allowed us to develop five pairs of maize (Zea mays L.) near-isogenic lines (NILs) suitable for the fine characterization of three major heterotic QTL previously detected. Here we describe the results of the detailed genomic characterization of these NILs that we undertook to establish their genotypic structure, to verify the presence of the expected genotypes within target QTL regions, and to determine the extent and location of residual non-isogenic genomic regions. Results The SNP genotyping approach allowed us to determine the parent-of-origin allele for 14,937 polymorphic SNPs and to describe in detail the genotypic structure of all NILs. The correct introgression was confirmed for all target QTL in the respective NIL and several nonisogenic regions were detected genome-wide. Possible linkage drag effects associated to the specific introgressed regions were observed. The extent and position of other non-isogenic regions varied among NIL pairs, probably deriving from random segregating sections still present at the separation of lineages within pairs. Conclusions The results of this work strongly suggest that the actual isogenicity and the genotypic architecture of near-isogenic materials should be monitored both during the introgression procedure and on the final materials as a paramount requisite for a successful mendelization of target QTL. The information here gathered on the genotypic structure of NILs will be integrated in future experimental programs aimed at the fine mapping and isolation of major heterotic QTL, a crucial step towards the understanding of the molecular bases of heterosis in maize

Joining smallholder farmers’ traditional knowledge with metric traits to select better varieties of Ethiopian wheat

Smallholder farming communities face highly variable climatic conditions that threaten locally adapted, low-input agriculture. The benefits of modern crop breeding may fail to reach their fields when broadly adapted genetic materials do not address local requirements. To date, participatory methods only scratched the surface of the exploitability of farmers’ traditional knowledge in breeding. In this study, 30 smallholder farmers in each of two locations in Ethiopia provided quantitative evaluations of earliness, spike morphology, tillering capacity and overall quality on 400 wheat genotypes, mostly traditional varieties, yielding altogether 192,000 data points. Metric measurements of ten agronomic traits were simultaneously collected, allowing to systematically break down farmers’ preferences on quantitative phenotypes. Results showed that the relative importance of wheat traits differed by gender and location. Farmer traits were variously contributed by metric traits, and could only partially be explained by them. Eventually, farmer trait values were used to produce a ranking of the 400 wheat varieties identifying the trait combinations most desired by farmers. The study scale and methods lead to a better understanding of the quantitative basis of Ethiopian smallholder farmer preference in wheat, broadening the discussion for the future of local, sustainable breeding efforts accommodating farmers’ knowledge

Targeting environmental adaptation in the monocot model Brachypodium distachyon: a multi-faceted approach

Background The local environment plays a major role in the spatial distribution of plant populations. Natural plant populations have an extremely poor displacing capacity, so their continued survival in a given environment depends on how well they adapt to local pedoclimatic conditions. Genomic tools can be used to identify adaptive traits at a DNA level and to further our understanding of evolutionary processes. Here we report the use of genotyping-by-sequencing on local groups of the sequenced monocot model speciesBrachypodium distachyon. Exploiting population genetics, landscape genomics and genome wide association studies, we evaluate B. distachyonrole as a natural probe for dentifying genomic loci involved in environmental adaptation. Results Brachypodium distachyonindividuals were sampled in nine locations with different ecologies and characterized with 16,697 SNPs. Variations in sequencing depth showed consistent patterns at 8,072 genomic bins, which were significantly enriched in transposable elements. We investigated the structuration and diversity of this collection, and exploited climatic data to identify loci with adaptive significance through i) two different approaches for genome wide association analyses considering climatic variation, ii) an outlier loci approach, and iii) a canonical correlation analysis on differentially sequenced bins. A linkage disequilibrium-corrected Bonferroni method was applied to filter associations. The two association methods jointly identified a set of 15 genes significantly related to environmental adaptation. The outlier loci approach revealed that 5.7% of the loci analysed were under selection. The canonical correlation analysis showed that the distribution of some differentially sequenced regions was associated to environmental variation. Conclusions We show that the multi-faceted approach used here targeted different components of B. distachyon adaptive variation, and may lead to the discovery of genes related to environmental adaptation in natural populations. Its application to a model species with a fully sequenced genome is a modular strategy that enables the stratification of biological material and thus improves our knowledge of the functional loci determining adaptation in near-crop species. When coupled with population genetics and measures of genomic structuration, methods coming from genome wide association studies may lead to the exploitation of model species as natural probes to identify loci related to environmental adaptation

Two-Dimensional Differential in Gel Electrophoresis (2D-DIGE) analysis of grape berry proteome during post-harvest withering

The practice of postharvest withering is commonly used to correct quality traits and sugar concentration of high quality wines. To date, changes in the metabolome during the berry maturation process have been well documented; however, the biological events which occur at the protein level have yet to be fully investigated. To gain insight into the postharvest withering process, we studied the protein expression profiles of grape (Corvina variety) berry development focusing on withering utilizing a twodimensional differential in gel electrophoresis (2D-DIGE) proteomics approach. Comparative analysis revealed changes in the abundance of numerous soluble proteins during the maturation and withering processes. On a total of 870 detected spots, 90 proteins were differentially expressed during berry ripening/withering and 72 were identified by MS/MS analysis. The majority of these proteins were related to stress and defense activity (30%), energy and primary metabolism (25%), cytoskeleton remodelling (7%), and secondary metabolism (5%). Moreover, this study demonstrates an active modulation of metabolic pathways throughout the slow dehydration process, including de novo protein synthesis in response to the stress condition and further evolution of physiological processes originated during ripening. These data represent an important insight into the withering process in terms of both Vitis germplasm characterization and knowledge which can assist quality improvement

Localization and fine mapping of gaMS-1, a male gametophytic mutant of maize

Post-meiotic mutants affecting pollen development are fundamental tools for defining the genetic program controlling microsporogenesis and pollen function. An example of such mutants is gametophytic male sterile-1 (gaMS-1). Heterozygous plants gaMS-1/+ that have a normal phenotype and are female fertile, segregate 1:1 normal:sterile pollen grains and their selfed progeny segregates 1:1 normal:semi-sterile plants. With the final aim of isolating the gene, a positional cloning strategy was adopted. In this paper, we report the results of fine mapping GaMS-1 by different types of molecular markers. Two back crosses were used as mapping populations. They were obtained by crossing the line carrying the mutation with the inbred lines Mo17 and WF9, used as recurrent male parents. Linkage disequilibrium analysis allowed assigning GaMS-1 to the short arm of chromosome 2. By the combined use of SSR, AFLP, PCR markers and ESTs a region of 1 cM containing GaMS-1 was delimited

Genome wide association study to identify the genetic base of smallholder farmer preferences of durum wheat traits

The study was conducted during the 2012 wheat growing season in two locations in the Ethiopian highlands. The first location was in the Geregera area, in the village of Workaye, Meket district (Amhara region, 11◦40′N/38◦52′E, WGS84). The second location was in the Hagreselam district, in the village of Melfa (Tigray region, 13◦39′N/39◦10′E, WGS84). In each location, 30 smallholder farmers growing wheat were selected on a voluntary basis, but keeping a 50:50 gender representation Farmers were asked to list the traits they used to evaluate wheat varieties, hereafter termed farmer traits (FT), and these were ranked by importance. Technicians collected 10 metrics traits on these sites and farmers provided a score for their overall plot evaluation. The genetic material here analyzed is a diversity panel comprising 400 Ethiopian wheat accessions conserved ex situ at the Ethiopian Biodiversity Institute. DNA extraction for genotyping was conducted in Ethiopia, at the Mekelle University Molecular and Biotechnology Laboratory (Mekelle,Tigray)