Population structure, allelic variation at Rht-B1 and Ppd-A1 loci and its effects on agronomic traits in Argentinian durum wheat.

Exploring the genetic variability in yield and yield-related traits is essential to continue improving genetic gains. Fifty-nine Argentinian durum wheat cultivars were analyzed for important agronomic traits in three field experiments. The collection was genotyped with 3565 genome-wide SNPs and functional markers in order to determine the allelic variation at Rht-B1 and Ppd-A1 genes. Population structure analyses revealed the presence of three main groups, composed by old, modern and genotypes with European or CIMMYT ancestry. The photoperiod sensitivity Ppd-A1b allele showed higher frequency (75%) than the insensitivity one Ppd-A1a (GS105). The semi-dwarfism Rht-B1b and the Ppd-A1a (GS105) alleles were associated with increases in harvest index and decreases in plant height, grain protein content and earlier heading date, although only the varieties carrying the Rht-B1 variants showed differences in grain yield. Out of the two main yield components, grain number per plant was affected by allelic variants at Rht-B1 and Ppd-A1 loci, while no differences were observed in thousand kernel weight. The increases in grain number per spike associated with Rht-B1b were attributed to a higher grain number per spikelet, whereas Ppd-A1a (GS105) was associated with higher grain number per spikelet, but also with lower spikelets per spike.

Allelic Variation at Glutenin Loci (Glu-1, Glu-2 and Glu-3) in a Worldwide Durum Wheat Collection and Its Effect on Quality Attributes.

Durum wheat grains (Triticum turgidum L. ssp. durum) are the main source for the production of pasta, bread and a variety of products consumed worldwide. The quality of pasta is mainly defined by the rheological properties of gluten, an elastic network in wheat endosperms formed of gliadins and glutenins. In this study, the allelic variation at five glutenin loci was analysed in 196 durum wheat genotypes. Two loci (Glu-A1 and Glu-B1), encoding for high-molecular-weight glutenin subunits (HMW-GS), and three loci (Glu-B2, Glu-A3 and Glu-B3), encoding for low molecular weight glutenin subunits (LMW-GS), were assessed by SDS-PAGE. The SDS-sedimentation test was used and the grain protein content was evaluated. A total of 32 glutenin subunits and 41 glutenin haplotypes were identified. Four novel alleles were detected. Fifteen haplotypes represented 85.7% of glutenin loci variability. Some haplotypes carrying the 7 + 15 and 7 + 22 banding patterns at Glu-B1 showed a high gluten strength similar to those that carried the 7 + 8 or 6 + 8 alleles. A decreasing trend in grain protein content was observed over the last 85 years. Allelic frequencies at the three main loci (Glu-B1, Glu-A3 and Glu-B3) changed over the 1915-2020 period. Gluten strength increased from 1970 to 2020 coinciding with the allelic changes observed. These results offer valuable information for glutenin haplotype-based selection for use in breeding programs.

Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes.

BACKGROUND: Durum wheat (Triticum turgidum L. ssp. durum Desf. Husn) is the main staple crop used to make pasta products worldwide. Under the current climate change scenarios, genetic variability within a crop plays a crucial role in the successful release of new varieties with high yields and wide crop adaptation. In this study we evaluated a durum wheat collection consisting of 197 genotypes that mainly comprised a historical set of Argentinian germplasm but also included worldwide accessions. RESULTS: We assessed the genetic diversity, population structure and linkage disequilibrium (LD) patterns in this collection using a 35 K SNP array. The level of polymorphism was considered, taking account of the frequent and rare allelic variants. A total of 1547 polymorphic SNPs was located within annotated genes. Genetic diversity in the germplasm collection increased slightly from 1915 to 2010. However, a reduction in genetic diversity using SNPs with rare allelic variants was observed after 1979. However, larger numbers of rare private alleles were observed in the 2000-2009 period, indicating that a high reservoir of rare alleles is still present among the recent germplasm in a very low frequency. The percentage of pairwise loci in LD in the durum genome was low (13.4%) in our collection. Overall LD and the high (r2 > 0.7) or complete (r2 = 1) LD presented different patterns in the chromosomes. The LD increased over three main breeding periods (1915-1979, 1980-1999 and 2000-2020). CONCLUSIONS: Our results suggest that breeding and selection have impacted differently on the A and B genomes, particularly on chromosome 6A and 2A. The collection was structured in five sub-populations and modern Argentinian accessions (cluster Q4) which were clearly differentiated. Our study contributes to the understanding of the complexity of Argentinian durum wheat germplasm and to derive future breeding strategies enhancing the use of genetic diversity in a more efficient and targeted way.

Cytochrome P450 Herbicide Metabolism as the Main Mechanism of Cross-Resistance to ACCase- and ALS-Inhibitors in Lolium spp. Populations From Argentina: A Molecular Approach in Characterization and Detection.

Knowledge about the mechanisms of herbicide resistance provide valuable insights into evolving weed populations in response to selection pressure and should be used as a basis for designing management strategies for herbicide-resistant weeds. The selection pressure associated with reactive management against glyphosate-resistant Lolium spp. populations would have favored the herbicide resistance to ACCase- and ALS-inhibitors. This work was aimed to determine the sensitivity of 80 Argentinean Lolium spp. populations to ALS- and ACCase-inhibitor herbicides for use in wheat or barley and to study the mechanisms of resistance involved. Sensitivity to pinoxaden and iodosulfuron-mesosulfuron were positively correlated (r = 0.84), even though both affect different target sites. Inhibitors of cytochrome P450 monooxygenases (P450s) increased the sensitivity to pinoxaden and iodosulfuron-mesosulfuron in 94% of herbicide-resistant populations and target-site ACCase resistance mutations were detected only in two cases. Polymorphic variants were obtained with a pair primer designed on P450 sequences, cluster analysis discriminated around 80% of susceptible and P450-metabolic resistant plants sampled from a single population or different populations. Five markers corresponding to herbicide sensitivity were identified to be significantly associated with phenotypic variance in plants. Resistance to ALS- and ACCase-inhibitor herbicides were closely related, challenging the rotation of herbicides of both sites of action as a practice against resistance. In that sense, the use of pinoxaden and iodosulfuron-mesosulfuron would have provoked a selection on P450 genes that conduced a convergence of P450-metabolism based resistant Lolium spp. populations, which was detected by markers in a contribution to elucidate the molecular basis of this type of resistance.

Genetic diversity and linkage disequilibrium using SNP (KASP) and AFLP markers in a worldwide durum wheat (Triticum turgidum L. var durum) collection.

The aim of this work was to analyze the genetic diversity and linkage disequilibrium in a collection of 168 durum wheat accessions (Triticum turgidum L. var. durum) of different origins. Our collection was mainly composed of released and unreleased Argentinian germplasm, with additional genotypes from Italy, Chile, France, CIMMYT, Cyprus, USA and WANA region. To this end, the entire collection was characterized with 85 Single Nucleotide Polymorphism (SNP) markers obtained by Kompetitive Allele Specific PCR (KASP), giving a heterozygosity (He) mean value of 0.183 and a coefficient of genetic differentiation (Gst) value of 0.139. A subset of 119 accessions was characterized with six Amplified Fragment Length Polymorphism (AFLP) primer combinations. A total of 181 polymorphic markers (125 AFLP and 56 SNP) amplified across this subset revealed He measures of 0.352 and 0.182, respectively. Of these, 134 were selected to estimate the genome-wide linkage disequilibrium obtaining low significant values (r2 = 0.11) in the subset, indicating its suitability for future genome-wide association studies (GWAS). The structure analysis conducted in the entire collection with SNP detected two subpopulations. However, the structure analysis conducted with AFLP markers in the subset of 119 accessions proved to have greater degree of resolution and detect six subpopulations. The information provided by both marker types was complementary and showed a strong association between old Argentinian and Italian germplasm and a contribution of CIMMYT germplasm to modern Argentinian, Chilean and Cypriot accessions. The influence of Mediterranean germplasm, mainly from Italy, on part of the modern Argentinian cultivars or breeding lines was also clearly evidenced. Although our analysis yields conclusive results and useful information for association mapping studies, further analyses are needed to refine the number of subpopulations present in the germplasm collection analyzed.