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.Fil: Roncallo, Pablo Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; ArgentinaFil: Beaufort, Valeria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; ArgentinaFil: Larsen, Adelina Olga. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Barrow; ArgentinaFil: Dreisigacker, Susanne. Centro Internacional de Mejoramiento de Maiz y Trigo; MéxicoFil: Echenique, Carmen Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentin

SSR and Pedigree Analyses of Genetic Diversity among CIMMYT Wheat Lines Targeted to Different Megaenvironments

Improved bread wheat (Triticum aestivum L.) cultivars for diverse agroecological environments are important for success in the effort to increase food production. In the 1980s, CIMMYT introduced the megaenvironment (ME) concept to breed wheats specifically adapted to different areas. Our objective was to analyze the genetic diversity among 68 advanced CIMMYT wheat lines targeted to different MEs by using 99 simple sequence repeats (SSRs) and the coefficient of parentage (COP). The average number of alleles detected was higher for the 47 genomic SSRs (5.4) than for the 52 SSRs derived from expressed sequence tags (EST) (3.3), but gene diversity between MEs was similar for both types of markers. No significant differences among the five MEs were observed for the means of SSR-based genetic similarities (GS), calculated as 1 − Rogers' distance, and COP values. Both measures showed a low correlation (r = 0.43). High levels of genetic diversity were found within the germplasm targeted to each ME. However, principle coordinate analysis based on modified Rogers' distances did not separate the genotypes according to their targeted MEs. We conclude that presence of a single core germplasm can reflect large phenotypic differences. A sufficient number of diverse breeding lines for each ME is required because MEs generally combine various production areas. SSRs represent a powerful tool to quantify genetic diversity in wheat, but genotypic differentiation for adaptation to specific MEs in the CIMMYT program could not be proven

Multi-environment QTL analysis using an updated genetic map of a widely distributed Seri × Babax spring wheat population

Seri/Babax spring wheat RIL population was developed to minimize the confounding effect of phenology in the genetic dissection of abiotic stress traits. An existing linkage map (< 500 markers) was updated with 6470 polymorphic Illumina iSelect 90K array and DArTseq SNPs to a genetic map of 5576.5 cM with 1748 non-redundant markers (1165 90K SNPs, 207 DArTseq SNPs, 183 AFLP, 111 DArT array, and 82 SSR) assigned to 31 linkage groups. We conducted QTL mapping for yield and related traits phenotyped in several major wheat growing areas in Egypt, Sudan, Iran, India, and Mexico (nine environments: heat, drought, heat plus drought, and yield potential). QTL analysis identified 39 (LOD 2.5–23.6; PVE 4.8–21.3%), 36 (LOD 2.5–15.4; PVE 2.9–21.4%), 30 (LOD 2.5–13.1; PVE 3.6–26.8%), 39 (LOD 2.7–14.4; PVE 2.6–15.9%), and 22 (LOD 2.8–4.8; PVE 6.8–12.9%) QTLs for grain yield, thousand-grain weight, grain number, days to heading, and plant height, respectively. The present study confirmed QTLs from previous studies and identified novel QTLs. QTL analysis based on high-yielding and low-yielding environmental clusters identified 11 QTLs (LOD 2.6–14.9; PVE 2.7–19.7%). The updated map thereby provides a better genome coverage (3.5-fold) especially on the D genome (4-fold), higher density (1.1-fold), and a good collinearity with the IWGSC RefSeq v1.0 genome, and increased the number of detected QTLs (5-fold) compared with the earlier map. This map serves as a useful genomic resource for genetic analyses of important traits on this wheat population that was widely distributed around the world.info:eu-repo/semantics/acceptedVersio

Changes in durum wheat root and aerial biomass caused by the introduction of the Rht-B1b dwarfing allele and their effects on yield formation

Aims This study aimed to quantify the changes in root and aerial biomass of durum wheat brought about by the introduction of the Rht-B1b dwarfing allele and their effects on yield formation. Methods A historical series of 24 Mediterranean cultivars with allelic variants a (tall) and b (semi-dwarf) at Rht-B1 locus was tested in tubes in three greenhouse experiments and six field experiments. Results The dwarfing allele reduced the aerial biomass of each plant at anthesis by 7.6 % and the root by 28.1 % (25.4 %, 26.7 % and 36.0 % in the upper, middle and lower root sections, respectively). Aerial and root biomass were reduced by 27.0 g y−1 and 7 g y−1 respectively, but the relative rate of change was much greater for roots (−0.73 % y−1) than for aerial organs (−0.17 % y−1). Aerial biomass at anthesis was negatively associated with spike number, harvest index and yield in tall cultivars, but no significant relationship was found for semi-dwarf ones. Conclusions The root/aerial biomass ratio was 29 % lower in semi-dwarf than in tall cultivars. In tall cultivars large aerial biomass at anthesis was detrimental to yield formation, while in semi-dwarf cultivars high aerial biomass at anthesis had no effect on yield formation.info:eu-repo/semantics/publishedVersio