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

Genetic diversity in elite lines and landraces of CIMMYT spring bread wheat and hybrid performance of crosses among elite germplasm

Wheat (Triticum aestivum) is one of the major cereals in the world. During the past years, the world consumption of wheat increased up to nearly 600 million tones, whereas wheat production continuously decreased. Due to land limitations, new production gains must be achieved from improved plant management systems as well as from the development of high yielding varieties. The International Maize and Wheat Improvement Center (CIMMYT) employs different strategies to enhance yield potential in wheat especially for developing countries. For instance, the wheat breeding program focuses on defined mega-environments (MEs), assuming similar growing conditions in certain countries. In the search for useful alleles, breeders often turn back to wild relatives of wheat stored in the CIMMYT gene bank. With the production of synthetic hexaploid bread wheat (SHWs), characteristics from T. durum and T. tauschii can be combined and via backcrossing incorporated into modern breeding materials. Wheat landraces (LCs) are an additional reservoir of resistances to pests and diseases as well as for environmental adaptation. The production of wheat hybrids is seen as a further option to improve yield potential. A considerable amount of genetic diversity among the materials is a prerequisite for all strategies. Due to the worldwide importance of CIMMYT wheat varieties, they represent a suitable source to examine different breeding strategies in wheat. The main objective of our research was to determine the genetic diversity in modern wheat breeding materials and genetic resources at CIMMYT. Specific research questions were: (i) Is the systematic breeding targeted for different MEs reflected in the genetic diversity among breeding lines (Experiment 1)? (ii) Does the production of SHWs (Experiment 2) and the use of LCs (Experiment 3) enhance the genetic variation in modern breeding materials? (iii) Does the development of hybrids represent an option to improve yield potential in wheat? (iv) Is it possible to predict levels of heterosis with the determination of genetic distance (GD) among hybrid parents? (v) Do genomic and EST- derived SSRs differ in the measurement of genetic diversity (Experiments 1 and 3)? (vi) Are GD values based on SSRs correlated with the coefficient of parentage (COP) (Experiments 1 to 4)? In Experiment 1, a total of 68 CIMMYT advanced breeding lines was analyzed with 99 SSRs, of which 51 were EST- and 46 genomic derived SSRs. A high level of genetic diversity (GD = 0.41) was observed among the breeding lines. The majority of variation (91%) was detected among lines targeted to one specific ME, which indicates a broad genetic base of the current CIMMYT breeding materials. Principal coordinate analysis (PCoA) could clearly separate the lines, but they clustered independently from their target MEs. Main explanations are: (i) alleles were selected that provide fitness to several MEs, (ii) adaptation depends only on a small number of genes that were not detected with the SSRs applied, or (iii) too few cycles of selection were considered to separate the germplasm. In Experiment 2, a total of 11 SHWs, 7 recurrent parent lines, and 13 families of backcross-derived lines (SBLs) were analyzed with 90 SSRs. The SHWs clustered far from the SBLs and the recurrent parents in the cluster analyses and PCoA, and formed a distinct germplasm pool with high allelic variation. Two families of SBLs were tested for a selective advantage of the SHW alleles. Six SSRs revealed non-Mendelian inheritance, indicating that the genomic region of SHWs was actively selected for. Thus, the production of SHWs provides a promising approach for the enhancement of genetic variation in modern breeding materials. In Experiment 3, gene bank accessions of 36 LCs from different countries and a total of 119 accessions from nine LCs populations collected in Turkey and Mexico were analysed with 44 and 76 SSRs, respectively. Both LC materials revealed high allelic variation (GD = 0.69 and 0.54). The 36 LC accessions could not be separated according to their continent of origin. An unexpected relationship was observed between the Chilean LC ?Trigo africano? and the Nigerian LCs ?Dikwa?. All of the nine LC populations could be discriminated except for two Turkish LCs collected from the same location. In accordance with previous studies, considerable genetic variation was observed within the LC populations. Our results contributed a lot to the characterisation of the LCs and generated important knowledge for the management of seed bank accessions. In Experiment 4, a total of 112 wheat hybrids and their 22 parental lines were evaluated at two locations in Mexico for grain yield, plant height, days to flowering and maturity. The level of heterosis varied between -15.3% and 14.1%, but was generally too low to compensate for the high costs of hybrid seed production. The correlations between mid-parent values and hybrid performance, as well as between parental line per se performance and general combining ability were significant (P < 0.01) for all traits, and particularly high for grain yield (r = 0.86 and 0.91). PCoA based on 113 SSR markers revealed three groups of parents. However, the correlations of GDs and COPs with the values of heterosis were negative and not significant. Thus, the prospects of large-scale cultivation of hybrid wheat in developing countries are low. The correlations between GDs and COP in Experiments 1 and 3 were generally significant but low. This can be explained by unrealistic assumptions in the calculation of COPs, which ignore the effects of selection and genetic drift. Similarly to genomic SSRs, EST-SSRs did not reflect functional diversity. The latter revealed lower degrees of polymorphism than genomic SSRs in all experiments, but the allele designation was simpler and more reliable. Across all experiments, our study demonstrates that plant breeding does not inevitably lead to a loss of genetic diversity. We confirmed that CIMMYT?s breeding strategies contributed to a successful increase in genetic variation. These results provide useful information to wheat breeders in CIMMYT and other national programs, regarding the use of wild relatives and landraces for the enhancement of the genetic base of wheat germplasm. In addition, our research provides a base of knowledge for future association studies, identification of useful alleles, and their use in marker-assisted selection.Weizen (Triticum aestivum) ist eine der wichtigsten Getreidearten der Welt. Während in den letzten Jahren der Weizenverbrauch weltweit auf knapp 600 Mio. t anstieg, ist die Produktion rückläufig. Ein erneuter Produktionszuwachs kann angesichts weltweit limitierter Anbauflächen nur über verbesserte Anbauverfahren und die Züchtung verbesserter Weizensorten erfolgen. Mit verschiedenen Strategien versucht das Internationale Institut für Mais und Weizenzüchtung (CIMMYT) in Mexiko das Ertragspotential des Weizens speziell in Entwicklungsländern zu erhöhen. Aufgrund der in vielen dieser Länder vergleichbaren Anbaubedingungen züchtet das Weizenprogramm u.a. für definierte Makro-Umwelten (MEs). Auf der Suche nach wertvollen Allelen greifen die CIMMYT-Züchter häufig auf Wildtypen in der Genbank zurück. Mit der Erzeugung von synthetischen Weizen (SHWs) werden Eigenschaften von T. durum und T. tauschii kombiniert und anschließend mittels Rückkreuzungen in modernes Zuchtmaterial von T. aestivum eingebracht. Landrassen (LCs) stellen ein zusätzliches Reservoir für Resistenzen und verbesserte Umweltanpassung dar. Die Züchtung von Hybridweizen wird als weitere Option zur Erhöhung des Ertragspotentials angesehen. Die genetische Diversität im Ausgangsmaterial ist gleichermaßen wichtig für alle diese Züchtungsstrategien. Aufgrund seiner weltweiten Bedeutung stellt das Weizenmaterial des CIMMYT eine ausgezeichnete Quelle zur Untersuchung der verschiedenen Optionen für die Weizenzüchtung dar. Hauptzielsetzung der vorliegenden Studie war die Erforschung der genetischen Diversität in aktuellem Zuchtmaterial und genetischen Ressourcen des CIMMYT. Im Einzelnen wurden folgende Fragestellungen bearbeitet: (1) Spiegelt sich die systematische Züchtung für verschiedene MEs in der genetischen Diversität zwischen Weizenlinien wieder (Experiment 1)? (2) Kann durch die Erzeugung von SHWs (Experiment 2) bzw. die Nutzung von LCs (Experiment 3) eine Erweiterung der genetischen Variation in modernem Zuchtmaterial erreicht werden? (3) Welche Möglichkeiten zur Anhebung des Ertragspotentials bietet die Erzeugung von Hybriden (Experiment 4)? (4) Inwieweit kann mit der Bestimmung genetischer Distanzen (GD) zwischen Elternlinien die Heterosis in Weizenhybriden vorausgesagt werden? (5) Zeigen genomische und EST-abgeleitete SSRs Unterschiede in der Bestimmung genetischer Diversität (Experimente 1 bis 4)? (6) Ist die genetischer Diversität, berechnet anhand von SSRs, mit dem Abstammungskoeffizienten (COP) korreliert (Experimente 1 und 3)? In Experiment 1 wurden 68 Hochleistungslinien mit 99 SSR Markern untersucht, von denen 51 EST- und 46 genomische SSRs waren. Es wurde ein hohes Ausmaß an genetischer Diversität ermittelt (GD = 0,41). Der Hauptteil der genetischen Variation (91%) wurde innerhalb der für MEs gezüchteten Linien gefunden, was auf eine außerordentliche Breite des CIMMYT-Zuchtmaterials hinweist. In der Hauptkoordinatenanalyse (PCoA) gruppierten die Linien unabhängig von ihrer Anpassung an fünf MEs. Mögliche Ursachen dafür sind: (a) Es wurden Allele selektiert, welche hohe Fitness in mehreren MEs bewirken; (b) die für die Anpassung verantwortlichen Allele wurden nicht mit den untersuchten SSRs erfasst; (c) die Selektion auf Anpassung an die MEs erstreckte sich über zu wenige Selektionszyklen. In Experiment 2 wurden 11 SHWs, 7 rekurrente Elternlinien (BWs) und 13 davon abgeleitete Familien von Rückkreuzungslinien (SBLs) mit 90 SSRs untersucht. Anhand einer Clusteranalyse und PCoA konnten die SHWs eindeutig von den SBLs sowie BWs getrennt werden. Sie stellen somit einen eigenständigen Pool an Genmaterial mit hoher Allelvariation dar. Zwei SBL-Familien wurden auf einen selektiven Vorteil der SHW-Allele getestet. Sechs SSRs zeigten dabei eine signifikante Abweichung von den unter Mendelscher Vererbung erwarteten Genfrequenzen, was auf eine gerichtete Selektion der SHW-Allele schließen lässt. Die Erzeugung von SHWs bietet somit ein Potential zur Erweiterung der genetischen Variation in modernem Zuchtmaterial. In Experiment 3 wurden Akzessionen von 36 LC aus verschiedenen Ländern sowie 119 Akzessionen von neun LC-Populationen aus der Türkei und Mexiko mit 44 bzw. 76 SSRs analysiert. Beide Materialgruppen zeigten ein hohes Maß an genetischer Diverstät (GD = 0,69 bzw. 0,54). Die 36 LCs konnten nicht entsprechend ihren Ursprungskontinenten getrennt werden. Jedoch wurde eine bisher unbekannte Beziehung zwischen einer chilenischen und nigerianischen LC aufgedeckt. Mit Ausnahme zweier türkischer LC-Populationen konnten alle neun untersuchten LCs differenziert werden. Der Großteil der genetischen Variation wurde jedoch innerhalb der LC-Populationen ermittelt. Die Ergebnisse dieses Experiments leisteten somit einen wesentlichen Beitrag zur Charakterisierung der LCs und führten zu wichtigen Erkenntnissen für das künftige Management von Genbank?Akzessionen. In Experiment 4 wurden 112 Weizenhybriden sowie deren Elternlinien in zwei mexikanischen Umwelten für Ertrag, Wuchshöhe, Blütezeit und Reife evaluiert. Die Heterosiswerte für Ertrag schwankten zwischen -15,3% und 14,1% und waren im Durchschnitt zu niedrig, um die höheren Produktionskosten für das Hybridsaatgut zu amortisieren. Die Korrelationen zwischen Elternmittel und Hybridleistung sowie Eigenleistung und Testkreuzungsleistung der Hybrideltern waren signifikant und für alle Merkmale inklusive Ertrag sehr hoch (r = 0,86 bzw. 0,91). Mit Hilfe von 113 SSRs konnten die Elternlinien in drei Gruppen eingeteilt werden. Die Korrelation zwischen GD und Heterosis war jedoch niedrig und nicht signifikant. Nach diesem Ergebnis sind die Aussichten für den potentiellen Erfolg von Hybridweizen in Entwicklungsländern als gering einzustufen. In Experiment 1 und 3 waren die Korrelationen zwischen den GD und COP-Werten signifikant aber niedrig. Dies beruht vermutlich auf unrealistischen Annahmen bei der Berechnung des COP, da hierbei Selektion und genetische Drift ignoriert werden. Im Vergleich zu genomischen SSRs spiegelten auch EST-SSRs keine funktionelle Diversität wieder. Die EST-SSRs waren in allen Experimenten weniger polymorph, jedoch einfacher auszuwerten als die genomischen SSRs. Über alle Experimente hinweg zeigt unsere Studie, dass Pflanzenzüchtung nicht notwendigerweise zum Verlust genetischer Variation führen muss. Sie belegt, dass die am CIMMYT verfolgten Strategien erfolgreich zu einer Verbreiterung der genetischen Variation beitragen. Die Ergebnisse geben den Weizenzüchtern am CIMMYT und in nationalen Zuchtprogrammen wertvolle Hinweise zur Nutzung von Wildarten bzw. Landsorten für die Erweiterung der genetischen Basis bei Weizen. Zudem bieten sie eine Basis für weitere Assoziationskartierungsstudien zur Identifizierung von wertvollen Allelen und deren Nutzung im Rahmen der marker-gestützten Selektion

Agronomic performance of durum wheat landraces and modern cultivars and its association with genotypic variation in vernalization response (Vrn-1) and photoperiod sensitivity (Ppd-1) genes

This study analyzed the relationship between important agronomic traits and major genes regulating flowering time in a panel of 151 Mediterranean durum wheat landraces and 20 modern cultivars. Field experiments were conducted under rainfed conditions during six crop seasons in northeastern Spain. Multivariate analysis of agronomic traits and genotypic data allowed the modern cultivars to be differentiated from the landraces and germplasm pools to be identified within the landraces associated with their geographic origin. The high frequency of the Vrn-A1c allele and the photoperiod insensitive alleles GS105 and GS100 at Ppd-A1 reduced time to anthesis and enlarged the grain filling period of the modern cultivars compared with the landraces. Ancient durums collected close to the domestication area of wheat showed a high frequency of the winter allele vrn-B1 and the photoperiod sensitivity allele Ppd-B1b. None of the allele variants or allelic combinations accounted significantly for variations in any agronomic trait of modern cultivars. Vernalization and photoperiod genes acted additively in explaining the genotypic variance for the agronomic traits of the landraces. Vrn-A1 alleles and Vrn-A1+Vrn-B1 allelic combinations significantly affected the number of grains per spike (NGS), thousand kernel weight (TKW) and grain filling rate (R), accounting for 9%–12% of the genotypic variance for these traits. Ppd-1 accounted for 6%–21% of the genotypic variance for R, grain filling duration (GFD), plant height (PH), biomass at anthesis (CDW) and harvest index (HI). Vrn-1+Ppd-1 allelic combinations accounted for 21%–26% of the genotypic variance for these traits. Except for NGS, the effect of vernalization and photoperiod genes on the agronomic traits was linked to their effect on anthesis time. The three-day delay in anthesis time caused by the allele Vrn-A1d irrespective of the allele Vrn-A1c resulted in increases of 10 % in R and 7% in TKW. The eight-day delay in anthesis time caused by the allele Ppd-A1(DelCD) compared with Ppd-A1(GS105) increased R by 19 % and PH by 28 %, but reduced GFD and HI by 10 %. None of the allele variants or allelic combinations at the Vrn-1 or Ppd-1 genes accounted significantly for variations in yield or number of spikes m−2 (NSm2).info:eu-repo/semantics/publishedVersio

Hybrid performance and heterosis in spring bread wheat, and their relations to SSR-based genetic distances and coefficients of parentage

Development of hybrids is considered to be a promising avenue to enhance the yield potential of crops. We investigated (i) the amount of heterosis observed in hybrid progeny, (ii) relative importance of general (GCA) versus specific (SCA) combining ability, and (iii) the relationship between heterosis and genetic distance measures in four agronomic traits of spring bread wheat. Eight male and 14 female lines, as well as 112 hybrids produced in a factorial design were grown in replicated trials at two environments in Mexico. Principal coordinate analysis based on Rogers’ distance (RD) estimates calculated from 113 SSRs revealed three different groups of parents. Mid-parent heterosis (MPH) for grain yield averaged 0.02 t ha−1 (0.5%) and varied from−15.33% to 14.13%. MPH and hybrid performance (F1P) were higher for intra-group hybrids than for inter-group hybrids, with low values observed in inter-group crosses involving two non-adapted Chinese parents. Combined analyses of variance revealed significant differences among parents and among hybrids. Estimates of GCA variances were more important than SCA variances for all traits. Tight correlations of GCA with line per se performance, and mid-parent value with F1P were observed for all traits. In contrast, correlations of MPH with RD and coefficient of parentage were not significant. It was concluded that the level of heterosis in spring wheat was too low to warrant a commercial exploitation in hybrids. SSRs proved to be a powerful tool for the identification of divergent groups in advanced wheat breeding materials

Haplotypes-based genetic analysis: benefits and challenges

The increasing availability of Single Nucleotide Polymorphisms (SNPs) discovered by Next Generation Sequencing will enable a range of new genetic analyses in crops, which was not possible before. Concomitantly, researchers will face the challenge of handling large data sets at the whole-genome level. By grouping thousands of SNPs into a few hundred haplotype blocks, complexity of the data can be reduced with fewer statistical tests and a lower probability of spurious associations. Owing to the strong genome structure present in breeding lines of most crops, the deployment of haplotypes could be a powerful complement to improve efficiency of marker-assisted and genomic selection. This review describes in brief the commonly used approaches to construct haplotype blocks and some examples in animals and crops are cited where haplotype-based dissection of traits were proven beneficial. Some important considerations and facts while working with haplotypes in crops are reviewed at the end

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