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

Abstract

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.

The Global Durum Wheat Panel (GDP): An International Platform to Identify and Exchange Beneficial Alleles

“…In the GDP, the mean PIC values of 0.27 for landraces and 0.28 for modern lines and ranging from 0.09 to 0.38 (Table 2B) indicated a generally higher or similar level of genetic diversity captured within the GDP compared to previously studied collections. Recent studies reported PIC values of 0.26 for durum modern germplasm ( Chao et al, 2017 ), 0.19 for a set of both landraces and modern lines ( Ren et al, 2012 ), and 0.18 in a collection of 168 durum wheat accessions of different origins ( Roncallo et al, 2019 ). Analogously, AMOVA on clusters within GDP based on geography and breeding program of origin showed that only 13% of the total genetic variance could be captured among groups, while most diversity remained among individuals within clusters.…”

Data_Sheet_2.ZIP

“…Analogously, AMOVA on clusters within GDP based on geography and breeding program of origin showed that only 13% of the total genetic variance could be captured among groups, while most diversity remained among individuals within clusters. These results concur with those reported by Soriano et al (2016) with 172 landraces from 21 countries, by Roncallo et al (2019) with a panel of 168 durum accessions and by N'Diaye et al (2018) with a panel of Canadian durum cultivars where only 10% of variation was captured among groups. Other studies considering similar panels reported capturing over 30% of the total genetic variance by clustering germplasm based on kinship matrix, but using relatively higher k values (Kabbaj et al, 2017;Robbana et al, 2019).…”

“…It is therefore evident that the passport information alone, while of great historical interest, is unable to capture the true genetic diversity of durum wheat worldwide. AMOVA on stratified groups may reveal much more variance among sub-populations, as indeed reported by other authors (Kabbaj et al, 2017;Roncallo et al, 2019). The moderate diversification among breeding groups (11.67% of the total variance) and very little among decades of release (2.95% of the total variance) revealed by AMOVA on the 473 modern durum wheat accessions (Tables 2D,E) was probably due to the wide and frequent exchange of parents among durum breeders worldwide.…”

“…In the GDP, the mean PIC values of 0.27 for landraces and 0.28 for modern lines and ranging from 0.09 to 0.38 (Table 2B) indicated a generally higher or similar level of genetic diversity captured within the GDP compared to previously studied collections. Recent studies reported PIC values of 0.26 for durum modern germplasm (Chao et al, 2017), 0.19 for a set of both landraces and modern lines (Ren et al, 2012), and 0.18 in a collection of 168 durum wheat accessions of different origins (Roncallo et al, 2019). Analogously, AMOVA on clusters within GDP based on geography and breeding program of origin showed that only 13% of the total genetic variance could be captured among groups, while most diversity remained among individuals within clusters.…”

Start codon targeted (SCoT) polymorphism reveals genetic diversity of Manilkara in Thailand

“…Molecular markers have been used very frequently in ecological, taxonomical, diversity, conservation, phylogenic and genetic studies amongst organisms (Avise 1994;Weising et al 2005;Sheth and Thaker 2017;Srivastava et al 2020). After the advent of Polymerase chain reaction (PCR) several advancements and introduction of new concepts were employed in the improvement of various types of molecular marker technologies like amplified fragment length polymorphism (AFLP) (Vos et al 1995;Roncallo et al 2019), inter simple sequence repeats (ISSRs), (Vanijajiva 2012;Husnudin et al 2019), random amplified polymorphic DNA (RAPD) (Vanijajiva et al 2005;Ihwan and Hakim 2019), Simple Sequence Repeats (SSR (Dewi et al 2020), Single Sequence Polymorphism (SNP) (Trick et al 2009;Luo et al 2010;Bayerl et al 2018). For distinct genetic applications amongst diverse plant species, different markers have been used by various researchers in commercial fruit accessions.…”