Spatial and temporal genetic variation in Ethiopian barley (Hordeum vulgare L.) landraces as revealed by simple sequence repeat (SSR) markers

Abstract

Background Ethiopia is considered as center of diversity for barley (Hordeum vulgare L.) and it is grown across different agro-ecologies of the country. Unraveling population structure and gene flow status on temporal scales assists an evaluation of the consequences of physical, demographic and overall environmental changes on the stability and persistence of populations. This study was to examine spatial and temporal genetic variation within and among barley landrace samples collected over a period of four decades, using simple sequence repeat markers. Results Results from STRUCTURE, neighbor joining tree and discriminant analysis of principal component (DAPC) analysis revealed presence low-to-high genetic diversity among the landraces and grouped the landraces into three clusters. The cluster analysis revealed a close relationship between landraces along geographic proximity with genetic distance increases along with geographic distance. From analysis of molecular variance (AMOVA) in terms of collection year, it was observed that within-population genetic diversity much higher than between population and that the temporal differentiation is considerably smaller. The low-to-high genetic differentiation between landraces could be attributed to gene flow across the region as a consequence of seed exchange among farmers. Conclusion The results demonstrate that this set of SSRs was highly informative and useful in generating a meaningful classification of barley germplasms. Furthermore, results obtained from this study also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change and in situ conservation strategies following adaptation to local environments.

Single nucleotide polymorphism (SNP) markers for genetic diversity and population structure study in Ethiopian barley (Hordeum vulgare L.) germplasm

“…Comparatively overall lower heterozygosity is obtained in all the regions, this may be due to the factor explained by the cleistogamy in barley that, the flower sheds its pollen before opening, forcing plants with this habit to be entirely autogamous, which can reduce the heterozygosity [ 55 ]. Our result is lower than the reported ranges observed from 0.594 to 0.662, and the expected 0.688 to 0.773 heterozygosity for Ethiopian barley landraces [ 33 ]. This is probably due to the source of genotypes and the samples included improved varieties, which are obtained in the lower heterozygosity ranges in our study.…”

“…Therefore, our results showed that the SNP markers were informative and polymorphic. The average and range values of polymorphism observed in the present study were lower than the reported range values of 0.474 to 0.652 with an average value of 0.552 in barley landraces [ 33 ], 0.34 to 0.83 with an average of 0.57 in barley collections [ 51 ]. Another study with Ethiopian durum wheat by Alemu et al [ 52 ] estimated the ranged value from 0.01 to 0.…”

“…The AMOVA also showed the genetic variation (46.43%) within accessions (Table 2 ), this could be associated with climatic variability and agro-ecological heterogeneity in the region of origins. The presence of diversity within accessions confirmed the potential of a genetic variant, which is the source material for barley breeding [ 30 , 33 ]. The utilization of diversity within accessions using pure-bred selection has been confirmed to provide germplasm for desirable traits [ 8 ].…”

“…The genetic variance fixation index (F ST ) was an evaluation of population variations because of genetic structure [ 33 , 58 ]. In the present study, lower values of (F ST = 0.019, 0.022, 0.038) genetic differentiations were shown in Table 3 .…”

“…Previous studies have used DNA markers to determine the genetic diversity of barley. Markers such as amplified fragment length polymorphism (AFLP) [ 28 ], restriction fragment length polymorphisms (RFLPs) [ 29 ], and simple sequence repeats (SSR) [ 27 , 30 – 33 ] have been employed and provided crucial information for barely breeding programs.…”