Association mapping for morphological traits relevant to registration of barley varieties

Abstract

Elucidating marker-trait associations would have fruitful implications in distinctness, uniformity, and stability (DUS) tests of new varieties required for both variety registration and granting plant breeders' rights. As the number of new varieties with narrow genetic bases increases, the necessity for deployment of molecular markers to complement morphological DUS traits gets particular attention. We used simple sequence repeats (SSRs) and sequence related amplification polymorphisms (SRAPs) markers in association mapping of morphological traits in a collection of 143 barley landraces and advanced breeding lines. This panel represented a diverse and uniform sample in terms of both quantitative and categorical traits whilst it was structurally partitioned by number of ear rows (six-and two-rowed) and seasonal growth habit (winter and spring types) characteristics. SSRs were more powerful compared with SRAPs in separating six-and two-rowed genotypes based on both model-based Bayesian and neighbor joining clustering methods. A number of associated SSR and SRAP markers were found for 15 out of 36 DUS traits after considering Bonferroni correction through linear models (GLM and MLM) and chi-square-based tests (SA and AAT). This is also the first report of association of awn roughness and grain color with molecular markers in barley. Moreover, SSR marker BMAC0113 appeared associated with time of ear emergence (TEE), confirming previous findings. These markers could be beneficial to complement and speed up DUS testing of new varieties, as well as for improving management of barley reference collections.Additional keywords: LD mapping; Hordeum vulgare L.; DUS traits; SSRs & SRAPs markers. Abbreviations used: AAT (allelic association test); AFLP (amplified fragment length polymorphism); AR (awn roughness); DUS (distinctness, uniformity, stability); ED (ear density); GLM (general linear model); GSLN (spiculation of inner lateral nerves of lemma); KCAL (color of grain aleurone layer); MLM (mixed linear model); NER (number of ear rows); SA (stratified analysis); SGH (seasonal growth habit); SRAP (sequence-related amplified polymorphism); SSR (simple sequence repeats); TEE (time of ear emergence).

Development of a multiparent advanced generation intercross (MAGIC) population for genetic exploitation of complex traits in Brassica juncea: Glucosinolate content as an example

“…The term MAGIC was first coined in 2007 [4], and the first MAGIC population in plant species was developed in Arabidopsis thaliana (L.) [5]. Then, dozens of MAGIC populations were established in a wide range of various crops, including rice [6][7][8][9][10], tomato [11,12], fava bean [13], cowpea [14], maize [15], barley [16,17], strawberry [18], sorghum [19], and wheat [3,[20][21][22][23]. However, no MAGIC populations in Brassicaceae have been reported to our knowledge.…”

Diversity Maintenance of Some Barley (Hordeum Spp) Genetic Resources Using SSR-Based Marker

“…SSR markers have been extensively used in barley genetic diversity (Elakhdar et al, 2016a;Ferreira et al, 2016;Elakhdar et al, 2018;Arya et al, 2019), Association mapping (Jamali et al, 2017) linkage mapping and phylogenetic analysis (Lakew et al, 2013;Zhang et al, 2014). Among different DNA marker types used in barley, microsatellites have proven to be the markers of choice for genetic diversity studies for this plant species (Wang et al, 2010;Hua et al, 2015;Todorovska et al, 2019).…”

Single nucleotide polymorphism assay to distinguish barley (Hordeum vulgare L.) varieties in support of seed certification

“…It has been proposed that molecular testing may be a way to make variety registration and certification more efficient and cost effective (for example in barley, Cockram et al 2012;Jones et al 2013;Jamali et al 2017). Molecular methods combined with appropriate sampling strategies have the potential to determine whether a variety is distinct from other varieties of the same species, and whether it is uniform and stable through propagation.…”