Analysis of diversity and relationships among orchardgrass (Dactylis glomerata L.) accessions using start codon-targeted markers

Abstract

ABSTRACT. Orchardgrass, or cocksfoot, is an important perennial forage grass worldwide. The comprehensive understanding of orchardgrass accessions will benefit germplasm collection and breeding progress, and it will enhance efforts to improve forage yield and quality. Therefore, 24 novel, simple, polymorphic, and reliable start codon-targeted (SCoT) markers were used to analyze the diversity and genetic relationships among 95 orchardgrass accessions. In total, 273 polymorphic bands were detected with an average of 11.4 bands per primer. The average polymorphic rate for the species was 83.4%, suggesting a high discriminating ability of the SCoT technique for orchardgrass. The molecular variance analysis revealed that 69.13 and 30.87% of variation resided within and among groups, respectively, demonstrating that the orchardgrass germplasms had a higher level of Analysis of Dactylis glomerata using SCoT markers genetic diversity within groups than among geographical regions and distributions. The distinct geographical divergence of orchardgrass was revealed between North America and Oceania. The unweighted pairgroup method with arithmetic mean dendrogram revealed a separation of 7 main clusters between 95 accessions according to the geographical origin. Furthermore, each cluster was divided into subgroups mainly according to the origin of its state. The genetic divergence of orchardgrass might be influenced by the ecogeographical conditions, climatic types, breeding systems and gene flow with variations in cultures, bird migration, and breeder selection. These results could facilitate orchardgrass germplasm collection, management, and breeding worldwide.

Potential of Start Codon Targeted (SCoT) Markers to Estimate Genetic Diversity and Relationships among Chinese Elymus sibiricus Accessions

“…SCoT markers were used for the first time in E. sibiricus due to several advantages to other marker techniques: easier development of species-specific primers than SSR [ 22 ], lower cost than AFLP [ 22 ] and higher reproducibility than RAPD [ 18 ]. The results of the present study showed that SCoT markers were efficient in assessing the genetic diversity among E. sibiricus accessions.…”

Genotyping by Sequencing and Plastome Analysis Finds High Genetic Variability and Geographical Structure in Dactylis glomerata L. in Northwest Europe Despite Lack of Ploidy Variation

“…Genetic diversity of Dactylis was assessed using a range of protein and DNA markers including allozymes [27,31]; SSR [24,[32][33][34][35] [24,32,33,34,35]; RAPD/ISSR/SCoT [35][36][37][38] [35,36,37,38]; AFLP [38] and SNPs [32]. Nuclear genotyping by sequencing (GBS) was used by Bushman et al [39], but not for genetic diversity studies.…”

Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated castor (Ricinus communis L.) genotypes

“…Using 37 SCoT markers we were able to distinguish all 111 genotypes of the ricin. FANG-YONG et al, 2014;JIANG et al, 2014;HUANG et al, 2014;SATYA et al, 2015) and these values presented a high level of polymorphism of genotypes detected by SCoT markers. HUANG et al (2014) assessed the genetic diversity of six Hemarthria cultivars using seven SCoT primers, which together amplified 105 bands with an average of 15 bands per sample.…”

“…In principle, SCoT is similar to RAPD and ISSR because the same single primer is used as the forward and reverse primer (COLLARD and MACKILL, 2009). Suitability of SCoT markers system has been successfully employed in genetic diversity analysis and fingerprinting of a number of agricultural and horticultural crop species, such as oat (BALÁŽOVÁ et al, 2017), rye (PETROVIČOVÁ et al, 2017), maize (VIVODÍK et al, 2016, date palm (AL-QURAINY et al, 2015), orchardgrass (JIANG et al, 2014), pepper (TSABALLA et al, 2015, ramie (SATYA et al, 2015), castor (KALLAMADIA et al, 2015), sugarcane (QUE et al, 2014) and mango (GAJERA et al, 2014).…”