Genome-Wide Identification and Development of LTR Retrotransposon-Based Molecular Markers for the Melilotus Genus

Abstract

Melilotus is an important genus of legumes with industrial and medicinal value, partly due to the production of coumarin. To explore the genetic diversity and population structure of Melilotus, 40 accessions were analyzed using long terminal repeat (LTR) retrotransposon-based markers. A total of 585,894,349 bp of LTR retrotransposon sequences, accounting for 55.28% of the Melilotus genome, were identified using bioinformatics tools. A total of 181,040 LTR retrotransposons were identified and classified as Gypsy, Copia, or another type. A total of 350 pairs of primers were designed for assessing polymorphisms in 15 Melilotus albus accessions. Overall, 47 polymorphic primer pairs were screened for their availability and transferability in 18 Melilotus species. All the primer pairs were transferable, and 292 alleles were detected at 47 LTR retrotransposon loci. The average polymorphism information content (PIC) value was 0.66, which indicated that these markers were highly informative. Based on unweighted pair group method with arithmetic mean (UPGMA) dendrogram cluster analysis, the 18 Melilotus species were classified into three clusters. This study provides important data for future breeding programs and for implementing genetic improvements in the Melilotus genus.

Transposable elements: multifunctional players in the plant genome

“…RBIP has been used to study the origin of Asian rice varieties and generate markers for marker-assisted breeding of pears ( Kim et al., 2012 ; Roy et al., 2015 ). Genome-wide analysis of RBIP markers in Melilotus genomes revealed high polymorphism information content (PIC), making them valuable tools for genetic improvement of the genus Melilotus ( Ouyang et al., 2021 ).…”

Retrotransposons: How the continuous evolutionary front shapes plant genomes for response to heat stress

“…The RBIP marker was shown to be duplicated several times during the development of Asian pear cultivars and may provide a comprehensive picture of the complex relationship and evolution of Pyrus species (Jiang et al, 2015). Likewise, genome-wide analysis of RBIP markers in the Melilotus genome revealed considerable polymorphism information content (PIC), indicating that these markers are highly informative and may be used for implementing genetic improvement in the Melilotus genus (Ouyang et al, 2021). Furthermore, RBIP markers used for DNA profiling of Japanese, Chinese, and European pear cultivars revealed that retrotransposons have transposed during Asian pear evolution or reflect the genetic relationship between Asian and European pears.…”

“…Recently, genome relationships and LTR retrotransposon diversity in three cultivated Capsicum strains were analyzed and a close relationship among the species was revealed (de Assis et al, 2020). Moreover, genome-wide analysis of LTR retrotransposons and their impact on evolution has been explored in several plants (Roulin et al, 2009;Beuléet al, 2015;Giordani et al, 2016;Mascagni et al, 2017;Keidar et al, 2018;Liu et al, 2018;Akakpo et al, 2020;Mascagni et al, 2020;Ouyang et al, 2021). TE amplification is the main mechanism behind plant genome size increase and evolution (Gantuz et al, 2022).…”

Identification and antibiotic susceptibility profile of methicillin and erythromycin resistant genes in clinical and environmental strains of Staphylococcus aureus in Minna Nigeria

“…A GeneAmp 9700 PCR System was used to perform the PCR (Nadeen et al, 2018). Applied Biosystem Inc.'s (USA) Thermalcycler has a profile that includes an initial 5-minute denaturation at 94°C for 5 min, 30 cycles of 94°C for 30 sec, 50°C for 60 sec, and 72°C for 1 min 30 sec, and a final termination at 72°C for 10 min and chill at 4 o C. (Ouyang et al, 2021).…”