Cross-genera amplification of informative microsatellite markers from common bean and lentil for the assessment of genetic diversity in pigeonpea

Abstract

A total of 24 pigeonpea (Cajanus cajan L. Millspaugh) cultivars representing different maturity groups were evaluated for genetic diversity analysis using 10 pigeonpea specific and 66 cross-genera microsatellite markers. Of the cross-genera microsatellite markers, only 12 showed amplification. A total of 45 alleles were amplified by the 22 markers. Nine markers showed 100 % polymorphism. Markers Lc 14, BMd 48 and CCB 9 amplified maximum number (5) of alleles each. One genotype specific unique band in Pusa 9 was generated by markers CCB 8. Maximum genetic diversity (74 %) was observed between cultivars MA 3 and CO 6, while the minimum diversity (12 %) was observed between NDA 1 and DA 11. The average diversity among the cultivars was estimated to be 45.6 %. SSR primers from pigeonpea were found to be more polymorphic (37 %) as compared to common bean and lentil markers. The arithmetic mean heterozygosity (Hav) and marker index (MI) were found to be 0.014 and 0.03, respectively, indicating the potential of common bean and lentil microsatellite markers for genetic mapping, diversity analysis and genotyping in Cajanus.

A comparative in silico analysis on frequency and distribution of microsatellites in coding regions of three formae speciales of Fusarium oxysporum and development of EST-SSR markers for polymorphism studies

“…Although the number of useful markers was low, all the isolates could be differentiated from each other. These marker can be further utilized for addressing genetic relatedness in other species of Fusarium because EST-derived SSR markers have a reputation of being highly transferable (Datta et al, 2010).…”

A Comparison of Microsatellites in Phytopathogenic Aspergillus Species in Order to Develop Markers for the Assessment of Genetic Diversity among Its Isolates

“…Microsatellites can be found in the protein-coding (Li et al, 2004 ; Garnica et al, 2006 ; Lawson and Zhang, 2006 ; Mahfooz et al, 2012a ) and non-coding regions of the genome (Kim et al, 2008 ; Araujo et al, 2012 ). Microsatellite loci show extensive length polymorphism, and hence they are widely used for DNA fingerprinting and diversity studies in bacteria (Mrazek et al, 2007 ; Guo and Mrazek, 2008 ), fungi (Kim et al, 2008 ; Araujo et al, 2012 ; Mahfooz et al, 2012a , b ), plants (Datta et al, 2010 ; Yu et al, 2017 ), and human (Subramanian et al, 2003 ; Shin et al, 2017 ). The utility of microsatellites as a molecular marker is well-known, however, its presence and absence in a particular species are of great functional and evolutionary significance (Gibbons and Rokas, 2009 ; Mahfooz et al, 2015 , 2016 ).…”

A Comprehensive Characterization of Simple Sequence Repeats in the Sequenced Trichoderma Genomes Provides Valuable Resources for Marker Development

“…The sequence data generated from the sequencing projects of these fungal species can be mined for the presence of microsatellites or simple sequence repeats (SSRs) in genic ( Li et al, 2004 ; Mahfooz et al, 2012 ) as well as genomic ( Toth et al, 2000 ; Lim et al, 2004 ; Kim et al, 2008 ) portions. These SSRs are useful as a marker for a variety of applications because of their reproducibility, multiallelic nature, codominant inheritance, relative abundance and good genome coverage ( Datta et al, 2010 ). However, despite the many advantages of SSR markers in various biological studies, only few reports ( Shahid et al, 2013 ; Geistlinger et al, 2015 ) on experimental data on polymorphic SSR markers is still a major limitation for utilizing SSR markers in biological studies in fungal systems especially in mycoparasitic fungi.…”