Development of new microsatellite markers and their application in the analysis of genetic diversity in lentils

Abstract

This paper reports the development of new microsatellite markers for lentil (Lens culinaris subsp. culinaris) and their use for genetic diversity analysis of a lentil core collection developed at ICARDA (Aleppo-Syria). Fourteen new markers were developed from microsatellite flanking sequences of a genomic library from a cultivated lentil accession ILL5588. The core collection used comprises 109 accessions from 15 countries representing 57 cultigens (including 18 breeding lines) from 8 countries and 52 wild types of germplasm (L. culinaris subsp. orientalis, L. culinaris subsp. tomentosus and L. culinaris subsp. odemensis) from 11 countries. Total number of alleles detected across all microsatellite loci was 182, with a mean of 13 alleles per locus. The wild accessions were rich in alleles (151 alleles) compared to cultigens (114 alleles). The genetic diversity index for the microsatellite loci in the wild accessions ranged from 0.16 (for locus SSR28 in L. culinaris subsp. odemensis) to 0.93 (for locus SSR66 in L. culinaris subsp. orientalis) with a mean of 0.66, while in the cultigens genetic diversity varied between 0.03 (locus SSR28) and 0.87 (locus SSR207) with a mean of 0.65. The cluster analysis indicated two major clusters, mainly one with the cultigens and the other with the wild accessions.

Diversification of indigenous gene- pool by using exotic germplasm in lentil (Lens culinaris Medikus subsp. culinaris)

“…These results suggested that most of the genotypes are diverse for maximum morphological traits compared SSR markers and hence first three components could be able to explain the most of variance available among the genotypes. However, existence of genetic diversity among the present genotypes found to be quite high compared to previous studies that showed high genetic similarity among the accessions originating from South Asia (Agrawal and Katiyar 2008;Hamwieh et al 2009;Datta et al 2011). The limited genetic variability observed in the Indian lentils was probably due to the founder effect, restriction brought to genetic variability in the indigenous gene pool, which is further narrowing the gene pool due to the adaptation in specialized environments in south Asia (Erskine et al 1989(Erskine et al , 1998Ferguson et al 1998;Kumar et al 2004).…”

“…Earlier molecular markers have been preferred for genetic diversity analysis in lentil (Udupa et al 1999;Abe et al 2003;Hamwieh et al 2009;Reddy et al 2009). Among the various molecular markers, microsatellites or simple sequence repeats (SSR) have shown to be very useful, because these markers showed high polymorphism, reproducible and easy to handle (Varshney et al 2005(Varshney et al , 2009Datta et al 2011).…”

“…Among the various molecular markers, microsatellites or simple sequence repeats (SSR) have shown to be very useful, because these markers showed high polymorphism, reproducible and easy to handle (Varshney et al 2005(Varshney et al , 2009Datta et al 2011). Though in lentil, a number of SSR markers have been developed (Hamwieh et al 2005;Kaur et al 2011;Datta et al 2011), availability of polymorphic SSR markers and their use in analysis of the genetic diversity is still limited in lentil compared to other pulses such as chickpea (Hamwieh et al 2005(Hamwieh et al , 2009Kaur et al 2011;Datta et al 2011). Therefore, present investigation was aimed to assess diversification of Indian gene-pool on the basis of SSR markers and morphological traits among 21 lentil genotypes involving the exotic lines.…”

Legume Crops Phylogeny and Genetic Diversity for Science and Breeding

“…The DNA-based markers, such as RFLP (Havey and Muehlbauer, 1989;Muench et al, 1991;Rajora and Mahon, 1994), RAPD (Sharma et al, 1995;Ferguson et al, 2000;Sonnante and Pignone, 2001;Toklu et al, 2009;Tewari et al, 2012), AFLP (Sharma et al, 1996;Zavodna et al, 2000;Duran and Perez de le Vega, 2004;Kahraman et al, 2004;Rubeena et al, 2006;Fiocchetti et al, 2009;Toklu et al, 2009), microsatellite markers (Duran and Perez de le Hamwieh et al, 2009;Liu et al, 2008;Babayeva et al, 2009;Reddy et al, 2010;Gupta et al, 2012, Tewari et al, 2012Zaccardelli et al, 2012), inter simple sequence repeat (ISSR) (Zavodna et al, 2000;Sonnante and Pignone, 2001;Toklu et al, 2009), internal transcribed spacers (ITS) (Fernandez et al, 2000;Mayer and Bagga, 2002;Sonnante et al, 2003), non-transcribed spacer (NTS) (Fernandez et al, 2005), sequenced tagged microsatellite site (STMS) (Inder et al, 2008;Datta et al, 2011), single-nucleotide polymorphisms (SNPs) (Alo et al, 2011), and resistance gene analogue (RGA) (Yaish et al, 2004;Sari et al, 2013) were used to analyze phylogenetic relationships among taxa in the genus Lens, as well as the genetic diversity of cultivated lentil.…”

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

“…Despite its importance in nutritional security, pigeonpea has not benefited much from the advances made in the field of genomic tools and molecular markers (Datta et al, 2009). As compared to large number of markers in common bean (L'taief et al, 2008;Blair et al, 2003), chickpea (Choudhary et al, 2009;Sethy et al, 2006), and lentil (Hamwieh et al, 2009;Hamwieh et al, 2005), only 109 microsatellite markers are reported so far in pigeonpea (Burns et al, 2001;Odeny et al, 2007;Odeny et al, 2009). Therefore, there is an urgent need to increase the number of polymorphic microsatellite markers in pigeonpea for diversity analysis and mapping of important traits.…”