Assessment of genetic diversity in lentils (Lens culinaris Medik) based on single nucleotide polymorphisms

Basheer-Salimia, Rezq; Camilli, B; Scacchi, Silvia; Noli, Enrico; Awad, Murad K.

doi:10.4238/2015.june.1.4

Cited by 9 publications

(3 citation statements)

References 21 publications

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“…SNPs are the most abundant type of polymorphism in all genomes, which allows high-throughput genotyping that is low cost, locus specific, and co-dominant with simple documentation. So far, only a limited number of SNP markers have been used to study the genetic diversity in lentil (Lombardi et al, 2014; Basheer-Salimia et al, 2015). The population structure of global lentil accessions has not been extensively characterized based on their agro-ecological adaptation zones.…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity of Cultivated Lentil (Lens culinaris Medik.) and Its Relation to the World's Agro-ecological Zones

et al. 2016

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Assessment of genetic diversity and population structure of germplasm collections plays a critical role in supporting conservation and crop genetic enhancement strategies. We used a cultivated lentil (Lens culinaris Medik.) collection consisting of 352 accessions originating from 54 diverse countries to estimate genetic diversity and genetic structure using 1194 polymorphic single nucleotide polymorphism (SNP) markers which span the lentil genome. Using principal coordinate analysis, population structure analysis and UPGMA cluster analysis, the accessions were categorized into three major groups that prominently reflected geographical origin (world's agro-ecological zones). The three clusters complemented the origins, pedigrees, and breeding histories of the germplasm. The three groups were (a) South Asia (sub-tropical savannah), (b) Mediterranean, and (c) northern temperate. Based on the results from this study, it is also clear that breeding programs still have considerable genetic diversity to mine within the cultivated lentil, as surveyed South Asian and Canadian germplasm revealed narrow genetic diversity.

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Section: Introductionmentioning

confidence: 99%

Genetic Diversity of Cultivated Lentil (Lens culinaris Medik.) and Its Relation to the World's Agro-ecological Zones

et al. 2016

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“…These markers have been used for various genetic studies in various crops including soybean [13], and chickpea [14]. However, in lentils, the InDels are very scantily reported in the public databases [15][16][17] and no PCR-based InDel markers have been developed till now. This study used QTL-seq to map QTLs and identify the candidate genes associated with earliness and identify and validate the PCR-based InDel markers linked with earliness trait in lentils.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide discovery of InDels and validation of PCR-Based InDel markers for earliness in a RIL population and genotypes of lentil (Lens culinaris Medik.)

Shivaprasad,

Aski,

Mishra

et al. 2024

PLoS ONE

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The systematic identification of insertion/deletion (InDel) length polymorphisms from the entire lentil genome can be used to map the quantitative trait loci (QTL) and also for the marker-assisted selection (MAS) for various linked traits. The InDels were identified by comparing the whole-genome resequencing (WGRS) data of two extreme bulks (early- and late-flowering bulk) and a parental genotype (Globe Mutant) of lentil. The bulks were made by pooling 20 extreme recombinant inbred lines (RILs) each, derived by crossing Globe Mutant (late flowering parent) with L4775 (early flowering parent). Finally, 734,716 novel InDels were identified, which is nearly one InDel per 5,096 bp of lentil genome. Furthermore, 74.94% of InDels were within the intergenic region and 99.45% displayed modifier effects. Of these, 15,732 had insertions or deletions of 20 bp or more, making them amenable to the development of PCR-based markers. An InDel marker I-SP-356.6 (chr. 3; position 356,687,623; positioned 174.5 Kb from the LcFRI gene) was identified as having a phenotypic variance explained (PVE) value of 47.7% for earliness when validated in a RIL population. Thus, I-SP-356.6 marker can be deployed in MAS to facilitate the transfer of the earliness trait to other elite late-maturing cultivars. Two InDel markers viz., I-SP-356.6 and I-SP-383.9 (chr. 3; linked to LcELF3a gene) when tested in 9 lentil genotypes differing for maturity duration, clearly distinguished three early (L4775, ILL7663, Precoz) and four late genotypes (Globe Mutant, MFX, L4602, L830). However, these InDels could not be validated in two genotypes (L4717, L4727), suggesting either absence of polymorphism and/or presence of other loci causing earliness. The identified InDel markers can act as valuable tools for MAS for the development of early maturing lentil varieties.

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“…In earlier studies, molecular markers such as Simple Sequence Repeat (SSR), Restriction Fragment Length Polymorphism (RFLP), Amplified Fragment Length Polymorphism (AFLP) and Random Amplified Polymorphic DNA (RAPD) have been preferred for genetic diversity analysis in lentil (Havey and Muehlbauer, 1989;Abo-Elwafa et al, 1995;Sharma et al, 1995Sharma et al, , 1996Ahmad et al, 1996;Ford et al, 1997;Udupa et al, 1999;Abe et al, 2003;Hamwieh et al, 2005Hamwieh et al, , 2009Reddy et al, 2010) and gene mapping (Eujayl et al, 1998;Tullu et al, 2003;Duran et al, 2004;Kahraman et al, 2004;Hamwieh et al, 2005). SNPs were identified across Palestinian lentil accessions for development of cost-effective and robust genotyping assays (Basheer-Salimia et al, 2015). Kaur et al (2014) identified SSR and SNP markers from transcriptome and EST for construction of gene-based genetic linkage map in lentil.…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity of Bio-fortified Lentils (Lens culinaris Medik.) through Simple Sequence Repeat Markers

Darai,

Dhakal,

Pandey

et al. 2023

SAARC J Agric

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Nepalese lentils are comparatively rich in iron and zinc, making it a potential crop of whole food solution to aid in the global battle against the micronutrient malnutrition. Understanding the genetic basis for uptake of grain iron and zinc is required to increase their stable concentrations along with these minerals in lentils. This study aimed at characterizing genetic variation in micronutrient high grain iron and zinc concentrations and exploring the potential in lentil accessions. A set of 25 lentil accessions was evaluated in two seasons across the three locations and genotyped by using 40 simple sequence repeat (SSR) markers that are linked with lentil iron and zinc concentrations. Out of the 40 SSR markers, 23 markers were found polymorphic while 12 were monomorphic, and 5 markers were null. These 23 polymorphic markers produced a total of 584 alleles, of which 52 were polymorphic alleles, and average alleles per locus was 11.49. The linkage disequilibrium (LD) analysis was done using a mixed linear model (MLM) that identified three SSR markers, PBALC 13, PBALC 206, and GLLC 563, associated with grain Fe concentration, explaining 9% to 11% phenotypic variation, respectively, and four SSR markers (PBALC 353, SSR 317–1, PLC 62, and PBALC 217) associated with grain Zn concentration, explaining 14% to 21% phenotypic variation, respectively. The pairwise genetic similarity index among 25 lentil accessions varied from 0.16 to 0.83. The identified SSRs exhibited consistent performance across two seasons and have potential for utilization in lentil molecular breeding program. SAARC J. Agric., 21(2): 27-40 (2023)

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Assessment of genetic diversity in lentils (Lens culinaris Medik) based on single nucleotide polymorphisms

Cited by 9 publications

References 21 publications

Genetic Diversity of Cultivated Lentil (Lens culinaris Medik.) and Its Relation to the World's Agro-ecological Zones

Genetic Diversity of Cultivated Lentil (Lens culinaris Medik.) and Its Relation to the World's Agro-ecological Zones

Genome-wide discovery of InDels and validation of PCR-Based InDel markers for earliness in a RIL population and genotypes of lentil (Lens culinaris Medik.)

Genetic Diversity of Bio-fortified Lentils (Lens culinaris Medik.) through Simple Sequence Repeat Markers

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