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. 2024 May 22;19(5):e0302870.
doi: 10.1371/journal.pone.0302870. eCollection 2024.

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.)

K M Shivaprasad  1   2 , Muraleedhar Aski  1 , Gyan Prakash Mishra  1 , Subodh Kumar Sinha  3 , Soma Gupta  1 , Dwijesh C Mishra  4 , Amit Kumar Singh  5 , Akanksha Singh  6 , Kuldeep Tripathi  7 , Ranjeet Ranjan Kumar  8 , Atul Kumar  9 , Shiv Kumar  6 , Harsh K Dikshit  1
Affiliations

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.)

K M Shivaprasad et al. PLoS One. .

Abstract

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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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Distribution of InDels between the lentil genotypes Globe Mutant and L4775 on the seven lentil chromosomes.
Fig 2
Fig 2. InDels density plot showing several InDels within 1Mb window size distributed on the seven lentil chromosomes.
Fig 3
Fig 3. Genotyping of 230 RIL individuals using InDel marker I-SP-356.6.
Fig 4
Fig 4. InDel marker polymorphism details in nine lentil genotypes differing for maturity duration.
Fig 5
Fig 5
Digital gene expression analysis of (A) FRI, and (B) ELF3 genes using Arabidopsis orthologs.
See this image and copyright information in PMC

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References

    1. Mishra GP, Dikshit HK, Kumari J, Priti, Tripathi K, Devi J, et al.. Identification and characterization of novel penta‐podded genotypes in the cultivated lentil. Crop Science. 2020; 60(4):1974–85. 10.1002/csc2.20156. - DOI
    1. FAOSTAT statistical database. Food and Agriculture Organization of the United Nations. 2020. https://www.fao.org/faostat/en/#home.
    1. Bhatty R. Composition and quality of lentil (Lens culinaris Medik): a review. Canadian Institute of Food Science and Technology Journal. 1988; 21(2):144–60. 10.1016/S0315-5463(88)70770-1. - DOI
    1. Summerfield R, Roberts E, Erskine W, Ellis R. Effects of temperature and photoperiod on flowering in lentils (Lens culinaris Medik.). Annals of Botany. 1985; 56(5):659–71. 10.1093/oxfordjournals.aob.a087055. - DOI
    1. Dutta H, KM S, Aski MS, Mishra GP, Sinha SK, Vijay D, et al.. Morpho-biochemical characterization of a RIL population for seed parameters and identification of candidate genes regulating seed size trait in lentil (Lens culinaris Medik.). Frontiers in Plant Science. 2023; 14:1091432. 10.3389/fpls.2023.1091432. - DOI - PMC - PubMed

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