SSR markers in revealing extent of genetic diversity and phylogenetic relationships among chickpea core collection accessions for Western Himalayas

Mir, Asma Hamid; Bhat, Mohd Ashraf; Fayaz, Humara; Wani, Aijaz A.; Dar, Shabir Ahmad; Maqbool, Showkat; Yasin, Mohammad; Mir, Javid Iqbal; Khan, M. A.; Sofi, Parvaze A.; El-Sappah, Ahmed H.; Thudi, Mahendar; Varshney, Rajeev K.; Mir, Reyazul Rouf

doi:10.1007/s11033-022-07858-4

Cited by 7 publications

(7 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The principal coordinate analysis clearly separated the whole population into four clusters, and wild and cultivated types in seperate clusters. Results from the present study are consistant with the previous studies 71 , 82 the grouping followed a clear pattern between cultivated chickpea and the wild species. It is also clear as the wild progenitor, Cicer reticulatum showed close proximity with the cultivated chickpea.…”

Section: Discussionsupporting

confidence: 90%

Genome-wide discovery of di-nucleotide SSR markers based on whole genome re-sequencing data of Cicer arietinum L. and Cicer reticulatum Ladiz

Sarı

Sari

İkten

et al. 2023

Sci Rep

View full text Add to dashboard Cite

Simple sequence repeats (SSRs) are valuable genetic markers due to their co-dominant inheritance, multi-allelic and reproducible nature. They have been largely used for exploiting genetic architecture of plant germplasms, phylogenetic analysis, and mapping studies. Among the SSRs, di-nucleotide repeats are the most frequent of the simple repeats distributed throughout the plant genomes. In present study, we aimed to discover and develop di-nucleotide SSR markers by using the whole genome re-sequencing (WGRS) data from Cicer arietinum L. and C. reticulatum Ladiz. A total of 35,329 InDels were obtained in C. arietinum, whereas 44,331 InDels in C. reticulatum. 3387 InDels with 2 bp length were detected in C. arietinum, there were 4704 in C. reticulatum. Among 8091 InDels, 58 di-nucleotide regions that were polymorphic between two species were selected and used for validation. We tested primers for evaluation of genetic diversity in 30 chickpea genotypes including C. arietinum, C. reticulatum, C. echinospermum P.H. Davis, C. anatolicum Alef., C. canariense A. Santos & G.P. Lewis, C. microphyllum Benth., C. multijugum Maesen, C. oxyodon Boiss. & Hohen. and C. songaricum Steph ex DC. A total of 244 alleles were obtained for 58 SSR markers giving an average of 2.36 alleles per locus. The observed heterozygosity was 0.08 while the expected heterozygosity was 0.345. Polymorphism information content was found to be 0.73 across all loci. Phylogenetic tree and principal coordinate analysis clearly divided the accessions into four groups. The SSR markers were also evaluated in 30 genotypes of a RIL population obtained from an interspecific cross between C. arietinum and C. reticulatum. Chi-square (χ2) test revealed an expected 1:1 segregation ratio in the population. These results demonstrated the success of SSR identification and marker development for chickpea with the use of WGRS data. The newly developed 58 SSR markers are expected to be useful for chickpea breeders.

show abstract

Section: Discussionsupporting

confidence: 90%

Genome-wide discovery of di-nucleotide SSR markers based on whole genome re-sequencing data of Cicer arietinum L. and Cicer reticulatum Ladiz

Sarı

Sari

İkten

et al. 2023

Sci Rep

View full text Add to dashboard Cite

show abstract

“…The microsatellite marker analysis result indicated moderate allelic richness per locus and relatively moderate to high PIC, Ho and He values. A high level of genetic diversity indicated the existence of higher molecular variation among the 40 tested chickpea genotypes, in agreement with the previous studies (Mir et al, 2022). During present study, the most of the loci (20) exhibited a low level of observed heterozygosity in comparison to the expected heterozygosity and high fixation index (Choudhary et al, 2012).…”

Section: Polymorphism Among Chickpea Genotypessupporting

confidence: 92%

“…Population one was Prioritization of Microsatellite Markers Linked with Drought Tolerance Associated Traits in Chickpea (Cicer arietinum L.) exclusively grouped in quadrant I, showing their distinctness from the rest of the populations evenly spread in all four quadrants because of their highly diverse nature. Similar results have also been reported in various earlier studies using microsatellite markers (Mir et al, 2022).…”

Section: Analysis Of Molecular Variance (Amova)supporting

confidence: 92%

“…Modern chickpea improvement program largely necessitates the identification of highly diverse chickpea germplasm, highly polymorphic trait-specific molecular markers, which can be effectively utilized for the development of improved varieties. Thus, the characterization of chickpea germplasm has the great potential for playing a vital role in future international breeding programs (Mir et al, 2022), especially in India (Asati et al, 2022;Yadav et al, 2023), which is the largest chickpeaproducing nation (Dixit, 2021). Consequently, for identification of new sources of germplasm having valuable genes/QTLs to improve yield and enhance resistance/tolerance to various abiotic and biotic stresses, investigation of structure and nature of genetic diversity and phylogenetic relationship within and among cultivated chickpea varieties, breeding lines and its wild relatives is obviously needed (Mir et al, 2022).…”

Section: Resultsmentioning

confidence: 99%

“…Thus, the characterization of chickpea germplasm has the great potential for playing a vital role in future international breeding programs (Mir et al, 2022), especially in India (Asati et al, 2022;Yadav et al, 2023), which is the largest chickpeaproducing nation (Dixit, 2021). Consequently, for identification of new sources of germplasm having valuable genes/QTLs to improve yield and enhance resistance/tolerance to various abiotic and biotic stresses, investigation of structure and nature of genetic diversity and phylogenetic relationship within and among cultivated chickpea varieties, breeding lines and its wild relatives is obviously needed (Mir et al, 2022). For Indian chickpea genotypes, molecular diversity and population structure studies using drought tolerance related traits linked microsatellite markers are very limited, hence this study was initiated to analyze the nature and structure of genetic diversity and phylogenetic relatedness among 40 chickpea genotypes.…”

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

Prioritization of Microsatellite Markers Linked with Drought Tolerance Associated Traits in Chickpea (Cicer arietinum L.)

Tiwari,

Sapre

et al. 2023

View full text Add to dashboard Cite

Background: Being a vital source of high-quality dietary protein, chickpea is an unavoidable legume. The present investigation was performed to study the applicability of the microsatellite markers linked with drought tolerance in Indian chickpea genotypes collected from different genetic background. Methods: In Rabi 2021-22, forty chickpea genotypes including national check for drought tolerance, elite cultivars, released varieties and advanced breeding lines were screened employing forty microsatellite markers linked with drought tolerance associated traits. Results: Among forty drought tolerance related microsatellite markers, twenty-six were found to be polymorphic and produced a total of 66 alleles, with a mean of 2.5 alleles per locus. Genotype NCPGR127 had highest numbers of alleles, gene diversity and polymorphism information content tracked by genotype TR19. These genotypes may be used for selecting drought tolerant genotypes through marker assistant selection (MAS). Model-based population structure analysis clearly distinguished the drought tolerant genotypes including ICC4958, JG74, JAKI9218, JG16, JG6, JG14 and JG11. Principle coordinate analysis (PCoA) and analysis of molecular variance (AMOVA) further confirmed these results. Findings of the present investigation have a greater potential for further utilization in breeding of drought specific chickpea cultivar(s).

show abstract

SSR markers in revealing extent of genetic diversity and phylogenetic relationships among chickpea core collection accessions for Western Himalayas

Cited by 7 publications

References 41 publications

Genome-wide discovery of di-nucleotide SSR markers based on whole genome re-sequencing data of Cicer arietinum L. and Cicer reticulatum Ladiz

Genome-wide discovery of di-nucleotide SSR markers based on whole genome re-sequencing data of Cicer arietinum L. and Cicer reticulatum Ladiz

Prioritization of Microsatellite Markers Linked with Drought Tolerance Associated Traits in Chickpea (Cicer arietinum L.)

In-silico identification of simple sequence repeat (SSR) markers and phylogenetic analysis from chloroplast genomes of the genus Bambusa

Contact Info

Product

Resources

About