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Estimation of genetic diversity using seed storage protein (SSP) profiling in wild and cultivated species of Cicer L

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Abstract

Background

The narrow genetic diversity of chickpea is a serious impediment to modern cultivar creation. Seed storage proteins (SSPs) are stable and have minimal or no degradation when subjected to isolation and SDS-PAGE.

Methods and results

We have characterized SSPs of 436 chickpea genotypes, belonging to nine annual Cicer species, originated from 47 countries by SDS-PAGE and determined the extent of genetic diversity in chickpea through clustering. Based on scoring, a total of 44 bands (10 to 170 kDa) were identified, which were all polymorphic. The least appeared protein bands were 11, 160 and 170 kDa where band of 11 and 160 kDa was present exclusively in wild type. Five bands were present in < 10% of genotypes. Bands appeared in 200–300 genotypes were suggested less polymorphic, on contrary bands present in 10–150 genotypes were suggested more polymorphic. Polymorphism of protein bands in context to their potential functions reported in literature were explored and suggested that the glubulins were most and glutelins were least abundant, whereas albumins with their known role in stress tolerance can be used as marker in chickpea breeding. Cluster analysis produced 14 clusters, interestingly three clusters contained only Pakistani genotypes and thus Pakistani genotypes appeared as a separate entity from the rest of the genotypes.

Conclusion

Our results indicate that SDS-PAGE of SSPs is a powerful technique in determining the genetic diversity plus it is easily adaptable, due to its cost effectiveness in comparison to other genomics tools.

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Data availability

All data generated or analysed during this study are being included in the manuscript and its supplementary information files.

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Acknowledgements

The authors are thankful to the Australian Grain Genebank, Victoria, Australia and chickpea group at NIAB, Pakistan for providing the seeds of exotic and Pakistani chickpea cultivars respectively.

Funding

No external funding was received for this work.

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    Authors and Affiliations

    1. Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan

      Uswah Khalid, Muhammad Qandeel Waheed, Mian Abdur Rehman Arif & Anjuman Arif

    2. Plant Breeding and Genetics, University of Agiculture (UAF), Faisalabad, Pakistan

      Najma Parveen

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    1. Uswah Khalid
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    2. Muhammad Qandeel Waheed
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    4. Mian Abdur Rehman Arif
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    Contributions

    AA conceived the idea; UK and MQW performed the original experiments and carried out the gel visualization and band scoring; MARA, AA, UK, MQW and NP performed the analysis; UK, MQW, AA & MARA wrote the manuscript; NP and AA reviewed the manuscript by providing inputs to improve the manuscript. All authors read and approve the final manuscript.

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    Correspondence to Anjuman Arif.

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    Competing interest

    The authors have no relevant financial and non-financial interest to disclose.

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    This article does not contain any studies with animals or humans performed by any of the authors.

    Additional information

    Uswah Khalid and Muhammad Qandeel Waheed shared first authors.

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    Supplementary Information

    Below is the link to the electronic supplementary material.

    Supplementary material 1 (TIFF 466.0 kb) Determination of number of clusters using the elbow method

    Supplementary material 2 (TIFF 825.2 kb) Determination of number of clusters using the silhouette method

    Supplementary material 3 (TIFF 37758.0 kb) Clusters representation using the silhouette method

    Supplementary material 4 (TIFF 37758.0 kb) 14 clusters using the gap statistic method

    11033_2023_8358_MOESM5_ESM.png

    Supplementary material 5 (PNG 67.7 kb) Sub clusters in cluster 1 where different shaded regions indicate different sub groups. For details, see Table S2

    11033_2023_8358_MOESM6_ESM.png

    Supplementary material 6 (PNG 30.3 kb) Sub clusters in cluster 2 where different colors indicate different sub groups. For details, see Table S3

    11033_2023_8358_MOESM7_ESM.png

    Supplementary material 7 (PNG 65.4 kb) Sub clusters in cluster 3 where different colors indicate different sub groups. For details, see Table S4

    11033_2023_8358_MOESM8_ESM.png

    Supplementary material 8 (PNG 28.0 kb) Sub clusters in cluster 4 where different colors indicate different sub groups. For details, see Table S5

    11033_2023_8358_MOESM9_ESM.png

    Supplementary material 9 (PNG 46.8 kb) Sub clusters in cluster 5 where different colors indicate different sub groups. For details, see Table S6

    11033_2023_8358_MOESM10_ESM.png

    Supplementary material 10 (PNG 45.6 kb) Sub clusters in cluster 6 where different colors indicate different sub groups. For details, see Table S7

    11033_2023_8358_MOESM11_ESM.png

    Supplementary material 11 (PNG 29.1 kb) Sub clusters in cluster 7 where different colors indicate different sub groups. For details, see Table S8

    11033_2023_8358_MOESM12_ESM.png

    Supplementary material 12 (PNG 30.7 kb) Sub clusters in cluster 8 where different colors indicate different sub groups. For details, see Table S9

    11033_2023_8358_MOESM13_ESM.png

    Supplementary material 13 (PNG 48.0 kb) Sub clusters in cluster 9 where different colors indicate different sub groups. For details, see Table S10

    11033_2023_8358_MOESM14_ESM.png

    Supplementary material 14 (PNG 54.0 kb) Sub clusters in cluster 10 where different colors indicate different sub groups. For details, see Table S11

    11033_2023_8358_MOESM15_ESM.png

    Supplementary material 15 (PNG 49.7 kb) Sub clusters in cluster 11 where different colors indicate different sub groups. For details, see Table S12

    11033_2023_8358_MOESM16_ESM.png

    Supplementary material 16 (PNG 58.4 kb) Sub clusters in cluster 12 where different colors indicate different sub groups. For details, see Table S13

    11033_2023_8358_MOESM17_ESM.png

    Supplementary material 17 (PNG 43.8 kb) Sub clusters in cluster 13 where different colors indicate different sub groups. For details, see Table S14

    11033_2023_8358_MOESM18_ESM.png

    Supplementary material 18 (PNG 44.1 kb) Sub clusters in cluster 14 where different colors indicate different sub groups. For details, see Table S15

    Supplementary material 19 (XLSX 89.6 kb)

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    Khalid, U., Waheed, M.Q., Parveen, N. et al. Estimation of genetic diversity using seed storage protein (SSP) profiling in wild and cultivated species of Cicer L. Mol Biol Rep 50, 4175–4185 (2023). https://doi.org/10.1007/s11033-023-08358-9

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