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Strategies of molecular diversity assessment to infer morphophysiological and adaptive diversity of germplasm accessions: an alfalfa case study

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Abstract

Germplasm collections of major crops include thousands of accessions whose agronomic evaluation is prevented by high costs, while their molecular characterization is getting increasingly affordable. This study aimed to assess the consistency between alfalfa (Medicago sativa L.) landrace diversity measures relative to adaptation pattern, eleven morphophysiological traits, and four genotyping strategies using SSR or genotyping-by-sequencing (GBS) SNP markers recorded on either five individual plants or three bulks of 100 plants each per accession. We focused on eleven landraces from Northern Italy featuring large genotype × environment interaction for biomass yield across environments with contrasting level of summer drought. We recorded 34 SSR and 237 SNP polymorphic markers for individual plants, and 41 SSR and 1274 SNP markers for bulked plants. Landrace diversity based on SNP data from bulked plants was the only molecular diversity measure associated with both adaptive diversity as expressed by pattern analysis (r = 0.34) and drought stress at collecting sites (r = 0.50). No molecular diversity measure was associated with overall morphophysiological diversity. Molecular diversity was highly consistent only between SSR and SNP data from bulked plants (r = 0.67). SSR-based diversity from individual plants exhibited marked inconsistency with other molecular diversity measures but was useful for genetic structure assessment, indicating much smaller among-population variation relative to within-population variation (7.5% in terms of variance ratio; 7.8% as global FST). Moderate inferences on germplasm adaptive diversity may be achieved by molecular characterization that maximizes the sampling of genomic areas and genotypes within accession through GBS applied to bulked plants.

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Acknowledgements

We are grateful to Y. Wei for her contribution to generation of SNP marker data and to P. Gaudenzi for technical assistance in SSR marker genotyping.

Funding

This research was funded by the Italian Ministry of Agricultural, Food and Forestry Policies within the project Plant Genetic resources/FAO Treaty and by the Samuel Roberts Noble Foundation.

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Authors and Affiliations

  1. Council of Agricultural Research and Economics (CREA), Research Centre for Animal Production and Aquaculture, Lodi, Italy

    P. Annicchiarico, M. Carelli & N. Nazzicari

  2. Plant Sciences Department, University of California, Davis, CA, USA

    E. C. Brummer

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  1. P. Annicchiarico
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  2. E. C. Brummer
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  3. M. Carelli
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  4. N. Nazzicari
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Contributions

Conceptualization and funding acquisition, PA and ECB; data generation, PA, MC and NN; data analysis, NN and PA; draft preparation, PA. All authors reviewed and commented on the manuscript and approved the final version.

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Correspondence to P. Annicchiarico.

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Molecular and morphophysiological data are provided as Online Resource 2.

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Online Resource 1

Name, origin, linkage group, locus, observed size range, and numbers of total polymorphic alleles, for 41 SSR markers used for bulked plants and 34 SSR markers used for analysis of individual genotypes of 11 alfalfa landraces (PDF 23 kb)

Online Resource 2

Molecular and morphophysiological data of 11 alfalfa landraces (XLS 540 kb)

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Annicchiarico, P., Brummer, E.C., Carelli, M. et al. Strategies of molecular diversity assessment to infer morphophysiological and adaptive diversity of germplasm accessions: an alfalfa case study. Euphytica 216, 98 (2020). https://doi.org/10.1007/s10681-020-02637-3

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