Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Genetic Diversity and Population Structure of the Peruvian Andean Legume, tarwi (Lupinus mutabilis), With High Quality SNPs

Amelia Huaringa-Joaquin
ORCID logo ,
Carla L. Saldaña
ORCID logo ,
David Saravia
,
Sady García-Bendezú
,
Pedro Rodriguez-Grados
ORCID logo ,
Wilian Salazar
,
Felix Camarena
,
Pedro Injante
,
Carlos I. Arbizu
* ORCID logo
Version 1 : Received: 19 January 2023 / Approved: 19 January 2023 / Online: 19 January 2023 (03:57:25 CET)

A peer-reviewed article of this Preprint also exists.

Huaringa-Joaquin, A.; Saldaña, C.L.; Saravia, D.; García-Bendezú, S.; Rodriguez-Grados, P.; Salazar, W.; Camarena, F.; Injante, P.; Arbizu, C.I. Assessment of the Genetic Diversity and Population Structure of the Peruvian Andean Legume, Tarwi (Lupinus mutabilis), with High Quality SNPs. Diversity 2023, 15, 437. Huaringa-Joaquin, A.; Saldaña, C.L.; Saravia, D.; García-Bendezú, S.; Rodriguez-Grados, P.; Salazar, W.; Camarena, F.; Injante, P.; Arbizu, C.I. Assessment of the Genetic Diversity and Population Structure of the Peruvian Andean Legume, Tarwi (Lupinus mutabilis), with High Quality SNPs. Diversity 2023, 15, 437.

Abstract

Lupinus mutabilis Sweet (Fabaceae), “tarwi” or “chocho”, is an important grain legume in the Andean region. In Peru, studies on tarwi have been mainly focused on morphological features, however, the have not been molecularly characterized. Currently, it is possible to explore genetic parameters of plants with reliable and modern methods like genotyping-by-sequencing (GBS). We here for the first time used single nucleotide polymorphisms (SNPs) markers to infer the genetic diversity and population structure of 89 accessions of tarwi from nine Andean regions of Peru. A total of 5922 SNPs distributed along all chromosomes of tarwi were identified. STRUCTURE analysis revealed that this crop is grouped into two clusters. A dendrogram was generated using the UPGMA clustering algorithm and, similar to the principal coordinate analysis (PCoA), it showed two groups that correspond to the geographic origin of the tarwi samples. AMOVA showed a reduced variation between clusters (7.59 %) and indicated that variability within populations is 92.41 %. Population divergence (Fst) between clusters 1 and 2 revealed low genetic difference (0.019). We also detected a negative Fis for both populations, demonstrating that, similar to other Lupinus species, tarwi also depends on cross-pollination. SNPs markers were powerful and effective for the genotyping process in this germplasm. We hope that this information is the beginning of the path towards a modern genetic improvement and conservation strategies of this important Andean legume.

Keywords

Fabaceae; bioinformatics; molecular markers; neglected crop; genomics

Subject

Biology and Life Sciences, Biochemistry and Molecular Biology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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