Consequences of introgression and gene flow on the genetic structure and diversity of Lima bean (Phaseolus lunatus L.) in its Mesoamerican diversity area

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RT @JorgeCBerny: Consequences of introgression and gene flow on the genetic structure and diversity of Lima bean (Phaseolus lunatus L.) in…
Consequences of introgression and gene flow on the genetic structure and diversity of Lima bean (Phaseolus lunatus L.) in its Mesoamerican diversity area Lots of consequences https://t.co/Lp7eMSrK5r https://t.co/QXb0OeAE8M
Plant Biology

Main article text

 

Introduction

Survey Methodology

Study sites and plant material

DNA extraction

SNP detection

Data analysis

Introgression at the local scale

Structure, genetic diversity and gene flow at the regional scale

Results

Introgression at local scale

Structure, genetic diversity and wild-crop gene flow in Lima bean at regional scale

Discussion

Introgression and gene flow in Lima bean of the Yucatan Peninsula

Genetic structure and diversity of Lima bean in the Yucatan Peninsula

Conclusions

Supplemental Information

Analysis of Principal Coordinates (PCoA) of Lima bean from the Itzinté complex, using 15,168 SNP markers

The colors assigned to the observed groups correspond to those used in the STRUCTURE analysis with K = 2 (Fig. 3-A).

DOI: 10.7717/peerj.13690/supp-1

Analysis of Principal Coordinates (PCoA) of Lima bean from the Dzitnup complex, using 15,168 SNP markers

The colors assigned to the observed groups correspond to those used in the STRUCTURE analysis with K = 2 (Fig. 3-B).

DOI: 10.7717/peerj.13690/supp-2

Models used for the ABBA-BABA tests

In these models, wild MII populations from Mexico (outside the Yucatan Peninsula) were assigned as the sister group (P1) of wild populations within the complexes or within the Yucatan Peninsula assigned as P2, and wild MI populations from Mexico were assigned as the sister group (P1) of domesticated populations within the complexes or within the Yucatan Peninsula assigned as P2. In each model P3, the tested group, was appropriately chosen to test gene flow between P3 and P2. In all these models, the Andean wild gene pool (AI) was fixed as outgroup.

DOI: 10.7717/peerj.13690/supp-3

Distribution of df values per chromosome

The figure shows the proportion of introgression (df) per chromosome in the Itzinté (a) and Dzitnup (b) complexes in the direction domesticated to wild (d-w) (red bars) and wild to domesticated (w-d) (yellow bars). Gray dashed lines indicate df = 0, red and yellow dashed lines indicate median df values observed in the direction d-w and w-d, respectively.

DOI: 10.7717/peerj.13690/supp-4

Analysis of Principal Coordinates (PCoA) of Lima bean from the Yucatan Peninsula and the control group, using 15,168 SNP markers

The colors assigned to the observed groups correspond to those used in the Neighbor-Joining analysis (Fig. 6).

DOI: 10.7717/peerj.13690/supp-5

Estimated ancestry coefficients for wild and domesticated Lima bean accessions from the Yucatan Peninsula and considering the control group, using STRUCTURE and 15,168 SNP markers

The colors correspond to the observed groups using different K values: (A) K = 2; (B) K = 3; (C) K = 4. Colors with K = 4 match to those used in the Neighbor-Joining analysis (Fig. 6) and in the PCoA (Fig. S5).

DOI: 10.7717/peerj.13690/supp-6

Analysis of Principal Coordinates (PCoA) of Lima bean using only accessions collected in the Yucatan Peninsula and 15,168 SNP markers

The colors assigned to the observed groups correspond to those used in the STRUCTURE analysis with K = 3 (Fig. 7).

DOI: 10.7717/peerj.13690/supp-7

Data of accessions collected within Dzitnup and Itzinté complexes

DOI: 10.7717/peerj.13690/supp-8

Data of accessions used at the regional level (Table S2), Models used for the ABBA-BABA tests (Table S5). D and df values evaluating introgression between wild and domesticated populations within the complexes Itzinté and Dzitnup (Table S6)

DOI: 10.7717/peerj.13690/supp-9

Genbank Accession Numbers: GBS Data

DOI: 10.7717/peerj.13690/supp-10

NGSEP results with the two complexes studied

DOI: 10.7717/peerj.13690/supp-11

S6.1, Chromosomal regions with evidence of introgression and location of domestication QTL and S8, Number of introgression bolcks unique and shared among the Dzitnup and Itzinté complexes

DOI: 10.7717/peerj.13690/supp-12

SNP data of Dzitnup complex

DOI: 10.7717/peerj.13690/supp-13

SNP data of Itzinté complex

DOI: 10.7717/peerj.13690/supp-14

SNP data of Yucatan peninsula

DOI: 10.7717/peerj.13690/supp-15

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Mauricio Heredia-Pech conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Mariana Chávez-Pesqueira conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Matilde M. Ortiz-García performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Rubén Humberto Andueza-Noh conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

María Isabel Chacón-Sánchez conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Jaime Martínez-Castillo conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Field Study Permissions

The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):

The seed collection was carried out with the approval of the CICY Herbarium, wich has permission from Secretaria de Medio Ambiente y Recursos Naturales (SEMARNAT)-Mexico (SGPA/DGVS/008421/18).

Data Availability

The following information was supplied regarding data availability:

The raw sequence data are available in the NBCI Sequence Read Archive (SRA): PRJNA596114 and PRJNA823361. Further information about the SRX number for each accession is available in Table S3.

Funding

This work was supported by CONACYT-Mexico (project code CB2014-240984). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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