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Genetic diversity and inter-gene pool introgression of Mesoamerican Diversity Panel in common beans

  • Plant Genetics • Original Paper
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Abstract

Brazil is among the largest producers and consumers of common bean (Phaseolus vulgaris L.) and can be considered a secondary center of diversity for the species. The aim of this study was to estimate the genetic diversity, population structure, and relationships among 288 common bean accessions in an American Diversity Panel (ADP) genotyped with 4,042 high-quality single nucleotide polymorphisms (SNPs). The results showed inter-gene pool hybridization (hybrids) between the two main gene pools (i.e., Mesoamerican and Andean), based on principal component analysis (PCA), discriminant analysis of principal components (DAPC), and STRUCTURE analysis. The genetic diversity parameters showed that the Mesoamerican group has higher values of diversity and allelic richness in comparison with the Andean group. Considering the optimal clusters (K), clustering was performed according to the type of grain (i.e., market group), the institution of origin, the period of release, and agronomic traits. A new subset was selected and named the Mesoamerican Diversity Panel (MDP), with 205 Mesoamerican accessions. Analysis of molecular variance (AMOVA) showed low genetic variance between the two panels (i.e., ADP and MDP) with the highest percentage of the limited variance among accessions in each group. The ADP showed occurrence of high genetic differentiation between populations (i.e., Mesoamerican and Andean) and introgression between gene pools in hybrids based on a set of diagnostic SNPs. The MDP showed better linkage disequilibrium (LD) decay. The availability of genetic variation from inter-gene pool hybridizations presents a potential opportunity for breeders towards the development of superior common bean cultivars.

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Funding

This research was funded by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), grant number Proc. 2017/24711–4 and scholarships 2017/01753–3, 2018/15526–1, and 2019/19670–2, and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior through scholarship grants.

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Authors and Affiliations

  1. Common Bean Genetic Group, Natural Center of Plant Genetics, Agronomic Institute (IAC), Campinas, SP, Brazil

    Jean Fausto de Carvalho Paulino, Caléo Panhoca de Almeida & Luciana Lasry Benchimol-Reis

  2. Soybean Genomics and Improvement Lab, USDA-ARS, Beltsville, MD, USA

    Qijian Song

  3. Common Bean Breeding Group, Grain and Fiber Center, Agronomic Institute (IAC), Campinas, SP, Brazil

    Sérgio Augusto Morais Carbonell & Alisson Fernando Chiorato

Authors
  1. Jean Fausto de Carvalho Paulino
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  2. Caléo Panhoca de Almeida
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  3. Qijian Song
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  4. Sérgio Augusto Morais Carbonell
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  5. Alisson Fernando Chiorato
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  6. Luciana Lasry Benchimol-Reis
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Contributions

L.L.B.R., A.F.C., and J.P.C. P., designed the study, and L.L.B.R. was responsible for the project funding. J.F.C.P. and C.P.A. conceived the structure of the manuscript, and J.F.C.P. wrote the initial manuscript. J.F.C.P. and C.P.A. conducted the experiments. J.F.C.P. and C.P.A., performed the date analyzes. Q.S. analyzes accuracy. L.L.B.R., A.F.C., Q. S, and S.A.M.C. supported the data curation and conducted reviewed the manuscript. All the authors have approved the final version of the manuscript.

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Correspondence to Jean Fausto de Carvalho Paulino.

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Communicated by Izabela Pawłowicz.

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Jean Fausto de Carvalho Paulino and Caléo Panhoca de Almeida are co-first authors

Supplementary Information

Below is the link to the electronic supplementary material.

13353_2021_657_MOESM1_ESM.xlsx

Supplementary file1 Details of the 288 cultivars: gene pool, commercial classification, grain size, institution of origin and ancestry coefficient (STRUCTURE) for K = 2 and K = 4 and pedigree.  (XLSX 57 KB)

13353_2021_657_MOESM2_ESM.xlsx

Supplementary file 2 The 288 genotypes genotyped with 4,042 SNPs of the panel grouped in by K = 4 were obtained by the analysis of the genetic structure and their respective main characteristics, and MDP selection with 2,437 SNPs. (XLSX 21 KB)

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de Carvalho Paulino, J.F., de Almeida, C.P., Song, Q. et al. Genetic diversity and inter-gene pool introgression of Mesoamerican Diversity Panel in common beans. J Appl Genetics 62, 585–600 (2021). https://doi.org/10.1007/s13353-021-00657-w

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