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Article

Genetic Diversity, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding

1
Centro de Pesquisa em Recursos Genéticos Vegetais, Instituto Agronômico (IAC), Campinas, São Paulo 13075-630, Brazil
2
Centro de Grãos e Fibras, Instituto Agronômico (IAC), Campinas, São Paulo 13075-630, Brazil
3
Soybean Genomics and Improvement Laboratory, US Department of Agriculture–Agricultural Research Service (USDA-ARS), Beltsville, MD 20705, USA
4
Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica dele Marche, 60131 Ancona, Italy
5
Max-Planck-Institute of Molecular Plant Physiology, Am Müehlenberg 1, 14476 Potsdam-Golm, Germany
6
Dipartimento di Agraria, Università degli Studi di Sassari, 07100 Sassari, Italy
7
Centro per la Cobservazione e Valorizzazione della Biodiversità Vegetale (CBV), Università degli Studi di Sassari, 07040 Alghero, Italy
*
Author to whom correspondence should be addressed.
Genes 2020, 11(11), 1298; https://doi.org/10.3390/genes11111298
Received: 2 October 2020 / Revised: 27 October 2020 / Accepted: 28 October 2020 / Published: 30 October 2020
(This article belongs to the Special Issue Food Legume Genomics)
Brazil is the largest consumer and third highest producer of common beans (Phaseolus vulgaris L.) worldwide. Since the 1980s, the commercial Carioca variety has been the most consumed in Brazil, followed by Black and Special beans. The present study evaluates genetic diversity and population structure of 185 Brazilian common bean cultivars using 2827 high-quality single-nucleotide polymorphisms (SNPs). The Andean allelic introgression in the Mesoamerican accessions was investigated, and a Carioca panel was tested using an association mapping approach. The results distinguish the Mesoamerican from the Andean accessions, with a prevalence of Mesoamerican accessions (94.6%). When considering the commercial classes, low levels of genetic differentiation were seen, and the Carioca group showed the lowest genetic diversity. However, gain in gene diversity and allelic richness was seen for the modern Carioca cultivars. A set of 1060 ‘diagnostic SNPs’ that show alternative alleles between the pure Mesoamerican and Andean accessions were identified, which allowed the identification of Andean allelic introgression events and shows that there are putative introgression segments in regions enriched with resistance genes. Finally, genome-wide association studies revealed SNPs significantly associated with flowering time, pod maturation, and growth habit, showing that the Carioca Association Panel represents a powerful tool for crop improvements. View Full-Text
Keywords: Phaseolus vulgaris L.; common bean; Carioca variety; variability gain; genomic introgression; genome-wide association study Phaseolus vulgaris L.; common bean; Carioca variety; variability gain; genomic introgression; genome-wide association study
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MDPI and ACS Style

Almeida, C.P.d.; Paulino, J.F.d.C.; Morais Carbonell, S.A.; Chiorato, A.F.; Song, Q.; Di Vittori, V.; Rodriguez, M.; Papa, R.; Benchimol-Reis, L.L. Genetic Diversity, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding. Genes 2020, 11, 1298. https://doi.org/10.3390/genes11111298

AMA Style

Almeida CPd, Paulino JFdC, Morais Carbonell SA, Chiorato AF, Song Q, Di Vittori V, Rodriguez M, Papa R, Benchimol-Reis LL. Genetic Diversity, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding. Genes. 2020; 11(11):1298. https://doi.org/10.3390/genes11111298

Chicago/Turabian Style

Almeida, Caléo Panhoca de, Jean Fausto de Carvalho Paulino, Sérgio Augusto Morais Carbonell, Alisson Fernando Chiorato, Qijian Song, Valerio Di Vittori, Monica Rodriguez, Roberto Papa, and Luciana Lasry Benchimol-Reis. 2020. "Genetic Diversity, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding" Genes 11, no. 11: 1298. https://doi.org/10.3390/genes11111298

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