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

Author(s)

Almeida, Caleo Panhoca de ^[1] ; Paulino, Jean Fausto de Carvalho ^[1] ; Morais Carbonell, Sergio Augusto ^[2] ; Chiorato, Alisson Fernando ^[2] ; Song, Qijian ^[3] ; Di Vittori, Valerio ^{[4, 5]} ; Rodriguez, Monica ^{[6, 7]} ; Papa, Roberto ^[4] ; Benchimol-Reis, Luciana Lasry ^[1]

Affiliation

^[1] Inst Agron IAC, Ctr Pesquisa Recursos Genet Vegetais, BR-13075630 Campinas, SP - Brazil

^[2] Inst Agron IAC, Ctr Graos & Fibras, BR-13075630 Campinas, SP - Brazil

^[3] USDA ARS, Soybean Genom & Improvement Lab, Beltsville, MD 20705 - USA

^[4] Univ Politecn Marche, Dipartimento Sci Agr Alimentari & Ambiental, I-60131 Ancona - Italy

^[5] Max Planck Inst Mol Plant Physiol, Muehlenberg 1, D-14476 Potsdam - Germany

^[6] Univ Sassari, Dipartimento Agr, I-07100 Sassari - Italy

^[7] Univ Sassari, Ctr Cobservaz & Valorizzaz Biodiversita Vegetale, I-07040 Alghero - Italy

• Document type: Journal article
• Source: GENES; v. 11, n. 11 NOV 2020.
• Web of Science Citations: 8

Abstract

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. (AU)

• FAPESP's process: 17/01753-3 - Marker assisted selection and genotyping by sequenecing (GBS) toward angular leaf resistance in common beans
• Grantee: Caléo Panhoca de Almeida
• Support Opportunities: Scholarships in Brazil - Master
• FAPESP's process: 17/24711-4 - A wide genome association study for resistance to Fusarium oxysporum f. sp. phaseoli and for tegument color in common bean
• Grantee: Luciana Lasry Benchimol-Reis
• Support Opportunities: Regular Research Grants
• FAPESP's process: 19/19670-2 - Population genomics and GWAS for disease resistance and identification of Andean pool introduction regions in carioca bean access
• Grantee: Caléo Panhoca de Almeida
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• FAPESP's process: 18/15526-1 - Genome-wide association study for identifying agronomic candidate loci in common bean
• Grantee: Caléo Panhoca de Almeida
• Support Opportunities: Scholarships abroad - Research Internship - Master's degree