Genetic diversity analysis of common beans based on molecular markers

Abstract

A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

Genetic Relationship among Common Bean Cultivars with Enhanced Accumulation of Bioactive Compounds

“…Genetic diversity analysis was performed among cultivars using seven microsatellite loci (BM143, BM154, BM164, BM181, BM188, GATs54, GATs91) achieved from previous reported genomic sequences (Gill-Langarica et al, 2011). Amplified PCR was obtained for each SSR according to conditions reported by Gill-Langarica et al, (2011).…”

“…Amplified PCR was obtained for each SSR according to conditions reported by Gill-Langarica et al, (2011). Total reaction volume included DNA (75 ng), 0.16 μM of each primer (sense and antisense), 2 μL of PCR buffer 10X, 1.5-2.5 mM of Mg (depending on each primer), 2 mM of dNTPs and 1 U of Taq DNA polymerase.…”

Expression profiling and sequence diversity of novel DREB genes from common bean (Phaseolus vulgaris L.) and their association with drought-related traits

“…This variability is observed in different leaf shapes, growth habits, flower colors, but especially for seeds in terms of colors, shapes and sizes (SINGH; GEPTS; DEBOUCK, 1991). Further studies with DNA markers confirmed the high genetic diversity of common bean at the molecular level: RAPD (CARVALHO et al, 2008;KUMAR et al, 2014), microsatellites BURLE et al, 2010;PERSEGUINI et al, 2011;GIL-LANGARICA et al, 2011), AFLP (MACIEL et al, 2003;GIL-LANGARICA et al, 2011;PERSEGUINI et al, 2011), ISSR (GONZÁLEZ et al, 2005 and SNP (CORTÉS; GALEANO et al, 2012;. Furthermore, an investigation of the variability at the transcriptome level showed how domestication has shaped nucleotide and gene expression diversity (BELLUCCI et al, 2014).…”

Diversidade genética entre acessos cultivados de feijão comum (Phaseolus vulgaris L.): uma abordagem in silico a partir dos genes -Phs e FR01

“…Esses dois pools gênicos são distinguidos tanto morfologicamente (GEPTS; DEBOUCK, 1991;CHIORATO et al, 2005) quanto molecularmente (GEPTS; BLISS, 1985;GEPTS et al, 1986;KOENIG;SINGH;GEPTS, et al 1990;SINGH;BECERRA-VELÁSQUEZ;GEPTS, 1994;FREYRE et al, 1996;THOME et al, 1996;GEPTS, 2003;CHACÓN;PICKERSGILL;DEBOUCK, 2005;BLAIR et al, 2006;HANAI et al, 2007;BENCHIMOL et al, 2007;KWAK;GEPTS, 2009;GILL-LANGARICA et al, 2011).…”

“…Os polimorfismos podem ser morfológicos, de natureza bioquímica ou molecular; neste caso, deve haver diferença na sequência de nucleotídeos do DNA, levando a um fenótipo molecular distinto (VIEIRA; VELLO; SILVA-FILHO, 2004). O conhecimento atual da estrutura populacional e da origem da domesticação do feijoeiro é baseado em estudos que utilizaram diversos marcadores moleculares, tais como: RFLPs (BECERRA-VELÁSQUEZ; GEPTS, 1994); RAPDs (FREYRE et al, 1996, BEEBE et al, 2000; AFLPs (THOME et al, 1996;BEEBE et al, 2001;PAPA;GEPTS, 2003); SSRs HANAI et al, 2007;BENCHIMOL et al, 2007;GILL-LANGARICA et al, 2011); DNA mitocondrial (KHAIRALLAH; SEARS; ADAMS, 1992) e cloroplastidial (CHACÓN et al, 2005); SNPs (MCCLEAN; LEE; MIKLAS, 2004;CHEN et al, 2010). Todavia, na maioria desses estudos, o baixo nível de polimorfismo e o reduzido número de marcas usado tem impedido uma caracterização detalhada da estrutura populacional e das relações genéticas entre os acessos dentro dos grupos gênicos (KWAK; GEPTS,…”