Analyses of African common bean (Phaseolus vulgaris L.) germplasm using a SNP fingerprinting platform: diversity, quality control and molecular breeding

Abstract

Common bean (Phaseolus vulgaris L.) is an important staple crop for smallholder farmers, particularly in Eastern and Southern Africa. To support common bean breeding and seed dissemination, a high throughput SNP genotyping platform with 1500 established SNP assays has been developed at a genotyping service provider which allows breeders without their own genotyping infrastructure to outsource such service. A set of 708 genotypes mainly composed of germplasm from African breeders and CIAT breeding program were assembled and genotyped with over 800 SNPs. Diversity analysis revealed that both Mesoamerican and Andean gene pools are in use, with an emphasis on large seeded Andean genotypes, which represents the known regional preferences. The analysis of genetic similarities among germplasm entries revealed duplicated lines with different names as well as distinct SNP patterns in identically named samples. Overall, a worrying number of inconsistencies was identified in this data set of very diverse origins. This exemplifies the necessity to develop and use a cost-effective fingerprinting platform to ensure germplasm purity for research, sharing and seed dissemination. The genetic data also allows to visualize introgressions, to identify heterozygous regions to evaluate hybridization success and to employ marker-assisted selection. This study presents a new resource for the common bean community, a SNP genotyping platform, a large SNP data set and a number of applications on how to utilize this information to improve the efficiency and quality of seed handling activities, breeding, and seed dissemination through molecular tools.Electronic supplementary materialThe online version of this article (10.1007/s10722-019-00746-0) contains supplementary material, which is available to authorized users.

Genetic diversity of Pseudocercospora griseola resistance loci in common beans

“…According to Colombari Filho et al (2010), the characterization of diversity may be more useful when evaluated in combination with genotype and phenotypic information of interest. Even though there are several studies on the genetic (Corrêa et al 2001;Mahuku et al 2011;Miller et al 2018;Nay et al 2019b) and phenotypic (Sannazzaro et al 2003;Reis-Prado et al 2006;Chataika et al 2010;Pereira et al 2019a, b) characterization of ALS resistance, as well as evaluation of the general genetic diversity of common bean accessions (Campa et al 2018;Raatz et al 2019;Valentini et al 2018;Gioia et al 2019), this is the first study involving phenotypic resistance evaluation in combination with genetic diversity of loci associated with ALS resistance.…”

Breeding tepary bean (Phaseolus acutifolius) for drought adaptation: A review

“…A congruity backcross method has been used to transfer genes from tepary bean to common bean (Mejía‐Jiménez, Muñoz, Jacobsen, Roca, & Singh, 1994; Muñoz et al, 2004; Souter et al, 2017). Tepary bean has a narrow genetic base compared to common bean which shows extensive genetic diversity (Blair et al, 2012; Okii et al, 2018; Raatz et al, 2019). Common bean also shows wide genetic variation for yield and yield‐related traits which can be useful for breeding of tepary bean genotypes with enhanced yield performance (Asfaw et al, 2017; Okii et al, 2018; Rana et al, 2015).…”

Population Structure and Genome‐Wide Association Analysis of Bruchid Resistance in Ethiopian Common Bean Genotypes

“…With the current advances in molecular markers, a number of studies have been conducted to assess genetic diversity, population structure, and genome-wide association in the common bean. A wide range of molecular markers, including restriction fragment length polymorphisms (RFLPs; Velasquez and Gepts, 1994;Freyre et al, 1998), random amplified polymorphic DNA (RAPD; Beebe et al, 2000;Durán et al, 2005), inter simple sequence repeats (ISSRs; González et al, 2005;Dagnew et al, 2014), amplified fragment length polymorphisms (AFLPs; Beebe et al, 2001;Papa and Gepts, 2003), simple sequence repeats (SSRs; Blair et al, 2007Blair et al, , 2009Blair et al, , 2010aAsfaw et al, 2009;Kwak and Gepts, 2009;Burle et al, 2010;McClean et al, 2012;De La Fuente et al, 2013;Mercati et al, 2013;Okii et al, 2014Okii et al, , 2017Gioia et al, 2019;Pereira et al, 2019), and single nucleotide polymorphisms (SNPs; Cortés et al, 2011;Blair et al, 2013;Goretti et al, 2013;Cichy et al, 2015a;Rodriguez et al, 2016;Lobaton et al, 2018;Raatz et al, 2019), have been used in common bean.…”