Abstract
Common bean ( L.) is the most important grain legume for human consumption and is a major nutrition source in the tropics. Because bean production is reduced by both abiotic and biotic constraints, current breeding efforts are focused on the development of improved varieties with tolerance to these stresses. We characterized materials from different breeding programs spanning three continents to understand their sequence diversity and advance the development of molecular breeding tools. For this, 37 varieties belonging to , (A. Gray), and L. were sequenced by whole-genome sequencing, identifying more than 40 million genomic variants. Evaluation of nuclear DNA content and analysis of copy number variation revealed important differences in genomic content not only between and the two other domesticated species, but also within , affecting hundreds of protein-coding genomic regions. A large number of inter-gene pool introgressions were identified. Furthermore, interspecific introgressions for disease resistance in breeding lines were mapped. Evaluation of newly developed single nucleotide polymorphism markers within previously discovered quantitative trait loci for common bacterial blight and angular leaf spot provides improved specificity to tag sources of resistance to these diseases. We expect that this dataset will provide a deeper molecular understanding of breeding germplasm and deliver molecular tools for germplasm development, aiming to increase the efficiency of bean breeding programs.
Highlights
Common bean is the most important grain legume for direct human consumption and is a staple food in different countries in Latin America and Eastern and Southern Africa (Broughton et al, 2003)
Because common bean is a major source of protein and micronutrients complementing the caloric contribution of cereal and root crops, this crop has a particular importance for resource-limited smallholder farmers living in tropical regions that are characterized by widespread poverty and malnutrition
As alleles from the species P. coccineus and P. acutifolius were successfully introgressed in some P. vulgaris elite cultivars, WGS was performed on one genotype of each of these species
Summary
Common bean is the most important grain legume for direct human consumption and is a staple food in different countries in Latin America and Eastern and Southern Africa (Broughton et al, 2003). Large WGS projects have been recently conducted on different crops such as rice (Oryza sativa L.) (Huang et al, 2012; Duitama et al, 2015), sorghum [Sorghum bicolor (L.) Moench.] (Mace et al, 2013), bell pepper (Capsicum annuum L.)(Qin et al, 2014), tomato (Solanum lycopersicum L.) (Lin et al, 2014), and even in other legumes such as lupin (Lupinus angustifolius L.) (Yang et al, 2015) These studies revealed the footprints of domestication and population dynamics within each species and allowed the assembly of large-scale databases of intra-species genomic variation including millions of single nucleotide polymorphisms (SNPs) and thousands of small indels, facilitating, in some cases, the genetic mapping of agronomically relevant traits through genome-wide association studies. Because genetic resistance to CBB is relatively low in P. vulgaris compared with P. acutifolius, breeding lines with acceptable levels of resistance have been developed from crosses with P. acutifolius (Miklas et al, 2011; Viteri et al, 2015)
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