A reference genome for common bean and genome-wide analysis of dual domestications

Abstract

Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement.

Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy

“…Genome sequences for most of the grain legumes are now available, for instance soybean (Schmutz et al, 2010), groundnut progenitors (Bertioli et al, 2016;Chen et al, 2016), chickpea (Varshney et al, 2013d;Parween et al, 2015), pigeonpea (Varshney et al, 2012a), common bean (Schmutz et al, 2014;Yang et al, 2015), and adzuki bean (Kang et al, 2015;Yang et al, 2015) (Table 1). Efforts are underway to sequence the remaining legume genomes.…”

“…BeadChip (Akond et al, 2013) • SoySNP50K array (Song et al, 2013) • 384 SNP GoldenGate assay (Hyten et al, 2008 (Varshney et al, 2012a) • 292 lines • 20 (crossing parentals of recombinant inbred lines, introgression lines, MAGIC and NAM population; Kumar et al, 2016) • 60K Axiom®Cajanus SNP array (Saxena et al, 2017 and unpublished) (Gupta et al, 2017) • 35 (parental genotypes of mapping populations; Thudi et al, 2016a) • 129 released varieties (Thudi et al, 2016b) • 300 lines (ICRISAT, unpublished) • 3000 lines (ICRISAT, unpublished) • GoldenGate assays based on VeraCode technology (Roorkiwal et al, 2013) • 60K Axiom®Cicer SNP array (Roorkiwal et al, 2017 (Chen et al, 2016) • 11 genotypes including synthetics and their diploid parents (Chen et al, 2016) • 41 diverse genotypes (30 tetraploids and 11 diploids) (Clevenger et al, 2017;Pandey et al, 2017a) • 58K Axiom®Arachis SNP array (Pandey et al, 2017a) •1536 SNP GoldenGate assay (Nagy et al, 2012) Common bean • 80.57% of Phaseolus vulgaris var G19833 genome (587 Mb); 26 279 protein coding genes (Schmutz et al, 2014) • 17 varieties • BARCBean6K_1, BARCBean6K_2 chips, BARCBean6K_3 SNP chips (Song et al, 2013 (Deulvot et al, 2010) • Combines custom-made growth vessels and new image analysis algorithms to non-destructively monitor RSA development over space (2D) and time • Allows information on soil properties (e.g. moisture)…”

Origin of year-long bean (Phaseolus dumosusMacfady, Fabaceae) from reticulated hybridization events between multiplePhaseolusspecies

“…The common bean, Phaseolus vulgaris, is a staple crop throughout South America, Central America and Africa, where it is an important source of dietary protein and a target of ongoing breeding and biofortification programmes Schmutz et al, 2014). To meet current and emerging production challenges, novel genetic variation needs to be identified within the genetic diversity of germplasm collections and in situ populations (Ramırez-Villegas et al, 2010;Beebe et al, 2012;Porch et al, 2013).…”

Genome-wide identification and characterization of aquaporin gene family in common bean (Phaseolus vulgaris L.)

“…These two gene pools were independently domesticated in what is now Mexico and South America (Gepts et al 1986;Bitocchi et al 2013) about 8,000 years ago. The release of a reference P. vulgaris genome sequence (Schmutz et al 2014), together with the development and application of Next Generation Sequencing technologies in plant species (Bräutigam and Gowik 2010) and synteny among plants, such as soybean and Arabidopsis, enabled a genome-wide identification of actual or putative loci involved in the domestication process of this species (Repinski et al 2012;Kwak et al 2012;Bellucci et al 2014;Schmutz et al 2014).…”