Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean

Abstract

Lima bean (Phaseolus lunatus L.), one of the five domesticated Phaseolus bean crops, shows a wide range of ecological adaptations along its distribution range from Mexico to Argentina. These adaptations make it a promising crop for improving food security under predicted scenarios of climate change in Latin America and elsewhere. In this work, we combine long and short read sequencing technologies with a dense genetic map from a biparental population to obtain the chromosome-level genome assembly for Lima bean. Annotation of 28,326 gene models show high diversity among 1917 genes with conserved domains related to disease resistance. Structural comparison across 22,180 orthologs with common bean reveals high genome synteny and five large intrachromosomal rearrangements. Population genomic analyses show that wild Lima bean is organized into six clusters with mostly non-overlapping distributions and that Mesomerican landraces can be further subdivided into three subclusters. RNA-seq data reveal 4275 differentially expressed genes, which can be related to pod dehiscence and seed development. We expect the resources presented here to serve as a solid basis to achieve a comprehensive view of the degree of convergent evolution of Phaseolus species under domestication and provide tools and information for breeding for climate change resiliency.

Genome-wide association study for grain mineral content in a Brazilian common bean diversity panel

“…Regarding to the distribution of the SNPs obtained by GBS, it was observed a higher density towards the ends of the chromosomes, and similar results was obtained in other bean materials (Ariani et al 2016;Garcia et al 2021). Mapping resolution and statistical power are the main aspects considered in GWAS, with the former being strongly in uenced by LD.…”

Comparative cytogenomics reveals genome reshuffling and centromere repositioning in the legume tribe Phaseoleae

“…Furthermore, in the ancestral Phaseolus karyotype (APsK) two reciprocal translocations occurred: between APnK1 and 8, resulting in APsK1 (A+B) and APsK8 (P+Q); and between APK2 and 3, generating APsK2 (C+E+C+D+F) and APsK 3 (G+H), followed by inversions and intrachromosomal translocations on APsK2 (C and E) and APsK3 (H) (Figure 1.B3). We also detected previously described inversions between P. vulgaris and P. lunatus (Bonifácio et al, 2012;Garcia et al, 2021) in Chr1 (in B); Chr2 (C, D and E); Chr3 (within H4); Chr7 (in N and O); Chr9 (in R), and Chr10 (in S and T). The complex, multiple inversions in chromosome 2 and 7, also involving intrachromosomal translocations, occurred independently in P. vulgaris and P. lunatus, while the intrachromosomal translocations on chromosomes 1 and inversions on chromosomes 1, 3, 9 and 10 occurred in P. lunatus (Pl1) and P. vulgaris (Pv1, 3, 9 and 10) lineages, respectively (Figure 1.B4 and 1.B5 and 2).…”

“…Few translocations and a large number of inversions were detected within Phaseolinae, some of which were previously identified by BAC-FISH, oligo-FISH and comparative genomics in P. vulgaris, P. lunatus and V. unguiculata (Bonifácio et al, 2012;Vasconcelos et al, 2015;Lonardi et al, 2019;Oliveira et al, 2020;do Vale Martins et al, 2021;Garcia et al, 2021;Bustamante et al, 2021). Based on our APK and oligo-FISH approaches, we can propose the direction of these rearrangements in a phylogenetic context.…”

“…The centromeric regions were defined based on the centromeric data available in the genome assemblies (Schmutz et al, 2014;Pecrix et al, 2018;Lonardi et al, 2019;Liu et al, 2020;Garcia et al, 2021). Because the centromere positions for S. suberecuts were not indicated in the genome assembly, we hypothesized the centromere region according to the peaks of TE accumulations along the chromosomes (Qin et al, 2019).…”

History and impact of a bean (Phaseolus spp., Leguminosae, Phaseoleae) collection

“…Wild forms and wild species should thus be better represented in the collection, with due consideration to the regeneration capacity and disclosure of the potential. There are two points here: first, given the possibilities opened by comparative mapping in the Phaseoleae (Schmutz et al, 2014;Vlasova et al, 2016;Garcia et al, 2021;Moghaddam et al, 2021) and by gene editing (Bhatta and Malla, 2020;Ku and Ha, 2020), it may be time to think beyond direct interspecific hybridization for the use of alien germplasm. In that sense, species of clade A that may represent half of genus (Delgado-Salinas et al, 2006;Porch et al, 2013;Debouck, 2021) may be opportunities of genes to imitate and/or to regulate differently instead of genes to transfer.…”