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. 2022 Dec 13;6(12):e470.
doi: 10.1002/pld3.470. eCollection 2022 Dec.

Large genomic introgression blocks of Phaseolus parvifolius Freytag bean into the common bean enhance the crossability between tepary and common beans

Santos Barrera  1 , Jorge C Berny Mier Y Teran  2 , Juan David Lobaton  3 , Roosevelt Escobar  4 , Paul Gepts  2 , Steve Beebe  4 , Carlos A Urrea  1
Affiliations

Large genomic introgression blocks of Phaseolus parvifolius Freytag bean into the common bean enhance the crossability between tepary and common beans

Santos Barrera et al. Plant Direct. .

Abstract

The production of the common bean (Phaseolus vulgaris L.), one of the most important sources of protein and minerals and one of the most consumed grain legumes globally, is highly affected by heat and drought constraints. In contrast, the tepary bean (Phaseolus acutifolius A. Gray), a common bean-related species, is adapted to hot and dry climates. Hybridization to introduce complex traits from the tepary bean into the common bean has been challenging, as embryo rescue is required. In this study, we report three novel interspecific lines that were obtained by crossing lines from prior common bean × tepary bean hybridization with Phaseolus parvifolius Freytag in order to increase the male gametic diversity to facilitate interspecific crosses. These interspecific lines enhanced the crossability of the common bean and tepary bean species while avoiding the embryo rescue process. Crossing these three interspecific lines with tepary beans resulted in 12-fold more hybrid plants than crossing traditional common beans with tepary beans. Whole-genome sequencing analysis of these three interspecific lines shows large introgressions of genomic regions corresponding to P. parvifolius on chromosomes that presumably contribute to reproductive barriers between both species. The development of these lines opens up the possibility of increasing the introgression of desirable tepary bean traits into the common bean to address constraints driven by climate change.

Keywords: embryo rescue; haplotype blocks; interspecific; introgressions; recombinant populations; whole‐genome sequencing.

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Conflict of interest statement

The authors declare that they have no conflict of interest related to this manuscript.

Figures

FIGURE 1
FIGURE 1
Relatedness tree based on the distance matrix between the interspecific lines (VAP and INB lines), the tepary bean genotype (G40001), the common bean genotype (RWR719), and the Phaseolus parvifolius genotype (G40264). The distance matrix was calculated, and the plot was created in the software TASSEL v.5.0 (Bradbury et al., 2007).
FIGURE 2
FIGURE 2
Interspecific hybridization between common bean and tepary bean. (a) Flowers abscised at a very early stage and pods without seeds, from crosses between tepary beans and common beans. (b) Mature pods and seeds from crosses between the VAP lines and tepary beans
FIGURE 3
FIGURE 3
Comparison of the ability to cross tepary beans with traditional common bean lines and the interspecific VAP lines. Left) 22 crosses of VAP lines (used as female parents) with tepary beans (used as male parents). Right) 23 crosses of traditional common beans (female parents) with tepary beans (male parents)
FIGURE 4
FIGURE 4
Mapping of the interspecific introgressions in the VAP lines, INB lines, two common bean genotypes (Andean and Mesoamerican), and two tepary bean genotypes in the 11 chromosomes. Light blue indicates the common bean background. Brown indicates the tepary bean background. Purple indicates heterozygous SNPs. The heat map shows the SNP density. G40001, which is the tepary bean reference genome is presented in this figure only to compare Phaseolus parvifolius and Phaseolus acutifolius genomes.
FIGURE 5
FIGURE 5
Flapjack visualization of introgressions from Phaseolus parvifolius (G40264) in the VAP lines in chromosome Pv09. Highlighted heterozygous introgression regions in the line VAP3 in replication 01 (R1) and replication 02 (R2). Heterozygous regions are defined as regions that share nucleotides from both reference haplotypes (G19833 and G40264). G40001, which is the tepary bean reference genome is presented in this figure only to compare P. parvifolius and Phaseolus acutifolius genomes.
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