Overview of the genus Phaseolus by Alfonso Delgado and Susana Gama Lopez (in Spanish)

In a recent issue of Revista Digital Universitaria of UNAM (National Autonomous University of Mexico), Alfonso Delgado and Susana Gama Lopez present – in Spanish – a synopsis of the ecological distribution of the genus Phaseolus in Mexico, the core distribution area of this genus.

A few salient points:

1/ There are currently 52 species distributed in the Mexican territory of which 31 are endemic. The highest species richness is concentrated in the staes of Durango, Jalisco, and Oaxaca, the lowest in the Yucatan peninsula, Tabasco, and Tlaxcala.

2/ The majority of species (49) grow in temperate to cold environments, subhumid to subarid, in juniper, pine, pine-oak, and oak forests.

3/ Lima bean (P. lunatus), distributed from the north of Argentina to Mexico, has the broadest ecological distribution as it occurs in  14 types of vegetation, more than any other Phaseolus species.

4/ Species diversity of Phaseolus will probably affected because the environments in which species currently are distributed will suffer the brunt of temperature increases: see point 2/ above.

5/ Ex situ conservation efforts of Phaseolus germplasm in Mexico include those organized by INIFAP (some 30,000 accessions) and SAGARPA (Centro Nacional de Recursis Geneticos in Tepatitlan de Morelos, Jalisco)

6/ In situ conservation projects include the MILPA project, which was funded by the McKnight Foundation, and the program of ANPs (Areas Naturales Protegidas)

7/ One species – Phaseolus leptophyllus – appears to be extinct. It was described first in the 18th centure in mountains near Chilpancingo in the state of Guerrero, but has not been collected since.

Plant & Animal Genome XXIII: 10-14 January, 2015

A belated report on some of the contributions – oral or poster – on beans (Phaseolus sp.) at the last Plant & Animal Genome conference from our own lab (in a following post, contributions from other labs).

One of the central questions currently is: to GBS/WGS or not to GBS/WGS? GBS at least appears to be cheaper than chip/SNP genotyping but this may be deceiving. There is a larger component of bioinformatics with GBS than with chip SNP genotyping; that additional component should be taken into account.

To be fully effective in breeding, an efficient, user-friendly pipeline should be available so that polymorphisms can be identified, viewed, and exported. We would be happy to test any pipeline.

a) W219 : https://pag.confex.com/pag/xxiii/webprogram/Paper15229.html
Determinacy in Common Bean: Duplications, Redundancies, and Multiple Domestications
Myoung-hai Kwak , WGRC, National Institute of Biological Resouces, Incheon, South Korea
Dianne M. Velasco , University of California, Davis, CA
Shelby Ellison , Department of Horticulture, University of Wisconsin, Madison, WI
Tamara Iva Miller , University of California, Davis, CA
Andrea Ariani , University of California, Davis, CA
The domestication syndrome is a suite of morphological and physiological traits that distinguish domesticated plants from their wild progenitors. Investigations into the inheritance of this syndrome have shown that the constituent traits involve sometimes genes with major effects, in addition to quantitative genes. In common bean (Phaseolus vulgaris L.), one of these genes is the fin gene, which leads to an early appearance of an inflorescence at the endings of the main stem and branches. Compared to indeterminate plants, determinate plants have, therefore, a bush growth habit and are early-flowering. We have been able to identify the causal gene for this trait (PvTFL1y), through a combination of large-scale co-segregation, candidate gene approaches based on Arabidopsis flowering time mutations, and transformation. Determinacy appears to have appeared as a de novo mutation and was not part of the standing variation in wild beans. Further analyses have shown that determinacy had multiple origins in different parts of the centers of origin, as suggested by the different mutations in PvTFL1y, including a retrotransposon insertion, a whole-locus deletion, frame shift mutations, and a putative splicing site mutation. Further research is needed to better understand the linked genetic backgrounds of the different mutations, possible selective sweeps around the PvTFL1y locus, and variation at another duplicate, unlinked locus, PvTFL1z.

b) P0754
Characterization of Genetic Diversity and Climatic Selection in Wild Common Bean (Phaseolus vulgaris) Using Genotyping By Sequencing (GBS) Technology
Andrea Ariani , University of California, Davis, CA
Jorge C. Berny , University of California, Davis, CA
Paul Gepts , University of California, Davis, CA
During domestication, and subsequent selection, plants were subjected to a severe bottleneck that drastically reduced genetic diversity in cultivated crops. This reduced diversity restricts the ability of breeding improvement in crop plants. Crop wild relatives constitute a valuable genetic resource for broadening the domesticated gene pools, even though they have been poorly characterized and exploited in breeding programs. Common bean (Phaseolus vulgaris) originated in the Americas and diverged into two separated gene pools (e.g., Mesoamerican and Andean), that underwent domestication independently. Wild common beans have a wide geographical distribution from north Mexico to north Argentina, that reflects an adaption to different environments. In this project we aim to genotype, using GBS technology, 284 wild common beans distributed from central to south America. The goal of the project is to generate a high density SNPs resource for wild common beans. These data will be useful for a comprehensive analysis of genetic diversity and signature of climatic selection in this species. After an in silico digestion of common bean reference genome we selected CviAII as the most suitable enzyme for our goals. We tested the approach with a sample of 17 wild and domesticated common bean, and a domesticated P. dumosus. We identified >47k high-quality variants located in ~11k annotated genes. SNPs distribution was positively correlated with chromosome size (r=0.79), with a median of 79 variants/Mb. These results suggest a dense variant distribution suitable for a comprehensive analysis of genetic diversity and signature of climatic selection in common bean. Funded by USDA-NIFA-AFRI.

3) P0748
Genome Sequencing of 15 Phaseolus vulgaris Genotypes in the African Bean Consortium Disease Resistance Breeding Program
Tamara Iva Miller , U.C. Davis, Davis, CA
The African Bean Consortium, funded by the Kirkhouse Trust, seeks to pyramid resistance genes for five major diseases that drive yield reduction in common bean grown in East Africa. In order to compare the nucleotide diversity and polymorphism of disease resistance loci relative to other loci and infer the evolutionary pressure driving genome diversity at disease resistance regions, genome sequencing of 15 parental lines used in the breeding programs was performed. In a first stage, genome sequences for the parents will be used to compare the frequency of Single Nucleotide Polymorphisms and Simple Sequence Repeat polymorphisms throughout the genome in order to both determine genome diversity in resistance loci, as well as access the distribution and overall usefulness of different markers for marker-assisted breeding. Paired-end 100 bp Illumina sequencing has been performed on disease resistance donor parents and preferred varieties that have seed and growth traits desirable to farmers and consumers in Uganda, Tanzania, Ethiopia, Rwanda and Kenya. Sequencing returned an average coverage per genotype of 13.09X. Variant analysis is underway using a pipeline that utilizes Burrows Wheeler Alignment to the G19833 Phaseolus vulgaris reference genome, Mpileup to call SNPs, and SSRIT, SSR Finder, and QDD to detect Simple Sequence Repeat motifs. These data will be hosted on the PhaseolusGenes database and genome browser (http://phaseolusgenes.bioinformatics.ucdavis.edu/), a molecular marker and genome database for common bean, which will facilitate marker use in future breeding programs.

That other bean: rescuing its wild ancestor

No, not soybean, but the revered coffee bean, which wakes us up (or keeps us awake) at crucial moments of the day. A recent letter to the editor of the journal Science highlights some of the problems associated with the conservation of wild coffee stands in the mountain forests of southern Ethiopia, the center of origin and domestication of arabica coffee.