Phaseolus Crop Germplasm Committee Report
Contributors to the 1996 update:
P. Gepts, Phaseolus CGC Chair
P. Miklas, Phaseolus CGC Secretary
I. INTRODUCTION: P. Gepts 3
A. World Production 3
B. U.S. Production 3
C. Domestic Use: 5
D. Export Markets: 5
E. Bean Germplasm 6
II. PRESENT GERMPLASM ACTIVITIES 6
A. Collection: P. Gepts 7
B. Evaluation: J. Steadman and D. Coyne 8
C. Enhancement: P. Miklas 9
D. Preservation: R. Hannan 10
E. Genetic Stocks Collection: J. Myers 13
F. Phaseolus Electronic Databases P. McClean 14
III. STATUS OF CROP VULNERABILITY 16
A. Trends in Genetic Diversity within Different Production Regions:
M. Brick and J. Myers 17
B. Cytoplasmic Genetic Diversity: C. Chase 20
IV. GERMPLASM NEEDS 21
A. Collection: P. Gepts 21
B. Evaluation: J. Steadman and D. Coyne 22
C. Enhancement: P. Miklas 23
D. Preservation: R. Hannan 23
E. Genetic Stocks Collection: J. Myers 24
F. Phaseolus Electronic Databases P. McClean 24
V. RECOMMENDATIONS 25
VI. LITERATURE CITED 25
I. INTRODUCTION: P. Gepts
A. World Production
Phaseolus dry beans are the leading grain legume crop with an annual world production of 20
million metric tons (mmt) or 30% of the total world pulse production of 60 mmt in 1994 (Parker
1995b). World figures for green bean production are not individually available hence are
included in the above figure. Green beans are becoming an increasingly important crop in
developing countries as consumers demand more diversity in their daily food consumption and
farmers seek additional sources of income.
The major dry bean producers are Brazil with 2.8 mmt, Mexico with 1.0 mmt, the U.S. with 1.3
mmt, and Europe at 0.8 mmt (1994 figures; Parker 1995b). Beans play a major role in the diets
of people throughout America and Africa with cumulative production of 1.1 mmt in other Latin
American countries and 1.8 mmt in E. Africa. Although Brazil is the leading producer of beans,
it consumes all its production. The U.S. is the leading export nation marketing 40% (0.4 mmt)
of all dry bean production overseas while Argentina exports all (99.5%) of its production of 0.25
B. U.S. Production
Phaseolus dry beans are planted on 2.0 (1.6-2.2) million acres in the U.S. (USDA 1: 1994 figure
with range over 1989-1994). Production reached around 29 million hundred weight (cwt)
annually, ranging from a low of 22 million in 1993 to a high of almost 34 million cwt in 1991.
This production has a farm gate value at between $400 to $675 million depending on the season
and the availability of export markets (USDA 2: period of 1987-1992). In 1995, the major
production states of dry beans ranked in order of production are: North Dakota, Michigan,
Nebraska, California, Colorado, Idaho, Minnesota, Washington, Wyoming, and New York
recognizing that there are seasonal changes (USDA 3). Average yields range from 13 cwt/a
under rainfed conditions in the Midwest to highs of 22 cwt/a under irrigated production in
California and the Northwest.
Dry bean classes are categorized based on differences in seed size, shape, and color. The white
seeded classes include navy and great northern beans; mottled classes include pinto and
cranberry beans while the remainder have color included in the market class name. Seed size
varies from small navy and black turtle beans (2200 to 3000 seed per pound or 15-20 g per 100
seeds) to medium-sized pinto, great northern, pink, and red Mexican beans (1200 to 1400 seeds
per pound or 32-38 g per 100 seeds) to large-seeded kidney and cranberry beans (800 to 1000
seeds per pound or 45-57 g per 100 seeds). In addition to the obvious seed trait differences,
other major differences in growth habit, disease reaction, and adaptation exist. The U.S.
produces 9 commercial market classes of dry beans ranked here in order of their 1994
production: Pinto, Navy, Black Turtle Soup, Kidney (light and dark), Great Northern, Red
Mexican (or Small Reds), Pink, Cranberry, and Small White (USDA 3). Pinto beans replaced the
navy bean as the number one market class in the late 1980s. The other classes have maintained a
fairly consistent annual production with exception of the Black Turtle Soup class which rose
dramatically in the 1980-81 season as a result of export markets. Subsequently, Black Turtle
Soup consumption has sharply increased since the beginning of the 1990s presumably because of
the popularity of ethnic foods (Lucier 1995a). The different bean classes are produced in
localized production areas within specific states listed. Navy bean production is concentrated in
Michigan and the Red River Valley of North Dakota and Minnesota; pintos mainly in Colorado,
North Dakota, and Idaho; great northerns primarily in Nebraska; pinks in Idaho, Washington,
and California; and red Mexican beans in Idaho and Washington. The localized intense
production of market classes of different evolutionary origins (Table 1) potentially decreases the
risk of genetic vulnerability within a production region or state. For example, in California the
two main classes (kidneys and pinks) belong to different gene pools (Andean and Middle
American, respectively). In addition, these common bean classes are grown with other bean
classes belonging to other species such as lima bean (P. lunatus), cowpea or blackeyed-pea
(Vigna unguiculata), and garbanzo bean or chickpea (Cicer arietinum).
Table 1. Evolutionary origin of major dry bean classes in the U.S.
(after Brown et al. 1982, Gepts et al. 1988, Singh et al. 1991)
|Dry bean class
|Black Turtle Soup
|Kidneys (light and dark)
|Red Mexican (or Small Reds)
Common bean cultivars belonging to the same race are more likely to be vulnerable to the same
pathogen strain than cultivars belonging to different races and a fortiori to different gene pools.
Snap beans are grown for processing or the fresh market. In 1995, the snap bean acreage for
processing in the U.S. was estimated at 218,000 acres (USDA 4). For the period of 1990-1992,
the production value ranged between $ 112-144 million annually (USDA 2). The major
production states in 1995 were Wisconsin with 68,000 acres, Oregon with 23,600 acres, New
York with 21,400 acres, and Michigan with 21,500 acres (USDA 5). In 1995, the fresh market
acreage under production was estimated at 89,600 acres (USDA 4). The 1992 value of the fresh-market crop was estimated at $138 million (USDA 2). Florida accounts for about a third of the
U.S. fresh market snap bean production with most of the remainder in California, Georgia, and
Tennessee (USDA 4).
C. Domestic Use:
Approximately 80% of total U.S. dry bean production is consumed nationally (Lucier 1995b).
Over 95% of navy beans are canned as baked bean products, whereas over 80% of the pintos are
sold as a dry pack commodity. The canned pinto usually is marketed as refried beans. The
majority of kidney beans are canned in brine in both small and large institutional packs for use in
salad bars, dark red kidneys being preferred in the northern U.S. and light reds in the south.
Great northerns are canned in brine, pinks in spicy barbeque sauce, and red Mexicans in chili
sauce although a portion of all of these classes are marketed as a dry pack commodity. Dry bean
consumption has increased in the U.S. by 40% over the last fifteen years (Lucier 1995a).
The recognition that the soluble fiber (pectins) content of dry bean seed can reduce cholesterol
has been documented in clinical studies conducted by Dr. J. Anderson of the HCF Nutritional
Research Foundation, Lexington, KY. He has demonstrated that 100 g of dry beans consumed
daily lowers total cholesterol by 19% but more importantly it lowers the low density lipoproteins
by 24% while preserving the desirable high density lipoprotein fraction.
Processed snap beans are either canned (75%) or frozen (25%). Since this production is
concentrated, variety selection is decided as part of the contract based on quality and maturity
specifications. The varieties preferred for fresh market generally have more fiber in the pods
which help retain shape during shipping and marketing. A small percentage of the fresh market
types are traditional string (half runner) bean types.
D. Export Markets:
The diversity in seed size, shape, and color permits the targeting of commercial classes to
specific regional and cultural market needs overseas. Hence, an increasing share of U.S.
produced dry beans is now targeted at export markets. Currently 20% of U.S. production is
exported; red kidneys average 25%, great northerns average 33%, and 50% of the navy beans are
exported (Lucier 1995b). Cranberry types are grown exclusively for export notably in Italy.
Navy beans are marketed in the UK, great northerns in Europe and North Africa, pinto and black
beans in Mexico, Dominican Republic, Venezuela, and Brazil. Argentina is the dominant
competitor in the great northern and black bean markets whereas Chile, Canada, and Australia
compete in navy bean markets. Successful overseas marketing is directly linked to the
availability of PL480 funds directed towards beans in those countries where foreign currency is
scarce. Exports of beans to Africa are likely to increase (Parker 1995a).
E. Bean Germplasm
Genetic diversity is a prerequisite for all plant improvement programs and certain significant
germplasm sources have played a major role in bean breeding programs. The N203 source of
root rot resistance from the PI203958 line (Silbernagel and Hannan, 1992); halo blight resistance
from PI150414; the dominant Are gene for resistance to six races of anthracnose found in the
Cornell breeding line 49-242 originally from Venezuela; the inhibitor I gene, described by Ali
(1950) in Corbett Refugee, conditions hypersensitive resistance to all strains of bean common
mosaic virus; the Mexico 309 gene block and the Mexico 235 and Aurora gene for resistance to
many U.S. rust races was identified by Stavely (1984) and Stavely and Grafton (1985); and
blight resistance introgressed from the tepary bean by Honma (1956) are a few examples of
widely used germplasm sources. More recently, R. Stavely has identified new sources of rust
resistance in the Pullman PI collection. A high frequency of resistance was found among
accessions from Guatemala. PI 181954, of the Mesoamerican gene pool, is the original donor of
the bc-3 gene for resistance against all know strains of the Bean Common Mosaic Virus,
including the necrotic strains (Johnson et al. 1996).
Interestingly, novel genetic variability created using mutations has played a major role in the
alteration of growth habit in navy beans. The determinate bush variety Sanilac was the product
of a X-ray mutation breeding program while the recent architectural upright indeterminate
varieties like C-20 all have utilized the NEP-2 variety developed through a chemical mutation
program in Costa Rica (Moh, 1971).
Recent evidence for genetic resistance to weevils implicates the role of the unique seed storage
protein arcelin (Osborn, et al., 1988). First identified in wild bean relatives from Mexico,
arcelin does not exist in the cultivated Phaseolus vulgaris, suggesting that wild beans could
represent a valuable source of additional genetic diversity.
II. PRESENT GERMPLASM ACTIVITIES
Different types of molecular markers have been used to further characterize the organization of
genetic diversity in common bean. These markers include RFLPs for single copy genomic
sequences (Becerra Velásquez and Gepts 1994), RFLPs for M13-related sequences (Sonnante et
al. 1994; Stockton and Gepts 1994), RAPDs (Freyre et al. 1996), and AFLPs (Tohme et al.
1996). These studies have further clarified the relationships among various segments of the
common bean gene pool and documented the reduction in genetic diversity during its evolution.
The categorization of Phaseolus germplasm into six races within two primary centers of origin;
the Jalisco, Durango and Mesoamerican races within the Mesoamerican gene pool and Nueva
Granada, Peru, and Chilean races within the Andean gene pool, has contributed immensely to
our knowledge about the genetic diversity within the Phaseolus collection (Singh et al.,
1991a,b). This classification of the Phaseolus germplasm should enable more efficient
utilization and access of the germplasm by bean breeders and researchers. This information also
provides us with a better understanding of the genetic incompatibility factors which prevent
good general combining ability between beans from each center and in fact for many cases
results in lethality of F1 hybrid plants (Singh and Gutiérrez 1984; Gepts and Bliss 1985;
Koinange and Gepts 1992). The significance of this concept is that these and other
incompatibilities reduce the effective introgression between germplasm from each center.
Studies in a common bean pathogen, Phaeoisariopsis griseola, causal agent of angular leafspot,
has revealed a remarkably similar arrangement of genetic diversity in the pathogen and the host,
namely both show a divergence into Mesoamerican and Andean components. The Andean
strains are more compatible (i.e. more pathogenic) with the Andean hosts and vice-versa for the
Mesoamerican genotypes (Guzmán et al. 1995). Similar distributions of genetic diversity appear
to exist in the anthracnose and rust pathogens (see below).
Within the domestic market classes, kidney and cranberry beans belong to the Andean center
whereas the pinto, small red, navy, pink, black, and great northern beans are Middle American in
origin (Table 1). Recent evidence reveals that snap beans have more Andean than Mesoamerican
germplasm in their background (Weeden 1984; Gepts and Bliss 1988; Skroch and Nienhuis,
Low to medium levels of outcrossing in beans have been reported to occur in California and
Puerto Rico (Wells et al. 1988; Brunner and Beaver 1989). Outcrossing has caused delays in the
release of certain bean cultivars and will need further monitoring to confirm safe isolation
distances in order to maintain the genetic integrity of pure line increases. An important factor in
determining levels of outcrossing appears to be the type of pollinator and actual numbers of
pollinators. To date, all estimates of outcrossing in common bean have been obtained outside the
centers of origin and distribution of wild beans. It is possible that, in these centers, specific
pollinators that have coevolved with the bean plant could be responsible for higher levels of
cross-pollination than those measured outside the centers of origin.
An exhaustive list of all germplasm activities is not possible in this report. The Annual Report of
the Bean Improvement Cooperative, however, is an excellent source for identifying bean
researchers and some of their current research activities.
A. Collection: P. Gepts
Recent collection trips include the following countries and collectors: Ecuador and Bolivia --
Gepts and Debouck in 1990 and 1994, respectively (Debouck et al. 1993, Freyre et al. 1996);
Argentina -- Steadman in 1995 and 1996.
The collections by Gepts and Debouck were focused on wild Phaseolus given the dearth of these
materials in germplasm collections (for an example, see the Pullman collection below: Table 2).
Both collections led to a better understanding of the ecological distribution of the species. The
Ecuador exploration was particularly remarkable because it allowed the identification of a
"missing link" between the Mesoamerican and Andean gene pools (Debouck et al. 1993).
Subsequent DNA sequence analyses of phaseolin genes suggest that the wild P. vulgaris
populations of Ecuador and northern Peru could actually be the ancestral populations from the
entire species is derived (Kami et al. 1995).
The collections by J. Steadman in 1995 and 1996 were focused on gathering materials pertinent
to a study of coevolution between the bean host and the rust pathogen. In both years wild and
landrace materials were collected.
B. Evaluation: J. Steadman and D. Coyne
From information presented at the 1995 BIC/NDBC and the W-150 Regional Research Project
meeting as well as the most recent Bean Improvement Cooperative Annual Reports, it would
appear that the most active area of evaluation is with Andean/Middle American germplasm
comparisons. As long as research publications are the primary criteria for promotion and tenure
at public institutions and funding for this type of activity is poor, PI/germplasm testing activity
will continue to be somewhat limited, except where a researcher is looking for resistance to a
Many reports on screening for stress tolerance (including diseases and pests) involve breeding
lines and common cultivars. CIAT recently has reported on screening Phaseolus vulgaris races
for water stress and low soil fertility tolerance and anthracnose and angular leaf spot resistance.
J. R. Stavely has completed resistance testing a sampling of 3500 PIs and now has 31 with broad
resistance to about 66 races of rust. These PIs are being tested in other countries and
incorporated into US bean market class germplasm releases at present. Andean bean race
specificity has been reported for the rust pathogen while Andean/Middle American specificities
are known for both the anthracnose and angular leaf spot fungal pathogens. In particular the
research groups of Michel Dron and Claire Neema at the University of Paris XI are conducting
in-depth studies on the variability of host and anthracnose pathogens in Latin America.
New sources of germplasm from landrace/wild bean populations in Dominican Republic,
Honduras, Malawi, Bolivia and Argentina await testing in the US. These collections have been
evaluated in their country of origin for some traits and the data indicate that characteristics exist
in these materials that would benefit US breeding programs.
The evaluation of cultigens, wild species, and interspecific populations for traits useful for
enhancing dry bean germplasm continues. Miklas et al. (1994b), Miklas and Santiago (1996),
and Salgado et al. (1994) have screened tepary bean PIs for multiple disease resistance and
adaptability to different environments. The multivariate cluster analyses of cultivar (McClean et
al., 1993) and landrace (Singh et al., 1991b) P. vulgaris accessions based on agroecological,
isozyme, seed protein and/or DNA marker data are helping to identify: i) genetic bottlenecks
(Garvin and Weeden, 1994), ii) areas of extreme genetic diversity, and iii) strategies for
attempting, through wide crosses, to increase yield and other quantitatively inherited traits of
relatively low heritability (e.g., Singh and Urrea 1995; Urrea and Singh 1996).
Many of the Phaseolus accessions maintained in collections throughout the world are
photoperiod sensitive and/or have Type IV growth habits (especially those of races Jalisco and
Peru) making them nearly impossible to evaluate in temperate climates. These accessions remain
an untapped source of genetic diversity and useful traits for enhancement of temperate snap and
dry bean germplasm. A program has been initiated by USDA/ARS scientists in Mayagüez, PR
and Prosser, WA to convert photoperiod sensitive germplasm into day-length neutral phenotypes
for evaluation and use in temperate regions.
C. Enhancement: P. Miklas
Disease, pest, and abiotic stress resistance of dry and snap beans continue to be improved
through introgression of novel and distinct genetic resistance resources into adapted phenotypes.
Specifically USDA/ARS scientists like Dr. Stavely continue to actively pyramid new resistance
genes identified from PI lines with existing genes like Ur-3, Ur-4, Ur-5, and Ur-6 to combat the
variable rust pathogen (Stavely and McMillan, Jr. 1992; Stavely et al. 1992, 1994). Stavely is
currently combining resistances to other diseases like bean golden mosaic virus (BGMV),
common bacterial blight and bean common mosaic virus (BCMV) with pyramided resistance to
rust to obtain multiple disease resistant germplasm (Stavely and Silbernagel, 1993). He is
developing germplasm with specific combinations of resistances for targeted areas, for instance,
(1) rust and BGMV resistances combined in McCaslan pole beans for southeastern U.S. snap
bean production; (2) rust and common bacterial blight resistances combined in great northern,
pinto and navy dry beans for eastern Colorado and the Midwestern production states of
Nebraska, North Dakota, and Michigan; and (3) rust and BCMV resistances combined so beans
can be produced more effectively in the seed production states of Idaho and Washington were
the virus is problematic.
New small red (formerly red mexican) beans with upright architecture, good canning quality
traits, and various disease resistances have been developed by Hosfield et al. (1995). He used
recurrent and pedigree selection to capture useful traits from a wide array of tropical and
temperate dry bean germplasm. Recently, Miklas et al. (1994a) developed multiple disease
resistant dry bean germplasm from P. vulgaris x P. coccineus interspecific populations.
Freytag et al. (1982) successfully introgressed wild P. coccineus into cultivated vulgaris and
released germplasm line XR235 which conditions resistance to common blight. Active work
continues with the introgression of both wild and cultivated tepary (P. acutifolius) into cultivated
vulgaris to transfer traits as diverse as blight resistance (Scott and Michaels, 1992), drought
tolerance and reproductive fitness under high temperatures.
The extensive use of PI203958 for Fusarium root rot resistance by Burke (Silbernagel and
Hannan, 1992) resulted in the development of 11 dry bean cultivars in 3 commercial classes. The
tropical black bean A55 has been used by Dr. Silbernagel (USDA/ARS, 1994) as a novel source
of root rot resistance and I gene for enhancement of pinto bean germplasm.
Enhancement is often a slow process. PI150414 was recognized as a source of resistance to halo
blight in 1966 by Patel and Walker. This resistance is only now being incorporated into
commercially acceptable snap bean cultivars. The advent of the random amplified polymorphic
DNA (RAPD) as a genetic marker for indirect selection will undoubtedly facilitate: i)
introgression of qualitative and perhaps quantitative resistance factors, ii) development of
multiple disease resistance, and iii) building of gene pyramids for multiple resistance against a
single race of pathogen. Tightly-linked RAPD markers already exist for rust, anthracnose,
BCMV, BGMV, and common bacterial blight resistance genes and QTLs (Haley et al., 1994b;
Kelly, 1995; Miklas et al., 1993; Nodari et al., 1993). The placement of these RAPD markers
and associated genes/QTLs on integrated linkage maps (Gepts et al. 1993; Freyre et al. 1996;
Phaseolus - Vigna Genome mapping information) will enable breeders to develop strategies for
combining resistance genes in coupling phase linkage or located on different chromosomes
versus breaking (recombining) resistance genes linked in repulsion.
The works above were critically backed by the ability to identify new sources of resistance in the
current PI collection. The availability of a Phaseolus core collection should facilitate further
identification of new resistance genes from the PI collection and flag regions or pockets of
germplasm where genetic variability may exist for such traits.
D. Preservation: R. Hannan
The USDA, ARS National Plant Germplasm System (NPGS) Phaseolus collection is maintained
at the Western Regional Plant Introduction Station, Pullman, Washington. As of the end of
1996, the collection totaled nearly 13,500 accessions, 1,650 of which are listed in the W6
category and are pending decision for PI assignment (Table 2). The biggest increases in W6
numbers are among the Phaseolus species, resulting from revived accessions from the old Oliver
Norvell collection. As these are being grown, sometimes from only two to three viable seed,
they are being processed through the virus clean-up program, as well as getting some
confirmation on their taxonomic identity. A large part of the W6, Phaseolus vulgaris material
(around 600 accessions) is a collection from Eastern Europe that has not been dealt with yet, and
another 407 W6 accessions are from the Honduras collection sent to Pullman by P. Miklas. The
Honduras material will be addressed first, but there is apparently a lot of redundancy in this
collection and this is being sorted out.
Table 2. Status of the Phaseolus collection at W-6, 1996
||Total no. of
||Accessions with W6
|vulgaris var. aborigineus
|Total (28 species)
Primary efforts have been focused on accession availability and back up at NSSL. General
increases are done in 19,000 ft.2 of greenhouse space at the Pullman and Central Ferry locations.
In concert with the seed increase program, all of the Phaseolus grown goes through the virus
clean-up program to eliminate seed borne viruses from the distribution samples. Financial,
physical and human resources have been provided to expand the virus testing program to
accomplish this formidable task. Virus testing is conducted on all bean plants grown. The
protocol for this program is available upon request. Although special problems exist in
increasing some accessions of the Phaseolus collection due to photoperiod sensitivity (short day-length requirements) or necessity for insect pollinators, WRPIS has discontinued off-site
increase of this genus for all but a few species. All accessions are grown under greenhouse
conditions and if necessary, flowers are hand-tripped or hand-cross pollinated within an
accession. Discontinuation of contract seed production was deemed necessary due to the level of
outcrossing in the off-site increases.
Distribution ranges from 1300-2000 accessions per year. It is important to note that the trend
over the last few years has shown that requests for bean germplasm are much more specific and
refined. For example, recent requests have averaged only around 30 accessions per request. This
trend is attributed to the ability to identify new sources of resistance in the current PI collection.
The availability of a Phaseolus core collection should facilitate further identification of
additional resistance genes from different PIs and regions where genetic variability exists for
In 1994, a subcommittee of the Phaseolus CGC was formed to establish guidelines for an
approach to develop a core subset for the Phaseolus collection. In subsequent meetings and
communications, it was decided that we would begin Phaseolus vulgaris, and partition this large
collection into logical sub-groups that would be of a reasonable size that the core concept could
be tested. The sub-groupings consisted of the P. vulgaris collection from Mexico as one, and the
combined P. vulgaris collections from the Latin American countries of El Salvador, Guatemala,
Honduras, Nicaragua, Costa Rica, Panama, Colombia, Ecuador, Peru and Bolivia as another.
The CGC started with these two sub-groupings to test the following hypothesis: Will a stratified
logarithmic selection based on a defined set of selection criteria be more efficient than a
complete random selection in producing a subset that represents the widest range of variability
(diversity) with the fewest number of accessions? Since the best and most complete set of
morphological data for the NPGS bean collection was the seed characteristic data, the selection
criteria were: i) geographical origin, ii) seed color (primary), iii) seed pattern, and iv) seed size.
A tentative core subset has been selected for these two sub-groups. Base statistics for each are
available. Furthermore, a randomly selected core with the same number of accessions as are in
the stratified core has been selected. A list of the accessions in each of these cores is available
Outside of the NPGS, collections of breeding materials and exotic germplasm are maintained by
state, federal, and private sector plant breeders. Efforts by the collection curator continue to
locate these collections, identify unique and/or valuable genotypes, and incorporate the material
into the NPGS, especially as plant breeders retire.
E. Genetic Stocks Collection: J. Myers
The genetics stocks collection as a subset of the overall Phaseolus collection is a relatively
recent effort to preserve unique genetic material used in fundamental studies of the bean
genome. Because of the newness of this effort, relatively few marker lines are available. At
present, 25 accessions in the Plant Introduction collection are flagged as genetic stocks. These
are lines that contain well characterized genes for various traits. Most are morphological
markers that affect foliage or pods. One flower color mutant and one seed coat color stock are
included. An additional 8 chromosome translocation stocks are preserved in the collection.
Other material already exists in the collection that could be designated as genetics stocks, but
awaits thorough classification before being flagged. Sets of host differentials for distinguishing
pathotypes or near-isogenic lines and other unique germplasm could be incorporated as 'genetic
stock-like' materials and flagged accordingly.
Phaseolus Electronic Databases P. McClean
The BeanGenes Database
Recent efforts have been made to develop internet accessible database that are of interest to
researchers in the field of bean genetics and production. BeanGenes, a database dedicated to
Phaseolus and Vigna research, first went on-line in January 1995. Initial funding for the project
came from a sub-contract through Dr. Randy Shoemaker, USDA/ARS, Iowa State University.
The primary funding source was the USDA Plant Genome project.
Currently, the majority of BeanGenes data is stored in the ACeDB software application. This is
a frequently used plant genome database application. Richard Durbin (MRC, England) and Jean
Thierry-Mieg (CNRS, France) initially developed ACeDB (an acronym for A C. elegans
database) to archive information about Caenorhabditis elegans. The database runs under the
X-Windows environment on machines utilizing some flavor of a UNIX operating system. To
access the database as an X-window application, the user must login on the server. Alternatively,
a user can obtain a copy of the database and install it on a local X-Windows server. Remote
users will need to access the database from a computer running a form of X-Windows. The
database can be accessed from any personal computer or MacIntosh computer which has
The data base is populated with several classes of data. Molecular mapping data contains all of
the mapping information for the two RFLP maps developed by Vallejos et al. (1992) and Gepts
et al. (1993) and the RFLP/RAPD map of Dron and colleagues (Adam-Blondon et al. 1994).
Nevin Young, University of Minnesota, has contributed RFLP map data of mung bean (Vigna
radiata) and cowpea (V. unguiculata). Associated with each molecular map are loci and probe
data. The loci data describes the molecular location and the probes or RAPDs used to define the
locus. The probe data provides specific details about a given probe.
All of the genetic information compiled by Dr. Mark Bassett at the
University of Florida is included in the database. This collection
describes all of the genes, along with their symbols and descriptions
accepted by the bean community. This list is identical to the recently
published list [Bassett (1993) Ann. Report of Bean Imp. Coop. 36:vi].
References to each gene are included.
The pathologies of bean are described in detail. The symptoms,
causal agents, and suggested solutions are described. Known sources of
resistance and the genes that provide that resistance are described.
The taxonomy of fungal, bacterial and viral pathogen is also included.
Images of many of the pathologies provided by CIAT can also be viewed.
Data from the GenBank database was collected for all DNA and protein sequence submissions of
Phaseolus and Vigna species. References for these sequences are also included.
Information is available for many dry bean cultivars. This includes
market class, pedigree, release date and developer of each cultivar.
Resistance alleles that the cultivar is known to possess are also included.
Finally, the database lists the address of many individuals working in the field of bean research.
Accessing the ACeDB Version of BeanGenes
The BeanGenes database can be accessed in two manners. For those users with X-Windows
capability, a login on the BeanGenes server can be established. If you would like to have an
account on the BeanGenes machine contact Phil McClean at firstname.lastname@example.org.
nodak.edu and an account will be established.
The ACeDB form of BeanGenes can be searched on the Agricultural Genome WWW Server.
The National Agricultural Library Genome Informatic Group developed a WWW interface to
the ACeDB databases. To connect to the WWW version of the BeanGenes data base go to
http://probe.nalusda.gov:8300/cgi-bin/browse/beangenes. This WWW site can be accessed by
such client software as Netscape, MS Explorer and Mosaic. Once the site is reached, the
database can be navigated using standard point-and-click techniques.
The BeanGenes WWW Site
A BeanGenes WWW site is in operation. The address for the site
is: http://beangenes.cws.ndsu.nodak.edu. The data in the database is
listed under "The BeanGenes Database" section of the homepage. You can
directly link to the Agricultural Genome WWW Server by clicking on "WWW
Version of BeanGenes".
The WWW site also has two other data sets that are not found in the ACeDB-based version. A
summary of all of the variety trial data from the dry bean production regions of the United States
can be accessed by selecting the "United States Common Bean Variety Trial Data" entry. Also
included is a list of the pedigrees of many dry bean cultivars. To view this data in both a textual
and graphical format select the "Dry Bean Pedigrees" entry. Most recently, a Java program was
developed that displays the pedigrees of common bean in the traditional tree diagram.
Links to other sites related to beans are listed under the "Links to
Other Phaseolus/Vigna Sites" section. Finally, links to WWW sites
containing information relevant to growing beans can be found under the
"Bean Production Information" section.
Other Phaseolus Databases
Although BeanGenes is most significant database effort in the US,
other exist throughout the world. BeanRef is a database developed by
Mario Nenno, a graduate student in the Division of Cell Biology at the
University of Kaiserslautern in Germany. This WWW
(http://scaffold.biologie.uni-kl.de/Beanref/) site is rich in links to
on-line resources in the Phaseolus research field. The National Plant
Germplasm System (GRIN) can be searched directly on-line via the
WWW at http://www.ars-grin.gov/npgs/. This is a direct link to the
material held by the germplasm repositories.
Valuable production information is also available. Users can contract Extension Service
computers at: North Dakota State University (http://ndsuext.nodak.edu/extnews/procrop/dbn/)
for specific production information for dry bean; Colorado State University
(http://www.colostate.edu/Depts/CoopExt/PUBS/CROPS/pubcrop.html) to download bean
production guides; University of Arkansas (http://uaexsun.uaex.arknet.edu/Vegfacs/
greenbean.html) for snap bean production information; and the University of Florida
(http://hammock.ifas.ufl.edu/txt/fairs/12231) for a description of how to produce a variety of
beans used as vegetable crops.
III. STATUS OF CROP VULNERABILITY
Botanical, archaeological, and biochemical data suggests that domestication of common bean in
the Americas occurred in two distinct regions. This evidence indicates that domestication took
place as separate events in both South and Middle America a few thousand years ago (Kaplan
1994). Molecular marker analysis clearly shows that domestication has induced a strong
bottleneck in genetic diversity (Gepts et al. 1986; Sonnante et al. 1994).
Caches of bean seed from cliff dweller sites in the Southwest U.S. that date back to 1000 AD are
evidence of the spread of beans from these centers of domestication to other regions in the
Americas. Seed types of the commercial market classes in the U.S. appear to have independent
points of entry into the U.S. One via the Inter-mountain western states from Mesoamerica and
another along the eastern Atlantic coast where beans were introduced by early colonists from
South and Central America via Europe. The latter types were later moved to the Midwest by
early settlers. Medium-sized vine beans dominated the introductions from Mesoamerica, while
the smaller navy and larger kidney and garden beans were first introduced into the eastern U.S
(Gepts et al. 1988).
A. Trends in Genetic Diversity within Different Production Regions: M. Brick and J. Myers
There is a concern about genetic vulnerability of the bean crop in the U.S. and the lack of
adequate genetic diversity to meet specific eventualities. Although commercial production is
relatively isolated across a dozen geographically isolated areas, there is a potential threat from
localized genetic vulnerability within specific production regions. The tradition of growing only
one or a few market classes within a geographic region, coupled with genetic similarities among
varieties of a class increases the problem. For example, in Michigan, where navy beans
constitute approximately 70% of the acreage, five commercial cultivars dominate the market and
three of these share C-20 in the parentage. The situation in Michigan has improved in recent
years with the shift away from Seafarer and Sanilac that constituted 90% of the acreage in 1989.
In addition, black, dark red kidney, light red kidney and cranberry cultivars that possess unique
genetic backgrounds from navy have expanded to 30% of the acreage in Michigan.
In Colorado and the contiguous production zones of SW Nebraska and NW Kansas, pinto beans
are produced on over 200,000 acres. The variety mix has shifted in the past ten years to several
cultivars with Bill Z, UI 126, Othello, NW 410, and private cultivars dominating the acreage.
However, most of these cultivars share a fairly narrow genetic base from the Durango race of the
Mesoamerican gene pool. New pinto cultivars such as Sierra, Chase, Apache and others have
recently been introduced that were developed by introgression of germplasm from the
Mesoamerican race and others. The private sector has a portion of that acreage of which the
pedigrees and relationships to other varieties are not generally known.
In adjacent states like Nebraska, the situation with great northerns is similar. In 1982, cultivar
Valley occupied 60% of the acreage; currently, the private variety Beryl occupies 60 to 70% of
the 193,000 acres planted to great northerns. Since the pedigree of Beryl is unknown, its genetic
relationship to the other varieties planted is of concern as this could affect the vulnerability of
the region. Within the great northern class, there is a close relationship between cultivars
Valley, Harris, Tara, and Sapphire because of the extensive use of Neb #1 sel 27 for bacterial
In North Dakota, the diversification of navy bean cultivars has increased in the past ten years. In
1989, 90% of the 170,000 acres planted to navy beans was occupied by the single cultivar
Upland. Today, the cultivars Norstar, Upland, Schooner and Agri I occupy 26, 20, 18 and 11%
of the acreage, respectively. In the pinto market class, over 350,000 acres were harvested in
1995. The pinto cultivars Othello, Topaz, Nodak, and Fiesta encompassed 44, 22, 16 and 2% of
that acreage, respectively. This represents a change from 1989 where the private variety Topaz
occupied 65% of the 220,000 acres planted to pinto beans.
In Idaho, more than 80% of dry and snap bean seed production takes place in the southern
portion of the state for shipment throughout the U.S., Canada and globally. This means that
many different cultivars are grown within the state, and consequently, genetic variability is
likely the highest in the nation. While genetic variability is high, the concentration of the crop
leaves bean seed production vulnerable to a regional crop failure. Seed-borne diseases
introduced from elsewhere as well as natural disasters could strongly affect the supply of bean
seed. The dry climate in combination with disease quarantines limits the spread of bacterial and
fungal diseases, but the crop is susceptible to attack by seed-borne virus diseases such as BCMV
and BCMNV. However, the region has never had a regional crop failure since beans were first
produced in the early 1900s. Approximately 120,000 acres of commercial dry beans and 60,000
acres of seed beans are produced in Idaho annually. While the seed acreage is genetically
diverse, the commercial acreage relies on relatively few cultivars. Of total commercial bean
acreage grown in 1994, 52% were pintos, 19% were small reds, 17% were pinks, and 3% were
great northerns, all of which belong to race Durango. Idaho is the number one producer of small
reds and pinks, ranks second in production of great northerns, and fourth in production of pintos.
Nearly all of the small red acreage is dominated by NW 63, although a new cultivar, UI 239
appears to be increasing. For pinks, the acreage is dominated by two cultivars, Viva and UI 537,
in roughly equal proportions. The great northerns grown in Idaho are predominately UI 60, UI
425, and US 1140. Within the pinto market class, Othello, NW 410, Olathe, and Nodak
predominate. However, Bill Z and Arapaho are increasing in acreage.
In California, common bean production represented in 1995 about 25 % of the total area
(145,000 acres) grown in beans. Lima beans (baby and large) were grown on about 33%,
blackeyes on 30%, and garbanzos on 13%.
In attempting to access the vulnerability of U.S. snap beans, the problem appears less acute
initially for a number of reasons. Snap beans are a minor crop with less than a quarter of a
million acres planted across ten states. In those states with relatively high concentration of bean
acreage, Wisconsin, Oregon, Florida, Georgia, and New York, there is intercrop buffering and
dispersion of relatively small bean fields of several different cultivars. It is unlikely that
horizon-to-horizon plantings of single snap bean cultivars will occur as with wheat, corn, or
soybean production, in part due to the small acreage, but also due to the diversity in cultivars
developed specifically for the canning, frozen, and fresh market. In addition, there is a well
regulated seed production industry for snap beans and a wide geographic separation of basic seed
stocks in the arid western states from the major Midwestern and/or eastern production states.
This separation of seed stocks and commercial production greatly reduces the likelihood of
buildup of seed-borne pathogens. This system of seed production, however functional for snap
beans, has been utilized less with dry beans in Michigan and North Dakota. Furthermore, recent
molecular evidence suggests that snap beans possess much greater genetic diversity than dry
beans (Weeden 1984; Haley et al., 1994a; Skroch and Nienhuis, 1995).
Another assessment of the relative genetic vulnerability differences exhibited by snap and dry
bean cultivars is demonstrated by their respective reactions to different races of the rust fungus.
Stavely (pers. comm.) reported in 1989, that 66 bush snap bean cultivars and 15 bush wax beans
had the same reaction to rust races 38 to 70, similar to one of the original processing type snap
bean cultivars, Early Gallatin. In addition, similar reactions were exhibited by the majority of
commercial light and dark red kidney cultivars. This similarity of reaction to rust was exhibited
by many of the PI lines originated from the Andean domestication center. The host cultivar's
reaction to these races indicated greater genetic diversity in U.S. dry bean cultivars than in U.S.
snap bean cultivars. In recent years new snap and dry bean cultivars have been released that
confer resistance to races of rust in the U.S. The resistance genes utilized by cultivars released
in the past five years has been dominated by the Ur-3 allele in dry beans and Ur-4 allele in snap
Genetic diversity is usually thought of as the amount of genetic variability among individuals of
a variety, population, or species. Although genetic vulnerability may result from a reduction in
genetic variability, it is known that genetic diversity per se does not prevent vulnerability unless
that diversity includes genetic resistance to the particular pathogen or stress causing the problem.
This point is underscored by the obvious diversity in landrace beans in Malawi. Martin and
Adams (1987) described extensive phenological, morphological, and seed type variation in
landrace beans grown in the same field in Malawi, yet the overall productivity is low because of
susceptibility to diseases and seasonal fluctuations of stress factors. Breeders should strive to
increase the genetic diversity in cultivars released, but in the absence of unusual disease or
environmental stress, they tend to concentrate on crosses of elite lines and cultivars, thus
reducing genetic diversity of newly released cultivars. Lack of knowledge about the
characteristics of accessions in the collections and difficulty of transferring some of the traits
from an exotic genotype to cultivated beans restricts utilization. Furthermore, applied breeding
programs which emphasize germplasm utilization are being replaced by laboratory-oriented
programs with emphasis on DNA technology and computer modeling.
The need to pyramid multiple disease, insect, and environment stress resistances into
commercially acceptable genetic backgrounds utilized by commercial breeders and to focus
more basic research on quantitative traits like yield and population improvement strategies is
critical. The loss of public breeding programs would further increase the problems of genetic
vulnerability since the private sector does not have an orientation toward long-term population
improvement. In order to meet the challenges posed by lack of diversity, the bean industry must
rely on the in-depth genetic reserves within the genus. There are long established state and
regional breeding programs in each of the major production areas, supplying a continuous flow
of genetically improved germplasm and cultivars, with an ever-broadening genetic base in the
form of multiple disease and environmental stress resistant factors sufficient to raise and
stabilize yields. These programs must be enhanced to maintain a stable snap and dry bean
industry in the U.S.
The present system of utilizing exotic germplasm materials has been improved by the
introgression of specific pest resistance genes from different races in the Mesoamerican gene
pools. The potential for greatly expanding our genetic germplasm base in commercial cultivars,
while carrying the industry to new levels of yield, adaptation, and quality characteristics, still
exists. There is a tremendous backlog of information and enhanced genetic materials that are
only a few steps away from commercial utilization. However, to accomplish those
breakthroughs will require the utilization of new molecular techniques such as RAPDs, SCARs,
RFLPs and others to facilitate identification of novel genetic recombinations not present in
germplasm collections or cultivars. Only new administrative approaches that foster integrated
collaborative team research with adequate resources will ensure the success of these endeavors.
Furthermore, new collaborative ventures between the public and private sectors will enhance
progress in cultivar development. Perhaps the NPGS can be a catalyst to provide the resources
and organizational focus to bring together these diverse agencies to develop the protocols to
accomplish these objectives.
B. Cytoplasmic Genetic Diversity: C. Chase
In beans, chloroplast DNA variability is limited (Llaca et al. 1994), but restriction fragment
length polymorphisms (RFLPs) were detected among four varieties (Mecosta, Tuscoloa,
Swedish Brown and Swan Valley) when DNAs were fractionated by polyacrylamide gel
electrophoresis (Lee, 1988).
Mitochondrial DNA RFLPs are more readily detected than chloroplast DNA RFLPs. This is due
in part to the structural complexity of plant mitochondrial genomes (reviewed by Mackenzie et
al., 1995). These complex multipartite genomes are subject to rearrangements and changes in the
stoichiometry of the various genome components. Mitochondrial genome alterations can be
influenced by nuclear genes, and mitochondrial genome variation therefore reflects, at least in
part, variation in the nuclear genome.
Khairallah et al. (1990) examined the mitochondrial genomes of 20 Malawian land races and 3
cultivars of P. vulgaris. This work identified 5 RFLPs, which divided the entries according to
the Andean and Mesoamerican gene pools. Mitochondrial genomes of wild Phaseolus vulgaris
accessions were more variable, as 20 RFLPs were identified among 6 accessions (Khairallah et
al., 1992). Accessions from the Southern Andes were distinguished from those originating in the
Northern Andes and Mesoamerica.
Sterility-inducing cytoplasms have been identified in P. vulgaris, P. coccineus, and P.
polyanthus (Hervieu et al., 1993). Surprisingly, all sterility-inducing cytoplasms characterized to
date possess the same mitochondrial-encoded sterility determinant (designated pvs) (Hervieu et
al., 1993). An examination of the overall mitochondrial genome diversity among normal and
sterility inducing cytoplasms of these species revealed a number of RFLPs. Overall, the
mitochondrial RFLPs indicated the CMS and normal P. coccineus cytoplasms were more closely
related than the CMS P. coccineus and CMS P. vulgaris cytoplasms, suggesting the sterility
determinant predated the divergence of P. vulgaris and P. coccineus (Hervieu et al., 1994).
Cytoplasms analyzed in this study were crossed into a common nuclear background, so the
influence of nuclear genome upon mitochondrial genome organization
The pvs determinant was also identified in wild P. vulgaris and P. coccineus accessions.
Male-fertility in a number of the P. vulgaris accessions carrying this determinant suggests the
presence of nuclear fertility restoration systems in these materials. The relationship of these
fertility restorers to the two restoration systems already identified (Mackenzie et al., 1988;
Mackenzie, 1991) will be of considerable interest.
IV. GERMPLASM NEEDS
A. Collection: P. Gepts
Additional collection in the South Andean Center is justified by the presence of many phaseolin
types (Gepts, et al., 1986) indicating wider diversity than in any other center. The A and H
phaseolins are represented in seed banks by only 1 and 4 accessions, respectively; it is unlikely
that these types are represented by so few genotypes in nature while the other S, T, and C types
are present in thousands of accessions.
Collection priorities for P. vulgaris in the American centers of diversification should be for
landraces from central and southern Peru and Bolivia. The wild ancestral forms should be
collected everywhere, but mainly in Central America. These could be used directly in bean
breeding, but wild collections will also serve as geographical markers for thousands of seed
accessions which lack any passport data. Debouck (1988) states that the plotting of all
accessions available suggests that more collections of the wild form could be advantageously
carried out in (modified following collections in 1990 and 1994 by Debouck and Gepts - see
Debouck et al. (1993) and Freyre et al. 1996)):
Mexico: in the mountainous range north of Guadalajara, east of Sinaloa, the mountainous range
around the Balsas, the Sierra Madre Oriental, the States of Oaxaca and Chiapas.
Guatemala: everywhere in the mountainous areas.
Honduras: everywhere in the mountainous areas.
Nicaragua: in the region of Estelí.
Costa Rica: in the meseta Central.
Panama: in the Chiriquí Province.
Colombia: Santander, Huila.
Peru: everywhere in inter-Andean valleys with the exception of places previously visited by
Debouck and co-workers in Cajamarca, Junin, and Apurimac.
Argentina: more materials could be collected in Catamarca, Cordoba, and San Luis.
Documentation about sites is excellent thanks to the explorations of Burkhart, Brücher, and
Countries such as Colombia and Costa Rica, which have a high degree of germplasm exchange,
would benefit from a link between germplasm explorations with biochemical analysis (e.g.,
phaseolin studies) in order to develop more appropriate sampling strategies. The same statement
seems also valid for secondary centers of diversity in the Caribbean. Specific germplasm
explorations in limited geographical areas such as Peru have revealed that the germplasm
represented in the collection was not representative and that it could be increased over 400%
after more careful field work. Rapid economic changes (e.g., globalization of trade), continued
high population growth, unsustainable agricultural practices, and destruction of natural
vegetation throughout the Americas, suggest high priority should be given to continued
collection of both wild forms and landraces. Beside the fact that more field work is still needed
for the wild ancestral forms of all four cultigens and for the species which are still unrepresented
in seed banks, evaluation and crossability studies can now begin. Such studies can now be done
on half of the genus and should benefit further from information fed back from collection
Some concern for loss of germplasm exists in eastern Africa with the current focus by both
CIAT and CRSP on germplasm enhancement and the introduction of improved lines into that
region. The input of new materials will most certainly put into jeopardy the current landrace
variability that exists in the cultivated Phaseolus species within the entire region. The potential
to market specific seed types and classes further risks the loss of native germplasm. Molecular
analyses, however, reveal few if any new variants among beans from secondary centers of
diversity compared to the diversity in the centers of origin (e.g., Gepts and Bliss 1988). This
observation suggests that evolution for 400 years in isolation from the centers of origin has
generated little new diversity although new recombinants and changes in gene frequency have
been observed. Collections in secondary centers of diversity should therefore be given lower
priority from the standpoint of the U.S. (Local collections should, however, be established
because they would include local materials that have reasonably good adaptation and reflect the
local agronomic and culinary preferences.)
Since progress in bean breeding has frequently been erratic and not decisive, the absence of
major breakthroughs may be linked to the very narrow variability of the progenitors, often
selected within the same gene pool or race. Biochemical studies have demonstrated that the wild
common beans are much richer in genetic diversity than their cultivated relatives (Gepts et al.
1986; Koenig et al. 1990; Sonnante et al. 1994), where the obvious diversity in seed colors and
types may result from very few genes. Further collecting should be oriented towards preserving
all variation for its potential benefits to humanity.
B. Evaluation: J. Steadman and D. Coyne
Scientists will be more likely to screen a subsample of the 13,000 Phaseolus accessions for traits
such as pest or pathogen resistance than the entire collection or a series of numbers. With the
core project underway, a representative sample of the core needs to be selected and then
evaluated at least for reaction to certain diseases. White mold, rust, web blight, root rot, bean
common mosaic, bacterial brown spot and Fusarium wilt (yellows) are important diseases where
finding improved resistance would benefit our bean industry. However, core collections may
not be valuable where resistance to a particular pathogen or pest, or some other particular trait is
expected to occur at a very low frequency. Core collections will be particularly useful where it
is desired to improve the level of a particular trait and where considerable diversity exists in the
collection. In addition any associations between resistances to different diseases and/or other
traits would be beneficial to know. Testing a core subsample would be a high priority for
germplasm evaluation under many circumstances.
C. Enhancement: P. Miklas and P. Gepts
After germplasm has been evaluated, the potentially useful characteristics need to be transferred
into a phenotype useful to private and public cultivar development programs. This often entails
years of hybridization, screening, and recurrent selection to put the new character into an
adapted background, essentially one or several crosses from a finished variety. Public
researchers are not likely to undertake this kind of long-term work because it does not lead to
frequent original publications which are the major basis for promotion. General genetic linkage
maps and genetic markers for specific qualitative and quantitative traits and other
biotechnological activities will likely continue to contribute to germplasm evaluation and
enhancement, and in increasing genetic diversity in Phaseolus, but they constantly need to be
integrated with traditional breeding programs.
Wild vulgaris and the related cultigens, P. acutifolius and P. coccineus, still remain an
relatively untapped novel source of useful traits for dry and snap bean improvement. The
usefulness of interspecific populations could be maximized by screening them against many
different biotic and abiotic stresses. This would be best accomplished by circulating the
interspecific materials among many programs for screening in different environments. The
potential of converting tropical photoperiod sensitive dry beans into day neutral lines for
evaluation and utilization in temperate environments for contributing to genetic diversity should
continue to be examined. A similar program in sorghum has generated genetic diversity and
provided novel resistance genes and traits for US breeding programs. The larger-seeded kidney
and cranberry beans would especially benefit from increased genetic diversity as yields have
stayed the same in these market classes the past 10 to 20 years.
The relative dearth of diversity within commercial classes and cultivated races of common bean
are leading bean breeders and geneticists to explore the usefulness of crosses between more
distantly related crosses (e.g., Beaver and Kelly 1994, Singh et al. 1992a,b) and to identify
natural examples of introgression between the Mesoamerican and Andean gene pools (Paredes
and Gepts 1994) or between wild and cultivated beans (Singh et al. 1991b; Freyre et al. 1995;
Beebe et al. 1997). Additional genetic diversity and a better understanding of the transfer of
quantitative traits across wider crosses in the cultivated gene pool of common bean can be
exoected from these studies.
D. Preservation: R. Hannan
Continued efforts need to be made to reduce duplication in the collection. Careful scrutiny of
the passport information needs to be made. With the recent molecular technologies, parameters
need to be established whereby the curator can refer duplicate accessions to one active accession
and then eliminate the duplicate from the active collection. This could conceivably impact the
long term efforts of seed regeneration.
Even though greenhouse seed increase has been successful for the majority of Phaseolus species
in the collection, there are species that need to be grown in short day tropical sites. A site such
as the Molokai, Hawaii, NRCS, Plant Materials Center needs to be identified and established for
some of these very special increase needs. This can be incorporated into an NPGS-wide
tropical, short-day increase program.
E. Genetic Stocks Collection: J. Myers
Over 100 genes for morphological traits, disease resistances, and isozyme markers have been
described and published (Bassett, 1993). As detailed above, only 25 genetic marker accessions
are publicly available from the PI collection. Many of marker lines may be lost, particularly
those described in the older papers. As an example, much of the genetic analysis of common
bean was done by H. Lamprecht from the early 1930's to the early 1960's. Upon his death, his
extensive collection of genetic stocks was neglected for many years before seed was obtained by
the Plant Introduction Station. As a result, a number of lines in this collection are now extinct
along with the traits that they carry. Even with marker lines used in more contemporary studies,
there has not been a concerted effort to place these in the PI collection.
Efforts should be made to increase seed without mixtures of all lines in the collection, and some
effort is needed to reduce the amount of duplication in the collection. This is generally true for
beans except for the more recent introductions, but is not true for some other species.
F. Phaseolus Electronic Databases P. McClean
The initial funding for the BeanGenes database has all been spent. We know have in place the
hardware and software to maintain a reasonable size database available to the bean community.
The majority of the basic information has been deposited and is available to all with electronic
access to the internet. Without additional funding, all of the additional efforts will be on a
volunteer basis by Phil McClean.
The database will continue to populated with variety trail data as it
is made available to the curator. The gene symbols will be updated as
that information is made available by the Genetics Committee. The last
major effort will be the conversion of all of the Cooperative Dry
Bean Nursery data in WWW table format, and the development of a search
engine to look at that data in a systematic manner.
Any other BeanGenes efforts would require additional funding. One
data source that has not been tapped to any significant extent is the
information at CIAT. The development of a systematic method of searching
their databases would certainly contribute significantly to the
knowledge needed by US plant breeders to use the CIAT material as
germplasm resource. As the use of molecular markers becomes a tool at the
applied level, access to digital representations of informative
polymorphisms becomes more pressing. Funds to support archiving that
information from all researchers is also necessary. Previous discussion
about the need to develop core collection is very valid. If such an
effort is instituted, archiving that information will be essential.
BeanGenes would certainly be one vehicle to organize and distribute that
information to the breeding community.
In general, there has been an emphasis on projects relating to evaluation of the P.I. collection for
commercially important characteristics and on enhancement. Projects should show substantial
results or be complete within 1 to 3 years, with options for renewed support for that period. Past
annual levels of funding have been around $20,000. In the past, rust screening and development
of a marker gene collection in a related genetic background for seed coat color, have been
funded. (BCMV cleanup is now part of the Western Regional Station budget.) The other
projects would be new.
1. Proposal for the establishment of a core collection representing 10% of the base collection to
facilitate germplasm evaluation. A strategy for the development of a Phaseolus core collection
is being formulated by a subcommittee of the Phaseolus CGC. A proposal for validating and
comparing the amount of genetic diversity of the base collection represented by different core-sampling techniques using RAPD markers.
2. Many researchers have expressed interest in evaluating the core collection, once established
and readily available, for different traits including heat tolerance, white mold resistance, root rot
resistance, and bean golden mosaic virus resistance among others. Compiling multiple data on
the same core would probably be the most beneficial in the long term. The problem in
evaluating accessions assigned to the core that are photoperiod sensitive and have Type IV long
vining growth habits needs to be addressed. Perhaps these accessions could be converted to day-neutral non-Type-IV plants.
3. Screening wild Phaseolus vulgaris for resistance to BCMV, and other traits has been
proposed. A core collection of this material could be flagged in the PI collection, also, to
4. Methods to efficiently introgress quantitative genetic variability (e.g., yield) from wild,
ancestral beans need to be developed.
5. Competitive Grants program for Genetic Resources: Long term advances in the safeguard
and utilization of genetic resources will depend on more reliable, long-term funding. This could
be modeled after the Plant Genome section of the NRI. Alternatively, more innovative funding
schemes could be developed that represent a partnership between the public and private sector.
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USDA 3: gopher://usda.mannlib.cornell.edu:70/00/data-sets/crops/9X180/96180/3/fieldcrp.txt
USDA 4: gopher://usda.mannlib.cornell.edu:70/00/data-sets/crops/9X180/96180/3/vegtbles.txt
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