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Common bean originated from central Mexico (Bitocchi et al. 2012). From that region, wild P. vulgaris moved north and south and can be found today from northern Argentina to Chihuahua in northern Mexico (Ariani et al. 2018). There were more domestication events in the Mesoamerican than Andean gene region, which may explain the narrower genetic variation within the Andean gene pool observed in many genetic studies. The two gene pools of common beans have been clearly defined based on morphological, biochemical, and molecular characterization (Gepts 1988). One of the most noticeable differences is the larger seed sizes found in Andean gene pool in contrast to members of the Middle American gene pool. Interestingly, similar seed size differences are observed between the Andean (large‐seeded) and Middle American (smaller‐seeded) gene pools for lima bean. A further classification of gene pools of common bean into six races based on agronomic and adaptive characteristics was proposed by Singh et al. (1991). A fourth race, named Guatemala, was added as the climbing beans from Chiapas, Mexico, are unique from the three other MA races (Beebe et al. 2000). Beans also differ in plant growth habit, ranging from determinate types to climbing pole beans that require support.

Singh (1982) classified beans into four types that differ in growth habit (Table 2.2). The typical type‐I determinate bush bean does not produce a vine and vegetative growth ceases at flowering. Most large‐seeded kidney and green beans are determinate. The other three types have an indeterminate growth habit and differ in vine extension. Type‐II is an upright short vine habit similar to soybean that is best suited to direct harvest. Type III is a decumbent long vine habit best suited to semiarid production areas where harvest loss due to wet weather is rare. Type‐IV is the climbing bean that is not grown commercially in the US other than as pole beans in gardens, but is widely grown in many parts of Latin America or East Africa, where they are supported on either trellises, or poles or grown in association with corn.

Table 2.2. Gene pools, races, and growth habits of US dry bean market classes.

Gene pool	Race	Growth habit	US market class
Andean:	Nueva Granada	Determinate Type I	Kidney
Bush cranberry
Chile	Indeterminate Type III	Vine cranberry
Peru	Determinate Type I	Yellow, Mayacoba
Middle American:	Mesoamerican	Indeterminate Type II	Black
Indeterminate Type II & Determinate Type I	Navy
Durango	Indeterminate Type II & III	Pinto
Great northern
Jalisco	Indeterminate Type II & III	Small red
Pink
Guatemala	Climbers Type IV	Red and blacks – Mexico, Central American only

Bean germplasm collections include contemporary and heirloom varieties, landraces, exotic plant introductions from foreign countries, and wild accessions of P. vulgaris (Acosta et al. 2007). These collections provide the greatest genetic potential for future improvements essential in breeding programs. Germplasm collections are maintained by the Plant Germplasm System in the US (17,653 Phaseolus accessions) and in germplasm banks at CIAT (37,938 accessions) and in countries where beans originated, were domesticated, and are grown.

To enhance beans, breeders need free access to a wide array of bean germplasm, but with the current climate of protectionism and intellectual property (IP) rights, that free exchange of germplasm has been severely curtailed in recent years. Not only have IP rights restricted free and liberal exchange of bean germplasm but the same rules contributed to a recent example of plant piracy. The system of plant patents and plant variety protection in the US was used effectively to protect a yellow bean variety from Mexico. The yellow bean variety “Enola” was successfully protected by both plant (no. 5894079) and plant variety protection (no. 9700027) patents. Using DNA analysis, Pallottini et al. (2004) proved that Enola was identical to the Azufrado Peruano 87 variety developed and released in Mexico in 1987. The AP87 variety had simply been transported to the US and was claimed to be unique because yellow beans were a new market class in the US. The patent was successfully challenged in court by CIAT for the Commission of Genetic Resources for the Food and Agriculture Organization (FAO) as a clear example of plant piracy. Before being refuted, the plant patent had the potential to jeopardize the entire system of free exchange of bean germplasm and its use in future breeding efforts to improve bean varieties for the public good. This issue opened a new discussion on the ownership of plant germplasm and the role of IP rights in controlling its use (Gepts 2004).

Within dry beans, the small‐ and medium‐seeded markets – including black, navy, pinto, great northern, pink, and small red beans – belong in the MA gene pool. The large‐seeded kidney, cranberry, and yellow beans are Andean in origin. These gene pools are so distinct that in crosses they produce semi‐lethal progeny, suggesting a genetic separation equivalent to subspecies classification. Dwarf lethal DL₁ genes found in the root of MA beans are not compatible with the DL₂ gene functional in the shoots of Andean germplasm. Crosses between gene pools produce a weak semi‐lethal F₁ intergene pool hybrid that severely restricts free gene exchange (Hannah et al. 2007). Breeders have successfully transferred single genes between gene pools, and the beneficial genetic contrast between gene pools has been a useful strategy in controlling pathogens adapted to a specific gene pool (Kelly and Miklas 1998). The greatest challenge for breeders is to use the diversity in one gene pool to enhance the other (Singh 1995). This has proved difficult for complex traits due to a lack of recombination between the gene pools (Kornegay et al. 1992).

Attempting to transfer yield potential from black beans to enhance yield of kidney beans was met with limited success, as a determining factor in bean breeding is seed size that corresponds with market class (Kelly et al. 1998). Kidney beans with one of the largest seed sizes (60g/100 seed) are generally lower yielding than small‐seeded black beans (20 g/100 seeds). In addition to genetic differences, each gene pool utilizes different physiological mechanisms to produce yield. Adams (1967) demonstrated the concept of yield component compensation in dry beans, where gain in one yield component was generally reflected by losses in another. Thus, selection for large seed size will result in either fewer pods per plant or fewer seeds per pod, either of which contributes to less yield. Limited genomic recombination is another factor limiting the exchange of genetic diversity between the gene pools. Segregation distortion is common in inter‐gene pool crosses (Blair et al. 2003) and the existence of incompatibility genes that result in gamete elimination in the species have also been suggested (Checa and Blair 2008). As a result of these gene pool incompatibilities, little progress has been made in the breeding of Andean type beans. Only modest gains in performance have been reported over years of breeding kidney and cranberry bean classes in the US. This lack of success has resulted in decreased acreage being planted to kidney and cranberry beans in the US. Likewise, the dominant bean class in Brazil is the MA carioca bean that was introduced in the late 1940s and has replaced the traditional large‐seeded Andean Jalo seed types. There is some optimism that new molecular tools and technologies might provide opportunities to correct this limitation in breeding Andean beans. Expanded crossing with landraces within the gene pools is a recommended strategy (Gioia et al. 2019) to increase genetic diversity that is being implemented (Cichy et al. 2015) for Andean beans. An alternative approach is to use the wild species with its “hidden” genetic potential rather than trying to focus on recombination within or between species where these gene pool incompatibilities exist.