and the same elevators purchase back the production at harvest at either contracted or free market prices.
BREEDING FOR SPECIFIC TRAITS
Breeding for yield
For a complete description of approaches used to improve yield in beans, the reader is referred to the review by Kelly (2018). Many genetic studies in the literature focus on specific traits by necessity as they present important information for breeders on genetic inheritance, heritability, location, and effect of QTL. However, bean breeders must combine multiple economic traits into a single successful variety with a combination of favorable traits with few minor deficiencies. When selection is practiced for individual traits, invariably other traits are affected, and unless selection is practiced to maintain them at optimum levels, they will tend to diminish. In the 1970s, the breeding program at Michigan broadened the genetic base of navy beans by crossing with black beans from Central America (Adams 1982). The resulting progeny were higher yielding with favorable upright architecture, but they lacked satisfactory canning quality present in the older navy bean varieties (Hosfield and Uebersax 1980). Correcting this problem required another series of crosses to reintroduce favorable canning quality traits. In order to maintain stability in most traits, a three‐tiered breeding pyramid (Figure 2.5, Kelly et al. 1998) based on the level of genetic variability available to the breeder was proposed as the most effective and flexible method to enhance yield in beans. Different breeding methods were proposed, depending on whether a private breeder was only crossing elite lines from the same market class, in contrast to a public sector USDA breeder working to enhance germplasm using wide genetic crosses, whereby the goal might not be an actual commercial variety.
Fig. 2.5. Breeding pyramid. A three‐tiered approach to breeding for yield in common bean.
Source: Kelly et al. (1998).
The choice of breeding systems is dictated by contrasting goals as well as the type of germplasm and the traits being improved. Having flexibility to change methods is critical due to the unpredictability of genetic recombination in certain crosses. Over the years, many breeders have identified specific genotypes/varieties not only as specific donor of economic traits but as good general combiners (i.e., they generally produce useful progeny). Other varieties that may be high yielding may prove to be poor general combiners, producing an array of mediocre progeny regardless of the other parents used in the cross. This information is only accumulated after years of experience of making crosses and from sharing similar information with breeder colleagues.
Disease resistance
Beans are attacked by a wide array of bacterial, fungal, and viral pathogens. Bean‐breeding programs that ignore disease resistance do so at their own peril, as many high‐yielding varieties are lost due to susceptibility to diseases. Most programs focus on the few major pathogens that are problematic in their local production areas, but some seed‐borne diseases such as Bean common mosaic virus (BCMV) are a universal problem, so all new varieties, regardless of production region, need to possess resistance. Rather than list all the pathogens that attack beans, and potential sources of resistance, the authors refer the reader to a few recent reviews on the subject (Miklas et al. 2006; Terán et al. 2009; Singh and Schwartz 2010). Two major types of disease resistance exist in beans and are broadly categorized into major single gene or qualitative resistance in contrast to partial resistance that is quantitatively inherited. Resistance to the highly specialized pathogens – such as bean anthracnose, bean rust, and BCMV – are controlled by major genes, whereas resistance to those pathogens such as Sclerotinia white mold that attack a broad array of crops is more complex. Breeders have identified many single‐resistance genes that control specific races (strains) of bean anthracnose (Kelly and Vallejo 2004), bean rust (Liebenberg and Pretorius 2010), and BCMV (Kelly et al. 2003). Molecular markers linked to these major genes have been developed that facilitate the pyramiding of multiple genes for resistance in single varieties as a way of increasing the durability (shelf life) of the resistance genes (Miklas et al. 2006; Kelly and Bornowski 2018). Recent progress has been made in identifying the actual proteins underpinning some of the resistance genes. For example, a truncated CRINKLY4 kinase conditions anthracnose resistance at the Co‐1 locus (Richard et al. 2021) and a mutated eIF4E translation initiation factor underlies the bc‐3 recessive gene for resistance to BCMV (Naderpour et al. 2010). These highly specialized pathogens have the ability to mutate and evolve new strains that overcome individual resistance genes, so breeders need to be vigilant for changes in pathogen virulence in order to deploy effective resistance genes in future varieties.
Resistance to those pathogens that cause root rots, white mold, and common bacterial blight (CBB) is only partial and is usually under large environmental effects. The partial resistance is quantitative in nature and QTL analysis is used to measure the size (effect) and chromosomal location of each locus that contributes to the overall resistance (Vasconcellos et al. 2017). Complete resistance is not possible to achieve, as many environmentally sensitive QTL contribute to resistance, and a large number of QTL need to be accumulated to provide effective resistance. Limited progress in breeding for resistance to these diseases has been reported, with the exception of CBB (Singh and Miklas 2015), where QTL with major effects have been identified (Viteri et al. 2014) and combined to achieve high levels of CBB resistance. The transfer of two major QTL from tepary to common bean is a major success story for interspecific hybridization using embryo rescue methods (Thomas and Waines 1984). The two major QTL exhibit recessive epistasis, and when combined confer a high level of resistance to CBB in common bean (Vandemark et al. 2008). A combination of single gene resistance to individual races (Miklas et al. 2014) with QTL conferring resistance to most races (Tock et al. 2017) has been used to breed for resistance to halo bacterial blight.
Abiotic stress tolerance
Breeding for improved tolerance to drought, heat, and low soil fertility have been the focus of breeding programs targeting abiotic stress tolerance. However, with increasing flooding and wet soil problems in the Upper Midwest during the spring and early summer months adversely affecting bean plantings and stands, an effort was made to search for genetic tolerance to flooding. Genotypes with improved tolerance to flooding were found in both Meso American (MA) and Andean (A) backgrounds (Soltani et al. 2018).
Two of the most flooding‐tolerant Andean beans were PR9920‐171 and one of its parents Indeterminate Jamaica Red (IJR) landrace, and the tolerance, in part, was attributable to physical seed dormancy conditioned by a pectin acetylesterase 8 candidate gene (Soltani et al. 2021). Interestingly, IJR is also a major source of heat tolerance that was used to develop heat‐tolerant kidney beans (Porch et al. 2010). Due to increasing heat‐ and drought‐related stresses resulting from climate change, there has been renewed emphasis in breeding for abiotic stress tolerance using wild germplasm resources (Porch et al. 2013). To screen for abiotic stress tolerance in bean, yield response in field trials with reduced inputs are used. Similarly, yield for the same set of breeding lines are grown under optimum inputs. Yield under stress and nonstress is then combined in a geometric mean analysis to identify the best performing lines across both sets of conditions. The bean breeders in Prosser, WA, have used a purgatory plot since 1960 to impose multiple stresses (drought, low soil fertility, compacted soils, high incidence of root rot, and short rotations) in the screening of breeding lines for abiotic stress tolerance using yield as the selection criteria. Only lines that yield well in the purgatory plot and in the yield trials with optimum inputs are advanced in the breeding program. Other breeders use similar stress plots to screen breeding materials for tolerance to low soil nitrogen or phosphorus levels and for drought tolerance by limiting water to simulate intermittent or terminal drought conditions. Tolerance