**2. Genetic resources**

#### **2.1. Center of origin and domestication of common bean**

Beans belong to the Fabaceae family (Leguminosae, Papilionoidae) and genus *Phaseolus*. About 55 species of *Phaseolus* are described but only five are cultivated: *P. vulgaris*, *P. acutifolius*, *P. lunatus*, *P. polyanthus*, and *P. coccineus* [8].

*P. vulgaris* is naturally distributed in a wide area from northern Mexico to northeastern Argentina. High morphological diversity has been found among wild populations of *P.* *vulgaris* from one to the other extreme of the geographical distribution of the species [9, 10]. This variability is observed in different leaf shapes, growth habits, flower colors but especially for seeds in terms of colors, shapes, and sizes [10]. This variability has also been observed at the molecular level, with several molecular marker studies such as with microsatellites [11– 15], AFLP [14–16], and SNPs [17–20].

Several of these studies recognized two major ecogeographical gene pools of wild beans: Mesoamerican and Andean. However, the geographic structure of the wilds reveals more complexity, with an additional third pool between Peru and Ecuador, characterized by a particular storage seed protein, phaseoline type I [21, 22]. Further examinations showed wild populations from Colombia to be intermediates. A marked geographic structure in popula‐ tions from the Mesoamerican pool has also been described [23, 24]. Originally, the population from northern Peru and Ecuador was considered an ancestral population from which *P. vulgaris* originated. From this core location, beans probably were spread north and south, resulting in the Mesoamerican and Andean pools, respectively [22, 25, 26].

Nevertheless, based on several studies [27–29], there has been a discussion over an alternative and older hypothesis which considers that ancestral beans were distributed through Mesoa‐ merica. The high genetic diversity encountered within these gene pools has been used to support this hypothesis. Furthermore, the Mesoamerican origin of the common bean has been suggested based on sequence analysis of data from five small gene fragments [32]. A wholegenome comparison among 30 individuals from each Mesoamerican and Andean wild populations showed high genetic differentiation among gene pools and, a demographic inference for the Andean gene pools, suggested it was derived from a Mesoamerican popula‐ tion with only a few thousands of individuals [20]. Nevertheless, the debate on the origin of the species remains and more studies are on their way to better understand the core center of origin of common bean.

Likewise, the domestication process of *P. vulgaris* has been another matter of debate and extensive molecular studies. Initially, morphological and enzyme profiles showed the existence of two major centers of bean domestication: Mesoamerica and Andean, encompass‐ ing six races [10]. There are indications that nearly 8,000 years ago common bean was inde‐ pendently domesticated in Mexico and South America [30–33]. Domestication was followed by local adaptations resulting in landraces with different characteristics [20]. However, much more has yet to be deciphered and the recent application of genomic approaches is promising to a better understanding of the domestication processes of common bean and other crops [34].

#### **2.2. Core collections**

beans are considered nutritionally rich and when consumed as part of the diet can lead to an increase in the use of maize and rice proteins since their amino acids are complementary [2]. They are also a good non-meat source of iron, providing 23–30% of the daily recommended

In Latin America, Africa, and Asia, common bean is primarily a small farmer crop cultivated with few purchased inputs and is subject to a large amount of biological, edaphic, and climatic issues [2–4]. Conditions under which common beans are regularly cultivated in this regions are extremely variable [3], and such factors coupled with the highly specific local preferences for seed characteristics (size, shape, color) have been challenging to establishing the breeding

Beans from these regions usually present low yielding [2], since they are frequently cultivated employing low to non-mechanized irrigation systems. Common bean is mostly grown in drought-prone areas, and long-term drought exposure periods seems to be a global and endemic threat affecting the majority of the production areas [4]. It has been observed that common bean is particularly susceptible to drought especially during the flowering and grainfilling stages (R5 and R8, respectively) [5, 6]. Moderate levels of water deficit usually lead to a reduction in plant biomass, lower seed number per pods, earlier maturation, lower seed yield

Not only abiotic factors but also several biotic constraints represent a significant threat to common bean cultivation. Fungi, bacteria, viruses, and nematodes cause a series of diseases, concurring for the death of some plants or even significant areas from whole plantations, causing a severe reduction in yield. Examples of such diseases are rust, white mold, anthrac‐ nose, root rots, bacterial blights (halo, yellow, common), powdery mildew, mosaic viruses, etc. Environmental conditions (temperature, soil moisture) and management practices (varieties, crop rotation, irrigation, and chemical control) may prevent the establishment of some diseases and reduce losses, but for some of them the most appropriate strategy for controlling consists

This chapter is especially driven to describe the most recent developments in the understand‐ ing of the molecular mechanisms involved in drought tolerance and anthracnose resistance. In that purpose, we outline important genetic resources of *Phaseolus vulgaris*, as well as the

Beans belong to the Fabaceae family (Leguminosae, Papilionoidae) and genus *Phaseolus*. About 55 species of *Phaseolus* are described but only five are cultivated: *P. vulgaris*, *P. acutifolius*, *P.*

*P. vulgaris* is naturally distributed in a wide area from northern Mexico to northeastern Argentina. High morphological diversity has been found among wild populations of *P.*

levels of this element in a regular adult diet [2–3].

122 Abiotic and Biotic Stress in Plants - Recent Advances and Future Perspectives

strategies in accordance with what is needed.

and weight, and reduction in nitrogen fixation [7].

on the development of resistant varieties and high-quality seeds.

technologies and methods used toward these findings.

**2.1. Center of origin and domestication of common bean**

*lunatus*, *P. polyanthus*, and *P. coccineus* [8].

**2. Genetic resources**

The high diversity of common bean has been collected in germplasm banks in which those are not only kept but also constantly improved, generating new genetic materials by adding new combinations obtained through many crosses and new generated populations. Several bean germplasm collections are available, but some of the core collections that must be highlighted here are held at the Centro Internacional de Agricultura Tropical (CIAT), in Cali, Colombia. Information on every wild and domesticated beans from this collection may be obtained in the website http://isa.ciat.cgiar.org/urg/main.do?language=en. Another core collection is from the United States Department of Agriculture (USDA), found on http://iapreview.ars.usda.gov. Brazil has held a very significant collection of landraces and domesticated beans at EMBRAPA Arroz e Feijão and also at the Agronomic Institute of Campinas, which has been developing several new commercial varieties (http://www.iac.sp.gov.br/areasdepesquisa/graos/ feijao.php). Much more details about bean collections are found on Genesys (https:// www.genesys-pgr.org/welcome), a portal to information about Plant Genetic Resources for Food and Agriculture, describing many bean accessions and the places where they are kept. These collections comprise a very rich source of genetic materials that possess several features to be exploited in functional genomic and molecular breeding studies for the species. Among the genetic resources available are wild beans, landraces, breeding lines, recombinant inbred populations, all distinguished between the Andean and Mesoamerican gene pools.

#### **2.3.** *Phaseolus vulgaris* **– The genome**

A recent publication showed the work that has been done for many years to sequence the genome of the common bean, whose assembly has been made public by a consortium between the USDA-NIFA project "A sequence map of the common bean genome for bean improve‐ ment" and DOE-JGI and ARRA (Phaseolus vulgaris v1.0 – http://phytozome.jgi.doe.gov/). In total, 472.5 Mb of the 587-Mb genome were assembled and 98% of the sequence were geneti‐ cally anchored on the 11 chromosomes, using a SNP high-density map (7,015 markers) genotyped in the RIL (recombinant inbred lines) population derived from the cross Stampede × Red Hawk and another map with 261 SSRs and a set of Infinium markers. The 472.5 Mb were arranged in 41,391 contigs (~9.32% gap) and the annotation revealed 27,197 total proteincoding genes and 31,638 protein-coding transcripts, resulting in 4,441 total alternatively spliced transcripts [23]. The publication of this genome opened a series of new resources for developing research in many fields such as the mechanisms involved in biotic and abiotic stresses in common bean.
