Genetic Resources (2021), 2 (4), 21–43 REVIEW DOI: 10.46265/genresj.WJEU8358 https://www.genresj.org ISSN: 2708-3764 History and impact of a bean (Phaseolus spp., Leguminosae, Phaseoleae) collection Daniel G Debouck *, Marcela Santaella and Lúıs Guillermo Santos Genetic Resources Program, Alliance of Bioversity International and International Center for Tropical Agriculture (CIAT), Km 17 recta Cali-Palmira, Cali, AA 6713, Colombia Abstract: This work explains the reasons why a bean collection was established in 1973 at the International Center of Tropical Agriculture (CIAT) near Palmira in Colombia. It shows the impact of the collection on plant breeding and in agricultural development through the distribution of germplasm to the center’s bean breeding program, to successively find resistances to pests and diseases, adaptation to low phosphorus and drought, and more recently higher content of iron and zinc in seeds. The collection was also used to progress knowledge in biological sciences, as shown by a dozen of examples. A reason behind these successes was foresight and focus on diversity per se in the collection. The paper ends with a number of suggestions for the way ahead for the genetic resources conservation and management of these bean crops, and possible take-home lessons for curators in charge of other similar collections. Keywords: distribution, yield, biotic stress, abiotic stress, breeding, Phaseolus Citation: Debouck, D. G., Santaella, M., Santos, L. G. (2021). History and impact of a bean (Phaseolus spp., Leguminosae, Phaseoleae) collection. Genetic Resources 2 (4), 21–42. doi: 10.46265/genresj.WJEU8358. © Copyright 2021 the Authors. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The purpose for establishing a collection of (IRRI) in Los Baños, Philippines, on rice and that of the genetic resources at CIAT Centro Internacional para el Mejoramiento del Máız y Trigo (CIMMYT) in El Batán, Mexico, on wheat, and as Created in 1967, the International Center of Tropical an outcome of international conferences (Hernández- Agriculture (CIAT for its Spanish acronym) was the Bravo, 1973; Rachie, 1973; Voysest-Voysest, 1983), third international center of agricultural research whose CIAT moved from a Food Legumes Production Systems mandate was to increase the agricultural productivity Program into a program focused on common bean, in the tropics. Because of population growth a sure Phaseolus vulgaris L. (Hidalgo, 1991); the Bean Program food availability crisis was anticipated and yields of initiated in January 1974 (Voysest-Voysest, 2000). key staple crops had to increase (Kastner et al, 2012) Given the production problems faced for this and, fortunately, this actually happened, namely in crop (Hernández-Bravo, 1973; Singh, 1992), very often Asia (Evenson and Gollin, 2003). Although CIAT was managed by small-holder farmers with limited access originally designed to improve agricultural systems in to inputs (Broughton et al, 2003), the next strategic the lowland tropics (the Center had a couple of animal decision was to increase productivity by transferring production programs), it became clear that the level of resistance to diseases and pests into target varieties. human talents, physical and financial resources required By then, the most severe diseases, out of more than for such a task was beyond the donors’ capacity and one hundred affecting the crop (Zaumeyer and Thomas, time frame, and these limits indicated to re-focus 1957; Singh, 1999), often caused a 70-100% loss in instead (Lynam and Byerlee, 2017). After the successful yield (Sanders and Schwartz, 1980; Singh, 1999). The experience of the International Rice Research Institute first cycle of breeding (which took about 8-10 years in beans in the 1960s) aimed at securing the potential yield of the landraces (Rachie, 1973). Thus, farmers would ∗Corresponding author: Daniel G Debouck have a secure food stock at home and a surplus for (d.debouck@cgiar.org) Received: 25.06.2021 Accepted: 06.10.2021 Published online: 08.11.2021 22 Debouck et al Genetic Resources (2021), 2 (4), 21–43 ciency and impact of the breeding efforts. The need for multiple sources for disease and pest resistance and abi- otic stress tolerance was also related to the wide diver- sity of conditions of deployment in the many countries benefiting from that technology. Note that apart from assembling collections, it was also the time of setting the founding principles of genebank management (Allard, 1970; Frankel and Hawkes, 1975). How the Phaseolus collection was assembled With the establishment of the CIAT Bean Program, the first introductions of bean collections from other insti- Figure 1. Evolution of the breeding strategy in bush common tutes (e.g. United States Department of Agriculture bean in the tropics over the last decades. [USDA], Pullman, USA; Instituto Nacional de Investi- gación Agŕıcola, Chapingo, Mexico; Instituto de Ciencias y Tecnoloǵıa Agŕıcola, Chimaltenango, Guatemala; Cen- sale in local markets. This strategy was likely to work tro Agronómico Tropical de Investigación y Enseñanza because in subsistence agriculture beans were planted [CATIE], Turrialba, Costa Rica) (Hernández-Xolocotzi, in mixtures to where resistant genotypes would lower 1973; Vieira, 1973) were made thanks to the constant the disease pressure for the total crop (Clawson, 1985), cooperation of the Instituto Colombiano Agropecuario, and in market-oriented agriculture with fewer genotypes Palmira, Colombia on plant quarantine matters (Fig- under cultivation a higher part of the production would ure 2). Accessions were registered as Germplasm num- be saved for sale. bers (e.g. G4017 for ‘Carioca’, perhaps the most planted It was envisioned to tackle the next most limiting bean variety in the world; Voysest-Voysest (2000). factor to productivity in a cumulative way, through the Thanks to the support of the International Board for production and distribution of elite varieties, with the Plant Genetic Resources (IBPGR), Rome, Italy (estab- active participation of the national partners, who then lished in 1974), several collecting missions were orga- would work with extension services for the diffusion nized for landraces and wild species. Before the entry of such a technological package. That participation was into force of the Convention on Biological Diversity critical for impact, given the high number and regional (CBD), these crop genetic resources were considered variation of commercial seed types (Voysest-Voysest, as common heritage of humankind, and there was free 1983; Voysest and Dessert, 1991). Figure 1 shows how exchange of genetic resources for breeding and agricul- this strategic approach has worked for common bean tural research purposes. After December 1993, acquisi- over five decades. With each breeding cycle tackling tion by introduction of copies of germplasm collections a new challenge, the strategy had to be cumulative, and explorations came to a halt (as experienced in other because the entire production chain and the final users genebanks of the Consultative Group on International would hardly accept to go backwards. In this regard, Agricultural Research (CGIAR); Halewood et al (2020). it is worth noting that after fifty years, diseases and But in recent years, target explorations were carried pests continue to be among the highest priorities of bean out under the legal framework set by the International breeding, especially in Africa (Assefa et al, 2019). Treaty on Plant Genetic Resources for Food and Agricul- While the first breeding cycle was under way, ture (FAO, 2002), for example in Costa Rica. improvements were introduced to agronomical prac- Because beans as a staple are often associated with tices, taking into account planting density, plant- maize, collections of bean germplasm have been estab- ing date versus water availability versus solar radi- lished across the tropics and subtropics, particularly in ation/photoperiod, minimum of nitrogen-phosphorus- Latin America (e.g. in Chapingo in Mexico, Medelĺın in potassium fertilization, or pH correction by lime applica- tion (Thung, 1991). Once these improved agronomical practices were implemented, it was clear that progress in yield had to come from plant breeding (Borlaug, 1983), but there was a critically important assumption for the whole strategy to work: the immediate availability of well characterized and evaluated genetic resources, which would be the ultimate source of all desirable genes. Practically, because there were none at the Cen- ter, this meant assembling large collections of genetic resources of beans and evaluating such collections by multidisciplinary teams. In the early years of CIAT, that Figure 2. Increase in size of the bean collection introduced into assumption had to quickly become reality for the effi- the CIAT genebank. Genetic Resources (2021), 2 (4), 21–43 Impact of a bean collection 23 Colombia or Campinas in Brazil) (Vieira, 1973), which Table 1. Accessions of the in-trust Phaseolus collection kept at could be introduced into CIAT. It was not rare for a CIAT Palmira (information also available in Genesys: https:// maize breeder to pick up seeds of local bean landraces www.genesys-pgr.org/a/overview/v2ZW8lQwlep) when visiting a farmer or a local market and give them Species Biological status No. to colleagues in charge of bean breeding. As a gen- accessions eral practice in Latin America the maintenance of bean P. vulgaris, cultivated (landraces, 30,571 germplasm collections was a side activity of the bean common bean commercial varieties) breeders. Given this kind of attention, it is no surprise wild and weedy forms 1,804 that the landraces of the market classes worked on cultivated (landraces, 3,031 by the breeders were well represented in the respec- P. lunatus,Lima bean commercial varieties) tive collections. Retrospectively, this is positive because wild and weedy forms 274 some of these collections were made in the 1940-1960s, just before massive rural transportation blurred the ori- P. coccineus, cultivated (landraces, 760 gins of many local landraces. By that time, the vari- scarlet runner commercial varieties) eties selected or bred over the last decade were starting wild and weedy forms 198 to replace many landraces. This replacement was seen P. dumosus, cultivated (landraces) 475 in small black and red-seeded bean varieties of Central year-bean wild and weedy forms 15 America. Consequently, the most original genetic vari- P. acutifolius, cultivated (landraces, 161 ation in landraces that existed in the 1940s is by now tepary commercial varieties) either in genebanks or lost. Collecting today will only wild and weedy forms 165 result in duplicates or in samples of bred materials. Other species wild forms only 484 The focus on common bean and the need to find (411) resistances for several market classes of beans as 1 This figure represents half of the number of species of the final targets influenced the makeup of the collection genus (Debouck, 2021). (Table 1). As the Bean Program was working with Central American countries and Brazil (Voysest-Voysest, collection was safely duplicated at GSSV. In addition, 1983), many small-seeded collections were introduced, CIAT safeguards in its vault the seed backups of the but because CIAT also worked together with Andean food legume collection of the International Institute of countries, large-seeded collections were included as Tropical Agriculture (IITA), Ibadan, Nigeria, and the well (both collections but particularly the last ones tropical forage legumes of the International Livestock were important for Africa: Martin and Adams (1987). Research Institute (ILRI), Addis Ababa, Ethiopia. Cultivated P. vulgaris makes up the biggest part of the collection, the other cultivated species follow, with a The diversity in the bean collection and its total of 32,183 landraces and 2,797 improved varieties. use The wild forms of the cultivated species and the wild species are represented by over 2,000 accessions Given the breeding priorities (Figure 1), the bean collec- (Table 1). tions were evaluated by multidisciplinary teams in mul- The number of country depositors is 110. The top tiple locations in Colombia, first in Palmira, in Quilichao five countries that have contributed most are: Mexico since 1977 and in Popayán since 1978 (Cuellar, 2003). (6,237 accessions), Colombia (3,927 accessions), Peru Resistances to several highly damaging diseases (e.g. (3,798 accessions), Guatemala (2,853 accessions) and anthracnose, angular leaf spot (ALS), bean common the United States (1,863 accessions), followed by mosaic virus (BCMV), rust) were found (Table 2) Brazil, Ecuador, Turkey, Malawi and Costa Rica (with and transferred as their mode of inheritance was pro- around 1,000 accessions each). Restoration of national gressively defined (Singh, 1992; Beebe et al, 1997; bean diversity has been done for Bhutan, Chile, Costa Beebe, 2012). However, bean breeders soon realized Rica, India, Iran, and Mexico, based on institutional that further genetic progress would be obtained only agreements. by screening the diversity outside the respective market After partial safety duplications at CATIE and classes, and that for many traits (e.g. Ascochyta blight, Centro Nacional de Pesquisa de Recursos Genéticos e bean golden mosaic virus (BGMV), bean golden yellow Biotecnologia, Brasilia, it was decided in 1996 to make mosaic virus (BGYMV), common bacterial blight, halo a complete backup at CIMMYT because extra space was blight, web blight, white mold, bruchids and leafhop- kindly offered by Bent Skovmand then in charge of pers) there were very few or no sources of workable the wheat collection. This included a check for viability resistance (Miklas et al, 2006; Singh and Schwartz, and absence of diseases of quarantine importance. By 2010; Beebe, 2012). In a copy of the USDA collection 2019, 92% of the bean collection had been safely there were a few accessions of wild common bean from duplicated at CIMMYT. When the Global Svalbard Seed Mexico collected in the 1960s by Howard Scott Gen- Vault (GSSV, Longyearbyen, Norway) was opened in try in which, later on, César Cardona and his team February 2008 (Fowler, 2016), a second safety backup found bruchid resistance associated with a particular was implemented there. By 2019, 94% of the bean seed protein (Osborn et al, 1988). The screening for the right variants of that protein by electrophoresis 24 Debouck et al Genetic Resources (2021), 2 (4), 21–43 opened the way for marker assisted selection (Kelly and cross QTL analysis using a wild form. The accessions of Miklas, 1999), widely applied in breeding for BGYMV wild P. vulgaris G12947 (Acosta-Gallegos et al, 2007), resistance (Broughton et al, 2003), anthracnose resis- G19892 (Buend́ıa et al, 2003), G24404 (Blair et al, tance (Kelly, 2004) and other traits. The wide sec- 2006) and G24423 (Kelly, 2004) were found to con- ondary gene pool (e.g. P. coccineus, P. costaricensis, P. tribute a significant QTL for yield (a 27% increase as dumosus) has just started to be evaluated, and has compared to the recurrent parent in the last example). already shown promise against Ascochyta blight (Schmit In some cases, the use of weedy types would help reduce and Baudoin, 1992), angular leaf spot (Mahuku et al, the number of backcrosses needed to recover the appro- 2003) and white mold (Singh et al, 2013). Such resis- priate seed size (Acosta-Gallegos et al, 2007). Another tances were expected because the species of the sec- innovative approach has been the use of lines coming tion Phaseoli thrive in montane humid forests (Debouck, from crosses with the year-bean (for transfer of high iron 2000) where these fungi diseases are frequent selec- in the grain) or with tepary (for transfer of bacterial tion pressures (Cattan-Toupance et al, 1998) and have blight resistance) in order to bring more monocarpism likely been present over hundreds of thousands of years, into common bean (Klaedtke et al, 2012; Mej́ıa-Jiménez given the age of these species (approximately 1 million et al, 1994). The bean crop with exceptions in growth years) (Delgado-Salinas et al, 2006; Rendón-Anaya et al, habits 1 and 2 still has the ancestral trait of continuing 2017). shoot production and lateral flowering, while the first Once disease resistances were transferred to the pre- pods already enter into maturity. In the wild it makes ferred varieties in the different market classes, yield all sense, but not in a crop aimed at mechanical har- came as the next challenge, in order to keep bean as a vesting. The desert ephemerals of the genus such as P. competitive (mono-)crop as compared to soybean, cow- acutifolius A. Gray, P. filiformis Benth, or P. microcar- pea or sorghum. An early approach, in line with the pus Mart. (Freytag and Debouck, 2002) invest much less spirit of the Green Revolution in wheat (Donald, 1968), in profuse branching but soon move all photosynthesis was to optimize the ideotype under favorable environ- products into their seeds. Thus, under heat or drought ments (Adams, 1973). That breeding effort on plant stress, it makes sense to quickly redirect such products architecture continued (Kelly, 2001), although with lim- to the only part that will be harvested (Rao et al, 2013; ited success in the tropics (Beebe, 2012). An impor- Suárez et al, 2020). tant outcome, however, has been the rise of growth One outcome of the increase in size of the collection habit 2 or bush erect indeterminate (race 3 of Evans and the first phase of germplasm evaluations at CIAT (1973) for mechanical harvesting in bean improved was the establishment of core collections (along the germplasm, little present in traditional landraces of concept introduced by Frankel and Brown (1984). The Latin America. This also offered opportunities to enrich CIAT common bean core collection was established the collection (Hidalgo et al, 1992). Another breed- by use of Geographic Information Systems maximizing ing goal was to combine the productivity of the small- the environmental diversity of landraces, and a few seeded varieties with the grain size of the large-seeded morpho-agronomic descriptors (Tohme et al, 1995a). ones, many of them demonstrated to be of Mesoamer- The core collection, consisting of 1,556 accessions, ican and Andean origin, respectively (Evans, 1976). has been used for the identification of germplasm Thus came the works evidencing the two major gene tolerant to low phosphorus (Beebe, 1997) or containing pools (Gepts et al, 1986; Singh et al, 1991b; Kwak high levels of micronutrients (Islam et al, 2002). For and Gepts, 2009; Bitocchi et al, 2013), and the races both traits less than 10% of the total collection had within them (Singh et al, 1991a; Beebe et al, 2000b; been evaluated at that time (Beebe et al, 2000b,a), Blair et al, 2007, 2012). The presence of races was a explaining the recourse to the core collection. Using bit unexpected in an autogamous crop but could be core collections was, in part, the consequence of internal explained by the role of outcrossing during early domes- duplication or redundancy in general collections, which tication (Chacón-Sánchez et al, 2021). Some genetic iso- for cultivated common bean has been estimated at lation and poor recombination have been shown to exist 50% across the major genebanks (Lyman, 1984). This between the two major genepools (Singh and Gutiérrez, figure is perhaps on the high side but reflects the 1984) and since the wild state (Koinange and Gepts, amount of commercial and breeding materials kept 1992). But significant heterosis was demonstrated to in genebanks as compared to primary sources of exist (Nienhuis and Singh, 1986; Bannerot, 1989), espe- variation (landraces, wild species). As mentioned, the cially between races (Singh et al, 1993; Singh and management of germplasm collections was often a Urrea, 1995), while genetic disorders between races side activity of bean breeders who would hesitate to were sometimes observed (Singh and Molina, 1996). eliminate all variants close to the target market class. The significant interactions with the environment, how- Given the cost of keeping accessions versus the cost of ever, have resulted in a narrow commercial applica- tracking down internal copies (this was then achieved bility of this approach (Gutiérrez and Singh, 1985; by multi-site characterization, in addition to passport Nienhuis and Singh, 1986). Another strategy inspired data) (Koo et al, 2004), the problem was not given from the quantitative developments in tomato breed- high priority in the past. With the development of SNP ing (Tanksley et al, 1996) was the advanced back- genotyping technology, this issue should be revisited, Genetic Resources (2021), 2 (4), 21–43 Impact of a bean collection 25 Table 2. Bean accessions from the CIAT collection used as sources of resistance to diseases and pests. Trait Material used References Diseases angular leaf spot G10613 from Guatemala Pastor-Corrales et al (1998) interspecific hybrids with P. coccineus; G4691 Pastor-Corrales et al (1998); Islam et al (2002); Mahuku et al (2003) angular leaf spot and G3991 from Costa Rica Schwartz et al (1982) anthracnose anthracnose Aliya G02333 Young and Kelly (1996) Kaboon G1588; Cornell 49-242 G5694 Melotto and Kelly (2000) interspecific hybrids with P. coccineus G35252 Mahuku et al (2002) Ascochyta blight P. dumosus G35369 from Costa Rica Schmit and Baudoin (1992) P. dumosus G35182 from Guatemala Garzón et al (2011) bacterial wilt wild P. vulgaris G12883 from Mexico Urrea and Harveson (2014) Bean Golden Yellow P. coccineus G35172 from Rwanda Beaver et al (2005) Mosaic Virus (BGYMV) Bean Common Mosaic Porillo Sintético G04495, Royal Red G04450 Singh et al (2000) Virus (BCMV) beet curly top virus California Pink G06222, Red Mexican G05507 Larsen and Miklas (2004) Porillo Sintético G04495, Burtner, Tio Canela 75 Singh and Schwartz (2010) common bacterial interspecific hybrids with acutifolius VAX4, MBE7 Zapata et al (1985); Singh and Muñoz blight (1999); Michaels et al (2006); Navabi et al (2012) Montana No. 5; PI 207262 Miklas et al (2003, 2006) halo blight Montcalm G06416, ICA Tundama G14016 Beaver (1999) Palomo G12669 Schwartz (1989) Pinto US 14 G18105 Singh and Schwartz (2010) Wis HBR 72 G03954 Taylor et al (1996) Fusarium root rot Porillo Sintético G04495; wild P. vulgaris G12947 Beebe et al (1981); Acosta-Gallegos et al (2007) Pythium root rot PI 311987 G02323 Beebe et al (1981) Rhizoctonia solani rot N203 G00881 Beebe et al (1981) rust Compuesto Negro Chimaltenango G05711 Stavely (1984) Ecuador 299 G05653 Stavely and Pastor-Corrales (1989) Redlands Pioneer G05747 Liebenberg et al (2006) PI 260418 Singh and Schwartz (2010) web blight BAT 93; Flor de Mayo G14241 Beaver et al (2002) white mold P. coccineus PI 175829 from Turkey Abawi et al (1978) P. dumosus PI 417603 from Mexico Hunter et al (1982) interspecific hybrids with P. coccineus G35172 Singh et al (2009) interspecific hybrids with P. costaricensis G40604 Singh et al (2013) Pests Acanthoscelides weevil wild P. vulgaris from western Mexico G12952; QUES van Schoonhoven et al (1983); Zaugg et al (2013) Apion godmani pod Amarillo 154 G03982; G03578 Beebe et al (1993); Garza et al (2001) weevil Empoasca leafhoppers Turrialba 1 G03712 Galwey (1983) California Dark Red Kidney, from USA G17638 Schaafsma et al (1998) Ophiomyia bean fly P. coccineus G35023 and G35075, and interspecific Kornegay and Cardona (1991) hybrids whiteflies Aleyrodidae DOR 303 Blair and Beaver (1992) Zabrotes weevil wild P. vulgaris from Chiapas, Mexico G24582 Acosta-Gallegos et al (1998) 26 Debouck et al Genetic Resources (2021), 2 (4), 21–43 with the merging of near identical accessions and the USA (26,093 samples), Colombia (18,444 samples), review of the core collection (as already suggested for Brazil (9,198 samples), Guatemala (7,430 samples) and the USDA core collection by Kuzay et al (2020). The Mexico (6,787 samples). The term ‘samples’ is preferred most significant costs ahead are likely to be about over ‘accessions’ as a country recipient could ask for a regeneration and evaluation, not the chasing of internal specific accession more than once. copies helped by robotics! Apart from germplasm, the genebank also distributed information related to the in-trust collections. An Distribution of the bean collection indicator of this service is given by the number of consultations of the genebank website (https://ciat.cgia Since being established in August 1977 as an inter- r.org/what-we-do/crop-conservation-and-use/) to have nal service unit (Hidalgo, 1991), the genebank has access to data (Figure 5). distributed to the Bean Program and the Biotechnol- Statistics about access to genebank information and ogy Research Unit of CIAT a total of 318,148 samples services in recent years show that most of the visi- (or 69.4 % of the total distributed) (Figure 3). Exter- tors (81%) reach the genebank website directly, indi- nally, the genebank has distributed 140,109 samples (or cating a user knowledge and confidence that relevant 30.6% of the total) to users in 105 countries. The total information can be found there, while 19% of visi- distributed was 458,257 samples of 37,657 accessions, tors find the website through a browser search or are or 99% of the bean collection. These figures indicate referred to it through another link. Users also benefit that: i) the collection has been studied and used ini- from specialized technical information currently consist- tially by the scientists of CIAT, ii) the number of coun- ing of 658 documents (including articles, book chapters, tries benefiting from the conservation work through dis- conference proceedings, germplasm exploration reports, tribution almost matches with the number of country posters and presentations). These documents can be depositors, and iii) the collection has been distributed accessed through the genebank website or the institu- almost entirely (this percentage could be even higher tional document repository CGSpace (https://cgspace.c since some accessions have not been distributed due giar.org/handle/10568/35697), that registered 27,278 to lack of seeds). One should note that apart from downloads in 2017-2019. CIAT programs, the most important users were national agricultural research services, universities and research Impact of the bean genetic resources institutes. The shares of farmers, commercial companies collection and non-governmental organizations in the distribution were low in comparison. Assuming farmers are aware of The 225 varieties released in 17 countries of Latin the existence of germplasm collections, reasons for the America and the 88 varieties released in 14 countries low number of requests might be related to the farmers’ of Africa in 1974-1999 by the Bean Program (Voysest- access to on-line request processes (mail requests were Voysest, 2000), the check of BGYMV in Central honored), as well as the capacity to deal with phytosan- America (Beebe, 2012), as well as the yield gain from itary regulations in the respective countries. As dry bean 688 kg/ha to 782 kg/ha in eastern Africa (Lynam breeding has been mostly carried out by public institu- and Byerlee, 2017) eventually have their origin in tions, requests of genetic diversity by the private sec- the CIAT genebank. Once the interesting traits were tor were few, often related to specific sources of varia- identified (Table 2); (Hidalgo and Beebe, 1997), tion for snap bean breeding (e.g. sources of resistance to through different breeding schemes, elite varieties anthracnose). were produced, tested and released via international The purposes of distribution have generally followed nurseries such as the International Bean Yield and the breeding priorities shown in Figure 1: interest in Adaptation Nursery (Voysest-Voysest, 1983; Beebe, resistances to diseases and pests, nutritional quality 2012), generating significant economic and social and more recently tolerance to abiotic stresses such benefits (Johnson et al, 2003). In this last work, over the as drought and high temperature. As discussed below period of analysis, and because of the varieties involved, and shown in Figure 4, a significant part of the some countries of Latin America and the Caribbean were distribution has been for the purpose of advancing net beneficiaries (Argentina, Brazil), while others were knowledge. In Figure 4, breeding activities (38.9%) net contributors (Mexico, El Salvador). Overall, and and applied research (e.g. in pathology or entomology: over the duration, however, it seems that all countries 37.1%) were the top purposes for seed requests, benefit from conservation and unrestricted international followed by agronomy (11.7%) and basic research exchange of germplasm (Johnson et al, 2003). (e.g. in genetics or evolutionary studies: 9.6%). The As an example of changing context over time, the variation in number of distributed samples from one gene gy. originating from Peru and conferring an intense year to another can be significant, namely if the core and sustained yellow color (Bassett et al, 2002) was used collection with over 1,500 accessions was requested since 1978 in northwestern Mexico (Lépiz-Ildefonso and and sent. The peak in distribution in the period 1978- Navarro-Sandoval, 1983), because it gave a premium 1996 practically matches with that of the activities of price as compared to the fading color in yellow- CIAT Bean Program (Voysest-Voysest, 2000). For the seeded traditional landraces. It ended up in the variety period 1973-2019, the top five recipient countries were: ‘Azufrado Peruano 87’ (Voysest-Voysest, 2000) and also Genetic Resources (2021), 2 (4), 21–43 Impact of a bean collection 27 Figure 3. Number of samples distributed in the period 1973-2019. Important recipients were the Bean and Biotechnology Programs of CIAT, the national agricultural research services (NARS), universities and research institutes. an undue patent granting (genetically dissected in great G14519, an old landrace named ‘Hickman Pole Bean’ detail by Pallottini et al (2004). It is because the in-trust from the United States and belonging to the Mesoamer- collection was rich in yellow-seeded accessions from ican genepool, also has shown potential (Blair et al, Mexico and Peru, and because the CIAT genebank kept 2010). From the start, the genebank had interest in past records such as old catalogs of varieties (Hedrick, assembling variation for any future need, and this is 1931), it was possible to demonstrate ample prior art, precisely the wide scope that made biofortification pos- and the patent was turned down in 2008. sible thirty years later and with a lasting impact where Legumes have been called the ’meat of the it is today most needed, e.g. in East Africa (Sellitti et al, poor’ (Heiser, 1990) and in many parts of Latin Amer- 2020). ica (e.g. Brazil, Mexico, Cuba) people with low income With changing context of bean production over the eat beans daily. Similarly, the highest consumption last forty years, for example, common bean being rates per capita are currently registered in eastern pushed towards the west in the Plains of the USA or Africa (OECD, 2015). Given this, it was becoming in the Canadian prairie, the northwest in Mexico and evident that improved varieties should also fight the the northeast in Brazil (Singh, 2001), new challenges ‘hidden hunger’ or the deficiency in minor minerals like drought, cold, heat or low phosphorus are set such as iron and zinc where the diet is not sufficiently for breeding. Some drought tolerance can be found in diverse. Using the core collection, the evaluation to find the ‘Durango’ race (Singh, 2007; Beebe et al, 2013), accessions with high iron and zinc was expanded (Islam in other landraces such as G21212 (Beebe et al, et al, 2002), and good sources were identified (G21242, 2008) and in wild forms (Cortés and Blair, 2018). G23818, G23834) (Blair et al, 2011), primarily from Root architectural and physiological traits identified the Andean region. Nothing on the seed aspect indi- in an Andean landrace, G19833, may contribute to cates high values in these micronutrients. Likewise, phosphorus acquisition (Beebe et al, 2006). 28 Debouck et al Genetic Resources (2021), 2 (4), 21–43 Figure 4. Number of samples distributed annually to users in the period 1973-2019, according to the purposes of requests. The impact of the bean germplasm collection has also been through the direct adoption of genebank accessions by farmers after the screening of international nurseries. No less than thirty-four accessions have been registered in national catalogs of varieties in thirty-eight countries in 1974-1999 (Voysest-Voysest, 2000), or 13% of the total of improved genetic materials distributed by CIAT. This figure may not look impressive, but bean varieties produced by breeding have been released in the same geographic areas since the 1940s. That said, it is anticipated that apart from the use of landraces for specific niche markets (see popping beans below), for specialized studies for example in pathology (e.g. Figure 5. Number of consultations of the CIAT genebank disease differential sets) or for servicing gardeners, website (https://ciat.cgiar.org/what-we-do/crop-conservation a significant coming impact of genetic resources will -and-use/) in the period 2009-2019. materialize through libraries of genetic stocks (van Genetic Resources (2021), 2 (4), 21–43 Impact of a bean collection 29 Treuren and van Hintum, 2014), targeted diversity et al, 2015; Mina-Vargas et al, 2016). As expected, panels (Cichy et al, 2015; Moghaddam et al, 2016), that founder effect was less marked in the scarlet and sequence tagged traits (Lobaton et al, 2018). But runner (Guerra-Garćıa et al, 2017). That knowledge in order to allow the ‘molecular’ breeder to do advanced also helped in the development of disease indexing searches throughout the collection substantial changes methods for the safe movement of germplasm (Kumar must be brought to databases (McCouch et al, 2012; et al, 2021). Some examples are provided in Table 3 Byrne et al, 2018). Learning from experience, the design (by tracking accessions distributed in 1973-2019). The should be for use by non-database experts, modular breadth of disciplines, evidenced by the diversity of and scalable, moving from passport data into accession peer-reviewed journal titles and linked to genebank traits and ending into annotated genes. Somehow, this accessions, is striking but just reflecting the diversity of focus re-emphasizes the role of genebanks as keepers the collection. No less important are the opportunities of the primary genetic variation, and perhaps less of scientific collaborations around ‘problems’ set up of all allelic combinations of that variation (i.e. the by the bean crops and materials provided by the sister lines of simple crosses), since tools now exist to genebank, as reflected by the institutions and countries recombine that variation to better meet human needs or of authorships. agricultural contexts (towards precision agriculture for instance). Appraising that variation by curators might Knowledge often overlooked, although be difficult (what should be kept in the genebank associated with crop germplasm for remains a cornerstone and recurrent question), although millennia they will be helped by sequence information. From a pragmatic perspective genebanks may keep interest in Because germplasm collections were assembled at old landraces since these have been tested over long CIAT primarily in relation to breeding, traditional durations in farmers’ fields. For similar efficiencies in knowledge associated with specific accessions was rarely breeding, genebanks might be interested in keeping documented. As the first phase of breeding was focused recombinants between gene pools, for example from on resistance to diseases and pests, with systematic southern Europe (Gioia et al, 2013), part of the inoculation of known strains, there were often no Guarani area in Brazil (Burle et al, 2010) or the incentives for a time-consuming effort to document northern Andes (Chacón-Sánchez et al, 2021), especially vernacular names, culinary and other folk practices. if they represent novelties in agronomic or nutritional One such example is that of popping beans consumed attributes. toasted (National Research Council, 1989). That group of landraces still exists in the Andes, from Cajamarca The other impact: the contribution to in Peru down to Chuquisaca in Bolivia (Tohme et al, knowledge 1995b). Elder farmers in the countryside will tell which variety can pop, while migrants to urban areas one The in-trust collections, because of the open access generation after will simply process them all in water set forth by FAO in the early years and then the cooking, even with a slight increase in digestibility (van facilitated access approved by the parties to the Beem et al, 1992). Documenting this property by International Treaty (FAO, 2002), have helped increase the genebank is doubly important. First, consumer knowledge in many fields of biological sciences (Dudnik preferences change over time (Voysest-Voysest, 2000) et al, 2001). Conversely, the increased knowledge and, in contrast to the 1960s, there is a renewed interest contributed tremendously to the efficiency of the nowadays in local gastronomy that can provide a better breeding and varietal deployment efforts. This was income to mountain farmers (Zimmerer, 1992). Second, particularly applicable to the mandate crops of CIAT, water and fossil energy might become expensive inputs since with the exception of rice, not much basic to food processing or transportation, as it is still the case biology and genetics was known in the late 1960s in many parts of rural eastern Africa. In pre-ceramic when crop improvement efforts were launched. For times in the Andes, these two inputs (excepting fire) instance, the ancestry of common bean became firmly were either difficult to carry or to access. Producing established at a time not far away from the founding of a hot surface with the help of solar energy might not CIAT (Burkart and Brücher, 1953; Gentry, 1969). The be an excessively difficult or expensive technology to double domestication of common bean became obvious implement in the Andes or in eastern Africa. In altitude, only in 1986 (Gepts et al, 1986), and that of Lima bean this kind of germplasm and the unique way to make in 1989 (Debouck et al, 1989), and the existence of a it ready for human consumption may also contribute fifth case of domestication in the genus was clarified as to reduce deforestation for fuel wood, while montane late as 1991 (Schmit and Debouck, 1991)! forests usually occupy a small acreage (National Such increased knowledge also helped to better Research Council, 1989). Finally, it is worth noting that define what should be conserved in genebanks; for this group has a high number of phaseolin types (Tohme example, studies on the founder effect due to bean et al, 1995b), indicating a high diversity in contrast to domestications have stressed the importance of wild other Andean landraces (Beebe et al, 2001). Evaluation forms for accessing the total genetic diversity of three of popping beans is continuing in Peru (Cruz-Balarezo bean crops (Sonnante et al, 1994; Mart́ınez-Castillo et al, 2009) and Colombia (Otálora et al, 2006), while 30 Debouck et al Genetic Resources (2021), 2 (4), 21–43 Table 3. Examples of impact of CIAT bean in-trust collection for the advance of knowledge. Field Output, problem solved References Botany new species described Salcedo-Castaño et al (2011) Plant taxonomy taxonomic status of bean species re-assessed Schmit et al (1996) review of the genus and species Freytag and Debouck (2002) Agricultural botany founder effect of bean domestication Schinkel and Gepts (1988) definition of a 3rd gene pool in Lima bean Motta-Aldana et al (2010) fifth case of domestication in the genus Schmit and Debouck (1991) Crop evolution recombination between gene pools Gioia et al (2013) Phylogeography past trans-isthmic migrations of wild bean Chacón-Sánchez et al (2007) Plant breeding gene pools/ races of common bean defined Singh et al (1991a) Plant pathology inheritance of ANT/ALS resistance genes Gonçalves-Vidigal et al (2011) coevolution of ALS in bean gene pools Guzmán et al (1995) Plant virology resistance to Clover yellow vein virus Hart and Griffiths (2014) Entomology resistance to bean bruchids Cardona et al (1990) resistance to bean weevil Kamfwa et al (2018) Plant genetics common bean genomic map Schmutz et al (2014) common bean genome history & evolution Rendón-Anaya et al (2017) inheritance of pod dehiscence Parker et al (2020) inheritance of leaf mutation Garrido et al (1991) Plant biotechnology genetic transformation in tepary bean Dillen et al (1997) Plant physiology flowering response to daylength White and Laing (1989) identification of phosphorus-efficient genotypes Beebe et al (1997) low phosphorus tolerance in bean Rao (2001) variation in photosynthetic activity Lynch et al (1992) Plant root physiology tolerance to NaCl salinity in early growth Bayuelo-Jiménez et al (2002) Plant microbiology coevolution of Rhizobium etli Aguilar et al (2004) Human nutrition content in micronutrients such as iron Beebe et al (2000a) phaseolin type and digestibility Montoya et al (2008) Archaeology crop domestication and ancient diet Piperno and Dillehay (2008) Intellectual Property Protection rebuttal of an undue crop utility patent Pallottini et al (2004) the inheritance of the trait is being investigated (Campa in countries of origin over the last forty years, shows et al, 2011; Yuste-Lisbona et al, 2012). the ever-changing nature of markets. Thus, examples of unpredictability abound, indicating for the genebank to focus on diversity per se, independently from immediate Serving the breeders community and and local interests. beyond This example of success brings a strong message to focus scarce resources, at a time when there As shown in Figure 3 and Table 3, distribution has is risk of repeating previous work because many been significant to a high diversity of users, going disciplinary continuums have been broken. Thus, it beyond CIAT breeding activities in Colombia and in seems of paramount importance to document at eastern Africa. The trend that in some countries accession level what is already known: phaseolin type, dry bean consumption is declining (Khoury et al, alleles of allozyme, RAPD markers, SCARs, SSRs, also 2014) (contradictory to health and global environment evaluation data (trait, location, strain as applicable). benefits: Foyer et al (2016) may mean fewer requests Individual accessions should be linked with references for that kind of germplasm but an increased interest into and supporting documents. Keeping in mind that one snap bean, often of Andean origin (Myers and Baggett, third of the collection has not been evaluated, there 1999). With the development of urban gardening, snap is still a lot of work for pathologists, entomologists bean might be on the rise, either through the planting and virologists. Evaluations were done on up to 23,000 of old heirloom varieties (Kaplan and Kaplan, 1992; accessions only for anthracnose, angular leaf spot and Zeven, 1997) or new ones. In CIAT, the priority was on common bacterial blight; for the other limiting pests dry bean, little on snap bean for the tropics, but with the figures are much lower (Hidalgo and Beebe, 1997). possibilities of using a wide range of resistance sources The reaction should be reported at each accession level, developed for the former commodity (Silbernagel et al, and not restricted to the best performers. Evaluation 1991). The changing fate of the popping beans, even Genetic Resources (2021), 2 (4), 21–43 Impact of a bean collection 31 should obviously capitalize on knowledge generated by Discussion previous protocols. For example, on bruchids, it is likely The afore-mentioned facts suggest the following points that evaluation of the rest of cultivated common bean for discussion. First, one can ask whether this bean germplasm will lead to nowhere (van Schoonhoven germplasm collection meets the expectations for which and Cardona, 1982), because domestication occurred it was established. Many sources of disease resistance elsewhere (Chacón-Sánchez et al, 2005; Bitocchi et al, were found (Table 2), and one should note that in 2013; Kwak et al, 2009). But the right arcelin can many cases the findings were unpredicted, and largely be picked by screening for the protein or the gene(s) independent of geographic origin or gene pool. As well involved instead of testing thousands of accessions in noted by Harlan (1978), page 351) “resistance is where contact with the insects. you find it”. For those diseases where no good sources From previous experience, it seems likely that of resistance have been found, in the light of a similar genebanks will face periodic shortages in skilled, experience with the USDA collection (e.g. the case of highly specialized staff (a challenge also mentioned white mold: Schwartz and Singh (2013), it seems more by Fu (2017). This is a recurrent limitation for a deficiency of the common bean crop species itself than germplasm evaluation (thus resulting in limited use a severe lack of representativeness. Thus, the breeders of the collection in the future). Sending the core turned logically to the wild forms and the secondary collection or more accessions abroad for specialized gene pools (Debouck, 1999), where the collection evaluations is an option, although perhaps not as fast provided some solutions but also means for the needed as having it evaluated by a multidisciplinary team as preliminary studies in taxonomy and wide crossing. This done at CIAT in the 1970s. Incidentally, blocks of links with a second point: given the above evidence resistance genes (Gonçalves-Vidigal et al, 2020) that of return on investment and incompleteness of the can be traced by molecular markers are giving an task (Hidalgo and Beebe, 1997), it might be important unexpected support to that approach. But in view to continue with evaluation, namely for abiotic stresses of complex traits such as heat or drought tolerance, such as drought or heat caused by global warming, as for which just a fraction of the entire collection has these will impact on yield (Lobell and Gourdji, 2012; been evaluated, multi site evaluation of thousands Beebe et al, 2013). In view of the numbers of accessions of accessions seems extremely time-consuming and and facing the need for developing novel evaluation expensive. New evaluation schemes have to be designed schemes for abiotic stresses including a network of and are a true challenge at the organ level (Zhao et al, well characterized (climate, soil) experimental plots, 2019), but not impossible when focused for example on it might be cost effective to cooperate with other pulvini-caused movements of leaflets in relation to solar et al bean germplasm repositories (e.g. Instituto Nacionalradiation avoidance (Thomas , 1983). de Investigaciones Forestales, Agŕıcolas y Pecuarias, For location-related abiotic stresses, geographical Tepatitlán, Mexico; Institut für Pflanzengenetik und approaches (targeted towards the surviving germplasm Kulturpflanzenforschung, Gatersleben, Germany; USDA, where the stress has been present for thousands of USA). Incidentally, this cooperation might also include years, and thus logically the wild forms) may help. a reciprocative safety backup and the development of a But these GIS approaches did not pick up outstanding novel database because it is a shared concern. Third, wild forms under low phosphorus stress (eighteen to the question whether the genebank has made any accessions tested, Beebe et al (1997), while there impact, the answer came from bean breeding but also seems some promise for drought tolerance (eighty-six many actors in the global community. The figures of accessions tested, Cortés and Blair (2018). Internally, germplasm distribution for applied and basic research these approaches requires the genebank to be strict (Table 3 and Figure 4) have shown a vibrant research on passport data accuracy (van Hintum et al, 2011). community worldwide adding value to the collection. However, this is not always possible; for example, They invite the genebank to a permanent capacity to accession G40001 with promise for heat tolerance is respond to requests (because of the ‘on-line shopping from a market in Veracruz (Suárez et al, 2020). Given syndrome’) but also to document these impacts. some intrinsic limitations of common bean, coming heat The question whether the collection will make any and drought stress in the tropics and subtropics (Battisti et al impact in the future should also consider technologicaland Naylor, 2009; Beebe , 2011) may be the innovations such as transgenesis and gene editing (e.g. opportunity to re-balance the collection towards the using CRISPR-Cas9) (Doudna and Charpentier, 2014). tepary and Lima bean, more hardy crops in this These approaches of genetic engineering bring new regard (Freeman, 1913; Rachie, 1973), respectively). light on using diversity, as they have the potential Eventually, bean breeders may realize that they have five to add a new function such as herbicide tolerance crops instead of one, each one with a different ecological or improve an existing one, such as seed protein head start (Debouck, 1992). With the advances in quality, beyond the trait offer of the primary gene marker assisted selection and genetic maps, it might be pool (Gepts, 2002). Transformation in common bean faster to correct a shortcoming in seed or growth habit in has proven to be particularly difficult (Jacobsen, 1999), tepary than expecting the common bean to fully change and with limited success (Aragão et al, 1998, 2002; its ecological background. Estrada-Navarrete et al, 2007). Transformation seems 32 Debouck et al Genetic Resources (2021), 2 (4), 21–43 quite possible in tepary bean (Zambre et al, 2005), the last fifty years. The same germplasm collections but apparently little exploited for tepary improvement. allowed inheritance studies and the improvement of The CRISPR technology in soybean aims at editing bean breeding methods, when looking for combining genes involved in a biosynthetic pathway for seed oil ability, tolerance to abiotic stress or tagging a resistance. quality, for herbicide tolerance, or changing photoperiod The coming storms in areas of bean production (e.g. sensitivity (Bandyopadhyay et al, 2020; Xu et al, 2020). increased demand due to demography in eastern New technologies will continue to appear, but under Africa, extinction of crop wild relatives in Mesoamerica, currently available evidence and costs they seem likely drought in 60% of bean growing areas worldwide) are to contribute to a wider and/or faster use of the resetting the timing to meet all breeding challenges at collection rather than to replace it. Finally, in this once and soon, but they also involve the genebanks context, in order to continue to meet the broader to have the genetic solutions ready on the shelf or expectations of human societies, the genebanks should on the screen (or both). The contributions of the fill gaps which were identified early on, in terms bean collections to advance knowledge on the nature, of geography, e.g. the northern Andes: (Hidalgo and structure and evolution of Phaseolus genetic resources Beebe, 1997; Beebe and Debouck, 2019); or in terms can now help the genebanks to check two extinctions: of biological coverage (Ramı́rez-Villegas et al, 2010, the extinction of populations in the wild, and the 2020). Wild forms and wild species should thus be better extinction of knowledge about cultivated diversity. represented in the collection, with due consideration Buying time on these two fronts will be difficult to the regeneration capacity and disclosure of the for genebanks, but the continuing improvement of potential. There are two points here: first, given the conservation methods and efficiencies will contribute to possibilities opened by comparative mapping in the find and enable the human talents for these daunting Phaseoleae (Schmutz et al, 2014; Vlasova et al, 2016; tasks. The above history shows many ways forward to Garcia et al, 2021; Moghaddam et al, 2021) and by ensure global food security in uncertain times. gene editing (Bhatta and Malla, 2020; Ku and Ha, 2020), it may be time to think beyond direct interspecific Acknowledgments hybridization for the use of alien germplasm. In that sense, species of clade A that may represent half of The authors warmly thank the following individu- the genus (Delgado-Salinas et al, 2006; Porch et al, als for providing or confirming specific data about 2013; Debouck, 2021) may be opportunities of genes to introduction and/or distribution of accessions: Sandra imitate and/or to regulate differently instead of genes Albarraćın, Alejandro Borrero, Juan Carlos Guerrero, to transfer. But given the speed of the technological Ángela Hernández, Rigoberto Hidalgo, Dimary Libreros, development in breeding (Hickey et al, 2019), the Celia Lima, Carmenza Llano, Josefina Mart́ınez, Daniel action should be initiated now with the most threatened Eduardo Salazar, Orlando Toro (deceased), Alba Marina habitats (Williams et al, 2007), species (Goettsch Torres and Eliana Urquijo. The invitation by Peter et al, 2021), or unpredictable conditions, or time- Wenzl to the first author to write down a few mem- consuming work. This leads to a second point, as ories is fully acknowledged. The first author expresses forsaking millenary crops (Mamidi et al, 2011) does deep gratitude to the following institutions for sup- not improve humankind’s food security. The four other port during four decades: Administration Générale de bean crops mean four more opportunities for plant la Coopération au Développement, Bundesministerium breeding. Following the diversity criteria prevailing für Wirtschaftliche Zusammenarbeit und Entwicklung, during the establishment of the common bean collection, the Department for International Development, Euro- similar efforts should be carried out for these bean pean Union, Global Crop Diversity Trust, International crops. The change experienced by soybean from an Board for Plant Genetic Resources, International Cen- oriental soy sauce in North America in 1767 into ter for Tropical Agriculture, United States Agency for an animal feeding and agro-industrial crop in just International Development, United States Department one hundred years (Hymowitz and Bernard, 1991) of Agriculture, and the World Bank. The agricultural is a strong message to not lose options. Along the research services of the following countries are fully concept of a societal insurance provided by crop genetic acknowledged for support in the field work and sub- resources (Gepts, 2006), keeping more crops alive goes sequent germplasm introduction: Argentina, Bolivia, in line with productive, sustainable and locally adapted Chile, Colombia, Costa Rica, Ecuador, El Salvador, agriculture and, as a consequence, with reducing rural Guatemala, Mexico, Panama and Peru. poverty and increasing appreciation towards indigenous cultures. More than ever before, genebanks should Author contributions continue to be the reserve of all options. DGD conceptualized and wrote the paper. DGD collated Concluding remarks the data about use and impact for the first period of the genebank, while MS covered the most recent period. Figure 1 presented breeding challenges in Latin America LGS compiled the data about germplasm distribution. in a time sequence, which were largely met by use MS and LGS re-checked the data of accession numbers. of genetic resources assembled and evaluated over All authors read, revised and approved the manuscript. Genetic Resources (2021), 2 (4), 21–43 Impact of a bean collection 33 Conflict of interest statement tolerant to the herbicide glufosinate ammonium. Crop Sci 42, 1298–1302. doi: https://doi.org/10.2135/ The first author has been responsible of CIAT genebank, cropsci2002.1298 as Head of the Genetic Resources Unit (1996-2009) and as Leader of the Genetic Resources Program (2009- Assefa, T., Assibi-Mahama, A., Brown, A. V., Cannon, E. 2016), with over seventy Staff members operating in K. S., Rubyogo, J. C., Rao, I. M., Blair, M. W., and five experimental stations and three labs, for three Cannon, S. B. (2019). A review of breeding objectives, germplasm collections (bean, cassava and tropical genomic resources, and marker-assisted methods in forages) of over 67,000 accessions. The second author common bean (Phaseolus vulgaris L.). Mol. Breeding has been responsible for all genebank operations in 2017 39, 1–23. doi: https://doi.org/10.1007/s11032-018- to date, which include the regeneration of bean and 0920-0 tropical forages collections in the experimental stations Bandyopadhyay, A., Kancharla, N., Javalkote, V. 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