Chapter 7 Marker-assisted Selection In Common Beans And .

Chapter 7Marker-assisted selection incommon beans and cassavaMathew W. Blair, Martin A. Fregene, Steve E. Beebe and Hernán Ceballos

82Marker-assisted selection – Current status and future perspectives in crops, livestock, forestry and fishSummaryMarker-assisted selection (MAS) in common beans (Phaseolus vulgaris L.) and cassava(Manihot esculenta) is reviewed in relation to the breeding system of each crop and thebreeding goals of International Agricultural Research Centres (IARCs) and NationalAgricultural Research Systems (NARS). The importance of each crop is highlighted andexamples of successful use of molecular markers within selection cycles and breeding programmes are given for each. For common beans, examples are given of gene tagging forseveral traits that are important for bean breeding for tropical environments and aspectsconsidered that contribute to successful application of MAS. Simple traits that are taggedwith easy-to-use markers are discussed first as they were the first traits prioritized forbreeding at the International Center for Tropical Agriculture (CIAT) and with NARSpartners in Central America, Colombia and eastern Africa. The specific genes for MASselection were the bgm-1 gene for bean golden yellow mosaic virus (BGYMV) resistanceand the bc-3 gene for bean common mosaic virus (BCMV) resistance. MAS was efficientfor reducing breeding costs under both circumstances as land and labour savings resultedfrom eliminating susceptible individuals. The use of markers for other simply inheritedtraits in marker-assisted backcrossing and introgression across Andean and Mesoamericangene pools is suggested. The possibility of using MAS for quantitative traits such as lowsoil phosphorus adaptation is also discussed as are the advantages and disadvantages ofMAS in a breeding programme. For cassava, the use of multiple flanking markers for selection of a dominant gene, CMD2 for cassava mosaic virus (CMV) resistance at CIAT andthe International Institute of Tropical Agriculture (IITA) as well as with NARS partners inthe United Republic of Tanzania using a participatory plant breeding scheme are reviewed.MAS for the same gene is important during introgression of cassava green mite (CGM) andcassava brown streak (CBS) resistance from a wild relative, M. esculenta sub spp. flabellifolia. The use of advanced backcrossing with additional wild relatives is proposed as a wayto discover genes for high protein content, waxy starch, delayed post-harvest physiologicaldeterioration, and resistance to whiteflies and hornworm. Other potential targets of MASsuch as beta carotene and dry matter content as well as lower cyanogenic potential are given.In addition, suggestions are made for the use of molecular markers to estimate averageheterozygosity during inbreeding of cassava and for the delineation of heterotic groupswithin the species. A final section describes the similarities and differences between theMAS schemes presented for the two crops. Differences between the species can be ascribedpartially to the breeding and propagation systems of common beans (seed propagated, selfpollinating) and cassava (clonally propagated, cross-pollinating). In addition, differencesin growth cycles, breeding methods, availability of genetic markers, access to selectionenvironments and the accompanying opportunities for phenotypic selection influence thedecisions in both crops of when and how to apply MAS. Recommendations are made forapplying MAS in breeding of both crops including careful prioritization of traits, markersystems, genetic stocks, scaling up, planning of crosses and the balance between MAS andphenotypic selection.

Chapter 7 – Marker-assisted selection in common beans and cassavaCommon beans: importance andgeneticsCommon beans (Phaseolus vulgaris L.)are the most important grain legume fordirect human consumption, especially inLatin America and eastern and southernAfrica. They are seed-propagated, true diploids (2n 22) and have a relatively smallgenome (650 Mb) (Broughton et al., 2003).Originating in the Neotropics, commonbeans were domesticated in at least twomajor centres in Mesoamerica and theAndes (Gepts, 1988) and possibly in athird minor centre in the northern Andes(Islam et al., 2002). Wide DNA polymorphism is expressed between the twomajor gene pools. Mesoamerican beanstypically have small to medium size seedsand can be classed into four races that aredistinguished by randomly amplified polymorphic DNA (RAPD) polymorphisms(Beebe et al., 2000). Andean beans usuallyhave medium to large seeds, and landraceshave been classed into three races basedon plant morphology and agro-ecologicaladaptation (Singh, Gepts and Debouck,1991). These can be differentiated by microsatellites (M. Blair, unpublished data) butthe genetic distance among Andean races isnarrower than that among Mesoamericanraces (Beebe et al., 2001). A large numberof gene tagging studies have been conducted in common beans, predominantlywith RAPD markers, some of which havebeen converted subsequently to sequencecharacterized amplified regions (SCARs;reviewed most recently by Miklas et al.,2006).Beans display a wide range of growthhabits (Van Schoonhoven and PastorCorrales, 1987), from determinate bushtypes, to indeterminate upright or vinybush types, to vigorous climbers. Bushtypes are the most widely grown, and are a83relatively short season crop, maturing in aslittle as 60 days from seeding in a tropicalclimate and yielding from 700 to 2 000 kg/ha on average. On the other hand, in smallholder agriculture where land is scarce,labour-intensive, high-yielding climbingbeans enjoy continuing or even expandingpopularity. Climbing beans can mature in100 to 120 days at mid-elevations, but candelay as long as ten months at higher elevations and can produce the highest yields forthe crop, up to 5 000 kg/ha. These featureshave significant implications for breedingprogrammes. In bush types it is possibleto obtain up to three cycles per year inthe field, or even four cycles in greenhouse conditions. Breeding bush beans isthus quite agile with regard to advance ofgenerations, although seed harvest of individual plants is sometimes limited. Withclimbing beans, on the other hand, at bestit is possible to obtain two cycles per yearwith field grown plants, while managingclimbing beans in the greenhouse is logistically difficult. However, while bush beansproduce on average 20 to 50 seeds/plant,individual plants of climbing beans oftenproduce enough seeds to plant several rows(100 to 150 seeds).Beans are self-pollinating and thusbreeding methods for autogamous cropsare employed. Pedigree selection or someadaptation thereof is most common, andboth recurrent (Muñoz et al., 2004) andadvanced (or inbred) backcrossing (Sullivanand Bliss, 1983; Buendia et al., 2003; Blair,Iriarte and Beebe, 2003) have been used.Recurrent selection has also been employed(Kelly and Adams, 1987; Beaver et al.,2003) but seldom in a formal sense with adefined population structure. Singh et al.(1998) suggested a system that they calledgamete selection in which individual F1plants of multiple parent crosses give rise

84Marker-assisted selection – Current status and future perspectives in crops, livestock, forestry and fishto families. This system takes advantage ofthe variability among F1 plants that is created between segregating parental plants.The choice of breeding method and itsadaptation to specific circumstances, thegrowth cycle of the crop in relation todifferent planting seasons, the access toselection environments and the accompanying opportunities for phenotypicselection and the ease of implementing thespecific markers to be used will all influence the decisions about where and howMAS will be most cost effective and usedto best advantage.MAS in bean breeding: experiences ofCIAT and NARSMolecular markers have been sought forboth simple and complex traits in beans,with an eye to eventual application in MAS.Tagging of genes and QTL in common beanand their application to MAS have beenreviewed previously (Kelly et al., 2003;Miklas et al., 2006). In the present chapter,some of the aspects that contribute to thesuccessful use of MAS are considered ingreater detail, referring to examples takenfrom bean breeding in the tropics at CIATand within NARS. Simple and complextraits are discussed separately, as they represent two contrasting sorts of experience.Simple traitsBean golden yellow mosaic virus resistanceBean golden yellow mosaic virus (BGYMV)is a white fly-transmitted Gemini virus, anda major production limitation of beans inthe mid-to-low altitude areas of CentralAmerica, Mexico and the Caribbean.Host resistance to the virus is the mostpractical means of control, and any newvariety in these production areas must carryresistance. Studies on inheritance of resistance revealed a major gene denominatedbgm-1 in breeding line A429 (Blair andBeaver, 1993) that originates in the Mexican(Durango race) accession “Garrapato” orG2402. Minor genes (Miklas et al., 2000c)as well as additional recessive and dominantresistance genes exist for the virus (Miklaset al., 2006). In most production areaswhere BGYMV exists, it is necessary topyramid genes for adequate disease control.Although lines developed in CIAT targetthese areas, BGYMV does not exist at levelsthat would permit selection under fieldconditions in Palmira, Colombia, at CIATheadquarters. Therefore, MAS was desirable to assure recovery of at least the mostimportant resistance genes. MAS has alsobeen employed in the Panamerican Schoolin Zamorano, Honduras, as a complementto field screening, to extend selection tosites and seasons with less disease pressure(J.C. Rosas, personal communication).A co-dominant RAPD marker wasidentified for the bgm-1 gene (Urrea etal., 1996) that was subsequently convertedto a SCAR marker named SR2 (CIAT,1997). The DNA fragment associated withbgm-1 gene has only been observed inone genotype other than G2402 and itsderivatives, and thus the polymorphismhas been very useful for recognizing thepresence of the gene in different geneticbackgrounds. This SCAR was evaluated onas many as 7 000 plants in a single sowing(CIAT, 2001; 2003). The uniqueness of themarker’s polymorphism and its reliabilityover laboratories, seasons and geneticbackgrounds have facilitated its wide use.More recently, a second SCAR (SW12.700)was developed from the W12.700 RAPDfor a QTL located on linkage group b04(Miklas et al., 2000c), and this has alsobeen incorporated into the breedingprogramme of CIAT. The combination ofbgm-1 and the QTL is expected to offer an