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Mark J. Bassett, Rian Lee, Tim Symanietz and Phillip E. McClean

Two common bean (Phaseolus vulgaris L.) genes, J (modifies seedcoat color and pattern) and L (modifies partly colored seedcoat pattern), were tested for allelism using genetic tester stocks. Those stocks have a common genetic background by backcrossing to the recurrent parent, Florida dry bean breeding line 5-593, that has black self-colored seeds and purple flowers due to the genotype T P [C r] Z J G B V Rk. Specifically, the L gene from `Thuringia' and the lers gene from `Early Wax' were tested for allelism with the j gene from various genetic tester stocks. L was found to be identical with j, but l ers was a different allele at J. We propose the gene symbols J (formerly l), j (formerly L), and j ers (formerly l ers). The seedcoat genotype of `Thuringia' was found to be t P C z j g b v lae rk d. A new seedcoat pattern called reverse margo was found to be determined by the genotype T/t z/z j/j ers in a P C G B V genetic background. A randomly amplified polymorphic DNA marker was developed for the j gene (formerly L) from `Thuringia' using bulk segregant analysis in an F2 population segregating for j vs. J in a t z genetic background, i.e., from the cross t z j × t z J in BC1 to 5-593. The linkage distance between marker OL4525 and j was determined to be 1.2 cM. In a population segregating for J and j ers, the distance between the marker and j ers was determined to be 4.7 cM. The utility of marker OL4525 is limited primarily to the Middle American gene pool.

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Mark J. Bassett, Lee Brady and Phil E. McClean

Common bean (Phaseolus vulgaris L.) plants with partly colored seeds and colored flowers were derived from PI 507984 in two genetic tester stocks, `2-points t cf BC1 5-593' and `2-points t cf BC2 5-593'. These stocks were produced by backcrossing to the recurrent parent, Florida dry bean breeding line 5-593, which has black self-colored seeds and purple flowers due to the genotype T P V. The crosses `2-points t cf BC1 5-593' × 5-593 and `2-points t cf BC2 5-593' × 5-593 produced F2 populations in which all plants had colored flowers. Those results, when considered with previously published work, do not support the previously reported hypothesis that the genes t Fcr Fcr-2 produce partly colored seedcoats and flower color restoration with t. The crosses `2-points t cf BC1 5-593' × `self-colored t BC2 5-593' and `2-points t cf BC2 5-593' × `minimus t BC3 5-593' produced F2 populations that segregated 3:1 for colored:white flowers, respectively. Those results are consistent with the revised hypothesis that t cf can produce partly colored seedcoats without affecting flower color. The RAPD marker OM19400, which is linked in repulsion to T, was used with the F2 populations from the crosses `2-points t cf BC2 5-593' × 5-593 and `2-points t cf BC2 5-593' × `minimus t BC3 5-593' and established that the t cf gene from PI 507984 is either an allele at T or tightly linked to T. F3 data from the cross `2-points t cf BC2 5-593 × 5-593 also support the t cf hypothesis. On the basis of the above experiments, the gene symbol t cf is proposed for an allele at T that pleiotropically produces partly colored seeds and colored flowers.

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Gino E. Beltrán, Geunwha Jung, James Nienhuis and Mark J. Bassett

The development of a complete linkage map, including both classical (visible) and molecular markers, is important to understand the genetic relationships among different traits in common bean (Phaseolus vulgaris L.). The objective of this study was to integrate classical marker genes into previously constructed molecular linkage maps in common bean. Bulked segregant analysis was used to identify 10 random amplified polymorphic DNA (RAPD) markers linked to genes for five classical marker traits: dark green savoy leaf (dgs), blue flower (blu), silvery [Latin: argentum] green pod (arg), yellow wax pod (y) and flat pod (a spontaneous mutation from round to flat pod in `Hialeah' snap bean). The genes for dark green savoy leaf (dgs) and blue flower (blu) were located in a previously constructed molecular linkage map. These results indicate that classical marker genes and molecular markers can be integrated to form a more complete and informative genetic linkage map. Most of the RAPD markers were not polymorphic in the two mapping populations used, and molecular markers from those mapping populations were not polymorphic in the F2 populations used to develop the RAPD markers. Alternative genetic hypotheses for the pod shape mutation in `Hialeah' are discussed, and the experimental difficulties of pod shape classification are described.

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Jose J. Velez, Mark J. Bassett, James S. Beaver and Albeiro Molina

The inheritance of resistance to bean golden mosaic virus (BGMV) in common bean (Phaseolus vulgaris L.) was studied in crosses between susceptible bean variety XAN176 and resistant breeding lines 9236-6 (T446/A429) and 9245-94 (DOR303/T968). Disease response data were taken on plants from four generations derived from each cross (parents, F1, F2, and backcrosses (BCs) of F1 to both parents) at 25 days after plants were inoculated with BGMV, using whiteflies (Bemisia argentifolii Bellows & Perring) as vectors. The segregation ratios obtained from F2 and BC generations were consistent with the hypothesis that resistance in 9236-6, which prevents a chlorotic response, is conferred by a single recessive gene. The disease response in 9245-94 was controlled by two genes—a dominant gene controlling a dwarfing reaction and a recessive resistance gene preventing a chlorotic response to BGMV infection. An allelism test demonstrated that the gene controlling resistance in 9236-6 is nonallelic with the recessive gene controlling resistance in 9245-94. The gene symbol bgm is proposed for the recessive resistance gene (originally from A429) in 9236-6. The gene symbol bgm-2 is proposed for the recessive resistance gene (originally from DOR303) in 9245-94.

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Luwbia Aranda, Timothy G. Porch, Mark J. Bassett, Laura Lara and Perry B. Cregan

Circumlineatus (cl) in common bean (Phaseolus vulgaris L.) is identified by a precipitation line in the seedcoat at the boundary of the white and colored zones. Cl is recessive and is expressed in partly colored seedcoats (t) with restricted patterns such as virgarcus. In this study, amplified fragment length polymorphism (AFLP) and single nucleotide polymorphism (SNP) markers, and the common bean genome sequence were used in combination with bulk segregant analysis and bidirectional selective genotyping to identify the genetic location of Cl. Markers were identified that cosegregated with Cl using Cl/Cl and cl/cl F3 and F5 progeny bulks from the cross t z cl G b v virgarcus BC3 5-593 × t z sel Cl G b v sellatus BC3 5-593. Two bands from an AFLP primer combination, which yielded unambiguous polymorphisms between the bulks, were cloned and sequenced. The two sequences were used to interrogate the common bean whole genome sequence identifying a region also found through cosegregation analysis using bidirectional selective genotyping with SNPs. Thus, the Cl gene was localized on Pv09 using cosegregating AFLP and SNP markers, and the physical location was confirmed with the whole genome sequence.

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Clifford W. Beninger, George L. Hosfield, Mark J. Bassett and Shirley Owens

Three common bean (Phaseolus vulgaris L.) seedcoat color (or glossiness) genotypes, differing from each other by a single substitution at a seedcoat locus, were analyzed for presence and concentration of three anthocyanins: delphinidin 3-O-glucoside, petunidin 3-O-glucoside, and malvidin 3-O-glucoside. The three anthocyanins were present in Florida common bean breeding line 5-593 (P C J G B V Asp), matte black (P C J G B V asp), and dark brown violet (P C J G b V Asp), but the amounts varied greatly depending on the genotype. Dark brown violet had 19% of the total anthocyanin content when compared to 5-593, whereas matte black had amounts intermediate between the two other genotypes. The B gene acts to regulate the production of precursors of anthocyanins in the seedcoat color pathway above the level of dihydrokaempferol formation, perhaps at the chalcone synthase or chalcone isomerase steps in the biosynthetic pathway. We hypothesize that B regulates simultaneously the flavonoid (color) and isoflavonoid (resistance) pathways. The I gene for resistance to bean common mosaic virus (BCMV) is known to be linked closely to B. It is therefore hypothesized that the I gene function may be to respond to BCMV infection by dramatically increasing (over a low constituitive level) production in the 5-dehydroxy isoflavonoid pathway, which leads to synthesis of the major phytoalexin, phaseollin, for resistance to BCMV. Alternatively, the B and I genes may be allelic. The Asp gene affects seedcoat glossiness by means of a structural change to the seedcoat. We demonstrate that Asp in the recessive condition (asp/asp) changes the size and shape of the palisade cells of the seedcoat epidermis, making them significantly smaller than either 5-593 or dark brown violet. Asp, therefore, limits the amounts of anthocyanins in the seedcoat by reducing the size of palisade cells.

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Phillip N. Miklas, Richard Delorme, Valerie Stone, Mark J. Daly, J. Rennie Stavely, James R. Steadman, Mark J. Bassett and James S. Beaver

Understanding the genomic associations among disease resistance loci will facilitate breeding of multiple disease resistant cultivars. We constructed a genetic linkage map in common bean (Phaseolus vulgaris L.) containing six genes and nine quantitative trait loci (QTL) comprising resistance to one bacterial, three fungal, and two viral pathogens of bean. The mapping population consisted of 79 F5:7 recombinant inbred lines (RILs) derived from a `Dorado'/XAN 176 hybridization. There were 147 randomly amplified polymorphic DNA (RAPD) markers, two sequence characterized amplified region (SCAR) markers, one intersimple sequence repeat (ISSR) marker, two seedcoat color genes R and V, the Asp gene conditioning seed brilliance, and two rust [Uromyces appendiculatus var. appendiculatus (Pers.:Pers) Unger] resistance genes: one conditioning resistance to Races 53 and 54 and the other conditioning resistance to Race 108. These markers mapped across eleven linkage groups, one linked triad, and seven linked pairs for an overall map length of 930 cM (Kosambi). Genes conditioning resistance to anthracnose (Co-2) [Colletotrichum lindemuthianum (Sacc. and Magnus) Lams.-Scrib.], bean rust (Ur-5), and bean common mosaic virus (I and bc-3) (BCMV) did not segregate in this population, but were mapped by inference using linked RAPD and SCAR markers identified in other populations. Nine previously reported quantitative trait loci (QTL) conditioning resistance to a variety of pathogens including common bacterial blight [Xanthomonas campestris pv. phaseoli (Smith) Dye], ashy stem blight [Macrophomina phaseolina (Tassi) Goid.], and bean golden mosaic virus (BGMV), were located across four linkage groups. Linkage among QTL for resistance to ashy stem blight, BGMV, and common bacterial blight on linkage group B7 and ashy stem blight, BGMV, and rust resistance loci on B4 will complicate breeding for combined resistance to all four pathogens in this population.

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Juan M. Osorno, Carlos G. Muñoz, James S. Beaver, Feiko H. Ferwerda, Mark J. Bassett, Phil N. Miklas, Teresa Olczyk and Bill Bussey

Bean golden yellow mosaic virus (BGYMV), incited by a whitefly (Bemisia tabaci Gennadius) transmitted geminivirus, is an important disease that can limit common bean (Phaseolus vulgaris L.) production in Central America, the Caribbean, and southern Florida. Only a few genes are currently deployed in BGYMV-resistant common bean cultivars. The identification of novel sources of resistance would help bean breeders broaden the genetic base of resistance to this important virus. Phaseolus coccineus L. germplasm accession G35172 was found by International Center for Tropical Agriculture scientists to be resistant to BGYMV. Populations derived from an interspecific cross between P. vulgaris and P. coccineus were evaluated to study the inheritance of resistance to BGYMV. Segregation ratios of F2 plants and other populations suggest that BGYMV resistance from P. coccineus is controlled by two genes. A recessive gene, with the proposed symbol bgm-3, confers resistance to leaf chlorosis and a dominant gene, with the proposed name Bgp-2, prevents pod deformation in the presence of BGYMV. Results from allelism tests with previously reported BGYMV resistance genes (bgm, bgm-2, and Bgp) and the absence of the SR-2 sequence-characterized amplified region marker for bgm support the hypothesis that bgm-3 and Bgp-2 are different genes for BGYMV resistance.

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Geunhwa Jung, Paul W. Skroch, Dermot P. Coyne, James Nienhuis, E. Arnaud-Santana, H.M. Ariyarathne, Shawn M. Kaeppler and Mark J. Bassett

Randomly amplified polymorphic DNA (RAPD) molecular markers were used to construct a partial genetic linkage map in a recombinant inbred population derived from the common bean (Phaseolus vulgaris L.) cross PC-50 × XAN-159 for studying the genetics of bacterial disease resistance in common bean. The linkage map spanned 426 cM and included 168 RAPD markers and 2 classical markers with 11 unassigned markers. The seventy recombinant inbred lines were evaluated for resistance to two strains of common bacterial blight [Xanthomonas campestris pv. phaseoli (Smith) Dye] (Xcp). Common bacterial blight (CBB) resistance was evaluated for Xcp strain EK-11 in later-developed trifoliolate leaves and for Xcp strains, DR-7 and EK-11, in first trifoliolate leaves, seeds, and pods. One to four quantitative trait loci (QTLs) accounted for 18% to 53% of the phenotypic variation for traits. Most significant effects for CBB resistance were associated with one chromosomal region on linkage group 5 and with two regions on linkage group 1, of the partial linkage map. The chromosomal region (a 13-cM interval) in linkage group 5 was significantly associated with resistance to Xcp strains DR-7 and EK-11 in leaves, pods, and seeds. The regions in linkage group 1 were also significantly associated with resistance to both Xcp strains in more than one plant organ. In addition, a seedcoat pattern gene (C) and a flower color gene (vlae) were mapped in linkage groups 1 and 5, respectively, of the partial linkage map. The V locus was found to be linked to a QTL with a major effect on CBB resistance.