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Jan Tivang, Paul W. Skroch, James Nienhuis and Neal De Vos

The magnitude of genetic differences among and heterogeneity within globe artichoke cultivars is unknown. Variation among individual heads (capitula) from three artichoke cultivars and two breeding populations were evaluated using RAPD markers. One vegetatively propagated cultivar (`Green Globe'), two seed-propagated cultivars (`Imperial Star' and `Big Heart') and two breeding populations were examined. Two to thirteen polymorphic bands were observed for 27 RAPD primers, which resulted in 178 scored bands. Variation was found within and among all cultivars, and breeding populations indicating that all five groups represent heterogeneous populations with respect to RAPD markers. The genetic relationships among individual genotypes were estimated using the ratio of discordant bands to total bands scored. Multidimensional scaling of the relationship matrix showed five independent clusters corresponding to the three cultivars and two breeding populations. The integrity of the five clusters was confirmed using pooled chi-squares for fragment homogeneity. Average gene diversity (Hs) was calculated for each population sample, and a one-way analysis of variance showed significant differences among populations. `Big Heart' had an Hs value equivalent to the two breeding populations, while clonally propagated `Green Globe' and seed propagated `Imperial Star' had the lowest Hs values. The RAPD heterogeneity observed within clonally propagated `Green Globe' is consistent with phenotypic variability observed for this cultivar. Overall, the results demonstrate the utility of the RAPD technique for evaluating genetic relationships and contrasting levels of genetic diversity among populations of artichoke genotypes.

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Soon O. Park, Dermot P. Coyne, James R. Steadman, Paul W. Skroch and Geunhwa Jung

The objective was to detect molecular markers associated with QTL for partial physiological resistance (PPR) to two white mold (WM) isolates, partial field resistance (PFR), plant architecture (PA), and plant height (PH) in a genetic linkage map constructed using recombinant inbred lines (RILs) from the cross `PC-50' (resistant to WM) × XAN-159 (susceptible to WM). Significant correlations (+0.39 and +0.47) were noted between the WM reactions in the greenhouse and field. A significant but negative correlation (–0.33) was observed between the WM reaction and PH in the field. Six QTL affecting PPR to isolate 152 were found on LGs 4, 5, 7, and 8. Six QTL affecting PPR to isolate 279 were found on LGs 2, 3, 4, 7, and 8. Five QTL for PFR were observed on LGs 2, 5, 7, 8, and 11. Two QTL affecting PA were detected on LGs 7 and 8. Two QTL affecting PH were identified on LGs 7 and 8. On one end of LG 8 marker H19.1250 was significant for PPR to both isolates. On the other end of LG 8 the region closely linked to the C locus was significantly associated with PPR to both isolates, PFR, PA and PH. Marker J09.950 on LG 7 was significantly associated with PPR to both isolates, PFR, PH and seed weight. Marker J01.2000 on LG 2 was the most significant locus for both PPR to the isolate 279 and PFR. QTL on LG 5 were found for PPR to the isolate 152 and PFR. Overall, four of the five QTL affecting PFR were also found for PPR to one or both isolates.

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Geunhwa Jung, Paul W. Skroch, Dermot P. Coyne, James Nienhuis and E. Arnaud-Santana

Common bacterial blight (CBB) incited by the bacterial pathogen Xanthomonas campestris pv. phaseoli (Smith) Dye is an important disease of common bean. In a previous study, QTL associated with CBB resistance were described based on RAPD marker analysis of a recombinant inbred population derived from the common bean cross BAC-6 (R) × HT-7719 (S) (resistant × susceptible). The objective of this research is to confirm these previously described candidate marker locus-QTL associations using an inbred backcross PC-50 (S) × BAC-6 (R) and a recombinant inbred Venezuela 44 (S) × BAC-6 (R) population. Two markers previously found to be associated with QTL for CBB resistance in the BAC-6 × HT-7719 population were found to account for 30% of the phenotypic variation for CBB resistance in the PC-50 × BAC-6 inbred backcross population. The three most resistant BC2F3 lines based on marker locus genotypes were ranked 1, 3, and 7 (out of 64) based on phenotypic evaluation. These results provide important confirmation of marker locus-QTL associations and indicate that RAPD markers linked to loci controlling the expression of CBB resistance in common bean may be used to transfer resistance genes into susceptible breeding material.

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Geunhwa Jung, Dermot P. Coyne, E. Arnaud-Santana, James Bokosi, Shawn M. Kaeppler, Paul W. Skroch and James Nienhuis

Common bacterial blight(CBB) and rust diseases, incited by the bacterial pathogen Xanthomonas campestris pv. phaseoli (Smith) Dye (Xcp) and Uromyces appendiculatus, respectively, are important diseases of common beans (Phaseolus vulgaris L.). The objectives were to construct a molecular linkage map, to locate CBB resistances, rust resistances and leaf pubescence using RAPDs. Sixteen linkage groups with 22 unassigned markers were identified. 178 RAPD markers and 8 morphological markers were mapped in a Population of 70 RI lines. Regression analysis and interval mapping using MAPMAKER/QTL were used to identify genomic regions involved in the genetic control of the traits. One, two, and three putative QTLs were identified for seed, pod and leaf reactions. These regions accounted for 18%, 25%, and 35% of the phenotypic variation in CBB resistance. A chromosome region on linkage group 1 carried factors influencing all three traits. Rust resistance genes controlling the reactions on the primary and on the 4th trifoliolate leaves (adult plant resistance) were located in linkage group 16. The genes for abaxial leaf pubescence was located on linkage group 9.

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Soon O. Park, Dermot P. Coyne, Geunhwa Jung, Paul W. Skroch, E. Arnaud-Santana and James R. Steadman

Our objective was to identify QTL for seed weight (SW), length, and height segregating in a recombinant inbred line (RIL) population from the cross `PC-50' (Larger SW) × XAN-159 (Smaller SW). The parents and RILs were grown in two separate greenhouse experiments in Nebraska, and in field plots in the Dominican Republic and Wisconsin. Data analysis was done for individual environments separately and on the mean over all environments. A simple linear regression analysis of all data indicated that most QTL appeared to be detected in the mean environment. Composite interval mapping (CIM) analysis was then applied to the means over environments. Eight QTL for SW were detected on common bean linkage groups (LGs) 3, 4, 5, 6, 7, and 8. All eight markers associated with these QTL were significant in a multiple regression analysis (MRA), where the full model explained 63% of the variation among SW means. Six QTL for seed length were detected on LGs 2, 3, 4, 8, and 11 using CIM. The markers associated with the three seed length QTL on LGs 2, 8, and 11 were significant in a MRA with the full model explaining 48% of the variation among seed length means. Three QTL for seed height on LGs 4, 6, and 11 explained 36% of the phenotypic variation for trait means. Four of the six QTL for seed length and two of three QTL for seed height also appeared to correspond to QTL for SW.

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Soon O. Park, Dermot P. Coyne, Geunhwa Jung, Paul W. Skroch, E. Arnaud-Santana, James R. Steadman, H.M. Ariyarathne and James Nienhuis

Our objective was to identify quantitative trait loci (QTL) for seed weight, length, and height segregating in a recombinant inbred line population derived from the common bean (Phaseolus vulgaris L.) cross `PC-50' × XAN-159. The parents and progeny were grown in two separate greenhouse experiments in Nebraska, and in field plots in the Dominican Republic and Wisconsin. Data analysis was done for individual environments separately and on the mean over all environments. A simple linear regression analysis of all data indicated that most QTL appeared to be detected in the mean environment. Based on these results, composite interval mapping (CIM) analysis was applied to the means over environments. For seed weight, strong evidence was indicated for five QTL on common bean linkage groups (LGs) 3, 4, 6, 7, and 8. Multiple regression analysis (MRA) indicated that these QTL explained 44% of the phenotypic variation for the trait. Weaker evidence was found for three additional candidate QTL on bean LGs 4, 5, and 8. All eight markers associated with these QTL were significant in a MRA where the full model explained 63% of the variation among seed weight means. For seed length, CIM results indicated strong evidence for three QTL on LG 8 and one on LG 2. Three additional putative QTL were detected on LGs 3, 4, and 11. The markers associated with the three seed length QTL on LG 8, and the QTL on LGs 2 and 11 were significant in a MRA with the full model explaining 48% of the variation among seed length means. For seed height, three QTL on LGs 4, 6, and 11 explained 36% of the phenotypic variation for trait means. Four of the seven QTL for seed length and two of three QTL for seed height also appeared to correspond to QTL for seed weight. Four QTL for common bacterial blight resistance [Xanthomonas campestris pv. phaseoli (Smith Dye)] and for smaller seed size were associated on LGs 6, 7, and 8. The implications of these findings for breeders is discussed.

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Geunhwa Jung, Dermot P. Coyne, Paul W. Skroch, James Nienhuis, E. Arnaud-Santana, James Bokosi, H.M. Ariyarathne, James R. Steadman, James S. Beaver and Shawn M. Kaeppler

Random amplified polymorphic DNA (RAPD) markers were used to construct a partial linkage map in a recombinant inbred population derived from the common bean (Phaseolus vulgaris L.) cross BAC 6 × HT 7719 for studying the genetics of disease resistance in common bean. The linkage map spanned 545 cM and included 75 of 84 markers used in this study. The population of 128 recombinant inbred lines was evaluated for resistance to common bacterial blight, foliar resistance to web blight [WB; Thanatephorus cucumeris (Frank) Donk], and resistance to rust [Uromyces appendiculatus var. appendiculatus (Pers.:Pers) Unger]. Common bacterial blight [CBB; Xanthomonas campestris pv. phaseoli (Smith) Dye] resistance was evaluated for CBB strain Epif-IV in later-developed trifoliolate leaves and for CBB strain EK-11 in seeds, first trifoliolate leaves, later-developed trifoliolate leaves, and pods. In addition, lines were rated for plant uprightness and branch density. Two to six markers accounted for 14% to 34% of the phenotypic variation for each trait. Significant marker locustrait associations were found for 14 mapped loci and 7 of the 9 unmapped markers. The distribution of detected QTL appeared to be nonrandom with most significant markers associated with more than one trait or closely linked to markers significantly associated with variation for a different trait. One marker, BC4091250, was significantly associated with WB resistance, resistance for CBB strain Epif-IV in later-developed trifoliolate leaves, and resistance for CBB strain EK-11 in first trifoliolate leaves, later-developed trifoliolate leaves, and pods. A rust resistance gene was mapped in an interval 14.6 cM from RAPD marker H191050 and 12.5 cM from marker AJ16250.

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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.

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Geunhwa Jung, Dermot P. Coyne, Paul W. Skroch, James Nienhuis, E. Arnaud-Santana, James Bokosi, H.M. Ariyarathne, James Steadman and James S. Beaver

Common blight, web blight, and rust, incited by the bacterial pathogen Xanthomonas campestris pv. phaseoli (Smith) Dye (Xcp) and the fungal pathogens Thanatephorus cucumeris (Frank) Donk (Tc) and Uromyces appendiculatus (Pers.:Pers) Unger, respectively, are important diseases of common beans (Phaseolus vulgaris L.). The objectives of were to construct a linkage map, and to locate CBB, rust, and WB resistances and plant architecture traits using RAPDs. Ten linkage groups were identified. Eighty-nine RAPD markers and rust resistance were mapped in 128 RI lines of the cross BAC-6 and HT-7719. Regression analysis and interval mapping using MAPMAKER/QTL were used to identify genomic regions involved in the genetic control of the traits. One, two, two, and three putative QTLs were identified for leaf, seed, and pod reactions to Xcp, and foliar reaction to Tc. These regions accounted for 11%, 9%, 32%, and 30% of the phenotypic variation in the resistances. Two, two, and three regions were identified for plant uprightness, branch density, and pod distribution. These regions accounted for 27%, 13%, and 16% of the phenotypic variation. Unassigned marker G17d influenced some of the phenotypic variation in all three traits. A rust resistance gene controlling pustule size on primary leaves was located in linkage group 1.