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I. Paran, I.L. Goldman and D. Zamir

Quantitative trait loci influencing morphological traits were identified by restriction fragment length polymorphism (RFLP) analysis in a population of recombinant inbred lines (RIL) derived from a cross of the cultivated tomato (Lycopersicon esculentum) with a related wild species (L. cheesmanii). One-hundred-thirty-two polymorphic RFLP loci spaced throughout the tomato genome were scored for 97 RIL families. Morphological traits, including plant height, fresh weight, node number, first flower-bearing node, leaf length at nodes three and four, and number of branches, were measured in replicated trials during 1991, 1992, and 1993. Significant (P ≤ 0.01 level) quantitative trait locus (QTL) associations of marker loci were identified for each trait. Lower plant height, more branches, and shorter internode length were generally associated with RFLP alleles from the L. cheesmanii parent. QTL with large effects on a majority of the morphological traits measured were detected at chromosomes 2, 3, and 4. Large additive effects were measured at significant marker loci for many of the traits measured. Several marker loci exhibited significant associations with numerous morphological traits, suggesting their possible linkage to genes controlling growth and development processes in Lycopersicon.

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Steven R. Triano and Dina A. St. Clair

The inbred backcross (IBC) breeding method is being used to introgress genes controlling high fruit soluble solids from a wild tomato species (Lycopersicon cheesmanii f. minor) into a California processing tomato cultivar (Lycopersicon esculentum cv. UC204B). One IBC tomato population (i.e. P1: 106 lines) is being used to map quantitative trail loci (QTL) for soluble solids and other traits. A genetically related but independently generated IBC population (i.e. P2: 96 lines) is being used to lest the efficiency of QTL-linked RPLPs for indirect marker-assisted selection (MAS) to improve soluble solids. P1 was analyzed for fruit quality traits in a replicated field design over 2 years. Twelve P1 lines were significantly greater than UC204B for soluble solids and also had acceptable fruit weights and horticultural traits. All twelve lines have been publicly released for further breeding efforts. In P1. we have identified RPLP markers that have significant correlations to QTL. Some of these markers map to regions previously reported by other researchers to contain QTL for the same traits. We will use 70-80 markers spaced approximately 10-20 cM apart across the genome to screen PI and map QTL. The RPLP analyses are currently in progress. P2 was replicated for one year using the same field design as P1. and analyzed for the same traits. P2 will be screened with QTL-linked RFLPs identified in P1 to test the consistency of QTL locations between independently derived populations. P2 lines selected using RFLP data will be compared to P2 lines identified by classical selection indices. This will indicate if MAS for QTL is effective in a population (P2) genetically independent from the mapping population (P1).

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Gennaro Fazio, Yizhen Wan, Dariusz Kviklys, Leticia Romero, Richard Adams, David Strickland and Terence Robinson

manual, the location of the QTL peaks was refined by multiple-QTL mapping analysis, which uses nearby markers as cofactors in the analysis. Locus interaction analysis. Individual phenotypic data (parametric) and corresponding JoinMap 4.1-coded marker data

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Yanbin Su, Yumei Liu, Huolin Shen, Xingguo Xiao, Zhansheng Li, Zhiyuan Fang, Limei Yang, Mu Zhuang and Yangyong Zhang

were not identified. Major gene/polygene genetic segregation analysis and QTL mapping are the main approaches used to clarify the genetic basis of quantitative traits ( Gai et al., 2007 ; Zhang et al., 2003 ). These methods have been successfully

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Tae-Ho Han, Herman J. van Eck, Marjo J. De Jeu and Evert Jacobsen

An F1 population, derived from an intraspecific cross between two Alstroemeria aurea accessions, was used to map quantitative trait loci (QTL) involved in ornamental and morphological characteristics. One QTL for leaf length was mapped on linkage group three of both parents near marker E+ACCT/M+CGCA-I165 explaining 20% and 14.8% phenotypic variation. Two putative QTL were detected on leaf width on A002-3 and A002-6. One QTL and three putative QTL, involved in the leaf length/width ratio were identified accounting for 46.7% of the phenotypic variance in total. Significant interaction was observed between two QTL, S+AC/M+ACT-I162 and S+AC/M+AGA-I465 in a two-way analysis of variance (ANOVA). For the main color of the flower one QTL and putative QTL accounted for up to 60% of phenotypic variance suggesting simple genetic control of flower color. A two-way ANOVA of these QTL suggested an epistatic interaction. A QTL was detected for color of the inner side of outer lateral tepal with 26.5% of the phenotypic variance explained. This QTL was also associated with main color of the flower just below the 95% threshold value. Two QTL were detected with the Kruskal-Wallis test for the tip color of inner lateral tepal near QTL for other flower color traits. Consequently flower color traits were significantly correlated. A QTL and a putative QTL for the flower size was mapped near marker E+ACCG/M+CGCT-I193 and E+ACCG/M+CGCG-197, respectively. One putative QTL was detected for the stripe width of the inner lateral tepal.

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J. Steven Brown, R.J. Schnell, J.C. Motamayor, Uilson Lopes, David N. Kuhn and James W. Borrone

A genetic linkage map was created from 146 cacao trees (Theobroma cacao), using an F2 population produced by selfing an F1 progeny of the cross Sca6 and ICS1. Simple sequence repeat (SSR) markers (170) were used principally for this map, with 12 candidate genes [eight resistance gene homologues (RGH) and four stress related WRKY genes], for a total of 182 markers. Joinmap software was used to create the map, and 10 linkage groups were clearly obtained, corresponding to the 10 known chromosomes of cacao. Our map encompassed 671.9 cM, approximately 100 cM less than most previously reported cacao maps, and 213.5 cM less than the one reported high-density map. Approximately 27% of the markers showed significant segregation distortion, mapping together in six genomic areas, four of which also showed distortion in other cacao maps. Two quantitative trait loci (QTL) for resistance to witches' broom disease were found, one producing a major effect and one a minor effect, both showing important dominance effects. One QTL for trunk diameter was found at a point 10.2 cM away from the stronger resistance gene. One RGH flanked the minor QTL for witches' broom resistance, implying possible association. QTLs mapped in F2 populations produce estimates of additive and dominance effects, not obtainable in F1 crosses. As dominance was clearly shown in the QTL found in this study, this population merits further study for evaluation of dominance effects for other traits. This F2 cacao population constitutes a useful link for genomic studies between cacao and cotton, its only widely grown agronomic relative.

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Antonio J. Matas, Eward D. Cobb, Dominick J. Paolillo Jr. and Karl J. Niklas

The mechanical properties and anatomy of fruit wall peels and their enzyme-isolated cuticular membranes (CM) are reported for three cherry tomato (Lycopersicon esculentum Mill.) cultivars that are crack-resistant, crack-intermediate, and crack-prone (i.e., Inbred 10, Sweet 100, and Sausalito Cocktail, respectively). The resistant and intermediate fruit peels strain-hardened when extended progressively; those of the crack-prone cultivar did so only modestly. The CM of all cultivars strain-hardened when extended with small forces; the CM of the intermediate and crack-prone cultivars strain-softened under tensile forces that did not strain-soften the crack-resistant cultivar. The peels and CM of the resistant cultivar were stiffer, stronger, and required more energy to break than crack-prone peels. The CM of crack-resistant peels developed deeper within the subepidermis than in the crack-prone or crack-intermediate peels. The CM in the outer epidermal periclinal walls of the crack-resistant and crack-intermediate cultivars was thicker than that of crack-prone peels. These data indicate that CM thickness can be used to gauge crack susceptibility among cherry tomato fruit, which can be useful in breeding programs and would facilitate QTL mapping of the underlying genetic factors.

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Rajeswari Srinivasan* and Richard Manshardt

QTL mapping gives an insight into the number, position and effect of loci controlling quantitative traits. Although a few linkage maps already exist for papaya, not many economically important traits have been studied. An investigation was undertaken to map two qualitative traits: 1) fruit flesh color and 2) an isozyme locus, phosphoglucomutase (PGM); as well as two quantitative traits: 1) number of nodes to first flowering and 2) stamen carpellody. An F2 population consisting of 281 plants derived from the parents Kapoho X Saipan Red was used for this study. Field observations suggested that there may be a linkage between PGM locus and one of the major QTLs controlling number of nodes to first flowering. Also, phenotypic data suggested that there may be a linkage between flesh color and carpellody. Marker genotyping was performed on a subset of 84 plants chosen from the phenotypic extremes of the population for node number and carpellody. Using AFLP (Amplified fragment length polymorphism) method, 510 markers were generated with 161 primer pairs. Although papaya has a haploid chromosome number of 9, at LOD score 5.0 and a maximum recombination frequency of 0.25, 25 linkage groups with number of markers ranging from 2 to 109 were generated using the software Mapmaker\EXP. Linkage and QTL maps are being constructed to reveal the molecular markers linked with the traits of interest and the nature of QTLs controlling the quantitative traits.

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H.A. Agrama and J.W. Scott

The genetic basis of resistance to tomato yellow leaf curl virus (TYLCV) and tomato mottle virus (ToMoV) was studied in three different mapping populations of tomato (Lycopersicon esculentum Mill.). Bulked segregant analysis (BSA) was used to identify random amplification of polymorphic DNA (RAPD) markers linked to TYLCV and ToMoV resistance. Segregated RAPD markers associated with resistance were linked to morphological markers self-pruning (sp) and potato leaf (c) on chromosome 6. RAPD genetic linkage maps of chromosome 6 were constructed for each of the three populations. Common mapped markers revealed straightforward homologies between the chromosome 6 linkage group of the three populations. Multiple-QTL mapping (MQM) was used to identify quantitative trait loci (QTL) for resistance linked to chromosome 6. These revealed that the resistance against TYLCV and ToMoV was mainly explained by two QTL in two populations and one QTL in another. For all of the resistance QTL detected, the favorable allele was provided by the resistant parents. The presence of three different sources of TYLCV and ToMoV resistance, and the markers in tight linkage with them, provide a means of systemically combining multiple resistance genes. Successful cloning of the R gene from tomatoes would lead to deeper understanding of the molecular basis of resistance to TYLCV and ToMoV, and might also shed light on the evolution of resistance genes in plants in general.

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Yan Cheng, Qian Wang, Qingyu Ban, Jianfeng Geng, Xiao Wei Zhang, Ying Yi and Xilin Hou

molecular basis of such complex traits. A prerequisite for QTL mapping studies is the availability of genetic maps, and many of these have been produced for Brassica rapa ( Ajisaka et al., 1995 ; Choi et al., 2007 ; Chyi et al., 1992 ; Kim et al., 2006