Microsatellite or simple sequence repeat (SSR) markers were developed from Rosa wichurana Crépin to combine two previously constructed tetraploid rose (Rosa hybrida L.) genetic maps. To isolate SSR-containing sequences from rose a small-insert genomic library was constructed from diploid Rosa wichurana and screened with several SSR probes. Specific primers were designed for 43 unique SSR regions, of which 30 primer pairs gave rise to clear PCR products. Seventeen SSR primer pairs (57%) produced polymorphism in the tetraploid rose 90-69 mapping family. These markers were incorporated into existing maps of the parents 86-7 and 82-1134, which were constructed primarily with AFLP markers. The current map of the male parent, amphidiploid 86-7, consists of 286 markers assigned to 14 linkage groups and covering 770 cm. The map of the female tetraploid parent, 82-1134, consists of 256 markers assigned to 20 linkage groups and covering 920 cm. Nineteen rose SSR loci were mapped on the 86-7 map and 11 on the 82-1134 map. Several homeologous linkage groups within maps were identified based on SSR markers. In addition, some of the SSR markers provided anchoring points between the two parental maps. SSR markers were also useful for joining small linkage groups. Based on shared SSR markers, consensus orders for four rose linkage groups between parental maps were generated. Microsatellite markers developed in this study will provide valuable tools for many aspects of rose research including future consolidation of diploid and tetraploid rose genetic linkage maps, genetic, phylogenetic and population analyses, cultivar identification, and marker-assisted selection.
L.H. Zhang, D.H. Byrne, R.E. Ballard, and S. Rajapakse
8 COLLOQUIUM 1 (Abstr. 001–005) Genome Mapping of Horticultural Crops
John McCallum, Gail Timmerman-Vaughan, Tonya Frew, and Adrian Russell
Developmental, environmental, and genetic factors affecting seed color were studied in the progeny of a cross between two white-flowered (aa) green cotyledon (ii) field peas (Pisum sativum L.): the pale large-seeded Marrowfat cultivar Primo and the greener small-seeded Prussian Blue OSU442-15. Changes in chlorophyll and carotenoid content during seed development of the parental genotypes were determined by high performance liquid chromatography analysis. Both cultivars accumulated similar pigment quantities per seed, but pigment loss was greater during maturation of `Primo'. Bleached and unbleached mature seed tissues also were compared for pigment composition. Lutein was the predominant pigment in bleached cotyledons of both cultivars. Only trace amounts of pheophytins were detected in unbleached seed. In both genotypes, chlorophyll A : B ratios were ≈1:1 in seed coats compared to 3:1 in cotyledons. Objective measurements of seed color in terms of luminance (lightness) and chrominance (hue and saturation) were made in YUV color space by video image analysis. Inheritance of seed color was studied in an F2 population derived from the `Primo' × `OSU442-15' cross and inbred descendants. Quantitative trait loci (QTL) for seed color were localized by interval mapping using a linkage map of 199 molecular markers spanning most of the genome and by bulked segregant analysis and selective genotyping. Four genomic regions affecting seed color were detected. A major gene accounting for 61% of the phenotypic variance in seed lightness (Y luminance component) was identified on linkage group V linked to r locus. Another major gene, which accounted for 56% of the phenotypic variance in seed hue (U chrominance component), was mapped to a linkage group containing group III and IV markers. A QTL with smaller effect on seed hue (U and V chrominance components) was detected on linkage group VII. Support for overdominant allelic interaction for a QTL on linkage group I, adjacent to the legumin locus Lg-J, was obtained by selective genotyping of the seed lightness distributional extremes.
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.
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.
Dror Sharon, Jossi Hillel, Samir Mhameed, Perry B. Cregan, Emanuel Lahav, and Uri Lavi
The detection of association between DNA markers and traits of interest in an outbred population is complicated and requires highly polymorphic markers. A genetic linkage map of avocado (Persea americana Mill.) recently generated consists of simple sequence repeat (SSR) markers as well as DNA fingerprint (DFP) and randomly amplified polymorphic DNA (RAPD) markers. These markers were used to detect putative quantitative trait loci (QTLs) of eight avocado fruit traits. Two statistical methods were used: one-way analysis of variance and interval mapping. Six traits were found to be associated with at least one of the 90 DNA markers. Based on the two statistical approaches, a putative QTL associated with the presence of fibers in the flesh, was found to be located on linkage group 3. This putative QTL was found to be associated with the SSR marker AVA04 having a high significant value (P = 4.4 × 10-8). The haplotype analysis of linkage group 3 showed a putative dominant interaction between the alleles of this locus.
Chunxiao Jiang and Kenneth C. Sink
RAPD (Random Amplified Polymorphic DNA) is being utilized to construct a molecular genetic linkage map. The mapping population used is comprised of 65 individuals. Of the 240 decamer primers (Operon) tested to date, 50 polymorphic bands have been resolved. The 50 markers are divided into two groups according to the genotypes of the two parents. The first group is where the female parent is heterozygous and male parent is homozygous and it has 17 markers, while the second group, in which male parent is heterozygous and female parent is homozygous, has 33 markers. Analysis of the two groups by MAPMAKER indicated that two linkage groups are formed in the first group, and five linkage groups are formed in the second group. Sex type is controlled by the M locus. Genetic experiments have demonstrated that females are homogametic (mm) while male plants are heterogametic (Mm) for the sex locus. Two bulks of genomic DNA created by using 10 male and 10 female individuals in the population were screened to identify RAPD markers associated with the sex locus. RAPD marker OCP15-984 is closely linked with the M locus (7.6 cM).
H.M. Ariyarathne, D.P. Coyne, G. Jung, P.W. Skroch, A.K. Vidaver, J.R. Steadman, P.N. Miklas, and M.J. Bassett
Diseases of beans (Phaseolus vulgaris L.) are primary constraints affecting bean production. Information on tagging and mapping of genes for disease resistance is expected to be useful to breeders. The objectives of this study were to develop a random amplified polymorphic DNA (RAPD) marker linkage map using 78 F9 recombinant inbred (RI) lines derived from a Middle-American common bean cross Great Northern Belneb RR-1 [resistant to common bacterial blight (CBB) and halo blight (HB)] × black A 55 [dominant I gene resistance to bean common mosaic potyvirus] and to map genes or QTL (quantitative trait loci) for resistance to CBB, HB, BCMV (bean common mosaic virus), and BCMNV (bean common mosaic necrosis virus) diseases. The RI lines were evaluated for resistance to leaf and pod reactions to Xanthomonas campestris pv. phaseoli (Xcp) (Smith Dye) strain EK-11, leaf reactions to two Pseudomonas syringae pv. phaseolicola (Psp) (Burkholder) Young et al. (1978) strains HB16 and 83-Sc2A, and BCMV strain US-5 and BCMNV strain NL-3. The linkage map spanned 755 cM, including 90 markers consisting of 87 RAPD markers, one sequence characterized amplified region (SCAR), the I gene, and a gene for hypersensitive resistance to HB 83-Sc2A. These were grouped into 11 linkage groups (LG) corresponding to the 11 linkage groups in the common bean integrated genetic map. A major gene and QTL for leaf resistance to HB were mapped for the first time. Three QTL for leaf reactions to HB16 were found on linkage groups 3, 5, and 10. Four regions on linkage groups 2, 4, 5, and 9, were significantly associated with leaf reactions to HB strain 83-Sc2A. The gene controlling the hypersensitive reaction to HB 83-Sc2A mapped to the same region as the QTL on LG 4. The I locus for resistance to BCMV and BCMNV was mapped to LG 2 at about 1.4 cM from RAPD marker A10.1750. Five and four markers were significantly associated with QTL for resistance to CBB in leaves and pods, respectively, with four of them associated with resistance in both plant organs. A marker locus was discovered on LG 10, W10.550, which could account for 44% and 41% of the phenotypic variation for CBB resistance in leaves and pods, respectively. QTL for resistance in pod to CBB, leaf resistance to HB, and the I gene were linked on LG 2.
Raymond J. Schnell and Robert J. Knight
Genetic relationships between commercial mango cultivars are often speculative and only the maternal parent is generally known. RAPD™ primers were used with the polymerase chain reaction (PCR) to provide markers useful in determining individual identity, family relationships, and linkage mapping analysis. In mango, 53 RAPD primers were screened for markers and 27 proved useful. Genomic DNA was isolated from 70 clones of mango maintained in the USDA germplasm collection. DNA from these clones was amplified with each of the 27 primers. Data were scored as the presence or absence of bands. Groupings of the clones using UPGMA based on Nei's genetic distance gave distinct clusters. RAPD clusters vs. clusters based on isozyme analysis are compared.
Harry S. Paris and Rebecca Nelson Brown
Pumpkin and squash (Cucurbita L. spp.) are important cucurbit crops and are grown in almost all arable regions of the world. The three economically important species, Cucurbita pepo L., Cucurbita moschata Duchesne, and Cucurbita maxima Duchesne are highly polymorphic in fruit characteristics, inspiring much research into their inheritance. A comprehensive list of genes for Cucurbita was last published more than a decade ago. This new gene list for pumpkin and squash includes descriptions of gene interactions and the genetic background of the parents that had been used for crossing to allow easy confirmation of previous work and provide a sound foundation for further investigation. This gene list includes 79 loci for phenotypic/morphological traits and 48 polymorphic allozyme loci. Linkage and mapping are discussed.