Sequence-based genetic markers for genes and gene families: single-strand conformational polymorphisms for the fatty acid synthesis genes of Cuphea

Slabaugh, Mary B.; Huestis, Gordon M.; Leonard, Jeffrey M.; Holloway, James L.; Rosato, Caprice; Hongtrakul, Vipa; Martini, Norbert; Toepfer, Reinhard; Voetz, Michael; Schell, Jeff; Knapp, Steven J.

doi:10.1007/s001220050429

Cited by 48 publications

(33 citation statements)

References 14 publications

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“…The final map included three additional, previously unpublished markers: HT39, HT135, and HT1490 (S. Tang and S. J. Knapp, unpublished data). HT39 amplicons were visualized via SSCP gel electrophoresis using 0.53 MDE gels that were run for 14 hr at 4 W (Slabaugh et al 1997) followed by silver staining (Sanguinetti et al 1994). HT135 exhibited a length polymorphism in this cross and was scored in the same manner as the SSRs described above.…”

Section: Methodsmentioning

confidence: 99%

Quantitative Trait Locus Analysis of the Early Domestication of Sunflower

2007

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Genetic analyses of the domestication syndrome have revealed that domestication-related traits typically have a very similar genetic architecture across most crops, being conditioned by a small number of quantitative trait loci (QTL), each with a relatively large effect on the phenotype. To date, the domestication of sunflower (Helianthus annuus L.) stands as the only counterexample to this pattern. In previous work involving a cross between wild sunflower (also H. annuus) and a highly improved oilseed cultivar, we found that domestication-related traits in sunflower are controlled by numerous QTL, typically of small effect. To provide insight into the minimum genetic changes required to transform the weedy common sunflower into a useful crop plant, we mapped QTL underlying domestication-related traits in a cross between a wild sunflower and a primitive Native American landrace that has not been the target of modern breeding programs. Consistent with the results of the previous study, our data indicate that the domestication of sunflower was driven by selection on a large number of loci, most of which had small to moderate phenotypic effects. Unlike the results of the previous study, however, nearly all of the QTL identified herein had phenotypic effects in the expected direction, with the domesticated allele producing a more crop-like phenotype and the wild allele producing a more wild-like phenotype. Taken together, these results are consistent with the hypothesis that selection during the post-domestication era has resulted in the introduction of apparently maladaptive alleles into the modern sunflower gene pool.

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Section: Methodsmentioning

confidence: 99%

Quantitative Trait Locus Analysis of the Early Domestication of Sunflower

2007

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“…Information on type of PCR-markers, primer sequences, annealing temperatures and restriction enzymes used for CAPS (cleaved ampliWed polymorphic sequences) markers are summarized in Table 1. The ampliWed DNA fragments were separated on agarose gels stained with ethidium bromide or by SSCP (single strand conformational polymorphism) analysis (Plomion et al 1999;Slabaugh et al 1997;Bormann et al 2004). For SSCP, 4 l of restriction digest was mixed with 8 l of denaturing solution (97% deionized formamide, 0.01 M NaOH, 0.05% xylene cyanol, 0.05% bromophenol blue), denatured by heating to 94°C for 4 min and put immediately on ice.…”

Section: Dna Isolation Pcr Polymorphism Of Ampliconsmentioning

confidence: 99%

Tagging QTLs for late blight resistance and plant maturity from diploid wild relatives in a cultivated potato (Solanum tuberosum) background

et al. 2007

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Phytophthora infestans causes an economically important disease of potato called late blight. The epidemic is controlled chemically but resistant potatoes can become an environment-friendly and Wnancially justiWed alternative solution. The use of diploid Solanum tuberosum derived from European tetraploid cultivars enabled the introgression of novel genes encoding foliage resistance and tuber resistance from other species into the modern cultivated potato gene pool. This study evaluated the resistance of the obtained hybrids, its quality, expression in leaXets and tubers and its relation to the length of vegetation period. We also identiWed genetic loci involved in late blight resistance and the length of vegetation period. A family of 156 individuals segregating for resistance to late blight was assessed by three laboratory methods: detached leaXet, tuber slice and whole tuber test, repeatedly over 5 years. Length of vegetation period was estimated by a Weld test over 2 years. The phenotypic distributions of all traits were close to normal. Using sequence-speciWc PCR markers of known chromosomal position on the potato genetic map, six quantitative trait loci (QTLs) for resistance and length of vegetation period were identiWed. The most signiWcant and robust QTL were located on chromosomes III (explaining 17.3% of variance observed in whole tuber tests), IV (15.5% of variance observed in slice tests), X (15.6% of variance observed in leaXet tests) and V (19.9% of variance observed in length of vegetation period). Genetic characterization of these novel resistance sources can be valuable for potato breeders and the knowledge that the most prominent QTLs for resistance and vegetation period length do not overlap in this material is promising with respect to breeding early potatoes resistant to P. infestans.

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“…To Wnd polymorphism within ampliWed DNA fragments, the PCR products were digested with the restriction enzymes MseI, AluI, HinfI, RsaI, DdeI, MspI, DraI, CfoI or TaqI, and separated on agarose gels stained with ethidium bromide [cleaved ampliWed polymorphic sequence (CAPS) markers]. Alternatively, amplicons were analyzed for single strand conformation polymorphism (SSCP) (Plomion et al 1999;Slabaugh et al 1997;Bormann et al 2004). For SSCP analysis, 4 l of restriction digest with 8 l of denaturing solution (97% deionized formamide, 0.01 M NaOH, 0.05% xylene cyanol, 0.05% bromophenol blue) were denatured at 94°C for 4 min and put immediately on ice.…”

Section: Dna Isolation Pcr and Electrophoresismentioning

confidence: 99%

The novel, major locus Rpi-phu1 for late blight resistance maps to potato chromosome IX and is not correlated with long vegetation period

et al. 2006

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Despite the long history of breeding potatoes resistant to Phytophthora infestans, this oomycete is still economically the most important pathogen of potato worldwide. The correlation of high levels of resistance to late blight with a long vegetation period is one of the bottlenecks for progress in breeding resistant cultivars of various maturity types. Solanum phureja was identiWed as a source of eVective late blight resistance, which was transferred to the cultivated gene pool by interspeciWc crosses with dihaploids of Solanum tuberosum. A novel major resistance locus, Rpiphu1, derived most likely from S. phureja and conferring broad-spectrum resistance to late blight, was mapped to potato chromosome IX, 6.4 cM proximal to the marker GP94. Rpi-phu1 was highly eVective in detached leaXet, tuber slice and whole tuber tests during 5 years of quantitative phenotypic assessment. The resistance did not show signiWcant correlation with vegetation period length. Our Wndings provide a well-characterized new source of resistance for breeding early and resistant-to-P. infestans potatoes.

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Sequence-based genetic markers for genes and gene families: single-strand conformational polymorphisms for the fatty acid synthesis genes of Cuphea

Cited by 48 publications

References 14 publications

Quantitative Trait Locus Analysis of the Early Domestication of Sunflower

Quantitative Trait Locus Analysis of the Early Domestication of Sunflower

Tagging QTLs for late blight resistance and plant maturity from diploid wild relatives in a cultivated potato (Solanum tuberosum) background

The novel, major locus Rpi-phu1 for late blight resistance maps to potato chromosome IX and is not correlated with long vegetation period

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