An ultradense genetic linkage map with .10,000 AFLP loci was constructed from a heterozygous diploid potato population. To our knowledge, this is the densest meiotic recombination map ever constructed. A fast marker-ordering algorithm was used, based on the minimization of the total number of recombination events within a given marker order in combination with genotyping error-detection software. This resulted in ''skeleton bin maps,'' which can be viewed as the most parsimonious marker order. The unit of distance is not expressed in centimorgans but in ''bins.'' A bin is a position on the genetic map with a unique segregation pattern that is separated from adjacent bins by a single recombination event. Putative centromeres were identified by a strong clustering of markers, probably due to cold spots for recombination. Conversely, recombination hot spots resulted in large intervals of up to 15 cM without markers. The current level of marker saturation suggests that marker density is proportional to physical distance and independent of recombination frequency. Most chromatids (92%) recombined once or never, suggesting strong chiasma interference. Absolute chiasma interference within a chromosome arm could not be demonstrated. Two examples of contig construction and map-based cloning have demonstrated that the marker spacing was in accordance with the expected physical distance: approximately one marker per BAC length. Currently, the markers are used for genetic anchoring of a physical map of potato to deliver a sequence-ready minimal tiling path of BAC contigs of specific chromosomal regions for the potato genome sequencing consortium (http:/ /www.potatogenome.net).
Cultivated potato (Solanum tuberosum L.), a vegetatively propagated autotetraploid, has been bred for distinct market classes, including fresh market, pigmented, and processing varieties. Breeding efforts have relied on phenotypic selection of populations developed from intra- and intermarket class crosses and introgressions of wild and cultivated Solanum relatives. To retrospectively explore the effects of potato breeding at the genome level, we used 8303 single-nucleotide polymorphism markers to genotype a 250-line diversity panel composed of wild species, genetic stocks, and cultivated potato lines with release dates ranging from 1857 to 2011. Population structure analysis revealed four subpopulations within the panel, with cultivated potato lines grouping together and separate from wild species and genetic stocks. With pairwise kinship estimates clear separation between potato market classes was observed. Modern breeding efforts have scarcely changed the percentage of heterozygous loci or the frequency of homozygous, single-dose, and duplex loci on a genome level, despite concerted efforts by breeders. In contrast, clear selection in less than 50 years of breeding was observed for alleles in biosynthetic pathways important for market class-specific traits such as pigmentation and carbohydrate composition. Although improvement and diversification for distinct market classes was observed through whole-genome analysis of historic and current potato lines, an increased rate of gain from selection will be required to meet growing global food demands and challenges due to climate change. Understanding the genetic basis of diversification and trait improvement will allow for more rapid genome-guided improvement of potato in future breeding efforts.
Pepper plants containing the dominant A gene accumulate anthocyanin pigments in the foliage, flower and immature fruit. We previously mapped A to pepper chromosome 10 in the F(2) progeny of a cross between 5226 (purple-fruited) and PI 159234 (green-fruited) to a region that corresponds, in tomato, to the location of Petunia anthocyanin 2 ( An2), a regulator of anthocyanin biosynthesis. This suggested that A encodes a homologue of Petunia An2. Using the sequences of An2 and a corresponding tomato expressed sequence tag, we isolated a pepper cDNA orthologous to An2 that cosegregated with A. We subsequently determined the expression of A by Northern analysis, using RNA extracted from fruits, flowers and leaves of 5226 and PI 159234. In 5226, expression was detected in all stages of fruit development and in both flower and leaf. In contrast, A was not expressed in the sampled tissues in PI 159234. Genomic sequence comparison of A between green- and purple-fruited genotypes revealed no differences in the coding region, indicating that the lack of expression of A in the green genotypes can be attributed to variation in the promoter region. By analyzing the expression of the structural genes in the anthocyanin biosynthetic pathway in 5226 and PI 159234, it was determined that, similar to Petunia, the early genes in the pathway are regulated independently of A, while expression of the late genes is A-dependent.
Potato (Solanum tuberosum L.) periderm is composed of the meristematic phellogen that gives rise to an external layer of suberized phellem cells (the skin) and the internal parenchyma-like phelloderm. The continuous addition of new skin layers and the sloughing of old surface layers during tuber maturation results in smooth, shiny skin. However, smooth-skin varieties frequently develop unsightly russeting in response to high soil temperatures. Microscopic observation of microtubers exposed to high temperatures (37 degrees C) suggested heat-enhanced development and accumulation of suberized skin-cell layers. To identify the genes involved in the periderm response to heat stress, skin and phelloderm samples collected separately from immature tubers exposed to high soil temperatures (33 degrees C) and controls were subjected to transcriptome profiling using a potato cDNA array. As expected, the major functional group that was differentially expressed in both skin and phelloderm consisted of stress-related genes; however, while the major up-regulated phelloderm genes coded for heat-shock proteins, many of the skin's most up-regulated sequences were similar to genes involved in the development of protective/symbiotic membranes during plant-microbe interactions. The primary activities regulated by differentially expressed peridermal transcription factors were response to stress (33%) and cell proliferation and differentiation (28%), possibly reflecting the major processes occurring in the heat-treated periderm and implying the integrated activity of the stress response and tissue development. Accumulating data suggest that the periderm, a defensive tissue, responds to heat stress by enhancing the production and accumulation of periderm/skin layers to create a thick protective cover. Skin russeting may be an indirect outcome; upon continued expansion of the tuber, the inflexible skin cracks while new layers are produced below it, resulting in a rough skin texture.
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