Genomic Analyses Yield Markers for Identifying Agronomically Important Genes in Potato.

@article{Li2018GenomicAY,
  title={Genomic Analyses Yield Markers for Identifying Agronomically Important Genes in Potato.},
  author={Yangping Li and C. Colleoni and Junjie Zhang and Q. Liang and Yufeng Hu and Holly Ruess and R. Simon and Yinghong Liu and Hanmei Liu and Guowu Yu and {\'E}. Schmitt and Chlo{\'e} Ponitzki and Guangjian Liu and Huanhuan Huang and F. Zhan and Lin Chen and Yubi Huang and D. Spooner and Binquan Huang},
  journal={Molecular plant},
  year={2018},
  volume={11 3},
  pages={
          473-484
        }
}
Wild potato species have substantial phenotypic and physiological diversity. Here, we report a comprehensive assessment of wild and cultivated potato species based on genomic analyses of 201 accessions of Solanum section Petota. We sequenced the genomes of these 201 accessions and identified 6 487 006 high-quality single nucleotide polymorphisms (SNPs) from 167 accessions in clade 4 of Solanum section Petota, including 146 wild and 21 cultivated diploid potato accessions with a broad geographic… Expand
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References

SHOWING 1-10 OF 77 REFERENCES
Genome diversity of tuber-bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potato
TLDR
A historic role of wild Solanum species in the diversification of long-day–adapted tetraploid potatoes is uncovered, showing that extant natural populations represent an essential source of untapped adaptive potential. Expand
QTL mapping of potato chip color and tuber traits within an autotetraploid family
TLDR
A biparental tetraploid potato population was evaluated across three field seasons and storage trials in order to identify quantitative trait loci (QTL) for multiple tuber traits including fried chip color after 5.5–7.2 °C storage. Expand
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes
TLDR
Thousands of genes with significantly lower diversity in cultivated but not wild rice are identified, which represent candidate regions selected during domestication and should be valuable for breeding and for identifying agronomically important genes in rice. Expand
Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection
TLDR
A high level of linkage disequilibrium in the soybean genome is identified, suggesting that marker-assisted breeding of soybean will be less challenging than map-based cloning and to facilitate future breeding and quantitative trait analysis. Expand
Genome sequence and analysis of the tuber crop potato
TLDR
The potato genome sequence provides a platform for genetic improvement of this vital crop and predicts 39,031 protein-coding genes and presents evidence for at least two genome duplication events indicative of a palaeopolyploid origin. Expand
Diversity of potato genetic resources
TLDR
Previously, primitive forms of cultivated potato and its wild relatives have been used in breeding programs and there is still an enormous and unimaginable potential for discovering desirable characteristics, particularly in wild species Different methods have been developed to incorporate useful alleles from these wild species into the improved cultivars. Expand
Retrospective View of North American Potato (Solanum tuberosum L.) Breeding in the 20th and 21st Centuries
TLDR
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. Expand
SSR Analysis of Genetic Diversity Among 192 Diploid Potato Cultivars
TLDR
Clustering results showed relatively low genetic diversity among 192 diploid cultivars, with closer relationship at the molecular level, which can provide molecular basis for diploids potato breeding. Expand
Genetic Diversity and Core Collection for Potato (Solanum tuberosum L.) Cultivars from Cameroon as Revealed by SSR Markers
TLDR
Analysis of molecular variance revealed that most of the genetic variations are found within geographic region, resulting in high gene flow (Nm > 4 individuals) and local varieties had significantly more alleles than exotic varieties. Expand
QTL mapping of yield, agronomic and quality traits in tetraploid potato (Solanum tuberosum subsp. tuberosum)
Interval mapping of quantitative trait loci (QTL) for 16 yield, agronomic and quality traits in potato was performed on a tetraploid full-sib family comprising 227 clones from a cross betweenExpand
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4
5
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