Shirasawa, K. and Kuwata, C. and Watanabe, M. and Fukami, M. and etc, .
(2016)
Target amplicon sequencing for genotyping
genome-wide single nucleotide polymorphisms
identified by whole-genome resequencing in Peanut.
Plant Genome, 9 (3).
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Abstract
Genome-wide genotyping data regarding breeding materials
are essential resources for improving breeding efficiency,
especially in plants with complex genomes with a high degree
of polyploidy. Several current breeding efforts in cultivated
peanut (Arachis hypogaea L.), which has a tetraploid genome,
are devoted to developing high oleic acid cultivars. Genetic
maps for such breeding programs have been developed using
simple-sequence repeat (SSR) markers, the use of which requires
time-consuming electrophoretic analyses. Next-generation
sequencing (NGS) technology can overcome this technical
hurdle. Initially, we attempted double-digest restriction siteassociated
DNA sequencing on peanut breeding materials used
to develop high oleic acid cultivars. However, this method was
not effective because few single nucleotide polymorphism (SNPs)
were available because of low genetic diversity of the lines.
The genome sequences of the probable diploid ancestors of
cultivated peanut, A. duranensis Krapov. & W. C. Greg. and A.
ipaënsis Krapov. & W. C. Greg., are available. Therefore, we
next employed whole-genome resequencing analysis to obtain
genome-wide SNP data. In this analysis, we observed large
biases in the numbers and genomic positions of interspecific and
intraspecific SNPs. For genome-wide genotyping, we selected
a subset of SNPs covering the peanut genome as the targets of
amplicon sequencing analysis. Using this technique, genomewide
genotypes of the breeding materials were easily and
rapidly determined. The SNP information and analytic methods
developed in this study should accelerate genetics, genomics,
and breeding in peanut.
| Item Type: |
Article
|
| Uncontrolled Keywords: |
Genome-wide, genotyping, genomes |
| Author Affiliation: |
Crop Science Society of America
5585 Guilford Rd., Madison, WI 53711 USA |
| Subjects: |
Crop Improvement |
| Divisions: |
Groundnut |
| Depositing User: |
Mr T L Gautham
|
| Date Deposited: |
20 Sep 2017 04:27 |
| Last Modified: |
20 Sep 2017 04:27 |
| URI: |
http://eprints.icrisat.ac.in/id/eprint/15054 |
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