Identification, characterisation and application of single nucleotide polymorphisms for diversity assessment in cassava (Manihot esculenta Crantz)
2009
E01467
Files
Details
Title
Identification, characterisation and application of single nucleotide polymorphisms for diversity assessment in cassava (Manihot esculenta Crantz)
Publication Date
2009
Call Number
E01467
Summary
To monitor genetic diversity in the field it is important that it is measured accurately. Here, we elucidate the potential of single nucleotide polymorphisms (SNPs) for measuring genetic diversity in cassava. The nature and frequency of SNPs was characterised and their utility in genetic diversity assessment compared to that of simple sequence repeats (SSRs). This was achieved by direct sequencing of amplicons in diverse cassava varieties. A total of 26 SNPs were identified from quality sequences of nine genes, giving an estimated frequency of one SNP every 121 nucleotides. Nucleotide diversity ranged from 7.8x10-4 to 5.6x10-3. Average haplotype-based polymorphic information content (PIC=0.414) was higher than for individual SNPs (PIC=0.228). The Mantel test indicated interdependence (r=0.219; P<0.001) between SNP and SSR genotypic data. Individual SNPs had lower PIC values than SSRs. For this reason larger numbers of SNPs may be necessary to achieve the same level of discrimination among genotypes provided by SSRs.
Journal Citation
v.23(4):669-684, MOLECULAR BREEDING
Contact Information
harvest@worldveg.org
Record Appears in
Research > Published Articles