Increasing cotton genome coverage with polymorphic SSRs as revealed by SSCP.
Simple sequence repeat (SSR) markers are widely used in plant genetics and breeding. However, there are many SSR markers that do not reveal polymorphism in cotton. Traditional SSR genotyping methods only provide information on product sizes. This leaves many marker polymorphism undetected, thus, lowering the utility of SSRs. In the present study, monomorphic SSRs between two mapping parents, 'Emian22' and 3-79, were subjected to single-strand conformation polymorphism (SSCP) analysis to reveal polymorphism. Of the 4194 monomorphic SSR primer pairs, 158 pairs (3.77%) showed polymorphism and revealed 174 polymorphic loci. Sequence analysis showed that the differences in PCR products between the mapping parents were solely due to base transition or transversion, which was in agreement with SSCP principles. SSCP also revealed SSRs with motifs of AT/TA and GAA/CTT were more polymorphic in dinucleotides and trinucleotides, respectively. Genetic mapping integrated 160 loci into our interspecific BC(1) linkage map, 5 of which associated with QTLs related to cotton fiber quality. The technique discussed in the present study enables us to detect polymorphism of monomorphic SSRs, and increase the utilization efficiency of the existing SSR primers.
National Key Laboratory of Crop Genetic Improvement & National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, Hubei, China.
Ximei
X
Li
Daojun
D
Yuan
Hantao
H
Wang
Xuemei
X
Chen
Bin
B
Wang
Zhongxu
Z
Lin
Xianlong
X
Zhang
D001483:Base Sequence; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D032561:Cotton Fiber; D017931:DNA Primers; D018744:DNA, Plant / Q000235:genetics*; D008040:Genetic Linkage; D018745:Genome, Plant; D005838:Genotype; D003368:Gossypium / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics*; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D018807:Polymorphism, Single-Stranded Conformational; D040641:Quantitative Trait Loci
D017931:DNA Primers; D018744:DNA, Plant