Development of SNP-based CAPS and dCAPS markers in eight different genes involved in starch biosynthesis in rice |
| |
Authors: | Gi-An Lee Hee-Jong Koh Hun-Ki Chung Anupam Dixit Jong-Wook Chung Kyung-Ho Ma Sok-Young Lee Jung-Ro Lee Gang-Seob Lee Jae-Gyun Gwag Tae-San Kim Yong-Jin Park |
| |
Institution: | 1. National Academy of Agricultural Science, RDA, 249, Seodun-Dong, Suwon, Gyunggi, 441-707, Republic of Korea 2. Crop Science and Biotechnology, Seoul National University, 599 Gwanak-Ro, Gwanak-Gu, 151-742, Republic of Korea 3. Rice DNA and Quality Testing Laboratory, Basmati Export Development Foundation, SVBP University of Agriculture and Technology, Meerut, 250110, India 4. College of Life and Environmental Sciences, Konkuk University, 1 Hwayang-dong, Gwangjin-Gu, Seoul, 143-701, Republic of Korea 5. Department of Plant Resources, Kongju National University, 1 Daehwari, Yesan, Chungnam, 340-702, Republic of Korea
|
| |
Abstract: | Single nucleotide polymorphisms (SNPs), which are inexhaustible, highly stable, and simply detectable sequence polymorphisms,
can lead to phenotypic variations by affecting protein composition changes. Here, we report development of 25 new cleaved
amplified polymorphic sequence or derived cleaved amplified polymorphic sequence markers that have discrete band sizes in
relation to the SNP genotypes in eight putative gene regions. The average frequency of DNA polymorphisms was 1 per 175 bp
(SNPs, 1 per 217 bp; In/dels, 1 per 906 bp). In primary statistical analysis of each marker on 55 diverse rice accessions,
including different ecotypes, the mean value of the major allele frequency was 0.658 (0.509–0.927). The average polymorphism
information content was 0.326 (0.126–0.375). The mean value of the inbreeding coefficient (f) was 0.950 and was positive (heterozygote deficiency) at all loci, corresponding to the inbreeding system in rice. In cluster
analysis, all rice accessions clustered mainly into three groups according to the ecotypes. The association analysis showed
that the SNP of Granule-bound starch synthase I and ADP-glucose pyrophosphorylase small subunit (ADPase-S) genes were highly associated with apparent amylose content variation than the others. These new SNP markers may be useful
in genotyping rice germplasm, in marker-assisted selection for improving starch quality and content, and in linkage as well
as association studies.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. |
| |
Keywords: | DNA marker Genotyping Rice SNP (single nucleotide polymorphism) Starch biosynthesis |
本文献已被 SpringerLink 等数据库收录! |
|