Development of SNP marker for Rice (Oryza sativa L.) lines contrasting for root traits using candidate genes
Loading...
Date
2009-08-10
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
University of Agricultural Sciences GKVK, Bangalore
Abstract
Rice (Oryza sativa L.) cultivation consumes significant amount of fresh water, which
needs to be saved. Introgressing relevant traits into a single genetic background are
envisaged to develop rice cultivars suitable for aerobic cultivation. Water mining, water
use efficiency, intrinsic tolerance and spikelet fertility are the important traits that need to
be exploited.
In the present investigation, a set of 35 contrasting rice germplasm lines were selected
and raised in root structure both under well watered (aerobic) and water limited (rainfed)
conditions. A strong relationship of root traits under aerobic and rainfed, as well as
between seasons reiterated the stability of root traits and exhibited strong genetic control.
Similar trend was observed for 13C, a time averaged surrogate for WUE. This
consistency in the important traits was also confirmed by gas exchange and other
alternate parameters like SLA and SCMR. Genotypes such as JBT-36/14, AC-35310, IET
-16348, PS-339, JBT-38/19 and AC-39020 have been identified as promising trait donor
parents. Traits introgression is best achieved through a marker assisted breeding program.
SNPs represent a highly polymorphic, co-dominant marker system which is very
frequently distributed in the genome. A large number of genes with relevence in root
growth and development have been cloned and validated. Among them, OsAGAP which
controls root length and adventitious root formation was used as candidate gene to
identify SNPs. Genomic DNA of a set of contrasting genotypes were PCR amplified
using gene specific primers and sequenced to discover SNP. A software ClustalW was
used to align the sequence and identify SNP. The software TASSEL was used to group
the genotype based on SNP haplotypes. The germplasm lines that were classified into
separate groups showed significant variability in root biomass and root density. Further
validation of these SNPs is in progress.
Description
Keywords
null