Molecular Characterisation of Upland and Lowland Rice from Sarawak, Malaysian Borneo
Keywords:
Maturase-K, Rice, Sarawak, Simple Sequence RepeatAbstract
A total of 39 Simple Sequence Repeat (SSR) markers distributed across the 12 chromosomes
were screened for polymorphism. Out of 39 tested SSR markers, eight primers displayed
polymorphic banding patterns and exhibited strong polymorphism among the accessions. The
primers with good amplification were RM1, RM489, RM552, RM444, RM257, RM489, RM166
and RM164. The highest PIC value (0.9316) was recorded by RM257. The lowest PIC value
(0.4029) was recorded by RM552 with average PIC value 0.6891. The observed number of
effective alleles (Ne) in lowland population recorded 1.543 and 1.566 in upland population. Nei’s
gene diversity (h) in upland and lowland population was 0.318 and 0.329, respectively,
indicating low level of divergence in current study. Shannon’s Information Index (I) was
recorded 0.475 in lowland population, and 0.490 in upland population. Analysis of Molecular
Variance indicated a percentage of 20% genetic variation among population. Meanwhile, genetic
variation within population was 80%. The UPGMA dendrogram based on the eight SSR markers
genotype classified the 44 rice accessions into two major clusters, Cluster I and Cluster II.
Cluster I was divided into two sub-clusters, sub-cluster IA and sub-cluster IB and Cluster II was
split into sub-cluster IIA and sub-cluster IIB. The clustering analysis did not show clear
clustering of the rice accessions according to their morphological traits nor geographical origin.
Simultaneously, the Maturase-K barcoding gene marker revealed the accessions were clustered
in one big cluster. Also in the cluster were 94 rice accessions from different origins and three
accessions of Oryza rufipogon. This clustering approach categories the accessions based on their
genome. The molecular markers used in the study provide valuable insights into the genetic
diversity of rice accessions and can be used in facilitating targeted breeding programs essential
for advancing sustainable agriculture.
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