**1. Introduction**

Information on adaptive evolution and genetic diversity of an organism are very important in supporting genetic improvement and germplasm conservation. Adaptive evolution implies evolutionary shifts within an organism which make it suitable for its environment. The improvements lead to improved chances of survival and reproduction. In order to conserve germplasm of an organism, information on genetic diversity is needed so that it can capture germplasm as a whole and efficiently in the implementation of germplasm conservation activities. In addition, information on the diversity of organisms needs to be documented to maintain information on the wealth and existence of certain types of an organism, including sago palm.

Several markers that can be used for accessing the diversity of an organism are morphology, protein, and DNA marker. Morphological and protein markers are not sufficiently used as indicators for measuring genetic characteristic because they are heavily affected by the surrounding factors. One of the markers that is not influenced by the surrounding factors is a molecular marker. Thereby, in expressing adaptive evolution and genetic characteristics, it is necessary to be based on molecular markers. Disclosure of the genetic characteristics of organism such as plant in Indonesia will be better focused on molecular-based markers.

Several DNA markers that can be used for accessing adaptive evolution of an organism are: Simple Sequence Repeat (SSR) in the nuclear genome and chloroplast genome (cpSSR), Random Amplified Polymorphism DNA (RAPD), functional gene such as Waxy gene in sago palm, 5S, Restriction Fragment Length Polymorphism (RFLP), and Amplified Fragment Length Polymorphism (AFLP), chloroplast DNA (cpDNA) such as *ma*tK gene, and mitochondrial DNA (mtDNA) such *nad* gene. These molecular markers are widely used as markers to express adaptive evolution of plant.

SSR markers have been shown to have high polymorphisms in soybean and in apples [1–4], thereby, can be used for revealing the adaptive evolution of an organism. SSR is composed of 1–6 base pairs (bp) of repeated DNA sequences with varying amounts [5]. The polymorphic fragments (alleles) are produced from variations in the length of the SSR repeats which can be separated by electrophoresis to display the genetic profile of the genome and the organelle genome. SSR alleles are codominant monogenic inherited and can be distinguished between homozygous and heterozygous in segregated populations [1].

The advantages of SSR DNA markers or microsatellite markers in genome analysis are that SSR sequences are found in many eukaryotic genomes, high diversity, stable inheritance, co-dominant markers and high accuracy detection [6]. The RAPD marker is a technique that is widely used for genetic characterization because the RAPD technique is simpler than other techniques. Molecular markers related to the expression of certain genes are interesting molecular markers because it can be seen the variation of genes encoding certain characters, making it easier to trace genes that have specific expressions and are desired for the improvement of certain gene of organisms.

The *Wx* gene molecular marker is a marker related to the starch biosynthesis process and amplifies the plant DNA sequences that linked to the starch formation. The Waxy (Wx) gene in cereals and *amf* in potato is called isoform gene, Granule-bound starch synthase I (GBSS I) that it encodes starch synthesis [7, 8]. Furthermore, starch synthesis process is regulated by one of the key genes, those the *Wx* gene [9]. Starch from rice plants consists of amylopectin and amylose [10]. Furthermore, it was stated that the *Wx* gene regulates the level of amylose content in starch-producing plants such as wheat and rice [10–12]. The motive structure of the *Wx* gene was reported that it has a very conservative sequence [8] so it fulfills the requirements to be used as a marker. The *Wx* gene marker have been used in various types of crops, i.e. rice [13], barley [9], wheat [14, 15], and sago palm [16, 17].

Large numbers of insertions and deletions in the genome can be detected using agaros gel separation techniques. A technique that is more suitable for small changes in DNA sequences, such as mutations or small deletions or insertions, is fragment analysis using sequencer tools. The technique can detect a change in the size of one base in a DNA fragment. The use of a separation technique that is able to distinguish the differences of one base pair makes it possible to detect the genetic diversity of sago palm that occur at the individual and population. The estimation of adaptive evolution that occurs over a long period of time (hundreds to thousands of years) can be determined based on the chloroplast Simple Sequence Repeat (cpSSR) marker and barcode *mat*K gene in the cpDNA genome. The barcode *mat*K gene was commonly use in the vascular plant, such as Dipterocarpaceae [18], Arecaceae [19]

**29**

and others).

years ago.

the refugee population [27, 28].

*Adaptive Evolution and Addressing the Relevance for Genetic Improvement of Sago Palm…*

and in the species of sago palm also [20]. The variation that occurs in a relatively short period of time can be determined based on RAPD markers and other markers

Diversity is a reflection adaptive evolution in an organism. Variations within a population and inter species that are affected by the occurrence of adaptive evolution. Adaptive evolution of sago palm can be measured by using various markers. The characteristics of sago palm in Indonesia were shown widely varies in morphological phenotypic. It was reported that around Sentani, Jayapura there are 15 varieties [21]. These varieties show variation in a broad sense, not only in morphological characters, but also in their adaptation to the environment (tolerant to fire and waterlogging). Furthermore, the variation of sago palm in Papua is very large based on morphological phenotypic, there are 96 varieties based on vernacular name [22]. The variation base on morphological phenotypic may differences from another population and location because morphological characters are strongly influenced by environmental factors. Observing the variation of sago palm need a marker that are not influenced by the environment so that they can reflect the actual state of plant variation. Markers developed in a wide variety of organisms including plants, namely chloroplast genome molecular markers (cpDNA) and nuclear genome molecular markers (RAPD, Wx gene expression,

The cpDNA molecular marker is a very conservative molecular marker, so it is very suitable to be used to estimate long-term adaptive evolution for a particular organism. The cpDNA locus mutation rates was estimated between 3.2 x 10–5 and 7.9 x 10–5 [23]. Apart from this, cpDNA sequences are conservative in comparison to nuclear genome because they do not undergo recombination in the genome and uniparental inherited [24, 25]. Based on the information found in the chloroplast genome, it is a difference that occurred hundreds or thousands of

The cpDNA markers were developed in plants showed that the cpDNA of sago palm varied, the total 10 haplotypes were found throughout Indonesia territorials [26]. Seven haplotypes were found on the island of Papua and three haplotypes were found apart from the island of Papua and two haplotypes were found on several islands (sharing haplotypes). Based on highly conservative cpDNA criteria, the variations in cpDNA detection were reflect conditions hundreds or thousands of years ago. It is hypothetically that gene flow of sago palm since ancient times moving from one island to another in various ways. It was found that only two haplotypes experienced displacement. This phenomenon was corresponded of *Pinus silvestris* L. and *Abies alba* Mill referred to as

Base on the largest number of haplotypes were found on several islands where sago samples were taken, the island of Papua is the center of sago diversity because the island of Papua has the highest number of cpDNA haplotypes. Large amount of diversity is found in natural populations [29]. Based on this statement, it can be said that the sago palm in Papua is a natural population (not refers to a migrant population). When talking about the source of diversity, the islands of Papua, Sulawesi and Kalimantan are the sources of diversity of sago palm because it has a specific haplotype. Large number of haplotypes reflects the high variation or diversity in a population [28] and differences in cpDNA

*DOI: http://dx.doi.org/10.5772/intechopen.94395*

used to investigate the nucleus genome.

**2. Adaptive evolution of sago palm**

and in the species of sago palm also [20]. The variation that occurs in a relatively short period of time can be determined based on RAPD markers and other markers used to investigate the nucleus genome.
