The Story of Rice, Nutrigenomics, and the Future of Our Nation
Tauhid Nur Azhar
Last weekend, as Indonesia was about to celebrate its 79th Independence Day in the new capital city, I was flooded with stories on my social media feed and WhatsApp chats. The questions and topics were intriguing, but there was a red thread that ran through them all, like a thread of sutures that were ready to be pulled tight to close the surface wound that had been gaping open, laughing at the world that was drunk on drama and acrobatic words that were deluding the meaning in the belly of perception born from various maya facts.
Our nation, like most nations in Asia and parts of Africa, has been nourished through the conversion of adenosine triphosphate from oxidative phosphorylation that occurs in the citric acid cycle. Where the citric acid cycle has eight enzymatic reactions that begin with the condensation of acetyl-CoA with oxaloacetate to form citrate, catalyzed by citrate synthase, and end with the dehydrogenation of malate to produce oxaloacetate by the enzyme malate dehydrogenase.
The citric acid cycle serves as a mitochondrial hub for the final step in the oxidative catabolism of carbon skeletons for carbohydrates, amino acids, and fatty acids. Each oxidative step, in turn, reduces coenzymes such as nicotinamide adenine dinucleotide (NADH) or flavin adenine dinucleotide (FADH2).
At the end of each cycle, a four-carbon oxaloacetate has been regenerated, and the cycle continues. At least six ATPs are produced in this process, which are used as vital energy. The question is, where does the raw material come from that is processed in this ATP-producing cycle?
From carbohydrates, for example, which in our culinary tradition are dominated by rice that is cooked or steamed from the original species of grass called Oryza sativa.
Homo sapiens are believed to have known rice that has been processed into rice and rice since 10,000 years ago. Not only did they exploit natural resources, but they also developed the concept of cultivation and production that is sustainable and part of the strategy and effort to maintain food security.
Given the importance of rice, the management of this living food resource has given rise to traditions and cultures that have become the womb of culture for the growth and development of various core values of life and various forms of participation.
Regarding this, Sensei Janoe San, who is in Kyoto on his summer pilgrimage, enthusiastically announced that he is studying the concept of INARI, or the goddess of rice (blessings), one of his favorite shrines is located in Kyoto.
Coincidentally, on August 10, the day of the national technology awakening, an expo of research and innovation results was held, titled: INARI expo 2021. Although the acronym is different, there is a strong connection between INARI, which is the acronym for Indonesia Research and Innovation Expo, and INARI, the Japanese goddess of rice. Firstly, many researchers and BRIN officials who have studied in Japan have a good understanding of the culture of the country where they studied. Secondly, of course, it is related to the issue of welfare that is closely related to the process of research and technology, as well as science and innovation that are its products.
Back to Sensei Janoe San in Kyoto, his pilgrimage to the ancient shrine far before the Meiji era brought him to a cultural atmosphere that placed INARI in a special position.
Inari (稲荷) is one of the Kami in Japanese belief. The honorable name of Inari is Inari no kami, Oinari-sama, Oinari-san, or Inari Daimyōjin (稲荷大明神).
In a philological approach and Japanese language, Ine (稲) means rice plant. Shrines that worship Inari are called Inari shrines (稲荷神社, Inari jinja). The center of various Inari shrines found throughout Japan is Fushimi Inari Shrine in the Fushimi district, Kyoto. The place where Sensei Janoe San came to better understand the role of rice in a construction of civilization.
In the shinbutsu shūgō system of belief, Inari is considered a manifestation of Dakini. In addition, Inari is believed to be Ukanomitama (agricultural god), Toyoukebime, and Ukemochi (food god) Inari is believed to be the goddess of agriculture, originating from the word of the harvest of the rice plant (ine) that is treated as a commodity or product (nari). Where INARI is the goddess of geishas, samurais, and merchants, as well as blacksmiths who are related to the figure of Kitsune or foxes.
How about in Nusantara? Don’t be mistaken, the legend of the goddess of fertility, Dewi Sri is still very close to the values and traditions of Javanese society, as well as in South Sulawesi and various other regions, of course with various articulations and terms that are diverse, in accordance with the dynamics of local, regional, and global culture.
In the Sunda region, there is a figure or character who is highly revered and respected by farmers and rulers whose foundation of power is based on agricultural products, Nyai Pohaci Sanghyang Sri.
Where Nyi Pohaci Sanghyang Sri is the highest and most important goddess for the agrarian community in the ancient Sundanese kingdom’s system of belief. She is a protective goddess who oversees the behavior and agricultural activities of the Sundanese people. Nyi Pohaci is also considered a construction of power relations from Batara or Bujangga led by Sunan Ambu.
Nyi Pohaci has various versions of stories, most of which involve Dewi Sri (Dewi Asri, Nyi Pohaci) and her brother Sedana (Sadhana or Sadono). These stories have a background of the Kingdom of Medang Kamulan, or heaven (with the involvement of gods such as Batara Guru), or both.
The mythology of Nyi Pohaci is not only stored in the memory of the Sundanese people, but it is also spread to the Javanese, Balinese, and Malay communities.
Even one of the daughters of the founder of the ancient Sundanese kingdom, Aki Tirem, was named Pohaci. Perhaps this is also part of the effort to negate the power relations that require ultra-natural legitimacy.
In the Wangsakerta Chronicle by Pangeran Wangsakerta, Aki Tirem is described as a Penghulu or regional leader in the western coast of West Java (Teluk Lada Pandeglang). Aki Tirem is also called Aki Luhur Mulya, his daughter’s name is Pohaci Larasati, who was married to Sang Dewawarman.
After Aki Tirem’s death, Sang Dewawarman succeeded him as ruler in the area with the name Prabu Darmalokapala Dewawarnan Haji Raksa Gapura Sagara, this figure is referred to by historians as Dewawarman the First. His wife, Pohaci Larasati, became queen with the name nobat Dewi Dwani Rahayu. The kingdom led by Dewawarman was named Salakanagara, which means the silver country with its capital in Rajatapura.
Sources that mention the existence of the Salakanagara kingdom include Chinese news (Dinasti Han), where in the news, King Yeh Tiao-pien sent an envoy to China in 132 M. Ye-tiao is believed to be the same as Yawadwipa or Yabadiu (Java Island), while Tiao-pien is believed to be Dewawarman.
Other sources of information about Salakanagara are a geographer named Claudius Ptolemeus who wrote in his book Geographia, written in 150 M, about the existence of the fertile island of Labadiou in the eastern world.
According to Geographia, at the western end of Labadiou (Java Island) is the city of Argyre (silver). Argyre is likely to be the capital of Salakanagara. A city with advanced use of metal elements, indicating the high level of metallurgy achieved by the Nusantara people at that time.
Discussing further about the spread of humans (Homo sapiens) and the development of agricultural culture that accompanies it will lead us to study further the matter of compatibility between biological entities, ecosystems, habitats, and biodiversity, as well as food and various types of food as a form of adaptation to environmental dynamics, including geographical position and its climatic consequences.
Various biological variations on the entity called humans, genetically can be studied through haplotypes and haplogroups. Where the relationship between the environment and food, as well as humans and their genes is now widely studied in nutrigenomics.
Nutrigenomics is the science that studies the interaction between human genomes and eating patterns, which can affect health and disease risk. One of the important aspects of nutrigenomics is the influence of haplogroups, genetic groups that are inherited through lineage, on food preferences and nutritional needs.
Nutrigenomics is a field of research that studies how genetic profiles can affect individual responses to food.
Meanwhile, Haplogroups, which are large categories in phylogenetics that describe the genetic origin of humans, have been proven to affect various biological aspects, including metabolism and nutritional needs.
In addition, geographical location and habitat also play an important role in shaping eating habits through food availability and genetic adaptation to a particular environment.
Haplogroups are large groups of haplotypes, combinations of alleles that are close to each other in the genome and are inherited together. Haplogroups are often categorized based on chromosome Y (for paternal lineage) and mitochondrial DNA (for maternal lineage).
Each haplogroup has a different geographical distribution, which often reflects human migration and adaptation throughout history.
Nutrigenomics is a branch of science that studies the interaction between an individual’s genes and their nutritional needs, and how nutrition can affect gene expression. For example, genetic variations in metabolic enzymes can affect how the body processes fats, carbohydrates, and proteins.
Certain genotypes may also affect the risk of diseases related to diet, such as type 2 diabetes and cardiovascular disease.
Studies have shown that certain haplogroups are correlated with genetic adaptations to the dominant diet in a specific geographic region. For example, populations from the polar region (such as haplogroup Q and C in the Inuit) have genetic adaptations to a diet high in fat and low in carbohydrates, which is dominant in the marine and terrestrial food of the region.
On the other hand, populations from the tropics (such as haplogroup L in Africa) may be more adapted to a diet high in carbohydrates and fiber from fruits, vegetables, and grains.
Human migration and modern urbanization have caused significant changes in eating patterns that are not always in line with their genetic profiles. This can lead to an increased risk of chronic diseases when populations with a specific haplogroup adopt a diet that is not in line with their genetic adaptations. For example, populations with a history of low-fat diets that now adopt high-fat and high-sugar diets are more prone to obesity and related diseases.
Lactose Intolerance and Haplogroup intolerance laktosa is one example of genetic adaptation to dietary patterns influenced by haplogroup. In European populations with haplogroup H, there is a high prevalence of alleles that allow lactose digestion until adulthood. This is related to the history of domestication of livestock and consumption of milk. On the other hand, haplogroups in Africa and Asia have a higher prevalence of lactose intolerance due to different dietary patterns.
Another example of the relationship between food types and environmental conditions can be seen in the genetic and dietary patterns of the Inuit.
Haplogroup Q, found in the Inuit or Eskimo population, has a habitat in the Arctic environment around the northern pole with very low temperatures and limited food availability.
Their diet is categorized as high in fat, with raw materials mainly from marine mammals such as seals and whales.
The Inuit population shows genetic adaptations to the dominant high-fat diet in their environment. Genes involved in fatty acid metabolism, such as FADS (Fatty Acid Desaturase), have evolved to increase the ability to metabolize fat from marine food sources. This is very important in the Arctic environment where carbohydrates are scarce and fat is the main source of energy.
Variations in the FADS gene allow individual Inuit to be more efficient in converting long-chain fatty acids (rich in omega-3 fatty acids) into energy.
Another example is Haplogroup L and the dominant plant-based diet in sub-Saharan Africa. Haplogroup L is common in populations living in sub-Saharan Africa. The habitat conditions are a tropical environment with high availability of plant-based foods such as fruits, vegetables, and grains.
Populations in sub-Saharan Africa belonging to haplogroup L have adaptations that support complex carbohydrate metabolism. They have genetic variations that support efficiency in breaking down carbohydrates and managing glucose, which is important in a diet rich in starchy plants.
In this population, the AMY1 gene, which encodes the salivary amylase enzyme, shows an increase in the number of copies in populations that historically consumed a high-carbohydrate diet. This allows for faster breakdown of starch into sugar in the mouth, which is very useful in a plant-based diet.
Genetic adaptations to specific dietary patterns often involve changes in gene expression. These changes can be triggered by mutations in gene regulatory regions (such as promoters) or changes in gene copy number (such as the AMY1 gene).
When individuals with specific genetic adaptations consume food in line with their genetic profile, gene expression is regulated in such a way that it supports efficient metabolism, reduces disease risk, and improves overall health.
In addition to genetic mutations, epigenetic factors such as DNA methylation can also affect the expression of genes related to dietary adaptations. For example, a high-fat diet can cause epigenetic changes that modulate the expression of genes related to lipid metabolism, which can affect the risk of metabolic diseases, etc.
Before we discuss further the compatibility of genetic profiles with environmental conditions (ecosystems and habitats) and available food, let’s discuss briefly, the technique for determining haplogroups.
There are several methods that can be used to identify haplotypes and haplogroups, which involve DNA analysis using various techniques, including:
SNP analysis (Single Nucleotide Polymorphism), where SNP is a variation in one nucleotide in a DNA sequence. SNP testing is used to identify specific genetic variations that define haplotypes and haplogroups.
This technique involves sequencing or genotyping using technologies such as microarray or next-generation sequencing (NGS).
PCR (Polymerase Chain Reaction), where PCR is a technique used to amplify specific DNA segments so that they can be analyzed further. PCR is used in combination with other techniques such as Restriction Fragment Length Polymorphism (RFLP) to map SNP or microsatellites that define haplotypes and haplogroups.
Mitochondrial DNA sequencing (mtDNA), where mtDNA is inherited maternally and does not undergo recombination is an ideal target for analyzing maternal haplogroups.
Techniques for sequencing mtDNA involve sequencing specific parts of the mitochondrial DNA, such as the Hypervariable Region (HVR), to identify haplogroups.
There is also STR analysis (Short Tandem Repeats), where STR is a short DNA sequence that is repeated multiple times along the Y chromosome or mtDNA.
STR analysis can be used to trace paternal lineage and determine haplotypes based on variations in the number of STR repeats.
Next-Generation Sequencing (NGS), where NGS allows for rapid and comprehensive sequencing of the entire genome or a large part of the genome. With NGS, researchers can map all the SNPs present in an individual’s genome and identify their haplogroup more accurately.
After haplotypes and haplogroups of a population have been mapped, mapping and analysis of specific genes can be used to evaluate the process of genetic adaptation of individuals to their dynamic environment.
Genes that can be observed, in addition to the AMY-1 gene involved in complex carbohydrate processing, also include many other genes such as TCF7L2. The AMY1 gene itself encodes the amylase enzyme, which plays a crucial role in breaking down starch into simple sugars (maltose and glucose) during the digestion process.
This enzyme can be found in saliva (salivary amylase) and is the first step in carbohydrate metabolism. The number of copies of the AMY1 gene varies among individuals and populations, with variations influenced by dietary patterns that have become traditions or habits.
Studies have shown that individuals with a higher number of copies of the AMY1 gene have a greater ability to digest carbohydrates. In populations that historically consumed high-carbohydrate foods (such as rice in Southeast Asia), the number of copies of the AMY1 gene tends to be higher.
The increased activity of amylase due to the high number of copies of the AMY1 gene can cause a rapid increase in blood glucose levels after consuming high-carbohydrate foods. This high glycemic response can increase the risk of insulin resistance, a condition in which cells in the body do not respond effectively to insulin.
Insulin resistance is one of the main factors in the development of type 2 diabetes. However, some studies have also shown that individuals with more copies of the AMY1 gene are more likely to have a lower risk of obesity, as they have more efficient carbohydrate metabolism. This shows that the relationship between AMY1 and the risk of diabetes mellitus is complex and may depend on environmental and dietary factors, as well as other aspects.
The TCF7L2 gene (Transcription Factor 7-Like 2) is one of the genes with the most significant association with the risk of type 2 diabetes. This gene encodes a transcription factor involved in the Wnt signaling pathway, which plays a crucial role in regulating cell growth, differentiation, and glucose homeostasis.
Polymorphisms in the TCF7L2 gene, such as the rs7903146 variant, have been associated with an increased risk of type 2 diabetes. TCF7L2 is involved in regulating the expression of genes involved in insulin secretion from pancreatic beta cells. Variants of TCF7L2 can reduce the ability of beta cells to produce and secrete insulin in response to glucose. As a result, blood glucose levels can remain high after eating, contributing to the development of type 2 diabetes.
TCF7L2 also plays a role in regulating glucose production in the liver. Certain variants of this gene can increase glucose production by the liver, even when blood glucose levels are already high, which worsens hyperglycemia in type 2 diabetes patients. Although TCF7L2 is better known for its effects on insulin secretion, there is also evidence that polymorphisms in this gene can affect insulin sensitivity in peripheral tissues, such as muscle and fat, which contributes to insulin resistance.
Now, how about the potential use of haplogroups and haplotypes in optimizing the quality of human resources in Indonesia?
Let’s imagine that we have a database or dataset of genomic data, including haplogroups of populations in various habitats in Indonesia, and also a database or dataset of precise composition of each nutritional element from various endemic foods in Indonesia. With the use of AI technology, we can bring about a precise nutrigenomics approach.
The existing dataset, such as the haplogroup of a particular tribe in a specific habitat, can be a good starting point in formulating a national food strategy and optimizing the quality of life of Indonesian people.
For example, the Y-DNA haplogroup J-M67 is found in 14% of Javanese people in Indonesia. The P* basal (P-PF5850*) haplogroup is also found in Southeast Asia.
The Javanese people are the largest ethnic group in Indonesia, with a genealogical origin in Central Java, East Java, Yogyakarta Special Region, Indramayu Regency, Cirebon Regency/City (West Java), and Serang-Cilegon Regency/City (Banten).
In 2010, at least 40.22% of the Indonesian population was of Javanese ethnicity. The Javanese people have several sub-ethnic groups, including Banyumasan, Cirebon, Osing, Samin, Tengger, Javanese Merauke, and Javanese Suriname, which are a transcontinental migrant community.
If we study further, there is a fact that the Javanese people also have a similarity in Y-DNA haplogroup O1b1a1a with people in Kalimantan and mainland Southeast Asia (Indo-China). This is different from people in Sumatra (O2), and Nusantara people who are scattered in various locations or habitats, which have different ecological characteristics, as we know through the Wallace and Weber imaginary boundaries.
With the availability of knowledge obtained through the analysis of genomic data (haplogroups), nutrigenomics of ecosystems, biodiversity, climate, and food processing technology, we will be able to:
- Plan a national food strategy based on:
- National genomic data
- Biodiversity data
- Relevant agricultural technology data
- Local, national, and regional climate data
- Food processing technology data
- Health data, including physiological and morbidity data
2. Design an improvement in the quality of human life
3. Design an improvement in the quality and carrying capacity of the environment
4. Design various comparative and competitive advantages related to global re-positioning
5. Design an educational and spatial planning model that is sustainable and can optimize the role of society in a comprehensive manner.
Great hope, the acquisition of knowledge and development of capacity in the context of efforts to improve the quality of life of Indonesian people based on genomics and eco-friendly methods can be a starting point for returning the glory of Nusantara in an integrated and science-based manner, while fully accommodating various local wisdom that have become the legacy of our ancestors.
