OMICS TECHNOLOGY FOR GENETIC SELECTION TOWARDS FEED EFFICIENCY TRAITS OF INDIGENOUS CATTLE IN
INDONESIA: A REVIEW
Hendrawan Soetanto1), and Fatchiyah Fatchiyah2), 3)
1) Department of Animal Nutrition, Faculty of Animal Science, Brawijaya University, Jl. Veteran, Ketawanggede, Kec. Lowokwaru, Kota Malang, Jawa Timur 65145
2) Department of Biology, Faculty of Mathematic & Natural Science, Brawijaya University, Jl. Veteran, Ketawanggede, Kec. Lowokwaru, Kota Malang, Jawa Timur 65145
3) RC Smart Molecule of Natural Genetics Resources, Brawijaya University, Jl. Veteran, Ketawanggede, Kec.
Lowokwaru, Kota Malang, Jawa Timur 65145 Email: [email protected] Diterima Pasca Revisi: 30 Agustus 2023
Layak Diterbitkan: 1 September 2023
ABSTRACT
Indigenous cattle in Indonesia seldom to reach their genetic potentials due to an interaction impact of harsh tropical climate and low-quality feed. Some indigenous breeds of cattle in Indonesia, such as Bali, Madura and Crossbred Ongole have demonstrated their successful adaptation to survive in the harsh environment, but their ultimate performances are still considered less than their genetic potentials when reared under comfortable environment like in the sub-tropical climate. This is primarily due to inefficient fermentation of feed originating from inadequate supply of essential nutrients required for optimum growth of microbes in the forestomach. A rapid advancement of omics technology has been the driver for ruminant nutritionists to use such a technology to study the interrelationship between nutrients and particular genes associated with the biochemical pathways of nutrients at molecular levels. This review highlights the current issues and challenges on the use of omics technologies to improve the efficiency of feed utilization by cattle consuming low-quality diets and its potential to be used in the genetic selection program.
Keywords: feed efficiency; indigenous cattle; nutrigenomics; omics technology
How to Cite:
Soetanto, H., & Fatchiyah, F. (2023).Omics Technology for Genetic Selection Towards Feed Efficiency Traits of Indigenous Cattle in Indonesia: A Review. Jurnal Nutrisi Ternak Tropis 6 (2) 113-132
*Corresponding author:
Hendrawan Soetanto
Email: [email protected]
Department of Animal Nutrition, Faculty of Animal Science, Brawijaya University, Jl.
Veteran, Ketawanggede, Kec. Lowokwaru, Kota Malang, Jawa Timur 65145
INTRODUCTION
Beef cattle in Indonesia have a wide role starting as a source of animal protein, a need for religious rituals to an indicator of social status in society. The government's efforts to meet the needs of beef through the Beef and Buffalo Self-Sufficiency Program have been in effect since 1995 and have not yet fulfilled domestic needs. The number of beef imports has always been increasing, namely around 8.44% / year since the last two decades and in 2018 the total import value of beef equivalent to beef reached 160,197.5 tons with a value of 707,730,100 USD (BPS, 2019).
Various efforts have been made to narrow the imbalance between demand and the ability to supply beef in the country through the Artificial Insemination Bluffing Program (GBIB) in 2015-2016 and continued with the UPSUS SIWAB program (Special Efforts for Mandatory Cows of Pregnancy) in 2017 and recently the name has changed as” Si Komandan” with approximately similar objectives as the previous program. The legal basis for the implementation of UPSUS SIWAB is the Regulation of the Minister of Agriculture of the Republic of Indonesia No. 48 / Permentan / PK.210 / 10/2016. The results of this program have been able to increase the cattle population from 14.24 million to 17.91 million heads.
In general, cattle in Indonesia face the constraints of a tropical climate which causes a decrease in the quality of basal feed due to the length of sun exposure of more than 12 hours per day, which stimulates plants to flower more quickly due to decreased protein content and increased crude fiber content in leaves and stems. It is therefore not surprising that during the dry season, local cattle generally experience a decrease in body weight, causing economic losses for small breeders. Besides, with the increasing conversion of common grazing land into residential and tourism areas, the main feed for cattle is more dependent on agricultural and industrial waste production.
This current condition is contradictory with the projected enormous growth of human population in 2025 that will reach more than 9 billion people living on earth (Lutz and Butz, 2017) and, undoubtedly, require adequate food production or otherwise a worldwide famine occurs.
The local beef cattle that are mostly kept by smallholder breeders in Eastern Indonesia are Bali cattle (which are descended from Bos sondaicus cattle, the result of the domestication of the Bull Bibos), Madura cattle (descendants of Bos Indicus and Bos Sondaicus), and Ongole Cross-breed cattle descendants of Bos Indicus). The three types of local cattle can survive in dry areas with low feed quality so that they are unique to be developed in Eastern Indonesia, where most beef cattle businesses are still dominated by smallholder beef cattle businesses.
Efficient use of feed is a complex mechanism resulting from the interaction between physical and chemical factors of feed, animal physiological stage, digestive tract carrying capacity, variety of microbes along the digestive tract, hormonal influence, and environmental factors through neural control mechanisms. The important aspect of feed use efficiency is reflected in the cost of feed which reaches more than 80% of total livestock production at certain growth stages (Seabury et al., 2017) so that if efficiency can be improved, farmers will get very profitable economic benefits (McCann et al., 2014).
Berry and Crowley, (2013) stated that the efficiency of feed use can be approached in two ways, namely (1) traits ratio and (2) regression or residual traits by using livestock that is in the growth phase. The traits ratio approach is a conventional method commonly used to calculate the feed conversion ratio (FCR), which is to calculate the ratio between dry feed matter consumption (DMI) and body weight gain (ADG). The smaller the FCR value, the more efficient the use of feed by the animal is. In addition to calculating the FCR, researchers also usually use partial
efficiency of growth (PEG) as a measure by calculating the ratio between body weight gain and the amount of food consumed after deducting energy needs for basic living. The disadvantage of FCR and PEG is that they cannot be used to measure the efficiency of feed use between individual animals in conditions according to energy needs for basic life so that they cannot be used to assist livestock selection programs based on the efficiency of feed use.
The second way is to calculate the residual feed intake (RFI), which is defined as the difference between actual feed consumption based on energy needs and expected feed consumption (Hernandez- Sanabria et al., 2012). Experts agree that RFI is a parameter that has the potential as a measure of the efficiency of feed used by the animals, so it is also known as net feed efficiency (Berry and Crowley, 2013).
The process of digestion of feed in ruminants is partly determined by the variety and size of the microbial population living in the front stomach (reticulum and rumen = RR) which ferment feed into compounds that are beneficial to the host in the form of VFA as a source of energy. As an ideal habitat, RR is inhabited by billions of bacteria, archaea, anaerobic fungi, and protozoa which actively ferment the feed consumed by livestock so that our knowledge of the diversity and dynamics of its development is the key to increasing the efficiency of feed use in ruminants (Kenny et al., 2018). This diversity of rumen microbial populations has long been the
object of research by experts but related to the use of molecular techniques to uncover the mystery of the efficiency of feed use is still relatively new (Ma et al., 2015).
However, the advent of omics knowledge and technology open opportunity to improve animal production outputs in the tropics where quality of feed resource is the main constraint (Ribeiro et al., 2020).
Local Cattle in Indonesia
Local cattle found in Indonesia have long existed in the archipelago and are thought to have existed since the first century based on the traces of the findings of inscriptions in the days of the Hindu kingdom of Mpu Sindok in the Medang Kemulan area, Malang Regency. These cows are descendants of Zebu cattle (Bos indicus), taurine cows (Bos taurus) and Bali cattle (Bos javanicus) which have adapted and produced offspring from crosses between these cattle breeds (Sutarno and Setyawan, 2016). Furthermore, it is stated by Sutarno and Setyawan (2016) that the largest population of crosses currently available can be grouped into three clumps of cattle, namely Bali cattle which are the result of domestication from Banteng, Madura cattle from crosses between Bos indicus and Bos javanicus and Ongole crossbreeds (PO). Besides, Zebu breeds were also found, among others, scattered in coastal areas such as West Sumatra, Aceh (Abdullah et al., 2012) and Sumba Ongole.
Until now, the distribution of local cattle in Indonesia can be found in various regions as shown in Table 1.
Table 1. Distribution of Local Breed of Cattle in Indonesia
Breed Group Regional Distribution
Bali South Sulawesi, South East Sulawesi, Central Sulawesi, West Sulawesi, Gorontalo, Bali, East Nusa Tenggara, West Nusa Tenggara, South Sumatera, South Kalimantan, Lampung
Crossbred Ongole West Java, Central Java, Lampung, South Sumatera. North Sumatera. Central Sulawesi, North Sulawesi
Aceh Aceh
Coastal Region Sumatera Barat
Madura Madura, Jawa Timur
Sumba Ongole NTT
Source: Directorate General of Livestock Production (2010) in Romjali (2018)
Besides that, based on our direct observations, Bali cattle have also spread to several provinces such as Central Kalimantan, Papua and West Papua which are integrated with oil palm plantations.
Likewise, Madura cattle have also been distributed in South Kalimantan.
Particularly for Bali cattle, the results of Surjoatmodjo's (1993) research are interesting to note that based on the analysis of the number of chromosomes owned by Bali cows, it turns out that the furthest relationship with Bos taurus is the possibility that Bali cattle are outside the Bos genus family. The reason stated was that there was an abnormality in the results of the cross between female Bali cattle and Bos taurus cattle, namely the male calves experienced aspermia (sterile, not containing sperm) until the second derivative. The results of research by Sutarno et al. (2015) relating to the genetic diversity of local cattle in Indonesia reported that among the five local cattle breeds in Indonesia, Madura cattle are a clump of cattle that shows uniqueness in terms of
established genetic diversity, although proven to have originated from crosses between Bos indicus X Bos javanicus. This uniqueness is thought to be the result of a breeder system with controlled mating management and has adapted to environmental conditions. The genetic linkages between local Indonesian cattle and cattle breeds from India are presented in Figure 1. Superior traits that can adapt to hot and humid environments and can survive in low feed quality conditions are traits that need to be investigated further as the dominant traits of local cattle for feed carrying capacity areas that are relatively lower than the ideal conditions generally carried out by commercial cattle farms with a feedlot maintenance pattern.
This important trait has been demonstrated in Zebu cattle for thermotolerance and resistance to parasites despite this cattle has reputation of lower grades of carcass-meat quality (Ribeiro et al., 2020). A summary of the adaptability and production capacity of Indonesian local cattle clumps is presented in Table 2.
Figure 1. Genetic relationship between Indonesian indigenous cattle and Indian breeds of cattle (Sutarno dan Setyawan, 2015)
Table 2. Superior comparison of three indigenous breeds of Indonesian cattle
Breed
Superiority Weakness
Remark Environmental
adaptability Reproduction
Response to low- quality
feed
% Carcass
Feed Efficiency
Resistance to diseases
Bali +++ +++ +++ ++ ++ -
Diseases that attack many Bali cows are malignant cataracts (which attack calves), and Jembrana disease (which attacks the brain of cows)
Madura +++ TI +++ +++ +++ NA
Madurese cattle are widely crossed with Limousine cattle so that genetic changes occur in the ability to consume low-quality feed, causing the forage feed given to be of high quality Crossbred
Ongole +++ +++ ++ + + NA
Notes: +++ :very good; ++ : good; + : moderate; - : bad; NA: no information available
(Source: Sutarno dan Setyawan, 2015) The productivity of Local Beef Cattle in Indonesia
The compilation of literature studies on three domestic cattle breeds in Indonesia reveals that the performance of Bali cattle raised in various regions in Indonesia with dry climates on average can increase body weight between 0.3 and 0.73 kg/head/day, during the dry and the rainy seasons, respectively (Panjaitan et al., 2003; Tahuk and Dethan, 2010; Mastika et al., 2017).
One of the advantages of Bali cattle is its ability to survive in hot humid environments with low feed quality, resistance to various diseases and has a relatively high fertility rate so that the birth spacing can reach 11.9 ± 1.9 months (Panjaitan et al., 2003). Comparatively, the performance of Madura cattle reported in the literature varied widely in terms of body dimensions under the rearing farm conditions.
Table 3. Summary of daily weight gain of Bali, Madura, and Crossbred Ongole cattle fed various diets
Local Breed
Initial Body
weight (kg) Final Body weight (kg) Daily Weight
Gain (kg/d) Treatment Sumber
Bali 222,75±9,74 286,08±9,11 0,70±0,16 Iso-energy feeding for cows aged 2- 2.5 years consisting of 12% CP and 72% TDN (the feed ingredients given were wild grass, gliricidia leaves, corn meal, and husks).
Tahuk et al., 2017
Bali 192,55±12,47 224,28±8,40 0,53±0,14 Giving 40% purea (urea mixed with putak flour) from concentrate given to bulls aged 18-24 months.
Lazarus et al., 2019
Bali 181,7 243,7 0,69 Feeding additives (Lannea
coromandelica) as much as 2000 ml in the ration of cows with an average body weight of 178 kg aged 2-3 years.
Sio et al., 2016
Bali 252,83±22,63 343,17±24,95 90,33±10,53 (120 days)
The addition of 5 kg of palm kernel cake, maize stover (ad libitum), and 400 grams of calcium (from palm oil fatty acids) to bulls aged 24-30 months grazed in oil palm plantations.
Leo et al., 2012
Bali 110-140 no available data 0,61±0,13 The addition of 20% leucaena leaves to the ration composed of 65% forage (45% fermented beetle grass + 20%
bengal grass) and 15% concentrate given to 1-year-old bulls.
Riswandi et al., 2015
Bali 222±13,55 ration containing 40% native grass + 60%
concentrate supplemented with 5% SOCS and 10%
CFF).
0,92±0,16 Addition of 5% soybean oil calcium soap and 10% cashew fruit flour to 40% weed + 60% concentrate given to bulls aged ±2 years.
Bain et al., 2016
Bali 122,1±2,66 208,0±9,2 0,76 Balanced feeding of 40% elephant
grass and 60% concentrate (20.74%
crude protein and 77.3% TDN) on young bulls (steers) with an average body weight of 112kg.
Mastika,et al. 2017
Bali 101,67 129,00 0,33 High-protein feeding (CP 15.05%) to
heifers aged 9 months.
Suryani et al., 2017
Madura 162 210 0,81 Feed treatment was made 14% CP and
55.1% TDN given to bulls aged 2 years.
Umar et al., 2015
Madura 112,50 167,83 0,61 The addition of coconut meal and
bioplus to feed (grass and legumes) given to bulls with a body weight of 136.62±21.61.
Ngadiyono dkk., 2000
Madura 236 ± 29 kg Quadratic response with increased amount of CB intake and reached the highest BWG at 40 % CB
0,72±0,29 – 0,83±0,11
Inclusion of CB in the diet of Madura bulls from 0 %- 70 % given forage (elephant grass) concentrate.
Cowley et al., 2020
PO 240-300 285,96±3,80 0,797±0,059 Sorghum-based feedlot feeding in silage form with the addition of commercial concentrates given to bulls aged I1-I4 (1.5 – 4.5 years).
Aditia dkk., 2013
PO 271,33±4,58 340,61±23,77 0,78±0,30 Giving concentrate as much as 50%
(consisting of husk, copra meal, beer waste, and minerals) of the dry matter needs of livestock with rice straw given ad libitum to cows aged 1.5-2 years.
Lestari et al., 2011
PO 272,67±26,84 354,00±23,26 0,83±0,2 Complete feeding supplemented with UDP in bulls aged 1.5 – 2 years
Nusi dkk., 2011
The report of Umar et al. (2015) showed that Madura cattle maintained in an intensive system using elephant grass and concentrates with various levels of energy content can increase body weight from 0.77 to 0.81 kg/head/day with the best efficiency achieved by feed with a medium level of energy content when compared with low and high energy. The addition of cassava bagasse (onggok) ranging from 30 to 70% to the concentrate as fattening Madura cattle feed with a balance between elephant grass:
concentrate, 20%: 80% resulted in weight gain in a quadratic pattern (Cowley et al., 2018). Meanwhile, for Ongole crossbreeds, Lestari et al. (2011) reported the results of observations in the Kebumen District, Central Java Province that Javanese and Ongole crossbred cows were able to increase body weight by 0.58 kg/head/day and 0.78 kg/head/day, respectively. The experimental animals were fed a basal feed containing rice straw and concentrate that consisted of rice bran, copra meal, beer dregs and minerals.
The results of various studies on the ability of Madura, Bali and PO cattle are presented in Table 3.
Beef Cattle Productivity Limiting Factors Hot and humid tropical climate conditions are one of the factors that trigger stress on cattle. Experts have long known the negative effects of increasing environmental temperature and humidity, which are expressed as the Thermal Humidity Index (THI) value. Brown-Brandl (2018) states that for beef cattle the THI value range can be divided into three groups, namely: (1) THI <74 = normal; (2) 74 <THI <79 = standby; (3) 79 <THI <84 = hazard; and (4) THI> 84 = emergency condition. The result of heat stress in dairy cows is more significant because it will have an impact on increasing the frequency of breathing, reducing the process of rumination and feed consumption, reducing milk production, increasing rectal temperature, increasing urination so that it increases energy requirements to maintain basic life and ultimately decreases body weight and decreases. body immunity.
Whereas in beef cattle the impact is not immediately apparent but will interfere with the homeostasis process such as signs in dairy cows and changes in behavior such as reduced activity, increased drinking water consumption and decreased feed consumption so that bodyweight will also decrease (Summer et al., 2019).
Apart from climatic factors, low feed quality conditions are a limiting factor for beef cattle production in the tropics. Long days of irradiation cause grass to flower more quickly resulting in a decrease in protein content, and vice versa accelerate the increase in crude fiber content, especially the formation of cross-links between cellulose, hemicellulose, and lignin in animal feed crops. Conditions will affect low feed digestibility. Various efforts to improve the digestibility of forage, especially those from agricultural waste have been carried out, such as by providing alkaline treatment throughout the world, but until now the level of technology adoption at the farmer level is almost nil except in China and parts of India (Owen et al., 2011). The same thing also happened to supplementation technology in the form of molasses block which was technologically successful but failed to be adopted at the farmer level because of the difficulty in obtaining raw materials for sugarcane milling waste in the form of molasses at affordable prices for smallholder farmers.
Other technologies offered by researchers such as making complete feeds (complete feed) and Total Mixed Ration (TMR) technology are also not developed at the smallholder farmer level because they require relatively expensive supporting equipment (Owen et al., 2011).
The development of molecular biology technology has opened a new page for the approach of nutritionists to overcome limiting factors for ruminant livestock production including beef cattle which are related to physiological processes and nutrient metabolism in livestock cells (Osorio and Moisa, 2019). The role of genes in regulating nutrients so that they can
influence changes in the body structure of beef cattle is new hope for increasing the productivity of beef cattle in tropical areas such as Indonesia.
However, before the nutrigenomics approach becomes a popular topic, molecular biology technology has brought about a change in the study approach in the field of nutrition with the role of microbes living in the RR organs. The conventional approach of microbiology technology through the efforts of microbial culture in the laboratory in anaerobic conditions and identification using the help of electron microscopes has not been able to provide a satisfactory understanding of the role of these microbes in increasing the efficiency of feed use and boosting the productivity of ruminants.
New microbiome studies can help explain that the efficiency of feed use is related to the diversity and size of certain microbial populations using molecular biology techniques as reported by several researchers such as Berry and Crowley (2013), Jewell et al. (2015), Kenny et al.
(2018), Deusch et al. (2017), Durso et al.
(2017) Myer et al. (2017), and Zhang et al.
(2018). Meanwhile, research in Indonesia is still relatively small, although molecular biology technology has been widely used for research in the health and agricultural fields.
One of the reports on the relationship between the rumen microbial population of beef cattle with silage and probiotic feeding in Indonesia was reported by Ridwan et al.
(2009). More recently Soetanto et al. (2022, unpublished) reported the diversity of rumen microbes from three indigenous cattle of Indonesia relating to the potential of fiber- utilizing bacteria.
The Importance of Feed Efficiency Traits in Cattle Production
It has been frequently reported in the literature, feed cost may constitute up to 70
% of the total production cost and therefore the ability of animals to convert the ingested nutrients into valuable animal’s products such meat, milk, draft power, and fur is of paramount to generate economical profits.
There is ample evidence to show that feed intake is correlated with live weight and level of production, but measuring individual feed intake is tedious and time demanding which explains the scarcity of results from experiments to use feed efficiency as genetic selection traits (Arthur and Herd, 2006). Feed efficiency is literally defined as the amount of ingested feed divided by the intended products. A more straightforward definition of feed efficiency is a ratio of inputs and outputs. Nevertheless, under integrated farming conditions measuring feed intake may not fit for the purpose of genetic selection program because this requires multiple inputs and outputs measurement of both breeding and replacement females and slaughter progeny (Carstens and Tedeschi, 2006). For this reason, feed efficiency may only be required to determine the amount of ingested feed to the outputs in targeted physiological stages, which indicates the variation in energy requirements.
Body weight gain and daily dry matter intake are generally used to measure ratio- based feed efficiency traits such as gross feed efficiency or inversely expressed as feed conversion ratio (FCR) although feed efficiency may also be measured as carcass or lean meat and input traits as digestible or metabolizable energy intake (Carstens and Tedeschi, 2006). Owing to this complexity in the relationship between feed intake and production traits, Arthur and Herd (2008) divide feed intake into four groups, namely gross efficiency, partial efficiency of growth, maintenance efficiency, cow/calf efficiency and residual feed intake (RFI).
The latter is a measure of feed efficiency which considers the variation in maintenance requirements.
In beef cattle the concept of RFI has been examined since70 years ago and concluded that feed intake could be adjusted to body weight and weight gain or other production traits that splits effectively feed intake into two components, namely (1) expected feed intake for the given level of production, and (2) a residual component.
The amount of residual component can be used as a predictor of feed efficiency induce as this correlates with the deviation from expected feed intake, meaning the negative value of RFI indicates efficiency in the use of nutrients to satisfy the given level of production (Arthur and Herd, 2008).
Nevertheless, from various studies reviewed by Arthur and Herd (2008) the genetic correlation between RFI and average daily gain of some breeds of beef cattle was low although the corresponding figure for feed intake was relatively high.
Additionally, RFI shows weak correlation to marbling and carcass rib eye area indicating that the complexity of physiological influences on growth involving protein turnover, tissue metabolism and stress, digestibility, heat increment and fermentation, physical activity, and body composition.
Nevertheless, as molecular technology has evolved in the last two decades, our knowledge on the relationship between nutrients intake and the operation of certain gens to response and influence the nature of production traits is promising. Lam et al.
(2020) reported their study on Nellore beef cattle and they concluded that the optimization of RNA sequencing pipelines is the key factor to maximize power and accuracy to identify genetic variants including SNPs which may serve as genetic markers to select for feed efficiency, leading to economic benefits for beef production.
Furthermore, Abdelrahman et al. (2022) have summarized from published literature on the mechanism of premature feeding strategy in ruminant animals to elucidate the expression of targeted genes at the gastro intestinal tract related to the RFI as a precursor to energy intake.
This finding suggests that there is a bright future of molecular approach to elucidate the genetic traits of feed efficiency in beef cattle for the sake of less feed
consumption but resulting optimum production leading to economic benefits.
Molecular Technology to Increase Beef Cattle Productivity
Abdelrahman et al. (2022) have reviewed from a published articles and defined that “omics” refers to methodologies associated with the knowledge of interaction between specific identified genes in an animal or the microbiome, genes transcribed to mRNA or protein, and metabolites present in particular cell, tissue, organ, fluid or population. The development of molecular biology technology has encouraged the adoption of
"omics" technology as well as bioinformatics research in the field of nutrition and physiology of ruminants (Figure 2). Both technologies can explain the main regulatory processes for nutrients through a series of complex metabolic processes at the molecular level of the body such as milk synthesis, changes in meat quality, fatty acid composition in meat and the mechanism for pathological conditions due to certain metabolic disorders such as ketosis, mastitis and heat stress. The combination of the increased understanding of chemical processes at the molecular level, as well as advances in equipment technology, have triggered the development of new disciplines, namely a combination of nutrition and genomics, known as
"nutrigenomics" (Osorio and Moisa, 2019).
Conventional approaches based on the appearance of livestock phenotypic variables in nutrition research have been the basis of nutrition science. However, since the rise of knowledge in the field of molecular biology, the research approach in the field of nutrition has shifted towards nutrigenomics, which studies the relationship between the role of the genome and the influence of nutritional factors (Zdunczyk and Pareek, 2009; Benitez et al., 2017; Osorio et al., 2017).
.
Figure 2. Dietary interaction with metabolites which potentially change the molecular metabolism in ruminant animals (Adapted from Abdelrahman et al., 2022) This is further explained by Osorio et
al. (2017) that the current nutrigenomics technology can be grouped into three, namely Transcriptomics, Gene receptor technology, Proteomics, and Metabolomics.
More recently, Abdelrahman et al. (2022) have drawn attention on the new development of nutritional genetic relationship approach called feedomics that
refers to a field of study that examine the gene expression as affected by the diet and gut and hence it is also called “feed-gut-gene scheme”.
The concept of feedomics in fact was formerly introduced by Sun and Guan (2018). By comparison nutrigenomics refers to the field of study focusing on nutrient molecules’ role in gene expression and the
regulatory mechanisms at cellular levels.
The schematic diagram of nutrition and genetic expression relationship in ruminant animals is presented in Figure 2One example of research on fat synthesis in ruminants is the one that gets the most attention of researchers because it is closely related to human health, which is influenced by diet and food quality, especially those derived from ruminant livestock products such as meat and milk. Nutrigenomics' approach to milk fat synthesis in dairy cows and intra-muscular fat synthesis in beef
cattle is the same, namely through transcription factor (TF) from the same nutritional stimulus, namely PUFA (polyunsaturated fatty acids), insulin, and others, which will activate PPARα in dairy cow liver and PPARγ in feeder fat in beef cattle intramuscular tissue as presented in Figure 4 below which is cited from Osorio and Moisa (2019). To provide an overview of the current use of omics technology in the field of nutrition, Zdunczyk and Pareek (2009) have summarized various literature sources as listed in Table 4.
Table 4. Important mediators associated with nutrient-gene interactions in ruminants via transcriptional regulatory factors (transcription factors) and epigenetic factors (DNA methyltransferases and non-coding RNAs) reviewed by Osorio and Moisa, (2019)
Common name Protein Symbol
Gen Symbol
Agonist Main Role Ruminants
Peroxisome
proliferator activated receptor α
PPAR α PPARA Fatty Acids Lipid Metabolism, inflamation, and tissue regeneration
Beef, Dairy cattle, Goats and Sheep
Peroxisome
proliferator activated receptor γ
PPAR γ PPARG Asam lemak Adipogenesis, insulin sensitivity, nnd
lipogenesis
Beef, Dairy cattle, Goats and Sheep
Peroxisome
proliferator activated receptor β
PPAR β PPARD Fatty Acids Fatty acid metabolism, fatty
acids, tissue regeneration, and
glucose uptake glukosa at udder
tissues
Beef, Dairy,Goat and Sheep
Liver X receptor α LXRα NR1H3 Oxysterol/
Fatty acids
Cholesterol homeostasis, macrophage function
and inflammation
Beef. Dairy cattle and goats
Retinoic X receptor α RXRα RXRA 9-cis- retinoic acids
Forming heterodimers with
other LdNR and neutrophil differentiation
Beef and Sheep
Sterol regulatory element binding protein 1
SREBP1 SREBF1 N/A Cholesterol and fatty acid synthesis
Beef, Dairy,Goat and Sheep DNA
methyltransferase 1
DNMT1 DNMT1 N/A Maintenance of
methylation patterns
Beef and dairy cattle
DNA
methyltransferase 3 α DNMT3a DNMT3A N/A Creates de novo methylation patterns.
Present in cytoplasm and nucleus
Beef and dairy cattle
DNA
methyltransferase 3 β DNMT3b DNMT3B N/A Creates de novo methylation patterns restricted to nucleus
Beef and dairy cattle
MicroRNA 33 miR33b Regulates lipogenesis Dairy cattle
MicroRNA 192 miR192 Regulates
myogenesis
Sheep
Figure 3. A Diagram of reaction pathway of Peroxisome proliferator-activated receptor (Somoza ,2006)
Notes:
PPARA/G : Peroxisome Proliferator- Activated Receptor α/γ
FABP : Fatty Acid Binding Protein SCD : Stearoyl CoA Desaturase FASN : Fatty Acid Synthase Gene ELOVL : Elongation of Very Long
Chain Fatty Acid
RXRA : Retinoic X Receptor Alpha
PUFA : Poly unsaturated fatty acids FASN : fatty acid synthase gene PPARA/G : Peroxisome proliferator
Alpha/Gamma
Fabp4 : fatty acid binding protein 4 RXRA : Retinoic and Retinoid receptors SCD : stearoyl CoA desaturase ELOVL6 : fatty acid elongase 6
Figure 4. Example of nutrigenomics linkage between beef and dairy cattle (Osorio and Moisa, 2019)
However, research on beef cattle is still relatively limited in the number that can be found in the current literature. Connor et al. (2009) stated that the discovery of genome sequence information in various livestock species encouraged researchers to further study livestock physiological processes related to the digestive process at the gene transcript level so that research that
investigates mRNA and protein expression from candidate genes expressing the normal and due to manipulation of feed nutrient content can be studied more deeply. The results of these studies have opened the horizons of nutritionists to be able to calculate and determine the need for certain nutrients as a strategy to increase ruminant livestock production.
Current Condition (State of The Art) Research on Nutrigenomics in Relation to Efficiency of Feed Use in Ruminants
Nutrigenomics is a new interdisciplinary field not only in nutrition science that introduces a new era of nutrition but also involves health science, molecular biology, biochemistry, food technology, and the food industry. Studying health cannot be separated from the role of food components and composition and how consumed nutrients interact with genes that cause certain diseases. Combining knowledge of genome-based nutrition will lead us to the right food choices. The interaction of these two things can be utilized to achieve optimal health and maintain general health in populations or individuals over a longer period of time. The field of nutrigenomics research continues to grow along with these developments. The connection between nutrients and genes is measured using quantitative polymerase chain reaction (PCR), real-time PCR, DNA microarray, and DNA sequencing. Currently, chip technology has enabled the sequencing of many genes and the advancement of an accurate insight into the changing patterns of gene expression (Dirong et al., 2021; Haq et al., 2022). Many new methods developed to examine the large-scale molecular adaptations in livestock breeds in the response to selected nutrients, dietary changes and their interactions in the past decade have yielded a wealth of biological information. The emergence of 'functional genomics' as a distinct field of research within the broader animal science underscores the utility of the molecular information in livestock populations as a way to better manage the growth and production capacity of animals. Innovative technologies in animal breeding to obtain quality meat or milk from farm animals based on genomic studies are currently developing rapidly (Haq et al., 2022).
Genetic diversity or similarity can be measured through genetic markers. These markers have been used to determine evolutionary relationships within and
between species, genera, or higher taxonomic categories. The RAPD marker, produced by Polymerase Chain Reaction (PCR) has been widely used since the 1990s to assess intra-specific genetic variation at the nuclear level. This procedure detects nucleotide sequence polymorphisms in a DNA amplification-based assay using only one primer of an arbitrary nucleotide sequence. Polymorphism between individuals is caused by sequence differences in one or both primer binding sites and can be seen from the presence or absence of certain RAPD bands (Khatun at al., 2012). The RAPD method is simple but has low reproducibility, another disadvantage is that it requires a wide variety of primers such as for forensic testing.
However, the RAPD technique is still used to amplify genomic DNA using a single short oligonucleotide primer under low stringency conditions, resulting in many amplification products from a locus distributed throughout the genome. In addition, livestock genome analysis also uses microsatellite DNA which is reliable because it is highly polymorphic and present in all chromosomal regions, with several dozen alleles at each locus; therefore, microsatellites can be easily assessed using PCR. Comparative analysis of RAPD and microsatellite polymorphisms on the genetic diversity of livestock populations showed that microsatellite analysis can generate population linkage groupings in closely related populations more accurately than RAPD (Dirong et al., 2021). Therefore, to determine the genetic diversity of native, exotic and crossbred cattle populations in Indonesia, this study was conducted using RAPD-PCR. Sensitive methods using mtDNA are generally used for the identification of species in dietary analysis.
This method, developed based on DNA technology, is useful in various livestock tissues. In meat specifications, nuclear or mitochondrial DNA genes (nDNA and mtDNA) have become the target of DNA amplification analysis. Chromosomal DNA
is a larger molecule organized in chromosomes and contains a larger variance in its sequence types as compared to mtDNA genes (Vaithiyanathan et al., 2016).
Most of the research results on gene expression in ruminants have focused on finding candidate genes that are capable of expressing them in relation to the normal livestock conditions, physiological processes that are considered important for livestock production, such as absorption and transport of nutrients (for example glucose, VFA and minerals) through Epithelial walls of dividing cells (barriers) at various
locations of the digestive tract segment (Connor et al. 2009). Riaz et al. (2014) conducted a meta-analysis of 45 research reports on voluntary feed intake and digestibility in 4 ruminant species, namely sheep, goats, buffalo, and cows which are affected by the nutritional content of the feed with the result that crude protein content affects the consumption of dry matter in ruminants, however, the response was varied between species. Among the ruminant species that are most responsive to the addition of crude protein is buffalo followed by sheep, goats, and cows.
Table 5. Some examples of research results using transcriptomics technology applications for the field of nutrition (Reviewed by Zdunczyk and Pareek, 2009)
Gene Expression Bioarray Research Objectives Research Model Affymetrix mouse genome
array containing probes for over 8000 genes
To determine the effect of soy protein on liver metabolism and the expression of gene clusters related to lipid metabolism
Rats were fed for 8 weeks with the addition of casein or soy protein
Affymetrix mouse genome array containing probes for over 8000 genes
To investigate the effect of soy protein on liver metabolism and expression of gene clusters related to lipid metabolism
Rats were given feed for 8 weeks with the addition of casein or soy protein to the feed
DNA microarray codelink containing 9028 gut-derived cDNA mice
To recognize the mechanism of chemopreventive properties of n-3 polyunsaturated fatty acids
Rats were given feed with different PUFA content Affymetrix gene chip with
cRNA derived from mouse duodenal mucosa
To test the effects of iron deficiency on known iron transport genes and to identify new genes involved in intestinal iron transport
Rats aged 8 days and 12 or 36 weeks after feeding feed containing iron as much as 198 or 3 ppm
The microarray contains about 2000 cDNA-derived from the large intestines of mice
To verify the hypothesis that the dietary heme (derived from read meat) and calcium are modulators of colon cancer risk
Rats were fed high and low calcium feed for 2 weeks, with or without heme
The cDNA microarray set up at the Maastricht Genome Centre contains 602 mouse genes
To recognize the genetic mechanism in vegetables, especially carrots, can prevent the risk of lung cancer
Rats were given feed without or with different doses of vegetables
In contrast, fiber content (ADF) has a negative correlation with dry matter consumption in all ruminant species except buffalo. Sheep and cattle show a very strong negative relationship between dry matter consumption and fiber content. Olivieri et al.
(2016) conducted a study on the identification of genomic areas and metabolic pathways related to dry matter consumption, body weight gain, feed efficiency, and residual feed intake in Nellore cattle, which are widely available in Brazil. The researchers found 9 gene
candidates related to the efficiency of feed use. Cantalapiedra-Hijar et al. (2018) stated that the efficiency of feed use in livestock is a complex attribute as well as multi-traits that can be seen.
For example, the most widely used parameters, namely dry matter consumption, increased body weight (PBB), feed conversion ratio (FCR), although this is a useful index, currently the use of FCR to be used in the evaluation process of beef cattle raising raises many questions because the results -Recent research results have
found a negative correlation between FCR and PBB. Thus, there is an undesirable effect on reaching body size when the cattle
are mature as well as an increase in maintenance costs, mostly in the form of feed costs.
Table 6. Summary of information about omics technology
Omics Definition Target
molecules researched
Information obtained Potential
Nutrigenomics Study of the effect of food or compounds in food on gene expression
DNA Genes that affect nutritional needs
Can provide information about optimizing nutritional
status, as well as helping information
about the effect of nutrients on a disease.
Transcriptomics Fully study the transcriptional components of RNA produced by
the genome
RNA Information about mRNA
Can be used to counteract the effects of
poisoning caused by toxic compounds Proteomics Extensive study of a
series of proteins produced by
organisms
Protein Research on proteins Improve the accuracy of diagnosis and monitoring of cures;
provide information about protein biomarkers that cause
disease Metabolomics Extensive study of
metabolites in cells or organisms
Metabolites (sugars, amino
acids, fats and hormones
Examining changes in the biochemical- homeostasis process of metabolites in cattle suffering from a disease
Can be used to accurately recognize biomarkers, ongoing biochemical processes, and the current condition of body cells Adapted from Sadeghi and Jenzer (2017)
Kenny et al. (2018) reported the results of a study on efforts to improve the efficiency of feed use in beef cattle from various research results where the residual feed intake parameters have the prospect of being used in breeding programs combined with other properties to obtain beef cattle that have advantages in the efficiency of feed use. Myer et al. (2017) reported the results of a recent analysis of the bacterial community of the digestive tract and their correlation to feed consumption, growth, and efficiency of feed use in beef cattle with the results that in the rumen there was a bacterial diversity of 1,098 382 Operational Taxonomic Unit (OTU) which can be grouped into 24 Phyla, 48 Class, 89 Ordo, 173 Families, and 397 Genus. This shows that by using molecular biology techniques, we can obtain more accurate information for
use in analyzing the relationship between the efficiency of feed use and the diversity of microbiota that actively live and carry out the fermentation process in the rumen or other segments of the digestive tract.
Especially for conditions in Indonesia, similar research has not been found to date.
CONCLUSION
The predicted explosion of human population by 2050 requires serious attention on the racing ground of food production systems under declining arable land, desertification, and other devastating climate change impacts to avoid malnutrition and famines. In this context, the sustainability of animal protein supply as the indispensable nutrients for quality human food may rely on the advancement of
knowledge and technology at cellular or molecular levels to manipulate the nutrient- gene interactions leading to efficient use of feed intake, reduce methane emitted from rumen fermentation without impairing animal production traits such as milk yield and daily gain potentials.
The use of omics technology seems promising in the future, but this technology requires massive and modern tools with the concomitant availability of pails of datasets.
Unfortunately, these pre-requites are the most significant limitation in the tropical countries like Indonesia, unless, otherwise, there will be consciously significant changes in mindsets and research priority to enhance the use of omics technology.
Further exploration on the genetic potential of indigenous breeds of cattle related to superiority traits under harsh environment such as heat tolerance, negative RFI indices, and disease-lowering production is warranted since this advancement will lead to increase economic benefits and hence the prosperity of smallholder farmers.
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