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Abstract

Rice (Oryza sativa L.) is the primary staple food for half of the world population. It is generally classified based on the grain color into black, red, purple, brown, green, and white. These colored rice are determined by the composition and concentration of anthocyanin pigments in different layers of aleurone, pericarp, and seed coat. Anthocyanins are also accumulated in various tissues of the rice plants, mostly in the grain, but are also presents in leaves, leaf sheath, floral organ, and hull. The type and concentration of the anthocyanins in rice tissues are influenced by the cultivars and developmental stages. Anthocyanin-enriched rice is related to the health effects, including antioxidant, antibacterial, and anti-inflammation activities that potentially use as functional food ingredients, dietary supplements, and natural colorants. Structural and regulatory genes are involved in anthocyanin biosynthesis of rice. Various molecular biology techniques have been applied to improve productivity, nutritional contents, and market value of pigmented rice. This review focused on the genetics, biochemistry and biophysical analysis of anthocyanin in rice that will facilitate rice breeding program to develop new high-yield pigmented rice varieties.
Advance Sustainable Science, Engineering and Technology (ASSET)
Vol. 4, No.1, April 2022, pp. 0220103-01 ~ 0220103-19
ISSN: 2715-4211 DOI: https://doi.org/10.26877/asset.v4i1.11659
0220103-01
Genetics, Biochemistry and Biophysical Analysis of Anthocyanin
in Rice (Oryza sativa L.)
Yheni Dwiningsih1*, Jawaher Al-Kahtani2
1Department of Crop, Soil and Environmental Sciences, University of Arkansas,
Fayetteville, Arkansas, United States of America
2Department of Botany and Microbiology, College of Science, King Saud University,
Riyadh, Saudi Arabia
* ydwining@uark.edu
Abstract. Rice (Oryza sativa L.) is the primary staple food for half of the world population. It is
generally classified based on the grain color into black, red, purple, brown, green, and white.
These colored rice are determined by the composition and concentration of anthocyanin
pigments in different layers of aleurone, pericarp, and seed coat. Anthocyanins are also
accumulated in various tissues of the rice plants, mostly in the grain, but are also presents in
leaves, leaf sheath, floral organ, and hull. The type and concentration of the anthocyanins in rice
tissues are influenced by the cultivars and developmental stages. Anthocyanin-enriched rice is
related to the health effects, including antioxidant, antibacterial, and anti-inflammation activities
that potentially use as functional food ingredients, dietary supplements, and natural colorants.
Structural and regulatory genes are involved in anthocyanin biosynthesis of rice. Various
molecular biology techniques have been applied to improve productivity, nutritional contents,
and market value of pigmented rice. This review focused on the genetics, biochemistry and
biophysical analysis of anthocyanin in rice that will facilitate rice breeding program to develop
new high-yield pigmented rice varieties.
Keywords: rice, anthocyanins, genetics, biochemistry, biophysics
(Received 2022-04-02, Accepted 2022-05-27, Available Online by 2022-05-31)
1. Introduction
Rice (Oryza sativa L.) has become the major staple food for almost half of the global population due
to the nutrients composition, including carbohydrate, protein, oil components, and other micronutrients
[1-5]. There are various kinds of rice are consumed that can be classified based on the grain color into
black, red, purple, brown, green, and white [6-9]. White rice is generally consumed, while pigmented
rice, such as black, red, purple, and brown contain natural pigment anthocyanins that accumulate in the
particular layers of the seed coat, pericarp, and aleurone [10-18]. Total anthocyanins in each pigmented
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Vol. 4, No.1, April 2022, pp. 0220103-01 ~ 0220103-19
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0220103-02
rice varieties are diverse in the range of 0-493 mg/100 g [19]. Black rice is the most common pigmented
rice in the market due to their sensory characteristics and organoleptic properties, such as good taste,
fragrant aroma, fluffiness texture, high nutrition values, and positive health effects [20-27]. China is the
biggest black rice producer followed by Sri Lanka, Indonesia, India, Philippines, Bangladesh, Malaysia,
Thailand, and Myanmar [17]. Pigmented rice genotypes have been cultivated in Asia for a long time,
such as Chinese black rice, Indonesian black rice, and Thai black rice [20]. Anthocyanins of the
pigmented rice has the potential to be applied as a dietary supplements, functional food ingredient, and
natural colorant for food, beverages, and pharmaceutical products. Anthocyanins show positive effects
for the human health, including antioxidant, antibacterial, anti-inflammatory, anticancer, anti-diabetic,
antitumor, anti-allergic agents, anticarcinogenic, anti-atherosclerosis, and others [23], [28-37], [38-40].
Consequently, anthocyanins play important roles in preventing human diseases, such as atherosclerosis
[12], [28], [41], diabetes [42-44], and cancer [45-49]. In the rice plants, anthocyanins involve in
pollination to attract the insects, UV-B protection, hormone responses regulation, photo-perception in
autumn leaves, stabilize photosynthetic activity, biotic and abiotic stress defense system [50-59].
Anthocyanins are water-soluble natural pigments classified to the phenolic compounds of
flavonoids group which responsible for attractive colors, such as purple, red or brown in different tissues
of the rice plants with various concentration and composition of anthocyanins [60-64]. There are six
anthocyanin types, including malvidin, peonidin, cyanidin, delphinidin, petunidin, and pelargonidin [65].
Different combinations of anthocyanins lead to different colors, the higher anthocyanins concentration
and combination, the blacker the color. The concentration and composition of anthocyanins in the rice
plants are vary depend on the rice variety and developmental stages [66-68]. The common anthocyanin
types in the pigmented rice are cyanidin-3-glucoside, while the minor is peonidin-3-glucoside [69-70].
Anthocyanins are important secondary metabolites in the rice plants and accumulate in various tissues
and organs that related to photosynthesis, reproduction, and defense, such as pericarp, aleurone, awn,
leaf blade, leaf sheath, palea, lemma, internode, stigma, apiculus, and root [71-74]. Different level of
purple color are identified in these tissues and organs of the rice plants. For example, purple and red rice
contain 20 times higher concentrations of the anthocyanin in their aleurone layer compared with brown
rice [75]. Black rice contain higher total antioxidant capacity compared to red rice; black rice have 0.5-
2.5% while red rice only 0.03-0.1% [76]. The purple pigmentation is regulated by the allelic variation
of genes, the co-segregation of the alleles do not always happen [72]. Anthocyanin biosynthesis is
controlled by the structural and regulation genes, and the stability of the anthocyanins also influenced
by the environmental conditions, including temperature, pH value, lights, enzymes, oxygen, and metallic
ions [51], [77-84]. Anthocyanin biosynthesis can be enhanced by environmental modification, such as
maintaining temperature ranging from 22 to 27oC and light intensity between 301-600 lx. Maintaining
the stability of anthocyanins is a crucial factor in food and pharmaceutical industry [85]. Accumulation
of anthocyanins in the rice plants are depend on the rice developmental stages, including seedling,
vegetative, reproductive, and mature stages. During maturity stage, black rice contains higher
anthocyanins in the aleurone layer compared with grain filling stage [75].
Anthocyanins have been used in human diet for centuries as herbal medicines to cure several
health problems, such as cold, diarrhea, and hypertension. Recently, anthocyanins are being applied as
natural colorant of food and beverages, and also dietary supplements due to their attractive colors and
health benefits. In the United States, estimated anthocyanins consumption is around 12.5 mg/day [86].
Black rice as the common pigmented rice in the market that contain various combinations of
anthocyanins, such as cyanidin-3-glucoside, peonidin-3-glucoside, and petunidin-3-glocoside in the
aleurone layer of the rice grain [13], [17], [70], [76], [87-88]. Cyanidin-3-glucoside is the most
anthocyanins composition in black rice around 631 mg/100 g, while peonidin-3-glucoside is around 363
mg/100 g [13], [70], [88-89]. Southeastern Asian countries are the primary producer of black rice.
Recently, California also produces black rice due to high market demand [90]. European countries that
cultivate black rice are Italy and Greece [23]. In Asian countries such as Thailand, China, Indonesia,
Advance Sustainable Science, Engineering and Technology (ASSET)
Vol. 4, No.1, April 2022, pp. 0220103-01 ~ 0220103-19
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India, Korea, and Japan, black rice is usually combine with white rice to increase the flavor [12], [91-
94]. The color of cooked black rice become regal purple [95]. Black rice is usually use as food
ingredients in fried rice, paella, risotto, porridge, bread, pasta, and rice cake [96 -97]. Black rice also
become an important material to produce alcoholic beverages with red color. There are many varieties
of black rice, including short and long grains, glutinous and non-glutinous rice, early and late maturity
period [98-100]. Red rice is generally used as a natural colorant in ice cream, bread, and liquor [11],
[101]. Pigmented rice also contains higher concentration of micronutrients, such as iron, manganese,
and zinc in the grain compared to white rice [102-107]. These pigmented rice has a potential to decrease
malnutrition around the world [66]. Many studies have been reported the nutritional values of black and
red rice [23], [41], [108-111]. Powdered anthocyanins extracts from black rice was produced with spray-
drying and freeze-drying processes of Italian black rice that contain rich anthocyanins and antioxidant
activity [112]. These powdered anthocyanins are more stable from environmental conditions of storage
and food processing, including temperature, pH value, and lights that give high economic value to use
for functional foods and pharmaceuticals products [6], [79], [113-114].
In China, red rice has been approved by the Chinese Ministry of Health as a food colorant in soybean
products, meat, and fish [115]. Meanwhile, in United States, Canada, European Union, Japan, Australia,
New Zealand, and South Africa restrict anthocyanins as a food colorant [116]. Red rice is commonly
use as food colorants and dietary supplements in China due to attractive and high stability color from
high light exposure, pH changes, and heat conditions; good taste and flavor; cheap; high availability;
and high yield rice variety [117]. The anthocyanin concentration in red rice is lower than black rice
around 1.5 to 9.4 mg/100 g [70], [118]. Fermented rice as a dietary supplement to decrease cholesterol
accumulation of the blood circulation has been marketed in China. Red rice as a herbal medicine to treat
cardiovascular disease and abdominal pain [11].
Analysis of biosynthesis, storage, and transportation mechanisms in anthocyanins have been
achieved a significant progress due to the development of molecular biology. These progress give a
positive impact on the food industry, pharmaceuticals, flavors, rice breeding program [119-121].
Identification of physicochemical properties, quantification, and extraction of anthocyanins in the rice
plants was based on Ultraviolet-Visible (UV-Vis) absorption spectrophotometer, High Performance
Liquid Chromatography (HPLC), mass spectrometry, liquid chromatography, and paper
chromatography [101], [104], [122-124]. Based on the UV-Vis absorption spectrophotometer data,
anthocyanins show maximum absorption range in the region 500-535 nm of the blue spectrum; malvidin
at 530 nm, peonidin at 517-520 nm, cyanidin at 512-520 nm, delphinidin at 525 nm, petunidin at 526-
529 nm, and pelargonidin at 502-506 nm [70]. By identification of phytochemical properties of
anthocyanins in pigmented rice gives insights to the application of pigmented rice as health promotion
agents [122], [125-126]. Based on the genetic analysis of pigmentation in pigmented rice, there are three
genes that regulates the pigmentation, including Ra, Rc, and Rd genes. The intensity of the pigmented
rice coloration is influenced by the presence of genes and the genes status (dominant or recessive). Ra
genes regulated purple pericarp, which purple color is dominant and white color is recessive. Brown
pericarp is produced when Rc gene presence and Rd gene absence. Both of the genes, Rc and Rd genes
are presence produce red pericarp. Meanwhile, if only Rd gene presence, it will not produce any color
[99], [127-128]. The alleles segregation of coloration in pigmented rice also presence, for example F2
population of the crossing between black rice and white rice varieties showed three phenotypes; black,
brown, and white color with the segregation ratio 9:3:4.
Pigmented rice cultivation since ancient time and in 1970s become more popular due to the
development of genetic engineering [129]. The famous pigmented rice varieties in Korea are dark red
Heugjinjubyeo, dark purple Heugnambyeo, dark blue Jakwangdo, red brown Sanghaehyeolla, black
purple Hongmi, and dark red-purple Kilimheugmi [130]. The quality of pigmented rice varieties have
been improve by employing recent technologies, including genome sequencing, gene expression
analysis, gene editing, and omics technologies [102], [131-134]. High-yield pigmented rice varieties
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have been developed by applying the characteristics of grain pigmentation inheritance, tagging the key
genes that controlled the rice quality traits, and identifying markers of these rice quality traits [135-136].
The advanced pigmented rice varieties can be developed by understanding the molecular basis of
anthocyanin biosynthesis in several organs of the rice plants [50]. In Japan, improved pigmented rice
variety was developed by crossing black rice variety ‘Okunomurasaki’ with high quality-white rice
variety ‘Koshihikari’ [137]. In Kazakhstan, adapted pigmented rice variety was developed by crossing
pigmented and non-pigmented rice varieties [138]. In Thailand, a new deep purple rice variety
‘Riceberry’ was developed by crossing between non-glutinous purple rice and an aromatic white jasmine
rice variety [139-140]. Brazil has been released two advanced pigmented rice varieties; the red rice
‘Rubi’ and the black rice ‘Onix’ [141]. In China, biofortified purple endosperm rice called ‘Zijingmi’
with high anthocyanins concentration was developed by editing anthocyanin biosynthesis [142]. New
foods and beverages from pigmented rice also have been develop by using improved processing
technologies. This review provides an update information on the genetics, biochemistry and biophysical
analysis of anthocyanin in pigmented rice that will facilitate rice breeding program to develop improved
pigmented rice varieties.
Anthocyanins in Rice Grains
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Anthocyanins in Rice Grains
Anthocyanins is mainly accumulated in the pericarp of the rice grains (Figure 1). Purple bran
color showed the highest total anthocyanin (2874 cyanidin 3-O-glucoside equivalent (CGE)/100g)
followed by black (1884 CGE/100 g), red (8.78 CGE/100g), and brown (3.09 CGE/100g). These rice
bran color has been reported to be correlated to the seed dormancy, red bran color rice have a longer
dormant compare to the white rice [143]. Based on the quantitative trait loci (QTL) analysis, one QTL
qSD7/qPC7 that regulated rice bran color and seed dormancy was identified on chromosome 7 [144].
Anthocyanin contents in the rice pericarp were significantly influenced by environmental conditions and
rice developmental stages (Figure 2). Rice developmental stages influence the anthocyanin
concentration in caryopsis that shows gradual color changes at each developmental stage. The
anthocyanin level increases as the increasing developmental stages and gradual grain filling. At 8-14
days after flowering (DAF), anthocyanins start accumulate in the caryopsis. At the milk stage, caryopsis
becomes black and at the maturity stage (35-45 DAF) is the highest anthocyanins concentration
accumulate in the caryopsis. The gradual changes of the anthocyanin concentration correlated with the
gene expression that control anthocyanin biosynthesis [145]. During maturity stage, the gene expression
level of OsDFR, OsF3H, OsAns, and OsCHS are increasing [146]. The anthocyanin accumulation in
black rice also influenced by photosynthetic activity.
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0220103-05
Figure 1. Cross-section of black rice grain showing anthocyanin accumulation in pericarp [66]
Anthocyanin is synthesized on the endoplasmic reticulum, transported through the Golgi
apparatus, and accumulated in the vacuole cells of vegetative and generative organs. Anthocyanin
biosynthesis is influenced by environmental conditions, such as salinity, drought, abscisic acid (ABA),
and rice diseases [147-149]. Black rice pigmentation is regulated by key activator loci for anthocyanin
(KALA), such as Kala1, Kala3 or MYB3, and Kala4 [137]. Based on the QTL analysis, Kala1 was
identified on chromosome 1 between SSR markers RM7405 and RM7419, Kala3 on chromosome 3
between RM15191 and RM3400, and Kala4 on chromosome 4 between RM1354 and RM7210.
LOC_Os04g0557500 within Kala4 region controls the purple color in the rice pericarp. Anthocyanin
concentration in the rice pericarp can be enhanced by overexpress LOC_ Os04g0557500 [20]. Red rice
pericarp is controlled by a QTL rg7.1 on chromosome 7 and LOC_Os07g11020 was identified within
the QTL region [150]. LOC_Os07g11020 encodes a bHLH TF. Two genes PURPLE PERICARP A (Pp,
Prpa and Prp1) on chromosome 1 and PURPLE PERICARP B (Pb, Prpb and Prp2) on chromosome 4
are regulates the purple color of rice pericarp [151-155].
Figure 2. Pigment gradient in brown rice, red rice, and black rice during developmental stages [66]
Transgenic pigmented rice varieties were developed by using transgene stacking system that
have higher nutritional and medical values for food and pharmaceutical industries [137]. Anthocyanin
concentration in the rice pericarp can be improved by using this genetic engineering technique that can
be enhanced their antioxidant activity and seed dormancy period [162]. By enhancing the anthocyanin
concentration in the rice pericarp may enhance the abiotic and biotic resistance [50]. Important genes
regulating the anthocyanin biosynthesis, such as CHS (chalcone synthase), F3H (flavanone 3]3-
hydroxylase), DFR (dihydroflavanol), and ANS1 (anthocyanin synthase) were identified by using whole
genome sequencing and transcriptomic sequencing in the pigmented rice plants [156]. Pigmented rice
produce lower yield and lower grain weight than white rice varieties [157-158]. Lower grain yield of
pigmented rice due to the anthocyanin deposition that reduce chlorophyll content in spikelet, decrease
photosynthetic rate and also grain filling rate [159]. The accumulation of anthocyanin in pericarp of the
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pigmented rice cause lower grain weight [145]. The lower grain yield and decreased grain size in black
rice near isogenic lines (NILs) population was identified in Japan [137].
Anthocyanins in Rice Floral Organs
Floral organs of the rice plants including stigma and apiculus showing red, purple, or brown
color because of anthocyanins accumulation (Figure 3). These obvious color is important in pollination
to attract insects and other animals but does not apply in the rice plants due to self-pollination.
Anthocyanins content in the floral organs also important as protective agents from ultraviolet radiation
and strong light intensity, and also become defense system from abiotic and biotic stresses including
salinity, drought, cold, heat, and diseases [160-162]. The specific color of stigma and apiculus is
important for rice taxonomy [73], [163-164]. Investigation about purple stigma and apiculus started in
1957 [165]. OsB2 is an important gene regulating anthocyanin biosynthesis in floral organs of the rice
plants. The variation color of apiculus is regulated by locus C, OsC1 [50].
Figure 3. Purple and white stigma of the rice plants [73]
The variation color of apiculus and stigma are regulated by several QTL regions. Diverse color of
apiculus is controlled by C-gene located between SSR markers RM19552-RM19565 [166-167]. Purple
apiculus is regulated by Pa-6 and red apiculus is coordinated by OSC [163], [166]. Purple stigma is
controlled by Ps-4(t) located in RM253, RM111, and RM6917 [168]. The first purple stigma gene OsC1
was identified on chromosome 6. Based on the map-based cloning strategy, two genes OsC1 and OsDFR
that responsible for the purple color of stigma and apiculi were identified in pigmented indica rice
cultivar Xieqingzao. A R2R3-MYB transcription factor is encoded by OsC1 on chromosome 6, while a
dihydroflavonol 4-reductase is encoded by OsDFR. OsPa gene responsible for apiculi color and OsPs
gene regulating the stigma color were identified by transcriptional expression analysis and
CRISPR/Cas9. Variety color of stigma and apiculus can be produced by gene interaction of OsC1,
OsDFR, OsPa, and OsPs. The purple color of stigma and apiculi is the result of genes interaction OsC1,
OsPa or OsPs , and OsDFR. Brown apiculi can be produced by gene interaction OsC1 and OsPa. Knock-
out of OsDFR resulting straw-white color stigma [169].
Anthocyanins in Rice Leaves
Leaves as the primary organ in photosynthesis promote the biosynthesis of anthocyanin and
starch. Anthocyanin accumulation in the rice leaves reduces the efficiency of photosynthetic activity
and consequently decrease the rice yield [170]. On the other hand, reducing the anthocyanin
concentration in the leaves will increase the photosynthetic activity and subsequently improve rice yield.
Consequently, in the rice variety selection process, purple leaf trait become a negative marker [50].
Based on the genomic sequence analysis, accumulation of anthocyanin in the rice leaves is regulated by
OsC1 and OsDFR [170]. OsC1 controls cyanidin 3-O-glucoside concentration in the rice leaves [171].
Rb gene on chromosome 1 involves in anthocyanins biosynthesis in the rice leaves was identified by
GWAS analysis. LOC_Os04g0577800 and LOC_Os04g0616400 on chromosome 4 also involve in
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anthocyanin biosynthesis in the purple rice leaves that identified by using bulk segregant and
transcriptome analysis [172].
Anthocyanins in Rice Leaf Sheath
Purple leaf sheath in rice due to the accumulation of anthocyanins. Leaf sheath color trait also
become a marker in rice variety selection. The level of anthocyanin accumulation in the leaf sheath also
influenced by the developmental growth stages. At V4 stage with 4-leaf, the anthocyanin concentration
in the leaf sheath ranging from 0.01 µmol/g until 0.06 µmol/g. The highest concentration of
anthocyanins starting at active tillering stage until maturity stage around 1.16 µmol/g [73].
Accumulation of the anthocyanins in the leaf sheath also correlated with defense system to the abiotic
stresses, including soil acidity, ultraviolet radiation, and temperature [173-174]. Diverse leaf sheath
color is regulated by OsC1 gene that has co-segregation with apiculus color [167]. A mutant rice plant
Z418 showing purple leaf sheath which was developed from C418 rice variety with green leaf sheet
color by modifying OsC1 gene [175]. OsC1 gene also identified in the F2 population of crossing
between purple leaf sheath rice (Tainung 72 / TNG72) and green leaf sheath rice (Taichung Sen 17 /
TCS17) [176]. There a segregation in that F2 population with ratio 3:1, 3 for purple leaf sheath and 1
for green leaf sheath, indicating that OsC1 is the dominant gene. Based on the RT-PCR analysis, the
gene expression of OsC1 in the leaf sheath tissue started at 5-leaf stages [177]. Another gene that
regulating the rice purple leaf sheath is PSH1(t) on chromosome 1 that identified in a recombinant inbred
line (RIL) population resulting from crossing rice variety IRBB60 and 9407 [152]. Variation of the leaf
sheath color also controlled by two QTLs on chromosome 1 and 6 [73], [178-179]. LOC_Os06g10350
on chromosome 6 as a gene controlling leaf sheath color was also identified by using F2 rice population
and 117 markers. LOC_Os06g10350 belong to the MYB family transcription factor.
Variation of leaf sheath color ranging from light to dark purple showing tyran rose, pansy
purple, red purple, and blackish purple. Anthocyanin accumulation in the leaf sheath ranged from 1.04
to 42.77 µmol/g, tyran rose color has the least anthocyanin concentration and blackish purple color has
the most anthocyanin content (Figure 4). The diverse leaf sheath color also associated with the rice
varieties [73].
Figure 4. Diverse rice leaf sheath color [73]
Anthocyanins in Rice Hulls
Colored rice hulls which are black and red due to the accumulation of anthocyanins [36]. About
15% of the rice varieties are colored hull and the most rice varieties (85%) have white-hulled. Colored
rice hull responsible to protect rice grain from oxidative stress [180]. China and Japan have been
cultivated rice variety with colored hulls since ancient time due to the health positive effects. Recently,
rice variety with colored hulls are cultivated in South Asia countries, United States, Italy, and Greece
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[181]. The type of anthocyanin in the purple rice hull is cyanidin 3-O-glucoside with concentration 2.8
mg/g [182]. Lemma and palea of the rice hull are associated with the rice floral organs and seed
characteristics including grain length, grain width, and grain weight [183-188]. The highest
anthocyanins accumulation is in purple hulls. Rice hull has been treated as one of residue material from
the rice plants, but right now colored rice hull is become antioxidant and anti-cancer sources. Straw-
white hull correlated with non-shattered rice grains and became an important marker during rice
domestication [189].
Figure 5. C-S-A gene system of rice hull pigmentation [182]
Methanol extracts of colored rice hulls from rice variety Heuginju with black hull, WD-3 with
purple hull, Jeoginju with red hull, and Ilpum with light-brown showed significantly high anti-cancer
and antioxidant activities. Black hull of Heuginju showed the highest anti-cancer and antioxidant
activities compared to the others colored hulls [190]. Acetone extract of rice hull contain procyanidins
[36]. Based on the molecular, genetic, metabolic, and phylogenetic analysis; colored rice hulls were
regulated by C-S-A gene system, which C1 encoding MYB transcription factor and become gene that
produce color, S1 encoding bHLH protein and acting as a tissue specific regulator, A1 encoding
dihydroflavonol reductase and only express when C1 co-ordinate with S1 (Figure 5). Brown hull color
is formed when A1 is not expressed. One QTL responsible for black hull trait is on chromosome 4 [191].
Gene Phr1 on chromosome 4 encoding polyphenol oxidase is found to be responsible for black hull
color of rice [192-193]. Black hull is also regulated by Bh4 gene on chromosome 4. Another genes that
responsible for black hull are Bh-a, Bh-b, and Bh-c as complementary genes [194]. Two QTLs qHC4
and qHC7 also responsible for black hull coloration, these QTLs were identified by using an F2
population of crossing between SS18-2 and EM93-1 [194].
Conclusions
Pigmented rice has been popular among rice consumers and increasing demand of pigmented
rice have become motivation for rice breeder to develop high yield pigmented rice. Anthocyanin is a
source of functional food ingredients, natural colorants, pharmaceuticals, and other industrial
biochemical products with the high health benefits. Anthocyanin accumulation in the rice plants can be
enhanced by genetic molecular techniques and environmental regulation. Advanced pigmented rice
varieties with enhanced anthocyanins content have been developed. To fulfill the consumer increasing
demand, it is important to explore deeply the genetic bases of pigmented rice in order to enhance
pigmented rice quality, sensory properties, and nutritional content. In this review provides important
information for rice breeder to develop high quality pigmented rice based on consumer demand.
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Rice (Oryza sativa L.) is primary dietary source for half of the global population that comprising both essential nutrients and toxic heavy metal elements for human health. A number of nutrients are required within the diet and generally lacking in human diets, and need to biofortify into the rice grains, such as iron (Fe), zinc (Zn), calcium (Ca), potassium (K), sodium (Na), magnesium (Mg), phosphorus (P), copper (Cu), iodine (I), selenium (Se), and Sulphur (S). Meanwhile, some elements are toxic to human, including arsenic (As), cadmium (Cd), chromium (Cr), cobalt (Co), mercury (Hg), manganese (Mn), nickel (Ni), and lead (Pb) which need to be eliminated from the rice grains. This article reviews the aspects of phenotypic variation of grain elemental concentration in the diverse rice genotypes, relationship of environmental conditions and rice grain elemental accumulation, correlation between rice grain elemental content and others agronomic traits, and also genetic basis of grain elemental concentration in rice. All of these aspects are important to develop rice varieties with a balanced elemental nutrients and lower toxic heavy metal elements. Enhancing the concentration of essential mineral elements and reducing the accumulation of toxic elements in the rice grain are important to improve the rice quality for human health in addressing mineral deficiency and toxicity that could be accomplished by using plant breeding, agronomic, and genetic engineering approaches.
... The majority of the agricultural pathogens are Xanthomonas oryzae (gram-negative) causes rice bacterial blight, Xanthomonas translucens (gram-negative) causes bacterial leaf streak, Pseudomonas spp (gram-negative) cause bacterial leaf spot, and Staphylococcus aureus (gram-positive) causes bumblefoot in chickens [35,36]. Additionally, the most popular bacteria that responsible for foodborne pathogens of contaminated products Escherichia coli (gram-negative), Salmonella typhimurium (gramnegative), Bacillus cereus (gram-positive), and Listeria monocytogenes (gram-positive) [37,38]. Minimizing agricultural and foodborne pathogens with chemical control has been ineffective due to safety concerns and bacterial resistance [39,40]. ...
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Zingiber cassumunar Roxb. is a powerful medicinal plant that has been used as traditional medicine to cure respiratory problems, pain, and inflammation in China, Indonesia, Thailand and other Asian countries by using the crude extracts. The objective of this research is to identify phytochemical composition of Z. cassumunar Roxb. and to analyze antibacterial activity of crude extract, purified compounds, and their microencapsulated products of Rhizome Z. cassumunar Roxb. Identification of phytochemical composition in crude extract of rhizome Z. cassumunar Roxb. was achieved by chromatography-mass spectrophotometer. The major phytochemical composition in crude extract of Z. cassumunar Roxb. is essential oils, including terpinen4-ol (37.7%), β-pinene (20.8%), and (E)-1-(3,4-dimethoxyphenyl)but-1-ene (13.3%). Crude extract of Z. cassumunar Roxb. was purified with silica gel flash column chromatography, resulting two purified compounds. The antibacterial activity of crude extract, purified compounds, and their microencapsulated products of Rhizome Z. cassumunar Roxb. were evaluated against agricultural and foodborne pathogens by using disc agar diffusion and broth microdilution techniques. All of the samples studied (crude extracts, purified compounds, and microencapsulated of Z. cassumunar Roxb.) were effective against all the bacteria. Based on the results of the disc-diffusion assay suggested that amongst the samples studied, purified compounds (compound 1 and 2) and microencapsulated purified compounds (compound 1 and 2) exhibited more effective against all the bacteria compared to the crude extracts. Antibacterial activity of the rhizome of Z. cassumunar Roxb. was contributed mainly by the essential oils components as the active compounds. Gram-negative bacteria (X. oryzae, X. translucens, Pseudomonas spp, E. coli, and S. typhimurium) appeared to the most resistant to the crude extracts, purified compounds, and microencapsulated of Z. cassumunar Roxb. compared to the gram-positive bacteria (S. aureus, B. cereus, and L. monocytogenes). Microencapsulated of the tested samples (crude extract, purified compound 1, and purified compound 2) of the rhizome Z. cassumunar Roxb. exhibited high antibacterial activity with no significantly different with the tested samples without microencapsulation. These results suggest potential antibacterial properties of Z. cassumunar Roxb., which useful for agricultural plant health, food preservation, natural therapies, and pharmaceuticals.
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Rice is important staple food and drought is the limiting factor for yield. US is the third largest exporter of rice, and Arkansas is the top rice-producing state. A RIL population, derived from Kaybonnet (drought resistant/DR) and ZHE733 (drought sensitive), termed K/Z RILs was chosen. The abscisic acid (ABA) is important in signaling responses to drought. Under drought, ABA triggers stomatal closure to reduce transpiration leading to drought resistance. Roots can be screened for ABA sensitivity, which reflects their stress response. The objectives of this research were to evaluate the ABA response of the K/Z RIL population on root architectural traits related to drought resistance and to identify QTLs and candidate genes for root architectural traits related to ABA response. The RIL population of 198 lines were screened for drought stress in the field at R3 stage and for ABA sensitivity. The effect of drought stress in the field was quantified by calculating the filled grains per panicle number (FG). Drought stress effect in ABA sensitivity were quantified by measuring root architectural traits at V3 stage: root length (RL), root to shoot ratio (RSR), total root number (TRN), shallow root number (SRN), deep root number (DRN), and root fresh weight (RFW). Kaybonnet and 48 drought resistant lines under control display more FG, longer RL, higher RSR, more DRN, and heavier RFW compared to ZHE733 and 150 drought sensitive lines. Under exogeneous ABA, Kaybonnet and 48 drought resistant lines exhibited an ABA-sensitive phenotype, implying that they regulate osmotic stress tolerance via ABA-mediated cell signaling. A total of 147 QTLs and 510 candidate genes within the QTL regions were identified for ABA sensitivity. The RT-qPCR analysis of the candidate genes revealed that a high number of abscisic acid-regulated genes were up-regulated in Kaybonnet. This study provides information to develop drought resistant rice.
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Heavy metal pollution in soil, forage, and animals is serious concern nowadays. Current research was conducted in Sargodha to find out the relationship of animals related to the forages and soil pollution. Three sites were selected with three different treatments; site I irrigated with ground water, site II irrigated with the canal water, and site III irrigated with the wastewater. Samples of soil, forage, and animals (blood, hair, feces) were collected from selected sites and were analyzed for metal analysis using atomic absorption spectroscopy. Results indicated that Zn in soil ranged from 24.12 to 37.39 mg/kg; forage, 31.98–44.47 mg/kg; blood of animals, 1.49–2.72 mg/L; hair of animals, 1.37–2.41 mg/kg; and feces of animals, 1.06–2.97 mg/kg. The concentration of zinc in soil and forage was less than permissible limit, but concentration in blood of animals was greater than critical limit suggesting the presence of metal. Bio-concentration factor indicated that metal was accumulated in forages growing at irrigated site. HRI concentration (2.024 mg/kg/day) suggests the accumulation of zinc in animal tissues. Pollution load index and enrichment factor were within the range.
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Rice (Oryza sativa L.) is the primary food for half of the global population. Recently, there has been increasing concern in the rice industry regarding the eating and milling quality of rice. This study was conducted to identify genetic information for grain characteristics using a recombinant inbred line (RIL) population from a japonica/indica cross based on high-throughput SNP markers and to provide a strategy for improving rice quality. The RIL population used was derived from a cross of “Kaybonnet (KBNT lpa)” and “ZHE733” named the K/Z RIL population, consisting of 198 lines. A total of 4133 SNP markers were used to identify quantitative trait loci (QTLs) with higher resolution and to identify more accurate candidate genes. The characteristics measured included grain length (GL), grain width (GW), grain length to width ratio (RGLW), hundred grain weight (HGW), and percent chalkiness (PC). QTL analysis was performed using QTL IciMapping software. Continuous distributions and transgressive segregations of all the traits were observed, suggesting that the traits were quantitatively inherited. A total of twenty-eight QTLs and ninety-two candidate genes related to rice grain characteristics were identified. This genetic information is important to develop rice varieties of high quality.
Thesis
Rice (Oryza sativa L.) is the staple food for a majority of the world’s population, and uses 30% of the global fresh water during its life cycle. Drought at the reproductive stage is the most important abiotic stress factor limiting grain yield. The United States is the third largest exporter of rice, and Arkansas is the top rice-producing state. The Arkansas rice-growing region in the Lower Mississippi belt is among the 10 areas with the highest risk of water scarcity. Adapted U.S. rice cultivars were screened for drought resistant (DR) traits to find sources for breeding U.S. rice cultivars for a water saving agricultural system. A recombinant inbred line (RIL) population, derived from varieties Kaybonnet (DR) and ZHE733 (drought sensitive), termed K/Z RILs was chosen for genetic analysis of DR traits. The objectives of this research were to 1) analyze the phenotypic and grain yield components of the K/Z RIL rice population for drought-resistance-related traits, 2) evaluate the Abscisic Acid (ABA) response of the K/Z RIL rice population on root architectural traits in relation to drought stress resistance, 3) screen polymorphic molecular markers to identify genes linked to productivity traits of grain yield under drought stress, measured by number of filled grain per panicle using bulk segregant analysis (BSA), and 4) identify QTLs and candidate genes in the K/Z RIL population for drought resistance associated with vegetative morphological traits, grain yield components under drought stress and well-watered conditions, and root architectural traits related to ABA response. The RIL population was screened in the field at Fayetteville (AR) by controlled drought stress (DS) treatment at the reproductive stage, and the effect of DS quantified by measuring drought-related traits. ABA sensitivity was quantified by measuring root architectural traits at the V3 stage. Based on the filled grain per panicle number, 13.13% of K/Z RIL population and parent Kaybonnet were highly drought resistant, while 75.75% of RILs and parent ZHE733 were drought sensitive. Under ABA conditions, Kaybonnet and 48 drought resistant lines exhibit ABA sensitivity, implying regulation of osmotic stress tolerance via ABA-mediated cell signaling. Based on BSA screening, 13 polymorphic markers potentially linked to DR traits were identified. QTL analysis was performed with 4133 SNPs markers by using QTL IciMapping. A total of 213 QTLs and 628 candidate genes within the QTL regions were identified for droughtrelated traits. The RT-qPCR analysis of the candidate genes revealed that a high number of drought resistance genes were up-regulated in Kaybonnet as the drought-resistant parent. Information from this research will serve an important step towards improvement of adapted Arkansas rice cultivars for higher grain production under DS conditions.