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Towards Understanding Rice Domestication and its Implication

Nihar Ranjan Chakraborty*

Department of Crop Improvement Horticulture and Agricultural Botany,

Palli Siksha Bhavana, Visva-Bharati, Sriniketan 731 236, India

*E-mail: nrchakraborty@gmail.com

Geneconserve: 12(47) - 1:22

Abstract:

Domestication is a long term process and continues today. Crop domestication can be considered a model system of plant evolution. The origin of cultivated rice is related to complex evolutionary dynamics in rice cultivars and wild progenitors, particularly rapid adaptive differentiation and continuous gene flow within and between cultivated and wild rice. A growing body of phylogenetic evidence suggested that the diverged genetic background of indica and japonica rice cultivars were derived independently from genetically distinct wild populations. Many genes such as sh4, Wx, G1F1 etc contributed to rice domestication process. The wild species of the genus Oryza offered enormous potential to make a significant impact on agricultural productivity. The domestication-selected gene can be used for further crop improvement. Genes for resistance to diseases, insects and abiotic stresses have also been introgressed across crossability barriers from distantly related species into cultivated rice. Key words: Domestication, Oryza, Wild rice, Phylogeny, Introgression,

Introduction

Green plants are the ultimate source of resources required for human life, food, clothing

and energy requirements. Prehistoric people, who depended on their skills as hunters,

drew upon abundant natural vegetation to collect nutritious and nonpoisonous fruits,

seeds, tubers, and other foods. The domestication of crops historically has been

influenced by ecological and agricultural conditions, as well as by food gathering

preferences. Genotypes that have adopted to a wide range of climatic and edaphic

conditions typically have been selected for cultivation. The achievement of higher

yielding crops facilitated population growth, sedentary settlement and further

development. Which crops were domesticated depended not only on the number of

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seeds or the size of fruits, but also on taste, palatability and other factors. Rice has a

long pre-history and plays an important role both for economic importance and human

culture. Rice (Oryza sativa) was domesticated approximately 10000 years ago

(Diamond, 2002) and now provides staple food for half of the world‟s population. It

accounts for 35-60% of the calories consumed by 2.9 billion Asians (Brar and Sing,

2011). As a diploid crop with a relatively small genome, rice holds a great potential for

understanding the genetic mechanisms of crop domestication and improvement.

Completion of the sequencing of the rice genome offered an unprecedented opportunity

for studying rice genetics (Goff et al., 2002; Yu et al., 2002). World rice production has

increased mainly through the application of principles of classical Mendelian genetics

and conventional plant breeding. The current world population is increased rapidly and

rice production must increase more to meet the growing demand. Rice productivity is

continually threatened by several biotic and abiotic stresses. The major challenge is

how to overcome these constraints particularly in the context of global climatic changes

and newly emerging diseases and pathogen types. The other major concern is how to

produce more rice with less land, water, chemicals and labor. Plant domestication

primarily solved the problem of food shortage and instability and allowed steady human

population growth and modernization of society. Understanding of the genetic basis of

domestication has leapt forward owing to rapid advances in genomics. In particular, the

cloning of genes controlling key domestication traits in major crops has opened up a

new avenue through which to investigate the molecular genetic mechanisms and

population processes of domestication (Doebley et a.,l 2006). On the basis of rice

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domestication knowledge scientists are able to develop rice varieties with higher yield

potential and durable resistance to diseases, insect and abiotic stresses.

Cultivated and Wild relatives of the Oryzeae tribe

Recent advances in cellular and molecular biology, particularly genomics, have

provided new opportunities to develop improved germplasm with new genetic properties

and to understand the function of rice genes (Khush and Brar, 2001). The cultivated rice

(O. sativa) belongs to the tribe Oryzeae, subfamily Oryzoideae of the grass family

poaceae (Gramineae). The tribe has 11 genera, of which genus Oryza is the only one

with cultivated species. The genus Oryza has 22 wild species (2n=24, 2n=48)

representing ten genomes: AA, BB, CC, BBCC, CCDD, EE, FF, GG, HHJJ, HHKK (Ge

et al., 1999). The genus Oryza has been divided into four species complexes (1) sativa

complexes (2) officinalis complexes (3) meyeriana complexes (4) ridleyi complexes.

Two species, O. brachyantha and O. schlechteri cannot be placed in any of these

groups (Vaughan, 1994).

O. sativa complexes: This complex consists of two cultivated species, O. sativa (Asian

rice) and O. glaberrima (African rice), and six wild taxa: O. nivara, O. rufipogon, O.

breviligulata (O. barthii), O. longistaminata, O. meridionalis, and O. glumaepatula. All of

these are diploid with AA genome. O. glaberrima is distinguished from O. sativa by its

short, rounded ligule, panicle-lacking secondary branches, and almost glabrous lemma

and palea. O. glaberrima is not as variable as O. sativa.

O. officinalis complexes: It is the largest complex in the genus consists of nine species.

It comprises five diploid (O. punctata, O. officinalis, O. rhizomatis, O. eichingeri, and O.

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australiensis) and four allotetraploid species (O. minuta, O. latifolia, O. alata, and O.

glandiglumis). Species of this complex can be easily identified by virtue of their

truncated ligules, straight rachilla, small sized spikelets, and linearly arranged tubercles

on the surface of lemma and palea. Some species grow in partial shade or moist soil.

Others are adopted to swamps and seasonal pools of water and open habitat (Brar and

Singh, 2011).

O. meyeriana complexes: This complex has two diploid species with GG genome: O.

meyeriana and O. granulata. This is the only group of species in the genus Oryza that is

not found in or near permanently or seasonally standing or flooded water. All members

of this species complex grow in the shade or partial shade of degraded primary or well

established secondary forests, often on sloping terrain. All species of this complex have

unbranched panicles with small spikelets.

O. ridleyi complexes: This complex comprises two tetraploid species with HHJJ

genome: O. ridleyi and O. longiglumis. The plants of this complex are tufted erect, 1-2 m

tall, with truncate ligule and straight rachilla of spikelet. They usually grow in shaded

habitats beside rivers, streams, or pools.

Unknown complexes: O. brachyantha - It is a diploid species with genome FF. Annual

tufted grass is up to 60 cm tall, thin leaves, 15-20 cm long, 6-7 mm wide, ligule flat or

acute not split. This species grows in the Sahel zone and in East Africa in small

temporary pools, often in laterite soils.

O. schlechteri - It is a tetraploid species with genome HHKK, the least studied species

in the genus. It is tufted perennial, 30-40 cm tall, with an erect, 4-5 cm panicle and

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small, unwanted spikelets. Roots with short underground shoots are covered by broad

scale like leaves. It is a stoloniferous species of unstable stony soil, such as riverbanks,

and grows in full or semi-shade (Brar and Singh, 2011).

Related Genera: Beyond Oryza, the tribe Oryzeae contains ten other genera. Vaughan

(1994) has given brief description of these genera. These genera include: Chikusichloa,

Hygrooryza, Leersia, Luziola, Prosphytochloa, Rhynchoryza, Zizania, Zizaniopsis,

Potaomophila and Porteresia.

Wild progenitors

Molecular phylogenetic studies have confirmed that the closest wild relatives of

cultivated rice (Asian rice) were O. nivara and O. rufipogon, which are distributed from

southeastern Asia to India. The two wild species are ecologically distinct. O. nivara is

annual, photoperiod insensitive, self-fertilized, and adapted to seasonally dry habitats,

whereas O. rufipogon is perennial, photoperiod sensitive, largely cross-fertilized, and

adapted to persistently wet habitats (Sharma et al., 2000). The identity of the species

that served as the direct progenitor of cultivated rice remains controversial. The

hypothesis of rice domestication from O. nivara was based on the phenotypic similarity

between O. nivara and O. sativa, including an annual life history, self-fertilization, and

high reproductive allocation (Sharma et al., 2000; Chang, 2003). Proponents of the

hypothesis that O. rufipogon is the ancestor of cultivated rice emphasize the benefit of

higher genetic diversity of an outcrossing progenitor (Oka, 1988). A greater effort to

correctly identify and distinguish these two ecologically distinct taxa should help better

characterizing the wild progenitor of rice (Zhu et al., 2007). O. nivara evolved from an O.

rufipogon-like ancestor as a result of habitat shift (Grillo et al., 2009).

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O. sativa (Asian rice) is widely cultivated whereas O. glaberrima (African rice) is

cultivated on a limited scale in western Africa. The Perennial and annual relatives of the

West African cultivated rice O. glaberrima are O. longistaminata and O. breviligulata,

respectively. The perennial relative is easily distinguished from the annual wild relative

of this complex by its strong rhizomes and long anthers (Brar and Singh, 2011).

Fig .1 Relationships of Wild progenitors:

South and Southeast Asia West Africa

Wild Perennial

Wild Annual

Cultivated

Origin of rice

To understand the domestication of Asian and African rice it is necessary to understand

the gene pools from which they came. That requires understanding these gene pools as

they are found today and also how they might have been in the past. Asian O. sativa

has two major varietal groups or subspecies, japonica (keng) and indica (hsien), that

Common Ancestor

Oryza rufipogon

Oryza nivara

Oryza sativa

Oryza longistaminata

Oryza breviligulata

Oryza glaberrima

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have traditionally been recognized in the Chinese language (Bray and Needham, 1984).

Kato et al. (1928) expressed the opinion that indica and japonica rice originated

independently from a wild ancestor. Ting (1957), on the other hand, proposed that

japonicas were derived from the indicas. Glaszmann (1987) recognized six groups of

rice varieties by using isozymes: indica, aus (early summer), ashwina (early deep

water), rayada (long duration deep water), aromatic and japonica. The vast majority of

varieties belonged to group I (73.4%) and group VI (23%). Less than 1% of the varieties

could be assigned to each group II, III, IV, and V. Information from genetic affinity

(isozyme analysis), isolation barriers (F1 sterility), and morphological classification

suggests that the six groups may have been domesticated from different populations of

O. nivara at different locations and on different time scales. Two major hypotheses

have been proposed on the origin of rice (1) monophyletic origin and (2) multiple,

geographically independent (diphyletic) domestication from its wild ancestor.

Archeological evidence, based on ancient rice grains and some genetic markers

support a single domestication of O.sativa ssp. Indica from O. rufipogon populations.

The alternative hypothesis, of at least two separate domestication events leading to

indica and japonica rice, has been suggested by genetic distance studies (Londo et al.,

2006). The genetic distance data reveal that japonica and indica are genetically distinct

from each other, raising the possibility that the two major rice types may have arisen

from different ancestral gene pools. The hypothesis of an origin from O. nivara was

based on the phenotypic similarity between O. nivara and O. sativa, including annuality,

self-fertilization, and high reproductive allocation (Sharma et al., 2000). Cheng et al.

(2003) determined polyphyletic origin of cultivated rice based on the interspersion

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pattern of SINEs(Short Interspersed Nuclear Element). When an indica cultivar was

crossed with O. nivara, no segregation of the mating system or life history traits was

observed in the F2 population (Li et al., 2006). There were two explanations for this

result. First, indica rice may have been domesticated from O. nivara so that their

phenotypic similarity was genetically based. Alternatively, indica rice may have been

domesticated from O. rufipogon, but the genes responsible for the independent origins

of annual habit and self-fertilization in O. nivara and O. sativa were the same. This

would imply that natural selection for annual life history and self-fertilization in the wild

O. nivara and artificial selection for these traits in domesticated rice acted on the same

gene targets. It is more parsimonious to consider the origin of indica rice from O. nivara.

While O. nivara could have been the primary genome donor for indica, it cannot be the

sole genome donor for all rice cultivars. Cultivars with relatively strong photoperiod

sensitivity and ability to grow in deep water conditions might have acquired O. rufipogon

genes through introgression or independent domestication. Moreover, the comparison

of indica and japonica genome sequences identified highly divergent linkage blocks,

suggesting that more distantly related wild species might have also contributed to the

domesticated rice gene pool through introgression probably assisted by breeders (Tang

and Shi, 2007). Phylogenetic and population studies using a variety of molecular

markers as summarized by Sang and Ge (2007) seemed to have reached the following

consensus. First, the sampled accessions of the wild proginators O. rufipogon and O.

nivara, did not form monophyletic groups within each species. Second, cultivated rice

did not show a clearly closer relationship with one wild species compared with the other.

Third, the major types of cultivars, such as subspecies indica and japonica, tended to

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form monophyletic groups separated by a relatively large genetic distance thereby

supporting diphyletic origin. West African O. glaberrima is similar to that of O. sativa in

Asia but O. glaberrima has less genetic diversity. Asian and African rice is primarily

grown where it evolved and, hence, where it‟s wild relatives occurs. Knowledge of the

genetics of O. glaberrima is far less than O. sativa although it is thought that the two

species have similar genetic architecture for many traits (Oka, 1988). Molina et al.

(2012) examined the evolutionary history of domesticated rice by resequencing 630

gene fragments on chromosomes 8, 10, and 12 from a diverse set of wild and

domesticated rice accessions and concluded their opinion for a single domestication

origin of rice.

Gene flow within and between cultivated rice and wild rice

Gene flow between rice cultivars and wild relatives coupled with taxonomic

inconsistency poses a major challenge to trace the origin of cultivated rice through

molecular phylogenetics. Gene flow between cultivated and wild rice occurs in both

directionnt (Khush, 2001). The introgression of valuable genes from wild to cultivar

species has been a continuous breeding practice for cultivar improveme Introgression

from cultivated rice to its wild progenitors is a common occurrence where they are

sympatric (Chen et al., 2004; Song et al., 2006), has created an array of phenotypic

intermediates known as weedy rice (Olsen et al., 2007). Although weedy rice is

classified as a subspecies of cultivated rice, namely O. sativa ssp. spontanae or ssp.

fatua, it has also been particularly recognized as wild species, O. rufipogon or O. nivara

(Li et al., 2006). Due to floral structure perennial outcrossing wild rice is more likely to

be a pollen receiver than annual inbreeding wild rice (Chen et al., 2004). During

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cultivation of rice, selection pressure would have been favoured high seed producing

populations and hence inbreeding. Subsequently when rice was fully domesticated

(non-shattering) it would have been sympatric with wild rice as it spread. Introgression

from wild rice of different genetic backgrounds into newly domesticated rice could

readily have occurred enabling domesticated rice to adapt to new environments. Most of

the germplasm in gene banks of wild rice was collected from human-disturbed or

human-made habitats such as roadside ditches and irrigation channels. These are

areas where introgression may have occurred between wild rice and rice. In Asia,

introgression from wild rice to cultivated rice is more likely to occur in indica varieties

than japonica varieties because of where these two varietal groups are grown. Tropical

japonica varieties in mainland Asia are generally grown in highland where wild rice does

not grow and in insular Asia, particularly Java, where A-genome wild rice is rarely in

proximity to rice fields. Indica varieties are mainly lowland varieties that on mainland

Asia often grow sympatric with wild rice. Many accessions of African cultivated rice, O.

glaberrima, have genes introgressed from O. sativa (Semon et al., 2005). Weedy rice

grows in rice fields and is adapted to the rice cropping system. Due to its genetic

similarity to rice it is difficult to eliminate from rice field without careful attention to land

preparation.

Recent phylogenetic analyses of rice domestication

Phylogenetic analyses of rice domestication have focused on addressing questions of

when, where, and how many times rice was domesticated. Isozymes and other

molecular markers such as restriction fragment length polymorphism (RFLP), random

amplified polymorphic DNA (RAPD), simple sequence repeat (SSR), inter simple

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sequence repeat (ISSR), transposable element (TE), and rDNA including chloroplast

DNA and mitochondrial plasmid-like DNAs have been used in evolutionary studies in

Oryza. The earliest effort to trace the geographic origin of rice with molecular markers

was undertaken by using 40 allozyme loci (Second, 1982). That study suggested that

japonica rice was domesticated in China and indica rice was domesticated in other

places of tropical Asia. Using restriction fragment length polymorphism (RFLP) markers

and 93 accessions of 21 Oryza species, Wang et al. (1992) found that the indica and

japonica cultivars were more closely related to the wild species than to each other.

Aggarwal et al. (1999) used amplified fragment length polymorphism (AFLP) markers to

study phylogenetic relationships in Oryza species. The results showed common

ancestry to the genus Oryza. Further evolution in Oryza has followed a polyphyletic path

where in multiple lineages underwent independent divergence after separation from a

common ancestor/pool of related taxa. In another study, Joshi et al. (2000) using ISSR

markers suggested that the genus may have evolved following polyphyletic pathway.

Sun et al. (2002) studied 75 cultivated varieties and 118 O. rufipogon strains using

markers from nuclear, mitochondrial, and chloroplast genomes, and demonstrated a

relatively high level of genetic differentiation between indica and japonica cultivars in

both nuclear and cytoplasmic genomes. Quantitative trait locus (QTL) mapping has

proven to be an effective initial step to reveal the genetic basis of phenotypic evolution

under natural and human selection (Paterson 2002). Yamanaka et al. (2003) concluded

that O.sativa has diphyletic origin based on the retrotransposon p-SINE1-r2, ashort

interspersed nuclear element (SINE) at the waxy locus of the three regions. Their study

had two major limitations (1) sampling of the wild species accessions did not represent

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the whole geographical region of their distribution. It represented only a small region in

Thailand, Cambodia, and Vietnam, leaving out the vast regions in china and India where

O. rufipogon and O. nivara, respectively, are widely distributed and (2) the amplification

patterns overlapped in both the forms for all the three regions. Cheng et al. (2003)

determined polyphyletic origin of cultivated rice based on the interspersion pattern of

SINEs. Zhu and Ge (2005) used sequences of four nuclear loci to investigate the

phylogenetic relationships between the A-genome species of Oryza. They found that

the cultivars fell into two monophyletic groups, with one containing indica rice and some

accessions of O. nivara and O. rufipogon, and the other containing japonica rice and

other accessions of both wild species. Recent phylogenetic and population studies

using a variety of molecular markers seemed to have reached the following consensus.

First, the sampled accessions of the wild progenitors O. rufipogon and O. nivara did not

form monophyletic groups within each species (Zhu and Ge, 2005; Kwon et al., 2006).

Second, cultivated rice did not show a clearly closer relationship with one wild species

compared with the other (Zhu and Ge, 2005). Third, the major types of cultivars, such

as subspecies indica and japonica, tended to form monophyletic groups separated by a

relatively large genetic distance (Zhu and Ge, 2005; Kwon et al., 2006; Zhu et al.,

2007). A phylogeographic study of 203 cultivars and 129 wild accessions suggested

that indica was domesticated within a region south of the Himalayan mountain range,

including eastern India, Myanmar, and Thailand, whereas japonica may have originated

from southern China (Londo et al., 2006). The results are consistent, to some extent,

with archaeological findings of ancient rice cultivation in the Yangtze basin of southern

China and northeastern India (Fuller, 2006). Several studies have examined

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evolutionarily neutral DNA markers at genome wide loci and domestication related QTL

in several collections, including various cultivars of Asian rice O.sativa and its wild

relative O. rufipogon (Izawa et al., 2009). These studies all seem to suggest, in one way

or another, that divergent rice cultivars were domesticated independently from

genetically differentiated wild populations at different geographic locations.

Rice domestication traits

Regardless of which wild species was the direct wild progenitor, a basic set of

morphological and physiological transitions known as the domestication syndrome must

have occurred during rice domestication (Hancock, 2004). These included reduction in

grain shattering and seed dormancy, synchronization of seed maturation, reduction in

tiller number, increase in tiller erectness, increase in panicle length and branches, and

reduction in coloration and awn length (Li et al., 2006). The reduction in shattering and

seed dormancy and synchronization of seed maturation, which may have been selected

unconsciously on most occasions (Harlan, 1975), were necessary for improving the

efficiency of harvest and planting to make the earliest efforts of cultivation worthwhile.

The decrease in tiller numbers in cultivated rice facilitates a synchronous tiller

production and maturation and, consequently, minimizes non-productive tillers that

flower too late to contribute to harvest. Tiller erectness reduces the degree of tiller

overlap and, thus, also increases the capacity of tiller cultivation per unit field. The

increase in panicle length and branches resulted in the production of a larger number of

grains per panicle. Therefore, selection for higher yield was most likely the driving force

for the morphological modifications. Additional phenotypic changes had to occur if rice

was domesticated from O. rufipogon rather than from O. nivara, including the switches

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from out-crossing to a selfing mating system, and from perennial to annual habit. A

number of genes such as shattering (qSH1, sh4), plant stature (PROG1), red pericarp

(RC, Rd), grain filling (GIF1), flowering time (Ghd7), grain number per panicle (Gn1a),

and taste/texture of cooked grains (Wx) contributed to rice domestication process

(Izawa et al., 2009).

Table 1: Main features of cloned domestication-related genes in rice

Gene name Trait Reference

Wx Taste/texture of cooked rice Olsen et al., 2006, Mikami

et al., 2008

sh4 Seed shattering Li et al., 2006, Lin et al.,

2007

qSH1 Seed shattering Konishi et al., 2006

Rc Seed pericarp color Sweeney et al., 2007

Rd Seed pericarp color Furukawa et al., 2007

qSW5 Seed width Shomura et al., 2008

Gn1a Grain number/panicle Shomura et al., 2008

Ghd7 Flowering time Xue et al., 2008

sd1 Plant height Nagano et al., 2005

PROG1 Plant stature Tan et al., 2008

GIF1 Grain filling Wang et al., 2008

Utilization of wild relatives of Oryza

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Wild species are reservoirs of many useful genes, particularly for resistance to major

biotic and abiotic stresses. However, these wild species are associated with several

weedy traits, such as grain shattering, poor plant type, poor grain characteristics, and

low seed yield. Besides, several incompatibility barriers also limit the transfer of useful

genes from wild species into cultivated species (Khush and Brar, 1992). Strategy to

transfer genes from wild species into rice depends on the nature of the target trait(s),

relatedness of the wild species, and incompatibility barriers. In several cases, genetic

variability for target agronomic traits is limited in the cultivated gene pool. Under such

situations, interspecific hybridization is an important plant breeding approach to

introduce novel genes for different agronomic traits from wild species into rice.

Interestingly, the introgression has been facilitated continuously by breeding programs

that more effectively moved beneficial genes from wild to cultivated plants. With

technical advances in molecular breeding, wild gene pools will play an increasingly

important role in the genetic improvement of cultivars (Zeder et al., 2006). To achieve

precise transfer of genes from wild to cultivated species, strategies involving a

combination of conventional plant breeding methods with tissue culture and molecular

approaches have become important (Brar and Khush, 2002, 2006). Interspecific hybrids

are produced between elite breeding lines with the wild species accessions carrying

useful genes for target traits of immediate interest to the breeder. Such hybrids are

produced through direct crosses between rice and AA-genome wild species. The major

emphasis has been on utilizing indica and japonica germplasm through intraspecific

hybridization (indica x indica, japonica x japonica, indica x japonica). More recently

indica x javanica(tropical japonica) crosses have been used to develop new plant type

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rice and the commercial high yielding hybrids. Cultivars of Asian rice O. sativa are high

yielding, whereas those of African rice, O. glaberrima, are low yielding. However, O.

glaberrima has several desirable traits, such as resistance to rice yellow mottle virus,

African gall midge, and nematodes, and tolerance to drought, acidity and iron toxicity.

Another important feature of O. glaberrima is its strong weed competitive ability. Thus,

the interspecific hybridization among Asian and African species offers tremendous

potential for combining the high productivity of O.sativa with tolerance to biotic and

abiotic stresses of O. glaberrima (Brar and Singh, 2011).

Conclusion

To understand evolutionary mechanisms in genus Oryza by using new tools of

genomics with rapid technical advances in genetic mapping and genome analysis

(Ross-Ibarra et al. 2007), the functional and population genetic studies of domestication

genes will play an increasingly important role in our understanding of the history and

genetic mechanism of plant domestication. This will in turn enable a more effective

utilization of natural resources for cultivar improvement and new domestications, such

as the domestication of energy crops (Ragauskas et al., 2006) to meet the future needs

of our society. Advances in tissue culture, genetic engineering, molecular cytogenetic,

comparative genetics and genomics, particularly the rice genome sequencing, have

opened new opportunities to develop improved rice germplasm with novel genetic

properties and in understanding the function of rice genes. Breeders have successfully

used conventional breeding methods and exploited the rice gene pool to develop high

yielding improved rice varieties resistant to pests and abiotic stresses with improved

quality characteristics. Identification and introgression of yield-enhancing “wild species

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alleles” into elite breeding lines need to be explored to further increase the yield

potential of indica and japonica rice cultivars. Extinction of wild species is a thread to

genetic diversity and international efforts are needed to overcome the trend in the loss

of valuable biodiversity. Integration of new tools of genetics to accelerate alien gene

introgression is emphasized.

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