This document discusses classical and innovative approaches for improving seed and seedling traits in rice. It describes classical breeding approaches like wide hybridization and backcrossing. It also discusses innovative approaches like marker-assisted breeding and genetic transformation. Several case studies are presented on improving traits like cold tolerance, flooding adaptation, seed shattering and dormancy. Quantitative trait loci (QTLs) associated with these traits have been identified and used to develop rice varieties with improved agronomic performance.

1. CLASSICAL AND INNOVATIVE APPROACHES FOR
THE IMPROVEMENT OF SEED AND SEEDLING
TRAITS IN RICE
Student:
T. Mithraa,
2016601602,
II M.Sc.,(Ag.) PGR.

2. CONTENT
 Introduction
 Classical approaches
 Innovative approaches
 Seed Vs seedling
 Seed traits & Case studies
 Seedling traits & Case studies

3. Introduction
 Plant breeding is an art and science of genetically improving plants for the benefit of
humankind.
 It can be considered as a co-evolutionary process between humans and edible plants.
 The genetic diversity of crop plants is the foundation for the sustainable development of
new varieties for present and future challenges which arises due to the various biotic and
abiotic stresses.
 Pre-breeding refers to all activities designed to identify desirable characteristics and/or
genes from unadapted materials that cannot be used directly in breeding populations, and to
transfer these traits to an intermediate set of materials that breeders can use further in
producing new varieties for farmers.

4. Characteristics of landraces
 (i) high levels of genetic diversity within populations, characterized by a limited range of
variation between individuals, with distinctive traits that make the landrace identifiable
 (ii) adaptation to soil and climate conditions typical of the region, combined with resistance to
common pests
 (iii) edible parts that are valued by local people, normally shaping and being shaped by the local
cuisine
 (iv) modest but stable yield, conferring food security to the local community under normal
environmental variation.

5. Pre breeding approaches
Classical approaches Innovative approaches
Introgression Incorporation
Wide
hybridization
1) Recurrent
backcross
2) Inbred
backcross
3) Congruity
backcross
1) Interspecific
2) Intergeneric
1) Direct
transfer /
biolistic
method
2) Indirect
transfer
using
vectors
(1)Diversity assessment
(2) Somatic Hybridization
(3) Anther culture
(4) Embryo rescue
(5)Marker assisted breeding
(6) Mapping of quantitative trait
loci (QTL)
(7) Introgression libraries,
association studies
(8) Genetic transformation

6. Seed:
Ripened ovule containing embryo
Any part of plant has the capability to regenerate ‘Embryo’, a living organism
embedded in the supporting tissue and a protective coat
Seedling:
A very young plant that grows from a seed
When the moisture , light and temperature conditions are correct , the seedlings
development begins with the seed germination and formation of three main parts:
1.Radicle-embryonic root
2. hypocotyl-embryonic shoot
3. cotyledons-seed leaves.

7. Importance of seed and seedling traits
 Good crop establishment is a key factor for the success of subsequent crop growth.
 Direct seeding succeeds based on the topography of land, seedbed condition, oxygen level in the
vicinity of germinating seed and method of sowing.
 Dry and wet seeding methods are popular among the rice farmers of rainfed lowland and gaining
its place in irrigated ecology, as they require less labour and time than transplanting (Sarkar
and Das 2003).
 Farmers commonly practise wet seeding with pre-germinated seeds, where there is good control
over the water supply.
 In areas where water supply is unpredictable, dry seeding is usually practised .

8.  Delay in transplanting reduces grain yield and seed quality because of poor seed set and biotic stresses due
to high temperature and high humidity at flowering.
 Therefore, farmers tend to shift the crop establishment methods for lowland rice from transplanting to
the direct seeding system(Joshi et al. 2013; Weerakoon et al. 2011).
 At present,rice cultivation as direct seeding is practised in many countries such as America, Western Europe
including Italy and France, Russia, Japan, Cuba, India, Korea, Malaysia,Thailand, Vietnam, Sri Lanka, the
Philippines and in some parts of Iran, due to high technology, high labour cost and shortage of skilled
labour.

9.  On the other hand, yield performance of DSR varies from place to place and contributes 23 %
of rice production globally (Rao et al. 2007).
 Factors such as soil physical and chemical properties, land preparation, seed viability and
genotypic characteristics for seed dormancy,seedling vigour, seeding depth,etc., affect early crop
establishment (Ladha et al. 2009; Tripathi et al. 2005) under DSR

10. Seed shattering
 Loss of seed shattering was a key event in the domestication of major cereals.
• Konishi et al.,2006, revealed that the qSH1 gene, a major quantitative trait locus
of seed shattering in rice, encodes a BEL1-typehomeobox gene and demonstrated
that a single-nucleotide polymorphism (SNP) in the regulatory region of the qSH1
gene caused loss of seed shattering owing to the absence of abscission layer
formation.
• Haplotype analysis and association analysis in various rice collections revealed
that the SNP was highly associated with shattering among japonica subspecies
of rice, implying that it was a target of artificial selection during rice domestication.

11.  Crop domestication might have proceeded during relatively short periods (less than 10,000years)
through the occurrence of nucleotide polymorphisms, such as by spontaneous mutation,recombination,
and fixation in populations.
 Because rice is a self-pollinated plant, such newly occurring nucleotide polymorphisms would have
easily become fixed in individuals.
 If such individuals propagated and contributed to the establishment of cultivated rice, it should be able
to follow step by step the haplotype changes that occurred during rice domestication.
 Therefore, the examination of haplotypes around the qSH1 gene in the rice collections was done.
 The identified SNP was likely to be assigned as a mutation that occurred in early domesticates of
japonica subspecies but not as a preexisting natural variation.

12. Konishi et al.,2006

13.  In the hypothetical process of evolution of qSH1, the SNP distribution clearly revealed a strong selection by
ancient humans for the SNP during rice domestication .
 In addition, the estimated haplotype of the common ancestor at the qSH1 locus was found in a wild rice
accession,W1943 , which is closely related to the japonica subspecies.
 We could therefore follow how domestication proceeded at the level of DNA sequence change, from ancestors to
cultivated rice.
 Many agronomic traits are related to domestication events and could have been the targets of artificial selection
during domestication.
 Therefore, this type of evolutionary analysis may give us some insights into the domestication process and could
reveal practical, useful allele information for future breeding in cereals .
 For instance, introgression of the Nipponbare qSH1 allele into indica cultivars would reduce the seed-
shattering degree and could improve yield.

14. Low-temperature stress:
 Low-temperature stress is common for rice cultivation in temperate zones and high-elevation
environments.
 An important breeding objective of these regions is to develop cultivars tolerant to low
temperatures at critical growth stages (Nakagahra et al., 1997).
 In parts of south and south-east Asia, an estimated 7,000,000 hectares cannot be planted with
modern varieties because of low-temperature stress .
 Rice cultivars vary greatly in their tolerance to low temperature.
 The indica rice subspecies, associated with tropical environments, is more sensitive to low
temperature.
 The more tolerant japonica subspecies is divided into tropical and temperate groups
(Glaszmann, 1987; Glaszmann et al., 1990; Oka,1988).

15.  During the early growth stages in rice, the occurrence of low-temperature stress affects seed
germination that inhibits seedling establishment and eventually leads to non-uniform crop
maturation.
 Rice plants are injured at the seedling stage when they are grown in early spring in temperate
or subtropical environments.
 In a survey conducted by Kaneda and Beachell (1974), the types of low temperature effects on
seedlings can be manifested as poor germination, slow growth, discoloration or yellowing,
withering after transplanting, reduced tillering, and stunted growth.
 Screening for chilling sensitivity of different rice genotypes in breeding programmes
commonly relies on visual observations under natural conditions.
 However, this type of screening is subject to genotype x environment interactions and diurnal
or random fluctuations throughout the growing season and over years.

16.  Methods were also developed to assess cold tolerance under controlled conditions.
Chilling survival tests using 10 °C at the two-leaf stage
Measurement of oxygen-scavenging enzymes
ABA or polyamines
Measurement of radicle growth
Seedling vigour
mRNA derived from seedlings exposed to chilling temperatures

17. Case study

18.  Cold stress may cause various seedling injuries, delayed heading and yield reduction due to spikelet
sterility.
 In this study, 181 microsatellite marker loci were used to identify quantitative trait loci (QTLs)
associated with cold tolerance at the vegetative stage in 191 recombinant inbred lines (RILs) derived
from a cross of a cold-tolerant temperate japonica cultivar (M-202) with a cold-sensitive indica
cultivar (IR50).
 Different temperature regimes were applied in growth chambers on 191 RILs.
 The temperature regimes imposed in the growth chamber simulated cold-stress injuries at the seedling
and late vegetative stages.
 A major QTL was identified on chromosome 12, designated as qCTS12a, that was closely associated
with cold-induced necrosis and wilting tolerance, and accounted for 41% of the phenotypic variation.
 A number of QTLs with smaller effects were also detected on eight rice chromosomes.

19. A.) B.)
Cold-tolerance scale used in scoring seedlings treated at (A) 9 °C constant-temperature regime
for cold-induced wilting tolerance (CIWT), and (B) a day/night temperature of 25/9° C for cold
tolerance (CT) score. The pictures were taken at 18 d and 30 d of treatment, respectively.
Tolerant materials similar to M-202 were given a score of 1 and susceptible materials similar to
IR50 were given a score of 9.

20. Chromosomal positions of QTLs that exceeded the critical LOD score of 3.52 for cold-induced wilting
tolerance (CIWT), cold tolerance (CT), cold-induced necrosis tolerance (CINT), and cold-induced
yellowing tolerance (CIYT). Arrows indicate the approximate position of the centromere. The bars indicate
the chromosomal intervals associated with the QTL at the critical LOD score.

21.  In this study, several QTLs associated with cold tolerance in rice were identified under a controlled-
environment condition.
 Since the type of cold injury may vary depending on stress level and duration of exposure, and the
complex nature of plant response to tolerate cold stress , visual damage to seedlings exposed to
low-temperature stress was assessed.
 The major QTL on chromosome 12,associated with tolerance to wilting and necrosis, was
particularly interesting and it may be useful as a target for varietal improvement and positional
cloning.
 In the field, adequate cold tolerance at the seedling stage may allow early sowing, because cold-
tolerant seedlings should be able to survive and develop normally, thereby ensuring uniform crop
establishment.

22. Adaptation to flooding:
 Direct seeding of rice is being adopted in rainfed and irrigated lowland ecosystems because it
reduces labour costs in addition to other benefits.
 However, early flooding due to uneven fields or rainfall slows down seed germination and hinders
crop establishment.
 Conversely , early flooding helps suppress weeds and reduces the costs of manual weeding
and/or dependence on herbicides; however, numerous weed species are adapted to lowlands and
present challenges for the use of flooding to control weeds.
 Advancing knowledge on the mechanisms of tolerance of flooding during germination and early
growth in rice and weeds could facilitate the development of improved rice varieties and effective
weed management practices for direct-seeded rice.

23. Case study

24.  Rice genotypes with a greater ability to germinate and establish in flooded soils were identified
, providing opportunities to develop varieties suitable for direct seeding in flooded soils.
 Tolerance of flooding in these genotypes was mostly attributed to traits associated with better
ability to mobilize stored carbohydrates and anaerobic metabolism.
 The studies compared rice and weeds and related weed species such as Echinochloa crus-galli
and E. colona or compared ecotypes of the same species of Cyperus rotundus adapted to either
aerobic or flooded soils.

25.  Tolerant weeds and rice genotypes mostly developed similar adaptive traits that allow
them to establish in flooded fields, including the ability to germinate and elongate
faster under hypoxia, mobilize stored starch reserves and generate energy through
fermentation pathways.
 Remarkably, some weeds developed additional traits such as larger storage tubers that
enlarge further in deeper flooded soils (C. rotundus).
 Unravelling the mechanisms involved in adaptation to flooding will help design
management options that will allow tolerant rice genotypes to adequately establish in
flooded soils while simultaneously suppressing weeds.

26.  Rice genotypes tolerant of complete submergence at the vegetative stage, such as the Indian
landrace FR13A, were identified that can survive submergence for over 2 weeks, and a single
gene responsible for tolerance(SUB1A) was cloned and its role in conferring (Xu et al. 2006;
Bailey-Serres et al. 2010).
 Furthermore, a marker-assisted backcrossing system was developed and used to transfer SUB1
into several popular rice varieties, and some of them have already been released for commercial
use in several countries in Asia.
 These varieties showed a yield advantage of 1 to 3 t ha over the original varieties following
submergence for a few days to 18 days (Neeraja et al. 2007; Septiningsih et al. 2009; Singh et
al. 2009; Mackill et al. 2012).

27.  In addition , two genes, ‘SNORKEL1’ and ‘SNORKEL2’, that are responsible for this
internode elongation under deep water conditions were cloned (Hattori et al. 2009).
 Regardless of the challenges posed by submergence , rice has evolved features that allow it to
flourish in a wide range of environments affected by flooding .
 However, most of the traits associated with tolerance for different types of flooding stress
identified so far are expressed better in traditional landraces being grown by farmers.
 These landraces have low yield potential with poor combining ability, making progress to transfer
these characteristics into high-yielding genotypes through conventional breeding relatively slow.
 However, faster progress is now being witnessed after recent developments in molecular and
genomics tools and approaches (Xu et al. 2006; Bailey-Serres et al. 2010).

28. Seed dormancy
 Seed dormancy is defined as the inability of viable seed to germinate under environmental conditions favorable
to germination.
 However, it is difficult to measure such inability in seeds.
 Seed dormancy is usually estimated by germination rate, but complex inheritance of seed dormancy has been noted
by breeders and geneticists (Takahashi 1997).
 The recent development of molecular markers has made it possible to identify individual genetic factors controlling
such complex traits as seed dormancy (Tanksley 1993), and several genes affecting seed dormancy in barley and
wheat which have been identified using these markers(Anderson et al. 1993; Flintham and Gale 1995; Laura et al.
1995; Larson et al. 1996).

29. Case study

30.  In rice, however, only a few reports have been published on the genetics of seed dormancy (Seshu and
Sorrels 1986; Das 1995; Takahashi 1997).
 No gene for seed dormancy with its chromosomal location has been reported.
 This might also be due to complex inheritance and environmental interactions.
 Four rice molecular linkage maps have been developed by independent research groups
(McCouch et al. 1988;Saito et al. 1991; Causse et al. 1994; Kurata et al. 1994).
 These linkage maps have facilitated analyses of quantitative trait loci (QTLs) controlling several
complex traits, such as yield-related traits (Xiao et al. 1996), blast resistance (Wang et al. 1994),
heading date and plant height (Li et al. 1995; Yano et al. 1997), root morphology ( Champoux et al.
1995), and seedling vigor (Redona and Mackill 1996).

31.  In this study, they have developed BC1F5 lines (backcross inbred lines: BILs) as a permanent mapping population
to facilitate QTL analysis in rice.
 They describe the construction of a framework linkage map of the BILs and the identification of QTLs
associated with seed dormancy and heading date using these BILs.
 Seed dormancy is usually affected by environmental factors such as temperature, dryness and degree of maturity
(Seshu and Sorrells 1986; Takahashi 1995).
 These factors make the genetic study of seed dormancy complex because the grains of each individual in a given
segregation population usually ripen at different times in different weather conditions.
 Recently , QTL analysis with molecular marker has made it possible to detect multigenes affecting a trait such as
seed dormancy.
 They successfully detected five chromosomal regions controlling seed dormancy based on QTL analysis.
 It accounted for 48.2% of the total phenotypic variation in seed dormancy.
 The unexplained remainder of the phenotypic variation might be due to environmental effects or to undetected
QTLs with relatively smaller phenotypic effects.

32. Seed and Seedling vigour
 It is the ability of a seed to emerge rapidly from soil or water, mainly reference
to seed germination rate and early seedling growth (Huang et al.2004).
 Different systems of rice cultivation have been adapted worldwide and the
productivity of the rice crop has increased with shifting from direct-seeded rice
(DSR) to puddled-transplanted rice approach.
 Farmers of irrigated rice ecosystem germinate their seeds in the nursery and
seedlings are transplanted to puddled soil.

33.  The advantages of the transplanted-puddled rice (TPR) system of crop establishment includes
restrained weed growth (Surendra et al. 2001), easy seedling establishment (Farooq et al.2011) and
enhanced nutrient availability (e.g. iron, zinc,phosphorus) by creating an anaerobic condition.
 Transplanting and puddling require a large amount of water,sufficient rainfall, labour and energy.
 As these factors are becoming limited, it makes rice production more expensive and less profitable
(Mahajan et al. 2004).
 Therefore, improving the crop productivity with economic security is a major challenge to develop an
alternative solution.
 Hence,the situation demands a major shift in the rice cultivation system from puddled-transplanted rice
to direct-seeded rice(DSR).

34. Mahendar et al.2015

35.  Germination of rice seeds in paddy field that are either waterlogged or submerged are exposed to
hypoxia or even anoxia situation.
 Seedling vigour plays a major role in emergence of seedling above the water surface and the
seedling tissue gets exposed to anoxia (Yamauchi et al.1993).
 Germination under anaerobic condition is a complex trait, involving several essential
biochemical and metabolic processes of breaking down starch, fermentation and
glycolysis(Ismail et al. 2009, 2012).
 An effort in breeding for tolerance of anaerobic germination (AG) and increased seedling vigour
was started during 1990s (Biswas and Yamauchi 1997) and achieved with identification of QTL
since 2000s.
 It is well established that, seed ageing plays a role in seed germination by synthesis of reactive
oxygen species(ROS) or oxidative stress.

36. Mahendar et al.2015

37. Case study:

38.  The objectives of this study were to identify superior alleles with consistent effects on seedling
vigour across different temperature conditions and to investigate genotype x environmental
temperature interactions for seedling vigour QTL.
 A set of 282 F13 recombinant inbred lines (RILs) derived from a rice cross were assessed for four
seedling vigour traits at three temperatures (25 C, 20 C and 15 C).
 Using a linkage map with 198 marker loci, the main effect QTL for the traits were mapped by
composite interval mapping.

39.  A total of 34 QTL for the four seedling vigour traits were identified.
 Of these QTL, the majority (82 %)were clustered within five genomic regions, designated as
QTL qSV-3-1, qSV-3-2, qSV-5, qSV-8-1 and qSV-8-2.
 All of these five QTL had small individual effects on the traits, explaining 31–158 % of the
phenotypic variation with a mean of 73 %.
 QTL qSV-3-1, qSV-3-2 and qSV-8-1 showed almost consistent effects on the traits across all
three temperatures while qSV-5 and qSV-8-2 had effects mainly at the ‘normal’ temperatures of
20 C and 25 C.
 Among the five QTL identified, all and four showed additive effects on shoot length and
germination rate, respectively.

40.  The contributions of these five QTL to shoot length and germination rate were also
much larger than those to the other two traits.
 A few of genomic regions (or QTL) were identified as showing effects on seedling
vigour.
 For these QTL, significant genotype x environmental temperature interactions were
found and these interactions appeared to be QTL-specific.
 Among the four seedling vigour traits measured, shoot length and germination rate
could be used as relatively good indicators to evaluate the level of seedling vigour in
rice.

41. Molecular linkage map of rice showing locations of putativeQTLfor rice seedling vigour detected under different
temperature conditions. Short arms of chromosomes are at the top. Five chromosomal regions containing multiple
QTL for seedling vigour traits on chromosomes 3, 5 and 8 are circled and designated as QTL qSV-3-1, qSV-3-2, qSV-
5, qSV-8-1, and qSV-8-2.
Zhang et al.,2005

42. Salt stress
 Soil salinity is a key abiotic stress in crop productivity worldwide (Zhu 2001).
 Rice one of the most important crops in the world, as well as other crops, suffers deleterious effects when salt
accumulates in soil due to defective irrigation and fertilization(Lin et al. 2004).
 In fact, about 30% of the rice growing area in the world is affected by salinity (Prasad et al.2000).
 Rice experiences salt stress at different developmental stages, such as germination, vegetative and
reproductive growth stages.
 Recently, improving rice salt tolerance at germination stage become more important, because the direct
seeding method has become increasingly important in many Asian countries due to its lower cost and its
operational simplicity(Fujino et al. 2004).
 However, it is difficult to develop elite varieties with a high level of salt tolerance due to a lack of understanding
the mechanisms of salt tolerance during seed germination stage.

43. Case study

44.  Salt tolerance of rice (Oryza sativa L.) at the seed germination stage is one of the major determinants for
the stable stand establishment in salinity soil.
 One population of recombinant inbred lines (RILs, F2:9), derived from a cross between a japonica rice
landrace tolerant to salt stress and a sensitive indica rice variety, was used to determine the germination
traits including imbibition rate and germination percentage under control (water) and salt stress (100
mM NaCl) for 10 days at 30 C.
 The multiple interval mapping (MIM) were applied to conduct QTL for the traits.

45.  The results showed that seed germination was a quantitative trait controlled by several genes, and
strongly affected by salt stress.
 A total of 16 QTLs were detected in this study, and each QTL could explain 4.6–43.7% of the
total phenotypic variance.
 The expression of these QTLs might be developmentally regulated and growth stage-specific.
 In addition, only one digenic interaction was detected under salt stress, showing small effect on
germination percentage with .
 Among sixteen QTLs detected in this study, four were major QTLs and some novel alleles of salt
tolerance genes in rice.
 The results demonstrated that the japonica rice Jiucaiqing is a good source of gene(s)for salt
tolerance and the major or minor QTLs identified could be used to improve the salt tolerance by
marker-assisted selection (MAS) in rice.

46. Seed germination under different NaCl concentration between two parents
Wang et al.,2005

47. Low N tolerance
 Nitrogen (N) is one of the most important mineral nutrients for plant growth, and
thus, massive quantities of N fertilizers are used to enhance crop yield.
 N fertilizer application for field growth of rice has increased rapidly in the past
decades, but loss of 30–70% of the applied N fertilizer was reported in high-
yielding rice fields (Zhu and Chen2002).
 In addition, low N fertilizer efficiency and much N loss have directly and indirectly
led to a series of environmental problems (Erisman and Vries 2000).
 Improving N efficiency under low-N supply condition is believed to be one way to
resolve these problems.

48.  Currently, many studies of QTLs affecting various traits associated with low-N
tolerance and/or N-use efficiency have been documented in maize (Agrama et al.1999,
Presterl et al. 2002, Liu et al. 2008, Cai et al. 2012),wheat (Laperche et al. 2007, Guo et
al. 2012) and Arabidopsis(Rauh et al. 2002, Loudet et al. 2003).
 QTL analyses for N-related traits have also been widely reported in rice under different
N supply conditions.
 Two QTLs under high N level and eight QTLs under low N level for plant height in
both nutrient solution and soil culture experiments were detected in a double haploid
population of ‘IR64’/‘Azucena’ by Fang and Wu (2001).
 Lian et al. (2005) mapped some QTLs for low-N tolerance at the seedling stage using a
RIL population of ‘Zhenshan 97’/‘Minghui 63’ and noted that the locations of some
QTLs might correspond to the loci of genes for N assimilation and transfer such as
NADH-GOGAT, GS and GDH2.

49. Senthilvel et al. (2008) studied the genetic basis associated with N-use efficiency and N uptake under
varying N levels.
Wang et al. (2009) reported some QTLs for panicle number and grain yield related to N-deficiency
tolerance in a chromosome segment substitution line population with ‘Nipponbare’-.
Feng et al. (2010) detected seven QTLs for relative traits under low- and high-N conditions using a RIL
population of ‘R9308’/‘XQZ’.
The genetic mechanisms controlling rice N-use efficiency and low-N tolerance are complicated, because of
multiple controlled genes and their interactions as well as different experimental conditions.
More QTL analysis for traits in response to low-N stress in rice will provide useful information for
studying the genetic basis of N efficiency under N-limited conditions and for breeding high-N-efficiency
rice varieties using molecular breeding approaches.

50. Low phosphorous
 Phosphorous (P) is essential for cell growth and cell division in living organisms, and is an
important inorganic plant nutrient.
 Currently, widespread phosphorous deficiency in soil seriously constrains production in rice.
 Approximately 5.7 billion hectares of arable land lack sufficient P available for plant and
almost50% of rice soils are P-deficient worldwide (Batjes, 2012).
 In the past decades, P fertilizer application for crop growth has been increased rapidly, but P-use
efficiency has decreased to a low level of 10%–20% (Wissuwa et al., 2007).
 Furthermore, much of the applied P has caused serious pollution to environment.
 Development of cultivars with improved P-deficiency tolerance is believed to be an effective
solution to this problem.

51.  Phosphorous deficiency significantly affects rice growth and development. P-deficiency could stunt plant
growth showing dark green leaves, suppress root development ,and reduce tillering (Dobermann and
Fairhurst, 2000).
 High sterility, maturity delaying and plant height reduction are also common under P stress.
 Root elongation is also observed in P-deficiency soils in various plant species (He et al., 2003; Shimizu et
al., 2004).
 Root interception of Phosphate, P acquisition efficiency, and internal P-use efficiency are three main
mechanisms for plant to adapt to low P-deficiency (Ismail et al., 2007).
 Changes in root architecture under P-deficiency are considered an adaptation that enhances phosphorus
uptake (Lynch, 1995).
 Breeders have concentrated their efforts on breeding P-deficiency tolerant rice cultivar

52.  In practice, P-deficiency tolerance has been assessed by measuring dry weight or grain yield under low P
soils directly (Fageria et al., 1988),or by indirectly measuring relative tiller number and relative dry weight
(Chaubey et al., 1994).
 But the complexity of the traits involved in tolerance to P-deficiency and lacking of screening criterion
suitable for use in breeding programs have hampered past efforts to develop tolerant high yield varieties.
 Many plant traits are complex quantitative traits in nature,affected by many genes, and are profoundly
influenced by environment (Li et al., 2003).
 QTL analysis is a key tool for explaining the genetic basis of complex traits,such as those associated
with P-deficiency tolerance.
 Some QTLs for the traits correlated with tolerance to P-deficiency have been reported in rice (Ni et al.,
1998;Wissuwa et al., 1998, 2002; Wu and Ni, 2000; Shimizu et al., 2004, 2008).
 Ni et al. (1998) mapped QTLs for relative tillering ability, relative shoot dry weight, and relative root dry
weight using a recombinant inbred line (RIL) population from the rice cross between IR20 and IR55178-3B-
9-3grown in P-deficiency and P-sufficiency nutrient solutions.
 Wissuwa et al. (1998) mapped QTLs for P uptake, internal P-use efficiency, dry weight, and tiller number
using BC lines grown in P-deficiency soil.

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