1. Introduction
Rice (
During domestication process from wild species to cultivated rice, selecting desirable-agronomic traits to keep achieving high yield allows many genes to be either directly selected or filtered out, resulting in a significant reduction of genetic diversity in rice gene pool (Brar et al. 2003). Sun et al (2001) revealed that the number of alleles in cultivated rice had been reduced by 50-60% compared to wild rice. Thus, it is necessary to broaden the gene pool in rice breeding from diverse sources, especially from wild rice.
In the genus of Oryza, there are two cultivated species and more than 20 wild species. Both of the cultivated species, O. sativa and O. glaberrima, are diploid (2n = 24) and have the AA genome. Wild species have evolved in a wide range of environments over millions of years (Stebbins 1981). The wild species have either 2n = 24 or 2n = 48 chromosomes, and seven genomes (AA, BB, CC, BBCC, CCDD, EE, and FF) have so far been designated for 17 species (Vaughan 1994; Brar et al. 1997). Common wild rice (Oryza rufipogon Griff.), due to its long-term growth in the wild conditions, possesses numerous advantages such as genetic diversity, excellent agronomic traits, and resistance against various biotic and abiotic stresses, proved to be an important resource for genetic improvement of rice (Song et al. 2005). Dongxiang wild rice (O. rufipogon Griff.) is in the northern most habitats among O. rufipogon populations to be discovered in the world (Chen et al. 2008; Xie et al. 2010; Figure 1), and displays strong tolerance to low temperature (Figure 2). It is for certain that many valuable traits exist in the wild rice species, but the most challenges to us are how to explore the valuable genes from wild rice and effectively transfer them into the cultivated rice for diversifying genetic basis of cultivated rice. Recently, many genes and QTLs have been mined from the wild rice, which functions include disease and insect resistances, abiotic stress tolerances, high yield, and so on. In this chapter, we will summarize current research progresses in mining elite genes and QTLs from wild rice for cultivar improvement in breeding programs.
2. Disease resistance genes and QTLs in wild rice
Rice diseases such as blast, bacterial blight and sheath blight are major obstacles for achieving optimal yields. To complement conventional breeding method, molecular or transgenic method represents an increasingly important approach for genetic improvement of disease resistance and reduction of pesticide usage. During the past two decades, a wide variety of genes and mechanisms involved in rice defense response have been identified and elucidated. However, most of the cloned genes confer high level of race specific resistance in a gene-for-gene manner, and the resistance is effective against one or a few related races or strains of the pathogens. The resistance is effective for only few years because the pathogen race or strain keeps changing for survival in nature. Therefore, there is an urgent need to broaden the rice gene pool from diverse resources, of which the wild rice is an ideal option.
2.1. Rice blast resistance
Rice blast, caused by pathogen
Jeung et al (2007) identified a new gene in the introgression line IR65482-4-136-2-2 that has inherited the resistance gene from an EE genome wild
Li et al (2009) evaluated blast resistance for 21 progenies from crossing with common wild rice, and obtained three stably resistance progenies. Preliminary analysis showed that the rice blast resistance was controlled by dominant genes. Geng et al (2008) cloned rice blast resistance gene
2.2. Bacterial blight resistance
Bacterial blight is caused by
In 1977, Dr. S. Devadath found that a strain of
Jin et al (2007) identified a rice bacterial blight resistance germplasm (Y238) from the wild rice species
Gu et al (2004) performed disease evaluation to a
Guo et al (2010) transferred a new rice bacterial blight resistance gene
2.3. Others
Bacterial leaf streak (BLS) is caused by
Sheath blight disease, caused by a soilborne necrotrophic fungus
3. Insect resistance genes and QTLs identified in wild rice
Insects are serious constraints to rice production. In Asia alone, yield loss due to insects has been estimated at about 25% (Savary et al. 2000). Insects not only damage the plant by feeding on its tissue, but also are vectors of devastating rice viruses in many cases. All portions of the plant, from panicle to root, are possibly attacked by various insects. And all growth stages of the rice plant, from the seedling to mature stages, are vulnerable. Even after harvest, the grain in store might face the attack from insects (Cramer et al. 1967). Because the resistance sources in cultivated rice are limited, it is important to keep exploring resistant germplasm from wild rice species for cultivar improvements.
Brown planthopper (BPH) is a destructive insect pest to rice in Asian countries where most rice is produced in the world, including China, India, the Philippines, Japan, Korea, Vietnam, etc (Khush 1984). BPH directly damages the plant phloem by using its piercing-sucking mouthparts, resulting in “hopper burn” in the most serious cases. Furthermore, it is also a vector for rice grassy stunt virus and ragged stunt virus, which may cause further yield losses in many Asian countries (Chelliah et al. 1993). Identification and incorporation of new BPH resistance genes from wild rice into modern cultivars are important breeding strategies to control the damage caused by the BPH.
Ishii et al (1994) found an introgression line from wild species
Later, Jena et al (2006) identified a major BPH resistance gene
Rahman et al (2009) conducted a genetic analysis of BPH resistance using an F2 population derived from a cross between an introgression line, IR71033-121-15 from
4. Abiotic stress resistance genes and QTLs identified in wild rice
Abiotic stresses including high salinity, drought and flood, high and low temperatures are largely limiting productivity of rice crops in large areas of the world. According to Hossain (1996), abiotic stresses affect rice cultivation more than the biotic stresses. Improving the resistance to abiotic stresses will increase agricultural productivity and extend cultivatable areas of rice. There is, therefore, a strong demand for rice cultivars resistant to abiotic stresses.
Based on physiological studies on stress responses, recent progress in plant molecular biology has enabled discovery of many genes involved in stress tolerance. These genes include functional genes which protect the cell (e.g., enzymes for generating protective metabolites and proteins), and regulatory genes which regulate stress response (e.g., transcription factors and protein kinases). Wild rice is the ancestor of cultivated rice, having been an important gene pool due to its survival ability in wild conditions and suffering from natural selection. Therefore, it is of great significance to study genetic basis of abiotic stress resistance as well as to explore new related genes in wild rice.
4.1. Cold resistance
Cold stress is a common problem for rice cultivation, and is a significant factor affecting global food production since cold stress can cause poor germination, slow growth, withering, and anthers injury on rice plants (Andaya et al. 2007). Annually, about 15 million hectares of rice in the world suffered from cold damage (Zhang et al. 2005). In south Asia, about 7 million hectares cannot be planted timely because of the low temperature stress (Sthapit et al. 1998). Consequently, development of rice cultivars with cold tolerance is recognized as one of the important breeding objectives.
Various methods have been adapted to improve rice resistance to low temperature stress (Bertin et al. 1997; Takesawa et al. 2002). With increasing emphasis on F1 hybrid rice production in public institutions and private breeding companies, lots of landraces with diversified genetic background continue to decrease, which makes the genetic base of parental materials become more and more narrower. As a result, development of cultivars for strong cold tolerance becomes increasingly difficult using intra-variation. There is thus an urgent need to study the cold-tolerance character and excavate related genes in wild rice to broaden rice gene pool for developing cold tolerance cultivars.
Genetic analysis of cold tolerance at seedling and/or booting stage has resulted in the identification of many QTLs (Lou et al. 2007; Zeng et al. 2009). Zheng et al (2011) constructed chromosome segment substitution line (CSSL) populations using two core accessions of common wild rice (DP15 and DP30) as donor parents and cultivar 9311 as recipient parent. Thus, they identified cold tolerance QTLs effective at the seedling stage. Two donor lines, DP15 and DP30, are different in the number, location and effect of QTLs for cold tolerance. A total of 19 cold tolerance QTLs were detected, and clustered on chromosome 3 and chromosome 8. The survival rates ranged 8 – 74% after cold treatment among the CSSLs. A major QTL
Dongxiang wild rice can winter over successful in Wuhan, Hubei province, China, where the lowest temperature can be down to -12C in winter (Liu et al. 2003). In order to transfer cold tolerance gene from Dongxiang wild rice, we have developed introgression lines (ILs) through a backcrossing and single-seed descent program using an elite
4.2. Soil salinity resistance
Soil salinity is one of the major agricultural problems affecting crop productivity worldwide (Rozema et al. 2008). Of the cereals, rice is one of the most salt-sensitive crops (Shelden et al. 2013). The effects of salinity on rice have been reported to reduce seed germination (Hakim et al. 2010), decrease growth and survival of seedlings (Lutts et al. 1995), damage the structure of chloroplasts (Yamane et al. 2008), reduce photosynthesis (Moradi et al. 2007) and inhibit seed set and grain yield (Asch et al. 2000). Improving evaluation methodologies to identify genetic sources and excavating responsible genes for improving cultivar salt resistance is of continuing importance in rice.
4.3. Low-phosphorus resistance
Phosphorus is one of essential nutritive elements for rice growth and development (Abel et al. 2002). The phosphorus content may be too little in the soil to be able to meet the needs of rice growth. It has been estimated that 5.7 billion hectares of land are deficient in phosphorus worldwide. Phosphorus deficiency is considered as one of the greatest limitations in agricultural production (Schachtman et al. 1998; Lynch et al. 2008).
Chen et al (2011) identified the low-phosphorus resistance ability of Dongxiang wild rice at the seedling stage by using the cultivated low-phosphorus sensitive varieties as the control. The results showed that Dongxiang wild rice has strong low-phosphorus resistance ability. And then, they developed BILs by using Dongxiang wild rice as donor parent and the low-phosphorus sensitive variety Xieqingzao B as recurrent parent. By analyzing the morphological indices, they found that the low-phosphorus resistance lines under low-phosphorus stress had higher values of relative leaf age, relative plant height, relative shoot dry mass, and relative soluble content, but low values of relative yellow leaf number and relative malondialdehyde content, suggesting that the low-phosphorus resistance capability of the low-phosphorus resistance lines was mainly attributed to the high phosphorus utilization efficiency of the lines, namely, low-phosphorus resistance lines had stronger capability in synthesizing dry mass with per unit phosphorus uptake (Chen et al. 2011).
4.4. Drought resistance
Because of global climate warming and increasing scarcity of water resource, drought stress and water scarcity have severely impacted the security of rice production (Farooq et al. 2009). At least 23 million hectares of rice area in Asia are estimated to be drought-prone (Pandey et al. 2005). To date, however, the major challenge for research communities is the relatively limited progress achieved in developing high yielding rice cultivars with drought resistance (Rabello et al. 2008). Therefore, the improvement of drought resistance in newly developed cultivars, for the wide adaptability across rice-growing ecologies, has become a major priority in rice breeding programs. Accordingly, identifying genes from new germplasm resources such as wild rice has become extremely important for drought resistance, which will lay the foundation for utilization of drought resistance gene and genetic improvement of drought resistance (Xie et al. 2004).
Our group has already carried out preliminary experiments for many years on characterization of Dongxiang wild rice for genetic differentiation and conservation, and utilization (Xie et al. 2010). We proved that Dongxiang wild rice has strong drought resistance (Figure 3). Subsequently, Hu et al (2013) constructed BIL population using
5. Yield-enhancing QTLs from wild rice
In general, wild rice has smaller seeds and other undesirable traits compared to cultivars, and thus appears not to be appropriate for a donor to enhance yield in cultivars. However, molecular studies have demonstrated that phenotypically poor wild rice contains some genes important for improving cultivar yield (Tanksley et al. 1996). Some wild-QTL alleles are favorable for some traits, but may be associated with deleterious effects on other traits. The positive QTLs from
By using a BC2F5 population derived from the cross between Zhenshan 97 and a wild rice, Wu et al (2012) identified a QTL region flanked by SSR marker RM481 and RM2 on chromosome 7. This QTL has pleiotropic effects on heading date, spikelets per panicle, and grain yield per plant. The alleles from wild rice have increasing effects on these phenotypic traits contributable to grain yield.
Fu et al (2010) developed an advanced backcross population by using an accession of common wild rice collected from Yuanjiang County, Yunnan Province, China, as the donor and an elite cultivar 9311 as the recurrent parent. From this population, several QTLs originating from
Xiao et al (1998) identified two yield-enhancing QTLs,
6. Present problems and future directions
As the wild relatives and ancestor of cultivated rice, wild rice carries various characteristics resistant to biotic and abiotic stresses, beneficial agronomic traits, and abundant genetic diversity, which have been lost in the cultivated rice due to breeding activities (Sakai et al. 2010). Thus, it is an extremely important resource for improving important traits in cultivated rice (Xie et al. 2004). However, loss of wild rice genetic diversity was sped up by increasing deterioration of original habitat. For example, the Dongxiang wild rice was sharply reduced from nine populations in nine isolated areas in 1978 to three in 1995 (Hu et al. 2011). The dramatic reduction makes the unique gene pool endangered. Therefore, it is necessary to accelerate a rational conservation for effective utilization of these survived genetic resources.
Breeders have long recognized the intrinsic value of wild rice for improving the traits of modern cultivars. The most successful examples to utilize wild rice in the history of rice breeding include the use of
Nowadays, QTL studies for mining favorable genes from wild rice species are receiving more and more attentions in global rice community. Several studies have successfully identified and introduced the QTL enhancing alleles from wild rice for yield-related traits into high-yielding elite cultivars (He et al. 2006; Deng et al. 2007; Tan et al. 2008). In addition, some QTLs related to rice quality traits were also detected using wild rice introgression lines (Hao et al. 2006; Garcia-Oliveira et al. 2009). Molecular mapping of these good genes will help discover and make full use of the elite resources of wild species to broaden the genetic base of modern cultivars. However, only a few genes have been cloned from wild rice, and the mechanism for those excellent traits from wild rice are far from being clarified. Cloning more genes from wild rice should be emphasized in the future, which will help make full use of these elite resources more effectively.
In summary, as a rare germplasm resource, wild rice is of great significance to our agricultural heritage and biodiversity protection. Research reveals that wild rice not only has many elite genes which have lost in cultivated rice, but also maintains a greater genetic diversity than cultivated rice. We should use the wild rice to broaden genetic diversity of cultivated rice, by which new cultivars could withstand biotic and abiotic stresses. This is of great significance to assure both high yield and quality in rice production.
References
- 1.
Abel S, Ticconi CA, Delatorre CA (2002) Phosphate sensing in higher plants. Physiol Plant 115:1–8 - 2.
Amante-Bordeos A, Sitch LA, Nelson R, Damacio RD, Oliva NP, Aswidinnoor H, Leung H (1992) Transfer of bacterial blight and blast resistance from the tetraploid wild rice Oryza minuta to cultivated rice,Oryza sativa . Theor Appl Genet 84:345–354 - 3.
Andaya VC, Tai TH (2007) Fine mapping of the qCTS4 locus associated with seedling cold tolerance in rice (Oryza sativa L.). Mol Breeding 20:349–358 - 4.
Asch F, Dingkuhn M, Dorffling K, Miezan K (2000) Leaf K/Na ratio predicts salinity induced yield loss in irrigated rice. Euphytica 113:109–118 - 5.
Bal AR, Dutt SK (1986) Mechanism of salt tolerance in wild rice ( Oryza coarctata Roxb ). Plant and soil 92:399–404 - 6.
Bertin P, Bouharmont J (1997) Use of somaclonal variation and in vitro selection for chilling tolerance improvement in rice. Euphytica 96:135–142 - 7.
Brar DS, Khush GS (1997) Alien introgression in rice. Plant Mol Biol 35:35–47 - 8.
Brar DS, Khush GS (2003) Utilization of wild species of genus Oryza in rice improvement. In: Monograph of genusOryza , Nanda, J.S. and S.D. Sharma (eds). Science Publishers, Inc., UK., pp:283–310 - 9.
Brondani C, Rangel PHN, Brondani RPV, Ferreira ME (2002) QTL mapping and introgression of yield-related traits from Oryza glumaepatula to cultivated rice (Oryza sativa ) using microsatellite markers. Theor Appl Genet 104:1192−1203 - 10.
Chelliah S, Bharathi M (1993) Biotypes of the brown planthopper, Nilaparvata lugens (homoptera: Delphacidae) – host inxuenced biology and behavior. Chemical ecology of phytopathogous insects. International Science Publishers, New York:133–148 - 11.
Chen XR, Chen M, He HH, Zhu CL, Peng XS, He XP, Fu JR, Ouyang LJ (2011) Identification of low-phosphorus-tolerance in Dongxiang wild rice ( Oryza rufipogon Griff.). Acta Agriculturae Universitatis Jiangxiensis 33:405–411 (Chinese with English abstract) - 12.
Chen XR, Chen M, He HH, Zhu CL, Peng XS, He XP, Fu JR, Ouyang LJ (2011) Low phosphorus tolerance and related physiological mechanism of Xieqingzao B // Xieqingzao B / Dongxiang wild rice BC1F9 populations. Chinese Journal of Applied Ecology 22:1169–1174 (Chinese with English abstract) - 13.
Chen XR, Yang KS, Fu JR, Zhu CL, Peng XS, He P, He HH (2008) Identification and genetic analysis of fertility restoration ability in Dongxiang wild rice ( Oryza rufipogon ). Rice Sci 15:21–28 - 14.
Chen YL, Luo XD, Zhang FT, Dai LF, Hu BL, Xie JK (2013) Cloning and expression analysis of retrotransposon reverse transcriptase in introgression lines from Dongxiang wild rice. Chinese Bulletin of Botany 48:138–144 (Chinese with English abstract) - 15.
Cho YC, Suh JP, Choi IS, Hong HC, Baek MK, Kang KH, Kim YG, Ahn SN, Choi HC, Hwang HG, Moon HP (2003) QTLs analysis of yield and its related traits in wild rice relative Oryza rufipogon . Treat of Crop Res 4:19–29 - 16.
Cramer DA, Barton RA, Shorland FB, Chochanska Z (1967) A comparison of the effects of white clover ( Trifolium repens ) and of perennial ryegrass (Lolium perenne ) on fat composition and flavour of lamb. J Agric Sci 69:367−373 - 17.
Deng HB, Deng QY, Chen LY, Yang YS, Liu GM, Zhuang W, Xiong YD (2007) Yield-increasing effect of yield-enhancing QTLs from O .rufipogon transferred to 9311, a male parent of medium super hybrid rice. Hybrid Rice 22:49−52 (Chinese with English abstract) - 18.
Du B, Zhang WL, Liu BF, Hu J, Wei Z, Shi ZY, He RF, Zhu LL, Chen RZ, Han B, He GC (2009) Identification and characterization of Bph14 , a gene conferring resistance to brown planthopper in rice. PNAS 106: 22163–22168 - 19.
Farooq M, Wahid A, Kobayashi N, Fujita D, Basra SMA (2009) Plant drought stress: effects, mechanisms and management. Agron Sustain Dev 29:185–212 - 20.
Fischer J, Fazey I, Briese R, Lindenmayer DB (2005) Making the matrix matter: challenges in Australian grazing landscapes. Biodivers Conserv 14: 561–78 - 21.
Fu Q, Zhang PJ, Tan LB, Zhu ZF, Ma D, Fu YC, Zhan XC, Cai HW, Sun CQ (2010) Analysis of QTLs for yield-related traits in Yuanjiang common wild rice ( Oryza rufipogon Griff.). J Genet Genomics 37:147−157 - 22.
Garcia-Oliveira AL, Tan LB, Fu YC, Sun CQ (2009) Genetic identification of quantitative trait loci for contents of mineral nutrients in rice grain. J Integr Plant Biol 51:84−92 - 23.
Geng XS, Yang MZ, Huang XQ, Cheng ZQ, Fu J, Sun T, Li J (2008) Cloning and analyzing of rice blast resistance gene Pi-ta + allele from Jinghong erect type of common wild rice (Oryza rufipogon Griff) in Yunnan. Hereditas (Beijing) 30(1):109–114 (Chinese with English abstract) - 24.
Gu K, Tian D, Yang F, Wu L, Sreekala C, Wang D, Wang GL, Yin Z (2004) High-resolution genetic mapping of Xa27 (t ), a new bacterial blight resistance gene in rice,Oryza sativa L. Theor Appl Genet 108:800–807 - 25.
Guo SB, Zhang DP, Lin XH (2010) Identification and mapping of a novel bacterial blight resistance gene Xa35 (t ) originated fromoryza minuta . Sci Agri Sin 43:2611–2618 (Chinese with English abstract) - 26.
Hakim MA, Juraimi AS, Begum M, Hanafi MM, Ismail MR, Selamat A (2010) Effect of salt stress on germination and early seedling growth of rice ( Oryza sativa L.). Afr J Biotechnol 9:1911–1918 - 27.
Hao W, Jin J, Sun SY, Zhu MZ, Lin HX (2006) Construction of chromosome segment substitution lines carrying overlapping chromosome segments of the whole wild rice genome and identification of quantitative trait loci for rice quality. J Plant Physiol Mol Biol 32:354−362 (Chinese with English abstract) - 28.
He GM, Luo XJ, Tian F, Li KG, Su W, Zhu ZF, Qian XY, Fu YC, Wang XK, Sun CQ, Yang JS (2006) Haplotype variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice. Genome Res 16: 618−626 - 29.
Hossain M (1996) Economic prosperity in Asia: Implication for rice research. IRRI. Rice Genetics III. Proceedings of the third international rice genetics symposium. 16–20 Oct., 1995, Manila, Philippines - 30.
Hu BL, Fu XQ, Zhang T, Wan Y, Li X, Huang YH, Dai LF, Luo XD, Xie JK (2011) Genetic analysis on characteristics to measure drought resistance using Dongxiang wild rice ( Oryza rufupogon Griff.) and its derived backcross inbred lines population at seedling stage. Agricultural Sciences in China 10:1653–1664 - 31.
Hu BL, Yang P, Wan Y, Li X, Luo SY, Luo XD, Xie JK (2013) Comprehensive assessment of drought resistance of BILs population derived from Dongxiang wild rice ( Oryza rufupogon Griff.) at seedling stage and its genetic analysis. Journal of Plnat Genetic Resources 14:249–256 (Chinese with English abstract) - 32.
Huang DH, Cen ZL, Liu C, He WN, Chen YZ, Ma ZF, Yang L, Wei SL, Liu YL, Huang SL, Yang XQ, Li RB (2008) Identification and genetic analysis of resistance to bacterial leaf streak in wild rice. Journal of plant genetic resources 9:11−14 (Chinese with English abstract) - 33.
Ishii T, Brar DS, Multani DS, Khush GS (1994) Molecualar tagging of genes for brown lanthopper resistance and earliness introgressed from Oryza australiennsis into cultivated rice,O .sativa . Genome 37:217−221 - 34.
Jena KK, Jeung JU, Lee JH, Choi HC, Brar DS (2006) High-resolution mapping of a new brown planthopper (BPH) resistance gene Bph18 (t ), and marker-assisted selection for BPH resistance in rice (Oryza sativa L.). Theor Appl Genet 112:288–297 - 35.
Jena KK, Kim SM (2010) Current status of brown planthopper (BPH) resistance and genetics. Rice 3:161–171 - 36.
Jeung JU, Kim BR, Cho YC, Han SS, Moon HP, Lee YT, Jena KK (2007) A novel gene, Pi40 (t ), linked to the DNA markers derived from NBS-LRR motifs confers broad spectrum of blast resistance in rice. Theor Appl Genet 115:1163–1677 - 37.
Jian SR, Wan Y, Luo XD, Fang J, Chu CC, Xie JK (2011) Genetic analysis of cold tolerance at the seedling stage in Dongxiang wild rice ( Oryza rufipogon ). Chinese Bulletin of Botany 46: 21–27 (Chinese with English abstract) - 38.
Jin XW, Wang CL, Yang Q, Jiang QX, Fan YL, Liu GC, Zhao KJ (2007) Breeding of near-isogenic line CBB30 and molecular mapping of Xa30 (t ), a new resistance gene to bacterial blight in rice. Sci Agri Sin 40:1094–1100 (Chinese with English abstract) - 39.
Khush GS (1984) Breeding rice for resistance to insects. Protection Eco 7:147–165 - 40.
Khush GS, Mackill DJ, Sidhu GS (1989) Breeding rice for resistance to bacterial blight. In: Bacterial blight of rice. International Rice Research Institute, Manila, Philippines:207–217 - 41.
Khush GS (1997) Origin, dispersal, cultivation and variation of rice. Plant Mol Biol 35: 25–34 - 42.
Khush GS, Jena KK (2009) Current status and future prospects for research on blast resistance in rice ( Oryza sativa L.). Advances in genetics, genomics and control of rice blast disease. Berlin: Springer:1–10 - 43.
Lee FN, Rush MC (1983) Rice sheath blight: a major rice disease. Plant Dis 67:829−832 - 44.
Li SH, Yang QW, Zheng GB, Li H, Lu XL, Han GM (2009) The genetic analysis on resistance to rice blast of rice progeny introduced with wild rice genes. Seed 28:36–40 (Chinese with English abstract) - 45.
Li Z, Zhu Y (1988) Rice male sterile cytoplasm and fertility restoration. In: Hybrid Rice. International Rice Research Institute. Manila, Philippines:85–102 - 46.
Liu FX, Sun CQ, Tan LB, Fu YC, Li DJ, Wang XK (2003) Identification of QTL for cold tolerance at booting and flowering stage in Jiangxi Dongxiang wild rice. Chin Sci Bull 48:1864–1867 (Chinese with English abstract) - 47.
Liu G, Lu G, Zeng L, Wang GL (2002) Two broad-spectrum blast resistance genes, Pi9 (t ) andPi2 (t ), are physically linked on rice chromosome 6. Mol Genet Genomics 267:472–80 - 48.
Lou QJ, Chen L, Sun ZX, Xing YZ, Li J, Xu XY, Mei HW, Luo LJ (2007) A major QTL associated with cold tolerance at seedling stage in rice ( Oryza sativa L.). Euphytica 158: 87–94 - 49.
Lutts S, Kinet J M, Bouharmont J (1995) Changes in plant response to NaCl during development of rice ( Oryza sativa L.) varieties differing in salinity resistance. J Exp Bot 46:1843–1852 - 50.
Lynch JP, Brown KM (2008) Root strategies for phosphorus acquisition. Plant Ecophysiol 7:83–116 - 51.
Maclean JL, Dawe DC, Hardy B, Hettel GP (eds) (2002) Rice almanac (Third Edition). Philippines, IRRI, WARDA, CIAT and FAO - 52.
Mew TM, Alvarez AM, Leach JE, Swings J (1993) Focus on bacterial blight of rice. Plant Dis 77:5−12 - 53.
Miao LL, Wang CL, Zheng CK, Che JY, Gao Y, Wen YC, Li GQ, Zhao KJ (2010) Molecular mapping of a new gene for resistance to rice bacterial blight. Sci Agri Sin 43: 3051−3058 (Chinese with English abstract) - 54.
Moradi F, Ismail AM (2007) Responses of photosynthesis, chlorophyll fluorescence and ROS-scavenging systems to salt stress during seedling and reproductive stages in rice. Annals of Botany 99:1161–1173 - 55.
Nino-Liu DO, Ronald PC, Bogdanove AJ (2006) Xanthomonas oryzae pathovars: model pathogens of a model crop. Mol Plant Pathol 7:303−324 - 56.
Pandey S, Bhandari H, Sharan R, Naik D, Taunk SK, Sastri ASRAS (2005) Economic costs of drought and rainfed rice farmers’ coping mechanisms in eastern India, Final report. International Rice Research Institute, Los Baños, Philippine. - 57.
Plucknett DL, Smith NJH, Williams JT, Anishetty NM (1987) Gene banks and the world’s food. Princeton University Press, Princeton, New Jersey - 58.
Prasad B, Eizenga GC (2008) Rice sheath blight disease resistance identified in Oryzas pp .accessions .Plant Dis 92:1503−1509 - 59.
Qu SH, Liu GF, Zhou B, Bellizzi M, Zeng LR, Dai LY, Han B, Wang GL (2006) The broad-spectrum blast resistance gene Pi9 encodes a nucleotide-binding site-leucine-rich repeat protein and is a member of a multigene family in rice. Genetics 172:1901–1914 - 60.
Rabello AR, Guimaraes CM, Rangel PH, da Silva FR, Seixas D, de Souza E, Brasileiro AC, Spehar CR, Ferreira ME, Mehta A (2008) Identification of drought-responsive genes in roots of upland rice ( Oryza sativa L). BMC Genomics 9:485 - 61.
Rahman ML, Jiang W, Chu SH, Qiao Y, Ham TH, Woo MK, Lee J, Khanam MS, Chin JH, Jeung JU, Brar DS, Jena KK, Koh HJ (2009) High-resolution mapping of two brown planthopper resistance genes, Bph20 (t ) andBph21 (t ), originating fromOryza minuta . Theor Appl Genet 119:1237–1246 - 62.
Renganayaki K, Fritz AK, Sadasivam S, Pammi S, Harrington SE, McCouch SR, Kumar SM, Reddy AS (2002) Mapping and progress toward map-based cloning of brown planthopper biotype-4 resistance gene introgressed from Oryza officinalis into cultivated rice,O. sativa . Crop Science 42:2112−2117 - 63.
Ronald PC, Albano B, Tabien R, Abenes L, Wu KS, McCouch S, Tanksley SD (1992) Genetic and physical analysis of the rice bacterial blight disease resistance locus, Xa21 . Mol Gen Genet 236:113–120 - 64.
Rozema J, Flowers T (2008) Crops for a salinized world. Science 322:1478–1480 - 65.
Rush MC, Lee FN (1992) Sheath blight. Pages 22−23 in: Compendium of rice diseases. R. K. Webster and P. S. Gunnell, eds. American Phytopathological Society, St. Paul, MN - 66.
Sakai H, Itoh T (2010) Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis. BMC Genomics 11:121 - 67.
Sasaki T, Burr B (2000) International Rice Genome Sequencing Project: The effort to completely sequence the rice genome. Curr Opin Plant Biol 3:138–141 - 68.
Savary S, Mew TW (1996) Analyzing crop losses due to Rhizoctonia solani : Rice sheath blight, a case study. In:Rhizoctonia Species: Taxonomy, Molecular Biology, Ecology, Pathology and Disease Control. B. Sneh, S. Jabajihare, S. Neate, and G. Dijst, eds. Kluwer Academic Publisher, Dordrecht, The Netherlands:237−245 - 69.
Savary S, Willocquet L, Elazegui FA, Castilla N, Teng PS (2000) Rice pest constraints in tropical Asia: quantification of yield losses due to rice pests in a range of production situations. Plant Dis 84:357–369 - 70.
Schachtman DP, Reid RJ, Ayling SM (1998) Phosphorus uptake by plants: from soil to cell. Plant Physiol 116:447–453 - 71.
Shelden MC, Roessner U (2013) Advances in functional genomics for investigating salinity stress tolerance mechanisms in cereals. Frontiers in plant science 4:123 - 72.
Song WY, Wang GL, Chen LL, Kim HS, Pi LY, Holsten T, Gardner J, Wang B, Zhai WX, Zhu LH, Fauquet C, Ronald P (1995) A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21 . Science 270:1804–1806 - 73.
Song ZP, Li B, Chen JK, Lu BR (2005) Genetic diversity and conservation of common wild rice ( Oryza rufipogon ) in China. Plant Spec Biol 20:83–92 - 74.
Stebbins GL (1981) Why are there so many species of flowering plants? Bioscience 31:573–577 - 75.
Sthapit BR, Witcombe JR (1998) Inheritance of tolerance to chilling stressing rice during germination and plumule greening. Crop Sci 38:660–665 - 76.
Sun CQ, Wang XK, Li ZC, Yoshimura A, Iwata N (2001) Comparison on the genetic diversity of common wild rice ( Oryza rufipogon Griff.) and cultivated rice (O. sativa L.) using RFLP markers. Theor Appl Genet 102:157–162 - 77.
Takesawa T, Ito M, Kanzaki H, Kameya N, Nakamura I (2002) Over-expression of ζ glutathione S-transferase in transgenic rice enhances germination and growth at low temperature. Mol Breed 9:93–101 - 78.
Tan GX, Ren X, Weng QM, Shi ZY, Zhu LL, He GC (2004) Mapping of a new resistance gene to bacterial blight in rice line introgressed from Oryza officinalis . Acta Genetica Sinica 31:724–729 (Chinese with English abstract) - 79.
Tan LB, Zhang PJ, Liu FX, Wang GJ, Ye S, Zhu ZF, Fu YC, Cai HW, Sun CQ (2008) Quantitative trait loci underlying domestication and yield-related traits in Oryza rufipogon ×Oryza sativa advanced backcross population. Genome 51:692−704 - 80.
Tanksley SD, Grandillo S, Fulton TM, Zamir D, Eshed Y, Petiard V, Lopez J, Beck-Bunn T (1996) Advanced backcross QTL analysis in a cross between an elite processing line of tomato and its wild relative L. pimpinellifolium. Theor Appl Genet 92:213–224 - 81.
Tanksley SD, Nelson JC (1996). Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203 - 82.
Vaughan DA (1994) The wild relatives of rice: a genetic resources guide book. International Rice Research Institute, Los Banos, The Philippines - 83.
Wang CL, Qi HX, Pan HJ, Li JB, Fan YL, Zhang Q, Zhao KJ (2005) EST-markers flanking the rice bacterial blight resistance gene Xa23 and their application in marker-assisted selection. Sci Agri Sin 38:1996–2001 (Chinese with English abstract) - 84.
Wu B, Han ZM, Li ZX, Xing YZ (2012) Discovery of QTLs increasing yield related traits in common wild rice. Yi Chuan 34:215−22 (Chinese with English abstract) - 85.
Xiao JH, Li JM, Grandillo S, Ahn SN, Yuan LP, Tanksley SD, McCouch SR (1998) Identification of trait-improving quantitative trait loci alleles from a wild rice relative, Oryza rufipogon . Genetics 150:899–909 - 86.
Xie JK, Agrama HA, Kong D, Zhuang J, Hu B, Wan Y, Yan W (2010) Genetic diversity associated with conservation of endangered Dongxiang wild rice ( Oryza rufipogon ). Genet Resour Crop Evol 57:597–609 - 87.
Xie JK, Hu BL, Wan Y, Zhang T, Li X, Liu RL, Huang YH, Dai LF, Luo XD (2010) Comparison of the drought resistance characters at Seedling Stage between Dongxiang Common Wild rice ( Oryza rufipogon Griff.) and cultivars (Oryza sativa L.). Acta Ecologica Sinica 30:1665–1674 (Chinese with English abstract) - 88.
Xie JK, Kong XL, Bao JS, Wan Y (2004) Recent advances in molecular mapping and cloning of useful genes from wild rice and their application in breeding. Hereditas (Beijing) 26:115–121 (Chinese with English abstract) - 89.
Xie X, Song MH, Jin F, Ahn SN, Suh JP, Hwang HG, McCouch SR (2006) Fine mapping of a grain weight quantitative trait locus on rice chromosome 8 using near-isogenic lines derived from a cross between Oryza sativa andOryza rufipogon . Theor Appl Genet 113:885–894 - 90.
Yamane K, Kawasaki M, Taniguchi M, Miyake H (2008) Correlation between chloroplast ultrastructure and chlorophyll fluorescence characteristics in the leaves of rice ( Oryza sativa L.) grown under salinity. Plant Prod Sci 11:139–145 - 91.
Zeng YW, Yang SM, Cui H, Yang XJ, Xu LM, Du J, Pu XY, Li ZC, Cheng ZQ, Huang XQ (2009) QTLs of cold tolerance-related traits at the booting stage for NIL-RILs in rice revealed by SSR. Genes Genom 31:143–154 - 92.
Zhang Q (2005) Highlights in identification and application of resistance genes to bacterial blight. Chinese J Rice Sci 19:453–459 (Chinese with English abstract) - 93.
Zhang ZH, Li S, Wei L, Wei C, Zhu YG (2005) A major QTL conferring cold tolerance at the early seedling stage using recombinant inbred lines of rice ( Oryza sativa L.). Plant Sci 168:527–534 - 94.
Zheng CK, Wang CL, Yu YJ, Liang YT, Zhao KJ (2009) Identification and molecular mapping of Xa32 (t ), a novel resistance gene for bacterial blight (Xanthomonas oryzae pv.oryzae ) in rice. Acta Agronomica Sin 35:1173−1180 (Chinese with English abstract) - 95.
Zheng JX, Ma ZF, Song JD, Liu C, Li YT, Huang DH, Wei SL, Zhang YX, Mi K, Huang JY, Chen M, Meng JR, Li RB, Chen BS (2011) Identification and mapping of QTLs for cold tolerance at the seedling stage in common wild rice ( Oryza rufipogon ). Chinese J Rice Sci 25:52–58 (Chinese with English abstract)