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
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.
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