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IR64: a high-quality and high-yielding mega variety

Ricevolume 11, Article number: 18 (2018) | Download Citation

Abstract

High-yielding varieties developed in the 1960s and 1970s at the International Rice Research Institute (IRRI) and elsewhere benefited farmers and the public, ultimately increasing yields and reducing the cost of rice to consumers. Most of these varieties, however, did not have the optimum cooking quality that was possessed by many of the traditional varieties they replaced. In 1985, the IRRI-developed indica variety IR64 was released in the Philippines. In addition to its high yield, early maturity and disease resistance, it had excellent cooking quality, matching that of the best varieties available. These merits resulted in its rapid spread and cultivation on over 10 million ha in the two decades after it was released. It has intermediate amylose content and gelatinization temperature, and good taste. It is resistant to blast and bacterial blight diseases, and to brown planthopper. Because of its success as a variety, it has been used extensively in scientific studies and has been well-characterized genetically. Many valuable genes have been introduced into IR64 through backcross breeding and it has been used in thousands of crosses. Its area of cultivation has declined in the past 10 years, but it has been replaced by a new generation of high-quality varieties that are mostly its progeny or relatives. Continued basic studies on IR64 and related varieties should help in unraveling the complex genetic control of yield and other desirable traits that are prized by rice farmers and consumers.

Background

In November 2016, the International Rice Research Institute (IRRI) and others commemorated the 50th anniversary of the release of IR8, its first developed variety and a beginning of the Green Revolution in rice (http://irri.org/ir8). This variety established the basic plant type of the high-yielding varieties (HYVs) that have now spread over most rice growing areas.

IR8 had a very high grain yield, but also a number of defects, most importantly, poor grain quality, lack of disease and insect resistance, and late maturity. The varieties subsequently developed and released over the next two decades improved greatly on these traits (Khush 1999). During the early 1980s, one of the most popular varieties grown was IR36. In addition to its disease and insect resistance, it achieved its high yield in a period of only 111 days from seed to seed, compared to 130 days for IR8 (Khush and Virk 2005). It spread rapidly and was estimated to be planted on more than 10 million ha during the 1980s.

While much improved over IR8, IR36 still lacked the quality of the best varieties grown in the Philippines and Indonesia before the Green Revolution. IR64, released in the Philippines in 1985, represented a breakthrough in combining excellent palatability of cooked rice with the other traits found in previous IRRI HYVs. IR64 replaced IR36 in most growing areas and spread rapidly in new areas. Because of its wide adaptation, early maturity, and improved quality, it became a standard for high-quality rice and was highly desired by the rice industry. Because of its popularity, it has been used widely as a representative indica variety in research studies. It has also been used extensively as a parent in breeding programs, and to develop populations for genetic analysis.

In this article, we describe the development of IR64 and its major characteristics. We also discuss the use of this variety in further breeding and rice research.

Review

Breeding history, including parentage and selection history, evaluation and release

The breeding history of IR64 is summarized in Khush and Virk (2005). The breeding program at IRRI focused on combining the different traits desired by farmers, including high yield, resistance to biotic and abiotic stresses, early maturity, and improved grain quality. The Genetic Evaluation and Utilization (GEU) program was formulated at IRRI to focus research efforts on combining these traits through interdisciplinary collaboration (Khush and Coffman 1977). In segregating generations and in evaluation of fixed lines, plants and breeding lines were evaluated for these traits either in the pedigree breeding nursery or special screening nurseries. This improved the chance of combining multiple traits into a single variety.

The cross of IR5657-33-2-1/IR2061-465-1-5-5, was made in early 1977 and was designated IR18348. The female parent was noted for its good cooking quality (intermediate amylose), as well as having some tolerance to salinity. The male parent was a high-yielding breeding line derived from a highly productive cross that resulted in a number of other varieties from sister lines, including IR28, IR29 and IR34. The full pedigree (Fig. 1) shows the derivation of IR64 from 19 traditional rice varieties.

Fig. 1
figure1

Pedigree of IR64 showing the ultimate landraces in its ancestry (Khush and Virk 2005)

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The F2 population was evaluated in 1978, and the pedigree method of breeding was followed in the F3 and F4 populations, grown in 1979. The breeding line IR18348-36-3-3 resulted from the bulk harvest of a F5 family in 1980, and was subsequently evaluated in yield trials in 1981–83 at IRRI, as well as in the Philippine National Trials. It out-yielded IR36 by 21% in these trials (IRRI 1986). It was released by the Philippine Seed Board with the designation ‘IR64’ in 1985, and this designation has been subsequently used by IRRI (IRRI 1986).

The early varieties developed at IRRI were high yielding and had disease and insect resistance, but their grain quality was inferior to the best available varieties. At the time, the standard for grain quality in the Philippines was the variety BPI-76 and its sister line BPI-121, derived from the cross Fortuna/Seraup Besar 15 (Cada and Escuro 1972). The parent variety Fortuna is from the USA, and Seraup Besar 15 was originally introduced from Malaysia. BPI-76 was released in 1960 in the Philippines, and non-photoperiod sensitive selections, BPI-76 (n.s.) and BPI-76-1, were also released (Dalrymple 1978). Another popular variety noted for its quality was C4-63, and it was derived from the cross Peta/BPI-76. Before IR64, C4-63 was considered one of the main high-quality varieties in the Philippines. In 1970, a green-base C4-63 was released to replace the original seed stocks of C4-63. Because of its good eating quality (intermediate amylose content) it had spread in Indonesia, Malaysia, and Burma (Yoshida 1981). Rice was even widely marketed under the C4 name up to the 1980s; however, many of the market samples actually turned out to be other varieties or mixtures of varieties with inferior quality that were being grown by farmers (Juliano et al. 1989).

BPI-121-407 is considered the most likely contributor of superior quality in the pedigree of IR64, although BPI-76 is also in its pedigree. BPI-121-407 is a short-statured breeding line with superior quality, and was selected as an induced mutant of the original BPI-121 (Cada and Escuro 1972). In the advanced evaluation of the breeding line IR18348-36-3-3 at IRRI, taste panels were used to ensure that the quality of BPI-76 (or BPI-121) was captured. Taste panels were also applied in the government of the Philippines rice program to assist in providing the data for release of this variety.

Adoption and impact

The major breakthrough in the development of IR64 was the combination of the high yield and disease and insect resistance of earlier IRRI varieties with the superior grain quality associated with varieties like BPI-76 and C4-63. It’s first release was by the Philippine government in 1985. It was also released in the following countries: Bhutan, Burkina Faso (as FKR42), Cambodia, China, Ecuador (as NIAP11), Gambia, India, Indonesia, Mauritania, Mozambique, and Vietnam (as OM89) (Khush and Virk 2005). Its wide adaptation is notable, and it became widely grown in Southeast and South Asia. It is also noted to be well adapted to the Sahelian regions of West Africa (Devries et al. 2011; Julia and Dingkuhn 2013).

By 1995, IR64 was already estimated to be grown on 8 million ha (Khush 1995), and by the turn of the century this rose to over 10 million ha. The long persistence of IR64 in farmers’ fields after its release was attributed to its excellent eating quality (Champagne et al. 2010). The area of production gradually declined in the Philippines during the period 2000–2007, partly due to pressure from tungro disease (Laborte et al. 2015). Indonesia was a major producer of IR64, which was grown on more than 40% of its total area for around a decade (Fig. 2), and was still popular in 2009 (Brennan and Malabayabas 2011). It is also widely grown in India. During 1998–2006 IR64 accounted for over 10% of the breeder seed produced in India and was still above 3% in 2015, suggesting that it was grown on 2–3 million ha annually during the period (data provided by A. K. Singh).

Fig. 2
figure2

Share of leading varieties in Indonesia during 1985–2009 (Brennan and Malabayabas 2011)

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A specific estimate of the impact of this variety has not been attempted, even though it is known as the most popular variety in terms of area, particularly in tropical Asia. IR64 has contributed greatly to farmer incomes not only through higher yields, but through improved quality that results in higher price and earlier maturity that allows higher cropping intensity.

As with other IRRI varieties, seed of IR64 was distributed freely to researchers and farmers and no intellectual property protection was sought on it or any progeny developed from it.

Major characteristics, including key traits

IR64 is a semidwarf indica rice variety, with average mature plant height of approximately 100 cm in the Philippines (Fig. 3). It is a relatively early duration variety, with total growth duration of about 117 days (Khush and Virk 2005). It inherits the same semidwarf sd1 allele as other IRRI semidwarf varieties, ultimately derived from Dee-geo-woo-gen. According to Wei et al. (2016) it has the loss of function alleles for Hd1 and Ehd1, which confer earlier duration and insensitivity to photoperiod. At the time of its release, IRRI (1986) listed the valuable traits as resistance to brown planthopper (BPH) biotypes 1 and 3, green leafhopper (GLH), white backed planthopper (WBPH), bacterial blight, grassy stunt virus; and moderate resistance to blast, BPH biotype 2, and stem borer. It was the first IRRI variety to combine intermediate amylose content and intermediate gelatinization temperature (GT).

Fig. 3
figure3

Plot of IR64 growing in the field at IRRI, Los Baños, Philippines (photo from IRRI)

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IR64 has high yield, especially compared to earlier-released IRRI varieties, but not as high as some of the subsequently released varieties like IR72. Peng et al. (2000) list its grain yield as 8.76 and 8.28 t ha− 1 compared to 9.50 and 9.06 t ha− 1 for IR72 in the dry season at IRRI in 1996 and 1998, respectively. It has high grain filling percentage and grain weight, but a relatively low spikelet number per m2 (Peng et al. 2000). According to Ujiie et al. (2016), IR64 possesses a gene GS3 for grain size and the narrow-leaf gene (NAL1) that improve grain yields. IR64 is considered a typical high-tillering indica type cultivar, in contrast to the “new plant type” NPT varieties that have lower tillering but large tiller and panicle size (Okami et al. 2015).

IR64 has relatively durable resistance to BPH, and it is known to carry the major gene Bph1. However, it is reported to have better resistance than other varieties carrying Bph1 and has good field resistance to the pest, exhibiting antiobiosis, antixenosis and tolerance (Cohen et al. 1997). This is partly attributed to its possessing additional QTLs controlling BPH resistance which confer greater durability of the resistance (Alam and Cohen 1998).

IR64 has very good levels of resistance to blast disease, including major-gene resistance and partial resistance (Bastiaans and Roumen 1993; Grand et al. 2012; Roumen 1992). Sallaud et al. (2003) reported six resistance genes, designated Pi25(t), Pi-27(t), Pi29(t), Pi30(t), Pi31(t), and Pi32(t). It also has resistance genes Pita (Lee et al. 2011) and Pi20 (Khush and Virk 2005), as well as Pi33 on chromosome 8 which was derived from O. rufipogon (accession IRGC101508, sometimes referred to as O. nivara) in its pedigree (Ballini et al. 2007; Berruyer et al. 2003). Sreewongchai et al. (2010) found that IR64 has broad resistance to blast disease in Thailand and this was conferred mainly by QTLs on chromosomes 2 and 12. It was also resistant in a blast hotspot in India (Thakur et al. 2013). Kongprakhon et al. (2010) identified QTLs that may correspond to Pi25 (chromosome 2), Pi29 (chromosome 8), and Pi28 (chromosome 10).

IR64 is resistant to Bacterial Blight (BB) disease (caused by Xanthomonas oryzae pv. oryzae) and possesses the major gene Xa4 for resistance (Adhikari et al. 1994; Khush and Virk 2005). The gene is thought to confer additional agronomic benefits in addition to BB resistance (Hu et al. 2017). It is also resistant against African strains of X. oryzae, and several QTLs for resistance were identified (Djedatin et al. 2016).

IR64 is susceptible to tungro disease, including Rice Tungro Spherical Virus (RTSV) (Lee et al. 2010) and Rice Tungro Bacilliform Virus (RTBV) (Zenna et al. 2006).

IR64 was developed primarily for irrigated rice production, and abiotic stress resistance was not an objective. While it is generally considered susceptible to abiotic stresses, it has been widely grown in more favorable rainfed situations and under mildly unfavorable soils.

IR64 is considered susceptible to drought stress and yield reductions can be considerable (Anantha et al. 2016). Yields under aerobic conditions (favorable upland) are also relatively low (Zhao et al. 2010). Vikram et al. (2015) attributed drought susceptibility of many modern high-yielding varieties to linkage between a drought susceptibility QTL and the semidwarf gene sd1. IR64 has a relatively shallow root system and low root length density (Henry et al. 2011; Shrestha et al. 2014). Under water stress, IR64 has relatively low water uptake rate (Gowda et al. 2012).

IR64 is considered sensitive to heat (Coast et al. 2016; Gonzalez-Schain et al. 2016; Shanmugavadivel et al. 2017; Ye et al. 2015), although this has not been reported as a problem with previous or current production environments. However, Jagadish et al. (2008) indicated that IR64 is actually moderately tolerant of high temperature at flowering. It is also susceptible to Fe toxicity (Wu et al. 1997), anaerobic germination (Miro and Ismail 2013), and low temperature at the vegetative stage (Chawade et al. 2013). IR64 lacks the P deficiency gene PSTOL1 like a number of other high-yielding varieties (Gamuyao et al. 2012). IR64 was reported to be sensitive to low P conditions (Mori et al. 2016; Vejchasarn et al. 2016). It is also relatively sensitive to Zn deficiency (Impa et al. 2013). While IR64 does not possess the submergence tolerance allele of SUB1, it has some moderate tolerance to submergence during the vegetative stage (Singh et al. 2010; Singh et al. 2013).

Grain and market characteristics

IR64 grain has good physical appearance and is a typical long-grain variety with high head rice yield (IRRI 1986). As mentioned above, IR64 was the first IRRI variety to have both intermediate amylose content and intermediate GT. These traits are considered important for the ideal texture of cooked rice, especially for many rice consumers in South and Southeast Asia. However, these two traits alone do not account for the superior cooking quality of the variety, and methods to evaluate cooking quality are still inadequate aside from laborious sensory methods (Concepcion et al. 2015). This is why the use of taste panels was essential to identify the superior quality of IR64.

Rice texture is mostly controlled by the allele at the waxy locus (Wx) on chromosome 6. Among the major alleles at this locus, IR64 carries the Wxin allele at the waxy locus signifying intermediate amylose content (Zhang et al. 2012). However, various sequence features of the Wx gene are associated with grain quality of rice, including the number of CT repeats in the 5′ untranslated part of the gene and the SNPs at specific sites in intron 1, exon 6, and exon 10 (Bligh et al. 1998; Bligh et al. 1995; Larkin and Park 2003). Based on the DNA sequence, IR64 has the (CT)17 allele of Wx (Roferos et al. 2008; Teng et al. 2012). (CT)17 and (CT)20 are associated with intermediate amylose and soft to medium hardness (Roferos et al. 2008). The SNPs at the Wx locus are G-C-C for intron 1, exon 6 and exon 10, a common haplotype for intermediate amylose varieties (Chen et al. 2010).

Azucena and IR64 both have intermediate amylose and intermediate GT, and the doubled haploid population of the cross between the two was used to identify QTLs for several grain quality related traits, including starch properties measured by Rapid Visco Analyzer (RVA) (Bao et al. 2002). The study showed that there are genetic differences for these traits despite both varieties having similar amylose content and GT.

Part of the improved quality superiority is from improved flavor, including sweet and corn notes (Calingacion et al. 2015; Champagne et al. 2010). Reduced yellow color, improved texture and mouthfeel, and superior “sweet” taste were noted in IR64 vs. the lower-quality IRRI-132 (Champagne et al. 2010) (Table 1). Metabolomics analysis showed very different profiles for IR64 vs. the lower quality variety Apo (Calingacion et al. 2015).

Table 1 Comparison of flavor attributes of high quality IR64 and low-quality Apo (Calingacion et al. 2015)
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Calingacion et al. (2014) surveyed grain quality preferences in different countries and regions based on the most popular varieties in each area. However, two countries where IR64 dominated have different preferences (Indonesia and Philippines). These preferences can change over time.

Genetic and genomic characteristics

IR64 has been used extensively in genetic studies of rice, mainly because it represents a high-yielding and high-quality indica variety that is widely adapted to tropical lowland growing conditions. The most well-known mapping population was a doubled haploid population of about 146 lines derived from the cross IR64/Azucena (Guiderdoni et al. 1992), and first used by Huang et al. (1997) to map important agronomic traits and by Wu et al. (1997) to map tolerance to Fe toxicity. Other mapping populations with IR64 as a parent have been developed using both indica and japonica parents. A recombinant inbred line (RIL) population of 171 families was developed in a cross between IR64 and the wild relative O. rufipogon and tolerance to Al toxicity was mapped (Nguyen et al. 2003). Reciprocal chromosome segment substitution lines (CSSL) were also developed in IR64 and Koshihikari backgrounds to study the inheritance of grain shape (Nagata et al. 2015).

The original genome sequence of rice used the japonica variety Nipponbare (IRGSP 2005). In the first report of resequencing multiple varieties, IR64 was used among 20 diverse varieties, although this only included 100 Mb of the unique fraction of the genome (McNally et al. 2009). Schatz et al. (2014) reported whole genome de novo assembly for IR64 as well as the japonica variety Nipponbare and the aus variety DJ123. The genome coverage was 88.5% and included 37,758 genes. IR64 was estimated to have 381 genes not present in either of the other two varieties, and DJ123 and Nipponbare had 297 and 786 genes not found in the other varieties. Jain et al. (2014) also reported whole genome sequencing of IR64 along with Pokkali and N22, achieving 84.5% coverage. Methylation pattern has also been studied in IR64 and compared with a japonica variety Dianjingyou1 and two wild ancestors (Li et al. 2012). Gene expression and identification of functional roles of genes have been carried out with this model variety, for example drought responsive genes (Ray et al. 2011), gene expression changes during different stages of development (Sharma et al. 2012), and salinity tolerance (Wang et al. 2016).

Important progeny

The excellent grain quality of IR64 has become the standard for rice quality requirements in a number of countries. Because of its popularity with farmers, IR64 has been used widely as a parent in rice breeding, as a recipient of new genes through marker-assisted backcrossing and genetic transformation, and as a standard check for basic studies by many rice researchers. IR64 figured prominently in the mapping of many QTLs when genome-wide markers became available.

In the Philippines, IR64 was replaced by newer varieties in the early 2000s mainly due to its susceptibility to tungro disease. However, the breeders have attempted to retain the quality traits of IR64. PSB Rc82 is an example of a variety that became very popular, and IR64 is one of its grandparents. In India as well, the variety MTU 1010 became very popular, and it is a cross of Krishnaveni/IR64.

IR64 was a dominant variety in Indonesia for over two decades. In the last 10 years, it has been replaced by the variety Ciherang, which has very similar grain quality and improved yields. This variety is from the cross IR18349-53-1-3-1-3/IR19661-131-3-1//IR19661-131-3-1/IR64/IR64, and has high genetic similarity with IR64 (IRRI 2015; Septiningsih et al. 2014). It has very similar grain quality to IR64 and is also morphologically and genetically similar (Muhamad et al. 2017).

The availability of genome-wide molecular markers for marker assisted selection enabled the transfer of important traits into popular varieties like IR64 through marker-assisted backcrossing (MABC) (Collard and Mackill 2008). Early examples of this included varieties developed by pyramiding BB resistance genes into IR64, including Angke and Conde in Indonesia, and NSIC Rc142 in the Philippines (Verdier et al. 2012).

The rice submergence tolerance gene SUB1 was introduced by marker assisted backcrossing into IR64 and several other popular varieties (Septiningsih et al. 2009) (Fig. 4). Because IR64 had moderate tolerance to submergence, IR64-Sub1 tended to perform better under submergence than some of the other Sub1 lines, and its relatively early maturity allowed it to recover and produce yields after prolonged flooding and before the onset of low temperatures (Singh et al. 2010; Singh et al. 2013). IR64-Sub1 was released as Submarino 1 in the Philippines in 2009. The genetic similarity of Ciherang with IR64 was exploited to develop a submergence-tolerant version of Ciherang with only one backcross (Septiningsih et al. 2014). IR64-Sub1 was also used to develop submergence tolerant varieties in Vietnam (Lang et al. 2015).

Fig. 4
figure4

a IR64 and IR64-Sub1 under non-flooded conditions at IRRI. b Trials after submergence showing the survival of IR64-Sub1 compared to IR64. Fields were submerged for 17 days at 28 days after seeding. (Photos from IRRI)

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Many interesting genes and QTLs have been backcrossed into IR64 and these progeny are being evaluated for useful traits (Table 2). One of the most important is drought tolerance. This trait was introduced by backcrossing from drought tolerance donor Aday Sel into IR64 (Venuprasad et al. 2011), and some of the derived lines showed yield increases of 528 to 1875 kg ha-1 over IR64 under severe drought conditions (Swamy et al. 2013). Breeding lines with two drought-tolerance QTLs (qDTY2.2 + qDTY4.1) introgressed into IR64 showed improved performance under drought stress. These lines had improved hydraulic conductivity and higher root length density (Henry et al. 2015). The gene DRO1, conferring deeper rooting and drought tolerance, was also transferred into IR64 by backcrossing, and resulted in NILs with higher drought tolerance (Uga et al. 2013). According to the authors, a single bp deletion in DRO1 resulted in a stop codon in IR64 and caused shallow rooting and drought intolerance, and this deletion was observed in IR64 and some of its progeny but not in its ancestors. The IR64 Dro1-NIL had a 14% higher yield than IR64 (Deshmukh et al. 2017). IR64-Sub1 is being used as a recipient for drought tolerance QTLs to develop a version of IR64 tolerant of both stresses (Singh et al. 2016).

Table 2 Near Isogenic Lines (NILs) developed in IR64 genetic background with genes conferring novel and improved traits
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IR64 is generally considered a restorer line for hybrid rice, particularly in the WA CMS system widely used in indica “three-line” hybrid breeding (Xie et al. 2014). However, Toriyama and Kazama (2016) developed a new IR64 cms termed CW type (Chinese wild rice), restored by the Rf17 gene.

At IRRI, induced mutation was used to generate a large collection of mutants in IR64. This collection has been used to discover many genes controlling important traits in rice (Wu et al. 2005). Some of these mutants show favorable phenotypes that could be used directly in rice breeding. Examples include tolerance to salinity (Nakhoda et al. 2012), resistance to blast disease (Madamba et al. 2009), resistance to tungro disease (Zenna et al. 2008), and drought tolerance (Cairns et al. 2009).

Transgenic applications have been limited for rice and are currently not in commercial cultivation. However, Agrobacterium mediated transformation protocols are well developed and used for IR64 (Ignacimuthu and Raveendar 2011). For example, it has been transformed with genes conferring higher Fe and Zn content in the endosperm (Oliva et al. 2014; Trijatmiko et al. 2016) and herbicide tolerance (Chhapekar et al. 2015).

Conclusions

This brief review attempts to document the value of the variety IR64 for rice breeding and genetics but cannot contain all the information available. At one time, this variety was estimated to be grown on 9–10 million ha annually (Laird and Kate 1999). Considering the many years it has been in production, over approximately two decades, it has been providing hundreds of millions of consumers with high-quality rice. In this sense it resembles some of the other mega varieties like Swarna and Samba Mahsuri, grown in India. However, breeders have been quick to take advantage of this variety to make further advances. As an example, IR64 has been replaced in most of the Philippines and Indonesia by new varieties with similar quality attributes but improved agronomic traits like disease resistance and higher grain yield.

Rice breeding is a continual process and all varieties are expected to be replaced by improved varieties over time. IR64 is still a popular variety in some areas, particularly in India where it is a popular variety in the north. Its area is gradually declining, due to release of improved varieties. However, as outlined here, it lives on through its progeny that are cultivated or under evaluation throughout the region. Some of the most important factors that enabled the development of such a superior variety include: a large breeding program where many crosses were made annually and large segregating populations were grown, well-defined objectives with focus on the most necessary traits including preferred quality attributes, systematic screening by skilled researchers for required traits, sensory data to confirm quality of the cooked rice, a suitable evaluation program to measure yield as early in the breeding program as possible, and an effective outreach effort to evaluate advanced selections under farmers’ conditions and ensure that seed was widely available.

The development of high-quality mega varieties like IR64 has provided a challenge to rice breeders to make further improvements to varieties that are widely-accepted by farmers. This challenge has been met well in the Philippines and Indonesia where new varieties have replaced IR64, but less well in India where the variety is still popular. In general, new varieties that aim to replace the mega varieties must offer a clear advantage, such as improved stress tolerance or higher yield. Additionally, the rice processing industry must be supportive of the efforts to replace existing varieties with new ones, so that farmers will have a suitable market for their crop produced from these new varieties.

Abbreviations

BB:

Bacterial blight

BPH:

Brown Planthopper

CSSL:

Chromosome segment substitution library

GEU:

Genetic Evaluation and Utilization

GLH:

Green leafhopper

GT:

Gelatinization temperature

HYV:

High-yielding variety

IRRI:

International Rice Research Institute

MABC:

Marker assisted backcrossing

RIL:

Recombinant inbred population

RTBV:

Rice tungro bacilliform virus

RTSV:

Rice tungro spherical virus

RVA:

Rapid visco analyzer

WBPH:

White backed planthopper

References

  1. Adhikari TB, Mew TW, Teng PS (1994) Progress of bacterial blight on rice cultivars carrying different Xa genes for resistance in the field. Plant Dis 78:73–77

  2. Ahmadi N, Albar L, Pressoir G, Pinel A, Fargette D, Ghesquiere A (2001) Genetic basis and mapping of the resistance to Rice yellow mottle virus. III. Analysis of QTL efficiency in introgressed progenies confirmed the hypothesis of complementary epistasis between two resistance QTLs. Theor Appl Genet 103:1084–1092

  3. Alam SN, Cohen MB (1998) Detection and analysis of QTLs for resistance to the brown planthopper, Nilaparvata lugens, in a doubled-haploid rice population. Theor Appl Genet 97:1370–1379

  4. Anantha MS, Patel D, Quintana M, Swain P, Dwivedi JL, Torres RO, Verulkar SB, Variar M, Mandal NP, Kumar A, Henry A (2016) Trait combinations that improve rice yield under drought: Sahbhagi Dhan and new drought-tolerant varieties in South Asia. Crop Sci 56:408–421

  5. Ballini E, Berruyer R, Morel JB, Lebrun MH, Notteghem JL, Tharreau D (2007) Modern elite rice varieties of the 'Green Revolution' have retained a large introgression from wild rice around the Pi33 rice blast resistance locus. New Phytol 175:340–350

  6. Bao JS, Wu YR, Hu B, Wu P, Cui HR, Shu QY (2002) QTL for rice grain quality based on a DH population derived from parents with similar apparent amylose content. Euphytica 128:317–324

  7. Bastiaans L, Roumen EC (1993) Effect on leaf photosynthetic rate by leaf blast for rice cultivars with different types and levels of resistance. Euphytica 66:81–87

  8. Berruyer R, Adreit H, Milazzo J, Gaillard S, Berger A, Dioh W, Lebrun MH, Tharreau D (2003) Identification and fine mapping of Pi33, the rice resistance gene corresponding to the Magnaporthe grisea avirulence gene ACE1. Theor Appl Genet 107:1139–1147

  9. Bimpong IK, Serraj R, Chin JH, Ramos J, Mendoza EMT, Hernandez JE, Mendioro MS, Brar DS (2011) Identification of QTLs for drought-related traits in alien introgression lines derived from crosses of rice (Oryza sativa cv. IR64) x O. glaberrima under lowland moisture stress. J Plant Biol 54:237–250

  10. Bligh HFJ, Larkin PD, Roach PS, Jones CA, Fu HY, Park WD (1998) Use of alternate splice sites in granule-bound starch synthase mRNA from low-amylose rice varieties. Plant Mol Biol 38:407–415

  11. Bligh HFJ, Till RI, Jones CA (1995) A microsatellite sequence closely linked to the waxy gene of Oryza sativa. Euphytica 86:83–85

  12. Brennan JP, Malabayabas A (2011) International Rice Research Institute’s contribution to rice varietal yield improvement in South-East Asia. ACIAR impact assessment No. 74. Australian Centre for International Agricultural Research, Canberra

  13. Cada EC, Escuro PB (1972) Rice varietal improvement in the Philippines. Rice breeding. International Rice Research Institute, Los Baños, pp 161–166

  14. Cairns JE, Acuna TLB, Simborio FA, Dimayuga G, Praba ML, Leung H, Torres R, Lafitte HR (2009) Identification of deletion mutants with improved performance under water-limited environments in rice (Oryza sativa L.) Field Crop Res 114:159–168

  15. Calingacion M, Fang L, Quiatchon-Baeza L, Mumm R, Riedel A, Hall RD, Fitzgerald M (2015) Delving deeper into technological innovations to understand differences in rice quality. Rice 8:1–10

  16. Calingacion M, Laborte A, Nelson A, Resurreccion A, Concepcion JC, Daygon VD, Mumm R, Reinke R, Dipti S, Bassinello PZ, Manful J, Sophany S, Lara KC, Bao JS, Xie LH, Loaiza K, El-hissewy A, Gayin J, Sharma N, Rajeswari S, Manonmani S, Rani NS, Kota S, Indrasari SD, Habibi F, Hosseini M, Tavasoli F, Suzuki K, Umemoto T, Boualaphanh C, Lee HH, Hung YP, Ramli A, Aung PP, Ahmad R, Wattoo JI, Bandonill E, Romero M, Brites CM, Hafeel R, Lur HS, Cheaupun K, Jongdee S, Blanco P, Bryant R, Lang NT, Hall RD, Fitzgerald M (2014) Diversity of global rice markets and the science required for consumer-targeted rice breeding. PLOS ONE 9(1): e85106. https://doi.org/10.1371/journal.pone.0085106

  17. Champagne ET, Bett-Garber KL, Fitzgerald MA, Grimm CC, Lea J, Ohtsubo K, Jongdee S, Xie LH, Bassinello PZ, Resurreccion A, Ahmad R, Habibi F, Reinke R (2010) Important sensory properties differentiating premium rice varieties. Rice 3:270–281

  18. Chawade A, Lindlof A, Olsson B, Olsson O (2013) Global expression profiling of low temperature induced genes in the chilling tolerant japonica rice Jumli Marshi. PLOS ONE 8(12): e81729. https://doi.org/10.1371/journal.pone.0081729

  19. Cheema KK, Bains NS, Mangat GS, Das A, Vikal Y, Brar DS, Khush GS, Singh K (2008) Development of high yielding IR64 x Oryza rufipogon (Griff.) introgression lines and identification of introgressed alien chromosome segments using SSR markers. Euphytica 160:401–409

  20. Chen MH, Fjellstrom RG, Christensen EF, Bergman CJ (2010) Development of three allele-specific codominant rice Waxy gene PCR markers suitable for marker-assisted selection of amylose content and paste viscosity. Mol Breed 26:513–523

  21. Chhapekar S, Raghavendrarao S, Pavan G, Ramakrishna C, Singh VK, Phanindra MLV, Dhandapani G, Sreevathsa R, Kumar PA (2015) Transgenic rice expressing a codon-modified synthetic CP4-EPSPS confers tolerance to broad-spectrum herbicide, glyphosate. Plant Cell Rep 34:721–731

  22. Chin JH, Gamuyao R, Dalid C, Bustamam M, Prasetiyono J, Moeljopawiro S, Wissuwa M, Heuer S (2011) Developing rice with high yield under phosphorus deficiency: Pup1 sequence to application. Plant Physiol 156:1202–1216

  23. Coast O, Murdoch AJ, Ellis RH, Hay FR, Jagadish KSV (2016) Resilience of rice (Oryza spp.) pollen germination and tube growth to temperature stress. Plant Cell Environ 39:26–37

  24. Cohen MB, Alam SN, Medina EB, Bernal CC (1997) Brown planthopper, Nilaparvata lugens, resistance in rice cultivar IR64: mechanism and role in successful N. lugens management in central Luzon, Philippines. Entomol Exp Appl 85:221–229

  25. Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the 21st century. Phil Trans Royal Soc B Rev 363:557–572

  26. Concepcion JCT, Ouk M, Zhao D, Fitzgerald MA (2015) The need for new tools and investment to improve the accuracy of selecting for grain quality in rice. Field Crop Res 182:60–67

  27. Dalrymple DG (1978) Development and spread of high yielding varieties of wheat and rice in the less developed nations. USDA Foreign Agricultural Economic Report No. 95. U. S. Department of Agriculture, Washington DC.

  28. Deshmukh V, Kamoshita A, Norisada M, Uga Y (2017) Near-isogenic lines of IR64 (Oryza sativa subsp indica cv.) introgressed with DEEPER ROOTING 1 and STELE TRANSVERSAL AREA 1 improve rice yield formation over the background parent across three water management regimes. Plant Prod Sci 20:249–261

  29. Devries ME, Leffelaar PA, Sakane N, Bado BV, Giller KE (2011) Adaptability of irrigated rice to temperature change in Sahelian environments. Exp Agric 47:69–87

  30. Djedatin G, Ndjiondjop MN, Sanni A, Lorieux M, Verdier V, Ghesquiere A (2016) Identification of novel major and minor QTLs associated with Xanthomonas oryzae pv. oryzae (African strains) resistance in rice (Oryza sativa L.) Rice 9:18

  31. Farooq M, Tagle AG, Santos RE, Ebron LA, Fujita D, Kobayashi N (2010) Quantitative trait loci mapping for leaf length and leaf width in rice cv. IR64 derived lines. J Integr Plant Biol 52:578–584

  32. Fujita D, Santos RE, Ebron LA, Telebanco-Yanoria MJ, Kato H, Kobayashi S, Uga Y, Araki E, Takai T, Tsunematsu H, Imbe T, Khush GS, Brar DS, Fukuta Y, Kobayashi N (2009) Development of introgression lines of an Indica-type rice variety, IR64, for unique agronomic traits and detection of the responsible chromosomal regions. Field Crop Res 114:244–254

  33. Fujita D, Trijatmiko KR, Tagle AG, Sapasap MV, Koide Y, Sasaki K, Tsakirpaloglou N, Gannaban RB, Nishimura T, Yanagihara S, Fukuta Y, Koshiba T, Slamet-Loedin IH, Ishimaru T, Kobayashi N (2013) NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars. Proc Natl Acad Sci U S A 110:20431-20436

  34. Gamuyao R, Chin JH, Pariasca-Tanaka J, Pesaresi P, Catausan S, Dalid C, Slamet-Loedin I, Tecson-Mendoza EM, Wissuwa M, Heuer S (2012) The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency. Nature 488:535–539

  35. Gonzalez-Schain N, Dreni L, Lawas LMF, Galbiati M, Colombo L, Heuer S, Jagadish KSV, Kater MM (2016) Genome-wide transcriptome analysis during anthesis reveals new insights into the molecular basis of heat stress responses in tolerant and sensitive rice varieties. Plant Cell Physiol 57:57–68

  36. Gowda VRP, Henry A, Vadez V, Shashidhar HE, Serraj R (2012) Water uptake dynamics under progressive drought stress in diverse accessions of the OryzaSNP panel of rice (Oryza sativa). Funct Plant Biol 39:402–411

  37. Grand X, Espinoza R, Michel C, Cros S, Chalvon V, Jacobs J, Morel JB (2012) Identification of positive and negative regulators of disease resistance to rice blast fungus using constitutive gene expression patterns. Plant Biotechnol J 10:840–850

  38. Guiderdoni E, Galinato E, Luistro J, Vergara G (1992) Anther culture of tropical japonica x indica hybrids of rice (Oryza sativa L.). Euphytica 62:219–224

  39. Henry A, Gowda VRP, Torres RO, McNally KL, Serraj R (2011) Variation in root system architecture and drought response in rice (Oryza sativa): phenotyping of the OryzaSNP panel in rainfed lowland fields. Field Crop Res 120:205–214

  40. Henry A, Swamy BPM, Dixit S, Torres RD, Batoto TC, Manalili M, Anantha MS, Mandal NP, Kumar A (2015) Physiological mechanisms contributing to the QTL-combination effects on improved performance of IR64 rice NILs under drought. J Exp Bot 66:1787–1799

  41. Hirabayashi H, Sasaki K, Kambe T, Gannaban RB, Miras MA, Mendioro MS, Simon EV, Lumanglas PD, Fujita D, Takemoto-Kuno Y, Takeuchi Y, Kaji R, Kondo M, Kobayashi N, Ogawa T, Ando I, Jagadish KSV, Ishimaru T (2015) qEMF3, a novel QTL for the early-morning flowering trait from wild rice, Oryza officinalis, to mitigate heat stress damage at flowering in rice, O. sativa. J Exp Bot 66:1227–1236

  42. Hu K, Cao J, Zhang J, Xia F, Ke Y, Zhang H, Xie W, Liu H, Cui Y, Cao Y, Sun X, Xiao J, Li X, Zhang Q, Wang S (2017) Improvement of multiple agronomic traits by a disease resistance gene via cell wall reinforcement. Nature Plants 3. https://doi.org/10.1038/nplants.2017.1039

  43. Huang N, Parco A, Mew T, Magpantay G, Mccouch S, Guiderdoni E, Xu JC, Subudhi P, Angeles ER, Khush GS (1997) RFLP mapping of isozymes, RAPD and QTLs for grain shape, brown planthopper resistance in a doubled haploid rice population. Mol Breeding 3:105–113

  44. Ignacimuthu S, Raveendar S (2011) Agrobacterium mediated transformation of indica rice (Oryza sativa L.) for insect resistance. Euphytica 179:277–286

  45. Impa SM, Morete MJ, Ismail AM, Schulin R, Johnson-Beebout SE (2013) Zn uptake, translocation and grain Zn loading in rice (Oryza sativa L.) genotypes selected for Zn deficiency tolerance and high grain Zn. J Exp Bot 64:2739–2751

  46. IRGSP (2005) The map-based sequence of the rice genome. Nature 436:793–800

  47. IRRI (1986) Annual report for 1985. International Rice Research Institute, Los Baños

  48. IRRI (2015) Growing rice, cultivating partnerships: 40 years of Indonesia-IRRI collaboration. Int. Rice Res. Inst, Los Baños

  49. Jagadish SVK, Craufurd PQ, Wheeler TR (2008) Phenotyping parents of mapping populations of rice for heat tolerance during anthesis. Crop Sci 48:1140–1146

  50. Jain M, Moharana KC, Shankar R, Kumari R, Garg R (2014) Genomewide discovery of DNA polymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance. Plant Biotechnol J 12:253–264

  51. Julia C, Dingkuhn M (2013) Predicting temperature induced sterility of rice spikelets requires simulation of crop-generated microclimate. Eur J Agron 49:50–60

  52. Juliano BO, Perez CM, Maranan CL, Abansi CL, Duff B (1989) Grain quality characteristics of rice in Philippine retail markets. Philipp Agriculturalist 72:113–122

  53. Kato Y, Okami M, Tajima R, Fujita D, Kobayashi N (2010) Root response to aerobic conditions in rice, estimated by Comair root length scanner and scanner-based image analysis. Field Crop Res 118:194–198

  54. Khush GS (1995) Modern varieties - their real contribution to food supply and equity. GeoJournal 35:275–284

  55. Khush GS (1999) Green revolution: preparing for the 21st century. Genome 42:646–655

  56. Khush GS, Coffman WR (1977) Genetic evaluation and utilization (GEU) program: the rice improvement program of the international rice research institute. Theor Appl Genet 51:97–110

  57. Khush GS, Virk PS (2005) IR varieties and their impact. Int. Rice Res. Inst, Los Baños

  58. Kongprakhon P, Cuesta-Marcos A, Hayes PM, Hongtrakul V, Sirithunya P, Toojinda T, Sangduen N (2010) Four QTL in rice associated with broad spectrum resistance to blast isolates from rice and barley. J Phytopathol 158:125–131

  59. Laborte AG, Paguirigan NC, Moya PF, Nelson A, Sparks AH, Gregorio GB (2015) Farmers’ preference for rice traits: insights from farm surveys in central Luzon, Philippines, 1966-2012. PLOS ONE 10(8): e0136562. https://doi.org/10.1371/journal.pone.0136562

  60. Laird SA, Kate K (1999) The commercial use of biodiversity : access to genetic resources and benefit-sharing. Earthscan, London.

  61. Lang NT, Phuoc NT, Ha PTT, Toan TB, Buu BC, Reinke R, Ismail AM, Wassmann R (2015) Development of submergence tolerant breeding lines for Vietnam. SABRAO. J Genet Breed 47:448–459

  62. Larkin PD, Park WD (2003) Association of waxy gene single nucleotide polymorphisms with starch characteristics in rice (Oryza sativa L.) Mol Breed 12:335–339

  63. Lee JH, Muhsin M, Atienza GA, Kwak DY, Kim SM, De Leon TB, Angeles ER, Coloquio E, Kondoh H, Satoh K, Cabunagan RC, Cabauatan PQ, Kikuchi S, Leung H, Choi IR (2010) Single nucleotide polymorphisms in a gene for translation initiation factor (eIF4G) of rice (Oryza sativa) associated with resistance to Rice tungro spherical virus. Mol Plant-Microbe Interact 23:29–38

  64. Lee S, Jia YL, Jia M, Gealy DR, Olsen KM, Caicedo AL (2011) Molecular evolution of the rice blast resistance gene Pi-ta in invasive weedy rice in the USA. PLOS ONE 6(10): e26260. https://doi.org/10.1371/journal.pone.0026260

  65. Li X, Zhu JD, Hu FY, Ge S, Ye MZ, Xiang H, Zhang GJ, Zheng XM, Zhang HY, Zhang SL, Li Q, Luo RB, Yu C, Yu J, Sun JF, Zou XY, Cao XF, Xie XF, Wang J, Wang W (2012) Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression. BMC Genomics 13:300. https://doi.org/10.1186/1471-2164-13-300

  66. Madamba MRS, Sugiyama N, Bordeos A, Mauleon R, Satoh K, Baraoidan M, Kikuchi S, Shimamoto K, Leung H (2009) A recessive mutation in rice conferring non-race-specific resistance to bacterial blight and blast. Rice 2:104–114

  67. McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR, Bureau TE, Stokowski R, Ballinger DG, Frazer KA, Cox DR, Padhukasahasram B, Bustamante CD, Weigel D, Mackill DJ, Bruskiewich RM, Ratsch G, Buell CR, Leung H, Leach JE (2009) Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U S A 106:12273–12278

  68. Miro B, Ismail AM (2013) Tolerance of anaerobic conditions caused by flooding during germination and early growth in rice (Oryza sativa L.) Front Plant Sci 4:269. https://doi.org/10.3389/fpls.2013.00269.

  69. Mori A, Fukuda T, Vejchasarn P, Nestler J, Pariasca-Tanaka J, Wissuwa M (2016) The role of root size versus root efficiency in phosphorus acquisition in rice. J Exp Bot 67:1179–1189

  70. Muhamad K, Ebana K, Fukuoka S, Okuno K (2017) Genetic relationships among improved varieties of rice (Oryza sativa L.) in Indonesia over the last 60 years as revealed by morphological traits and DNA markers. Genet Resour Crop Evol 64:701–715

  71. Nagata K, Ando T, Nonoue Y, Mizubayashi T, Kitazawa N, Shomura A, Matsubara K, Ono N, Mizobuchi R, Shibaya T, Ogiso-Tanaka E, Hori K, Yano M, Fukuoka S (2015) Advanced backcross QTL analysis reveals complicated genetic control of rice grain shape in a japonica x indica cross. Breed Sci 65:308–318

  72. Nakhoda B, Leung H, Mendioro MS, Mohammadi-nejad G, Ismail AM (2012) Isolation, characterization, and field evaluation of rice (Oryza sativa L., Var. IR64) mutants with altered responses to salt stress. Field Crop Res 127:191–202

  73. Nguyen BD, Brar DS, Bui BC, Nguyen TV, Pham LN, Nguyen HT (2003) Identification and mapping of the QTL for aluminum tolerance introgressed from the new source, Oryza rufipogon Griff., into indica rice (Oryza sativa L.) Theor Appl Genet 106:583–593

  74. Okami M, Kato Y, Kobayashi N, Yamagishi J (2015) Morphological traits associated with vegetative growth of rice (Oryza sativa L.) during the recovery phase after early-season drought. Eur J Agron 64:58–66

  75. Oliva N, Chadha-Mohanty P, Poletti S, Abrigo E, Atienza G, Torrizo L, Garcia R, Duenas C, Poncio MA, Balindong J, Manzanilla M, Montecillo F, Zaidem M, Barry G, Herve P, Shou HX, Slamet-Loedin IH (2014) Large-scale production and evaluation of marker-free indica rice IR64 expressing phytoferritin genes. Mol Breed 33:23–37

  76. Peng S, Laza RC, Visperas RM, Sanico AL, Cassman KG, Khush GS (2000) Grain yield of rice cultivars and lines developed in the Philippines since 1966. Crop Sci 40:307–314

  77. Ray S, Dansana PK, Giri J, Deveshwar P, Arora R, Agarwal P, Khurana JP, Kapoor S, Tyagi AK (2011) Modulation of transcription factor and metabolic pathway genes in response to water-deficit stress in rice. Funct Integr Genomics 11:157–178

  78. Roferos LT, Butardo VM, Fitzgerald MA, Juliano BO (2008) Association between alleles of the waxy gene and traits of grain quality in Philippine Seed Board rice varieties. Philipp Agric Sci 91:334–337.

  79. Roumen EC (1992) Effect of leaf age on components of partial resistance in rice to leaf blast. Euphytica 63:271–279

  80. Sallaud C, Lorieux M, Roumen E, Tharreau D, Berruyer R, Svestasrani P, Garsmeur O, Ghesquiere A, Notteghem JL (2003) Identification of five new blast resistance genes in the highly blast-resistant rice variety IR64 using a QTL mapping strategy. Theor Appl Genet 106:794–803

  81. Schatz MC, Maron LG, Stein JC, Wences AH, Gurtowski J, Biggers E, Lee H, Kramer M, Antoniou E, Ghiban E, Wright MH, Chia JM, Ware D, McCouch SR, McCombie WR (2014) Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol 15:506. https://doi.org/10.1186/s13059-014-0506-z

  82. Septiningsih EM, Hidayatun N, Sanchez DL, Nugraha Y, Carandang J, Pamplona AM, Collard BCY, Ismail AM, Mackill DJ (2014) Accelerating the development of new submergence tolerant rice varieties: the case of Ciherang-Sub1 and PSB Rc18-Sub1. Euphytica 202:259–268

  83. Septiningsih EM, Pamplona AM, Sanchez DL, Neeraja CN, Vergara GV, Heuer S, Ismail AM, Mackill DJ (2009) Development of submergence tolerant rice cultivars: the Sub1 locus and beyond. Ann Bot 103:151–160

  84. Septiningsih EM, Prasetiyono J, Lubis E, Tai TH, Tjubaryat T, Moeljopawiro S, McCouch SR (2003) Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor Appl Genet 107:1419–1432

  85. Shanmugavadivel PS, Mithra SVA, Prakash C, Ramkumar MK, Tiwari R, Mohapatra T, Singh NK (2017) High resolution mapping of QTLs for heat tolerance in rice using a 5K SNP array. Rice 10:28

  86. Sharma R, Agarwal P, Ray S, Deveshwar P, Sharma P, Sharma N, Nijhawan A, Jain M, Singh AK, Singh VP, Khurana JP, Tyagi AK, Kapoor S (2012) Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice. Funct Integr Genomics 12:229–248

  87. Shrestha R, Al-Shugeairy Z, Al-Ogaidi F, Munasinghe M, Radermacher M, Vandenhirtz J, Price AH (2014) Comparing simple root phenotyping methods on a core set of rice genotypes. Plant Biol 16:632–642

  88. Singh N, Dang TTM, Vergara GV, Pandey DM, Sanchez D, Neeraja CN, Septiningsih EM, Mendioro M, Tecson-Mendoza EM, Ismail AM, Mackill DJ, Heuer S (2010) Molecular marker survey and expression analyses of the rice submergence-tolerance gene SUB1A. Theor Appl Genet 121:1441–1453

  89. Singh R, Singh Y, Xalaxo S, Verulkar S, Yadav N, Singh S, Singh N, Prasad KSN, Kondayya K, Rao PVR, Rani MG, Anuradha T, Suraynarayana Y, Sharma PC, Krishnamurthy SL, Sharma SK, Dwivedi JL, Singh AK, Singh PK, Nilanjay, Singh NK, Kumar R, Chetia SK, Ahmad T, Rai M, Perraju P, Pande A, Singh DN, Mandal NP, Reddy JN, Singh ON, Katara JL, Marandi B, Swain P, Sarkar RK, Singh DP, Mohapatra T, Padmawathi G, Ram T, Kathiresan RM, Paramsivam K, Nadarajan S, Thirumeni S, Nagarajan M, Singh AK, Vikram P, Kumar A, Septiningshih E, Singh US, Ismail AM, Mackill D, Singh NK (2016) From QTL to variety-harnessing the benefits of QTLs for drought, flood and salt tolerance in mega rice varieties of India through a multi-institutional network. Plant Sci 242:278–287

  90. Singh US, Dar MH, Singh S, Zaidi NW, Bari MA, Mackill DJ, Collard BCY, Singh VN, Singh JP, Reddy JN, Singh RK, Ismail AM (2013) Field performance, dissemination, impact and tracking of submergence tolerant (Sub1) rice varieties in South Aisa. SABRAO J Breed Genet 45:112–131

  91. Sreewongchai T, Toojinda T, Thanintorn N, Kosawang C, Vanavichit A, Tharreau D, Sirithunya P (2010) Development of elite indica rice lines with wide spectrum of resistance to Thai blast isolates by pyramiding multiple resistance QTLs. Plant Breed 129:176–180

  92. Swamy BPM, Ahmed HU, Henry A, Mauleon R, Dixit S, Vikram P, Tilatto R, Verulkar SB, Perraju P, Mandal NP, Variar M, Robin S, Chandrababu R, Singh ON, Dwivedi JL, Das SP, Mishra KK, Yadaw RB, Aditya TL, Karmakar B, Satoh K, Moumeni A, Kikuchi S, Leung H, Kumar A (2013) Genetic, physiological, and gene expression analyses reveal that multiple QTL enhance yield of rice mega-variety IR64 under drought. PLOS ONE 8(5): e62795. https://doi.org/10.1371/journal.pone.0062795

  93. Tagle AG, Fujita D, Ebron LA, Telebanco-Yanoria MJ, Sasaki K, Ishimaru T, Fukuta Y, Kobayashi N (2016) Characterization of QTL for unique agronomic traits of new-plant-type rice varieties using introgression lines of IR64. Crop J 4:12–20

  94. Teng B, Zeng RZ, Wang YC, Liu ZQ, Zhang ZM, Zhu HT, Ding XH, Li WT, Zhang GQ (2012) Detection of allelic variation at the Wx locus with single-segment substitution lines in rice (Oryza sativa L.) Mol Breed 30:583–595

  95. Thakur S, Singh PK, Rathour R, Variar M, Prashanthi SK, Singh AK, Singh UD, Chand D, Singh NK, Sharma TR (2013) Positive selection pressure on rice blast resistance allele Piz-t makes it divergent in Indian land races. J Plant Interact 8:34–44

  96. Toledo AMU, Ignacio JCI, Casal Jr C, Gonzaga ZJ, Mendioro MS, Septiningsih EM (2015) Development of improved Ciherang-Sub1 having tolerance to anaerobic germination conditions. Plant Breed Biotech 3:77–87

  97. Toriyama K, Kazama T (2016) Development of cytoplasmic male sterile IR24 and IR64 using CW-CMS/Rf17 system. Rice 9:22

  98. Trijatmiko KR, Dueñas C, Tsakirpaloglou N, Torrizo L, Arines FM, Adeva C, Balindong J, Oliva N, Sapasap MV, Borrero J, Rey J, Francisco P, Nelson A, Nakanishi H, Lombi E, Tako E, Glahn RP, Stangoulis J, Chadha-Mohanty P, Johnson AAT, Tohme J, Barry G, Slamet-Loedin IH (2016) Biofortified indica rice attains iron and zinc nutrition dietary targets in the field. Sci Rep 6:19792

  99. Uga Y, Sugimoto K, Ogawa S, Rane J, Ishitani M, Hara N, Kitomi Y, Inukai Y, Ono K, Kanno N, Inoue H, Takehisa H, Motoyama R, Nagamura Y, Wu J, Matsumoto T, Takai T, Okuno K, Yano M (2013) Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions. Nat Genet 45:1097–1102

  100. Ujiie K, Yamamoto T, Yano M, Ishimaru K (2016) Genetic factors determining varietal differences in characters affecting yield between two rice (Oryza sativa L.) varieties, Koshihikari and IR64. Genet Resour Crop Evol 63:97–123

  101. Vejchasarn P, Lynch JP, Brown KM (2016) Genetic variability in phosphorus responses of rice root phenotypes. Rice 9:29

  102. Venuprasad R, Impa SM, Gowda RPV, Atlin GN, Serraj R (2011) Rice near-isogenic-lines (NILs) contrasting for grain yield under lowland drought stress. Field Crop Res 123:38–46

  103. Verdier V, Cruz CV, Leach JE (2012) Controlling rice bacterial blight in Africa: needs and prospects. J Biotechnol 159:320–328

  104. Vikram P, Swamy BP, Dixit S, Singh R, Singh BP, Miro B, Kohli A, Henry A, Singh NK, Kumar A (2015) Drought susceptibility of modern rice varieties: an effect of linkage of drought tolerance with undesirable traits. Sci Rep 5:14799

  105. Wang W-S, Zhao X-Q, Li M, Huang L-Y, Xu J-L, Zhang F, Cui Y-R, Fu B-Y, Li Z-K (2016) Complex molecular mechanisms underlying seedling salt tolerance in rice revealed by comparative transcriptome and metabolomic profiling. J Exp Bot 67:405–419

  106. Wei FJ, Tsai YC, Wu HP, Huang LT, Chen YC, Chen YF, Wu CC, Tseng YT, Hsing YIC (2016) Both Hd1 and Ehd1 are important for artificial selection of flowering time in cultivated rice. Plant Sci 242:187–194

  107. Wissuwa M, Kretzschmar T, Rose TJ (2016) From promise to application: root traits for enhanced nutrient capture in rice breeding. J Exp Bot 67:3605–3615

  108. Wu JL, Wu C, Lei C, Baraoidan M, Bordeos A, Madamba MR, Ramos-Pamplona M, Mauleon R, Portugal A, Ulat VJ, Bruskiewich R, Wang G, Leach J, Khush G, Leung H (2005) Chemical- and irradiation-induced mutants of indica rice IR64 for forward and reverse genetics. Plant Mol Biol 59:85–97

  109. Wu P, Luo A, Zhu J, Yang J, Huang N, Senadhira D (1997) Molecular markers linked to genes underlying seedling tolerance for ferrous iron toxicity. Plant Soil 196:317–320

  110. Xie F, He Z, Esguerra M, Qiu F, Ramanathan V (2014) Determination of heterotic groups for tropical Indica hybrid rice germplasm. Theor Appl Genet 127:407–417

  111. Ye C, Tenorio F, Redoña E, Morales-Cortezano P, Cabrega G, Jagadish KV, Gregorio G (2015) Fine-mapping and validating qHTSF4.1 to increase spikelet fertility under heat stress at flowering in rice. Theor Appl Genet 128:1507–1517

  112. Yoshida S (1981) Rice crop science. Int. Rice Res. Inst, Los Baños, Philippines

  113. Zenna NS, Cabauatan PQ, Baraoidan M, Leung H, Choi IR (2008) Characterization of a putative rice mutant for reaction to rice tungro disease. Crop Sci 48:480–486

  114. Zenna NS, Cruz FCS, Javier EL, Duka IA, Barrion AA, Azzam O (2006) Genetic analysis of tolerance to rice tungro bacilliform virus in rice (Oryza sativa L.) through agroinoculation. J Phytopathol 154:197–203

  115. Zhang ZJ, Li M, Fang YW, Liu FC, Lu Y, Meng QC, Jun CC, Yi XH, Gu MH, Yan CJ (2012) Diversification of the waxy gene is closely related to variations in rice eating and cooking quality. Plant Mol Biol Rep 30:462–469

  116. Zhao DL, Atlin GN, Amante M, Cruz MTS, Kumar A (2010) Developing aerobic rice cultivars for water-short irrigated and drought-prone rainfed areas in the tropics. Crop Sci 50:2268–2276

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    • David J. Mackill

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