QTL MAPPING FOR SUBMERGENCE TOLERANCE IN RICE
In lowland regions of Asia where flooding is common, submergence tolerance has always been an important trait for rice breeding. However, efforts to introgress this trait into agronomically viable lines were unsuccessful until the 1990s, when Quantitative Trait Loci (QTL) for submergence tolerance were mapped that allowed breeders to employ markers in selection. Sub1A, mapped to chromosome 9 of the rice genome, emerged as the gene primarily responsible for conferring tolerance. The tolerance specific allele Sub1A-1 was introgressed into a widely grown Asian rice variety in 2006, marking the first submergence tolerant cultivar widely adopted by farmers. This discovery of Sub1A as the primary contributor to submergence tolerance led to the release of many tolerant cultivars which ultimately improved yield in flood-ridden regions of the world. Efforts to map and characterize more submergence tolerance QTL are currently ongoing and will lead to the development of cultivars better adapted to an increased risk of submergence due to changing climatic conditions.
Submergence tolerance in rice is a highly important trait in cultivars grown in lowland areas of Asia where flooding is common. The Food and Agriculture Organization of the United Nations (FAO), found that 53% of crop loss due to natural disasters is caused by flooding worldwide (Baas, Trujillo, et al., 2015). Climate change is expected to cause a doubling in flood frequency for approximately 430 km2 of flood prone cropland, and the most adverse impacts are projected to be in Asia (Arnell and Gosling, 2016), where over 90% of rice is produced (Rai, Van Tran, et al., 2003). In the past 50 years, much progress has been made in increasing submergence tolerance in rice cultivars via the use of QTL mapping, trait introgression, and marker assisted selection. The locus Sub1 on chromosome 9 of the rice genome was identified in 1996 and accounted for approximately 69% of the phenotypic variance for submergence tolerance (Xu and Mackill, 1996). Over the next ten years, characterization and fine mapping of the Sub1 locus, in addition to marker assisted selection efforts (Kamolsukyunyong, Ruanjaichon, et al., 2001), (Toojinda, Siangliw, et al., 2003), (Xu, Xu, et al., 2000) led to the release of the first submergence tolerant cultivar of japonica variety Liaogeng (Xu, Xu, et al., 2006). Since then, the submergence tolerance allele of Sub1A has been introgressed into many previously intolerant rice varieties and has led to an incremental increase of about 0.8 million tons of paddy rice each year since the adoption of Sub1 varieties (Mackill, Ismail, et al., 2012). In this review, the methodology leading to the characterization and introgression of the Sub1 locus into widely used rice varieties will be discussed, in addition to current trends and future outlooks on breeding for submergence tolerance in rice, as well as applicability to other important crops.
Breeding for submergence tolerance in rice before Sub1
Submergence leads to reduced yield in rice mostly due to inhibition of photosynthesis, as light intensity is reduced under water. Also, ethylene accumulation and reduced respiration due to lack of oxygen lead to carbohydrate depletion (Setter, Jackson, et al., 1988). Due to the importance of submergence tolerance for cultivars at an increased risk of long-term submergence, breeding for this trait has been an ongoing effort since the dawn of modern history. In 1975, a simple screening method for submergence tolerant varieties was described (Vergara and Mazaredo, 1975) in which rice is directly seeded in greenhouse tanks, then screened after being submerged for 7 days and scored five days after the water was drained. This resulted in identification of 26 submergence tolerant cultivars. In 1982, various methods were tested in identifying submergence tolerant cultivars. In all tests, accessions FR13A, Thavalu 15314, Thavalu 15325, and Kurkaruppan performed well (HilleRisLambers and Vergara, 1982), (Mackill, 1996). The International Rice Research Institute (IRRI) has consistently used FR13A, (a flood tolerant cultivar from Orissa) as a tolerant check for scoring submergence tolerance in rice since its identification as an extremely tolerant accession (Vergara and Mazaredo, 1975) (HilleRisLambers and Vergara, 1982). Breeding efforts in the 1980s aimed to use FR13A as a submergence tolerance donor to well established, agronomically viable varieties. Viable donors such as FR13A, IR42, IR17494-32-1and RD19 were identified in 1985 (Mohanty and Khush, 1985), and inheritance of tolerance to submergence was investigated and found to follow the additive-dominance model, and additive and non-additive gene effects were highly significant (Haque, Hille Ris Lambers, et al., 1989). The breeding line IR49830-7-1-2-2 (derived from FR13A) was used for production of semi-dwarf varieties in the 1990s, as it was the only submergence tolerant line with high yield (Mackill, Amante, et al., 1993). Efforts to introduce submergence tolerance into established lowland semi-dwarf lines resulted in a few successful cultivars, but conventional breeding efforts produced cultivars with reduced yield that were not as desirable to farmers (Mackill, 1996). Submergence tolerance was later found to be controlled by a single dominant gene (Mishra, Senadhira, et al., 1996) (Xu and Mackill, 1996), which became known as the Sub1 locus that gave rise to modern-day submergence tolerant cultivars.
Discovery of rice locus Sub1 and introgression into agronomically productive cultivars
Despite the development of submergence tolerant lines in the 1980s, little progress was made in releasing an agronomically relevant cultivar that would be widely adopted by farmers. In 1996, a major QTL for submergence tolerance was mapped on chromosome 9 of the rice genome using random-amplified polymorphic DNA and RFLP (restriction fragment length polymorphism) markers in an F2 population and resulting G3 families of a cross between a tolerant Indica donor line (IR40931-26, derived from FR13A), and an intolerant japonica line (PI543851) (Xu and Mackill, 1996). This locus accounted for ~70% of the phenotypic variation. A high-resolution linkage map was later developed using bulked segregant analysis to identify AFLP (amplified fragment length polymorphism) makers within 0.2 cM of the Sub1 locus (Xu, Xu, et al., 2000). Other studies further confirmed the existence of a major QTL for submergence tolerance on chromosome 9 (Kamolsukyunyong, Ruanjaichon, et al., 2001), (Nandi, Subudhi, et al., 1997), (Siangliw, Toojinda, et al., 2003), and identified minor loci contributing to submergence tolerance on chromosomes 1, 2, 5, 7, 10, and 11 which were specific to particular environmental conditions or genetic backgrounds (Toojinda, Siangliw, et al., 2003). Marker assisted selection also provided opportunities for introgressing the submergence tolerance trait from FR13A into agronomically relevant cultivars (Siangliw, Toojinda, et al., 2003) (Toojinda, Tragoonrung, et al., 2005), but this process was time-consuming (>2 years) and less precise since the amount of genetic material transferred from the donor parent was not highly monitored and primarily relied on conventional breeding techniques. In 2006, a study using a mapping population of 4,022 plants derived from a cross between IR40931-26 (tolerant, indica), and intolerant japonica cultivar M-202, mapped Sub1 to a 0.06 cM interval on chromosome 9 (Xu, Xu, et al., 2006). This interval contained three Ethylene Response Factor (ERF) domains (Sub1A, Sub1B, and Sub1C) and ten non-ERF genes and spanned ~182kb. Quantification of gene transcript levels showed that Sub1A was expressed at higher levels in the tolerant line, while the other genes showed either minimal expression or no expression during submergence (Xu, Xu, et al., 2006). Of two Sub1A alleles (Sub1A-1 and Sub1A-2) possession of Sub1A-1 was found to be highly correlated with submergence tolerance. Using marker assisted selection, the Sub1A gene was introgressed into an established Indian cultivar, Swarma, which lacked Sub1A entirely (Xu, Xu, et al., 2006). Selection for individuals with the fewest FR13A derived chromosomal segments resulted in the first introgression of Sub1A into a widely grown Asian rice cultivar, conferring submergence tolerance while also maintaining important agronomic properties such as high yield and grain quality from the recurrent parent.
Breeding for submergence tolerance after Sub1A
The identification of Sub1A as the allele primarily responsible for conferring submergence tolerance led to the development of more tolerant mega-varieties and use of improved breeding techniques to achieve introgression. Marker-assisted backcrossing (MAB) used to rapidly and precisely transfer the Sub1A locus from IR49830-7-1-2-2 (FR13A derived line) into the mega-variety Swarna (Neeraja, Maghirang-Rodriguez, et al., 2007) within a 2-3 year period. This backcrossing technique allowed breeders to screen for individuals that were heterozygous for the Sub1 locus, homozygous (recombinant) for the recipient allele, and had the fewest markers derived from the donor genome in the generation derived from crossing the F1 generation back to Swarna (Neeraja, Maghirang-Rodriguez, et al., 2007). The resulting progeny were then backcrossed with Swarna a second time, and the same screening and backcrossing method was used to develop the second and third backcross generations. In addition to demonstrating that MAB could be used to efficiently transfer the submergence-tolerance-conferring loci into an agronomically important variety while retaining minimal genetic material from the donor parent, tightly linked flanking markers were identified to further stimulate breeding efforts for submergence tolerance in other mega-varieties (Neeraja, Maghirang-Rodriguez, et al., 2007). The MAB technique used in this study was used in a subsequent study to successfully develop five submergence tolerant mega-varieties (derived from Swarna, S. Mahsuri, IR64, TDK1, and CR1009) within a period of three years (Septiningsih, Pamplona, et al., 2009). Interestingly, differing levels of tolerance were observed among each Sub1 line. Furthermore, survival percentages after submergence seemed to be dependent on expression level of Sub1A (Septiningsih, Pamplona, et al., 2009). This suggested that more work could be done to identify additional mechanisms controlling submergence tolerance, such as identification of genes affecting expression of Sub1A, but that a MAB strategy could be used to successfully develop submergence tolerant mega-varieties in a <3 year time-frame. MAB has since been used to develop many varieties of Sub1 rice (Iftekharuddaula, Newaz, et al., 2011) (Cuc, Huyen, et al., 2012) (Khanh, Linh, et al., 2013).
Future directions and conclusions
Current Sub1 cultivars have led to yield advantages from 1 to 3 t/ha, and have been widely adopted by farmers in India, Bangladesh and Nepal due to widespread international collaboration between NGOs, governmental entities, and seed producers (Singh, Dar, et al., 2013). In 2014, Sub1 varieties were expected to cover >5 million ha (Singh, Dar, et al., 2013).
Despite successful efforts to develop submergence tolerant cultivars of rice, efforts to identify more submergence-related QTL and characterize expression patterns of Sub1 are currently ongoing. Additonal QTL for submergence tolerance were mapped on chromosomes 1, 8, and 10 with R2 values of 23.33, 14.98, and 15.80 % respectively (Gonzaga, Carandang, et al., 2016) (Gonzaga, Carandang, et al., 2017). Interestingly, lines without SUB1, but containing these additional QTLs were still tolerant (up to 95 % survival rate), showing that there is still potential to enhance tolerance beyond SUB1 (Gonzaga, Carandang, et al., 2016).
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