David J. Mackill

Identifying novel QTLs for submergence tolerance in rice cultivars IR72 and Madabaru

Short-term submergence is a recurring problem in many rice production areas. The SUB1 gene, derived from the tolerant variety FR13A, has been transferred to a number of widely grown varieties, allowing them to withstand complete submergence for up to 2xa0weeks. However, in areas where longer-term submergence occurs, improved varieties having higher tolerance levels are needed. To search for novel quantitative trait loci (QTLs) from other donors, an F2:3 population between IR72 and Madabaru, both moderately tolerant varieties, was investigated. After a repeated phenotyping of 466 families under submergence stress, a subset of 80 families selected from the two extreme phenotypic tails was used for the QTL analysis. Phenotypic data showed transgressive segregation, with several families having an even higher survival rate than the FR13A-derived tolerant check (IR40931). Four QTLs were identified on chromosomes 1, 2, 9, and 12; the largest QTL on chromosome 1 had a LOD score of 11.2 and R2 of 52.3%. A QTL mapping to the SUB1 region on chromosome 9, with a LOD score of 3.6 and R2 of 18.6%, had the tolerant allele from Madabaru, while the other three QTLs had tolerant alleles from IR72. The identification of three non-SUB1 QTLs from IR72 suggests that an alternative pathway may be present in this variety that is independent of the ethylene-dependent pathway mediated by the SUB1A gene. These novel QTLs can be combined with SUB1 using marker assisted backcrossing in an effort to enhance the level of submergence tolerance for flood-prone areas.

QTL mapping and confirmation for tolerance of anaerobic conditions during germination derived from the rice landrace Ma-Zhan Red

Wide adoption of direct-seeded rice practices has been hindered by poorly leveled fields, heavy rainfall and poor drainage, which cause accumulation of water in the fields shortly after sowing, leading to poor crop establishment. This is due to the inability of most rice varieties to germinate and reach the water surface under complete submergence. Hence, tolerance of anaerobic conditions during germination is an essential trait for direct-seeded rice cultivation in both rainfed and irrigated ecosystems. A QTL study was conducted to unravel the genetic basis of tolerance of anaerobic conditions during germination using a population derived from a cross between IR42, a susceptible variety, and Ma-Zhan Red, a tolerant landrace from China. Phenotypic data was collected based on the survival rates of the seedlings at 21xa0days after sowing of dry seeds under 10xa0cm of water. QTL analysis of the mapping population consisting of 175 F2:3 families genotyped with 118 SSR markers identified six significant QTLs on chromosomes 2, 5, 6, and 7, and in all cases the tolerant alleles were contributed by Ma-Zhan Red. The largest QTL on chromosome 7, having a LOD score of 14.5 and an R2 of 31.7xa0%, was confirmed using a BC2F3 population. The QTLs detected in this study provide promising targets for further genetic characterization and for use in marker-assisted selection to rapidly develop varieties with improved tolerance to anaerobic condition during germination. Ultimately, this trait can be combined with other abiotic stress tolerance QTLs to provide resilient varieties for direct-seeded systems.

Stress Tolerant Rice Varieties for Adaptation to a Changing Climate

Rising temperatures due to accumulation of greenhouse gasses are expected to result in declining rice yields in the tropics. In addition to the direct effect of high temperature in reducing yields, a rise in sea level coupled with more erratic and extreme weather events will result in reduced yields and increase the risks of rice farming. The abiotic stresses that are anticipated to worsen as the consequences of climate change include high temperature, drought, flooding and salinity stresses. While high temperature is not currently a major problem, the other stresses are already widespread yield limiting factors in the unfavorable environments of tropical Asia. Incorporating stress tolerance into high-yielding varieties has proven to be a very effective approach to developing varieties that can cope with these situations. These successes provide optimism that the problem of climate change can be addressed partially through development and dissemination of adapted germplasm.

Accelerating the development of new submergence tolerant rice varieties: the case of Ciherang-Sub1 and PSB Rc18-Sub1

Submergence is an escalating problem in many rice producing areas. A submergence tolerance gene, SUB1, derived from FR13A was previously introduced into six mega varieties through marker assisted backcrossing (MABC) with the final product selected at the BC2 or BC3 generation. Their phenotype was similar to the original varieties, but they could withstand complete inundation for up to 2 or 3xa0weeks. Several of these varieties have been released in South and Southeast Asia; nonetheless the development of additional submergence tolerant varieties is indispensable to provide farmers with diverse choices of varieties that are preferable for the local needs and to avoid ecological vulnerability due to planting only one variety across vast areas. To accelerate this effort, the SUB1 gene has now been introgressed into two new popular varieties from Indonesia and the Philippines, i.e. Ciherang and PSB Rc18, respectively, through MABC using only one backcross (BC1) with the previously developed IR64-Sub1 as the donor. Since this new donor is closely related to both recurrent parents, a more rapid MABC approach can be pursued due to the similarity of genetic backgrounds. Using this strategy, new submergence tolerant varieties Ciherang-Sub1 and PSB Rc18-Sub1 were developed in less than 2xa0years, presenting a promising approach to convert additional popular varieties in the future.

Mapping additional QTLs from FR13A to increase submergence tolerance in rice beyond SUB1

AbstractnSubmergence is a common naturally occurring disaster in rice production in South and Southeast Asia. The development of mega-varieties with tolerance conferred by the SUB1 gene on chromosome 9 derived from FR13A that can withstand up to 2xa0weeks of complete submergence has been one of the best solutions. However, the recent severe conditions of flooding because of climate change, which has been predicted to become worse in the near future, calls for the development of an improved variety with superior tolerance of submergence. To search for novel quantitative trait loci (QTLs) that can complement the SUB1 gene, recombinant inbred lines (RILs) derived from an IR42/FR13A mapping population were explored. Five QTLs were detected on chromosomes 1, 4, 8, 9, and 10, four of which were from FR13A and one was from IR42. The study confirms the SUB1 QTL on chromosome 9 with a maximum LOD score of 19.51 and R2 of 53.60xa0%. Additional novel QTLs coming from FR13A on chromosomes 1, 8, and 10 were identified with LOD scores of 5.16, 3.56, and 3.85 and R2 of 23.33, 14.98, and 15.80xa0%, respectively. Interestingly, lines without SUB1 were still tolerant, with a maximum survival rate up to 95xa0% because of the presence of these additional QTLs. The non-SUB1 QTLs identified have great potential to enhance tolerance as evidenced by the superior tolerance of FR13A compared with that of the developed Sub1 lines. By transferring selected potential QTLs that are mostly additive to SUB1, it is hoped that crop damage from severe flooding can be significantly decreased.

Evaluation of a M-202 × Oryza nivara advanced backcross mapping population for seedling vigor, yield components and quality

AbstractOryza nivara, the ancestral species of cultivated rice (O. sativa), has been the source of novel alleles for resistance to biotic and abiotic stress lost during domestication. Interspecific advanced backcross (ABC) populations permit the introgression of desirable alleles from the wild species into O. sativa and allow traits to be mapped to chromosomal regions by QTL mapping. An ABC population was developed by crossing M-202, a California medium grain, temperate japonica cultivar with O. nivara (IRGC100195). The population has 177 BC2F2:5 progeny lines and was evaluated for 17 traits including seedling vigor under cool temperature (mesocotyl, coleoptile, shoot and root lengths), agronomic (days to heading, plant height, culm angle, panicle type), yield components (panicles per plant, panicle length, florets and seeds per panicle, 100-seed weight) and quality [kernel length and width, apparent amylose content (AAC), alkali spreading value (ASV)]. Most exciting was that the O. nivara parent improved seedling vigor by increasing both the coleoptile and shoot lengths. Wild donor alleles increased the panicles per plant and seed weight, but M-202 alleles improved fertility. For one locus, the O. nivara alleles accounted for increased kernel length even though this parent had smaller seeds than M-202. The AAC mapped to the WAXY locus and ASV to the ALK locus, with most progeny being similar to M-202 for these quality traits. Select progeny lines could be useful for improving seedling vigor. This interspecific population is the first in the background of a U.S. temperate japonica rice cultivar.n