Increasing flooding tolerance in rice: combining tolerance of submergence and of stagnant flooding.

BACKGROUND AND AIMS: Rice ecosystems in the tropical coastal areas are subject to two types of flooding stress: transient complete submergence and long-term water stagnation (stagnant flooding). Here, we aimed to dissect the mechanisms for stagnant flooding tolerance of rice genotypes carrying SUB1, a quantitative trait locus for submergence tolerance. METHODS: We screened 80 elite genotypes under stagnant flooding stress in the lowland rice fields in the wet and dry seasons, and examined the tolerance mechanisms of promising genotypes for the two following seasons. KEY RESULTS: Yield reduction under stagnant flooding averaged 48 % in the dry season and 89 % in the wet season. Elite genotypes carrying SUB1 showed 49 % lower yield than those without SUB1 under stagnant flooding, with no differences under shallow water conditions. However, we identified a few high-yielding Sub1 genotypes that were as tolerant of stagnant flooding as a reference genotype that lacked SUB1. These genotypes had intermediate stature with more shoot elongation in response to rising water than a moderately tolerant Sub1 reference variety, resulting in greater canopy expansion and higher yield. It was important to increase lodging resistance, since plant height >140 cm increased lodging under stagnant flooding. The culm diameter was closely associated with culm strength; reduced aerenchyma formation and increased lignin accumulation in the culm should increase lodging resistance. CONCLUSIONS: The study demonstrated a successful combination of submergence and stagnant flooding tolerance in a rice breeding programme, and identified elite Sub1 genotypes that also tolerate stagnant flooding. Our results will support genetic improvement of Sub1 varieties for stagnant flooding tolerance.

Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines.

Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.

Comparison of phenotypic versus marker-assisted background selection for the SUB1 QTL during backcrossing in rice.

Marker assisted backcrossing has been used effectively to transfer the submergence tolerance gene SUB1 into popular rice varieties, but the approach can be costly. The selection strategy comprising foreground marker and phenotypic selection was investigated as an alternative. The non-significant correlation coefficients between ranking of phenotypic selection and ranking of background marker selection in BC(2)F(1), BC(3)F(1) and BC(3)F(2) generations indicated inefficiency of phenotypic selection compared to marker-assisted background selection with respect to recovery of the recipient genome. In addition, the introgression size of the chromosome fragment containing SUB1 was approximately 17 Mb, showing the effects of linkage drag. The significant correlation coefficient between rankings of phenotypic selection with the percentage of recipient alleles in the BC(1)F(1) generation suggested that background selection could be avoided in this generation to minimize the genotyping cost. The phenotypically selected best plant of the BC(3)F(1) generation was selfed and backcross recombinant lines were selected in the resulting BC(3)F(4) generation. The selection strategy could be appropriate for the introgression of SUB1 QTL in countries that lack access to high-throughput genotyping facilities.

Identification and characterization of high-yielding, short-duration rice genotypes for tropical Asia.

Previous efforts to increase the yield of tropical rice (Oryza sativa L.) have focused on medium-duration varieties. However, there is increasing demand for high-yielding short-duration varieties that can adapt to intensified cropping systems and climate change. Our goal was to identify physiological traits associated with high yield in elite short-duration genotypes suitable for tropical Asia. We conducted field experiments in five consecutive growing seasons at the International Rice Research Institute, the Philippines. We selected genotypes in the first two seasons, then performed a detailed characterization of the most promising genotypes in the following three seasons. Of the 50 advanced-generation genotypes, three had consistently high yield and early maturity, with yields 11 to 38% higher than that of 'IRRI104' ('IR50404-57-2-2-3'), a short-duration variety that is widely grown in Southeast Asia. These genotypes were 20 to 32 cm taller than IRRI104. We found that for grain growth, low source capacity, defined as stem nonstructural carbohydrates at heading plus biomass accumulation after heading, was the major factor for the low yield of IRRI104. Although sink capacity (spikelets m-2 × grain weight) in the promising genotypes was comparable to that of IRRI104, they had a 25 to 53% higher source-sink ratio (source capacity/sink capacity) than IRRI104, which was attributed to larger leaf area and greater biomass accumulation during the grain-filling stage. This result suggests that slight changes in plant development to promote height combined with increased leaf area around heading would improve the yield of short-duration rice varieties in tropical Asia.

Review: Improving global food security through accelerated plant breeding.

With an expected 9 billion people by 2050 and average income on the rise in the developing world, meeting future food demand will be a challenge. Climate change, urbanisation and land degradation are putting further pressure on the food supply. The multifaceted and self-reinforcing nature of these challenges calls for a fundamental transformation of the food system. In the past, crop improvement through breeding has been the major tool to lift people out of poverty and increase global food supply. To adequately address these food security challenges, new improved crop varieties need to be developed and reach farmers sooner as a partial solution. In this review, we focus on various proven conventional and biotechnological accelerating plant breeding methods that do not require genetic engineering or gene editing. We pay specific attention to the feasibility for implementation by national agricultural research systems in developing countries in the short term. We argue that postponing technologies that can accelerate breeding makes no economic sense and justify immediate adoption of accelerated breeding practices in the public sector. Considering a wide range of factors including the economics of accelerated breeding, we advocate the use of a method called rapid generation advance (RGA) as the most feasible method for accelerating breeding in the public sector.

Global survey data on rice breeders' characteristics and willingness to adopt alternative breeding methods.

The data presented in this article contains information on 189 rice breeders from 51 rice-growing countries around the world. Firstly, this unique dataset permits to lay down a baseline of currently used breeding methods. Secondly, the data allow to make an assessment of the adoption behavior of rice breeders towards alternative breeding methods, and in specific rapid generation advance. A global online survey in Google Forms was conducted to obtain information about the different aspects of the adoption process. Both the raw and cleaned data are made available, along with Stata code to promote further research into adoption of breeding methods by public and private breeding institutes.

Global survey of rice breeders to investigate characteristics and willingness to adopt alternative breeding methods.

BACKGROUND: Despite the critical role rice breeders play to ensure food security, there is a lack of information regarding their current socio-economic characteristics, constraints and attitudes towards technology adoption. Some key concepts like budget, experience, local ecosystems, level of education and even main breeding method have hardly been surveyed in the past. This not only clouds any policy making regarding scientists in national agricultural research programmes, it also makes it difficult to assess the needs and problems local rice breeders face around the world. METHODS: A global online survey was conducted reaching 189 rice breeders from 51 rice-growing countries around the world. The questionnaire was structured according to an adoption framework we proposed from the literature. We specifically investigated their attitudes to adopting an alternative breeding method called rapid generation advance (RGA) (also known as single seed descent). To provide some historical perspective, we compare our results with those reported by Hargrove (Rice breeders in Asia: a ten-country survey of their backgrounds, attitudes, and use of genetic materials, 1978), the only published survey on rice breeders. RESULTS: Overall, rice breeders are highly educated and have a long experience with their main breeding method. However, a gender gap with respect to education seems to persist. Large variation in resources (staff, land and budget) was observed with a small number of resource-rich institutes and a large number of resource-poor institutes. Most rice breeders are focused on breeding for irrigated conditions. Most breeders have a relatively high degree of risk taking and time preference towards shorter breeding cycles. The majority of breeders are aware of RGA and its benefits with more than half having observed RGA in practice. Finally, breeders are confident in the RGA technique and estimate its resource savings to be substantial. CONCLUSIONS: Breeders' willingness to adopt RGA was remarkably high. Surprisingly, adoption of RGA remains low (4% as main method). This may suggest that the benefits of using the RGA method still need to be further demonstrated in rice breeding. Our results could be useful to develop targeted extension material or interventions for implementing new technologies, which could be useful to high-level agricultural managers, international research centres and aid agencies.

Identification of QTLs for yield and agronomic traits in rice under stagnant flooding conditions.

BACKGROUND: Stagnant flooding, where water of 25-50 cm remains until harvest time, is a major problem in rainfed lowland areas. Most of the Sub1 varieties, which can withstand around 2 weeks of complete submergence, perform poorly in these conditions. Hence, varieties tolerant of stagnant flooding are essential. RESULTS: This paper presents the first study to map QTLs associated with tolerance to stagnant flooding, along with a parallel study under normal irrigation, using an F7 mapping population consisting of 148 RILs derived from a cross of Ciherang-Sub1 and the stagnant-flooding tolerant line IR10F365. Phenotypic data was collected for 15 key traits under both environments. Additionally, survival rate was measured under stress conditions. Genotyping was performed using the Illumina Infinium genotyping platform with a 6 K SNP chip, resulting in 469 polymorphic SNPs. Under stress and irrigated conditions, 38 and 46 QTLs were identified, respectively. Clusters of QTLs were detected in both stress and normal conditions, especially on chromosomes 3 and 5. CONCLUSIONS: Unique and common QTLs were identified and their physiological consequences are discussed. These beneficial QTLs can be used as targets for molecular breeding and can be further investigated to understand the underlying molecular mechanisms involved in stagnant flooding tolerance in rice.

Root Traits Enhancing Rice Grain Yield under Alternate Wetting and Drying Condition.

Reducing water requirements and lowering environmental footprints require attention to minimize risks to food security. The present study was conducted with the aim to identify appropriate root traits enhancing rice grain yield under alternate wetting and drying conditions (AWD) and identify stable, high-yielding genotypes better suited to the AWD across variable ecosystems. Advanced breeding lines, popular rice varieties and drought-tolerant lines were evaluated in a series of 23 experiments conducted in the Philippines, India, Bangladesh, Nepal and Cambodia in 2015 and 2016. A large variation in grain yield under AWD conditions enabled the selection of high-yielding and stable genotypes across locations, seasons and years. Water savings of 5.7-23.4% were achieved without significant yield penalty across different ecosystems. The mean grain yield of genotypes across locations ranged from 3.5 to 5.6 t/ha and the mean environment grain yields ranged from 3.7 (Cambodia) to 6.6 (India) t/ha. The best-fitting Finlay-Wilkinson regression model identified eight stable genotypes with mean grain yield of more than 5.0 t/ha across locations. Multidimensional preference analysis represented the strong association of root traits (nodal root number, root dry weight at 22 and 30 days after transplanting) with grain yield. The genotype IR14L253 outperformed in terms of root traits and high mean grain yield across seasons and six locations. The 1.0 t/ha yield advantage of IR14L253 over the popular cultivar IR64 under AWD shall encourage farmers to cultivate IR14L253 and also adopt AWD. The results suggest an important role of root architectural traits in term of more number of nodal roots and root dry weight at 10-20 cm depth on 22-30 days after transplanting (DAT) in providing yield stability and preventing yield reduction under AWD compared to continuous flooded conditions. Genotypes possessing increased number of nodal roots provided higher yield over IR64 as well as no yield reduction under AWD compared to flooded irrigation. The identification of appropriate root architecture traits at specific depth and specific growth stage shall help breeding programs develop better rice varieties for AWD conditions.

Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa).

Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models.

Physiological analyses of traits associated with tolerance of long-term partial submergence in rice.

Floods are major constraints to crop production worldwide. In low-lying, flood-prone areas of the tropics, longer-term partial submergence (stagnant flooding [SF]) greatly reduces rice yield. This study assesses shoot growth and several physiological mechanisms associated with SF tolerance in rice. Five rice genotypes with contrasting responses to SF were evaluated in field ponds. Following transplanting, floodwater was gradually increased at a rate of ∼2 cm day(-1) to reach a final depth of 50 cm and then maintained until maturity. Although plants were not fully submerged, the yield was reduced by 47 % across genotypes compared with those grown under control conditions (6.1 vs. 3.3 t ha(-1)). This reduction was mainly attributed to the reduction in biomass caused by reduced light interception and leaf growth above the water. Stagnant flooding also reduced panicle number per unit area by 52 % because of reduced tillering. Shoot elongation rate kept pace with rising floodwater and correlated positively with leaf growth and biomass production. Conversely, stem non-structural carbohydrate (NSC) concentration correlated negatively with shoot elongation rate, suggesting that fast-elongating genotypes actively consume NSCs to avoid complete submergence. Moderate shoot elongation rate strongly and positively correlated with grain yield under SF; however, elongation at rates >2.0 cm day(-1) was associated with reduced harvest index due to a smaller panicle size and increased lodging. Tolerant varieties were found to be either inherently tall or elongate moderately with rising floodwater. Our studies suggest that to improve tolerance of SF an appropriate phenotype should combine both of these traits. Fine-tuning for optimum shoot elongation with rising floodwater is, therefore, a priority for future work.

Marker-assisted selection: an approach for precision plant breeding in the twenty-first century.

DNA markers have enormous potential to improve the efficiency and precision of conventional plant breeding via marker-assisted selection (MAS). The large number of quantitative trait loci (QTLs) mapping studies for diverse crops species have provided an abundance of DNA marker-trait associations. In this review, we present an overview of the advantages of MAS and its most widely used applications in plant breeding, providing examples from cereal crops. We also consider reasons why MAS has had only a small impact on plant breeding so far and suggest ways in which the potential of MAS can be realized. Finally, we discuss reasons why the greater adoption of MAS in the future is inevitable, although the extent of its use will depend on available resources, especially for orphan crops, and may be delayed in less-developed countries. Achieving a substantial impact on crop improvement by MAS represents the great challenge for agricultural scientists in the next few decades.