Glenn B. Gregorio

Progress in breeding for salinity tolerance and associated abiotic stresses in rice

Abstract Saline soils are characterized by an array of properties that are adverse to rice cultivation. The problem of salinity is compounded by mineral deficiencies (Zn, P) and toxicities (Fe, Al, organic acids), submergence, deep water and drought. These soil stresses vary in magnitude and interactions over time and place, making long-term adaptability of a cultivar dependent on its level of tolerance to all the stresses that occur in its growing environment. Thus, in breeding rice for saline environments, multiple stress tolerance traits must be considered. Some degree of cultivar tolerance for these stresses is in rice germplasm. However, understanding the physiological mechanisms of these traits, their biochemical basis, inheritance and efficient screening techniques are needed to hasten breeding progress. Recent progress in breeding for rice for saline environments includes the development of rapid and reliable techniques of screening for elongation ability and tolerance for salinity, submergence, iron toxicity, aluminum toxicity and phosphorus efficiency. Donor germplasm has been identified and improved, and its inheritance for tolerance for most soil-related stresses has been studied. Physiological mechanisms of some stresses are now fairly well understood. Rice lines developed with tolerance for multiple stresses have been successfully used as donor parents, and released as cultivars for salt-affected areas by national agricultural research and extension systems (NARES). Present studies are directed toward increasing the selection efficiency and accelerating pyramiding of various soil-related tolerance traits. F 8 recombinant inbred line (RIL) mapping populations for various abiotic traits were developed and genotyped. Major genes and quantitative trait loci (QTLs) for elongating ability tolerance and for tolerance for salinity, submergence, P deficiency, and Al and Fe toxicities were mapped. Genotyping is in progress for other tolerance traits. Refined mapping using near-isogenic lines for the development of polymerase chain reaction (PCR)-based marker-assisted selection (MAS) is now possible and pursued. MAS techniques are being developed for elongation ability and tolerance of salinity, submergence, Al toxicity, P deficiency and Zn deficiency.

Characterizing the Saltol Quantitative Trait Locus for Salinity Tolerance in Rice

This study characterized Pokkali-derived quantitative trait loci (QTLs) for seedling stage salinity tolerance in preparation for use in marker-assisted breeding. An analysis of 100 SSR markers on 140 IR29/Pokkali recombinant inbred lines (RILs) confirmed the location of the Saltol QTL on chromosome 1 and identified additional QTLs associated with tolerance. Analysis of a series of backcross lines and near-isogenic lines (NILs) developed to better characterize the effect of the Saltol locus revealed that Saltol mainly acted to control shoot Na+/K+ homeostasis. Multiple QTLs were required to acquire a high level of tolerance. Unexpectedly, multiple Pokkali alleles at Saltol were detected within the RIL population and between backcross lines, and representative lines were compared with seven Pokkali accessions to better characterize this allelic variation. Thus, while the Saltol locus presents a complex scenario, it provides an opportunity for marker-assisted backcrossing to improve salt tolerance of popular varieties followed by targeting multiple loci through QTL pyramiding for areas with higher salt stress.

Breeding for Trace Mineral Density in Rice

In 1992 the International Rice Research Institute (IRRI) began to examine the effect of certain soil characteristics on the iron content of rice grains. As part of the Consultative Group for International Agricultural Research (CGIAR) Micronutrients Project, this effort was expanded in 1995 to include analysis of both iron and zinc, in collaboration with the University of Adelaide in Australia. Since then, germplasm screening has shown large genetic variation for iron and zinc concentrations in brown rice. Common cultivars contain about 12 mg of iron and 25 mg of zinc per kilogram. Some traditional varieties have double these amounts. Genetic-by-environmental interactions are sufficiently moderate that breeding for higher iron and zinc content is considered worthwhile. The next major research step will be to further study the genetics of trace mineral accumulation in the grain to determine the best selection techniques for use in breeding. High iron and zinc traits can be combined with improved agronomic traits. This has already been demonstrated in the serendipitous discovery in the IRRI testing programme of an aromatic variety (IR68144-3B-2-2-3) that has a high concentration of grain iron, about 21 mg/kg in brown rice. This elite line has good tolerance to rice tungro virus and to mineral-deficient soils and has excellent grain qualities. The yields are about 10% below those of IR72, but in partial compensation, maturity is earlier. After 15 minutes of polishing, IR68144-4B-2-2-3 had about 80% more iron than IR64, a widely grown commercial variety. It remains to be shown that this extra iron can improve the iron status of iron-deficient human subjects. A human feeding trial is being planned.

Genetic analysis of salinity tolerance in rice (Oryza sativa L.)

SummaryThe genetics of salinity tolerance in rice was investigated by a nine-parent complete diallel including reciprocals. Test materials involved susceptible (IR28, IR29, and MI-48), moderately tolerant (IR4595-4-1-13, IR9884-54-3-1E-P1, and IR10206-29-2-1), and tolerant (“Nona Bokra”, “Pokkali”, and SR26B) parents. Twoweek-old seedlings were grown in a salinized (EC = 12 dS/m) culture solution for 19 days under controlled conditions in the IRRI phytotron. Typical characteristics of salinity tolerance in rice were found to be Na+ exclusion and an increased absorption of K+ to maintain a good Na-K balance in the shoot. Genetic component analysis (GCA) revealed that a low Na-K ratio is governed by both additive and dominance gene effects. The trait exhibited overdominance, and two groups of genes were detected. Environmental effects were large, and the heritability of the trait was low. Our findings suggest that when breeding for salt tolerance, selection must be done in a later generation and under controlled conditions in order to minimize environmental effects. Modified bulk and single-seed descent would be the suitable breeding methods. Combining ability analysis revealed that both GCA and specific combining ability (SCA) effects were important in the genetics of salt tolerance. Moderately tolerant parents — e.g., IR4595-4-1-13 and IR9884-54-3-1E-P1 — were the best general combiners. Most of the best combinations had susceptible parents crossed either to moderate or tolerant parents. The presence of reciprocal effects among crosses necessitates the use of susceptible parents as males in hybridization programs. Large heterotic effects suggest the potential of hybrid rice for salt-affected lands.

Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding

BackgroundThis article describes the development of Multi-parent Advanced Generation Inter-Cross populations (MAGIC) in rice and discusses potential applications for mapping quantitative trait loci (QTLs) and for rice varietal development. We have developed 4 multi-parent populations: indica MAGIC (8 indica parents); MAGIC plus (8 indica parents with two additional rounds of 8-way F1 inter-crossing); japonica MAGIC (8 japonica parents); and Global MAGIC (16 parents – 8 indica and 8 japonica). The parents used in creating these populations are improved varieties with desirable traits for biotic and abiotic stress tolerance, yield, and grain quality. The purpose is to fine map QTLs for multiple traits and to directly and indirectly use the highly recombined lines in breeding programs. These MAGIC populations provide a useful germplasm resource with diverse allelic combinations to be exploited by the rice community.ResultsThe indica MAGIC population is the most advanced of the MAGIC populations developed thus far and comprises 1328 lines produced by single seed descent (SSD). At the S4 stage of SSD a subset (200 lines) of this population was genotyped using a genotyping-by-sequencing (GBS) approach and was phenotyped for multiple traits, including: blast and bacterial blight resistance, salinity and submergence tolerance, and grain quality. Genome-wide association mapping identified several known major genes and QTLs including Sub1 associated with submergence tolerance and Xa4 and xa5 associated with resistance to bacterial blight. Moreover, the genome-wide association study (GWAS) results also identified potentially novel loci associated with essential traits for rice improvement.ConclusionThe MAGIC populations serve a dual purpose: permanent mapping populations for precise QTL mapping and for direct and indirect use in variety development. Unlike a set of naturally diverse germplasm, this population is tailor-made for breeders with a combination of useful traits derived from multiple elite breeding lines. The MAGIC populations also present opportunities for studying the interactions of genome introgressions and chromosomal recombination.

New allelic variants found in key rice salt-tolerance genes: an association study.

Salt stress is a complex physiological trait affecting plants by limiting growth and productivity. Rice, one of the most important food crops, is rated as salt-sensitive. High-throughput screening methods are required to exploit novel sources of genetic variation in rice and further improve salinity tolerance in breeding programmes. To search for genotypic differences related to salt stress, we genotyped 392 rice accessions by EcoTILLING. We targeted five key salt-related genes involved in mechanisms such as Na(+) /K(+) ratio equilibrium, signalling cascade and stress protection, and we found 40 new allelic variants in coding sequences. By performing association analyses using both general and mixed linear models, we identified 11 significant SNPs related to salinity. We further evaluated the putative consequences of these SNPs at the protein level using bioinformatic tools. Amongst the five nonsynonymous SNPs significantly associated with salt-stress traits, we found a T67K mutation that may cause the destabilization of one transmembrane domain in OsHKT1;5, and a P140A alteration that significantly increases the probability of OsHKT1;5 phosphorylation. The K24E mutation can putatively affect SalT interaction with other proteins thus impacting its function. Our results have uncovered allelic variants affecting salinity tolerance that may be important in breeding.

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.

Evaluation of salt tolerance in rice genotypes by physiological characters

AbstractThe use of physiological characters as selection criteria in salt tolerance breeding requires the identification of the contribution each individual character makes to salt tolerance. Rice genotypes were evaluated for salt tolerance in terms of grain yield and physiological characters. Plants of twelve genotypes were grown in sand tanks in a greenhouse and irrigated with Yoshida nutrient solution. Sodium chloride and calcium chloride (5:1 molar ratio) were added at two concentrations to give moderate (4.5 dS m-1) and high (8.3 dS m-1) salinity treatments. One set of plants was harvested at 635 °Cċd (accumulative thermal time) after planting to determine LAI and mineral ion concentrations. Another set of plants was allowed to grow to maturity. High genotypic diversity for LAI and shoot ion contents was observed. LAI contributed the most to the variation of the grain yield under salt stress. Significant correlations between LAI and yield components in both salt-tolerant and-sensitive genotypes further confirmed the significant contribution of LAI to grain yield. K-Na selectivity increased with increasing salinity. Conversely, Na-Ca selectivity decreased with increasing salinity. Significant correlations were identified between grain yield and both Na-Ca and K-Na selectivity. Highly significant (p<0.001) correlations were identified between Na-Ca selectivity and the rankings among genotypes for grain yield. Thus, Na-Ca selectivity could be one salt tolerance component and an useful selection criterion in screening for salt tolerance.

Domestication history and geographical adaptation inferred from a SNP map of African rice

African rice (Oryza glaberrima Steud.) is a cereal crop species closely related to Asian rice (Oryza sativa L.) but was independently domesticated in West Africa ∼3,000 years ago. African rice is rarely grown outside sub-Saharan Africa but is of global interest because of its tolerance to abiotic stresses. Here we describe a map of 2.32 million SNPs of African rice from whole-genome resequencing of 93 landraces. Population genomic analysis shows a population bottleneck in this species that began ∼13,000–15,000 years ago with effective population size reaching its minimum value ∼3,500 years ago, suggesting a protracted period of population size reduction likely commencing with predomestication management and/or cultivation. Genome-wide association studies (GWAS) for six salt tolerance traits identify 11 significant loci, 4 of which are within ∼300 kb of genomic regions that possess signatures of positive selection, suggesting adaptive geographical divergence for salt tolerance in this species.

Development of the first salt-tolerant rice cultivar through indica/indica anther culture

Abstract Seventy-nine di-haploid lines were produced in rice through anther culture of the cross of two indica breeding lines (IR5657-33-2×IR4630-22-2-5-1-3). The cross was designed to combine the high-yielding ability of IR5657-33-2 with the salinity tolerance of IR4630-22-2-5-1-3. The anther culture (AC)-derived lines were evaluated in the greenhouse, field, and salinity affected areas. Several lines showed desirable traits such as high yield, salinity tolerance, early maturity, good plant type, and resistance to pests and diseases. IR51500-AC9-7 and IR51500-AC11-1 selected from evaluations were included in the National Cooperative Trials (NCT) for saline-prone areas conducted by the Rice Varietal Improvement Group (RVIG) of the National Seed Industry Council (NSIC) of the Philippines. Trials conducted from the 1990 wet season to 1994 dry season at nine sites revealed that IR51500-AC11-1 performed better than other cultivars grown in saline-prone lands. In 1995, the NSIC named IR51500-AC11-1 as PSBRc50 “Bicol” and recommended it for commercial cultivation in salt-affected rice lands. This is the first F 1 AC-derived line from an indica/indica cross to be released as a cultivar for cultivation in saline-prone areas.