Characterization of tissue tolerance to iron by molecular markers in different lines of rice

Ferrous iron (Fe2+) toxicity is a major disorder in rice prod uction on acid, flooded soils. Rice ( Oryza sativa L.) genotypes differ widely in tolerance to Fe2+ toxicity, which makes it possible to bre ed more tolerant rice varieties. Tissue tolerance to higher iron concentrations in plants has been considered to be important to Fe2+ tolerance in ri ce. Segregation for leaf bronzing and growth reduction due to Fe2+ to xicity was observed in a doubled haploid (DH) population with 135 lines derived from a Fe2+ tolerant japonica variety, Azucena, and a sensitive indic a variety, IR64 in a solution culture with Fe2+ stress condition at a Fe2+concentration of 250 mg L-1 at pH 4.5. To better understand the mechanism of tissue tolerance, Leaf Bronzing Index (LBI), total iron concentration in shoot tissue and the enzymes of ascorbate peroxidase (AP), dehydroascorbate reductase (DR) and glutathione reductase (GR), and concentrations of ascorbate (AS) and dehydroascorbate (DHA), which are involved in the ascorbate-specific H2O2-scavenging system, were determined for the population under Fe2+ stress. A non-normal distribution of LBI was found. About 38 lines showed no bronzing, while the lines with non-zero LBI values ranged from 0.05 to 0.85 and showed a normal distribution. The other parameters measured showed normal distribution. The total iron concentrations in the 38 tolerant lines ranged from 1.76 mg Fe g-1 to 4.12 mg Fe g-1 and was in a similar range as in the non-tolerant genotype (2.04 – 4.55 mg Fe g-1). No significant differences in the activities of the enzymes were found between the parents under normal culture, but remarkably higher Fe2+ induced enzyme activities were observed in the tolerant parent. AS was similar between the parents under both normal and Fe2+ stress, but its concentration was sharply decreased under Fe2+ stress. DHA was much lower in the tolerant parent than in the sensitive parent under Fe2+ stress. Single locus analysis and interval mapping analysis based on 175 molecular markers revealed that the interval flanked by RG345 and RZ19 on chromosome one was an important location of gene(s) for Fe2+ tolerance. The ascorbate-specific system for scavenging Fe2+-mediated oxygen free radicals may be an important mechanism for tissue Fe2+ tolerance. A gene locus with relative small effect on root ability to exclude Fe2+ was also detected.     

Molecular markers linked to genes underlying seedling tolerance for ferrous iron toxicity

A double haploid (DH) population consisting of 123 lines derived from a japonica variety, Azucena, and an indica variety, IR64, and 100 BC1F1 (Azucena) lines were cultivated hydroponically using two treatments: one with excess Fe2+ at the concentration of 250 mg L-1 and a control with standard nutrient solution. Genotypic tolerance was evaluated using an index scale based on degree of leaf bronzing and relative decease in shoot dry weight (RDSDW) Toxic symptoms were not observed for Azucena and BClFl plants. In contrast, index values for the DH population indicated segregation for tolerance, and IR64 was moderately sensitive. Molecular marker loci associated with variations in index values and in RDSDW, and gene loci for tolerance were detected using 175 Markers mapped on all 12 chromosomes by single marker loci and interval mapping. Two gene loci were identified to be flanked by RG345 and RG381, and linked to RG810, respectively, on chromosome 1 for both index values and RDSDW. They explained 32% and 13% of the total variation in the index values, and 15% and 21 % in the RDSDW in the population, respectively. The variation in RDSDW was also explained by a locus linked to RG978 on chromosome 8 by about 10%. Comparison of the two marker genotypic class means indicated that the tolerant alleles were from Azucena at the first locus on chromosome 1 and the locus on chromosome 8, and that at the second locus on chromosome 1 from IR64.     

Mapping QTLs for phosphorus deficiency tolerance in rice (Oryza sativa L.)

 The amplified fragment length polymorphism (AFLP) technique combined with selective genotyping was used to map quantitative trait loci (QTLs) associated with tolerance for phosphorus (P) deficiency in rice. P deficiency tolerant cultivar IR20 was crossed to IR55178-3B-9-3 (sensitive to P-deficiency) and 285 recombinant inbred lines (RILs) were produced by single-seed descent. The RILs were phenotyped for the trait by growing them in P-sufficient (10.0 mg/l) and P-deficient (0.5 mg/l) nutrient solution and determining their relative tillering ability at 28 days after seeding, and relative shoot dry weight and relative root dry weight at 42 days after seeding. Forty two of each of the extreme RILs (sensitive and tolerant) and the parents were subjected to AFLP analysis. A map consisting of 217 AFLP markers was constructed. Its length was 1371.8 cM with an average interval size of 7.62 cM. To assign linkage groups to chromosomes, 30 AFLP and 26 RFLP markers distributed over the 12 chromosomes were employed as anchor markers. Based on the constructed map, a major QTL for P-deficiency tolerance, designated PHO, was located on chromosome 12 and confirmed by RFLP markers RG9 and RG241 on the same chromosome. Several minor QTLs were mapped on chromosomes 1, 6, and 9. Received: 21 April 1998 / Accepted: 9 June 1998     

The effects of selection for sodium transport and of selection for agronomic characteristics upon salt resistance in rice (Oryza sativa L.)

A multiple cross was constructed with the aim of combining component traits for the complex salinity resistance character. The aim was to combine donors for physiological traits with the agronomically desirable semidwarf/intermediate plant type and with the overall salinity resistance of the traditional tall land races. We report a study of selection strategies in the resulting breeding population. The effects of early selection for agronomic traits and early selection for low sodium transport were compared with a control population in which minimal selection was practised. Conventional selection for agronomic characters at early generations selected against low sodium-transporting (and thus potentially salt-tolerant) genotypes. In contrast, mild early selection for low sodium transport enriched the population in potentially salt-resistant genotypes but did not select against agronomic (semi-dwarf/intermediate) genotypes. It is concluded that selection for agronomic traits should be made after selection for salt resistance and, ideally, should be delayed until the population has reached near-homozygosity.     

Genetic analysis of tolerance for phosphorous deficiency in rice (Oryza sativa L.)

The inheritance of phosphorous (P) — deficiency tolerance in rice was investigated by a sevenparent diallel. The parent materials involved were four P-efficient (IR20, IR54, IR28, and Mahsuri), one moderately P-efficient (TN1), and two P-inefficient (IR31406333-1 and IR34686-179-1-2-1), genotypes. Relative tilering ability (RTA) under P-deficient and P-supplemented soil conditions was the parameter used in determining the tolerance level of the different genotypes. Diallel graph analysis revealed that tolerant parents have an excess of recessive genes, while moderate and susceptible parents possess more dominant genes. Genetic-component analysis suggested that both additive and dominance gene effects are involved in the inheritance of P-deficiency tolerance in rice. The trait exhibited over doiminance as confirmed by the graphical analysis. Narrow-sense heritability of the trait was moderate (0.50) and environmental effects were low. Both the general combining ability (GCA) and the specific combining ability (SCA) were significant, but GCA was more prevalent than SCA. Tolerant parents exhibited a high GCA whereas susceptibles have a very poor GCA, suggesting that tolerant parents were mostly enriched in additive genes and susceptible parents in non-additive genes. Crosses involving two high general combiners showed low SCA effects whereas crosses between poor general combiners manifested highly-significant SCA values.     

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

Summary The 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.     

Variability and genetics of tolerance for aluminum toxicity in rice (Oryza sativa L.)

A study was undertaken to investigate the variability among lowland rice cultivars and the mode of gene action of aluminum (Al) toxicity tolerance in rice. Pregerminated seeds were grown in a nutrient solution containing 30 ppm Al and in normal nutrient solution, and relative root length (RRL) was determined at the 14-day-old stage to characterize genotypes for tolerance. Sixty-two traditional rice cultivars grown on lowland acid sulfate soil areas of Asia and West Africa were tested. Tolerant varieties Azucena, IRAT104, and Moroberekan, moderately sensitive IR29 and IR43, and sensitive IR45 and IR1552 were used to investigate the genetics of tolerance by diallel analysis. Of the 62 cultivars tested, only 3 were found to be sensitive to A l toxicity. Among the tolerant cultivars identified, 11 (Siyam Kuning, Gudabang Putih, Siyam, Lemo, Khao Daeng, Siyamhalus, Bjm-12, Ketan, Seribu Gantang, Bayer Raden Rati, and Padi Kanji) were found to possess higher levels of tolerance than the improved tolerant upland cultivar IRAT104. Diallel analysis revealed that high RRL is governed by both additive and dominance effects with a preponderance of additive effects. The trait exhibited partial dominance, and one group of genes was detected. Heritability was high, and environmenal effects were low. Findings suggest that when breeding for A1 toxicity tolerance, selection can be made in early generations. The pedigree method of breeding would be suitable. Combining ability analysis revealed the importance of both general combining ability (GCA) and specific combining ability (SCA) in the genetics of A1 toxicity tolerance in rice. GCA was more prevalent than SCA. Tolerant parens Azucena, IRAT104, and Moroberekan were the best general combiners. The presence of reciprocal effects among crosses suggested the proper choice of parents in hybridization programs. Results indicated that Azucena, IRAT 104, and Moroberekan should be used as the female in crosses for A1 toxicity tolerance.     

Mapping QTLs for submergence tolerance in rice by AFLP analysis and selective genotyping

By combining the amplified fragment length polymorphism (AFLP) technique with selective genotyping, we constructed a linkage map for rice and assigned each linkage group to a corresponding chromosome. The AFLP map, consisting of 202 AFLP markers, was generated from 74 recombinant inbred lines (RIL) which were selected from both extremes of the population (250 lines) with respect to the response to complete submergence. Map length was 1756 cM, with an average interval size of 8.5 cM. To assign linkage groups to chromosomes, we used 50 previously mapped AFLP markers as anchor markers distributed over the 12 chromosomes. Other AFLP markers were then assigned to specific chromosomes based on their linkage to anchor markers. This AFLP map is equivalent to the RFLP/AFLP map constructed previously as the anchors were in the same order in both maps. Furthermore, tests with two restriction fragment length polymorphism (RFLP) markers and two sequence-tagged site (STS) markers showed that they mapped in the expected positions. Using this AFLP map, a major gene for submergence tolerance was localized on chromosome 9. Quantitative trait loci (QTL) associated with submergence tolerance were detected on chromosomes 6, 7, 11, and 12. We conclude that the combination of AFLP mapping and selective genotyping provides a much faster and easier approach to QTL identification than the use of RFLP markers. Received: 20 December 1996 / Accepted: 21 January 1997     

Field performance of anther-culture-derived lines from F1 crosses of Indica rices under saline and nonsaline conditions

Summary Field experiments were conducted to evaluate and compare the yield and agronomic characteristics of anther-culture-derived (AC) lines in rice and the parents under saline and nonsaline soil conditions. The yield stability of two entries was also evaluated by comparing their performance under two distinct nonsaline soil environments. The test entries were planted in randomized complete block design with four replications at each test location. Data were collected on grain yield, yield components, and agronomic characteristics. This study demonstrates that through anther culture, it is possible to produce homozygous diploid lines in a short time. The possibility of regenerating recombinants with desirable characteristics such as good plant type and salinity tolerance, higher yield, and increased resistance to pests and diseases from both the parents is high.     

Genes/QTLs affecting flood tolerance in rice

The adaptation of deepwater rice to flooding is attributed to two mechanisms, submergence tolerance and plant elongation. Using a QTL mapping study with replicated phenotyping under two contrasting (water qualities) submergence treatments and AFLP markers, we were able to identify several genes/QTLs that control plant elongation and submergence tolerance in a recombinant inbred rice population. Our results indicate that segregation of rice plants in their responses to different flooding stress conditions is largely due to the differential expression of a few key elongation and submergence tolerance genes. The most important gene was QIne1 mapped near sd-1 on chromosome 1. The Jalmagna (the deepwater parent) allele at this locus had a very large effect on internal elongation and contributed significantly to submergence tolerance under flooding. The second locus was a major gene, sub1(t), mapped to chromosome 9, which contributed to submergence tolerance only. The third one was a QTL, QIne4, mapped to chromosome 4. The IR74 (non-elongating parent) allele at this locus had a large effect for internal elongation. An additional locus that interacted strongly with both QIne1 and QIne4 appeared near RG403 on chromosome 5, suggesting a complex epistatic relationship among the three loci. Several QTLs with relatively small effects on plant elongation and submergence tolerance were also identified. The genetic aspects of these flooding tolerance QTLs with respect to patterns of differential expression of elongation and submergence tolerance genes under flooding are discussed. Received: 13 December 1999 / Accepted: 14 March 2000<@head-com-p1a.lf>Communicated by G. Wenzel