Rice Cross Research Articles

Analysis of QTL×environment interaction for yield components and plant height in rice

An F2 and two equivalent F3 populations of an indica-indica cross of rice, Tesanai 2/CB, were constructed and grown in different environments. The identification of quantitative trait loci (QTL) for yield components and plant height and an analysis of QTL×environment interaction were conducted for three trials. Interval mapping of QTL for eight traits was employed with a threshold of LOD=2 using the computer package MAPMAKER/QTL. A total of 44 QTL were detected in 18 intervals of nine chromosomes, including 3 for the number of panicles (NP), 5 for the number of filled grains (NFG), 6 for total number of spikelets (TNS), 3 for spikelet fertility (SF), 7 for 1000-grain weight (TGWT), 5 for grain weight per plant (GWT), 8 for plant height (PH) and 7 for panicle length (PL). The numbers of QTL detected in two or three trials were 1 for NP, 1 for NFG, 1 for TNS, none for SF, 4 for TGWT, 3 for GWT, 2 for PH and 5 for PL, making a total of 17. When a QTL was detected in more than one trial the direction and magnitude of its additive effect, the dominance effect and the degree of dominance were generally in good agreement. In all three trials, QTL were frequently detected for related traits in the same intervals. The directions of additive effect of QTL for related traits in a given interval were in agreement with few exceptions, no matter whether they were detected in the same trial or not. This result suggested that pleiotropism rather than close linkage of different QTL was the major reason why QTL for different traits were frequently detected in the same intervals. When gene pleiotropism was considered, 23 of the 29 QTL for yield and its components and 9 of the 15 QTL for plant stature were detected in more than one trial. This indicated that the detection of chromosomal segments harboring QTL was hardly affected by environmental factors.

Molecularmarker diversity and hybrid sterility in indica-japonica rice crosses

The partial sterility of hybrids between the indica and japonica rice subspecies of Asian cultivated rice is a serious constraint for utilizing inter-subspecific heterosis in hybrid rice breeding. In this study, we have investigated the relationship between molecular-marker polymorphism and indica-japonica hybrid fertility using a diallel set involving 20 rice accessions including 9 indica and 11 japonica varieties. Spikelet fertility of the resulting 190 F1s and their parents was examined in a replicated field trial. Intra-subspecific hybrids showed much higher spikelet fertility than inter-subspecific hybrids except in crosses involving wide-compatibility varieties. The parents were surveyed for DNA polymorphism using 96 RFLP and ten SSR markers, which revealed extensive genetic differentiation between indica and japonica varieties. A large number of markers detected highly significant effects on hybrid fertility. The chromosomal locations for many of the positive markers coincided well with previously identified loci for hybrid sterility. The correlation between hybrid fertility and parental distance was low in both intra- and inter-subspecific crosses. The results suggest that the genetic basis of indica-japonica hybrid sterility is complex. It is the qualitative, rather than the quantitative, difference between the parents that determines the fertility of hybrids.

Two new loci for hybrid sterility in cultivated rice (Oryza sativa L.)

Female gamete abortion in Indica-Japonica crosses of rice was earlier identified to be due to an allelic interaction at the S-5 locus on chromosome 6. Recently, in other crosses of rice, similar allelic interactions were found at loci designated as S-7 and S-8, located on chromosomes 7 and 6 respectively. All of them are independent of each other. At the S-5 locus, Indica and Japonica rice have S-5 (i) and S-5 (j) alleles respectively and Javanicas, such as Ketan Nangka, have a neutral allele S-5 (n) .The S-5 (i) /S-5 (j) genotype is semi-sterile due to partial abortion of female gametes carrying S-5 (j) , but both the S-5 (n) /S-5 (i) and S-5 (n) /S-5 (j) genotypes are fertile. The S-5 (n) allele is thus a "wide-compatibility gene" (WCG), and parents homozygous for this allele are called wide-compatible varieties (WCV). Such parents when crossed with Indica or Japonica varieties do not show F1 hybrid sterility. Wide-compatible parents have been used to overcome sterility barriers in crosses between Indica and Japonica rice. However, a Javanica variety, Ketan Nangka (WCV), showed typical hybrid sterility when crossed to the Indian varieties N22 and Jaya. Further, Dular, another WCV from India, showed typical hybrid sterility when crossed to an IRRI line, IR2061-628-1-6-4-3(IR2061-628). By genetic analyses using isozyme markers, a new locus causing hybrid sterility in crosses between Ketan Nangka and the Indicas was located near isozyme loci Est-1 and Mal-1 on chromosome 4, and was designated as S-9. Another new locus for hybrid sterility in the crosses between Dular and the IR2061-628 was identified and was found linked to four isozyme loci, Sdh-1, Pox-2, Acp-1 and Acp-2, on chromosome 12. It was designated as S-15. On the basis of allelic interactions causing female-gamete abortion, two alleles were found at S-9, S-9 (kn) in Ketan Nangka and S-9 (i) in N22 and Jaya. In the heterozygote, S-9 (kn) /S-9 (i) , which was semisterile, female gametes carrying S-9 (kn) were aborted. The hybrid of Dular and IR2061-628, with a genetic constitution of S-15 (Du) /S-15 (i) , was semi-sterile and the female gametes carrying S-15 (Du) were aborted. A Japonica tester variety, Akihikari, and an Indica variety, IR36, were found to have neutral alleles, S-9 nand S-15 n, at these loci, in addition to S-7 nand at S-7. The accumulation of three neutral alleles into a breeding line should help solve the hybrid sterility problem in wide crosses of rice.

Detection of segregation distortions in an indica-japonica rice cross using a high-resolution molecular map

We have constructed a high-resolution rice genetic map containing 1383 DNA markers covering 1575 cM on the 12 linkage groups of rice using 186 F2 progeny from a cross between a japonica variety, 'Nipponbare', and an indica variety, 'Kasalath'. Using this high-resolution molecular linkage map, we detected segregation distortion in a single wide cross of rice. The frequencies of genotypes for 1181 markers with more than 176 genotype data were plotted along this map to detect segregation distortion. Several types of distorted segregation were observed on 6 of the chromosomes. We could detect 11 major segregation distortions at ten positions on chromosomes 1, 3, 6, 8, 9, and 10. The strongest segregation distortion was at 107.2 cM on chromosome 3 and may be the gametophyte gene 2 (ga-2). The 'Kasalath' genotype at this position was transmitted to the progeny with about a 95% probability through the pollen gamete. At least 8 out of the 11 segregation distortions detected here are new. The use of the high-resolution molecular linkage map for improving our understanding of the genetic nature and cause of these segregation distortions is discussed.

Identification of QTLs affecting traits of agronomic importance in a recombinant inbred population derived from a subspecific rice cross

To detect QTLs controlling traits of agronomic importance in rice, two elite homozygous lines 9024 and LH422, which represent the indica and japonica subspecies of rice (Oryza sativa), were crossed. Subsequently a modified single-seed-descent procedure was employed to produce 194 recombinant inbred lines (F8). The 194 lines were genotyped at 141 RFLP marker loci and evaluated in a field trial for 13 quantitative traits including grain yield. Transgressive segregants were observed for all traits examined. The number of significant QTLs (LOD [Symbol: see text] 2.0) detected affecting each trait ranged from one to six. The percentage of phenotypic variance explained by each QTL ranged from 5.1% to 73.7%. For those traits for which two or more QTLs were detected, increases in the traits were conditioned by indica alleles at some QTLs Japonica alleles at others. No significant evidence was found for epistasis between markers associated with QTLs and all the other markers. Pleitropic effects of single QTLs on different traits are suggested by the observation of clustering of QTLs. No QTL for traits was found to map to the vicinity of major gene loci governing the same traits qualitatively. Evidence for putative orthologous QTLs across rice, maize, oat, and barley is discussed.

Detection of segregation distortions in an indica-japonica rice cross using a high-resolution molecular map

Detection of segregation distortions in an indica-japonica rice cross using a high-resolution molecular map

Identification of QTLs affecting traits of agronomic importance in a recombinant inbred population derived from a subspecific rice cross

Identification of QTLs affecting traits of agronomic importance in a recombinant inbred population derived from a subspecific rice cross

Response to selection for high and low partial resistance to leaf blast in F2 populations of three rice crosses

Divergent selection for higher and lower partial resistance to leaf blast was applied in F2 populations of crosses between the rice cultivars IR36, IR64 and CO39 after exposure to a virulent isolate. IR36 and IR64 are partially resistant while CO39 is highly susceptible. As selection criteria the number of sporulating lesions in leaves of the main culm or the lesion density in the topmost leaf relative to other F2 plants with the same stage of development were used. A highly significant and meaningful response to selection was obtained in most cases, but the heritability was low. Realized heritabilities varied from 0.14 to 0.25 depending on the cross and were similar for both selection criteria. Selection for improved partial resistance to leaf blast is possible as early as the F2. The efficiency of selection is probably much higher if replicated tests could be made, and better results are therefore expected if selection among F3 lines is carried out. The results indicated that the relatively low infection efficiency in IR36 and IR64 is oligo- or polygenically controlled.

Non-allelic interaction conditioning spikelet sterility in an F2 population of indica/japonica cross in rice

Significant segregation of spikelet fertility occurred in an F2 population derived from a spikelet fertility-normal F1 hybrid produced by a cross between 'Palawan', a japonica variety, and 'IR42', an indica variety. To identify factors controlling the fertility segregation, we used 104 RFLP markers covering all 12 rice chromosomes to investigate the association of spikelet fertility and marker segregation. We found that the segregation of two sets of gene pairs was significantly (P < 0.001) associated with fertility segregation. The first pair of genes was linked to RFLP marker RG778 on chromosome 12 and RFLP markers RG690/RG369 on chromosome 1. A significant reduction in fertility was observed when the plants were homozygote at RG778 with the indica allele as well as homozygote at RG690/RG369 with the japonica allele. The second pair of genes was linked to RG218 on chromosome 12 and RG650 on chromosome 7, respectively. The recombinant homozygote at these two loci showed a significant reduction on spikelet fertility. The non-allelic interaction effect was further modified by a gene linked to RG778, resulting in even lower fertility. The results of this study provides the first evidence of chromosomal localization of sporophytic sterility genes whose interaction can result in a reduction of spikelet fertility in the F2 derived from fertility-normal F1.

Dominance is the major genetic basis of heterosis in rice as revealed by QTL analysis using molecular markers.

A set of 194 F7 lines derived from a subspecific rice cross showing strong F1 heterosis was backcrossed to the two parents. The materials (388 BC1F7 lines, 194 F8 lines, two parents, F1) were phenotyped for 12 quantitative traits. A total of 37 significant QTLs (LOD > or = 2.0) was detected through 141 RFLP markers in the BC1F7 populations. Twenty-seven (73%) quantitative trait loci (QTLs) were detected in only one of the BC1F7 populations. In 82% of these cases, the heterozygotes were superior to the respective homozygotes. The remaining 10 (27%) QTLs were detected in both BC1F7 populations, and the heterozygote had a phenotype falling between those of the two homozygotes and in no instances were the heterozygotes found to be superior to both homozygotes. These results suggest that dominance complementation is the major genetic basis of heterosis in rice. This conclusion was strengthened by the finding that there was no correlation between most traits and overall genome heterozygosity and that there were some recombinant inbred lines in the F8 population having phenotypic values superior to the F1 for all of the traits evaluated--a result not expected if overdominance was a major contributor to heterosis. Digenic epistasis was not evident.

COMBINING ABILITY FOR SOME METRIC TRAITS IN RICE

Combining ability and genetic variance were estimated through the use of 10 x 10 diallel cross of rice (Oryza sativa L.) for yield, maturity and plant characters. Both additive and non additive gene effects were important for the expression of the traits. Parents IR 54 and UPRM 500 were the best general combiners for grain yield in F as well as in F2 generations. The best two crosses IET 4141 x IET 6288 and UPRM 500 x IET 6288 which showed high sca effects for grain yield and other important traits involved both the parents having good gea effects.

Identification of A New Locus S-16 Causing Hybrid Sterility in Native Rice Varieties (Oryza sativa L.) from Tai-hu Lake Region and Yunnan Province, China.

The presence of semi-sterile panicles in Indica-Japonica crosses of rice is due to an allelic interaction at a gamete abortion locus, S-5 on ( hromosome 6 The S 5 n allcle s referred to as wide compatibility gene" (WCG), since one of the parents carrying this allele does not show hybrid sterility in the Fl' However. Ketan Nangka, which is a donor of S-5 n, sholved typical h.vbrid sterility when it was crossed to local varieties from Taihu Lake, such as Fengjingdao and Feilaifeng, as weil as to those from Yun-nan Provinco, sueh as Dabai, Luanjiaolong and Xiaobaigu. A new locus for the sterilitv in the hvbrid between Ketan Nangka and the local varieties was detected near the Est-5 locus on Chromosome 1, and designated as S-16 following our recent report.s on S-7, S-8 . S-9 and S-15 .

Inheritance and Selection of Field Resistance to Sheath Brown Rot Disease in Rice

Chilling temperatures induce sheath brown rot disease (ShBR) in rice (Oryza sativa) caused by Pseudomonas fuscovaginae. The major symptoms of the disease are poor exsertion of the panicle from the boot and spikelet sterility. The inheritance of field resistance was studied in F 3 families derived from three rice crosses involving a field-resistant (R) parent, two intermediate (I) parents, and a susceptible (S) parent. Each cross was assessed at a different altitude to give three independent data sets. Heritability (h 2 ) estimates of disease resistance traits were determined by analysis of F 3 family means in crosses Raksali (S) x Makwanpur-15L (I), Makwanpur-3L (I) x Chhomrong (R), and IR36 (S) x Chhomrong (R). There were highly significant differences between F 3 family means in all cases and heritabilities were consistently high (0.72 to 0.84). High h 2 estimates and high variance between F 3 families resulted in high predicted genetic gains from selection, so field screening in the F 3 generation for ShBR resistance should be effective. Mean, additive, and dominance gene effects were estimated from generation means analyses. A statistically significant model could be fitted in all three crosses, and additive effects were always important. Dominance was also an important genetic effect, and its direction was significantly toward resistance in two of the crosses but, with lower significance, toward susceptibility in the third. Significant correlations were found between ShBR field resistance and plant height and panicle exsertion from the boot. Selection, in the presence of the disease, for taller plants and better panicle exsertion will give a genetic gain for greater chilling tolerance and higher ShBR field resistance.

Improvement in Anther Culture of Japonica/Indica Crosses of Rice

Improvement in Anther Culture of Japonica/Indica Crosses of Rice

GENETIC STUDIES IN F2 AND F3 OF TALL X DWARF RICE CROSSES

F2 and F3 generations of three rice crosses were evaluated for various genetic parameters. In F2 of all crosses, PCV and GCV were high for number of productive tillers. grain number per panicle, and single plant yield, low for days to panicle emergence and hundred grains weight and moderate for plant height, while in F3, moderate variability for single plant yield and low variability for other traits were observed. In F2, high heritability combined with high genetic advance was recorded for plant height and single plant yield whereas in F3, high values of heritability and genetic advance were recorded in ASD 1/co 33 for plant height, hundred grain weight and single plant yield, in ASD 1/ADT 36 for plant height and in ASD 1/IR 50 for grain number per panicle and single plant yield. Days to panicle emergence had high heritability with low GCV and genetic advance indicating non-additive gene action.

Inheritance of Aroma in Two Rice Crosses

Two nonscented varieties, ADT38 and ADT39, were crossed with a scented variety, Badshabhog, to study the inheritance of aroma in rice. The parents, F1 and F2 were grown in Nov 1992. For each cross, 2 g of leaf blades from randomly selected parent and F1 plants and 200 F2 plants were soaked in 10 ml of 1.7 percent KOH solution in test tubes and evaluated for scent after 10 min by smelling the contents. All F1 plants were nonaromatic, indicating the recessive nature of the gene controlling aroma. A 15 non-aromatic: 1 aromatic segregation occurred for F2 plants in both crosses, suggesting that two recessive genes control aroma in Badshabhog. Pedigree breeding with a larger population for F2 selection is suggested for introducing scent into nonscented varieties

Genetical control of amylose content in a diallel set of rice crosses

Models proposed by Gale and Pooni, Kumar and Khush are applied to study the inheritance of amylose content in a diallel set of crosses produced from seven elite inbred lines of indica rice representing all the major rice consuming regions of the world. In theory, the standard (Hayman's and Griffing's) analyses of diallel tables and the Wr/Vr relationship are found to apply even though the trait under investigation is expressed in a triploid state. It is further revealed that reciprocal effects can only be detected unambiguously in the F 2 diallel and the additive and non-additive effects cannot be separated in the B 1 and B 2 diallels when they are analysed separately. Analysis of the experimental data reveals that additive and dominance effects are the main sources of variation among the 21 crosses of the 7 times 7 diallel. Comparisons of the B 1 and B 2 diallels also show that the single dosage dominance (h a1 type) effects differ significantly from the double dosage dominance (h a2 type) effects. In addition, cytoplasmic control of amylose content is confirmed unambiguously and a large proportion of the heritable variation is shown to be controlled by a series of multiple alleles with large effects.

Genetical control of amylose content in selected crosses of indica rice

Models of Pooni et al. (1992) were employed to investigate the genetic control of amylose content in 10 rice crosses produced by the pairwise crossing of five varieties representing almost the whole range of amylose levels from 0 to 28 per cent. Analyses of the first-degree statistics revealed an important role of the additive and the dominance effects in determining the genetic variability in all the crosses. Epistasis and cytoplasmic effects were also observed to contribute significantly to the variability among the generation means of most crosses. Dominance was generally towards the higher score and its effects were enhanced by a complementary dominance x dominance interaction in several sets of basic generations. The predominantly additive nature of the genetic variability was further revealed by the analyses of second-degree statistics. Component D was detected significant in all the crosses while components H1 and H2 were non-significant throughout. Significance of the covariance components F' and F, however, showed indirectly that dominance contributed significantly to variability at the variance level. Higher levels of transgression and considerable increases in the phenotypic ranges displayed by the segregating generations of various crosses, also pointed to their potency for yielding superior recombinants with diverse levels of amylose.

A major photoperiod-sensitivity gene tagged with RFLP and isozyme markers in rice

Photoperiod-sensitive rice (Oryza sativa L.) cultivars are widely grown in rainfed lowland areas with unfavorable water regimes. A molecular marker for the trait would be useful in genetic and physiological studies and in developing improved photoperiod-sensitive cultivars. Previous genetic studies identified a major gene for photoperiod sensitivity on chromosome 6. We have tested an isozyme marker and several RFLP probes mapping to chromosome 6 in an attempt to identify marker(s) tightly linked to photoperiod sensitivity in tropical rice cultivars. We report here that the isozyme gene Pgi-2 is linked (23.2±4.7 cM) to the photoperiod-sensitivity gene in the cultivar GEB-24. Although association of duration with Pgi-2 alleles can be used to detect segregation of the photoperiod sensitivity gene in crosses, it will probably not be useful as a marker in selection because of its loose linkage. In contrast, a gene for photoperiod sensitivity in the cultivar Puang Rai 2 was found to be closely linked to the rice genomic clone RG64. Among 15 F3 lines homozygous for photoperiod insensitivity, no recombinants were detected with RG64. This clone is thus an excellent probe to follow segregation of the major photoperiod-sensitivity gene in rice crosses.

Comparison of single seed descent and anther culture-derived lines of three single crosses of rice

Distribution parameters (mean, variance, skewness and kurtosis) of 12 quantitative traits were evaluated for inbred lines generated through single seed descent (SSD) and anther culture (AC) of two japonica x japonica hybrids and one japonica x indica hybrid of rice. For most of the traits the data were normally distributed, and the means and variances were found to be identical for SSD- and AC-derived lines of the given hybrids. However, for some other traits, differences between the two population types were observed, mainly in the lines derived from the intra-japonica crosses. A tentative explanation for these differences is given. Nevertheless, our results suggest that SSD and AC are equally effective breeding techniques for producing agronomically useful lines of rice.