The semidwarf gene,sd-1, of rice (Oryza sativa L.). II. Molecular mapping and marker-assisted selection

To establish the location of the semidwarf gene, sd-1, the anthocyanin activator (A), purple node (Pn), purple auricle (Pau), and the isozyme locus, EstI-2, in relation to DNA markers on the molecular linkage map of rice, 20 RFLP markers, previously mapped to the central region of chromosome 1 (McCouch et al. 1988), were mapped onto an F₂ population derived from the cross Taichung 65 (A,Pn,Pau)/Taichung 65 (sd-1). sd-1 and EstI-2 were determined to be linked most tightly to RFLP markers RG 109 and RG 220, which cosegregated with each other. The distance between these RFLP markers and sd-1 was estimated to be 0.8 cM, based on an observed recombination value of 0.8%. The order of genes and markers in this region of chromosome 1 was determined to be sd-1 — (EstI-2 — RG220 — RG109) — RG381 — A — Pn — Pau. To test the efficacy of selection for sd-1 based on these linked markers, 50-day-old F₂ seedlings derived from another cross, Milyang 23/Gihobyeo, were analyzed for marker genotype. At this age, the semidwarf character could not be clearly detected based on phenotype. In addition, plant height was normally distributed in this population, making it difficult to unambiguously identify plants carrying sd-1. Thirteen seedlings homozygous for the sd-1-associated allele at EstI-2, RG220 and RG109, and 13 seedlings homozygous for the Sd-1-associated allele at all three marker loci were selected for further genetic analysis. At 20 days after heading, the culm lengths of these 26 plants were measured and the expected phenotype was confirmed in every case. These 26 plants were then selfed for four generations and F₆ lines were again evaluated to determine whether any recombination among the three molecular markers, or between these markers and the sd-1 gene, could be detected. No recombinants were identified, confirming the tight linkage of these loci and the usefulness of genotypic selection for this recessive semidwarf character prior to the time when it can be evaluated based on phenotype.     

Genes for Dwarfness in Wheat, TRITICUM AESTIVUM L

The genetic control of plant height was studied in crosses of four spring wheats involving the standard height variety Ramona 50 and short-statured selections Olesen, D6301, and D6899. Data from parent, F₁, F₂, and F₃ populations indicated that four independently segregating loci account for most of the differences among the four varieties. Two major genes of a highly recessive nature condition reduced height in Olesen and the Norin 10 derivative D6301. Olesen also carries a third dwarfing gene which is partially dominant in its effects over genes for tallness. This gene, or a gene that acts in a similar manner, is also present in the standard height variety Ramona 50. Dwarfing in D6899, a derivative of Tom Thumb, is controlled primarily by a single gene with mainly additive effects which is not present in any of the other three varieties.

Genetic components estimated from generation means (parental, F₁, F₂, F₃, and backcross) indicated that additive gene effects were the major component of variation in four of the six crosses, and of similar magnitude to dominance effects in another cross. The primary source of genetic variation in the cross Olesen x D6899 was due to epistasis with both additive x additive and dominance x dominance effects of major importance. The results of the generation mean analyses were consistent with the models for major-gene control of plant height based on segregation patterns.

     

Genetic studies of yield contributing traits in Amaranthus

Summary Genetical studies on grain yield and its contributing traits were made in a six parent complete diallel in the F₁ and F₂ generations of one of the most widely grown grain species of grain amaranths (Amaranthus hypochondriacus L.). Graphical analysis indicated that epistasis exists for 1,000-grain weight in the F₁. Grain weight/panicle, yield/plant and harvest index indicated absence of non-allelic gene interaction. The harvest index in the F₁ and F₂ and grain weight/ panicle, 1,000-grain weight, yield/plant in the F₂ appeared to be controlled by overdominance effects. Higher grain yield appeared to be associated with dominant genes. Both additive and non-additive gene effects were responsible for the genetic variation in the diallel population. However, dominance variance was more important than additive variance in grain yield/ plant and harvest index in the F₁ and F₂. For 1,000-grain weight additive genetic variance was more important in the F₁ and non-additive in F₂. There was overdominance of a consistent nature in the two analyses for harvest index in the F₁ and F₂, grain weight/ panicle, 1,000-grain weight and yield/plant in the F₂ and partial dominance for 1,000-grain weight in the F₁.     

Diallel analysis for some quantitative characters in Petunia hybrida Hort

Summary Flowering time, plant height and flower size in Petunia hybrida Hort. (multiflora type) have been genetically analysed by means of a 5 × 5 diallel cross. The results indicated that: (1) the three characters are controlled by additive-dominance polygenic systems. The contribution of the additive gene actions to the genetic variance of flowering time was relatively higher than that of dominance. The reverse situation was found for plant height and flower size. (2) Dominance is ambi-directional for the three characters. Ratios of average dominance were in the range of partial for flowering-time, complete for plant height and overdominance for flower size. (3) Number of genes (or gene groups) controlling the characters are about 3, 3 and 5 for flowering time, plant height and flower size: respectively, (4) Heritability estimates are 0.84, 0.88 and 0.89 in the broad-sense and 0.40, 0.49 and 0.37 in the narrow-sense, for flowering time, plant height and flower size; respectively. (5) Heterosis as percent increase of the mean F₁-hybrid above the higher parent, or decrease below the lower parent, was observed for flowering time (+ 9.7% to +13.3%), for plant height (–13.6% to –20.3%) and for flower size (+2.5% to +16.0%).     

Inheritance of adult field resistance to yellow rust disease among broad-based hexaploid spring wheat germplasm

 Complete F₁ and F₂ diallel crosses were used to investigate the inheritance of yellow rust resistance among eight bread wheat lines, developed by CIMMYT for the East African Highlands, which showed a wide response to this disease. Both diallel sets were grown at a site with a high incidence of yellow rust, although for one season, during which the F₁ diallel was grown, disease incidence was unusually low. Analyses disclosed the presence of additive, dominance and epistatic effects among those genes controlling rust resistance, with the former being the most important. At normal disease levels, excluding two arrays having resistant common parents removed non-allelic interactions from the F₁ diallels. For all F₂ diallels, and the remaining F₁ diallel, omitting two arrays based on susceptible parents removed these interactions. Local selection of material from a broadly based germplasm appears to be a feasible method of developing adapted cultivars resistant to endemic diseases. Received: 1 March 1998 / Accepted: 19 March 1998     

Genetics of Heading Time in Wheat (TRITICUM AESTIVUM L.). II. the Inheritance of Vernalization Response

The inheritance of vernalization response was studied in crosses involving four spring wheats (Sonora 64 (S), Pitic 62 (P), Justin (J) and Thatcher (T)) and three winter wheats (Blackhull (B), Early Blackhull (E) and Extra Early Blackhull (EE)).—All winter cultivars were highly responsive to vernalization, and Pitic 62 was the only spring cultivar whose time to heading was significantly accelerated following cold treatments. When vernalized and grown under long days, spring and winter cultivars became comparable in their heading response, indicating that cold requirement is the major attribute differentiating the heading behavior of true spring and true winter wheats.—Inheritance of growth habit in the F₁ generation of a five-parent diallel cross showed dominance of the spring character in all spring x winter crosses. Depending on the cross, one or two duplicate major genes governing growth habit were detected in F₂, F₃ and backcross generations grown in the field under long days in the absence of vernalizing temperatures. In some spring x winter crosses most of the variation in heading time among spring segregates could be attributed to the effects of major genes conditioning growth habit. In other crosses the heading patterns appeared more complex, indicating that genes with smaller effects are also involved in the control of heading response under spring or summer environments.—Evidence was presented supporting the hypothesis that the cultivar Pitic 62 carries a different allele at one of the two major loci governing its spring habit. This allele was associated with some response to vernalization and acted as a dominant gene determining earliness under low temperature vernalization, but as a partially recessive gene determining lateness in the absence of vernalizing temperatures. Genotypes were assigned to five cultivars as follows: S, CC DD; P, CC D'D'; J, cc DD; B and EE, cc dd.—The presence of major and minor genes and of multiple alleles governing response to photoperiod and vernalization was discussed in relation to the genetic manipulation of the heading response and to breeding wheat cultivars with specific or broad adaptation.     

Diallel analysis of the latent period of stripe rust in wheat

A half diallel was made amongst five wheat (Triticum aestivum L.) genotypes of which one was susceptible, while the others had adult-plant resistance, to stripe rust (Puccinia striiformis West.). The five parent and ten F₁ progeny were grown in the glasshouse and were inoculated with three rust pathotypes at the seedling stage. The latent period was measured on the first leaf. Two procedures were used to analyze the half diallel. Both methods showed that the average effects of alleles were of much greater importance than was dominance in conditioning resistance in response to two of the pathotypes, while for the third pathotype dominance was important. Resistance was conditioned by partial dominance for two pathotypes whereas for the third it was determined by full dominance. Broad-sense heritabilities range from 60–73% and the number of genes involved was different (from 1 to 4), depending on the pathotype.     

Inheritance of resistance in cucumber to race 2 of Colletotrichum lagenarium

Summary The resistant breeding line, AR79-95, and the susceptible cultivar, Model, were crossed to develop F₁, F₂, F₃, and backcross populations for genetic analysis of resistance in cucumbers to race 2 of Colletotrichum lagenarium (Pass.) Ellis & Halsted., the causal agent of cucurbit anthracnose. There was no maternal effect on resistance and a small amount of F₁ heterosis toward the susceptible parent. Generation means analysis showed that there was additive and dominance but no epistatic gene action detected on the scale used. Additive and dominance genetic variances were estimated, and narrow-sense heritability was low to moderate. Based on effective factor formulae, at least five effective factors contrtolled the resistance. Some of these factors were dominant and others recessive. Implications for breeding procedures are discussed.     

Genetic Analysis of Oil Content in Brassica napus L. Using Mixed Model of Major Gene and Polygene

The joint segregation analysis of a mixed genetic model of major gene plus poly-gene was conducted to study the inheritance of oil content in Brassica napus L. Five populations, i.e the populations of 2 parents(P₁ and P₂), F₁, F₂ and F_2:3 (derived from F₂) family, from each of the two crosses (1141B × Ken C₁-1, 32B × Ken C₁-2) were investigated. The frequency distributions of oil content in F₂ and F_2:3 family populations show characteristics of a mixed normal distribution, which indicated that the inheritance of oil content followed a major gene plus poly-gene model. Twenty-one genetic models were established, which could be classified into five types: one and two major genes, polygenes, one and two major genes plus polygenes. The most suitable genetic model could be selected using Akaike's Information Criterion and the fitness of the selected one could be examined by a set of tests. Results show that genetic model D-2 is the most fitting genetic model for the trait. In other words, oil content in oilseed rape is controlled by one additive major gene plus additive and dominance polygenes. For cross 1 (1141B × Ken C₁-1) the heritabilities of major gene and poly-genes in F₂ are 68.21% and 27.17%, respectively, and in F_2:3 are 81.70% and 16.80%, respectively. The additive effect of major gene is-1.74, which indicates that the locus of the allele in parent 1141B may decrease the oil content, but that in parent Ken C₁-1 may increase it. The additive and dominance effects of the polygenes are 1.20 and -1.93, respectively. For cross 2 (32B × Ken C₁-2) the heritabilities of major gene and polygenes in F₂ are 66.20% and 28.10%, respectively, and in F_2:3 were 81.00% and 14.90%, respectively. The additive effect of major gene was -3.74, which also indicates that the locus of the allele in parent 32B may decrease the oil content, but that in parent Ken C₁-2 may increase it. The additive and dominance effects are -1.99 and 0.93, respectively. The heritability of the major gene in F_2:3 is higher than that in F₂ in both crosses, so it would be more efficent to conduct selection in F_2:3 families for high oil content in breeding.     

Epistasis in maize (Zea mays L.)

Summary Three flint and three dent maize (Zea mays L.) inbred lines, their possible F₁ crosses, F₂ and backcross progenies, and all possible three-way crosses were evaluated in a three-year experiment for yield, ear moisture, and plant height. The purpose was to estimate genetic parameters in European breeding materials from (i) generation means analysis, (ii) diallel analysis of generation means, and (iii) analysis of F₁ and three-way cross hybrids. Method (i) was based on the F-metric model and methods (ii) and (iii) on the Eberhart-Gardner (1966) genetic model; both models extended for heterotic maternal effects.Differences among generation means for yield and plant height were mainly attributable to dominance effects. Epistatic effects were significantly different from zero in a few crosses and considerably reduced heterosis in both traits. Additive x additive and domiance x dominance effects for yield were consistently positive and negative, respectively. Significant maternal effects were established to the advantage of generations with a heterozygous seed parent. In the diallel analysis, mean squares for dominance effects were greater than for additive effects for yield and plant height but smaller for ear moisture. Though significant for yield and plant height, epistatic variation was small compared to additive and dominance variation. Estimates of additive x additive epistasis for yield were significantly negative in 11 of 15 crosses, suggesting that advantageous gene combinations in the lines had been disrupted by recombination in the segregating generations. The analysis of hybrids supported the above findings regarding the analysis of variance. However, the estimates of additive x additive epistasis for yield were considerably smaller and only minimally correlated with those from the diallel analysis. Use of noninbred materials as opposed to materials with different levels of inbreeding is considered the main reason for the discrepancies in the results.     

Nature and type of gene action governing resistance to Helminthosporium turcicum leaf blight in maize (Zea mays L.)

Six generations, consisting of three resistant parents, three susceptible parents, their 15 possible F₁ crosses, 15 F₂'s, 15 BC₁'s (F₁ x resistant female parent) and 15 BC₂'s (F₁ x susceptible male parent) were analysed following Hayman (Heredity 12: 371–390, 1958) to evaluate the nature and type of gene action governing resistance to H. turcicum. The results showed that all types of gene effects, viz., additive, dominance and epistasis (i.e., additive x additive, additive x dominance and dominance x dominance) were operating in one cross or the other in controlling resistance. However, it was additive gene action and dominance x dominance type of epistasis with duplicate nature that were important in controlling resistance in most crosses. Depending upon the final objectives, one of the breeding methods, viz., recurrent selection, heterosis breeding, back-cross method or full-sib selection (bi-parental mating) may be followed.     

Genetic analysis of resistance to swede mildew

The incidence of swede mildew (Erysiphe cruciferarum) was analysed on three occasions in five swede varieties Crifel, Doon Major, Harvester, Ne Plus Ultra and Ruta Øtofte and their F₁ hybrids. Overall levels of infection were greater in Ne Plus Ultra and Harvester and least in Ruta Øtofte. Genetic analysis by the diallel method showed that initially resistance was recessive with Ruta Øtofte possessing most recessive genes but results from the final analysis showed partial dominance, with Ne Plus Ultra having most recessive and Harvester most dominant genes. The changing pattern of inheritance with time was due to variation in the rates of increase in disease incidence and diallel analyses of these rates, calculated by regression analyses over five observations, showed in almost entirely additive control. Although no variety was immune it was considered that except on soils of high pH or in the event of a marked change in the genetic composition of the pathogen the level of resistance in Ruta Øtofte was satisfactory.     

The semidwarf gene,sd-1, of rice (Oryza sativa L.). I. Linkage with the esterase locus,Estl-2

The linkage relationship between the semidwarf gene (sd-1) and the isozyme locus EstI-2 was elucidated using segregating populations derived from crosses between several semidwarf testers and tall rice varieties. Bimodal distributions for culm length were observed in F₂ populations of three cross combinations, including Shiokari/Shiokari (sd-1), Taichung 65 (A,Pn,Pau)/Taichung 65 (sd-1), and Milyang 23/Kasalath. Taking the valley of the distribution curves as the dividing point, two height classes were apparent with a segregation ratio of 3 tall1 short, demonstrating this character to be under the control of a single recessive gene. An inheritance study of esterase isozymes, based on isoelectric focusing (IEF), showed that the EstI-2 locus had two active allozymes of monomeric structure and one null form, which were designated a, b, and n, respectively (Eun et al. 1990). Semidwarf testers such as Shiokari (sd-1), Taichung 65 (sd-1) and Milyang 23 have an active allozyme designated as EstI-2^aa, while the tall parents, Shiokari and Taichung 65 (A,Pn,Pau), have the active allozyme, EstI-2^bb, and Kasalath has a null form of the allozyme, EstI-2ⁿⁿ. By dividing F₂ populations based on EstI-2 allozyme patterns, culmlength distributions exhibited trimodal curves. Most of the short plants had the homozygous EstI-2^aa pattern of the short parents, most of the tall plants had the homozygous pattern, EstI-2^bb or EstI-2ⁿⁿ, and most of the intermediate plants had the heterozygous EstI-2^ab or EstI-2^an banding pattern. Einkage analysis indicated that sd-1 and EstI-2 were tightly linked. These findings were also confirmed by segregation analyses in F₃ progenies. No recombinants among 171 F₃ families from the Shiokari/Shiokari (sd-1) combination, five recombinants among 267 F₃ families from Taichung 65 (A,Pn,Pau)/Taichung 65(sd-1), and only two recombinants out of 237 F₃ families from Milyang 23/Kasalath, were found. The recombination values were 0, 1.87 and 0.8%, respectively.     

Genetic analysis of resistance in Brussels sprout to cauliflower mosaic and turnip mosaic viruses

A total of 28 inbred lines of Brussels sprout were assessed in the glasshouse for their reaction to inoculation with cauliflower mosaic (CaMV) or turnip mosaic (TuMV) virus. There was significant variation for resistance to both viruses. From the 28 inbred lines parents were chosen for two 9 × 9 diallel crossing programmes. The parents and their F₁ progeny were assessed for their reaction to CaMV or TuMV in the field. There was significant additive and non-additive (dominance) variation but no maternal effects. Resistance to both viruses was generally dominant but with some evidence of a recessive gene for resistance to CaMV. Resistance to TuMV and CaMV was apparently controlled by at least four genes and two genes respectively. The heritability of resistance to each virus was high. The implications for breeding F₁ hybrid Brussels sprout cultivars are discussed.     

Epistatic gene effects on the yield of the parents of F1, F2, BC1 and BC2 progeny

The genetic analysis of 5 tomato hybrids (Danubius F₁, Luna F₁, Lido F₁, Balkan F₁ and Mi-10 F₁) was made. We produced their F₁, F₂, BC₁ and BC₂ generations and analysed their yield (on the first three flower branches) as well as some of the yield components of tomato fruits (mean fruit weight, mean fruit weight on the first flower branch, fruit length, fruit width, and number of locules). In order to estimate the gene effects, we applied the additive-dominance mode with three and six parameters. Epistatic gene effects were estimated by applying the six-parameter mode (Mather and Jinks 1982). As for yield and yield components, there were significant differences between the mean values of parents and their progeny. On the basis of the investigated genetic parameters, the obtained results suggested that the additive and dominance gene effects prevailed in the yield and yield components (Danubius F₁, Luna F₁, Lido F₁, Mi-10 F₁), whereas epistatic gene effects were excluded. As for the hybrid Balkan F₁, we recorded significant gene effects, both the additive and the dominance ones in the yield inheritance: additive x additive and dominance x dominance (with the negative sign). The estimated values of the epistatic gene effects were the most prominent in inheriting the feature average fruit weight on the first flower branch — additive x dominance gene effects. They represented the most frequent type of the interallele interaction recorded in the investigated hybrids.     

Relationships of differential gene expression in leaves with heterosis and heterozygosity in a rice diallel cross

Using differential display analysis, we assessed the patterns of differential gene expression in hybrids relative to their parents in a diallel cross involving 8 elite rice lines. The analysis revealed several patterns of differential expression including: (1) bands present in one parent and F₁ but absent in the other parent, (2) bands observed in both parents but not in the F₁, (3) bands occurring in only one parent but not in the F₁ or the other parent, and, (4) bands detected only in the F₁ but in neither of the parents. Relationships between differential gene expression and heterosis and marker heterozygosity were evaluated using data for RFLPs, SSRs and a number of agronomic characters. The analysis showed that there was very little correlation between patterns of differential expression and the F₁ means for all six agronomic traits. Differentially expressed fragments that occurred only in one parent but not in the other parent or in F₁ in each of the respective crosses were positively correlated with heterosis and heterozygosity. And conversely, fragments that were detected in F₁s but in neither of the respective parents were negatively correlated with heterosis and heterozygosity. The remaining patterns of differential expression were not correlated with heterosis or heterozygosity. The relationships between the patterns of differential expression and heterosis observed in this study were not consistent with expectations based on dominance or overdominance hypotheses.     

Inheritance of grain filling duration in spring wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L. em thell)

To understand the genetic control of grain filling duration (GFD), i.e., the number of days from anthesis to physiological maturity, we studied the F₁, F₂, BC1 and BC₂ generations of six spring wheat crosses from nine varieties/genotypes. Generation mean analysis for gene effects indicated that one or more types of epistasis were significant in all crosses. In each pairing, the F₁ and F₂ means were either intermediate or closer to the mean of the parent having the longer GFD. Our narrow-sense heritability estimate was reasonably high, at 47.67 (based on diallel analysis). This demonstrated that progress could be made from the selection in these crosses for either long or short GFD. The two early varieties that had identical maturity durations differed in their GFD values, indicating that maturity dates are not good criteria when choosing parents for modifying GFD. To utilize favorable additive × additive effects during this selection, we suggest that a single seed descent (SSD) or bulk popula-tion approach be adopted. In comparison, dominance effects would prove quite useful in hybrid wheat breeding programs.     

Gene effects for fibre properties in upland cotton (Gossypium hirsutum L.)

Summary Six populations — P₁,P₂,F₁,F₂,B₁ and B₂ — each of five Upland Cotton (Gossypium hirsutum L.) crosses were used to evaluate gene effects in the inheritance of fibre properties by Gamble's six-parameter model for the analysis of generation means. Partial dominance of long fibres over short fibres and of mature fibres over immature fibres was found in the material studied. Overdominance in gene action governed fibre fineness while additive gene action governed the fibre strength. Besides additive and dominance effects, significant epistasis was present in all crosses. These results indicate a significant potential for improving fibre properties through reciprocal recurrent selection.     

Transmission distortion and genetic incompatibilities between alleles in a multigenerational mouse advanced intercross line

While direct additive and dominance effects on complex traits have been mapped repeatedly, additional genetic factors contributing to the heterogeneity of complex traits have been scarcely investigated. To assess genetic background effects, we investigated transmission ratio distortions (TRDs) of alleles from parent to offspring using an advanced intercross line (AIL) of an initial cross between the mouse inbred strains C57BL/6NCrl (B6N) and BFMI860-12 [Berlin Fat Mouse Inbred (BFMI)]. A total of 341 males of generation 28 and their respective 61 parents and 66 grandparents were genotyped using Mega Mouse Universal Genotyping Arrays. TRDs were investigated using allele transmission asymmetry tests, and pathway overrepresentation analysis was performed. Sequencing data were used to test for overrepresentation of nonsynonymous SNPs (nsSNPs) in TRD regions. Genetic incompatibilities were tested using the Bateson–Dobzhansky–Muller two-locus model. A total of 62 TRD regions were detected, many in close proximity to the telocentric centromere. TRD regions contained 44.5% more nsSNPs than randomly selected regions (182 vs 125.9 ± 17.0, P < 1 × 10⁻⁴). Testing for genetic incompatibilities between TRD regions identified 29 genome-wide significant incompatibilities between TRD regions [P_(BF) < 0.05]. Pathway overrepresentation analysis of genes in TRD regions showed that DNA methylation, epigenetic regulation of RNA, and meiotic/meiosis regulation pathways were affected independent of the parental origin of the TRD. Paternal BFMI TRD regions showed overrepresentation in the small interfering RNA biogenesis and in the metabolism of lipids and lipoproteins. Maternal B6N TRD regions harbored genes involved in meiotic recombination, cell death, and apoptosis pathways. The analysis of genes in TRD regions suggests the potential distortion of protein–protein interactions influencing obesity and diabetic retinopathy as a result of disadvantageous combinations of allelic variants in Aass, Pgx6, and Nme8. Using an AIL significantly improves the resolution at which we can investigate TRD. Our analysis implicates distortion of protein–protein interactions as well as meiotic drive as the underlying mechanisms leading to the observed TRD in our AIL. Furthermore, genes with large amounts of nsSNPs located in TRD regions are more likely to be involved in pathways that are related to the phenotypic differences between the parental strains. Genes in these TRD regions provide new targets for investigating genetic adaptation, protein–protein interactions, and determinants of complex traits such as obesity.