Genetic analysis of two weak dormancy mutants derived from strong seed dormancy wild type rice N22 (Oryza sativa)

Two weak dormancy mutants, designated Q4359 and Q4646, were obtained from the rice cultivar N22 after treatment with 400 Gy ⁶⁰Co gamma‐radiation. Compared to the N22 cultivar, the dormancy of the mutant seeds was more readily broken when exposed to a period of room temperature storage. The mutants also showed a reduced level of sensitivity to abscisic acid compared to the N22 cultivar, although Q4359 was more insensitive than Q4646. A genetic analysis indicated that in both mutants, the reduced dormancy trait was caused by a single recessive allele of a nuclear gene, but that the mutated locus was different in each case. The results of quantitative trait locus (QTL) mapping, based on the F₂ population from Q4359 x Nanjing35, suggested that Q4359 lacks the QTL qSdn‐1 and carries a novel allele at QTL qSdn‐9, while a similar analysis of the Q4646 x Nanjing35 F₂ population suggested that Q4646 lacks QTL qSdn‐5, both qSdn‐1 and qSdn‐5 are major effect seed dormancy QTL in N22. Therefore, these two mutants were helpful to understand the mechanism of seed dormancy in N22.     

Inheritance of vector competence by the thrips Ceratothripoides claratris (Shumsher) (Thysanoptera: Thripidae)

The thrips Ceratothripoides claratris is an efficient vector of the Capsicum chlorosis virus (CaCV). Transmission studies with a natural population of C. claratris found in a greenhouse ‘GH’ and a ‘colony’ derived from this ‘GH’ population by selection and inbreeding resulted in lowering the percentage of viruliferous individuals within the ‘colony’. After passing through approximately 20 generations, the ‘colony’ lost the ability to transmit the CaCV. When either viruliferous or non‐viruliferous virgin females reproduced parthenogenetically, 81% of F1 arrhenotokous males inherited their viruliferous status from their mothers, whilst, no viruliferous offspring arose from non‐viruliferous virgin mothers. Crosses between viruliferous and non‐viruliferous individuals suggest that the competence of the thrips C. claratris as a vector for this virus is probably a heritable trait controlled by a recessive allele.     

Genotyping the Heading Date of Male-Sterile Rice Line II-32A

II-32A, an elite male-sterile line of rice （Oryza sativa L.）, has been widely used for the production of hybrid rice seed In China. Heading date In most combinations using II-32A shows transgressive Inheritance or similarity to the latter parent, but the genotype of II-32A with respect to major genes for heading time Is unknown. This limits the further exploitation of this sterile line In breeding and hybrid seed production. Using a number of major gene heading date Isogenlc lines and heading date QTL near-lsogenic lines, we genetically analyzed II-32B under both long- and short-day conditions. We show that II-32B carries two photoperlod-sensltlve genes, E1 and E3, a recessive late-heading gene, ef-l, and a photoperlod-sensltlve allele, Se-1^u. In addition we Identified In II- 32B a recessive Inhibitor for E1 or Se-1^n and other modified photoperlod-sensltlve genes. The heading-date constitution of II-32A was determined to be E1e2E3Se-1^uef-li-Se-1.     

The hybrid protein interactome contributes to rice heterosis as epistatic effects

Heterosis is the phenomenon in which hybrid progeny exhibits superior traits in comparison with those of their parents. Genomic variations between the two parental genomes may generate epistasis interactions, which is one of the genetic hypotheses explaining heterosis. We postulate that protein?protein interactions specific to F₁ hybrids (F₁‐specific PPIs) may occur when two parental genomes combine, as the proteome of each parent may supply novel interacting partners. To test our assumption, an inter‐subspecies hybrid interactome was simulated by in silico PPI prediction between rice japonica (cultivar Nipponbare) and indica (cultivar 9311). Four‐thousand, six‐hundred and twelve F₁‐specific PPIs accounting for 20.5% of total PPIs in the hybrid interactome were found. Genes participating in F₁‐specific PPIs tend to encode metabolic enzymes and are generally localized in genomic regions harboring metabolic gene clusters. To test the genetic effect of F₁‐specific PPIs in heterosis, genomic selection analysis was performed for trait prediction with additive, dominant and epistatic effects separately considered in the model. We found that the removal of single nucleotide polymorphisms associated with F₁‐specific PPIs reduced prediction accuracy when epistatic effects were considered in the model, but no significant changes were observed when additive or dominant effects were considered. In summary, genomic divergence widely dispersed between japonica and indica rice may generate F₁‐specific PPIs, part of which may accumulatively contribute to heterosis according to our computational analysis. These candidate F₁‐specific PPIs, especially for those involved in metabolic biosynthesis pathways, are worthy of experimental validation when large‐scale protein interactome datasets are generated in hybrid rice in the future.     

Genetics of gel consistency in rice (Oryza sativa L.)

Inheritance of gel consistency in rice was studied in crossés involving highamylose, low-gelatinizalion temperature parents with hard, medium, and soft gel consistency. The results of single-grain analysis of parents, F₁, F₂, B₁F₁, B₂F₂, and their reciprocal crosses from a single-season harvest showed that the differences between hard and soft, hard and medium, and medium and soft gel consistency are under monogenic control and that modifiers affect the expression of the trait. Multiple alleles at the same locus, hereby designated asgec ^a for medium gel consistency andgec ^b for soft gel consistency, were recessive to the wild type allele for hard gel consistency andgec ^a was dominant overgec ^b. The results indicate that selection for desired gel consistency can effectively be done in early segregating generations.     

Mapping quantitative trait loci associated with regeneration ability of seed callus in rice, Oryza sativa L.

 Quantitative trait loci (QTL) controlling the regeneration ability of rice seed callus were detected using 245 RFLP markers and 98 BC₁F₅ lines derived from two varieties, ‘Nipponbare’ and ‘Kasalath’. Regeneration ability was evaluated by two indices: average number of regenerated shoots per callus (NRS) and regeneration rate (RR). The BC₁F₅ lines showed continuous segregation for both indices. Five putative QTL for NRS (tentatively named qRg1, qRg2, qRg4a, qRg4b and qRg4c) located on chromosomes 1, 2 and 4 were detected. Digenic interaction among these detected QTL was not significant (P<0.01). Among the five QTL detected, four ‘Kasalath’ alleles and one ‘Nipponbare’ allele increased NRS. According to an estimate based on the nearest marker loci, the five QTL accounted for 38.5% of the total phenotypic variation of the BC₁F₅ lines. For RR, four putative QTL were detected on chromosomes 2 and 4, and all of these were in the same chromosomal regions as the NRS QTL. The four RR QTL accounted for 32.6% of the total phenotypic variation. Received: 7 November 1996 / Accepted: 25 April 1997     

Identifying signatures of sexual selection using genomewide selection components analysis

Sexual selection must affect the genome for it to have an evolutionary impact, yet signatures of selection remain elusive. Here we use an individual‐based model to investigate the utility of genome‐wide selection components analysis, which compares allele frequencies of individuals at different life history stages within a single population to detect selection without requiring a priori knowledge of traits under selection. We modeled a diploid, sexually reproducing population and introduced strong mate choice on a quantitative trait to simulate sexual selection. Genome‐wide allele frequencies in adults and offspring were compared using weighted F_ST values. The average number of outlier peaks (i.e., those with significantly large F_ST values) with a quantitative trait locus in close proximity (“real” peaks) represented correct diagnoses of loci under selection, whereas peaks above the F_ST significance threshold without a quantitative trait locus reflected spurious peaks. We found that, even with moderate sample sizes, signatures of strong sexual selection were detectable, but larger sample sizes improved detection rates. The model was better able to detect selection with more neutral markers, and when quantitative trait loci and neutral markers were distributed across multiple chromosomes. Although environmental variation decreased detection rates, the identification of real peaks nevertheless remained feasible. We also found that detection rates can be improved by sampling multiple populations experiencing similar selection regimes. In short, genome‐wide selection components analysis is a challenging but feasible approach for the identification of regions of the genome under selection.     

Identification of a New Rice Low-Tiller Mutant and Association Analyses Based on the SLAF-seq Method

By studying the regulatory mechanism by which rice tillers are controlled, many rice mutants were described as providing important insights into the investigation of tillering control. In this study, we surveyed a new rice mutant produced by ethyl methane sulfonate induction, designated as Oryza sativa low-tiller 1 (oslt1), which had been planted to the fourth generation and proved to stably inherit the low-tillering trait. The statistical analysis of the number of tillers in oslt1 showed that there was a significant lack of tillering in the mutant lines, with the average number being 2.33 as opposed to 8.00 in wild-type plants. The data from a series of crossed populations, including F₂ populations produced by selfing of the offspring of oslt1?×?ptb and backcross populations of the F₁ generation?×?oslt1, indicated that a single recessive gene controlled the low-tillering trait. To locate the recessive gene, the crossed population in the F₂ generation from two parents, oslt1 and Peiai 64, was constructed and the population was used for bulked segregate analysis based on specific locus amplified fragment-sequencing (SLAF-seq) method. The results showed that approximately 100 differential markers were procured by analyzing 7437 polymorphic SLAFs and 1 primary region associated with low-tillering characteristics located on Chr12. In the associated regions, there were 34 candidate genes of 0.24 Mb that might be related to the number of low tillers in oslt1 plants. All of these results are necessary for further fine mapping for this low tillering-related gene. In addition, these identified SLAF-tags will be valuable for marker-assisted selection in rice breeding.     

QTL analysis for rice grain length and fine mapping of an identified QTL with stable and major effects

Grain length in rice plays an important role in determining rice appearance, milling, cooking and eating quality. In this study, the genetic basis of grain length was dissected into six main-effect quantitative trait loci (QTLs) and twelve pairs of epistatic QTLs. The stability of these QTLs was evaluated in four environments using an F₇ recombinant inbred line (RIL) population derived from the cross between a Japonica variety, Asominori, and an Indica variety, IR24. Moreover, chromosome segment substitution lines (CSSLs) harboring each of the six main-effect QTLs were used to evaluate gene action of QTLs across eight environments. A major QTL denoted as qGL-3a, was found to express stably not only in the isogenic background of Asominori but also in the recombinant background of Asominori and IR24 under multiple environments. The IR24 allele at qGL-3a has a positive effect on grain length. Based on the test of advanced backcross progenies, qGL-3a was dissected as a single Mendelian factor, i.e., long rice grain was controlled by a recessive gene gl-3. High-resolution genetic and physical maps were further constructed for fine mapping gl-3 by using 11 simple sequence repeat (SSR) markers designed using sequence information from seven BAC/PAC clones and a BC₄F₂ population consisting of 2,068 individuals. Consequently, the gl-3 gene was narrowed down to a candidate genomic region of 87.5 kb long defined by SSR markers RMw357 and RMw353 on chromosome 3, which provides a basis for map-based cloning of this gene and for marker-aided QTL pyramiding in rice quality breeding.     

Occurrence and genetics of black‐eyed migratory locusts,Locusta migratoria (Orthoptera: Acrididae)

Black‐eyed Locusta migratoria appeared in albino locusts as a result of crossing between a short‐winged strain originating from Tsushima Island, Japan, and an albino strain originating from Okinawa Island. The black eye trait was recessive to the white eye trait because the crosses between black‐ and white‐eyed albino locusts produced only individuals with white eyes in the F₁ generation. In the F₂ generation, black‐ and white‐eyed individuals appeared in a ratio of 1:3, indicating that the black eye trait was controlled by a simple Mendelian unit. The black eye trait showed no genetic association with other traits including wing morph, adult body dimensions and classical morphometric ratios such as hind femur length / head width and forewing length / hind femur length.     

QST–FST comparisons with unbalanced half‐sib designs

Q_ST, a measure of quantitative genetic differentiation among populations, is an index that can suggest local adaptation if Q_ST for a trait is sufficiently larger than the mean F_ST of neutral genetic markers. A previous method by Whitlock and Guillaume derived a simulation resampling approach to statistically test for a difference between Q_ST and F_ST, but that method is limited to balanced data sets with offspring related as half‐sibs through shared fathers. We extend this approach (i) to allow for a model more suitable for some plant populations or breeding designs in which offspring are related through mothers (assuming independent fathers for each offspring; half‐sibs by dam); and (ii) by explicitly allowing for unbalanced data sets. The resulting approach is made available through the R package QstFstComp.     

Non‐random segregation of an autosomal gene in males of the flea beetle,Phyllotreta nemorum: implications for colonization of a novel host plant

The flea beetle, Phyllotreta nemorum (L.) (Coleoptera: Chrysomelidae: Alticinae), is currently expanding its host plant range in Europe. The ability to utilize a novel host plant, Barbarea vulgaris R. Br. (Brassicaceae), is controlled by major dominant genes named R‐genes. The present study used extensive crossing experiments to illustrate a peculiar mode of inheritance of the R‐gene in a population from Delemont (Switzerland). When resistant males from Delemont are mated with recessive females from a laboratory line, the female F₁ offspring contains the R‐allele and is able to utilize B. vulgaris, whereas the male offspring contains the r‐allele and is unable to utilize the plant. This outcome suggests X‐linkage of the R‐gene, but further crossing experiments demonstrated that this was not the case. When the R‐gene is present in offspring from males from a laboratory line that originates from Taastrup (Denmark), it is transmitted to female and male offspring in equal proportions as a normal autosomal gene. The results demonstrate a polymorphism in segregation patterns of an autosomal R‐gene in P. nemorum males. Males from Delemont contain a factor which causes non‐random segregation of the R‐gene (NRS‐factor). This factor is inherited patrilineally (from fathers to sons). Males with the NRS‐factor transmit the R‐gene to their female offspring, whereas males without the NRS‐factor transmit the R‐gene to female and male offspring in equal proportions. Various models for the non‐random segregation of autosomes in P. nemorum males are discussed – e.g., fusions between autosomes and sex chromosomes, and genomic imprinting. The implications of various modes of inheritance of R‐genes for the ability of P. nemorum populations to colonize novel patches of B. vulgaris are discussed.     

Die genetische Grundlage der Monogenie bei der Schmei?fliege Chrysomya rufifacies (Calliphoridae, Diptera)

Summary Recently in our wild stock of the monogenic blowfly Chrysomya rufifacies a recessive mutation white (w) causing white instead of red-brown eyes spontaneously appeared (Fig. 1). This marker gene enabled us to clarify the genetic basis of monogeny in this species. F₁ offspring produced by reciprocal crossings between normal (+/+) and white-eyed (w/w) flies were phenotypically wildtype (Table 1). In F₂ offspring of female-producing (thelygenic) and male-producing (arrhenogenic) F₁ females wildtype and white-eyed flies appeared in the expected 3:1 ratio; in several crossings a slight deviation of this ratio indicated a reduced viability of the w/w individuals (Table 2). Examination of F₂ progeny of thelygenic F₁+/w females, which had received the w allele from their father, showed that most of the F₂+/+ females were thelygenic, whereas most of the F₂ w/w females were arrhenogenic; among F₂+/w females thelygenic and arrhenogenic individuals occurred in almost equal numbers (Table 3). On the other hand, when F₂ offspring of thelygenic F₁+/w females which had inherited the w allele from their mother were tested, most of the F₂+/+ females turned out to be arrhenogenic and most of the F₂ w/w females thelygenic; among F₂+/w females thelygenic and arrhenogenic flies also were found in almost equal frequencies (Table 4). the sex-linked inheritance of the factor w following from these results was also confirmed by an analysis of the progeny of thelygenic F₁+/w females backcrossed with w/w males. Among the R₁ offspring of F₁+/w females, which had received the w allele from their father, the +/w females were predominantly thelygenic compared to their predominantly arrhenogenic w/w sisters (Table 5). Analysis of R₁ progeny of F₁+/w females, which had inherited the w allele from their mother, yielded reciprocal results (Table 6).This mode of incomplete sex-linkage of the mutation white observed in C. rufifacies (Figs. 2–5) supports the hypothesis that thelygenic females are heterozygous for a dominant female sex realizer (F') with predetermined sex-determining properties, and that arrhenogenic females as well as the males are homozygous for the recessive allele f (Fig. 6). The recombination frequency between F'/f and the w-Locus was calculated to be 12.72±0.72 per cent.

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Mit Unterstützung durch die Deutsche forschungsgemeinschaft.     

Investigation of partial sterility in advanced generation,sodium azide-induced lines of spring barley

Summary The partial sterility found in several advanced generation, sodium azide-induced lines of spring barley (Hordeum vulgare L.) was investigated. Plants of mutant lines were reciprocally crossed with plants of their untreated mother lines. Spike sterility was measured in the selfed offspring of the plants crossed and in F₁ and F₂ progeny. Pollen sterility and endosperm development were analyzed in the selfed offspring of the plants crossed. Results indicated that the sterility was inherited in the mutant lines and was not caused by translocations, inversions, endosperm lethals, embryo-endosperm lethals, or major gene mutations. Furthermore, the sterility was not cytoplasmically inherited, and was essentially eliminated in the F₁ and F₂ of crosses between partially sterile lines and their fertile parents. Results suggest that the sterility may be caused by an environmental interaction with deleterious, homozygous recessive, minor gene mutations that were in the heterozygous condition when the mutant lines were originally selected.Scientific paper No. 7441, College of Agriculture Research Center, Washington State University, Pullman, Wash., USA, Project No. 1006     

A loss‐of‐function allele of OsHMA3 associated with high cadmium accumulation in shoots and grain of Japonica rice cultivars

Excessive cadmium (Cd) accumulation in rice poses a risk to food safety. OsHMA3 plays an important role in restricting Cd translocation from roots to shoots. A non‐functional allele of OsHMA3 has been reported in some Indica rice cultivars with high Cd accumulation, but it is not known if OsHMA3 allelic variation is associated with Cd accumulation in Japonica cultivars. In this study, we identified a Japonica cultivar with consistently high Cd accumulation in shoots and grain in both field and greenhouse experiments. The cultivar possesses an OsHMA3 allele with a predicted amino acid mutation at the 380^th position from Ser to Arg. The haplotype had no Cd transport activity when the gene was expressed in yeast, and the allele did not complement a known nonfunctional allele of OsHMA3 in F₁ test. The allele is present only in temperate Japonica cultivars among diversity panels of 1483 rice cultivars. Different cultivars possessing this allele showed greatly increased root‐to‐shoot Cd translocation and a shift in root Cd speciation from Cd―S to Cd―O bonding determined by synchrotron X‐ray absorption spectroscopy. Our study has identified a new loss‐of‐function allele of OsHMA3 in Japonica rice cultivars leading to high Cd accumulation in shoots and grain.     

Inheritance of the red color in tilapias

The inheritance of the red color was studied in two different varieties of tilapia which are both considered as hybrids of Oreochromis mossambicus. Crosses between red tilapia from the Philippines (PRT) and Sarotherodon galilaeus, or Oreochromis aureus gave a 1:1 ratio of red: normal and crosses between F₁ black fish gave only black offspring. On the other hand crosses between the F₁ red fish gave a 3:1 ratio of red:black and crosses between F₁ red and black offspring gave a 1:1 ratio. These results lead to the conclusion that red color is dominant over the normal black color and controlled by a single autosomal gene (R). A unique phenotype named albino with black eyes was observed among offspring of PRT and a presumed model of inheritance of this trait is proposed. Genetic analysis of a second variety of red tilapia (derived from an unknown origin) showed the following results: crosses between parents and between their F₁ offspring consistently gave 100% red fish and crosses between this red tilapia and Oreochromis aureus gave 100% black offspring. The crosses between red and black F₁ of these last two crosses gave a 1:1 ratio and crosses carried out between the black F₁ offspring gave a 1:3 ratio of red:black. It may be concluded from these results that the black color is dominant in this strain and that this color is controlled by a single autosomal gene (B). The presumed mode of action of the dominant gene (R) as well as of the recessive gene (b) are discussed.     

QTL analysis and mapping of pi21, a recessive gene for field resistance to rice blast in Japanese upland rice

Field resistance is defined as the resistance that allows effective control of a parasite under natural field conditions and is durable when exposed to new races of that parasite. To identify the genes for field resistance to rice blast, quantitative trait loci (QTLs) conferring field resistance to rice blast in Japanese upland rice were detected and mapped using RFLP and SSR markers. QTL analysis was carried out in F₄ progeny lines from the cross between Nipponbare (moderately susceptible, lowland) and Owarihatamochi (resistant, upland). Two QTLs were detected on chromosome 4 and one QTL was detected on each of chromosomes 9 and 12. The phenotypic variation explained by each QTL ranged from 7.9 to 45.7% and the four QTLs explained 66.3% of the total phenotypic variation. Backcrossed progeny lines were developed to transfer the QTL with largest effect using the susceptible cultivar Aichiasahi as a recurrent parent. Among 82 F₃ lines derived from the backcross, resistance segregated in the expected ratio of resistant 1 : heterozygous 2 : susceptible 1. The average score for blast resistance measured in the field was 4.2 ± 0.67, 7.5 ± 0.51and 8.2 ± 0.66, for resistant, heterozygous and susceptible groups, respectively. The resistance gene, designated pi21, was mapped on chromosome 4 as a single recessive gene between RFLP marker loci G271 and G317 at a distance of 5.0 cM and 8.5 cM, respectively. The relationship to previously reported major genes and QTLs conferring resistance to blasts, and the significance of marker-assisted selection to improve field resistance, are discussed. Received: 8 June 2000 / Accepted: 24 November 2000     

A method for adjusting allele frequencies in the case of microsatellite allele drop‐out

A new method is proposed to adjust allele frequencies when allelic drop‐out is common. This method assumes Hardy–Weinberg equilibrium (HWE), and treats the problematic alleles as a one‐locus two‐allele system with dominance. By assuming that the homozygote frequency of the ‘recessive’ allele is measured correctly, we can back calculate the allele frequency of the ‘dominant’ allele, and adjust the heterozygote frequency accordingly. The drawback is that multilocus genotypes cannot be constructed and tests that use deviations from Hardy–Weinberg such as tests for bottlenecks become impossible. An example is given where a large homozygote excess (F_IS = 0.44) is adjusted to a reasonable level (F_IS = 0.046). The effect of scoring error was set in relation to sampling error and while F_IS values can be seriously biased, F_ST values are not necessarily so, if scoring error and sample size are both low. As sample size increases, the effect of scoring error increases.     

Mapping of QTLs conferring extremely early heading in rice (Oryza sativa L.)

Two genes related to extremely early heading were identified in populations derived from crosses between Hoshinoyume, a variety adapted to the northernmost limit of rice cultivation (Hokkaido), and Nipponbare, a variety adapted to the temperate region of Japan. The segregations for heading date clearly revealed that a two-gene model determined the extremely early heading in the F₂ and BC₁F₁ populations under natural field conditions in Hokkaido. Using molecular markers corresponding to ten known quantitative trait loci (QTLs) for heading date, we carried out QTL analysis in the BC₁F₁ population and detected two QTLs, qDTH-7-1 and qDTH-7-2, both on chromosome 7, and observed epistatic interaction between them. We conclude that the recessive alleles of these two genes contribute to extremely early heading for the adaptation to Hokkaido environment and to stable rice production in Hokkaido. The relationships between the two QTLs identified in this study and known QTLs are discussed.