Relationship between molecular marker heterozygosity and hybrid performance in intra- and inter-subspecific crosses of rice

The objective of this study was to investigate the relationship between molecular marker diversity and heterosis in both intra-and inter-sub-specific hybrids of rice to evaluate the feasibility of predicting hybrid performance using molecular markers. Eleven elite lines were intermated resulting in a diallel set including 10 indica × indica, 15 japonica × japonica and 30 indica × japonica crosses. The F₁ hybrids and parents were evaluated for agronomic performance in a replicated field trial. The parental lines were tested for DNA polymorphisms with 113 restriction fragment length polymorphism (RFLP) probes covering the 12 rice chromosomes. Inter-subspecific crosses showed better performance and higher heterosis than intrasubspecific hybrids. Correlations of marker heterozygosity with hybrid performance and heterosis differed considerably between the two subspecies; they were higher in crosses within japonica subspecies than within indica subspecies. Very little correlation was detected in intersubspecific crosses. It was concluded that relationships between marker heterozygosity and hybrid performance were complex owing to germplasm diversity and the complexity of the genetic basis of heterosis. The implications of the results in predicting hybrid performance using molecular markers are discussed.     

Heterosis in inter and intrasubspecific crosses over three-environments in rice

Moderate to high heterosis for yield and ten related characters was studied in 45 crosses involving six indica (I) and four tropical japonica (J) varieties of rice under three (E₁-optimum sowing and high fertility, E₂-both optimum sowing and fertility and E₃- late sowing and high fertility) environments. Trends of magnitude of heterosis for grain yield and plant height were I/J > I/I > J/J and for days to 50% flowering I/J > J/J > I/I hybrids. Estimates of standard heterosis (%) for grain yield were –64.5 to 146.1 in E₁, –70.4 to 82.2 in E₂ and –67.2 to 63.8 in E₃. Environment E₁ seemed to be more favorable for higher heterosis expression than others. Higher heterosis in yield also accompanied heterosis in panicle number, dry matter and spikelet and grain number per panicle. Most estimates for days to flower were negative. Heterotic I/J hybrids also recorded maximum heterosis for earliness. Moderate to low standard heterosis for plant height across environments (2.0 to 13.7%) was recorded. Hybrids were identified in specific environments for direct exploitation in hybrid breeding. Hybrids B4116 / Sarjoo 52, B4122 / Pant Dhan 4 and B4122 / Narendera 359 were more stable than others over three environments. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic effects and genotype × environment interactions for cooking quality traits in Indica-japonica crosses of rice (Oryza sativa L.)

Indica-japonica hybridization is an important approach for developing superior performing hybrids in rice (Oryza sativa L.). In view of the scanty information available on cooking quality characters in indica-japonica crosses, an investigation was undertaken to estimate genetic and genotype × environment variance and covariance components of amylose content, gel consistency and alkali digestion value, and to determine the relative importance of direct genetic effects, maternal genetic effects and cytoplasmic effects in the genetic variations of the three quality characters. Two indica photo-sensitive genic male sterile (PGMS) lines and four japonica varieties were used as parents to make crosses. Genetic model with genotype × environment interactions for triploid endosperm was used for genetic studies of the three cooking quality characters. Variance component analysis revealed that genetic variations of the three characters were mainly attributable to direct additive and maternal additive effects, and the three traits had significant direct and maternal heritabilities. Genotype × environment interactions were mainly dominance × environment (including direct dominance × environment and maternal dominance × environment) and cytoplasm × environment interactions. Environment factors could only affect the expression extent of dominant genes, without changing their directions. Predicted values of genetic effects indicated that the parental lines, ‘VI-70’ and ‘H9304-1’, appeared to be best for amylose content, ‘T 1950’ and ‘Suxuan’ appeared to be best for gel consistency and alkali digestion value. This revised version was published online in August 2006 with corrections to the Cover Date.     

Identification of restorers and maintainers for developing basmati and non-basmati hybrids in rice, Oryza sativa

Twenty‐seven improved aromatic lines of germplasm and 18 non‐aromatic disease‐resistant genotypes of rice were test‐crossed with four cytoplasmic male‐sterile lines (IR 58025A, IR 62829A, PMS 3A and PMS 10A). Thirteen aromatic and 10 non‐aromatic genotypes were selected based on pollen fertility, and crosses were repeated to confirm sterility‐maintaining and fertility‐restoring ability. Genotypes were categorized as effective restorers (> 80% spikelet fertility), partial restorers (21‐79% spikelet fertility) and maintainers (< 1% spikelet fertility). The effective basmati restorers identified were Basmati 385, Chandan, P1031‐8‐5‐1, HKR 241‐IET‐12020, SAF Khalsa 7 and Karnal Local. The basmati maintainers identified were Basmati 370, Pusa basmati 1, P615‐K‐167‐13 and P1173‐4‐1. The frequency of restorers obtained was higher for the non‐aromatic than the aromatic basmati type. The performance of restorers varied with cytoplasmic male‐sterile (CMS) line, location and season of testing. The differential ability to restore fertility in the CMS lines that have the wild abortive (WA) cytosterile system could result from different nuclear backgrounds of the CMS lines. These restorers and maintainers possess acceptable grain dimensions, a desirable degree of aroma, volume expansion through linear kernel elongation and cooking quality characteristics of basmati rice. These genotypes will contribute to developing basmati hybrids and provide restorers and maintainers with acceptable key basmati quality characteristics.     

Mapping and genetic analysis of two fertility restorer loci in the wild-abortive cytoplasmic male sterility system of rice (Oryza sativa L.)

Hybrid varieties developed by making use of the wild abortive cytoplasmic male sterility system account for 90% of hybrid rice produced. Previous inheritance studies have established that the fertility restoration in this system is controlled by two major loci, but the chromosomal locations of the fertility restorer (Rf) loci have yet to be resolved. In this study we determined the genomic locations of the two Rf loci by their linkage to molecular markers. The Rf gene containing regions were identified by surveying two bulks, made of 30 highly fertile and 46 highly sterile plants from a large F₂ population of the cross between Zhenshan 97A and Minghui 63, with RFLP markers covering the entire rice genome. The survey identified two likely Rf gene containing regions, located on chromosomes 1 and 10 respectively. This was confirmed by ANOVA using a large random sample from the same F₂ population and also with a genome-wide QTL analysis of a test-cross population. The results also showed that both loci have major effects of almost complete dominance on fertility restoration and the effect of the locus on chromosome 10 is larger than the one on chromosome 1. The two loci acted as a pair of classical duplicate genes; a single dominant allele at one of the two loci would suffice to restore the fertility to normal or nearly normal. Closely linked markers identified in this study may be used for marker assisted selection in hybrid rice breeding programs. This revised version was published online in July 2006 with corrections to the Cover Date.     

Identification of two types of differentiation in cultivated rice (Oryza sativa L.) detected by polymorphism of isozymes and hybrid sterility

Magnitudes of genetic variation within each of major varietal groups of cultivated rice were surveyed in terms of isozyme polymorphism and allelic differentiation of hybrid sterility loci, both of which are considered to have litt le selective value. Allelic differences for 20 isozyme loci were examined in a total of 337 accessions, including Indica and Japonica rices. Aus cultivars from India, Javanica cultivars and both landraces and cultivars from China. Eleven out of the 20 isozyme loci were polymorphic. The Aus cultivars contained more alleles per locus than others. The hybrid sterilities in the crosses among Chinese cultivars, Indica and Japonica cultivars were mainly controlled by locus S-5, whereas the hybrid sterilities of Aus cultivars, when they were crossed to Indica, Japonica or Javanica cultivars, were found to be controlled by allelic interaction at hybrid sterility loci S-5, S-7, S-9 and S-15. Also in terms of the number of alleles at S-5 and S-7, Aus cultivars contained more alleles than others. While the Aus group showed an extreme diversity for both hybrid sterility alleles and isozymes, modern cultivars from the south of YangZi River in China were classified into Indica type and those from the north were into Japonica, which were almost the same as those in Japan. On the basis of the measured polymorphism the Indica-Japonica differentiation was explained by founder effects, i.e., through selection and distribution of two original sources each with a unique set of markers. Contrastingly, the continuous and pronounced diversity in the Aus group was attributed to the absence of such a process. The intermediate groups in Yunnan province and Tai-hu Lake region of China are considered to be isolated from such founder effects, retaining an intermediate diversity in terms of isozymes and hybrid sterility genes. Since hybrid sterility hampers the exchange of genes between cultivars of different groups, the understanding of its genetic basis will be important in rice breeding, particularly in hybrid rice breeding. This revised version was published online in July 2006 with corrections to the Cover Date.     

An analysis of hybrid sterility in rice using a diallel cross of 21 parents involving indica, japonica and wide compatibility varieties

Summary There is much interest in the inter-varietal fertility of Asian cultivated rice. In this study, we analyzed the fertility of hybrids in a diallel set of 210 crosses involving 21 parents representing a broad range of the cultivated rice germplasm including landraces, primitive cultivars, modern elite cultivars and parents of hybrid rice. The materials were also carefully selected with respect to indica-japonica classification including typical indica/japonica, more or less intermediate and wide compatibility varieties. The level of hybrid fertility varied widely among the crosses from almost completely sterile to fully fertile. In general, hybrid fertility of intra-subspecific crosses, i.e., indica by indica (I×I) and japonica by japonica (J×J), is much higher than inter-subspecific crosses (I×J or J×I). The fertility varied widely in hybrids involving wide compatibility varieties and also in inter-subspecific crosses not involving wide compatibility varieties. An analysis of variance showed that both the main effects of indica and japonica parents and the interaction between the parents are highly significant in determining hybrid fertility. We speculate that, in addition to wide compatibility, the overall genetic difference between the indica and japonica parents, that may involve a series of minor mutations, play an important role in determining the hybrid fertility. There are also genes of sizable effect that influence fertility in hybrids resulting from specific combinations of the parents.Abbreviations I×I indica by indica cross - I×J indica by japonica cross - J×I japonica by indica cross - J×J japonica by japonica cross - WCV wide compatibility variety     

水稻籼粳杂种一代稻米加工和外观品质性状研究

采用不同稻米品质3个粳稻和4个籼稻按完全双列模型设计进行杂交，配组了24个籼粳杂种一代F1，对其主要稻米加工和外观品质性状进行研究。加工品质中糙米率和精米率均接近粳稻品种，与籼稻无关，无胞质效应；整精米率差异很大，但大多介于籼粳双亲之间，并且随粳稻亲本不同，其胞质效应表现不一致。外现品质中垩白度和透明度，大多数介于双亲之间．而垩白率多倾向于亲本的高值。     

Genetic analysis of methionine content in indica-japonica hybrid rice (Oryza sativa L.) at different grain developmental stages

Genetics of methionine content in indica-japonica hybrid rice (Oryza sativa L.) was studied in 35 F₁ hybrids derived from crossing 7 male-sterile indica rice cultivars with 5 restorer japonica rice cultivars. Two genetic models and their corresponding statistical methods for quantitative traits of triploid endosperm in cereal crops were used for the analysis. One is the unconditional model, which refers to the analysis of cumulative measurements along the developmental stages, while another is the conditional model, which relates to analysis throughout the developmental stages. Results showed that methionine content of indica-japonica hybrid rice was controlled by expression of triploid endosperm nuclear genes, cytoplasm genes, diploid maternal plant nuclear genes, and their genotype-environment interaction effects. Dominant effects were important at the first three developmental stages, while additive effects were important at the next two stages of grain development under both unconditional and conditional analyses. With regard to the components of heritability, maternal and cytoplasm general heritabilities and their environmental interaction heritabilities were important. It was suggested that enhancing methionine content could be more efficient when selection is based on maternal plants in early breeding generations.     

Selection in Early Generations of Dried Peas, Pisum sativum L. III. Plot Size and Plot Type

Investigations were carried out to study the effect of different plot sizes and plot types on the performance of peas and to determine plot size and plot type combinations suitable for the reliable evaluation of varietal yield performance realized in commercial stands of pea crops. Four pea varieties were tested in 1981 and 1982 in combinations of plot sizes ranging from 0.25 m2 to 19.50 in2 with plot types either unbordered, bordered with faba beans, surrounded with perforated plastic foil or only central sections of plots harvested (net plots). With decreasing plot size the performance mean as well as the error variance of grain yield and thousand grain weight increased disproportionately. Thus, changes in grain yield were much higher than those for thousand grain weight. The four varieties tested reacted differently to changing plot sizes and as a result, highly significant variety × plot size interactions were found. Although overestimation of grain yield in small plots could be strongly reduced by bordering the plots with faba beans or surrounding them with plastic foil, their suitibility for yield testing was limited by highly significant variety × plot type interactions. Compared to the largest net plot (15 m²) reliable results were still obtained with plot sizes larger than 6.5 m², no matter whether edge effects were eliminated or not. If only a small quantity of seed is available, plots may be reduced even to 1.00 m², if surrounded by plastic foil. The results presented in peas were compared to those in other crops and discussed concerning their relevance for variety testing as well as for selection of grain yield in early generations.     

Location-Specific and Across-Location Selections for Seed Yield in Populations of Common Bean, Phaseolus vulgaris L.

Two populations of common bean, Phaseolus vulgaris L., were used to make three independent location-specific selections at Palmira, Quilichao, and Popayán, Colombia. Also, three across-location selections were made by alternating generations between Palmira and Popayan, between Quilichao and Popayán, and among Palmira, Quilichao, and Popayán. The seven highest yielding lines selected from each environment and population along with 14 parents and two checks were evaluated for seed yield, seed weight, maturity, and reaction to an-thracnose, angular leaf spot, and common bacterial blight. Mean squares due to evaluation and selection environments, selected lines, and their interactions were significant for all traits. Mean yields of selected lines were higher than the mean of parents in both populations. Among location-specific selections, lines yielded higher at their respective selection site. Moreover, selections made at Popayán were higher yielding than those made at Quilichao or Palmira when tested across locations and years. Use of Popayán, a relatively wetter and cooler site, either alone or in combination with other locations resulted in higher yield, higher seed weight, and higher resistance to anthracnose. On the average, location-specific selections were lower yielding than the across-location selections. Among across-location selections, those selected between Palmira and Popayán were the highest yielding in both populations. Selections at Palmira and across all three locations resulted in greater stability.