Prediction of heterosis for grain yield in rice using 'key' informative EST-SSR markers

This study was undertaken to assess the comparative potential of 25 Expressed Sequence Tag derived simple sequence repeats (EST-SSRs) and 25 genomic SSRs in the prediction of grain yield heterosis using a set of nine cytoplasmic male sterile (CMS) lines and 32 restorer lines of rice. EST-SSRs and genomic SSRs exhibited an average Polymorphism Information Content value of 0.37 and 0.45, respectively. The coefficient of marker polymorphism among parental lines with respect to a set of hypervariable EST and genomic SSRs was correlated with standard heterosis for grain yield of six public bred rice hybrids. EST-SSRs gave a better correlation (r = 0.75) as compared with genomic SSRs (r = 0.09). When 10 'key' informative EST-SSR markers which showed a higher positive correlation with grain yield heterosis were validated in a new set of 14 experimental hybrids, the markers exhibited a higher correlation (r = 0.79), indicating the predictive value of these EST-SSRs. We recommend these 10 'key' informative EST-SSR markers for analysis of genetic diversity of parental lines and prediction of heterosis in hybrid rice breeding programmes.     

Relationship between heterosis and genetic divergence in 'Tongil'-type rice

Improving grain yield and quality of ‘Tongil’‐type rice (indica/japonica) continues to be a major breeding objective in Korea. In this study, genetic divergence among 13‘Tongil’‐type rice cultivars was evaluated and the relationship between genetic distance and hybrid performance in all possible nonreciprocal crosses between them assessed. The 78 F₁ hybrids together with the 13 parents were evaluated for eight traits of agronomic importance, including yield, in a replicated field trial. The 13 parents were examined for DNA polymorphism using 71 micro‐satellite or simple sequence repeats and 46 random decamer oligonucleotide primers. A total of 319 polymorphic variants were generated and, based on the polymorphism data, genetic distances (GDs) ranged from 0.021 to 0.437. Cluster analysis based on GDs revealed associations among cultivars which was in agreement with the pedigree data. Heterosis was observed in hybrids for most of the traits, and yield exhibited the highest heterosis among the eight traits examined. The correlation values of GDs with F₁ performance were mostly nonsignificant, except for yield, culm length and spikelets per panicle. The correlations of GDs with midparent and better‐parent heterosis were not significant enough to be of predictive value. These results indicate that GDs based on the microsatellite and random amplified polymorphic DNA (RAPD) markers may not be useful for predicting heterotic combinations in ‘Tongil’‐type rice and support the idea that the level of correlation between hybrid performance and genetic divergence is dependent on the germplasm used.     

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.     

A method of choosing locations based on genotype × environment interaction for regional trials of rice

An ideal test location with particular environmental conditions should generate a relatively large genotype × environment interaction (GE) value in regional trials. A method of selecting test locations based on GE was proposed. Using the statistic D_j, the ranking of ability to discriminate the best genotypes for locations could be obtained. The locations among the group with the smallest D_j value were deleted from the whole set step by step, and the number of locations was reduced to a rational level at which most (over 85%) of the GE sum of squares of trials were maintained. A comparative evaluation based on data collected from Zhejiang Province (China) rice regional trials showed that the new method was more feasible than two other methods without loss of accuracy and reliability.     

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.     

Effects of cytoplasm on heterosis and combining ability for agronomic traits in rice (Oryza sativa L.)

Summary Effect of sterilizing (WA) cytoplasm on heterosis and combining ability for days to flowering, plant height and grain yield in rice was studied in 70 crosses and their reciprocals produced by 10 cytoplasmic male sterile (A), their maintainer (B) and seven restorer (R) lines following line x tester design. The materials consisting of 140 hybrids (70 A/R and their reciprocal 70 R/B) plus 17 parental lines (10 B + 7 R) were evaluated under six environments, created by growing in three fields with different fertilizer doses (0, 60, 120 kg N/ha) and 2 seasons (dry and wet) during 1986 at IRRI farm. Reciprocal cross effect (A/R vs R/B) were highly significant for all the three traits. Interaction of reciprocal cross effects with environments were also highly significant for yield and days to flowering. Cytoplasmic effect for yield, days to flowering and plant height were estimated by comparing A/R and R/B combination and testing the significance of difference with LSD value. In order to avoid confounding effect of spikelet sterility on yields, twenty crosses showing normal spikelet fertility were selected. Both positive and negative cytoplasmic effects were observed for the three traits. The effects were modified by environments, except for plant height. Heterosis for all three traits was also affected by cytoplasm, however, manifestation of cytoplasmic effects was higher for heterosis for days to flower than in heterosis for yield and plant height. Effect of cytoplasm was more pronounced on general combining ability effects of parents than specific combining ability effects of crosses. Among the parents two CMS lines A4 (IR54752A) and A8 (IR22107-113-3-3A) and two R lines: R2 (IR46) and R7 (IR9761-19-1) showed consistent positive effect of cytoplasm on general combining ability. These lines have given several good heterotic combinations. The study indicated the usefulness of evaluating diverse cytoplasmic sources in various nuclear genotypes bred for hybrid rice breeding program.     

高粱主要品质性状的基因型与环境及互作效应分析

摘要： 选取10个高梁品种分别播种于山西榆次、辽宁沈阳、甘肃平凉、贵州贵阳和湖南长沙5个地区,淀粉、蛋白质、单宁和脂肪4项品质分析结果表明,不同品种、不同地点间4个品质性状均表现出较大的不同。不同区域试验结果表明,在各试点籽粒淀粉含量变异系数均为最小,平均值为2.59%,单宁最大,变异系数平均值为21.57%,蛋白质和脂肪的变异系数分别为11.13%和18.63%,远远高于淀粉和低于单宁,说明不同品种淀粉含量变化相对较小, 而单宁含量则有很大的变异,有较大的选择余地和改进潜力。分析影响品质性状的主次因素,结果表明,淀粉含量以基因型×环境效应为主,基因效应也较大。单宁含量以基因效应为主要因素,蛋白质含量以基因型×环境互作效应为主, 脂肪含量的环境、基因型、基因型×环境效应三者所占总平方和的百分比比较接近,几乎是基因型、环境和交互作用平均作用的结果。在今后品种的引进和选育方面应考虑这些性状的基因型、环境和互作效应,以提高品种的选育效果和生产水平。     

High embryo sac fertility and diversity of abnormal embryo sacs detected in autotetraploid indica/japonica hybrids in rice by whole‐mount eosin B‐staining confocal laser scanning microscopy

An eosin B staining procedure for use with confocal microscopy (WE‐CLSM) was used to examine the mature embryo sacs in 24 typical autotetraploid (2n = 4x = 48) indica/japonica hybrids and to compare with their original diploid (2n = 2x = 24) indica/japonica hybrids in rice. Four of the 24 hybrids showed >80% embryo sac fertility, and 13 hybrids over 70%. The average embryo sac fertility of the 24 autotetraploid indica/japonica hybrids was 68.08%, which was 17.33% higher than that in diploid hybrids. When compared with the diploid hybrids, 79.17% of the autotetraploid hybrids had higher embryo sac fertility. A diversity of abnormal embryo sacs occurred in autotetraploid indica/japonica hybrids. Embryo sac abnormalities were similar for both autotetraploid and diploid hybrid, but their frequencies were different. Some novel abnormal types were found in autotetraploid hybrids, such as enlarged egg apparatus. The embryo sac fertilities and frequencies of various abnormalities in autotetraploid hybrids varied with parental genotype and environment. The average seed set of the autotetraploid hybrids were higher than their diploid hybrids in different growing seasons.     

Pyramiding of insect- and disease-resistance genes into an elite indica, cytoplasm male sterile restorer line of rice,'Minghui 63'

The wild‐rice‐derived dominant gene Xa21 conferring multi‐race resistance to bacterial blight and a fused Bt gene cry1Ab/cry1Ac conferring resistance to lepidopteran insects were individually introduced into the same genetic background of an elite indica cytoplasm male sterile (CMS) restorer line ‘Minghui 63′. The line showed the desirable insect‐ and disease‐resistant phenotypes. To maximize the effect, the two genes were also pyramided into the same recipient plant of ‘Minghui 63’ by marker‐assisted selection. After being subjected to natural infestation of leaf‐folders and yellow stem borers and inoculation of Xoo strain mixtures, the pyramiding line and its derived hybrids showed high levels of resistance against both insect damage and disease. Furthermore, data from field trials demonstrated that the hybrids made by crossing this pyramiding line with the CMS lines ‘Zhenshan 97A’ and ‘Maxie A’ retained a similar level of yield under conditions without chemical spray, indicating that the pyramiding genes have a yield‐stabilizing effect on the recipient line and its hybrids.     

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.     

灌浆温度和氮肥及其互作效应对稻米贮藏蛋白组分的影响

灌浆结实期温度与氮肥施用量是影响稻米品质的两个重要生态因子,尤其是与稻米蛋白含量及米饭食味关系密切。本文以多个水稻主栽品种为材料,通迆灌浆结实期的人工控温试验、大田长期定位点的施氮处理试验和盆栽条件下的温氮两因素复合处理试验,探讨了水稻灌浆结实期温度对稻米贮藏蛋白含量与组分影响及其有别于氮肥处理效应的差异觃律,幵分析了温度与氮肥两个因素对稻米贮藏蛋白及其组分影响的交互作用特点。结果表明,高温胁迫和增施氮肥均引起水稻籽粒总蛋白及其谷蛋白组分含量(%)的显著增加,但两者对稻米醇溶蛋白影响却存在明显差别。其中,高温处理引起醇溶蛋白含量显著下降,提高稻米谷蛋白/醇溶蛋白比值,而增施氮肥引起稻米谷蛋白和醇溶蛋白含量明显增加,但对谷蛋白/醇溶蛋白比值与贮藏蛋白各亚基的组成比例影响相对较小。在高温处理下,谷蛋白的57kD前体亚基组分含量有所提高,而37kD酸性亚基和22kD碱性亚基随温度处理的差异变化却因品种而异,且高温处理对水稻籽粒蛋白绝对含量(mg grain^–1)的影响程度也进没有其对蛋白相对含量(%)的影响明显。高氮×高温处理组合对稻米总蛋白与谷蛋白含量的影响程度显著大...     

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     

杂交籼稻恢复系稻米淀粉RVA谱特征相关及聚类分析

测定早造种植收获的42个恢复系和7个不同蒸煮及食味对照稻米淀粉RVA谱特征值,对其进行了相关分析和系统聚类分析。结果表明如下：（1）恢复系RVA谱特征值变异系数最大是SBV,依次是BDV,CSV,CPV,HPV,最小是PKV。（2）各RVA谱特征值表现较好相关性。RVA谱特征值3个基本粘度间,只有HPV与CPV表现极显著正相关。PKV与BDV呈极显著正相关,与SBV和CSV均分别呈极显著负相关;HPV、CPV与BDV分别呈显著、极显著负相关,HPV、CPV分别与SBV和CSV均呈极显著正相关。BDV、SBV和CSV均分别呈极显著负相关,而SBV和CSV呈极显著正相关。（3）RVA谱特征值可分为3大类型,三类型区分主要依据SBV,Ⅰ类型SBV最高(37.4RVU～156.8RVU),Ⅱ类型SBV最低(-141.2RVU～-86.0RVU),而Ⅲ类型SBV介于两者之间(-83.6RVU～23.7RVU);在两极端类型Ⅰ类型和Ⅱ类型之间区分还可依据BDV和CSV指标。Ⅰ类型亚类间区分主要依据PKV和CPV,Ⅱ类型亚类区分依据PKV,Ⅲ类型亚类区分则比较复杂,依据PKV、HPV、BDV、SBV和CSV指标组合。     

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。     

Construction of chromosomal segment substitution lines and genetic dissection of introgressed segments associated with yield determination in the parents of a super‐hybrid rice

Heterosis is a phenomenon whereby hybrids of inbred lines produce favourable phenotypes that exceed those of their parents. Traits of interest are higher yield and stronger stress tolerance. The two‐line super‐hybrid rice ‘Liangyoupei9’ (LYP9) shows superiority to both its elite inbred line ‘93‐11’ and ‘Pei'ai64s’ (‘PA64s’) parents and conventional hybrids. However, the genetic basis of its hybrid vigour, especially yield determination, remains elusive. In the present study, a set of 156 chromosome segment substitution lines (CSSLs) carrying overlapping segments from ‘PA64s’ in a genetic background of ‘93‐11’ were constructed and planted in six environments. Three major agronomic traits, viz. panicle length (PL), heading date (HD) and plant height (PH), and five yield‐related traits, viz. grain weight per panicle (GWP), number of grains per panicle (GPP), 1000‐grain weight (TGW), seed set (SS) and number of panicles of per plant (PPP), were evaluated over 3 years. Quantitative trait loci (QTL) analysis was conducted using a likelihood ratio test based on stepwise regression. Forty‐six putative QTL distributed on 11 chromosomes were detected in more than one year. Remarkably, GWP of four CSSLs carrying positive yield QTL outperformed the recurrent parent ‘93‐11’ by more than 15%, in at least two environments. These results indicate that CSSLs are effective in identifying yield‐associated traits, and lines harbouring such QTL will be rich in resources for future molecular breeding programmes.