Genetic Components of Heterosis for Seedling Traits in an Elite Rice Hybrid Analyzed Using an Immortalized F_2 Population

Utilization of heterosis has greatly contributed to rice productivity in China and many Asian countries. Superior hybrids usually show heterosis at two stages: canopy development at vegetative stage and panicle development at reproductive stage resulting in heterosis in yield. Although the genetic basis of heterosis in rice has been extensively investigated, all the previous studies focused on yield traits at maturity stage. In this study, we analyzed the genetic basis of heterosis at seedling stage making use of an "immortalized F2" population composed of 105 hybrids produced by intercrossing recombinant inbred lines(RILs) from a cross between Zhenshan 97 and Minghui 63,the parents of Shanyou 63, which is an elite hybrid widely grown in China. Eight seedling traits, seedling height, tiller number, leaf number, root number, maximum root length, root dry weight, shoot dry weight and total dry weight, were investigated using hydroponic culture. We analyzed single-locus and digenic genetic effects at the whole genome level using an ultrahigh-density SNP bin map obtained by population re-sequencing. The analysis revealed large numbers of heterotic effects for seedling traits including dominance, overdominance and digenic dominance(epistasis) in both positive and negative directions. Overdominance effects were prevalent for all the traits, and digenic dominance effects also accounted for a large portion of the genetic effects. The results suggested that cumulative small advantages of the single-locus effects and two-locus interactions, most of which could not be detected statistically, could explain the genetic basis of seedling heterosis of the F_1 hybrid.     

Genome‐wide identification and analysis of heterotic loci in three maize hybrids

Heterosis, or hybrid vigour, is a predominant phenomenon in plant genetics, serving as the basis of crop hybrid breeding, but the causative loci and genes underlying heterosis remain unclear in many crops. Here, we present a large‐scale genetic analysis using 5360 offsprings from three elite maize hybrids, which identifies 628 loci underlying 19 yield‐related traits with relatively high mapping resolutions. Heterotic pattern investigations of the 628 loci show that numerous loci, mostly with complete–incomplete dominance (the major one) or overdominance effects (the secondary one) for heterozygous genotypes and nearly equal proportion of advantageous alleles from both parental lines, are the major causes of strong heterosis in these hybrids. Follow‐up studies for 17 heterotic loci in an independent experiment using 2225 F₂ individuals suggest most heterotic effects are roughly stable between environments with a small variation. Candidate gene analysis for one major heterotic locus (ub3) in maize implies that there may exist some common genes contributing to crop heterosis. These results provide a community resource for genetics studies in maize and new implications for heterosis in plants.     

The use of SSRs for predicting the hybrid yield and yield heterosis in 15 key inbred lines of Chinese maize

A challenge to maize breeders is to predict and identify inbred lines that can produce highly heterotic hybrids precisely. In the present study we surveyed the genetic diversity among 15 elite inbred lines of maize in China with SSR markers and assessed the relationship between SSR marker and hybrid yield/yield heterosis in a diallel set of 105 crosses. Forty-three SSR primers selected from all sixty-three primers gave stable profiles amplified in the sample of 15 inbred lines, which could clearly resolve on 4% metaphor agarose gel. The average number of alleles per SSR locus was 4.44 with a range from 2 to 9. The polymorphism information content (PIC) for the SSR loci varied from 0.28 to 0.81 with a mean of 0.6281. Genetic similarity (GS) among 15 lines was estimated with 191 alleles identified as raw data, the Nei's coefficient of GS ranged from 0.492 for 478 vs HZ4 up to 0.745 for E28 to ZH64 with a mean of 0.619. The cluster diagram based upon the SSR data grouped the 15 lines into families consistent with the yield heterotic response of these. Genetic distance (GD) based on SSR data was significantly correlated with hybrid yield/yield heterosis, the correlation coefficient (r) being 0.5432 and 0.4271 in 1999 and 0.4305 and 0.3614 in 1998 field test, respectively, whereas the determination coefficient (r2) was lower. The correlation between GD based on SSR data and hybrid yield/yield heterosis changed alone with the difference of number and pedigree relationship among parents that were used in this study. SSR makers showed high polymorphism and could be used to assess the relationship between inbred lines of maize, but it was difficult to predict the yield heterosis of maize.     

Understanding the genetic and molecular constitutions of heterosis for developing hybrid rice

The wide adoption of hybrid rice has greatly increased rice yield in the last several decades. The utilization of heterosis facilitated by male sterility has been a common strategy for hybrid rice development. Here, we summarize our efforts in the genetic and molecular understanding of heterosis and male sterility together with the related progress from other research groups. Analyses of F₁ diallel crosses show that strong heterosis widely exists in hybrids of diverse germplasms, and inter-subspecific hybrids often display higher heterosis. Using the elite hybrid Shanyou 63 as a model, an immortalized F₂ population design is conducted for systematic characterization of the biological mechanism of heterosis, with identification of loci controlling heterosis of yield and yield component traits. Dominance, overdominance, and epistasis all play important roles in the genetic basis of heterosis; quantitative assessment of these components well addressed the three classical genetic hypotheses for heterosis. Environment-sensitive genic male sterility (EGMS) enables the development of two-line hybrids, and long noncoding RNAs often function as regulators of EGMS. Inter-subspecific hybrids show greatly reduced fertility; the identification and molecular characterization of hybrid sterility genes offer strategies for overcoming inter-subspecific hybrid sterility. These developments have significant implications for future hybrid rice improvement using genomic breeding.     

Comparison of quantitative trait loci controlling seedling characteristics at two seedling stages using rice recombinant inbred lines

A better understanding of the genetics of seedling characteristics in rice could be helpful in improving rice varieties. Zhenshan 97 and Minghui 63, the parents of Shanyou 63, an elite hybrid developed during the last decade in China, vary greatly with respect to their physiological and morphological traits at the seedling growth stage. In this study, we used a population of 240 recombinant inbred lines derived from a cross between Zhenshan 97 and Minghui 63 to identify quantitative trait loci (QTL) for seedling characteristics. All plant material was grown in hydroponic culture. Data for the following characters were collected at 30 days and 40 days post-sowing: plant height, shoot dry matter weight (SDW), maximum root length, root dry weight (RDW), total dry weight , and root-shoot ratio (the ratio of SDW to RDW). Analysis using composite interval mapping detected 16 QTL for the six traits in 30-day-old seedlings. Of these 16 QTL, Minghui 63 alleles increased trait values at only two of them. The QTL in the vicinity of R3166 on chromosome 5 simultaneously influenced PH, SDW, MRL, RDW, and TDW in the same direction. Twenty QTL were detected for the same traits in the 40-day-old seedlings. However, at this stage Minghui 63 alleles increased trait values at eight QTL. The QTL linked to R3166 also affected PH, SDW, MRL, RDW, and TDW. Only four QTL were common to the two stages. These results clearly indicate that different genes (QTL) control the same traits during different time intervals. Zhenshan 97 alleles had positive effects during the first 30 days of seedling growth, but thereafter the positive effects of Minghui 63 alleles on seedling growth gradually became more pronounced.     

Determination of heterotic groups for tropical Indica hybrid rice germplasm

Key message

Two heterotic groups and four heterotic patterns were identified for IRRI hybrid rice germplasm to develop hybrid rice in the tropics based on SSR molecular data and field trials.

Abstract

Information on heterotic groups and patterns is a fundamental prerequisite for hybrid crop breeding; however, no such clear information is available for tropical hybrid rice breeding after more than 30 years of hybrid rice commercialization. Based on a study of genetic diversity using molecular markers, 18 parents representing hybrid rice populations historically developed at the International Rice Research Institute (IRRI) were selected to form diallel crosses of hybrids and were evaluated in tropical environments. Yield, yield heterosis and combining ability were investigated with the main objectives of (1) evaluating the magnitude of yield heterosis among marker-based parental groups, (2) examining the consistency between marker-based group and heterotic performance of hybrids, and (3) identifying foundational hybrid parents in discrete germplasm pools to provide a reference for tropical indica hybrid rice breeding. Significant differences in yield, yield heterosis and combining ability were detected among parents and among hybrids. On average, the hybrids yielded 14.8 % higher than the parents. Results revealed that inter-group hybrids yielded higher, with higher yield heterosis than intra-group hybrids. Four heterotic patterns within two heterotic groups based on current IRRI B- and R-line germplasm were identified. Parents in two marker-based groups were identified with limited breeding value among current IRRI hybrid rice germplasm because of their lowest contribution to heterotic hybrids. Heterotic hybrids are significantly correlated with high-yielding parents. The efficiency of breeding heterotic hybrids could be enhanced using selected parents within identified marker-based heterotic groups. This information is useful for exploiting those widely distributed IRRI hybrid rice parents.     

超高产杂交稻不同生育期的光合色素含量、净光合速率和水分利用效率

 较为系统地研究了两个超高产杂交稻‘两优培九’、‘华安3号’和多年来大面积推广的常规杂交稻‘汕优63’不同生育期的光合色素含量、净光合速率和水分利用效率。结果表明,在苗期,3个杂交稻的单位叶面积的叶绿素（Chl）含量差别不大,类胡萝卜素（Car）的含量以‘汕优63’为最高。然而,随着发育阶段的推进,到分蘖期,尤其是抽穗期剑叶的单位叶面积Chl和Car含量,两个超高产杂交稻高于‘汕优63’。从苗期到抽穗期,超高产杂交稻‘两优培九’和‘华安3号’的净光合速率（Pn）都比‘汕优63’高,而在苗期的午间强光条件下和分蘖期的早晨以及抽穗期的早晚相对弱光条件下其Pn的差别尤为显著。在苗期,‘汕优63’的水分利用效率（WUE）略高于‘两优培九’和‘华安3号’;到分蘖期和抽穗期,在上午10时之前和下午14时以后的时间段,则是两个超高产杂交稻明显高于‘汕优63’。这些结果说明,超高产杂交稻‘两优培九’和‘华安3号’不仅有较高的Pn和较强的抗光抑制能力,而且还能充分利用早晨和傍晚较弱的光强进行光合作用,这些是它们之所以高产的重要生理基础。此外,超高产杂交稻在生长发育的中后期（分蘖期和抽穗期）具有较高的WUE,有利于节约农业用水。     

A new AOX homologous gene OsIM1 from rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) with an alternative splicing mechanism under salt stress

"Zhenshan 97" is the female parent of a number of widely used hybrids for rice production in China. However, this line is of poor quality because of a high amylose content (AC), a hard gel consistency (GC) and a low gelatinization temperature (GT), together with a chalky endosperm. It had been determined that the three traits for cooking and eating quality, AC, GC and GT, are controlled by the Waxy locus and/or the tightly linked genomic region. In this study we improved the eating and cooking quality of Zhenshan 97 by introgressing the Waxy gene region from Minghui 63 (wx-MH), a restorer line, that has medium AC, soft GC and high GT. The wx-MH fragment was transferred to Zhenshan 97B by three backcrosses and one selfing, then from Zhenshan 97B to Zhenshan 97A by a cross and a backcross. Molecular marker-assisted selection was applied in the series to select for individuals carrying wx-MH, to identify recombination between the Waxy and flanking markers, and also to recover the genetic background of the recurrent parent. According to the marker genotypes, the improved versions of Zhenshan 97B and Zhenshan 97A, or Zhenshan 97B(wx-MH) and Zhenshan 97A(wx-MH), were the same as the originals except for the Waxy region of less than 6.1 cM in length. The selected lines and their hybrids with Minghui 63, or Shanyou 63(wx-MH), showed a reduced AC and an increased GC and GT, coupled with a reduced grain opacity. Field examinations of agronomic performance revealed that Zhenshan 97B(wx-MH) and Shanyou 63(wx-MH) were essentially the same as the originals except for a significant decrease in grain weight. The simultaneous improvement of AC, GA, GT and opacity, indicated that the Waxy region had major effects on the four quality traits. The improved versions of Zhenshan 97 A and B should be immediately useful in hybrid rice production.     

组学技术揭示水稻杂种优势遗传机制

杂种优势是杂交后代在生长或生殖性状上表现出优于亲本的现象。虽然杂种优势在农业生产上已广为应用,但其分子机理仍不清楚。最近,中国科学家通过分析17个代表性杂交稻(Oryza sativa)品种,共10 074个F2个体的全基因组序列和表型,对水稻产量杂种优势相关位点进行了系统定位和解析。此外,中国另一个科研小组通过整合杂交稻亲本和杂交种的表型组、转录组及基因组等多层次数据,深入研究了超级杂交稻两优培九产量的杂种优势基础。这些研究不仅为杂种优势理论的建立提供了新数据,也为水稻育种实践提供了有益的指导。     

ATP Determination of Parend Seedlings as Method to Evaluate the Heterosis of Rice

By bioluminescent assay the ATP content of rice seedings homogenate of parents, which produce a heterotic or nonheterotic hybrid, was determined. It was found that the sum of ATP content of parents, which produce a heterotic hybrid was >2.0 × 10-6 mmoles/g seedlings homogenate, while that of parents of nonheterotic hybrids was <2.0×10-6 mmoles/g seedlings homogenate. This method has been applied to evaluate the heterosis of 15 rice crosses in vitro. Results indicated that 14/15 of the experimental subjects were in coincidence with the above-mentioned findings.     

长链非编码RNA基因Ef-cd调控水稻早熟与稳产

水稻(Oryza sativa)育种中早熟和高产往往不能兼顾。最近一项研究分离鉴定了1个调控水稻早熟的基因Ef-cd (Early flowering-completely dominant)。Ef-cd编码一段长链非编码RNA (lncRNA), 该lncRNA与OsSOC1基因的一段反义转录本重叠, Ef-cd正调控H3K36me3的富集及OsSOC1基因的表达。在不同的纬度, 含有Ef-cd基因的品种及其杂交种与对照相比生育期缩短7-20天, 但产量不降低。对1 439份优质杂交稻品种的基因型分析显示, 含有Ef-cd基因的16份纯合子和299份杂合子均表现出明显的早熟特性。Ef-cd基因可能通过提高氮素利用率及光合效率来促进水稻早熟。因此, Ef-cd基因兼顾了水稻的早熟和产量, 在水稻分子育种中具有重要利用价值。     

Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. II. Grain yield components

The genetic basis underlying inbreeding depression and heterosis for three grain yield components of rice was investigated in five interrelated mapping populations using a complete RFLP linkage map, replicated phenotyping, and the mixed model approach. The populations included 254 F(10) recombinant inbred lines (RILs) derived from a cross between Lemont (japonica) and Teqing (indica), two backcross (BC) and two testcross populations derived from crosses between the RILs and the parents plus two testers (Zhong413 and IR64). For the yield components, the RILs showed significant inbreeding depression and hybrid breakdown, and the BC and testcross populations showed high levels of heterosis. The average performance of the BC or testcross hybrids was largely determined by heterosis. The inbreeding depression values of individual RILs were negatively associated with the heterosis measurements of the BC or testcross hybrids. We identified many epistatic QTL pairs and a few main-effect QTL responsible for >65% of the phenotypic variation of the yield components in each of the populations. Most epistasis occurred between complementary loci, suggesting that grain yield components were associated more with multilocus genotypes than with specific alleles at individual loci. Overdominance was also an important property of most loci associated with heterosis, particularly for panicles per plant and grains per panicle. Two independent groups of genes appeared to affect grain weight: one showing primarily nonadditive gene action explained 62.1% of the heterotic variation of the trait, and the other exhibiting only additive gene action accounted for 28.1% of the total trait variation of the F(1) mean values. We found no evidence suggesting that pseudo-overdominance from the repulsive linkage of completely or partially dominant QTL for yield components resulted in the overdominant QTL for grain yield. Pronounced overdominance resulting from epistasis expressed by multilocus genotypes appeared to explain the long-standing dilemma of how inbreeding depression could arise from overdominant genes.     

DNA methylation in cotton hybrids and their parents

The possible role of methylation in the performance of heterosis has been analyzed in many crops. To further study this possibility, we investigated both the differences in cytosine methylation patterns between cotton heterotic hybrid/nonheterotic hybrids and their parental lines and the change in methylation level from seedling stage to flowering stage by using the methylation-sensitive amplified polymorphism (MSAP) method. The results showed that the number of demethylation loci in highly heterotic hybrids was greater that in lowly heterotic hybrids, and the level of DNA cytosine methylation in cotton at the seedling stage is higher than that at the flowering stage. The altered methylation patterns at low-copy genomic regions can be confirmed by DNA gel blot analysis. A total of 39 fragments that showed different methylation patterns were cloned and sequenced. The methylation status of these genes was modified differentially in hybrid and parents, suggesting that these genes might play a role in the performance of heterosis.     

长链非编码RNA基因Ef-cd调控水稻早熟与稳产

水稻(Oryza sativa)育种中早熟和高产往往不能兼顾。最近一项研究分离鉴定了1个调控水稻早熟的基因Ef-cd (Early flowering-completely dominant)。Ef-cd编码一段长链非编码RNA (lncRNA), 该lncRNA与OsSOC1基因的一段反义转录本重叠, Ef-cd正调控H3K36me3的富集及OsSOC1基因的表达。在不同的纬度, 含有Ef-cd基因的品种及其杂交种与对照相比生育期缩短7-20天, 但产量不降低。对1 439份优质杂交稻品种的基因型分析显示, 含有Ef-cd基因的16份纯合子和299份杂合子均表现出明显的早熟特性。Ef-cd基因可能通过提高氮素利用率及光合效率来促进水稻早熟。因此, Ef-cd基因兼顾了水稻的早熟和产量, 在水稻分子育种中具有重要利用价值。     

Exploring the molecular basis of heterosis for plant breeding

Since approximate a century ago, many hybrid crops have been continually developed by crossing two inbred varieties. Owing to heterosis(hybrid vigor) in plants, these hybrids often have superior agricultural performances in yield or disease resistance succeeding their inbred parental lines. Several classical hypotheses have been proposed to explain the genetic causes of heterosis. During recent years, many new genetics and genomics strategies have been developed and used for the identifications of heterotic genes in plants. Heterotic effects of the heterotic loci and molecular functions of the heterotic genes are being investigated in many plants such as rice, maize, sorghum, Arabidopsis and tomato.More and more data and knowledge coming from the molecular studies of heterotic loci and genes will serve as a valuable resource for hybrid breeding by molecular design in future. This review aims to address recent advances in our understanding of the genetic and molecular mechanisms of heterosis in plants. The remaining scientific questions on the molecular basis of heterosis and the potential applications in breeding are also proposed and discussed.     

Extending the rapeseed gene pool with resynthesized <Emphasis Type="Italic">Brassica napus</Emphasis> II: Heterosis

Hybrid breeding relies on the combination of parents from two differing heterotic groups. However, the genetic diversity in adapted oilseed rape breeding material is rather limited. Therefore, the use of resynthesized Brassica napus as a distant gene pool was investigated. Hybrids were derived from crosses between 44 resynthesized lines with a diverse genetic background and two male sterile winter oilseed rape tester lines. The hybrids were evaluated together with their parents and check cultivars in 2 years and five locations in Germany. Yield, plant height, seed oil, and protein content were monitored, and genetic distances were estimated with molecular markers (127 polymorphic RFLP fragments). Resynthesized lines varied in yield between 40.9 dt/ha and 21.5 dt/ha, or between 85.1 and 44.6% of check cultivar yields. Relative to check cultivars, hybrids varied from 91.6 to 116.6% in yield and from 94.5 to 103.3% in seed oil content. Mid-parent heterosis varied from −3.5 to 47.2% for yield. The genetic distance of parental lines was not significantly correlated with heterosis or hybrid yield. Although resynthesized lines do not meet the elite rapeseed standards, they are a valuable source for hybrid breeding due to their large distance from present breeding material and their high heterosis when combined with European winter oilseed rape.     

杂交稻汕优36幼苗根系呼吸代谢特点的研究

本文报道了对杂交水稻汕优36及其亲本幼苗根系生长、蛋白质含量、呼吸强度和G_6PDH、IDH、PK三种呼吸酶的初步研究。结果表明,杂种汕优36和其亲本相比,前者具有生长量高和呼吸强度低的特点。在呼吸代谢特点上,母本珍汕97A具有较高的IDH活力,父本IR36具有较高的G_6PDH活力。杂种汕优36PK活力高于双亲.但它在三种酶活力中所占比重与其它两种酶活力所占比重一样均居于双亲之间。作者认为,以PK活力为代表的EMP途径运转状况及EMP、TCA和HMP三条呼吸代谢途径之间的关系可能对杂交水稻幼根生长优势的形成起作重要作用。     

Extensive heterosis in growth of yeast hybrids is explained by a combination of genetic models

Heterosis, also known as hybrid vigor, is the superior performance of a heterozygous hybrid relative to its homozygous parents. Despite the scientific curiosity of this phenotypic phenomenon and its significance for food production in agriculture, its genetic basis is insufficiently understood. Studying heterosis in yeast can potentially yield insights into its genetic basis, can allow one to test the different hypotheses that have been proposed to explain the phenomenon and allows better understanding of how to take advantage of this phenomenon to enhance food production. We therefore crossed 16 parental yeast strains to form 120 yeast hybrids, and measured their growth rates under five environmental conditions. A considerable amount of dominant genetic variation was found in growth performance, and heterosis was measured in 35% of the hybrid–condition combinations. Despite previous reports of correlations between heterosis and measures of sequence divergence between parents, we detected no such relationship. We used several analyses to examine which genetic model might explain heterosis. We found that dominance complementation of recessive alleles, overdominant interactions within loci and epistatic interactions among loci each contribute to heterosis. We concluded that in yeast heterosis is a complex phenotype created by the combined contribution of different genetic interactions.     

SSR heterogenic patterns of parents for marking and predicting heterosis in rice breeding

The most important concerns of hybrid rice breeders are selection of donors to improve parental lines and prediction of hybrid performance. In this study, SSR molecular marker technology and a half-diallel method were used to address these related hybrid production issues. The results show that genetic diversity among the parental lines is certainly related to heterosis. The heterozygosity of each parental pair is significantly associated with the general combining ability, not with the specific combining ability. However, neither genetic diversity nor heterozygosity is a good indicator for predicting heterosis. From these results, it is suggested that donors for improving parents of hybrids be selected from the improved inbred lines by conventional breeding programs. In this investigation, we also discovered that four favorable alleles and six favorable heterogenic patterns on the parental lines significantly contribute to the heterosis of their hybrids in grain yield, whereas six unfavorable alleles and six unfavorable heterogenic patterns significantly reduce heterosis. These noticeable findings could be, in practice, useful for hybrid rice breeding programs with SSR marker-assisted selection. It is suggested that the optimal combinations with the superior grain yield could be bred out by assembling those favorable alleles into their parental lines and by removing the unfavorable alleles from the parental lines. This study also indicates that there is still a great heterosis potential to be exploited in indica/indica hybrids by the same strategy. In indica/japonica hybrid breeding programs, it may also be important to remove unfavorable alleles rather than broaden genetic diversity or heterozygosity of the parents.     

Genome Properties and Prospects of Genomic Prediction of Hybrid Performance in a Breeding Program of Maize

Maize (Zea mays L.) serves as model plant for heterosis research and is the crop where hybrid breeding was pioneered. We analyzed genomic and phenotypic data of 1254 hybrids of a typical maize hybrid breeding program based on the important Dent × Flint heterotic pattern. Our main objectives were to investigate genome properties of the parental lines (e.g., allele frequencies, linkage disequilibrium, and phases) and examine the prospects of genomic prediction of hybrid performance. We found high consistency of linkage phases and large differences in allele frequencies between the Dent and Flint heterotic groups in pericentromeric regions. These results can be explained by the Hill–Robertson effect and support the hypothesis of differential fixation of alleles due to pseudo-overdominance in these regions. In pericentromeric regions we also found indications for consistent marker–QTL linkage between heterotic groups. With prediction methods GBLUP and BayesB, the cross-validation prediction accuracy ranged from 0.75 to 0.92 for grain yield and from 0.59 to 0.95 for grain moisture. The prediction accuracy of untested hybrids was highest, if both parents were parents of other hybrids in the training set, and lowest, if none of them were involved in any training set hybrid. Optimizing the composition of the training set in terms of number of lines and hybrids per line could further increase prediction accuracy. We conclude that genomic prediction facilitates a paradigm shift in hybrid breeding by focusing on the performance of experimental hybrids rather than the performance of parental lines in testcrosses.