Molecular marker heterozygosity and hybrid performance in indica and japonica rice

Molecular Genetic Diversity and Combining Ability for Some Physiological and Agronomic Traits in Rice under Well-Watered and Water-Deficit Conditions

Water deficit is a pivotal abiotic stress that detrimentally constrains rice growth and production. Thereupon, the development of high-yielding and drought-tolerant rice genotypes is imperative in order to sustain rice production and ensure global food security. The present study aimed to evaluate diverse exotic and local parental rice genotypes and their corresponding cross combinations under water-deficit versus well-watered conditions, determining general and specific combining ability effects, heterosis, and the gene action controlling important traits through half-diallel analysis. In addition, the research aimed to assess parental genetic distance (GD) employing simple sequence repeat (SSR) markers, and to determine its association with hybrid performance, heterosis, and specific combining ability (SCA) effects. Six diverse rice genotypes (exotic and local) and their 15 F₁ hybrids were assessed for two years under water-deficit and well-watered conditions. The results revealed that water-deficit stress substantially declined days to heading, plant height, chlorophyll content, relative water content, grain yield, and yield attributes. Contrarily, leaf rolling and the sterility percentage were considerably increased compared to well-watered conditions. Genotypes differed significantly for all the studied characteristics under water-deficit and well-watered conditions. Both additive and non-additive gene actions were involved in governing the inheritance of all the studied traits; however, additive gene action was predominant for most traits. The parental genotypes P₁ and P₂ were identified as excellent combiners for earliness and the breeding of short stature genotypes. Moreover, P₃, P₄, and P₆ were identified as excellent combiners to increase grain yield and its attributes under water-deficit conditions. The hybrid combinations; P₁ × P₄, P₂ × P₅, P₃ × P₄, and P₄ × P₆ were found to be good specific combiners for grain yield and its contributed traits under water-deficit conditions. The parental genetic distance (GD) ranged from 0.38 to 0.89, with an average of 0.70. It showed lower association with hybrid performance, heterosis, and combining ability effects for all the studied traits. Nevertheless, SCA revealed a significant association with hybrid performance and heterosis, which suggests that SCA is a good predictor for hybrid performance and heterosis under water-deficit conditions. Strong positive relationships were identified between grain yield and each of relative water content, chlorophyll content, number of panicles/plant, number of filled grains/panicle, and 1000-grain weight. This suggests that these traits could be exploited as important indirect selection criteria for improving rice grain yield under water-deficit conditions.

Assembly of yield heterosis of an elite rice hybrid is promising by manipulating dominant quantitative trait loci

In the past, rice hybrids with strong heterosis have been obtained empirically, by developing and testing thousands of combinations. Here, we aimed to determine whether heterosis of an elite hybrid could be achieved by manipulating major quantitative trait loci. We used 202 chromosome segment substitution lines from the elite hybrid Shanyou 63 to evaluate single segment heterosis (SSH) of yield per plant and identify heterotic loci. All nine detected heterotic loci acted in a dominant fashion, and no SSH exhibited overdominance. Functional alleles of key yield-related genes Ghd7, Ghd7.1, Hd1, and GS3 were dispersed in both parents. No functional alleles of three investigated genes were expressed at higher levels in the hybrids than in the more desirable parents. A hybrid pyramiding eight heterotic loci in the female parent Zhenshan 97 background had a comparable yield to Shanyou 63 and much higher yield than Zhenshan 97. Five hybrids pyramiding eight or nine heterotic loci in the combined parental genome background showed similar yield performance to that of Shanyou 63. These results suggest that dominance underlying functional complementation is an important contributor to yield heterosis and that heterosis assembly might be successfully promised by manipulating several major dominant heterotic loci.

Genetic Analysis of S5-Interacting Genes Regulating Hybrid Sterility in Rice

BACKGROUND

Asian cultivated rice (Oryza sativa L.) comprises two subspecies, O. sativa subsp. indica and subsp. japonica, and the hybrids between them display strong heterosis. However, hybrid sterility (HS) limits practical use of the heterosis between these two subspecies. S5 is a major-effect locus controlling the HS of female gametes in rice, consisting of three closely-linked genes ORF3, ORF4 and ORF5 that act as a killer-protector system. The HS effects of S5 are inconsistent for different genetic backgrounds, indicating the existence of interacting genes within the genome.

RESULTS

In the present study, the S5-interacting genes (SIG) and their effects on HS were analyzed by studying the hybrid progeny between an indica rice, Dular (DL) and a japonica rice, Balilla^ORF5+ (BL^ORF5+), with a transgenic ORF5+ allele. Four interacting quantitative trait loci (QTL): qSIG3.1, qSIG3.2, qSIG6.1, and qSIG12.1, were genetically mapped. To analyze the effect of each interacting locus, four near-isogenic lines (NILs) were developed. The effect of each specific locus was investigated while the other three loci were kept DL homozygous (DL/DL). Of the four loci, qSIG3.1 was the SIG with the greatest effects in which the DL allele was completely dominant. Furthermore, the DL allele displayed incomplete dominance at qSIG3.2, qSIG6.1, and qSIG12.1. qSIG3.1 will be the first choice for further fine-mapping.

CONCLUSIONS

Four S5-interacting QTL were identified by genetic mapping and the effect of each locus was analyzed using advanced backcrossed NILs. The present study will facilitate elucidation of the molecular mechanism of rice HS caused by S5. Additionally, it would provide the basis to explore the origin and differentiation of cultivated rice, having practical significance for inter-subspecific hybrid rice breeding programs.

Selection criteria for high-yielding and early-flowering bread wheat hybrids under heat stress

Hybrid performance during wheat breeding can be improved by analyzing genetic distance (GD) among wheat genotypes and determining its correlation with heterosis. This study evaluated the GD between 16 wheat genotypes by using 60 simple sequence repeat (SSR) markers to classify them according to their relationships and select those with greater genetic diversity, evaluate the correlation of the SSR marker distance with heterotic performance and specific combining ability (SCA) for heat stress tolerance, and identify traits that most influence grain yield (GY). Eight parental genotypes with greater genetic diversity and their 28 F1 hybrids generated using diallel crossing were evaluated for 12 measured traits in two seasons. The GD varied from 0.235 to 0.911 across the 16 genotypes. Cluster analysis based on the GD estimated using SSRs classified the genotypes into three major groups and six sub-groups, almost consistent with the results of principal coordinate analysis. The combined data indicated that five hybrids showed 20% greater yield than mid-parent or better-parent. Two hybrids (P2 × P4) and (P2 × P5), which showed the highest performance of days to heading (DH), grain filling duration (GFD), and GY, and had large genetic diversity among themselves (0.883 and 0.911, respectively), were deemed as promising heat-tolerant hybrids. They showed the best mid-parent heterosis and better-parent heterosis (BPH) for DH (-11.57 and -7.65%; -13.39 and -8.36%, respectively), GFD (12.74 and 12.17%; 12.09 and 10.59%, respectively), and GY (36.04 and 20.04%; 44.06 and 37.73%, respectively). Correlation between GD and each of BPH and SCA effects based on SSR markers was significantly positive for GFD, hundred kernel weight, number of kernels per spike, harvest index, GY, and grain filling rate and was significantly negative for DH. These correlations indicate that the performance of wheat hybrids with high GY and earliness could be predicted by determining the GD of the parents by using SSR markers. Multivariate analysis (stepwise regression and path coefficient) suggested that GFD, hundred kernel weight, days to maturity, and number of kernels per spike had the highest influence on GY.

QTL mapping for pre-harvest sprouting resistance in japonica rice varieties utilizing genome re-sequencing

Pre-harvest sprouting (PHS) leads to serious economic losses because of reductions in yield and quality. To analyze the quantitative trait loci (QTLs) for PHS resistance in japonica rice, PHS rates on panicles were measured in 160 recombinant inbred lines (RILs) derived from a cross between the temperate japonica varieties Odae (PHS resistant) and Unbong40 (PHS susceptible) under two different environmental conditions—field (summer) and greenhouse (winter) environments. Genome re-sequencing of the parental varieties detected 266,773 DNA polymorphisms including 248,255 single nucleotide polymorphisms and 18,518 insertions/deletions. We constructed a genetic map comprising 239 kompetitive allele-specific PCR and 49 cleaved amplified polymorphic sequence markers. In the field environment, two major QTLs, qPHS-3^FD and qPHS-11^FD, were identified on chromosomes 3 and 11, respectively, whereas three major QTLs, qPHS-3^GH, qPHS-4^GH, and qPHS-11^GH, were identified on chromosomes 3, 4, and 11, respectively, in the greenhouse environment. qPHS-11^GH and qPHS-11^FD had similar locations on chromosome 11, suggesting the existence of a gene conferring stable PHS resistance effects under different environmental conditions. The QTLs identified in this study can be used to improve the PHS resistance of japonica varieties, and they may improve our understanding of the genetic basis of PHS resistance.

Formation of heterotic pools and understanding relationship between molecular divergence and heterosis in pearl millet [Pennisetum glaucum (L.) R. Br.]

The present investigation was made to generate information on the heterotic pools amongst pearl millet hybrid parents. A set of 17 representative parents was selected from a diverse set of 147 hybrid parents using SSR based genetic distance (GD) and clustering pattern; 136 hybrids were developed in diallel fashion and evaluated at two locations in India. Moderate positive significant correlation (r = 0.37, p<0.01) and (r = 0.33, p<0.01) was found between GD and mid-parent heterosis (MPH) and better-parent heterosis (BPH), respectively, for grain yield for all the hybrids. Higher correlation between genetically closer individuals was observed for grain yield heterosis when the parents of B- and R- crosses had lesser genetic distance (<0.68 GD) in comparison to those parental combinations having GD higher than 0.68, indicating that the GD based predictions for grain yield are better when the parents are genetically related than when they are genetically diverse. In this study, all the pearl millet hybrid parents seems to exist in two broad-based heterotic pools; one each represented by seed and restorer parents as B × R hybrids showed highest mean heterosis for grain yield than either of B × B or R × R crosses. Further, four heterotic pools have been identified in this diverse set of hybrid parents of pearl millet, two each for seed parents (HPB1 and HPB2) and for restorer parents (HPR3 and HPR4). Among these, HPB1 × HPR3 was identified having the highest heterotic level, and could be further used to develop higher yielding pearl millet hybrids.

Assessment of Heterosis Based on Genetic Distance Estimated Using SNP in Common Wheat

This study assessed the genetic distance (GD) between parental genotypes using single nucleotide polymorphism (SNP) DNA markers and evaluated the correlation between GD and heterosis in common wheat. We examined the performance of parents and hybrids in a field experiment conducted in a randomized block design at a Shihezi location with three replications. Different traits such as the height of the parents and the F1 generation, number of harvested ears, number of grains per panicle, grain weight per panicle, 1000-grain weight, and grain yield were examined. Genotyping using a wheat 90K SNP chip determined the GD between the parents and analyzed the relationship between GD and heterotic performance of hybrids in wheat. Cluster analysis based on GD estimated using SNP chips divided the 20 elite parents into five groups which were almost consistent with the parental pedigree. Correlation analysis showed a significant association between GD and mid-parent heterosis (MPH) of 1000-grain weight. However, GD and high-parent heterosis (HPH) of 1000-grain weight showed no significant correlation. There was a weak correlation between GD and with spikelet number, harvested spikes, and yield at MPH or HPH. Hence, SNP analysis may be utilized in allocating wheat parents to heterotic groups. However, the correlation between SNP-based GD and hybrid performance still remains unclear.

Stacking S5-n and f5-n to overcome sterility in indica-japonica hybrid rice

Pyramiding of S5 - n and f5 - n cumulatively improved seed-setting rate of indica-japonica hybrids, which provided an effective approach for utilization of inter-subspecific heterosis in rice breeding. Breeding for indica-japonica hybrid rice is an attractive approach to increase rice yield. However, hybrid sterility is a major obstacle in utilization of inter-subspecific heterosis. Wide-compatibility alleles can break the fertility barrier between indica and japonica subspecies, which have the potential to overcome inter-subspecific hybrid sterility. Here, we improved the compatibility of an elite indica restorer line 9311 to a broad spectrum of japonica varieties, by introducing two wide-compatibility alleles, S5-n and f5-n, regulating embryo-sac and pollen fertility, respectively. Through integrated backcross breeding, two near isogenic lines harboring either S5-n or f5-n and a pyramiding line carrying S5-n plus f5-n were obtained, with the recurrent parent genome recovery of 99.95, 99.49, and 99.44 %, respectively. The three lines showed normal fertility when crossed to typical indica testers. When testcrossed to five typical japonica varieties, these lines allowed significant increase of compatibility with constant agronomic performance. The introgressed S5-n could significantly improve 14.7-32.9 % embryo-sac fertility in indica-japonica hybrids. In addition, with the presence of f5-n fragment, S5-n would increase the spikelet fertility from 9.5 to 21.8 %. The introgressed f5-n fragment greatly improved anther dehiscence, embryo-sac and pollen fertility in indica-japonica hybrids, thus leading to improvement of spikelet fertility from 20.4 to 30.9 %. Moreover, the pyramiding line showed 33.6-46.7 % increase of spikelet fertility, suggesting cumulative effect of S5-n and f5-n fragment in seed-set improvement of inter-subspecific hybrids. Our results provided an effective approach for exploiting heterosis between indica and japonica subspecies, which had a profound implication in rice breeding.

Metabolic prediction of important agronomic traits in hybrid rice (Oryza sativa L.)

Hybrid crops have contributed greatly to improvements in global food and fodder production over the past several decades. Nevertheless, the growing population and changing climate have produced food crises and energy shortages. Breeding new elite hybrid varieties is currently an urgent task, but present breeding procedures are time-consuming and labour-intensive. In this study, parental metabolic information was utilized to predict three polygenic traits in hybrid rice. A complete diallel cross population consisting of eighteen rice inbred lines was constructed, and the hybrids’ plant height, heading date and grain yield per plant were predicted using 525 metabolites. Metabolic prediction models were built using the partial least square regression method, with predictive abilities ranging from 0.858 to 0.977 for the hybrid phenotypes, relative heterosis, and specific combining ability. Only slight changes in predictive ability were observed between hybrid populations, and nearly no changes were detected between reciprocal hybrids. The outcomes of prediction of the three highly polygenic traits demonstrated that metabolic prediction was an accurate (high predictive abilities) and efficient (unaffected by population genetic structures) strategy for screening promising superior hybrid rice. Exploitation of this pre-hybridization strategy may contribute to rice production improvement and accelerate breeding programs.

Heterosis in elite hybrid rice: speculation on the genetic and biochemical mechanisms

Because of the tremendous advances in functional genomics and the current availability of a large number of superior hybrids, rice is an excellent model crop system for heterosis research. Genetic dissection of yield and yield component traits of an elite rice hybrid using an ultra-high density linkage map identified overdominance as the principal genetic basis of heterosis in this hybrid. This is not an expected finding based on the reported effects of single genes. Here we propose a gene expression and protein quality control hypothesis as one possible explanation for the overdominance in hybrids bred for yield. Future studies will be directed toward the identification of the genetic and biochemical mechanisms underlying the biology of hybrid vigor.

Demarcation of informative chromosomes in tropical sweet corn inbred lines using microsatellite DNA markers

A study of genetic variation among 10 pairs of chromosomes extracted from 13 tropical sweet corn inbred lines, using 99 microsatellite markers, revealed a wide range of genetic diversity. Allelic richness and the number of effective alleles per chromosome ranged from 2.78 to 4.33 and 1.96 to 3.47, respectively, with respective mean values of 3.62 and 2.73. According to the Shannon’s information index (I) and Nei’s gene diversity coefficient (Nei), Chromosome 10 was the most informative chromosome (I = 1.311 and Nei = 0.703), while Chromosome 2 possessed the least (I = 0.762 and Nei = 0.456). Based on linkage disequilibrium (LD) measurements for loci less than 50 cM apart on the same chromosome, all loci on Chromosomes 1, 6 and 7 were in equilibrium. Even so, there was a high proportion of genetic variation in Chromosomes 4, 5, 8, 9 and 10, thereby revealing their appropriateness for use in the genetic diversity investigations among tropical sweet corn lines. Chromosome 4, with the highest number of loci in linkage disequilibrium, was considered the best for marker-phenotype association and QTL mapping, followed by Chromosomes 5, 8, 9 and 10.

Use of random amplified polymorphic DNA markers to estimate heterosis and combining ability in tomato hybrids

Random Amplified Polymorphic DNAs (RAPD) were used to estimate genetic distances and determine the correlation between genetic distance and hybrid performance of 29 tomato lines that were the parents in a diallel mating design. Among 97 observed bands, 69 showed polymorphism and were used for establishing genetic distances based on the Nei coefficient between parents. A UPGMA dendrogram and Multi-Dimensional Scaling (MDS) analysis based on Nei genetic distances clearly clustered each group, confirming the variation at a molecular level. Correlations between genetic distances of the parents and performances of hybrids were established for various quantitative traits. Significant correlations were found between RAPD markers estimated genetic distances and MPH, HPH, SCA for some traits. The low correlation between parental genetic distances and hybrid performances for some quantitative traits suggested that RAPD markers have low linkage to Quantitative Trait Loci (QTLs) or have inadequate genome coverage for these traits. The results indicated that RAPD markers can be used as a tool for determining the extent of genetic diversity among tomato lines, for allocating genotypes into different groups and also to aid in the choice of the superior crosses to be made among tomato lines, so reducing the number of crosses required under field evaluation.

Differences of cytosine methylation in parental lines and F1 hybrids of Large White×Meishan crosses and their effects on F1 performance

In order to probe the effect of methylation on heterosis, the methylation-sensitive arbitrarily primed polymerase chain reaction (AP-PCR) technique was adopted to amplify pig genome DNA with 40 single arbitrary primers. The material involved parental lines and F1 hybrids of Large White×Meishan crosses. Nineteen differentially methylated sites with RsaI+HpaII digestion and 14 differentially methylated sites with RsaI+MspII digestion between parental lines and the hybrid were found. All fragments detected in this study were grouped into four classes: (1) the same level of methylation in both parental lines and the hybrid; (2) the same level of methylation in one parent and the hybrid; (3) an increased level of methylation in the hybrid compared to the parents, and (4) a decreased level of methylation in the hybrid. Five sites had significant effects on seven traits (P<0.05). Sequence analysis showed that three sequences had a high-identity match in GenBank (greater than 87%) and two sequences had no match in the database. The percentage of G+C in three sequences was over 50, and the observed/expected CpG of all sequences was above 0.6. Furthermore, one sequence contained G/C boxes. This study demonstrated that the sites in CpG islands within a gene promoter were differentially methylated in the hybrid compared to parental lines; methylated sites contributed differentially to F1 performance, showing that heterosis could benefit from either expression or repression of some genes.

Heterosis and polymorphisms of gene expression in an elite rice hybrid as revealed by a microarray analysis of 9198 unique ESTs

Despite the significant contributions of utilizing heterosis to crop productivity worldwide, the biological mechanisms of heterosis remained largely uncharacterized. In this study, we analyzed gene expression profiles of an elite rice hybrid and the parents at three stages of young panicle development, using a cDNA microarray consisting of 9198 expressed sequence tags (ESTs), with the objective to reveal patterns of gene expression that may be associated with heterosis in yield. A total of 8422 sequences showed hybridization signals in all three genotypes in at least one stage and 5771 sequences produced detectable signals in all slides. Significant differences in expression level were detected for 438 sequences among the three genotypes in at least one of the three stages, as determined by ANOVA validated with 100 permutations at P < 0.05. Significant mid-parent heterosis was detected for 141 sequences, which demonstrated the following features: a much larger number of sequences showed negative heterosis than ones showing positive heterosis; genes functioning in DNA replication and repair tended to show positive heterosis; genes functioning in carbohydrate metabolism, lipid metabolism, energy metabolism, translation, protein degradation, and cellular information processing showed negative heterosis; both positive and negative heterosis were observed for genes in amino acid metabolism, transcription, signal transduction, plant defense and transportation. The results are indicative of the biochemical and physiological activities taking place in the hybrid relative to the parents. Identification of genes showing expression polymorphisms among different genotypes and heterotic expression in the hybrid may provide new avenues for exploring the biological mechanisms underlying heterosis.

Delimitation of the rice wide compatibility gene S5 ( n ) to a 40-kb DNA fragment

Wide compatibility varieties (WCVs) are a special class of rice (Oryza sativa L.) germplasm that produces hybrids with normal pollen and spikelet fertility when crossed with both indica and japonica subspecies. The wide compatibility gene S5 ( n ) has been used extensively in inter-subspecific hybrid breeding programs. We previously mapped the S5 locus to a 2.2-cM genomic region between RM253 and R2349 on chromosome 6, using a population of 356 F(1) plants derived from the three-way cross 02428/Nanjing11//Balilla. In this study, a chromosome walking strategy was employed to construct a physical map covering this genomic region using these two closest markers as the starting points. A physical map consisting of six overlapping BAC clones was formed, spanning a genomic region of 540-kb in length. By analyzing recombination events from a population of 8,000 F(1) plants derived from a three-way cross based on near isogenic lines of the S5 locus, the S5 locus was localized to a DNA fragment of 40-kb in length, flanked by two shotgun subclones, 7B1 and 15D2. Sequence analysis of this fragment predicted five open reading frames, encoding xyloglucan fucosyltransferases, dnak-type molecular chaperone BiP, a putative eukaryotic aspartyl protease, and a hypothetical protein. This result will be very useful in molecular cloning of the S5 ( n ) allele and marker-assisted transferring of the wide compatibility gene in rice breeding programs.

Genetic distances revealed by morphological characters, isozymes, proteins and RAPD markers and their relationships with hybrid performance in oilseed rape (Brassica napus L.)

Genetic distances (GDs) based on morphological characters, isozymes and storage proteins, and random amplified polymorphic DNAs (RAPD) were used to predict the performance and heterosis of crosses in oilseed rape (Brassica napus L.). Six male-sterile lines carrying the widely used Shaan2A cytoplasm were crossed with five restorer lines to produce 30 F1 hybrids. These 30 hybrids and their parents were evaluated for seven agronomically important traits and their mid-parent heterosis (MPH) at Yangling, Shaanxi province in Northwest China for 2 years. Genetic similarity among the parents based on 34 isozyme and seven protein markers was higher than that based on 136 RAPDs and/or 48 morphological markers. No significant correlation was detected among these three sets of data. Associations between the different estimates of GDs and F1 performance for some agronomic traits were significant, but not for seed yield. In order to enhance the predicting efficiency, we selected 114 significant markers and 43 favoring markers following statistical comparison of the mean values of the yield components between the heterozygous group (where the marker is present only in one parent of each hybrid) and the homozygous group (where the marker is either present or absent in both parents of each hybrid) of the 30 hybrids. Parental GD based on total polymorphic markers (GDtotal, indicating general heterozygosity), significant markers (GDsign, indicating specific heterozygosity) and favoring markers (GDfavor, indicating favoring-marker heterozygosity) were calculated. The correlation between GDfavor or GDsign and hybrid performance was higher than the correlation between GDtotal and hybrid performance. GDsign and GDfavor significantly correlated with plant height, seeds per silique and seed yield, but not with the MPH of the other six agronomic traits with the exception of plant height. The information obtained in this study on the genetic diversity of the parental lines does not appear to be reliable for predicting F1 yield and heterosis.

DNA markers in plant improvement: an overview

The progress made in DNA marker technology has been tremendous and exciting. DNA markers have provided valuable tools in various analyses ranging from phylogenetic analysis to the positional cloning of genes. The development of high-density molecular maps which has been facilitated by PCR-based markers, have made the mapping and tagging of almost any trait possible. Marker-assisted selection has the potential to deploy favorable gene combinations for disease control. Comparative studies between incompatible species using these markers has resulted in synteny maps which are useful not only in predicting genome organization and evolution but also have practical application in plant breeding. DNA marker technology has found application in fingerprinting genotypes, in determining seed purity, in systematic sampling of germplasm, and in phylogenetic analysis. This review discusses the use of this technology for the genetic improvement of plants.