Heterotic Loci Research Articles

Identification of Heterosis-Associated Stable QTLs for Ear-Weight-Related Traits in an Elite Maize Hybrid Zhengdan 958 by Design III

Heterosis plays a decisive role in maize production worldwide, but its genetic basis remains unclear. In this study, we explored heterosis for ear-weight (EW)-related traits using a North Carolina Experiment III design (Design III) population derived from the elite maize hybrid Zhengdan 958. Quantitative trait loci (QTL) analysis was conducted based on phenotypic data collected from five environments using a high-density linkage map that consisted of 905 single nucleotide polymorphisms (SNP). A total of 38 environmentally stable QTLs were detected, and the numbers for the Z1 and Z2 populations were 18 and 20, respectively. All environmentally stable QTLs for Z2 were characterized by the overdominance effect (OD), which indicated that overdominance was one of the most important contributors to the heterosis of EW-related traits. Consistent with the significant positive correlations between EW-related traits, 9 genomic regions with overlapped QTLs for different traits were found and were located on chromosomes 1 (1), 3 (2), 4 (3), 7 (1), 8 (1), and 9 (1). Compared to previous reports, we found that the genomic regions for heterosis were not always congruent between different hybrids, which suggested that the combination of heterotic loci in different hybrids was genotype-dependent. Collectively, these data provided further evidence that the potential utilization of QTLs for heterosis may be feasible by pyramiding if we treat the QTLs as inherited units.

Mapping of QTLs and Heterotic Loci for Flowering Time-related Traits in Maize

Mapping of QTLs and Heterotic Loci for Flowering Time-related Traits in Maize

Identification of heterotic loci associated with grain yield and its components using two CSSL test populations in maize.

Heterosis has widely been used to increase grain yield and quality. In this study, the genetic basis of heterosis on grain yield and its main components in maize were examined over 2 years in two locations in two test populations constructed from a set of 184 chromosome segment substitution lines (CSSLs) and two inbred lines (Zheng58 and Xun9058). Of the 169 heterotic loci (HL) associated with grain yield and its five components identified in CSSL × Zheng58 and CSSL × Xun9058 test populations, only 25 HL were detected in both populations. The comparison of quantitative trait loci (QTLs) detected in the CSSL population with HL detected in the two test populations revealed that only 15.46% and 17.35% of the HL in the given populations respectively, shared the same chromosomal regions as that of the corresponding QTLs and showed dominant effects as well as pleiotropism with additive and dominant effects. In addition, most of the HL (74.23% and 74.49%) had overdominant effects. These results suggest that overdominance is the main contributor to the effects of heterosis on grain yield and its components in maize, and different HL are associated with heterosis for different traits in different hybrids.

Heterotic loci identified for plant height and ear height using two CSSLs test populations in maize

Heterosis is an important biological phenomenon, and it has been used to increase grain yield, quality and resistance to abiotic and biotic stresses in many crops. However, the genetic mechanism of heterosis remains unclear up to now. In this study, a set of 184 chromosome segment substitution lines (CSSLs) population, which derived from two inbred lines lx9801 (the recurrent parent) and Chang 72 (the donor parent), were used as basal material to construct two test populations with the inbred lines Zheng 58 and Xun 9058. The two test populations were evaluated in two locations over two years, and the heterotic loci for plant height and ear height were identified by comparing the performance of each test hybrid with the corresponding CK at P<0.05 significant level using one-way ANOVA analysis and Duncan's multiple comparisons. There were 24 and 29 different heterotic loci (HL) identified for plant height and ear height in the two populations at two locations over two years. Three HL (hlPH4a, hlPH7c, hlPH1b) for plant height and three (hlEH1d, hlEH6b, hlEH1b) for ear height were identified in the CSSLs×Zheng 58 and CSSLs×Xun 9058 populations as contributing highly to heterosis performance of plant height and ear height across four environments. Among the 29 HL identified for ear height, 12 HL (41.4%) shared the same chromosomal region associated with the HL (50.0%) identified for plant height in the same test population and environment.

Exploitation of heterosis loci for yield and yield components in rice using chromosome segment substitution lines.

We constructed 128 chromosome segment substitution lines (CSSLs), derived from a cross between indica rice (Oryza sativa L.) 9311 and japonica rice Nipponbare, to investigate the genetic mechanism of heterosis. Three photo-thermo-sensitive-genic male sterile lines (Guangzhan63-4s, 036s, and Lian99s) were selected to cross with each CSSL to produce testcross populations (TCs). Field experiments were carried out in 2009, 2011, and 2015 to evaluate yield and yield-related traits in the CSSLs and TCs. Four traits (plant height, spikelet per panicle, thousand-grain weight, and grain yield per plant) were significantly related between CSSLs and TCs. In the TCs, plant height, panicle length, seed setting rate, thousand-grain weight, and grain yield per plant showed partial dominance, indicating that dominance largely contributes to heterosis of these five traits. While overdominance may be more important for heterosis of panicles per plant and spikelet per panicle. Based on the bin-maps of CSSLs and TCs, we detected 62 quantitative trait loci (QTLs) and 97 heterotic loci (HLs) using multiple linear regression analyses. Some of these loci were clustered together. The identification of QTLs and HLs for yield and yield-related traits provide useful information for hybrid rice breeding, and help to uncover the genetic basis of rice heterosis.

Genetic analysis of heterosis for maize grain yield and its components in a set of SSSL testcross populations

The present study aimed to dissect the genetic basis of heterosis for grain yield and its components in maize (Zea mays L.). Quantitative trait loci (QTL) and heterotic loci (HL) were analyzed using a set of 203 single segment substitution lines (SSSLs) and its testcross population in three environments. Forty-one QTL were identified as responsible for grain yield, ear length, ear diameter, row number, kernel number per row, and 100-kernel weight in the SSSLs population, and 17 QTL were conserved across the three environments. In the heterosis analysis, 36 HL were identified for grain yield and five yield-related traits in the test population in the three environments. Among the HL, only six (16.7 %) for ear length, kernel number per row, 100-kernel weight, and grain yield were consistent with the results of QTL mapping. In addition, 16.7 % of the heterotic loci showed a dominant effect and 83.3 % showed an over-dominant effect. The results implied that dominance and over-dominance were two important components of heterosis in maize grain yield and yield-related traits in the present testcross population.

Identification of Heterotic Loci for Yield and Ear Traits Using CSSL Test Population in Maize

Heterosis plays an important role in enhancing crop yield and quality. Dissecting the genetic basis of heterosis can promote hybrid maize selection, however it is unclear up to now. In this study, a set of chromosome segment substitution lines (CSSLs) population, which was constructed using the inbred line lx9801 as the receptor parent and the inbred line Chang 7-2 as the donor parent, was crossed with the inbred line T7296 to construct the corresponding test population. The test population was used to identify the heterotic loci (HL) for grain yield and ear traits in maize, which showed significant difference in heterosis between the corresponding chromosomal region of the inbred line Chang 7-2 and lx9801 as well as the test inbred line T7296. A total of 64 HL were identified for gain yield and ear traits, and among them 23 HL were identified at the two environments simul- taneously, including 4 HL for ear length, 4 HL for ear width, 4 HL for row number, 7 HL for kernels per row, and 4 HL for grain yield. Additionally, the HL for both grain yield and its components simultaneously were found on many chromosomal regions. This study could offer a basic material for thoroughly dissecting the genetic basis of heterosis for grain yield and its components in maize.

Genetic distance revealed by genomic single nucleotide polymorphisms and their relationships with harvest index heterotic traits in rapeseed (Brassica napus L.)

Identifying and using heterotic loci in breeding programs is crucial for increasing crop yield. In this study, we planted 68 inbred lines and their 132 testcrosses at Wuhan and Xiangyang, China. We performed a phenotypic analysis of nine yield-related traits, including plant height, main inflorescence length, branch number, seeds per silique, effective silique number on the main inflorescence, thousand seed weight, biomass yield per plant, seed yield per plant, and harvest index (HI). Additionally, the mid-parent heterosis (MPH) and better-parent heterosis (BPH) for each trait were evaluated. The genetic distance (GD) calculated using high-throughput single nucleotide polymorphisms (SNPs) showed no correlation with HI heterosis, and the difference in GD in the two groups (H-154 and H-155) was not correlated with the difference in HI heterosis levels. The MPH and BPH of HI were significantly correlated with the MPH and BPH of biomass yield per plant, but not with the other traits. Our results indicate that yield-related traits heterosis, including HI heterosis, are extremely complex. The effectiveness of predicting heteroses with GD based on SNPs may be limited, though the SNPs can be used to instead of older markers for high-throughput and accurate genotyping. Our findings may contribute a better understanding to rapeseed breeding and the natural variations of HI heterosis.

Heterotic loci for various morphological traits of maize detected using a single segment substitution lines test-cross population

Heterosis has been exploited to increase grain yield, quality, and resistance in many crops, and it plays an important role in plant breeding. However, the genetic mechanism of heterosis remains unclear. To dissect the genetic basis of heterosis, a set of 203 single segment substitution lines (SSSLs) was developed, and its test-cross population was used to identify heterotic loci (HL) for plant morphological traits in maize, including plant height (PH), ear height (EH), leaf number (LN), tassel main axis length (TMAL), and tassel branch number (TBN). A total of 41 QTLs and 37 HL were identified for five morphological traits in the test-cross population derived from the 203 SSSLs and the parent, Xu178. Nine HL for PH, nine HL for EH, seven HL for LN, seven HL for TMAL, and five HL for TBN were detected in three different environments, respectively. Eight HL, ph1a, ph1b, ph2, ph5, eh3a, eh3b, eh10, and tmal1b, were simultaneously detected in the three environments. Among the 37 HL, only 10 (27.03 %; for PH, EH, LN, and TBN) had a corresponding QTL (24.39 %) sharing the same chromosomal region. Of all the HL, 21.4 % showed dominance effects, 76.8 % showed over-dominance effects, and only one (1.8 %) showed a partial-dominance effect. This result illustrated that heterosis and performance was controlled by different genetic mechanisms, and over-dominance effects were the main contributors to heterosis for plant-related traits at the single-locus level in maize.

Prediction of Heterosis in Crop Plants – Status and Prospects

Heterosis has been commercially exploited in many crops; however, its genetic and molecular basis is still not clear. The availability of advanced genomic tools has encouraged several research groups to dissect heterosis into genetic components. Prediction of heterosis using molecular markers is the first step towards this direction, as it may lead to the identification of markers and genomic regions associated with heterosis. Practically, it increases the efficiency of hybrid breeding by marker-assisted selection of superior parental combinations without large-scale field evaluation. Extensive studies in important crops like rice, wheat and maize have identified the genes / genomic regions associated with heterosis and also demonstrated the potential of molecular prediction. Recent trends in whole transcriptome and metabolome analyses will help in the identification of genes or metabolic networks involved in the expression of heterosis. Various genomic tools such as heterotic loci, molecular markers associated with heterotic gene blocks, ESTs and heterosisMini-Review Article Rajendrakumar et al.; AJEA, 9(3): 1-16, 2015; Article no.AJEA.19263 2 related gene databases provide better opportunities for understanding the molecular basis of heterosis and to develop reliable methodologies for a realistic prediction of heterosis. This review provides critical analysis of the prediction of heterosis in crop plants and its implications in hybrid development.

DNA divergence as a criterion of a sweet pepper (Capsicum annuum L.) selection for heterosis

The identification of perspective parental lines for the creation of highyield hybrids is the most laborconsuming stage of selection, because it needs exte nsive trials of combining ability. Based on evaluation of the genetic divergence of the parental lines, the prediction accuracy of F1 hybrids performance was inves� tigated. The value of the divergence was calculated using biometric and molecular methods, such as inter sim� ple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD). Based on estimates of diver� gence, 10 lines were chosen for cyclic cross (scheme I) and testcross (scheme II). In most crosses, the F1 hybrids were significantly superior to the parents in the main economically valuable traits. The level of het� erosis was higher among hybrids of scheme I. Analysis of the relationship between parental divergence and F1 performance showed that the hybrid productivity of scheme I was predetermined by ISSR divergence in 86%, and productivity was caused by RAPD divergence in 69%, whereas the F1 yield of scheme II was not related to the value of genetic distances. Since the values of DNA divergence were closely associated both with mid� parent level and F1 performance, we assumed that part of the polymorphic DNA fragments of the parental lines of scheme I is related to heterotic loci (HTL), which may be considered potential key markers for the heterotic selection of the sweet pepper.

Mapping Heterotic Loci for Yield and Agronomic Traits Using Chromosome Segment Introgression Lines in Cotton

In the present study, a set of chromosome segment introgression lines (CSILs) using Gossypium hirsutum L. TM-1 as the recipient parent and G. barbadense Hai7124 as the donor parent were used to explore the genetic basis of heterosis for interspecific hybrids. Two sets of F₁ populations individually derived from CSILs crossing with both parents were configured to investigate heterotic loci (HL) and substitution effect loci (SL). A total of 58 HL and 39 SL were identified in 3 years. One stable HL, hLP-A4-3, could be detected in all 3 years. Three HLs, hBS-A8-1, hLP-D6-1, and hSI-D7-11, could be detected in 2 years. Four SLs, sBS-D7-1, sLP-A8-1, sLP-D7-1, and sLP-D12-1, could be detected in 2 years. HL and SL tended to be distributed in some HL-rich chromosome segments with close positions. Compared with QTL detected in a former study, HL showed little overlap with QTL, indicating that trait phenotype and heterosis might be controlled by different sets of loci. All three forms of genetic effects (partial-, full-, over-dominant) were identified, while the over-dominant effect made the main contribution to heterosis. These results may help lay the foundation for clarifying the heredity mechanism of heterosis in cotton.

QTL-based analysis of heterosis for number of grains per spike in wheat using DH and immortalized F 2 populations

To map quantitative trait loci (QTL) and heterotic loci (HL) related to grain number per spike (GNS), 168 double haploid (DH) populations derived from Huapei 3 × Yumai 57 and an immortalized F2 population (IF2) generated by randomly permutated intermating of these DH populations were investigated. Using inclusive composite interval mapping (ICIM), a total of nine and eight significant QTLs for GNS were detected in three different environments in DH and IF2 populations, respectively. QTLs on chromosomes 1A, 2B, 3B, and 6A were observed between two populations. Five QTLs were detected on chromosome 1A. Of these QTLs, QGns1A-1 was a major QTL explaining 31.25 % of phenotypic variation. QGns2B-2 detected on chromosome 2B had the most significant additive effects, explaining 46.75 % of phenotypic variation with the favorable allele contributed by Yumai 57 corresponding to an increase of 5.69 kernels. Mid-parent heterosis of each cross in the IF2 population was used to map heterotic quantitative trait loci. A total of 17 HLs were detected. QTLs and HLs on chromosomes 2B and 6A were observed in the IF2 population. Three HLs, QHgns1B-2, QHgns2B, and QHgns6A-1, were detected in two environments and expressed stably. These results showed that some intervals on chromosomes 1B, 2B, and 6A play an important role in GNS heterosis in wheat, improving understanding of this phenomenon.

Genetic-basis analysis of heterotic loci in Dongxiang common wild rice (Oryza rufipogonGriff.)

Heterosis is widely used in genetic crop improvement; however, the genetic basis of heterosis is incompletely understood. The use of whole-genome segregating populations poses a problem for establishing the genetic basis of heterosis, in that interactions often mask the effects of individual loci. However, introgression line (IL) populations permit the partitioning of heterosis into defined genomic regions, eliminating a major part of the genome-wide epistasis. In our previous study, based on mid-parental heterosis (HMP) value with single-point analysis, 42 heterotic loci (HLs) associated with six yield-related traits were detected in wild and cultivated rice using a set of 265 ILs of Dongxiang common wild rice (Oryza rufipogon Griff.). In this study, the genetic effects of HLs were determined as the combined effects of both additive and dominant gene actions, estimated from the performance values of testcross F1s and the dominance effects estimated from the HMP values of testcross F1s. We characterized the gene action type at each HL. Thirty-eight of the 42 HLs were over-dominant, and in the absence of epistasis, four HLs were dominant. Therefore, we favour that over-dominance is a major genetic basis of 'wild-cultivar' crosses at the single functional Mendelian locus level.

Identification of heterotic loci associated with yield-related traits in Chinese common wild rice ( Oryza rufipogon Griff.)

Many rice breeding programs have currently reached yield plateaus as a result of limited genetic variability in parental strains. Dongxiang common wild rice ( Oryza rufipogon Griff.) is the progenitor of cultivated rice ( Oryza sativa L.) and serves as an important gene pool for the genetic improvement of rice cultivars. In this study, heterotic loci (HLs) associated with six yield-related traits were identified in wild and cultivated rice and investigated using a set of 265 introgression lines (ILs) of O. rufipogon Griff. in the background of the Indica high-yielding cultivar Guichao 2 ( O. sativa L.). Forty-two HLs were detected by a single point analysis of mid-parent heterosis values from test cross F 1 offspring, and 30 (71.5%) of these HLs showed significantly positive effects, consistent with the superiority shown by the F 1 test cross population in the six yield-related traits under study. Genetic mapping of hsp11, a locus responsible for the number of spikelets per panicle, confirmed the utility of these HLs. The results indicate that favorable HLs capable of improving agronomic traits are available. The identification of HLs between wild rice and cultivated rice could lead to a new strategy for the application of heterosis in rice breeding.

Genetic analysis of heterotic loci detected in a cross between indica and japonica rice (Oryza sativa L.)

The study on the genetic basis of heterosis has received significant attention in recent years. In this study, using a set of introgression lines (ILs) and corresponding testcross F1 populations, we investigated heterotic loci (HL) associated with six yield-related traits in both Oryza sativa L. subsp. indica and japonica. A total of 41 HL were detected on the basis of mid-parent heterosis values with single-point analysis. The F1 test-cross population showed superiority in most yield-related traits and was characterized by a high frequency of overdominant HL. Thirty-eight of the 41 HL were overdominant, and in the absence of epistasis, three HL were dominant, suggesting that heterotic effects at the single-locus level mainly appeared to be overdominant in rice. Twenty-four HL had a real positive effect, suggesting that they are viable candidates for the improvement of rice yield potential. Compared with the quantitative trait loci (QTLs) detected in the ILs, only six out of the 41 (14.6%) HL were detected in QTL analysis under the same statistical threshold, indicating that heterosis and trait performance may be conditioned by different sets of loci.

Analysis of Plant Height Heterosis Based on QTL Mapping in Wheat

This study aimed at studying the molecular genetic basis of plant height (PH) heterosis in wheat. From a set of doubled haploid (DH) lines derived from Huapei 3 × Yumai 57, an “immortalized F 2” population was constructed with 168 single crosses. The DH lines, IF 2 population, and the parents were evaluated for plant height in 3 environments, i.e., in Tai'an, Shandong Province, China, in 2007 and 2008 cropping seasons and in Jiyuan, Henan Province, China in 2008 cropping season. Based on the genetic map of quantitative trait locus (QTL) constructed in a previous study, the heterosis of PH of wheat was analyzed using the composite interval mapping method. A total of 3 additive QTLs, 2 dominance QTLs, 4 pairs of epistatic QTLs (including additive by additive, additive by dominance, dominance by additive, and dominance by dominance), and 20 heterotic loci were detected for PH in the 3 environments. Two QTLs, QPh2D and QPh4D, were detected on chromosomes 2D and 4D with a minor interaction of additive by environment. In addition, several heterotic loci for PH except QPh2D were also identified on chromosome 2D in close regions with similar marker intervals. Of them, QTLs QPh2D-2 and QPh2D-7 explained the PH variance by 29.77% and 55.77%, respectively. Another QTL associated with PH heterosis, QPh7D-2, was mapped in the marker interval between Xwmc273.2 and Xcfd175 on chromosome 7D in the 3 environments. These results indicated that a few QTLs on chromosomes 2D, 4D, and 7D play an important role in PH heterosis in wheat. These loci have potential use for the improvement of PH in wheat breeding assisted with molecular markers.

Dissection of the genetic basis of heterosis in an elite maize hybrid by QTL mapping in an immortalized F2 population

The genetic basis of heterosis for grain yield and its components was investigated at the single- and two-locus levels using molecular markers with an immortalized F(2) (IF(2)) population, which was developed by pair crosses among recombinant inbred lines (RILs) derived from the elite maize hybrid Yuyu22. Mid-parent heterosis of each cross in the IF(2) population was used to map heterotic quantitative trait loci. A total of 13 heterotic loci (HL) were detected. These included three HL for grain yield, seven for ear length, one for ear row number and two for 100-kernel weight. A total of 143 digenic interactions contributing to mid-parent heterosis were detected at the two-locus level involving all three types of interactions (additive x additive = AA, additive x dominance = AD or DA, dominance x dominance = DD). There were 25 digenic interactions for grain yield, 36 for ear length, 31 for ear row number and 51 for 100-kernel weight. Altogether, dominance effects of HL at the single-locus level as well as AA interactions played an important role in the genetic basis of heterosis for grain yield and its components in Yuyu22.

Detection of quantitative trait loci and heterotic loci for plant height using an immortalized F2 population in maize

A set of recombinant inbred lines (RIL) derived from Yuyu22, an elite hybrid widespread in China, was used to construct an immortalized F2 (IF2) population comprising 441 different crosses. Genetic linkage maps were constructed containing 10 linkages groups with 263 simple sequence repeat (SSR) molecular markers. Twelve and ten quantitative trait loci (QTL) were detected for plant height in the IF2 and RIL populations respectively, using the composite interval mapping method, and six same QTL were identified in the two populations. In addition, ten unique heterotic loci (HL) located on seven different chromosomes were revealed for plant height using the mid-parent heterosis as the input data. These HL explained 1.26%–8.41% of the genotypic variance in plant height heterosis and most expressed overdominant effects. Only three QTL and HL were located in the same chromosomal region, it implied that plant height and its heterosis might be controlled by two types of genetic mechanisms.

Single-locus heterotic effects and dominance by dominance interactions can adequately explain the genetic basis of heterosis in an elite rice hybrid.

The genetic basis of heterosis of an elite rice hybrid was investigated by using an "immortalized F(2)" population produced by randomly permutated intermating of 240 recombinant inbred lines from a cross between the parents of Shanyou 63, the most widely cultivated hybrid in China. Measurements of heterosis for crosses in the immortalized F(2) population were obtained from replicated field trials over 2 years by inter-planting the hybrids with the parental recombinant inbred lines. The analyses were conducted making use of a linkage map comprising 231 segregating molecular marker loci covering the entire rice genome. Heterotic effects were detected at 33 loci for the four traits with modified composite interval mapping. The heterotic loci showed little overlap with quantitative trait loci for trait performance, suggesting that heterosis and trait performance may be conditioned by different sets of loci. Large numbers of digenic interactions were resolved by using two-way ANOVA and confirmed by randomization tests. All kinds of genetic effects, including partial-, full-, and overdominance at single-locus level and all three forms of digenic interactions (additive by additive, additive by dominance, and dominance by dominance), contributed to heterosis in the immortalized F(2) population, indicating that these genetic components were not mutually exclusive in the genetic basis of heterosis. Heterotic effects at the single-locus level, in combination with the marginal advantages of double heterozygotes caused by dominance by dominance interaction at the two-locus level could adequately explain the genetic basis of heterosis in Shanyou 63. These results may help reconcile the century-long debate concerning the genetic basis of heterosis.