Overdominant Epistatic Loci Are the Primary Genetic Basis of Inbreeding Depression and Heterosis in Rice. I. Biomass and Grain Yield

Genetics ◽  
2001 ◽  
Vol 158 (4) ◽  
pp. 1737-1753 ◽  
Author(s):  
Zhi-Kang Li ◽  
L J Luo ◽  
H W Mei ◽  
D L Wang ◽  
Q Y Shu ◽  
...  
Keyword(s):  
Grain Yield ◽  
Inbreeding Depression ◽  
Genetic Basis ◽  
Mixed Model ◽  
Recombinant Inbred Lines ◽  
Hybrid Breakdown ◽  
Mixed Model Approach ◽  
Epistatic Qtl ◽  
Main Effect ◽  
Mapping Populations

AbstractTo understand the genetic basis of inbreeding depression and heterosis in rice, main-effect and epistatic QTL associated with inbreeding depression and heterosis for grain yield and biomass in five related rice mapping populations were investigated using a complete RFLP linkage map of 182 markers, replicated phenotyping experiments, and the mixed model approach. The mapping populations included 254 F10 recombinant inbred lines derived from a cross between Lemont (japonica) and Teqing (indica) and two BC and two testcross hybrid populations derived from crosses between the RILs and their parents plus two testers (Zhong 413 and IR64). For both BY and GY, there was significant inbreeding depression detected in the RI population and a high level of heterosis in each of the BC and testcross hybrid populations. The mean performance of the BC or testcross hybrids was largely determined by their heterosis measurements. The hybrid breakdown (part of inbreeding depression) values of individual RILs were negatively associated with the heterosis measurements of their BC or testcross hybrids, indicating the partial genetic overlap of genes causing hybrid breakdown and heterosis in rice. A large number of epistatic QTL pairs and a few main-effect QTL were identified, which were responsible for >65% of the phenotypic variation of BY and GY in each of the populations with the former explaining a much greater portion of the variation. Two conclusions concerning the loci associated with inbreeding depression and heterosis in rice were reached from our results. First, most QTL associated with inbreeding depression and heterosis in rice appeared to be involved in epistasis. Second, most (~90%) QTL contributing to heterosis appeared to be overdominant. These observations tend to implicate epistasis and overdominance, rather than dominance, as the major genetic basis of heterosis in rice. The implications of our results in rice evolution and improvement are discussed.

scholarly journals Overdominant Epistatic Loci Are the Primary Genetic Basis of Inbreeding Depression and Heterosis in Rice. II. Grain Yield Components

Genetics ◽  
2001 ◽  
Vol 158 (4) ◽  
pp. 1755-1771 ◽  
Author(s):  
L J Luo ◽  
Z-K Li ◽  
H W Mei ◽  
Q Y Shu ◽  
R Tabien ◽  
...  
Keyword(s):  
Grain Yield ◽  
Inbreeding Depression ◽  
Yield Components ◽  
Genetic Basis ◽  
Mixed Model ◽  
Gene Action ◽  
Recombinant Inbred Lines ◽  
Hybrid Breakdown ◽  
Multilocus Genotypes ◽  
Grain Yield Components

Abstract 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 F10 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 F1 mean values. We found no evidence suggesting that pseudooverdominance 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.

scholarly journals Genetic dissection of heterosis of indica–japonica by introgression line, recombinant inbred line and their testcross populations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wenqing Yang ◽  
Fan Zhang ◽  
Sundus Zafar ◽  
Junmin Wang ◽  
Huajin Lu ◽  
...  
Keyword(s):  
Grain Yield ◽  
Recombinant Inbred ◽  
Genetic Basis ◽  
Recombinant Inbred Lines ◽  
Introgression Line ◽  
Successful Implementation ◽  
Genetic Dissection ◽  
Single Nucleotide ◽  
Panicle Number ◽  
Main Effect

AbstractThe successful implementation of heterosis in rice has significantly enhanced rice productivity, but the genetic basis of heterosis in rice remains unclear. To understand the genetic basis of heterosis in rice, main-effect and epistatic quantitative trait loci (QTLs) associated with heterosis for grain yield-related traits in the four related rice mapping populations derived from Xiushui09 (XS09) (japonica) and IR2061 (indica), were dissected using single nucleotide polymorphism bin maps and replicated phenotyping experiments under two locations. Most mid-parent heterosis of testcross F1s (TCF1s) of XS09 background introgression lines (XSILs) with Peiai64S were significantly higher than those of TCF1s of recombinant inbred lines (RILs) with PA64S at two locations, suggesting that the effects of heterosis was influenced by the proportion of introgression of IR2061’s genome into XS09 background. A total of 81 main-effect QTLs (M-QTLs) and 41 epistatic QTLs were identified for the phenotypic variations of four traits of RILs and XSILs, TCF1s and absolute mid-parent heterosis in two locations. Furthermore, overdominance and underdominance were detected to play predominant effects on most traits in this study, suggesting overdominance and underdominance as well as epistasis are the main genetic bases of heterosis in rice. Some M-QTLs exhibiting positive overdominance effects such as qPN1.2, qPN1.5 and qPN4.3 for increased panicle number per plant, qGYP9 and qGYP12.1 for increased grain yield per plant, and qTGW3.4 and qTGW8.2 for enhanced 1000-grain weight would be highly valuable for breeding to enhance grain yield of hybrid rice by marker-assisted selection.

scholarly journals Effects of kinship correction on inflation of genetic interaction statistics in commonly used mouse populations

2021 ◽  
Author(s):  
Anna L Tyler ◽  
Baha El Kassaby ◽  
Georgi Kolishovski ◽  
Jake Emerson ◽  
Ann E Wells ◽  
...  
Keyword(s):  
Mixed Model ◽  
Linear Mixed Model ◽  
Genetic Interaction ◽  
Recombinant Inbred Lines ◽  
Test Statistics ◽  
Test Statistic ◽  
Kinship Matrix ◽  
Main Effect ◽  
Main Effects ◽  
Interaction Test

Abstract It is well understood that variation in relatedness among individuals, or kinship, can lead to false genetic associations. Multiple methods have been developed to adjust for kinship while maintaining power to detect true associations. However, relatively unstudied, are the effects of kinship on genetic interaction test statistics. Here we performed a survey of kinship effects on studies of six commonly used mouse populations. We measured inflation of main effect test statistics, genetic interaction test statistics, and interaction test statistics reparametrized by the Combined Analysis of Pleiotropy and Epistasis (CAPE). We also performed linear mixed model (LMM) kinship corrections using two types of kinship matrix: an overall kinship matrix calculated from the full set of genotyped markers, and a reduced kinship matrix, which left out markers on the chromosome(s) being tested. We found that test statistic inflation varied across populations and was driven largely by linkage disequilibrium. In contrast, there was no observable inflation in the genetic interaction test statistics. CAPE statistics were inflated at a level in between that of the main effects and the interaction effects. The overall kinship matrix overcorrected the inflation of main effect statistics relative to the reduced kinship matrix. The two types of kinship matrices had similar effects on the interaction statistics and CAPE statistics, although the overall kinship matrix trended toward a more severe correction. In conclusion, we recommend using a LMM kinship correction for both main effects and genetic interactions and further recommend that the kinship matrix be calculated from a reduced set of markers in which the chromosomes being tested are omitted from the calculation. This is particularly important in populations with substantial population structure, such as recombinant inbred lines in which genomic replicates are used.

scholarly journals Genetic dissection of yield-related traits and mid-parent heterosis for those traits in maize (Zea mays L.)

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Qiang Yi ◽  
Yinghong Liu ◽  
Xianbin Hou ◽  
Xiangge Zhang ◽  
Hui Li ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Recombinant Inbred Lines ◽  
Kernel Weight ◽  
Genetic Dissection ◽  
Hybrid Mapping ◽  
Maize Breeding ◽  
Phenotypic Variations ◽  
Selection For ◽  
Genomic Regions ◽  
Mapping Populations

Abstract Background Utilization of heterosis in maize could be critical in maize breeding for boosting grain yield. However, the genetic architecture of heterosis is not fully understood. To dissect the genetic basis of yield-related traits and heterosis in maize, 301 recombinant inbred lines derived from 08 to 641 × YE478 and 298 hybrids from the immortalized F2 (IF2) population were used to map quantitative trait loci (QTLs) for nine yield-related traits and mid-parent heterosis. Results We observed 156 QTLs, 28 pairs of loci with epistatic interaction, and 10 significant QTL × environment interactions in the inbred and hybrid mapping populations. The high heterosis in F1 and IF2 populations for kernel weight per ear (KWPE), ear weight per ear (EWPE), and kernel number per row (KNPR) matched the high percentages of QTLs (over 50%) for those traits exhibiting overdominance, whereas a notable predominance of loci with dominance effects (more than 70%) was observed for traits that show low heterosis such as cob weight per ear (CWPE), rate of kernel production (RKP), ear length (EL), ear diameter (ED), cob diameter, and row number (RN). The environmentally stable QTL qRKP3–2 was identified across two mapping populations, while qKWPE9, affecting the trait mean and the mid-parent heterosis (MPH) level, explained over 18% of phenotypic variations. Nine QTLs, qEWPE9–1, qEWPE10–1, qCWPE6, qEL8, qED2–2, qRN10–1, qKWPE9, qKWPE10–1, and qRKP4–3, accounted for over 10% of phenotypic variation. In addition, QTL mapping identified 95 QTLs that were gathered together and integrated into 33 QTL clusters on 10 chromosomes. Conclusions The results revealed that (1) the inheritance of yield-related traits and MPH in the heterotic pattern improved Reid (PA) × Tem-tropic I (PB) is trait-dependent; (2) a large proportion of loci showed dominance effects, whereas overdominance also contributed to MPH for KNPR, EWPE, and KWPE; (3) marker-assisted selection for markers at genomic regions 1.09–1.11, 2.04, 3.08–3.09, and 10.04–10.05 contributed to hybrid performance per se and heterosis and were repeatedly reported in previous studies using different heterotic patterns is recommended.

Detection of main-effect and epistatic QTL for yield-related traits in rice under drought stress and normal conditions

2014 ◽  
Vol 94 (4) ◽  
pp. 633-641 ◽  
Author(s):  
Wang Xing ◽  
Hongwei Zhao ◽  
Detang Zou
Keyword(s):  
Drought Stress ◽  
Crop Yields ◽  
Upland Rice ◽  
Recombinant Inbred Lines ◽  
Stress Conditions ◽  
Epistatic Qtls ◽  
Epistatic Qtl ◽  
Main Effect ◽  
Drought Resistant ◽  
Main Effect Qtls

Xing, W., Zhao, H. and Zou, D. 2014. Detection of main-effect and epistatic QTL for yield-related traits in rice under drought stress and normal conditions. Can. J. Plant Sci. 94: 633–641. Drought-resistant cultivars play an important role in maintaining high and stable crop yields under drought-stress conditions. However, the genetic mechanism of drought resistance must first be elucidated. Therefore, 220 recombinant inbred lines from a cross between Xiaobaijingzi (upland rice) and Kongyu 131 (Oryza sativa L.) were used to identify quantitative trait loci (QTLs) for yield and yield-component traits under drought stress and control conditions in Heilongjiang and Tieli. As a result, 23 main-effect QTLs and 11 digenic interactions were detected for four traits under the above two conditions. Of the main-effect QTLs, 10 and 8 were detected under control and drought-stress conditions, respectively; and five common QTLs were observed. In addition, five QTLs were found to be responsible for the difference across the two conditions. Among all epistatic QTLs, three types of epistatic QTLs were observed: one was between two main-effect QTLs, such as qPH-3-1 and qPH-7-2; one was between one locus with and another without main-effect, e.g., qPN-4 and qPN-3-2; and one was between two loci without main-effect, e.g., qYP-6-1 and qYP-12-2. In the above epistatic examples, their recombinant genotypes tended to reduce plant height and the number of grains per panicle and increase yield, respectively. Our results provide a good foundation for designed molecular breeding of drought-resistant rice.

scholarly journals Genetic Dissection of Hybrid Performance and Heterosis for Yield-Related Traits in Maize

2021 ◽  
Vol 12 ◽  
Author(s):  
Dongdong Li ◽  
Zhiqiang Zhou ◽  
Xiaohuan Lu ◽  
Yong Jiang ◽  
Guoliang Li ◽  
...  
Keyword(s):  
Grain Yield ◽  
Recombinant Inbred ◽  
Fixed Effects ◽  
Prediction Accuracy ◽  
Genetic Architecture ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Hybrid Performance

Heterosis contributes a big proportion to hybrid performance in maize, especially for grain yield. It is attractive to explore the underlying genetic architecture of hybrid performance and heterosis. Considering its complexity, different from former mapping method, we developed a series of linear mixed models incorporating multiple polygenic covariance structures to quantify the contribution of each genetic component (additive, dominance, additive-by-additive, additive-by-dominance, and dominance-by-dominance) to hybrid performance and midparent heterosis variation and to identify significant additive and non-additive (dominance and epistatic) quantitative trait loci (QTL). Here, we developed a North Carolina II population by crossing 339 recombinant inbred lines with two elite lines (Chang7-2 and Mo17), resulting in two populations of hybrids signed as Chang7-2 × recombinant inbred lines and Mo17 × recombinant inbred lines, respectively. The results of a path analysis showed that kernel number per row and hundred grain weight contributed the most to the variation of grain yield. The heritability of midparent heterosis for 10 investigated traits ranged from 0.27 to 0.81. For the 10 traits, 21 main (additive and dominance) QTL for hybrid performance and 17 dominance QTL for midparent heterosis were identified in the pooled hybrid populations with two overlapping QTL. Several of the identified QTL showed pleiotropic effects. Significant epistatic QTL were also identified and were shown to play an important role in ear height variation. Genomic selection was used to assess the influence of QTL on prediction accuracy and to explore the strategy of heterosis utilization in maize breeding. Results showed that treating significant single nucleotide polymorphisms as fixed effects in the linear mixed model could improve the prediction accuracy under prediction schemes 2 and 3. In conclusion, the different analyses all substantiated the different genetic architecture of hybrid performance and midparent heterosis in maize. Dominance contributes the highest proportion to heterosis, especially for grain yield, however, epistasis contributes the highest proportion to hybrid performance of grain yield.

Genetic progress in upland rice breeding program for grain yield and plant height

2021 ◽  
Vol 45 ◽  
Author(s):  
Amanda Mendes de Moura ◽  
Flávia Barbosa Silva Botelho ◽  
Laís Moretti Tomé ◽  
Cinthia Souza Rodrigues ◽  
Camila Soares Cardoso da Silva ◽  
...  
Keyword(s):  
Grain Yield ◽  
Plant Height ◽  
Mixed Model ◽  
Upland Rice ◽  
Breeding Program ◽  
High Yield ◽  
Joint Analysis ◽  
Rice Breeding ◽  
Genetic Progress ◽  
Mixed Model Approach

ABSTRACT In the context of plant breeding programs, it is necessary to evaluate the efficiency of genotype selection over successive years. However, evaluating the genotype selection efficiency is not an easy task, since there is not just a single way to precede it. Besides that, the programs need to be dynamic; that is, they should be able to track the introduction and discard of genotypes each year. As a result, the available data is quite unbalanced, leading to difficulties in certain analyses. Thus, the present study aims to propose some approaches to verify the genetic progress in the preliminary trial of the Federal University of Lavras (UFLA) upland rice breeding program. We utilized mixed models for grain yield and plant height. Trials were performed with a total of 120 genotypes in seven environments, defined by the interaction between locations and years. Due to the imbalance in the available data, the mixed model approach, i.e., Restricted Maximum Likelihood/Best Linear Unbiased Prediction (REML/BLUP), was adopted for the joint analysis. Besides the genetic and phenotypic parameters, the expected gains were also obtained with the selection, genetic progress, renewal rate (RR%), and dynamism of preliminary trials. The efficiency of the selection of superior genotypes per year was verified, with genetic progress favorable for reducing the medium-sized plants associated with high yield.

scholarly journals Combining QTL-seq and linkage mapping to uncover the genetic basis of single vs. paired spikelets in the advanced populations of two-ranked maize×teosinte

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhengjie Chen ◽  
Dengguo Tang ◽  
Kun Hu ◽  
Lei Zhang ◽  
Yong Yin ◽  
...  
Keyword(s):  
Fine Mapping ◽  
Linkage Mapping ◽  
Genetic Basis ◽  
Recurrent Selection ◽  
Epistatic Effect ◽  
Phenotypic Variance ◽  
Epistatic Qtl ◽  
Maize Domestication ◽  
Genomic Regions ◽  
Mapping Populations

Abstract Background Teosinte ear bears single spikelet, whereas maize ear bears paired spikelets, doubling the number of grains in each cupulate during maize domestication. In the past 20 years, genetic analysis of single vs. paired spikelets (PEDS) has been stagnant. A better understanding of genetic basis of PEDS could help fine mapping of quantitative trait loci (QTL) and cloning of genes. Results In this study, the advanced mapping populations (BC3F2 and BC4F2) of maize × teosinte were developed by phenotypic recurrent selection. Four genomic regions associated with PEDS were detected using QTL-seq, located on 194.64–299.52 Mb, 0–162.80 Mb, 12.82–97.17 Mb, and 125.06–157.01 Mb of chromosomes 1, 3, 6, and 8, respectively. Five QTL for PEDS were identified in the regions of QTL-seq using traditional QTL mapping. Each QTL explained 1.12–38.05% of the phenotypic variance (PVE); notably, QTL qPEDS3.1 with the average PVE of 35.29% was identified in all tests. Moreover, 14 epistatic QTL were detected, with the total PVE of 47.57–66.81% in each test. The QTL qPEDS3.1 overlapped with, or was close to, one locus of 7 epistatic QTL. Near-isogenic lines (NILs) of QTL qPEDS1.1, qPEDS3.1, qPEDS6.1, and qPEDS8.1 were constructed. All individuals of NIL-qPEDS6.1(MT1) and NIL-qPEDS8.1(MT1) showed paired spikelets (PEDS = 0), but the flowering time was 7 days shorter in the NIL-qPEDS8.1(MT1). The ratio of plants with PEDS > 0 was low (1/18 to 3/18) in the NIL-qPEDS1.1(MT1) and NIL-qPEDS3.1(MT1), maybe due to the epistatic effect. Conclusion Our results suggested that major QTL, minor QTL, epistasis and photoperiod were associated with the variation of PEDS, which help us better understand the genetic basis of PEDS and provide a genetic resource for fine mapping of QTL.

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