Heterosis

Birchler, James A.; Yao, Huilu; Chudalayandi, Sivanandan; Vaiman, Daniel; Veitia, Reiner A.

doi:10.1105/tpc.110.076133

Cited by 465 publications

(416 citation statements)

References 69 publications

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“…Reduction in CCA1 expression amplitudes or transcript levels promotes the expression of downstream genes that are negatively regulated by CCA1 abundance, as shown in Arabidopsis diploids and allopolyploids (Ni et al, 2009). This altered circadian regulation could affect photosynthetic and metabolic pathways that are altered in F1 hybrids (Fujimoto et al, 2012;Meyer et al, 2012) as well as overall regulatory networks related to growth and development (Birchler et al, 2010).…”

Section: A Model For Parent-of-origin Effects On Altered Circadian Rhmentioning

confidence: 99%

A Role for CHH Methylation in the Parent-of-Origin Effect on Altered Circadian Rhythms and Biomass Heterosis inArabidopsisIntraspecific Hybrids

Miller

et al. 2014

The Plant Cell

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Hybrid plants and animals often show increased levels of growth and fitness, a phenomenon known as hybrid vigor or heterosis. Circadian rhythms optimize physiology and metabolism in plants and animals. In plant hybrids and polyploids, expression changes of the genes within the circadian regulatory network, such as CIRCADIAN CLOCK ASSOCIATED1 (CCA1), lead to heterosis. However, the relationship between allelic CCA1 expression and heterosis has remained elusive. Here, we show a parent-of-origin effect on altered circadian rhythms and heterosis in Arabidopsis thaliana F1 hybrids. This parent-of-origin effect on biomass heterosis correlates with altered CCA1 expression amplitudes, which are associated with methylation levels of CHH (where H = A, T, or C) sites in the promoter region. The direction of rhythmic expression and hybrid vigor is reversed in reciprocal F1 crosses involving mutants that are defective in the RNA-directed DNA methylation pathway (argonaute4 and nuclear RNA polymerase D1a) but not in the maintenance methylation pathway (methyltransferase1 and decrease in DNA methylation1). This parent-of-origin effect on circadian regulation and heterosis is established during early embryogenesis and maintained throughout growth and development.

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Section: A Model For Parent-of-origin Effects On Altered Circadian Rhmentioning

confidence: 99%

A Role for CHH Methylation in the Parent-of-Origin Effect on Altered Circadian Rhythms and Biomass Heterosis inArabidopsisIntraspecific Hybrids

Miller

et al. 2014

The Plant Cell

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“…6). Heterozygous loci may be preferentially maintained during the early rounds of breeder selection, as individuals with higher rates of heterozygosity may exhibit greater yields or other advantageous traits due to heterosis (Birchler et al, 2010). Genetic theory predicts, on average, a halving of heterozygous loci with every self-pollination following a given cross.…”

Section: Selection and Intracultivar Heterogeneitymentioning

confidence: 99%

The Composition and Origins of Genomic Variation among Individuals of the Soybean Reference Cultivar Williams 82

et al. 2010

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Soybean (Glycine max) is a self-pollinating species that has relatively low nucleotide polymorphism rates compared with other crop species. Despite the low rate of nucleotide polymorphisms, a wide range of heritable phenotypic variation exists. There is even evidence for heritable phenotypic variation among individuals within some cultivars. Williams 82, the soybean cultivar used to produce the reference genome sequence, was derived from backcrossing a Phytophthora root rot resistance locus from the donor parent Kingwa into the recurrent parent Williams. To explore the genetic basis of intracultivar variation, we investigated the nucleotide, structural, and gene content variation of different Williams 82 individuals. Williams 82 individuals exhibited variation in the number and size of introgressed Kingwa loci. In these regions of genomic heterogeneity, the reference Williams 82 genome sequence consists of a mosaic of Williams and Kingwa haplotypes. Genomic structural variation between Williams and Kingwa was maintained between the Williams 82 individuals within the regions of heterogeneity. Additionally, the regions of heterogeneity exhibited gene content differences between Williams 82 individuals. These findings show that genetic heterogeneity in Williams 82 primarily originated from the differential segregation of polymorphic chromosomal regions following the backcross and single-seed descent generations of the breeding process. We conclude that soybean haplotypes can possess a high rate of structural and gene content variation, and the impact of intracultivar genetic heterogeneity may be significant. This detailed characterization will be useful for interpreting soybean genomic data sets and highlights important considerations for research communities that are developing or utilizing a reference genome sequence.

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“…Under the F ∞ (or F 2 ) metric model, the heritabilities for the ten main QTL varied from 0.00 to 12.69% (0.00 to 13.55%) in the L 1 population and from 0.00 to 5.44% (0.00 to 6.07%) in the L 2 population; those for the three epistatic QTL were 0.51, 7.31, and 0.00% (0.14, 4.10 and 0.00%) in the L 1 population, and 15.70, 7.83, and 4.98% (23.77, 2.18 and 9.47%) in the L 2 population; the total heritabilities explained by all the main and epistatic QTL were 51.28 and 42.02% (47.95 and 35.26%) in the above two populations, respectively (Table S4). Judged by pure main effects, QTL 3 and QTL 10 were additive; QTL 1 and QTL 4 were partially dominant; QTL 2 was completely dominant; QTL 6 , QTL 7 and QTL 9 were overdominant; and QTL 5 and QTL 8 had no pure main effects (Tables 3, 5, S5 and S7). While judged by augmented main effects under the F ∞ metric model, QTL 5 and QTL 8 turned to complete dominance; the other eight QTL had the same types as the original ones, although degrees of dominance for some QTL (QTL 4 and QTL 7 ) changed (Tables 3 and 5).…”

Section: Monte Carlo Simulation Studiesmentioning

confidence: 99%

“…The results showed that the RIL-based NCIII design was superior to the F 2 -based NCIII design for mapping heterotic QTL. Although the augmented main effects ( * a and * d ) were all unbiasedly estimated with satisfactory powers and the augmented epistatic effects (  i and  i ) between QTL 4 and QTL 7 , which consisted of two epistatic effects with the same sign, were also well mapped. The augmented epistatic effects ( i between QTL 5 and QTL 8 ), which consisted of two epistatic effects of equal strength in opposite directions, were very poorly mapped, even though both sample size and replication number were at high levels (n=500 and m=10), i.e., the powers in the detection of  58 i and  58 i in the F 2 -based NCIII design were 0.50 and 2.00% under the F ∞ metric model, and 0.50 and 18.5% under the F 2 metric model [41].…”

Section: Monte Carlo Simulation Studiesmentioning

confidence: 99%

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Genome-wide mapping of QTL associated with heterosis in the RIL-based NCIII design

Zhang

2012

Chin. Sci. Bull.

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Heterosis represents one of the most revolutionary advancements in crop improvement. In the genetic dissection of heterosis, NCIII design is one of the most powerful and widely used mating schemes. However, the methodologies for quantitative trait loci (QTL) detection in the design were mostly based on composite interval mapping. Therefore, in this study, our purpose was to develop a statistical method for mapping epistatic QTL associated with heterosis in the RIL-based NCIII design. First, we derivated the expectations of two classical linear transformations, Z 1 and Z 2 , while a quantitative trait was controlled by two QTL with digenic epistasis and arbitrary linkage under the F ∞ and F 2 metric models. Then, we constructed an epistatic genetic model that includes all markers on the whole genome simultaneously, and estimated all the parameters in the model by the empirical Bayes approach. Finally, a series of Monte Carlo simulation experiments was carried out to confirm the proposed approach. The results show that: (1) all the augmented genetic parameters for main-effect QTL could be rightly identified with satisfactory statistical power and precision; (2) the statistical powers in the detection of augmented epistatic effects were substantively affected by the signs of pure epistatic effects; (3) it is more difficult to detect epistatic QTL than to detect main-effect QTL; (4) statistical power is higher in the RIL-based NCIII design than in the F 2 -based NCIII design, especially in the detection of the augmented epistatic effect that consists of two pure epistatic effects in opposite directions.empirical Bayes, epistasis, NCIII design, heterosis, quantitative trait locus, recombinant inbred line Citation:He X H, Hu Z L, Zhang Y M. Genome-wide mapping of QTL associated with heterosis in the RIL-based NCIII design.

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Heterosis

Cited by 465 publications

References 69 publications

A Role for CHH Methylation in the Parent-of-Origin Effect on Altered Circadian Rhythms and Biomass Heterosis inArabidopsisIntraspecific Hybrids

A Role for CHH Methylation in the Parent-of-Origin Effect on Altered Circadian Rhythms and Biomass Heterosis inArabidopsisIntraspecific Hybrids

The Composition and Origins of Genomic Variation among Individuals of the Soybean Reference Cultivar Williams 82

Genome-wide mapping of QTL associated with heterosis in the RIL-based NCIII design

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