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

He, Xiaohong; Hu, Zhongli; Zhang, Yuan-Ming

doi:10.1007/s11434-012-5127-x

Cited by 11 publications

(13 citation statements)

References 41 publications

(101 reference statements)

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“…In TTC, Z 1 , Z 2 and Z 3 were used to detect augmented additive, augmented dominant and dominance-by-additive ( da ) interaction effects, respectively, in Kusterer et al [ 32 ] and Melchinger et al [ 33 ], and to unbiasedly estimate all the main and epistatic effects in He et al [ 34 ]. In the NCIII, pair mean Z 1 and pair difference Z 2 were used to detect augmented additive effect and augmented dominant effect in Melchinger et al [ 35 ], and epistasis in Garcia et al [ 36 ] and He et al [ 37 ]. In addition, Rebaϊ & Goffinet [ 38 ] and Lenarcic et al [ 39 ] developed a general regression-based method and Bayesian approach, respectively, for QTL detection in diallel design; Li et al [ 40 ] and Wang et al [ 41 ] proposed analysis of variance approach for the detection of main and interacted QTL of quantitative and endosperm traits in NCIII and TTC, respectively; and Reif et al [ 42 ] used TTC with near-isogenic lines as base population to detect epistasis.…”

Section: Introductionmentioning

confidence: 99%

Interacted QTL Mapping in Partial NCII Design Provides Evidences for Breeding by Design

Zhao

et al. 2015

PLoS ONE

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The utilization of heterosis in rice, maize and rapeseed has revolutionized crop production. Although elite hybrid cultivars are mainly derived from the F1 crosses between two groups of parents, named NCII mating design, little has been known about the methodology of how interacted effects influence quantitative trait performance in the population. To bridge genetic analysis with hybrid breeding, here we integrated an interacted QTL mapping approach with breeding by design in partial NCII mating design. All the potential main and interacted effects were included in one full model. If the number of the effects is huge, bulked segregant analysis were used to test which effects were associated with the trait. All the selected effects were further shrunk by empirical Bayesian, so significant effects could be identified. A series of Monte Carlo simulations was performed to validate the new method. Furthermore, all the significant effects were used to calculate genotypic values of all the missing F1 hybrids, and all these F1 phenotypic or genotypic values were used to predict elite parents and parental combinations. Finally, the new method was adopted to dissect the genetic foundation of oil content in 441 rapeseed parents and 284 F1 hybrids. As a result, 8 main-effect QTL and 37 interacted QTL were found and used to predict 10 elite restorer lines, 10 elite sterile lines and 10 elite parental crosses. Similar results across various methods and in previous studies and a high correlation coefficient (0.76) between the predicted and observed phenotypes validated the proposed method in this study.

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Section: Introductionmentioning

confidence: 99%

Interacted QTL Mapping in Partial NCII Design Provides Evidences for Breeding by Design

Zhao

et al. 2015

PLoS ONE

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“…In hybrid breeding for heterosis utilization, a genetic mating scheme is usually used to identify elite parents and hybrid combinations through the analyses of general combining ability (GCA), and specific combining ability (SCA), respectively. Recently, an association mapping approach was used for dependent variables such as GCA and SCA in triple testcross and North Carolina III mating designs 27 28 29 30 31 32 33 . The North Carolina II (NCII) mating designs based on different base populations, such as BC 1 F 8 34 , recombinant inbred lines 35 and introgression lines 36 37 , were reported, and a comparison across different base populations was also conducted 38 .…”

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confidence: 99%

Genetic dissection of heterosis using epistatic association mapping in a partial NCII mating design

Wen

Zhao

et al. 2015

Sci Rep

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Heterosis refers to the phenomenon in which an F1 hybrid exhibits enhanced growth or agronomic performance. However, previous theoretical studies on heterosis have been based on bi-parental segregating populations instead of F1 hybrids. To understand the genetic basis of heterosis, here we used a subset of F1 hybrids, named a partial North Carolina II design, to perform association mapping for dependent variables: original trait value, general combining ability (GCA), specific combining ability (SCA) and mid-parental heterosis (MPH). Our models jointly fitted all the additive, dominance and epistatic effects. The analyses resulted in several important findings: 1) Main components are additive and additive-by-additive effects for GCA and dominance-related effects for SCA and MPH, and additive-by-dominant effect for MPH was partly identified as additive effect; 2) the ranking of factors affecting heterosis was dominance > dominance-by-dominance > over-dominance > complete dominance; and 3) increasing the proportion of F1 hybrids in the population could significantly increase the power to detect dominance-related effects, and slightly reduce the power to detect additive and additive-by-additive effects. Analyses of cotton and rapeseed datasets showed that more additive-by-additive QTL were detected from GCA than from trait phenotype, and fewer QTL were from MPH than from other dependent variables.

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“…The genetic basis of heterosis has been debated for more than 100 years and has still not been completely resolved (Stuber et al, 1992;Frascaroli et al, 2007). Additive QTL do not contribute to heterosis, in contrast to non-additive QTL, including dominant, overdominant, and epistatic QTL (Lu et al, 2003;LeDeauxet al, 2006;Li et al, 2008b;He et al, 2012). The elite variety WanCao No.…”

Section: Discussionmentioning

confidence: 99%

Mapping quantitative trait loci for five forage quality traits in a sorghum-sudangrass hybrid

et al. 2015

Genet. Mol. Res.

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ABSTRACT. The identification of quantitative trait loci (QTLs) affecting forage quality traits enables an understanding of the genetic mechanism of these loci. The aim of the present study was to detect QTLs for the wholeplant protein content (WP), whole-plant fat content (WF), neutral detergent fiber (NDF), acid detergent fiber (ADF), and whole-plant ash content (WA) using a population of 184 F 2 individuals from a cross between sorghum Tx623A and sudangrass Sa. Correlation analysis was performed between the five forage quality traits. WP was found to be positively correlated with WF, NDF, and ADF. Furthermore, NDF was positively correlated with ADF but negatively correlated with WA. A genetic map with 124 SSR markers was constructed for QTL mapping. A total of 12 QTLs associated with the five forage quality traits were detected. Of these QTLs, qNDF3, qNDF8, and qADF8 explained more than 10% of the phenotypic variation. Additionally, although all of the QTLs exhibited additive and dominant effects, they mainly exhibited dominant effects. Our results provide important information for marker-assisted selection breeding of sorghum-sudangrass hybrids.

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

Cited by 11 publications

References 41 publications

Interacted QTL Mapping in Partial NCII Design Provides Evidences for Breeding by Design

Interacted QTL Mapping in Partial NCII Design Provides Evidences for Breeding by Design

Genetic dissection of heterosis using epistatic association mapping in a partial NCII mating design

Mapping quantitative trait loci for five forage quality traits in a sorghum-sudangrass hybrid

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