Orthogonal contrast based models for quantitative genetic analysis in autotetraploid species

Chen, Jing; Zhang, Fengjun; Wang, Lin; Leach, Lindsey; Luo, Zewei

doi:10.1111/nph.15284

Cited by 12 publications

(16 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These findings imply that methods for the genetic analysis of complex traits (e.g. quantitative trait locus analysis) in autotetraploid species such as potato should be designed to accommodate crossing over in multivalents, and the consequent features of allele segregation, including double reduction (Chen et al 2018 ; Chen et al 2020 ). Finally, meiosis in autopolyploids has to adapt to the external as well as the internal environment (Bomblies et al 2015 ); therefore, future work may focus on evaluating the generality of our findings not only in a larger more diverse potato germplasm collection, but also in field versus controlled growth environments.…”

Section: Conclusion and Future Researchmentioning

confidence: 99%

Varietal variation and chromosome behaviour during meiosis in Solanum tuberosum

et al. 2020

Self Cite

View full text Add to dashboard Cite

Naturally occurring autopolyploid species, such as the autotetraploid potato Solanum tuberosum, face a variety of challenges during meiosis. These include proper pairing, recombination and correct segregation of multiple homologous chromosomes, which can form complex multivalent configurations at metaphase I, and in turn alter allelic segregation ratios through double reduction. Here, we present a reference map of meiotic stages in diploid and tetraploid S. tuberosum using fluorescence in situ hybridisation (FISH) to differentiate individual meiotic chromosomes 1 and 2. A diploid-like behaviour at metaphase I involving bivalent configurations was predominant in all three tetraploid varieties. The crossover frequency per bivalent was significantly reduced in the tetraploids compared with a diploid variety, which likely indicates meiotic adaptation to the autotetraploid state. Nevertheless, bivalents were accompanied by a substantial frequency of multivalents, which varied by variety and by chromosome (7–48%). We identified possible sites of synaptic partner switching, leading to multivalent formation, and found potential defects in the polymerisation and/or maintenance of the synaptonemal complex in tetraploids. These findings demonstrate the rise of S. tuberosum as a model for autotetraploid meiotic recombination research and highlight constraints on meiotic chromosome configurations and chiasma frequencies as an important feature of an evolved autotetraploid meiosis.

show abstract

Section: Conclusion and Future Researchmentioning

confidence: 99%

Varietal variation and chromosome behaviour during meiosis in Solanum tuberosum

et al. 2020

Self Cite

View full text Add to dashboard Cite

show abstract

“…However, one could easily estimate eventual dominance effects from the detected QTL using simpler biallelic-based models as proposed previously (Hackett et al . 2014; Chen et al . 2018).…”

Section: Discussionmentioning

confidence: 99%

Multiple QTL mapping in autopolyploids: a random-effect model approach with application in a hexaploid sweetpotato full-sib population

Pereira

Gemenet

Mollinari

et al. 2019

Preprint

View full text Add to dashboard Cite

ABSTRACTIn developing countries, the sweetpotato,Ipomoea batatas(L.) Lam. (2n= 6x= 90), is an important autopolyploid species, both socially and economically. However, quantitative trait loci (QTL) mapping has remained limited due to its genetic complexity. Current fixed-effect models can only fit a single QTL and are generally hard to interpret. Here we report the use of a random-effect model approach to map multiple QTL based on score statistics in a sweetpotato bi-parental population (‘Beauregard’×‘Tanzania’) with 315 full-sibs. Phenotypic data were collected for eight yield component traits in six environments in Peru, and jointly predicted means were obtained using mixed-effect models. An integrated linkage map consisting of 30,684 markers distributed along 15 linkage groups (LGs) was used to obtain the genotype conditional probabilities of putative QTL at every cM position. Multiple interval mapping was performed using our R package QTLPOLY and detected a total of 41 QTL, ranging from one to ten QTL per trait. Some regions, such as those on LGs 3 and 15, were consistently detected among root number and yield traits and provided basis for candidate gene search. In addition, some QTL were found to affect commercial and noncommercial root traits distinctly. Further best linear unbiased predictions allowed us to characterize additive allele effects as well as to compute QTL-based breeding values for selection. Together with quantitative genotyping and its appropriate usage in linkage analyses, this QTL mapping methodology will facilitate the use of genomic tools in sweetpotato breeding as well as in other autopolyploids.

show abstract

“…; 4) are the corresponding orthogonal contrast scales for the genetic effects of genotype k for the jth contrast (j ¼ 1; 2; :::; 4). The rationale, statistical properties, and parameter estimation of the orthogonal quantitative genetic model are detailed in our recent work (Chen et al, 2018).…”

Section: Orthogonal Quantitative Genetic Model In Autotetraploidsmentioning

confidence: 99%

“…For example, the same likelihood profile is expected for genotype configuration (1) QQQQ Â qqqQ and an alternative configuration, QQQQ Â QQQq. However, the genetic effects would differ in sign under these two models, allowing the correct model to be distinguished, given that the monogenic effect must be positive by definition (Chen et al, 2018).…”

Section: Model Parameter Estimationmentioning

confidence: 99%

A tetrasomic inheritance model and likelihood‐based method for mapping quantitative trait loci in autotetraploid species

et al. 2020

Self Cite

View full text Add to dashboard Cite

Dissecting the genetic architecture of quantitative traits in autotetraploid species is a methodologically challenging task, but a pivotally important goal for breeding globally important food crops, including potato and blueberry, and ornamental species such as rose. Mapping quantitative trait loci (QTLs) is now a routine practice in diploid species but is far less advanced in autotetraploids, largely due to a lack of analytical methods that account for the complexities of tetrasomic inheritance. We present a novel likelihood-based method for QTL mapping in outbred segregating populations of autotetraploid species. The method accounts properly for sophisticated features of gene segregation and recombination in an autotetraploid meiosis. It may model and analyse molecular marker data with or without allele dosage information, such as that from microarray or sequencing experiments. The method developed outperforms existing bivalent-based methods, which may fail to model and analyse the full spectrum of experimental data, in the statistical power of QTL detection, and accuracy of QTL location, as demonstrated by an intensive simulation study and analysis of data sets collected from a segregating population of potato (Solanum tuberosum). The study enables QTL mapping analysis to be conducted in autotetraploid species under a rigorous tetrasomic inheritance model.

show abstract

Orthogonal contrast based models for quantitative genetic analysis in autotetraploid species

Cited by 12 publications

References 46 publications

Varietal variation and chromosome behaviour during meiosis in Solanum tuberosum

Varietal variation and chromosome behaviour during meiosis in Solanum tuberosum

Multiple QTL mapping in autopolyploids: a random-effect model approach with application in a hexaploid sweetpotato full-sib population

A tetrasomic inheritance model and likelihood‐based method for mapping quantitative trait loci in autotetraploid species

Contact Info

Product

Resources

About