Multivariate segregation analysis for quantitative traits in line crosses

Xiao, Jian; Wang, X; Hu, Zhiqiu; Tang, Zaixiang; Xu, Chenwu

doi:10.1038/sj.hdy.6800960

Cited by 6 publications

(4 citation statements)

References 30 publications

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Section: Discussionmentioning

confidence: 99%

“…Segregation analysis involves the estimation of normal mixtures, which is well known to be an ill-posed problem, particularly when the disparity between the component distributions is small (Xiao et al, 2007;Lourens et al, 2013). Methods for segregation analysis may therefore suffer from low statistical power in diploids, and even more so in autotetraploids (Xiao et al, 2007). We extended the concept of the overlapping coefficient (Inman & Bradley, 1989) to quantify the disparity between multiple component normal distributions for segregation analysis in autotetraploids.…”

Section: Discussionmentioning

confidence: 99%

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Orthogonal contrast based models for quantitative genetic analysis in autotetraploid species

et al. 2018

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Dissecting the genetic architecture of quantitative traits is a crucial goal for efficient breeding of polyploid plants, including autotetraploid crop species, such as potato and coffee, and ornamentals such as rose. To meet this goal, a quantitative genetic model is needed to link the genetic effects of genes or genotypes at quantitative trait loci (QTL) to the phenotype of quantitative traits. We present a statistically tractable quantitative genetic model for autotetraploids based on orthogonal contrast comparisons in the general linear model. The new methods are suitable for autotetraploid species with any population genetic structure and take full account of the essential features of autotetrasomic inheritance. The statistical properties of the new methods are explored and compared to an alternative method in the literature by simulation studies. We have shown how these methods can be applied for quantitative genetic analysis in autotetraploids by analysing trait phenotype data from an autotetraploid potato segregating population. Using trait segregation analysis, we showed that both highly heritable traits of flowering time and plant height were under the control of major QTL. The orthogonal model directly dissects genetic variance into independent components and gives consistent estimates of genetic effects provided that tetrasomic gene segregation is considered.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Orthogonal contrast based models for quantitative genetic analysis in autotetraploid species

et al. 2018

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“…It had been aware that the effect sizes of genes (loci) controlling quantitative traits are not entirely equal, but usually a few major genes and many minor genes are involved in most cases. On many occasions, there were large-effect genes (loci) that could be statistically detected 54 55. With introduction of application of molecular biology into quantitative genetics, the mixed model had gradually taken shape to modify the empirical assumptions of polygenic model in practice (Table 2), which, in a simple consideration, was realized by adding major gene(s) to the polygenic model.…”

Section: From Polygenic Model To Gene Network Modelmentioning

confidence: 99%

Understanding Quantitative Genetics in the Systems Biology Era

Zhu¹,

Yu²,

Zhao³

2009

Int. J. Biol. Sci.

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Biology is now entering the new era of systems biology and exerting a growing influence on the future development of various disciplines within life sciences. In early classical and molecular periods of Biology, the theoretical frames of classical and molecular quantitative genetics have been systematically established, respectively. With the new advent of systems biology, there is occurring a paradigm shift in the field of quantitative genetics. Where and how the quantitative genetics would develop after having undergone its classical and molecular periods? This is a difficult question to answer exactly. In this perspective article, the major effort was made to discuss the possible development of quantitative genetics in the systems biology era, and for which there is a high potentiality to develop towards "systems quantitative genetics". In our opinion, the systems quantitative genetics can be defined as a new discipline to address the generalized genetic laws of bioalleles controlling the heritable phenotypes of complex traits following a new dynamic network model. Other issues from quantitative genetic perspective relating to the genetical genomics, the updates of network model, and the future research prospects were also discussed.

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“…Segregation ratios that do not obey expected Mendelian ratios have been reported in a number of plants including pea ( Pisum sativum ) [28], common bean [29], mungbean ( Vigna radiata L Wilcek) [30], barley ( Hordeum vulgare ) [31,32], maize ( Zea mays ) [33,34], rice ( Oryza sativa ) [35,36] and wheat ( Triticum aestivum ) [37-39]. Segregation analysis may serve as an important intermediate tool to help investigators plan more sophisticated genomic studies [40] and further enable breeders to manipulate major genes [41,42]. …”

Section: Introductionmentioning

confidence: 99%

Growth, seed development and genetic analysis in wild type and Def mutant of Pisum sativum L

et al. 2011

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BackgroundThe def mutant pea (Pisum sativum L) showed non-abscission of seeds from the funicule. Here we present data on seed development and growth pattern and their relationship in predicting this particular trait in wild type and mutant lines as well as the inheritance pattern of the def allele in F2 and F3 populations.FindingsPod length and seed fresh weight increase with fruit maturity and this may affect the abscission event in pea seeds. However, the seed position in either the distal and proximal ends of the pod did not show any difference. The growth factors of seed fresh weight (FW), width of funicles (WFN), seed width (SW) and seed height (SH) were highly correlated and their relationships were determined in both wild type and def mutant peas. The coefficient of determination R2 values for the relationship between WFN and FW, SW and SH and their various interactions were higher for the def dwarf type. Stepwise multiple regression analysis showed that variation of WFN was associated with SH and SW. Pearson's chi square analysis revealed that the inheritance and segregation of the Def locus in 3:1 ratio was significant in two F2 populations. Structural analysis of the F3 population was used to confirm the inheritance status of the Def locus in F2 heterozygote plants.ConclusionsThis study investigated the inheritance of the presence or absence of the Def allele, controlling the presence of an abscission zone (AZ) or an abscission-less zone (ALZ) forming in wild type and mutant lines respectively. The single major gene (Def) controlling this phenotype was monogenic and def mutants were characterized and controlled by the homozygous recessive def allele that showed no palisade layers in the hilum region of the seed coat.

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Multivariate segregation analysis for quantitative traits in line crosses

Cited by 6 publications

References 30 publications

Orthogonal contrast based models for quantitative genetic analysis in autotetraploid species

Orthogonal contrast based models for quantitative genetic analysis in autotetraploid species

Understanding Quantitative Genetics in the Systems Biology Era

Growth, seed development and genetic analysis in wild type and Def mutant of Pisum sativum L

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