QTL linkage analysis of connected populations using ancestral marker and pedigree information

Bink, M.C.A.M.; Totir, Liviu R.; Braak, Cajo J. F. ter; Winkler, Christopher; Boer, Martin P.; Smith, O. S.

doi:10.1007/s00122-011-1772-8

Cited by 41 publications

(41 citation statements)

References 33 publications

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“…Boer et al 2007;van Eeuwijk et al 2010;ter Braak et al 2010;Bink et al 2012). The relative value of different founder haplotypes for economically important traits can influence selection decisions.…”

Section: Trend 22 Extending Germplasm Knowledge To the Sequence Levelmentioning

confidence: 99%

“…Thus, in addition to mapping and selection within specific crosses (e.g. Boer et al 2007), methods have been developed for mapping within multiparent, multi-cross, pedigree-related mating designs that are common within pedigree breeding programs (van Eeuwijk et al 2010;ter Braak et al 2010;Bink et al 2012). Mapping within such multi-cross mating designs has been enabled through utilisation of IBD information to connect haplotype diversity across multiple, pedigree-related segregating populations that are generated, tested and phenotyped during the course of conducting the cycles of the breeding program in the TPE (Figs 2, 13).…”

Section: Trend 23 Expanding Trait Genetic Knowledgementioning

confidence: 99%

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Predicting the future of plant breeding: complementing empirical evaluation with genetic prediction

et al. 2014

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Abstract. For the foreseeable future, plant breeding methodology will continue to unfold as a practical application of the scaling of quantitative biology. These efforts to increase the effective scale of breeding programs will focus on the immediate and long-term needs of society. The foundations of the quantitative dimension will be integration of quantitative genetics, statistics, gene-to-phenotype knowledge of traits embedded within crop growth and development models. The integration will be enabled by advances in quantitative genetics methodology and computer simulation. The foundations of the biology dimension will be integrated experimental and functional gene-to-phenotype modelling approaches that advance our understanding of functional germplasm diversity, and gene-to-phenotype trait relationships for the native and transgenic variation utilised in agricultural crops. The trait genetic knowledge created will span scales of biology, extending from molecular genetics to multi-trait phenotypes embedded within evolving genotype-environment systems. The outcomes sought and successes achieved by plant breeding will be measured in terms of sustainable improvements in agricultural production of food, feed, fibre, biofuels and other desirable plant products that meet the needs of society. In this review, examples will be drawn primarily from our experience gained through commercial maize breeding. Implications for other crops, in both the private and public sectors, will be discussed.

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Section: Trend 22 Extending Germplasm Knowledge To the Sequence Levelmentioning

confidence: 99%

Section: Trend 23 Expanding Trait Genetic Knowledgementioning

confidence: 99%

Predicting the future of plant breeding: complementing empirical evaluation with genetic prediction

et al. 2014

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“…The simplest is to consider that parents carrying the same allele at a given marker are IBD (Yu et al 2008;Liu et al 2012) as done in association mapping. Haplotype-based approaches also have been proposed to group parental alleles and tested by simulations (for instance Jansen et al 2003;Bink et al 2012;Leroux et al 2014). Advantages of LDLA have been shown experimentally in maize notably by using the nested association mapping (NAM) design developed in the United States (Yu et al 2008;McMullen et al 2009).…”

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confidence: 99%

Linkage Disequilibrium with Linkage Analysis of Multiline Crosses Reveals Different Multiallelic QTL for Hybrid Performance in the Flint and Dent Heterotic Groups of Maize

et al. 2014

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Multiparental designs combined with dense genotyping of parents have been proposed as a way to increase the diversity and resolution of quantitative trait loci (QTL) mapping studies, using methods combining linkage disequilibrium information with linkage analysis (LDLA). Two new nested association mapping designs adapted to European conditions were derived from the complementary dent and flint heterotic groups of maize (Zea mays L.). Ten biparental dent families (N = 841) and 11 biparental flint families (N = 811) were genotyped with 56,110 single nucleotide polymorphism markers and evaluated as test crosses with the central line of the reciprocal design for biomass yield, plant height, and precocity. Alleles at candidate QTL were defined as (i) parental alleles, (ii) haplotypic identity by descent, and (iii) single-marker groupings. Between five and 16 QTL were detected depending on the model, trait, and genetic group considered. In the flint design, a major QTL (R 2 = 27%) with pleiotropic effects was detected on chromosome 10, whereas other QTL displayed milder effects (R 2 , 10%). On average, the LDLA models detected more QTL but generally explained lower percentages of variance, consistent with the fact that most QTL display complex allelic series. Only 15% of the QTL were common to the two designs. A joint analysis of the two designs detected between 15 and 21 QTL for the five traits. Of these, between 27 for silking date and 41% for tasseling date were significant in both groups. Favorable allelic effects detected in both groups open perspectives for improving biomass production. MOST traits of agronomic interest present a continuous variation resulting from the sum of the effects of various quantitative trait loci (QTL). Mapping these QTL is a first step toward elucidating their molecular nature and offers important application perspectives for marker-assisted breeding. QTL mapping started in plants with segregating families derived from the cross of two inbred lines (Lander and Botstein 1989). However, such biparental designs address only a small portion of the diversity available (a maximum of two alleles can segregate at a given QTL) and the accuracy of QTL positions is usually poor. To overcome these limitations, Rebai and Goffinet (1993) and Charcosset et al. (1994) proposed models for joint QTL detection in several biparental families connected to each other by the use of common parental lines. When the number of parents is less than the number of families, connections can be taken into account to reduce the number of allelic effects to be estimated in the detection model. This increases power and accuracy of detection when QTL behave additively (see Blanc et al. 2006). However, such a model makes the assumption that each parental line carries a different allele, which limits its benefit when the number of parental lines is high relative to the number of families, a situation commonly encountered in breeding programs. Recent advances in sequencing and genotyping technologies make it possi...

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“…The Bayesian statistics and PBA methodology used in FlexQTL™, as described in Bink et al (2002Bink et al ( , 2008Bink et al ( , 2012 built from approaches and procedures developed in Sillanpää and Arjas (1999). The implementation of FlexQTL™ in QTL analyses has been described in detail in Bink et al (2014) in a proof of concept paper.…”

Section: Qtl Analysesmentioning

confidence: 99%

Two QTL characterized for soft scald and soggy breakdown in apple (Malus × domestica) through pedigree-based analysis of a large population of interconnected families

Howard

Weg

Tillman

et al. 2017

Tree Genetics & Genomes

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Soft scald and soggy breakdown are important postharvest physiological disorders of apple (Malus × domestica). 'Honeycrisp' and some of its offspring are particularly susceptible to developing these disorders. The purpose of this study was to identify molecular markers associated with high incidences of soft scald and soggy breakdown for use in marker-assisted breeding. Towards this aim, we employed a pedigree-based approach using mostly germplasm related to 'Honeycrisp.' Two quantitative trait loci (QTL) were consistently identified on linkage groups (LGs) 2 and 16 across the 2014 and 2015 harvest years. The same QTL were identified for both storage disorders, indicating that they may be physiologically related. 'Honeycrisp' is homozygous for an identical by state haplotype at the LG2 QTL that was consistently associated with a deleterious effect on soft scald and soggy breakdown incidence. This haplotype was traced through SNP-confirmed pedigrees to the following cultivars: 'Grimes Golden,' 'Northern Spy,' 'Rome Beauty,' and 'Fireside' and is common in derived apple germplasm. Haplotypes at the LG16 QTL could not be adequately characterized due to variation between years combined with effects of this QTL being of relatively smaller size and being most evident in individuals that carry two copies of the deleterious haplotype at the LG2 QTL. These results suggest that limiting homozygosity of the deleterious haplotype at the LG2 QTL through marker-assisted breeding would be a valid strategy to limit soft scald and soggy breakdown incidences in apple seedling populations.

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QTL linkage analysis of connected populations using ancestral marker and pedigree information

Cited by 41 publications

References 33 publications

Predicting the future of plant breeding: complementing empirical evaluation with genetic prediction

Predicting the future of plant breeding: complementing empirical evaluation with genetic prediction

Linkage Disequilibrium with Linkage Analysis of Multiline Crosses Reveals Different Multiallelic QTL for Hybrid Performance in the Flint and Dent Heterotic Groups of Maize

Two QTL characterized for soft scald and soggy breakdown in apple (Malus × domestica) through pedigree-based analysis of a large population of interconnected families

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