Detecting QTLs and putative candidate genes involved in budbreak and flowering time in an apple multiparental population

Allard, Alix; Bink, M.C.A.M.; Martinez, Sébastien; Kelner, Jean-Jacques; Legave, Jean Michel; Guardo, Mario Di; Pierro, Erica A. Di; Laurens, François; Weg, Eric van de; Costes, Evelyne

doi:10.1093/jxb/erw130

Cited by 94 publications

(93 citation statements)

References 68 publications

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“…Part of these populations have also been used in studies on the development of multiplexes of SSR markers, 42 validation of the pedigree-based analyses approach for QTL mapping on multiple pedigreed families 13 and QTL discovery for horticultural traits. 18 …”

Section: Methodsmentioning

confidence: 99%

A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species

et al. 2016

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Quantitative trait loci (QTL) mapping approaches rely on the correct ordering of molecular markers along the chromosomes, which can be obtained from genetic linkage maps or a reference genome sequence. For apple (Malus domestica Borkh), the genome sequence v1 and v2 could not meet this need; therefore, a novel approach was devised to develop a dense genetic linkage map, providing the most reliable marker-loci order for the highest possible number of markers. The approach was based on four strategies: (i) the use of multiple full-sib families, (ii) the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism (SNP) markers, (iii) the construction of a single backcross-type data set including all families, and (iv) a two-step map generation procedure based on the sequential inclusion of markers. The map comprises 15 417 SNP markers, clustered in 3 K HaploBlock markers spanning 1 267 cM, with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 cM. Moreover, chromosome 5 was oriented according to its homoeologous chromosome 10. This map was useful to improve the apple genome sequence, design the Axiom Apple 480 K SNP array and perform multifamily-based QTL studies. Its collinearity with the genome sequences v1 and v3 are reported. To our knowledge, this is the shortest published SNP map in apple, while including the largest number of markers, families and individuals. This result validates our methodology, proving its value for the construction of integrated linkage maps for any outbreeding species.

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Section: Methodsmentioning

confidence: 99%

A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species

et al. 2016

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“…The QTL on LG9 for entropy appeared as a new zone of importance, as it co-localized with a major QTL detected for the timing of vegetative and flowering bud break (Dyk et al, 2010; Celton et al, 2011; Allard et al, 2016). New QTLs were also detected for BBIs on LG5 and LG7, consistently with “Starkrimson® Red Delicious” and “Granny Smith” not being heterozygous for these QTLs.…”

Section: Discussionmentioning

confidence: 99%

“…The MCMC algorithms and details on the monitoring of Monte Carlo accuracy and length of the simulation chains can be found in Bink et al (2008) and Allard et al (2016), respectively. The number of QTLs was inferred from a pairwise comparison of models differing by one QTL, and considering twice the natural logarithm of the Bayes Factors (Kass and Raftery, 1995), denoted 2 * lnBF.…”

Section: Methodsmentioning

confidence: 99%

Predicting Flowering Behavior and Exploring Its Genetic Determinism in an Apple Multi-family Population Based on Statistical Indices and Simplified Phenotyping

et al. 2017

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Irregular flowering over years is commonly observed in fruit trees. The early prediction of tree behavior is highly desirable in breeding programmes. This study aims at performing such predictions, combining simplified phenotyping and statistics methods. Sequences of vegetative vs. floral annual shoots (AS) were observed along axes in trees belonging to five apple related full-sib families. Sequences were analyzed using Markovian and linear mixed models including year and site effects. Indices of flowering irregularity, periodicity and synchronicity were estimated, at tree and axis scales. They were used to predict tree behavior and detect QTL with a Bayesian pedigree-based analysis, using an integrated genetic map containing 6,849 SNPs. The combination of a Biennial Bearing Index (BBI) with an autoregressive coefficient (γg) efficiently predicted and classified the genotype behaviors, despite few misclassifications. Four QTLs common to BBIs and γg and one for synchronicity were highlighted and revealed the complex genetic architecture of the traits. Irregularity resulted from high AS synchronism, whereas regularity resulted from either asynchronous locally alternating or continual regular AS flowering. A relevant and time-saving method, based on a posteriori sampling of axes and statistical indices is proposed, which is efficient to evaluate the tree breeding values for flowering regularity and could be transferred to other species.

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“…Among the 6849 polymorphic SNPs, 3123 were used in this study, after a careful checking of their robustness consistency (Van de Weg et al, 2013; Di Guardo et al, 2015) and recombination pattern (Allard et al, 2016). In particular, all markers which were not strictly bi-allelic in at least one of the parent were discarded.…”

Section: Methodsmentioning

confidence: 99%

Combining Genome-Wide Information with a Functional Structural Plant Model to Simulate 1-Year-Old Apple Tree Architecture

Migault¹,

Pallas²,

Costes³

2017

Front. Plant Sci.

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In crops, optimizing target traits in breeding programs can be fostered by selecting appropriate combinations of architectural traits which determine light interception and carbon acquisition. In apple tree, architectural traits were observed to be under genetic control. However, architectural traits also result from many organogenetic and morphological processes interacting with the environment. The present study aimed at combining a FSPM built for apple tree, MAppleT, with genetic determinisms of architectural traits, previously described in a bi-parental population. We focused on parameters related to organogenesis (phyllochron and immediate branching) and morphogenesis processes (internode length and leaf area) during the first year of tree growth. Two independent datasets collected in 2004 and 2007 on 116 genotypes, issued from a ‘Starkrimson’ × ‘Granny Smith’ cross, were used. The phyllochron was estimated as a function of thermal time and sylleptic branching was modeled subsequently depending on phyllochron. From a genetic map built with SNPs, marker effects were estimated on four MAppleT parameters with rrBLUP, using 2007 data. These effects were then considered in MAppleT to simulate tree development in the two climatic conditions. The genome wide prediction model gave consistent estimations of parameter values with correlation coefficients between observed values and estimated values from SNP markers ranging from 0.79 to 0.96. However, the accuracy of the prediction model following cross validation schemas was lower. Three integrative traits (the number of leaves, trunk length, and number of sylleptic laterals) were considered for validating MAppleT simulations. In 2007 climatic conditions, simulated values were close to observations, highlighting the correct simulation of genetic variability. However, in 2004 conditions which were not used for model calibration, the simulations differed from observations. This study demonstrates the possibility of integrating genome-based information in a FSPM for a perennial fruit tree. It also showed that further improvements are required for improving the prediction ability. Especially temperature effect should be extended and other factors taken into account for modeling GxE interactions. Improvements could also be expected by considering larger populations and by testing other genome wide prediction models. Despite these limitations, this study opens new possibilities for supporting plant breeding by in silico evaluations of the impact of genotypic polymorphisms on plant integrative phenotypes.

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Detecting QTLs and putative candidate genes involved in budbreak and flowering time in an apple multiparental population

Abstract: HighlightQTLs and candidate genes for the regulation of budbreak and flowering time reveal new hypotheses on temperature perception in growth resumption at spring time in apple.

Cited by 94 publications

References 68 publications

A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species

A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species

Predicting Flowering Behavior and Exploring Its Genetic Determinism in an Apple Multi-family Population Based on Statistical Indices and Simplified Phenotyping

Combining Genome-Wide Information with a Functional Structural Plant Model to Simulate 1-Year-Old Apple Tree Architecture

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