The Genetic Architecture of Grain Yield and Related Traits in <i>Zea maize</i> L. Revealed by Comparing Intermated and Conventional Populations

Huang, Yung‐Fen; Madur, Delphine; Combes, Valérie; Ky, Chin Long; Coubriche, Denis; Jamin, Philippe; Jouanne, Sophie; Dumas, Fabrice; Bouty, Ellen; Bertin, Pascal; Charcosset, Alain; Moreau, Laurence

doi:10.1534/genetics.110.113878

Cited by 38 publications

(34 citation statements)

References 52 publications

(42 reference statements)

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“…Both GY and GM are considered to be highly polygenic traits, based on QTL mapping results (Schön et al 2004;Huang et al 2010). Several authors found in simulation studies and for real data sets that GBLUP models were superior to or equally well performing as Bayesian wholegenome regression methods for such traits (Zhong et al 2009;Hayes et al 2010;Clark et al 2011;Kärkkäinen and Sillanpää 2012;Wimmer et al 2013).…”

Section: Comparison Of Prediction Methodsmentioning

confidence: 99%

Genome Properties and Prospects of Genomic Prediction of Hybrid Performance in a Breeding Program of Maize

et al. 2014

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Maize (Zea mays L.) serves as model plant for heterosis research and is the crop where hybrid breeding was pioneered. We analyzed genomic and phenotypic data of 1254 hybrids of a typical maize hybrid breeding program based on the important Dent 3 Flint heterotic pattern. Our main objectives were to investigate genome properties of the parental lines (e.g., allele frequencies, linkage disequilibrium, and phases) and examine the prospects of genomic prediction of hybrid performance. We found high consistency of linkage phases and large differences in allele frequencies between the Dent and Flint heterotic groups in pericentromeric regions. These results can be explained by the Hill-Robertson effect and support the hypothesis of differential fixation of alleles due to pseudooverdominance in these regions. In pericentromeric regions we also found indications for consistent marker-QTL linkage between heterotic groups. With prediction methods GBLUP and BayesB, the cross-validation prediction accuracy ranged from 0.75 to 0.92 for grain yield and from 0.59 to 0.95 for grain moisture. The prediction accuracy of untested hybrids was highest, if both parents were parents of other hybrids in the training set, and lowest, if none of them were involved in any training set hybrid. Optimizing the composition of the training set in terms of number of lines and hybrids per line could further increase prediction accuracy. We conclude that genomic prediction facilitates a paradigm shift in hybrid breeding by focusing on the performance of experimental hybrids rather than the performance of parental lines in testcrosses.H YBRID breeding was pioneered in maize (Shull 1908) and plays an ever increasing role in other globally important field (Duvick 1999) and vegetable crops (Silva Dias 2010). Maize has also served as a model species for research in heterosis, the phenomenon behind the success of hybrid varieties, for which the genetic mechanisms have been elusive (Duvick 1999;Lippman and Zamir 2006). In recent years, evidence emerged for the importance of (pseudo-)overdominance in the manifestation of heterosis in maize (Lippman and Zamir 2006;Schön et al. 2010) and the particular role of the centromeres in this process (Gore et al. 2009;McMullen et al. 2009). Today, the availability of high-density marker data and whole-genome regression methods developed in the context of genomic prediction (Meuwissen et al. 2001) allows us to revisit this hypothesis by studying key genome properties such as allele frequencies and linkage phases.Consistency of linkage phases between quantitative trait loci (QTL) and markers is a key prerequisite for pooling of diverse breeds and germplams to increase sample size for genetic studies and transferability of their results to different populations (De Roos et al. 2008). Weber et al. (2012) used whole-genome estimates of marker effects of several cattle breeds to investigate across-breed marker-QTL linkage phase consistency. Such a study is still missing for maize and other important crops. For o...

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Section: Comparison Of Prediction Methodsmentioning

confidence: 99%

Genome Properties and Prospects of Genomic Prediction of Hybrid Performance in a Breeding Program of Maize

et al. 2014

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“…This may not necessarily be a disadvantageous feature of MAGIC populations if it allows the identification of QTL with consistent effects over a diverse set of complex backgrounds. It has also been suggested that with the increased number of recombinations, there could be a breakage of small QTL that were previously linked, reducing the ability to detect them (Huang et al 2010). Such an effect has not been seen Using average MAGIC line values (correlation is significant at *P = 0.003 level, which is the Bonferroni corrected level equivalent to P = 0.05; and correlation is significant at the **P = 0.001 level).…”

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confidence: 99%

The Genetic Basis of Natural Variation in Seed Size and Seed Number and Their Trade-Off Using Arabidopsis thaliana MAGIC Lines

Gnan¹,

Priest²,

Kover

2014

Genetics

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Offspring number and size are key traits determining an individual's fitness and a crop's yield. Yet, extensive natural variation within species is observed for these traits. Such variation is typically explained by trade-offs between fecundity and quality, for which an optimal solution is environmentally dependent. Understanding the genetic basis of seed size and number, as well as any possible genetic constraints preventing the maximization of both, is crucial from both an evolutionary and applied perspective. We investigated the genetic basis of natural variation in seed size and number using a set of Arabidopsis thaliana multiparent advanced generation intercross (MAGIC) lines. We also tested whether life history affects seed size, number, and their trade-off. We found that both seed size and seed number are affected by a large number of mostly nonoverlapping QTL, suggesting that seed size and seed number can evolve independently. The allele that increases seed size at most identified QTL is from the same natural accession, indicating past occurrence of directional selection for seed size. Although a significant trade-off between seed size and number is observed, its expression depends on life-history characteristics, and generally explains little variance. We conclude that the trade-off between seed size and number might have a minor role in explaining the maintenance of variation in seed size and number, and that seed size could be a valid target for selection.T HE reproductive output of an organism is a critical lifehistory trait defining its fitness and is the result of both offspring number and quality. In the case of cereal crops, the number and size of seeds are also the main constituents of yield. Thus, understanding the genetic architecture of seed size and number, and any possible genetic constraints to maximizing them, is crucial from both an evolutionary and applied perspective (Sadras 2007;Van Daele et al. 2012;Kesavan et al. 2013). Despite its importance, the genetic basis of natural variation in seed size and number and their interaction with life-history traits remain poorly understood.Previous studies on the genetic basis of seed traits have predominantly used mutant screens and identified genes in key pathways involved in seed development (Garcia et al. 2003;Tzafrir et al. 2004;Adamski et al. 2009;Fang et al. 2012). However, since this approach only allows for the comparison of phenotypic effects of genes that are "on" or "off" (Koornneef et al. 2004), genes' contribution to natural continuous variation in seed size or seed number remain largely uncharacterized. Because the effects of mutants are often dependent on the genetic background (Tonsor et al. 2005;Chou et al. 2011), a QTL mapping approach using multiple parents is ideal to identify genetic factors that can contribute to natural variation in these traits in a heterogeneous genetic background.Identification of genetic factors affecting seed traits is further complicated by potential trade-offs between them. Life-history the...

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“…For example, in a nine-generation advanced intercross used for fine mapping body weight in chickens, BESNIER et al (2011) could only detect five of the nine QTL that were earlier found with the original F2 population. Similar results have been found in advanced crosses of maize (HUANG et al 2010) and mice (WANG et al 2003;LIONIKAS et al 2010).…”

Section: Finer Scale Qtl Localisation and Annotation Of The Qtl-contasupporting

confidence: 87%

Genetic dissection of a major polymorphism underlying population divergence in sexually selected pheromones in Drosophila serrata

Rusuwa¹

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With the advent of QTL mapping in the late 1980s, evolutionary geneticists have actively dissected the genetic basis of adaptive phenotypes. In recent times, advances in whole genome sequencing have allowed for finer scale mapping of traits that have diverged due to natural selection. These relatively inexpensive sequencing technologies have also greatly facilitated adaptive trait dissection in non-model species that exhibit especially interesting patterns of adaptation. One class of trait that has largely escaped the attention of the next generation ecological and evolutionary genomics research programme, are sexually-selected traits. Sexual selection is a strong form of directional selection in nature and is thought to be responsible for the evolution of elaborate sexual ornaments and armaments. However we still know comparatively little of the genetic basis of such traits.The cuticular hydrocarbons (CHCs) of Drosophila serrata provide an opportunity for dissecting the divergence of sexually selected traits. Populations along the eastern Australian coast exhibit latitudinal variation in these traits in association with climatic factors and consistent with the action of divergent natural selection. Under experimental settings, divergent sexual as well as natural selection has been implicated in the evolution of CHCs. Natural populations of D. serrata along the northern part of the Eastern Australian coast have recently been observed to exhibit a polymorphism in three of their CHC compounds representing the shortest carbon chains; 5,9-tetracosadiene (5,9-C 24 ), 5,9-pentacosadiene (5,9-C 25 ) and 9-pentacosene (9-C 25 ). One class of phenotype only expresses these three compounds in trace amounts ('low' phenotype) whereas the other has normal levels ('high' phenotype). These short-chained CHCs also exhibit strong genetically-based latitudinal clines up to, but not beyond, 20 degrees south of the equator. Based on both traditional QTL and modern sequence-based genomic mapping approaches, the aim of this study was to dissect the genetic basis of the polymorphism in D. serrata CHCs and to examine its adaptive significance within the context of sexual and natural selection.Through F2 QTL mapping based on a cross between two inbred lines, from the opposite ends of the D. serrata CHC cline, one a 'low' phenotype and the other a 'high' phenotype, the genetic basis of all CHCs in this species was mapped to twenty two overlapping QTLs on chromosomes 2 and 3.The short-chain CHC polymorphism was traced to two major effect recessive QTLs on the right arm of chromosome 3, which including their interaction, accounted for more than 70% of the variance in the polymorphism (Chapter 2). Fine mapping of this major polymorphism was then conducted using next generation DNA sequencing and bulk segregant analysis of an advanced F60 cross of the same founding lines. Bulk segregant analysis revealed a single peak of genetic differentiation on chromosome 3R (~20kb), harbouring three adjacent fatty acyl-CoA reductase ii genes (Cha...

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The Genetic Architecture of Grain Yield and Related Traits in Zea maize L. Revealed by Comparing Intermated and Conventional Populations

Cited by 38 publications

References 52 publications

Genome Properties and Prospects of Genomic Prediction of Hybrid Performance in a Breeding Program of Maize

Genome Properties and Prospects of Genomic Prediction of Hybrid Performance in a Breeding Program of Maize

The Genetic Basis of Natural Variation in Seed Size and Seed Number and Their Trade-Off Using Arabidopsis thaliana MAGIC Lines

Genetic dissection of a major polymorphism underlying population divergence in sexually selected pheromones in Drosophila serrata

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