Academic journal article Genetics

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

Academic journal article Genetics

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

Article excerpt

MOST traits of agronomic interest present a continuous variation resulting from the sum of the effects of var- ious 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 ad- dress only a small portion of the diversity available (a max- imum 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 ??. (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 esti- mated 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 as- sumption 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 com- monly encountered in breeding programs.

Recent advances in sequencing and genotyping technol- ogies make it possible to genotype individuals for a large number of markers at reduced costs, so that one can expect to have markers closely linked to any QTL. This has paved the way toward association mapping, in which marker-trait associations are directly detected in populations com- posed of diverse inbred lines without the need to develop experimental segregating families. Association mapping, also often referred to as linkage disequilibrium (LD) mapping, has been widely used with success in the plant community (see for instance Bouchet et al. 2013 and Romay et al. 2013 for recent results of association mapping in maize). In this approach, it is important to use models ac- counting for potential underlying population structure and relatedness between individuals to prevent spurious QTL detection due to associations between loci that are not linked physically (Yu et al. 2006). As a consequence, the power to detect associations is low for causal polymor- phisms correlated with the underlying population structure or when they are present in the population at a low fre- quency (Rincent et al. 2014). In addition, associations are generally tested at SNP (single nucleotide polymorphism) markers, which leads to the implicit assumption that the QTL are biallelic. These limitations can be alleviated by combining information coming from LD at the level of the parents and linkage within families, as first proposed for animal populations by Meuwissen and Goddard (2001). In this approach, referred to as linkage disequilibrium and link- age analysis (LDLA), dense genotyping of parents is used to detect identity by descent (IBD) at putative QTL, i.e., the fact that two individuals carry the same allele transmitted by a common ancestor. Different types of LDLA analyses have been proposed to account for the LD component. The sim- plest 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). This design consists of 25 biparental recombinant inbred line (RIL) pop- ulations derived from the cross of the inbred B73 with 25 diverse lines representing the diversity of maize (tropical, temperate, sweet corn, and popcorn lines). …

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