Genetic Properties of a Nested Association Mapping Population Constructed With Semi-Winter and Spring Oilseed Rapes.

Jianlin Hu,Kede Liu,Chaocheng Guo,Jiaqing Ye,Qinghua Zhang,Yingjie Xiao,Meng Liu,Zhikun Wu,Bo Wang,Haitao Li,Graham J King

doi:10.3389/fpls.2018.01740

Abstract

Nested association mapping (NAM) populations have been widely applied to dissect the genetic basis of complex quantitative traits in a variety of crops. In this study, we developed a Brassica napus NAM (BN-NAM) population consisting of 15 recombination inbred line (RIL) families with 2,425 immortal genotypes. Fifteen high-density genetic linkage maps were constructed by genotyping by sequencing (GBS) based on all RIL families, with further integration into a joint linkage map (JLM) having 30,209 unique markers in common with multiple linkage maps. Furthermore, an ultra-density whole-genome variation map was constructed by projecting 4,444,309 high-quality variants onto the JLM. The NAM population captured a total of 88,542 recombination events (REs). The uneven distribution of recombination rate along chromosomes is positively correlated with the densities of genes and markers, but negatively correlated with the density of transposable elements and linkage disequilibrium (LD). Analyses of population structure and principal components revealed that the BN-NAM population could be divided into three groups with weak stratification. The LD decay distance across genome varied between 170 and 2,400 Kb, with LD decay more rapid in the A than in the C sub-genome. The pericentromeric regions contained large LD blocks, especially in the C sub-genome. This NAM population provides a valuable resource for dissecting the genetic basis of important traits in rapeseed, especially in semi-winter oilseed rape.

Highlights

Most important traits in crops are genetically determined by polygenes and interaction effects between genes and/or genes and the environment
The genetic architecture of complex traits has traditionally been dissected by QTL mapping using segregating populations derived from biparental crosses (Long et al, 2007), and more recently by Genome-wide association studies (GWAS) using landraces, cultivars and Number of bins
Number of bins distorted to D0 (%)b aNumber and frequency of segregation distortion bins of each recombination inbred line (RIL) family. bNumber and frequency of segregation distortion bins of each RIL family distorted to common parent (D0). cNumber and frequency of segregation distortion bins of each RIL family distorted to other donor parents (D1–15)

Summary

Introduction

Most important traits in crops are genetically determined by polygenes and interaction effects between genes and/or genes and the environment. QTL mapping has been successful in detecting contributions from thousands of loci in many crops, and greatly facilitated the identification of many agronomically important genes and molecular marker-assisted breeding This approach had proven to be efficient in detecting QTL effects at low resolution, it is often hard to identify closely linked markers for Genetic Properties of Rapeseed NAM Population fine mapping and marker-assisted selection due to the relatively low frequency and coverage of recombination events in single or several crosses. This initial success prompted the development of NAM populations in other crops such as rice, wheat, barley, soybean, and sorghum (Maurer et al, 2015; Schmutzer et al, 2015; Bajgain et al, 2016; Bouchet et al, 2017; Fragoso et al, 2017; Song et al, 2017)

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