A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits

Abstract

Background: The nematode Caenorhabditis elegans has been extensively used to explore the relationships between complex traits, genotypes, and environments. Complex traits can vary across different genotypes of a species, and the genetic regulators of trait variation can be mapped on the genome using quantitative trait locus (QTL) analysis of recombinant inbred lines (RILs) derived from genetically and phenotypically divergent parents. Most RILs have been derived from crossing two parents from globally distant locations. However, the genetic diversity between local C. elegans populations can be as diverse as between global populations and could thus provide means of identifying genetic variation associated with complex traits relevant on a broader scale.

Results: To investigate the effect of local genetic variation on heritable traits, we developed a new RIL population derived from 4 parental wild isolates collected from 2 closely located sites in France: Orsay and Santeuil. We crossed these 4 genetically diverse parental isolates to generate a population of 200 multi-parental RILs and used RNA-seq to obtain sequence polymorphisms identifying almost 9000 SNPs variable between the 4 genotypes with an average spacing of 11 kb, doubling the mapping resolution relative to currently available RIL panels for many loci. The SNPs were used to construct a genetic map to facilitate QTL analysis. We measured life history traits such as lifespan, stress resistance, developmental speed, and population growth in different environments, and found substantial variation for most traits. We detected multiple QTLs for most traits, including novel QTLs not found in previous QTL analysis, including those for lifespan and pathogen responses. This shows that recombining genetic variation across C. elegans populations that are in geographical close proximity provides ample variation for QTL mapping.

Conclusion: Taken together, we show that using more parents than the classical two parental genotypes to construct a RIL population facilitates the detection of QTLs and that the use of wild isolates facilitates the detection of QTLs. The use of multi-parent RIL populations can further enhance our understanding of local adaptation and life history trade-offs.

Keywords: C. elegans; Genetic map; Life-history; Multi-parent RILs; Natural variation; QTL.

Fig. 1

Crossing scheme used to make the four parental mpRIL population. Different populations of worms are shown in the colored circles. Magenta solid lines indicate the hermaphrodite parental lines, and the dashed blue lines show the male parental lines. A JU1511 hermaphrodite (yellow) was crossed with a JU1926 male (red) to create F1 population W. A JU1941 hermaphrodite (blue) was crossed with a JU1931 male (green) to create F1 population X. Individuals from populations W and X were reciprocally crossed to create seven separate populations. In this way, we obtained different populations of genotypes with mixed genetic background from the four parental lines. Individuals from the seven separate populations (A, B, Y1, Y2, Z, C, and D) where further intercrossed to obtain extra recombinations mainly to break up the X-chromosome, which lacks recombination in the male. These populations are labeled E to Q. From these populations (light blue), individuals were taken for inbreeding via self-fertilization for six generations to create mpRILs. For details, see also Additional file 1: Table S1 and Fig. 3

Fig. 2

Genome-wide SNP distribution in the four parental genotypes. Circle size shows the number of SNPs within 50 kb bin. Colors indicate SNP distribution patterns (SDP) as shown in the legend. These are SDP 12—difference between pair JU1511/JU1926 and pair JU1931/JU1941; SDP 13—difference between pair JU1511/JU1931 and pair JU1926/JU1941; and SDP 14—difference between pair JU1511/JU1941 and pair JU1926/JU1931

Fig. 3

Parental background of the multi parental recombinant inbred lines and recombination and allelic distribution per chromosome. a Colors indicate the parental background per genetic segment (x-axis) per RIL (y-axis) as estimated from the SNP distribution patterns. Chromosomes are in separate panels on the x-axis. mpRILs are grouped according to their cross history. The parental lines are shown in group Z. b Genome-wide distribution of parental alleles. Colors indicate the percentage of parental occurrence (y-axis) per genetic segment (x-axis) as estimated from the SNP distribution patterns. Chromosomes are in separate panels on the x-axis. c Recombination per chromosome. Chromosomes show on the x-axis. Numbers of recombinations per RIL are shown on the y-axis. d Recombination frequency per chromosome. e Genomic distance (x) vs genetic distance (y), the rug lines (small lines on the axis) indicate the marker positions

Fig. 4

Phenotypic variation in the mpRILs. On the y-axis, the number of mpRILs is shown. The x-axis values depend on the trait. Heat shock is the average number of dead animals per 50. Oxidative stress indicates activity. Lifespan is the average lifespan on NGM in days. Lifespan (DR) is the average lifespan on DR medium in days. DR effect is the difference in the average lifespan between NGM and DR medium in days. Males OP50 and males Erwinia is the occurrence of males on plates (0 = none , 0.5 = 1 plate, 1 = 2 plates). First egg Erw (1) is the time in hours until the first egg (1–10) for populations grown on Erwinia. First egg Erw (3) is the time in hours until the first egg (> 100) for populations grown on Erwinia. First egg OP50 (1) is the time in hours until the first egg (1–10) for populations grown on OP50. First egg OP50 (3) is the time in hours until the first egg (> 100) for populations grown on OP50. Pop growth shows worms per 5 μl of culture. Length and width in nanometers, LW ratio is the ratio between the length and width; volume in nanoliters. The parental values for these traits are not shown yet were measured in a different batch in Volkers et al. 2013. Distribution in the mpRILs are shown in gray, and parental strains are shown JU1511 (yellow), JU1926 (red), JU1931 (green), and JU1941 (blue)

Fig. 5

Correlations between traits in the mpRILs. Ewr Dev1 and Ewr Dev3 are the speed of development on Erwinia as measured by time until the first egg (1 = first egg, 3 = first > 100 eggs). OP50 Dev1 and OP50 Dev3 are the speed of development on OP50. Heat shock is the alive worms after 10 h of 35 °C. LSP DR is the lifespan on dietary restriction. DR Effect is the difference in lifespan between LSP DR and LSP. DSM PG, OP50 PG, BTd PG, BT PG, and Erw PG are the population growth on bacteria DSM, OP50, BT diluted, BT and Erwinia, respectively. LWrat is the length to width ratio. Volume is the animal volume. Width is the animal width. Length is the animal length. Erw males and OP50 males are the occurrence of males on Erwinia and OP50, respectively. LSP is the mean lifespan. Sph PG is the population growth on Sphingmonas. Ox stress is the oxidative stress survival

Fig. 6

QTL profiles of the lifespan and stress phenotypes. Genomic position on the x-axis against the significance on the y-axis. Triangles show the position of the co-factors used in the final mapping model. Significance was multiplied by the sign of the allelic effect to show the effect direction. Colors show SNP distribution patterns (SDP). These are SDP 12—difference between pair JU1511/JU1926 and pair JU1931/JU1941; SDP 13—difference between pair JU1511/JU1931 and pair JU1926/JU1941; and SDP 14—difference between pair JU1511/JU1941 and pair JU1926/JU1931

Fig. 7

Genome-wide overview of QTLs. QTLs are shown by the triangles; triangles pointing upwards show a positive allelic effect, and triangles pointing downwards show a negative allelic effect. Size indicates significance in −log10(p); colors show SNP distribution patterns (SDP). These are SDP 12—difference between pair JU1511/JU1926 and pair JU1931/JU1941; SDP 13—difference between pair JU1511/JU1931 and pair JU1926/JU1941; and SDP 14—difference between pair JU1511/JU1941 and pair JU1926/JU1931. Black dots show the exact location of the peaks and the black horizontal bars the 2 −log10(p) drop QTL intervals