A spontaneous complex structural variant in rcan-1 increases exploratory behavior and laboratory fitness of Caenorhabditis elegans

Abstract

Over long evolutionary timescales, major changes to the copy number, function, and genomic organization of genes occur, however, our understanding of the individual mutational events responsible for these changes is lacking. In this report, we study the genetic basis of adaptation of two strains of C. elegans to laboratory food sources using competition experiments on a panel of 89 recombinant inbred lines (RIL). Unexpectedly, we identified a single RIL with higher relative fitness than either of the parental strains. This strain also displayed a novel behavioral phenotype, resulting in higher propensity to explore bacterial lawns. Using bulk-segregant analysis and short-read resequencing of this RIL, we mapped the change in exploration behavior to a spontaneous, complex rearrangement of the rcan-1 gene that occurred during construction of the RIL panel. We resolved this rearrangement into five unique tandem inversion/duplications using Oxford Nanopore long-read sequencing. rcan-1 encodes an ortholog to human RCAN1/DSCR1 calcipressin gene, which has been implicated as a causal gene for Down syndrome. The genomic rearrangement in rcan-1 creates two complete and two truncated versions of the rcan-1 coding region, with a variety of modified 5' and 3' non-coding regions. While most copy-number variations (CNVs) are thought to act by increasing expression of duplicated genes, these changes to rcan-1 ultimately result in the reduction of its whole-body expression due to changes in the upstream regions. By backcrossing this rearrangement into a common genetic background to create a near isogenic line (NIL), we demonstrate that both the competitive advantage and exploration behavioral changes are linked to this complex genetic variant. This NIL strain does not phenocopy a strain containing an rcan-1 loss-of-function allele, which suggests that the residual expression of rcan-1 is necessary for its fitness effects. Our results demonstrate how colonization of new environments, such as those encountered in the laboratory, can create a1111111111 a1111111111 a1111111111 a1111111111 a1111111111

From QTL to gene: C. elegans facilitates discoveries of the genetic mechanisms underlying natural variation

“…Quantitative genetics mappings use three complementary approaches: linkage mapping, bulksegregant analysis (BSA), and genome-wide association (GWA) mapping. Although BSA has been shown to be a fast, powerful, and effective tool to identify QTL [20,49,73,95,98], linkage mapping is the most popular method for the detection of QTL in C. elegans. In this approach, investigators leverage statistical power to detect QTL using a large number of recombinant lines generated from a cross between two or more phenotypically and genotypically diverse strains.…”

“…These two strains were used to demonstrate that a QTV in the npr-1 gene, originally identified as a natural genetic variant that regulates feeding behavior, arose after isolation from the wild and increased the fitness of the N2 strain in laboratory conditions [84]. Mapping of phenotypic differences between the N2 and LSJ2 strains using a RIL panel generated between these two strains led to the identification of a number of additional beneficial QTVs in the glb-5, nurf-1, rcan-1, srg-36, and srg-37 genes [18,44,84,95,141,148]. These QTVs affect a number of behavioral, developmental, and reproductive traits, from feeding behaviors on bacterial lawns, to behavioral and developmental responses to pheromones, to reproductive output and lifespan.…”

“…This technique is especially powerful to establish candidate genes whose expression is controlled by loci far from the regulated gene, as most fine-mapping techniques only consider genes within the QTL confidence interval. In the case of tyra- After identification of a QTV, one common use of experimental evolution in C. elegans is to test the role of selection in the spread or loss of QTVs in a population [18,37,70,86,95,141,148,[154][155][156]. Typically, two strains with homozygous genotypes for alternate alleles compete against each other for multiple generations in specific environments.…”

“…in main text). Most C. elegans studies validate and narrow QTL using NILs[4,[17][18][19][20]34,36,37,[40][41][42]44,50,61,63,65,67,69,71,[74][75][76]81,84,86,87,90,92,93,95,100,101,104,149]. Any differences in phenotype between the NIL and the parental strain with the same genetic background can be attributed to the introgression of the QTL or the interaction of the introgression with the genetic background from the opposite genotype.…”

Deciphering complex genome rearrangements in C. elegans using short-read whole genome sequencing

“…More complex events, known as chromoanagenesis, combine a cascade of chromosomal rearrangements 1 . Over the past few years, structural variants and complex genomic rearrangements have been implicated in various phenotypes: cancer 2 , 3 , rare disorders 4 – 9 and common diseases 10 in humans, reproduction traits in pigs 11 , virulence traits in plant pathogenic fungi 12 , local adaptation in maize 13 , and behavior in Caenorhabditis elegans ( C. elegans ) 14 . However, the technologies and methods used to identify SVs and complex rearrangements are still multifaceted and no approach has yet been recognized as standard.…”