What causes mating system shifts in plants? Arabidopsis lyrata as a case study

Abstract

The genetic breakdown of self-incompatibility (SI) and subsequent mating system shifts to inbreeding has intrigued evolutionary geneticists for decades. Most of our knowledge is derived from interspecific comparisons between inbreeding species and their outcrossing relatives, where inferences may be confounded by secondary mutations that arose after the initial loss of SI. Here, we study an intraspecific breakdown of SI and its consequences in North American Arabidopsis lyrata to test whether: (1) particular S-locus haplotypes are associated with the loss of SI and/or the shift to inbreeding; (2) a population bottleneck may have played a role in driving the transition to inbreeding; and (3) the mutation(s) underlying the loss of SI are likely to have occurred at the S-locus. Combining multiple approaches for genotyping, we found that outcrossing populations on average harbour 5 to 9 S-locus receptor kinase (SRK) alleles, but only two, S1 and S19, are shared by most inbreeding populations. Self-compatibility (SC) behaved genetically as a recessive trait, as expected from a loss-of-function mutation. Bulked segregant analysis in SC × SI F2 individuals using deep sequencing confirmed that all SC plants were S1 homozygotes but not all S1 homozygotes were SC. This was also revealed in population surveys, where only a few S1 homozygotes were SC. Together with crossing data, this suggests that there is a recessive factor that causes SC that is physically unlinked to the S-locus. Overall, our results emphasise the value of combining classical genetics with advanced sequencing approaches to resolve long outstanding questions in evolutionary biology.

Adding Complexity to Complexity: Gene Family Evolution in Polyploids

“…(3) Amplicon-based approaches are inherently at risk of generating PCR recombinants between copies, making it difficult to distinguish errors from actual recombination, introgression in hybrids, or gene conversion between sequences. (4) It is also difficult to distinguish presence/absence of paralogs from amplification biases during PCR (Mable et al, 2017). (5) There is extensive length heterogeneity within and between members of the gene family, so it can be difficult to establish the positional homology necessary to interpret patterns of selection (Charlesworth et al, 2003a).…”

“…From our previous studies on the evolutionary dynamics of SRK alleles in diploids, we have already described challenges in generating robust data for interpreting these complex gene families in diploids, relevant for the sequencing strategies we apply here: (1) Primers designed to be general enough to recognize all SRK alleles also amplify the rest of the gene family, so a major challenge is assigning sequence variants to loci (Schierup et al, 2001;Charlesworth et al, 2003b;Mable et al, 2003Mable et al, , 2017Mable and Adam, 2007). (2) This is complicated by the fact that, due to the extensive polymorphism in SRK and evidence that gene conversion has contributed to allelic repertoire, paralogs that are not linked to the SI phenotype can be more similar to "real" alleles than "real" alleles are to one another, so similarity can't always be used to assign functionality (Schierup et al, 2001;Mable et al, 2003;Prigoda et al, 2005).…”

“…(5) There is extensive length heterogeneity within and between members of the gene family, so it can be difficult to establish the positional homology necessary to interpret patterns of selection (Charlesworth et al, 2003a). (6) The highly polymorphic nature of SRK alleles means that they are sometimes too divergent from the reference genome to be assembled using standard filtering strategies; this means that these types of alleles might frequently be found in the unassembled reads for resequencing projects (Mable et al, 2017).…”

“…Several known paralogs (Aly8, Aly9, Aly13-2/13-7) were expected to amplify with the primer set used. Polymorphic regions like the S-locus are known to be difficult to assemble in genome resequencing studies due to divergence from the reference genome (Mable et al, 2017) but we tested whether de novo assemblies from a genome resequencing study (Novikova et al, 2016) could be used to assess copy number of the SRK-related kinase gene family. We also attempted to pull out full-length sequences that spanned the S-domain (exon 1), transmembrane (exon 2) and kinase domains (exons 3-7) (Charlesworth et al, 2003a).…”

“…For example, genes controlling sporophytically controlled self-incompatibility (SI) in plants have been found to be missing from resequencing assemblies because they are too divergent from the reference genome and so trawling in the unassembled reads is necessary to characterize these highly polymorphic genes (Mable et al, 2017). Both male and female components are members of large gene families that show extensive trans-specific polymorphism, with highly similar alleles shared across species and even genera but high divergence between functional specificities (Schierup et al, 1998;Paetsch et al, 2006;Castric and Vekemans, 2007;Busch et al, 2008;Guo et al, 2011;Tedder et al, 2011;Leducq et al, 2014).…”