High‐resolution insight into recombination events at the SD1 locus in rice

Abstract

These authors contributed equally to this work. SUMMARYRecombination during meiosis plays an important role in genome evolution by reshuffling existing genetic variations into fresh combinations with the possibility of recovery of lost ancestral genotypes. While crossover (CO) events have been well studied, gene conversion events (GCs), which represent non-reciprocal information transfer between chromosomes, are poorly documented and difficult to detect due to their relatively small converted tract size. Here, we document these GC events and their phenotypic effects at an important locus in rice containing the SD1 gene, where multiple defective alleles contributed to the semidwarf phenotype of rice in the 'Green Revolution' of the 1960s. Here, physical separation of two defects allows recombination to generate the wild-type SD1 gene, for which plant height can then be used as a reporter. By screening 18 000 F 2 progeny from a cross between two semi-dwarf cultivars that carry these different defective alleles, we detected 24 GC events, indicating a conversion rate of~3.3 3 10 À4 per marker per generation in a single meiotic cycle in rice. Furthermore, our data show that indels and single-nucleotide polymorphisms (SNPs) do not differ significantly in GC rates, at least at the SD1 locus. Our results provide strong evidence that GC by itself can regain an ancestral phenotype that was lost through mutation. This GC detection approach is likely to be broadly applicable to natural or artificial alleles of other phenotyperelated functional genes, which are abundant in other plant genomes.

Mitotic gene conversion can be as important as meiotic conversion in driving genetic variability in plants and other species without early germline segregation

“…With respect to the relative frequencies of CO to NCO-GC events in mitosis, these data therefore indicate a ratio of 36 CO events (29 CO and 7 CO-GC) to 17 NCO-GC events, or 2.11:1 at the SD1 locus. This is highly similar to the previous estimate (34 CO versus 16 NCO-GC, 2.12:1) at the SD1 locus in meiosis [62]. Furthermore, 29.2% (here a total of 17 NCO-GC and 7 CO-GC, 7/(7+14) = 29.2%) of the conversion events in spontaneous mitotic recombination in our data are associated with COs, which is close to estimates of mitotic recombination events in yeast (27%, χ 2 = 0.086, P = 0.77) [27,46] or meiotic recombination at the SD1 locus in rice (33.3%, χ 2 = 0.27, P = 0.604) [62].…”

“…Similarly, H5 (Type 9 in Fig 2) is likely to have resulted from a relatively long tract conversion (93.3 kb) associated with a CO event. Collectively, with respect to the rate of GC per marker, we estimated that GC involving the SD1 locus per marker per haplotype occurs at a rate of PLOS BIOLOGY 1.36 × 10 −6 per marker per haplotype per plant (3 NCO-GCs and 3 CO-GCs for 2 haplotypes and 2 markers, (3+3)/1,100,000/2/2 = 1.36 × 10 −6 ), which is lower by 2 orders of magnitude than our estimate (3.3 × 10 −4 ) of the meiotic rate of GC at the same locus in rice [62].…”

“…3% lower tail), this approximating to less than 1 plant in our sample (if 24 observed = 97%, 100% = 24.7). As a negative control, we previously examined 98 random average sized individuals (in the range of 100 to 120 cm) and found no CO or GC events at the locus [62].…”

“…Both estimates differ markedly from what is seen in meiosis. Using the same low-resolution markers, we estimate a mean meiotic tract size of 9.8 kb (length range: 0.4 kb to 16.4 kb) using the same detection system at the same locus in rice [62]. From our prior analysis [7], we can also determine a higher-resolution WGS-based estimate, this being 3.121 kb.…”

“…To this end, we employ our method [62] for detecting both mitotic and meiotic CO and GC events at 1 specific locus (SD1). Hybrid plants (termed LYP9) have 2 different defective alleles (a frameshifting indel and a premature stop codon), thus enabling the possibility of recombinant rescue of the wild-type tall growth phenotype (>130 cm) by mitotic recombination (see Materials and methods, Fig 1 and S1 Fig).…”