Extended Data Fig. 10: Large-scale chromosomal rearrangements shaped the segregation and recombination patterns in progenies of 13 crosses from a working oat breeding program.

(a) Summary of 13 crosses (rows) by chromosome (columns). The top row in each cell shows the segregation ratios (AA:AB:BB). The bottom row shows the p-value for the chi-square goodness-of-fit tests of the expected F₆ ratio (31:2:31). Cell colors highlight significant P values to reject the fit (pink = p < 0.01; blue = p < 0.05). Boxes around cells represent suppressed recombination within or between chromosomes. Most crosses demonstrated expected segregation ratios and recombination patterns across the majority of chromosomes. Cross 19S29 showed segregation distortions across most chromosomes. All crosses had at least one chromosome that showed distorted segregation. The recombination patterns of half-sib crosses 19S32 and 19S43, which share the common parent OA1613-5, were investigated in further detail using recombination heatmaps. (b) The 19S32 progenies (n = 147) exhibited some suppressed recombination, but only on chromosomes 2C and 3C. There were insufficient markers to generate accurate scaled r values on chromosomes 4C and 7C. (c) In contrast, the 19S43 progenies (n = 122) exhibited pseudo linkage between chromosomes 1A and 1C, as well as between chromosomes 1D and 7C. Additional chromosomes that exhibited some recombination suppression include chromosomes 2C, 3A, 3C, and 4D. Karyotypes of the three parental lines confirmed that they have a complete set of 21 chromosome pairs. (d) The karyotype of OA1623-2, the female parent of 19S32, confirmed the presence of a heterozygous inversion on chromosome 3C as well as a homozygous chromosome 1A/1C translocation. (e) The karyotype of OA1613-5, the pollen donor for the two crosses, shows a homozygous 3C inversion (non-ancestral) and a homozygous 1A/C translocation. This is manifested in cross 19S32 by a partially suppressed recombination pattern on chromosome 3C and by the expected recombination patterns in 1A and 1C. (f) The karyotype of OA1568-6, the female parent of 19S43, shows a pair of ancestral 1A chromosomes (without the 1A/1C translocation), confirming the reason for pseudo-linkage between chromosomes 1A and 1C in cross 19S43. These crosses were not made intentionally for this purpose; rather, they are part of a breeding program that uses both conventional and genomic selection. Even though these populations were small and were advanced by modified single-seed descent, they still show evidence of known SVs and suggest additional SVs in oats. The companion study14, which detected chromosome inversions using a population-based approach, identified large-scale chromosomal inversions in all affected chromosomes except 7C. A pseudo-linkages similar to 1A/1C between 1D and 7C in 19S43 (c) suggests the possibility of an additional translocations.