Reference Report for AP20210805.1
| Title: | Nonallelic homologous recombination events responsible for copy number variation within an RNA silencing locus |
| Authors: | Cho, Y. B., Jones, S. I., Vodkin, L. O. |
| Source: | Cho et al. 2019 Plant Direct, 3(8): e00162 |
| Abstract: | The structure of chalcone synthase (CHS) gene repeats in different alleles of theI(inhibitor) locus in soybean spawns endogenous RNA interference (RNAi) that leads to phenotypic change in seed coat color of this major agronomic crop. Here, we examinedCHSgene copy number by digital PCR and single nucleotide polymorphisms (SNPs) through whole genome resequencing of 15 cultivars that varied in alleles of theIlocus (I,ii,ik, andi) that control the pattern distribution of pigments in the seed coats. Lines homozygous for theiiallele had the highest copy number followed by theIandikcultivars which were more related to each other than to the lines withiialleles. Some of the recessiveialleles were spontaneous mutations, and each revealed a loss of copy number by digital PCR relative to the parent varieties. Amplicon sequencing and whole genome resequencing determined that the breakpoints of severaliitoimutations resulted from nonallelic homologous recombination (NAHR) events betweenCHSgenes located in segmental duplications leading to large 138-kilobase deletions that erase the structure generating theCHSsiRNAs along with eight other non-CHSgenes. Functional hybridCHSgenes (designatedCHS5:1) were formed in the process and represent rare examples of NAHR in higher plants that have been captured by examining spontaneous mutational events in isogenic mutant lines. |
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