Comparative and phylogenetic study on the chloroplast genomes of CMS with the cytoplasm of Aegilops ovata and its maintainer line in wheat

BACKGROUND : Aegilops ovata a wild relative of wheat. As a valuable genetic source, it can be used for wheat breeding and improvement. However, the interspecific variation, evolutionary mechanism and phylogenetic relationship of the chloroplast genome from the nucleoplasmic hybrid between Ae. ovata and wheat are still unclear. RESULTS: In this study, the CMS line (Ae.ovata)-Xinong1376 and its maintainer line Xinong1376 were used as the materials. We compared their phenotypes. The anthers of (Ae.ovata)-Xinong1376 were indehiscent and lighter in color at the late stage of microspore development, and the male gametophytes lacked starch. The abortion appeared at binucleate stage. Subsequently, we assembled and compared the chloroplast genomes of the CMS line (Ae. ovata)-Xinong1376 and its maintainer line Xinong1376 via high-throughput sequencing technology for the first time. The data revealed the cp. genome was 136,170 bp long for the CMS (Ae.ovata)-Xinong1376 and 135,885 bp for common wheat Xinong1376, with typical quadripartite structures. The unique genes consisted of 66 protein-coding genes, 4 rRNA genes, and 27 tRNA genes. There were similar gene categories and numbers between (Ae.ovata)-Xinong1376 and Xinong1376, but different codon preferences. 186 possible SSRs were found in (Ae.ovata)-Xinong1376, and 183 possible SSRs in Xinong1376. Single nucleotide repeats are more abundant in SSRs. Phylogenetic analysis revealed that (Ae.ovata)-Xinong1376 was the most closely related to Ae. ovata, and Xinong1376 was the most closely related to common wheat. We identified two highly variable regions, and 20 nonsynonymous mutations through sequence comparison of two lines. In addition, the chlorophyll level was relatively low in the male sterile line (Ae.ovata)-Xinong1376, and correspondingly, most of 12 genes selected were downregulated via qRT-PCR. CONCLUSIONS: Our study provides valuable information on the chloroplast genome of the male sterile line with the cytoplasm of Ae.ovata and its maintainer line, evolutionary implications for the scientific community, and novel perspective on the exploration of wheat CMS.