Plastid Genotyping Reveals Uniformity of cms-T Maize Cytoplasms

Abstract

ORCID IDs: 0000-0003-4454-9882 (M.B.); 0000-0002-8063-653X (C.G.); 0000-0002-6202-0029 (P.M.).Cytoplasmic male-sterile (CMS) lines in maize (Zea mays) have been classified by their response to specific restorer genes into three categories: cms-C, cms-S, and cms-T. A mitochondrial genome representing each of the CMS cytotypes has been sequenced, and male sterility in the cms-S and cms-T cytotypes is linked to chimeric mitochondrial genes. To identify markers for plastid genotyping, we sequenced the plastid genomes of three fertile maize lines (B37, B73, and A188) and the B37 cms-C, cms-S, and cms-T cytoplasmic substitution lines. We found that the plastid genomes of B37 and B73 lines are identical. Furthermore, the fertile and CMS plastid genomes are conserved, differing only by zero to three single-nucleotide polymorphisms (SNPs) in coding regions and by eight to 22 SNPs and 10 to 21 short insertions/deletions in noncoding regions. To gain insight into the origin and transmission of the cms-T trait, we identified three SNPs unique to the cms-T plastids and tested the three diagnostic SNPs in 27 cms-T lines, representing the HA, I, Q, RS, and T male-sterile cytoplasms. We report that each of the tested 27 cms-T group accessions have the same three diagnostic plastid SNPs, indicating a single origin and maternal cotransmission of the cms-T mitochondria and plastids to the seed progeny. Our data exclude exceptional pollen transmission of organelles or multiple horizontal gene transfer events as the source of the mitochondrial urf13-T (unidentified reading frame encoding 13-kD cms-T protein) gene in the cms-T cytoplasms. Plastid genotyping enables a reassessment of the evolutionary relationships of cytoplasms in cultivated maize.

Complete Chloroplast Genome Sequence of Broomcorn Millet (Panicum miliaceum L.) and Comparative Analysis with Other Panicoideae Species

“…The GC content of the IR region (43.95%) was much higher than that of the LSC (36.47%) and SSC regions (33.09%) in the broomcorn millet cp genome. The higher GC content in the IR region was probably the result of the presence of four ribosomal RNA (rRNA) genes in this region, which is consistent with previous analyses in other plants [18,34] (Table 1 and Figure 1). Additionally, the GC content in the overall cp genome and IR region was nearly the same as in other Panicoideae cp genomes, suggesting that the cp genome in this subfamily had rather conserved genome organization [15,29].…”

“…Among all the SSR motifs identified in the broomcorn millet cp genome, 85.9% of mononucleotides were comprised of A or T, and a similar proportion of trinucleotides (73.8%) was composed of A or T. Similarly, the motif tended to have a higher percentage of A or T in the other five related species. Our results were consistent with previous studies that reported that potential SSR markers identified in the cp genome commonly consisted of polyA or polyT repeats, and seldom included C and G repeats, which partially explained why broomcorn millet had a higher frequency of AT content [34,36]. Based on the SSR dynamics in these six cp genomes, a total of 13 potential SSR markers were developed, which could be used for molecular identification of Panicoideae and other species (Table S2).…”

“…Among the coding regions, there were 76 protein-coding genes categorized into different functional groups, including nine genes for large ribosomal proteins, 12 genes for small subunit ribosomal proteins, seven genes for photosystem I, 15 genes for photosystem II, and six genes for ATP synthase. A similar gene composition was also found in other monocots [34] (Table 2). Furthermore, the 82 protein-coding genes comprise of 60,903 bp in length coding for 20,301 codons.…”

Chromosome-level Genome Assembly of a Regenerable Maize Inbred Line A188

“…Read depths for contigs were assessed using Illumina short reads generated independently from seedling and immature ear DNAs to identify potential contamination from organelle genomes or extraneous microbial DNA whose contigs were expected to have differential read depths between the two tissues. Based on this strategy, contigs identified as the chloroplast or mitochondrion sequences were replaced respectively with the previously complete assemblies of A188 organelle genomes 15,16 and contigs from extraneous contamination were discarded ( Supplementary Fig. 4).…”

Involvement of a universal amino acid synthesis impediment in cytoplasmic male sterility in pepper

“…However, in practical seed selection processes, a number of problems occurs, such as cytoplasm singularity, low combining ability and unstable sterility, and farmers may lack the theoretical knowledge required to solve these problems. The CMS line is an ideal material in the study of nucleo-cytoplasmic interactions; thus, scientists have reported numerous studies on the mechanisms of sterility 2 3 4 5 6 7 8 9 10 11 12 and identified many CMS-related genes (orf507 2 8 , atp6 10 and orf456 11 in pepper; AcPMS1 in onion 4 ; and MYB80/UNDEAD in Arabidopsis 7 , among others) and proteins (ATP synthase and Hsp60 in wheat 3 ). Because CMS widely occurs, plant pollen abortion has different symptoms, although its common morphological expression is as small floral organs, short filaments, and thin and small anthers.…”