Male-sterile (S) cytoplasm of onion is an alien cytoplasm introgressed into onion in antiquity and is widely used for hybrid seed production. Owing to the biennial generation time of onion, classical crossing takes at least 4 years to classify cytoplasms as S or normal (N) male-fertile. Molecular markers in the organellar DNAs that distinguish N and S cytoplasms are useful to reduce the time required to classify onion cytoplasms. In this research, we completed next-generation sequencing of the chloroplast DNAs of N- and S-cytoplasmic onions; we assembled and annotated the genomes in addition to identifying polymorphisms that distinguish these cytoplasms. The sizes (153 538 and 153 355 base pairs) and GC contents (36.8%) were very similar for the chloroplast DNAs of N and S cytoplasms, respectively, as expected given their close phylogenetic relationship. The size difference was primarily due to small indels in intergenic regions and a deletion in the accD gene of N-cytoplasmic onion. The structures of the onion chloroplast DNAs were similar to those of most land plants with large and small single copy regions separated by inverted repeats. Twenty-eight single nucleotide polymorphisms, two polymorphic restriction-enzyme sites, and one indel distributed across 20 chloroplast genes in the large and small single copy regions were selected and validated using diverse onion populations previously classified as N or S cytoplasmic using restriction fragment length polymorphisms. Although cytoplasmic male sterility is likely associated with the mitochondrial DNA, maternal transmission of the mitochondrial and chloroplast DNAs allows for polymorphisms in either genome to be useful for classifying onion cytoplasms to aid the development of hybrid onion cultivars.
The genus Magnolia (Magnoliaceae) comprises more than 130 species distributed predominantly in temperate and tropical regions in Southeast Asia and is valued worldwide for its ornamental traits as well as for timber and medicinal products, and in trade. Despite their favored status, many species of Magnolia are faced with threats from logging, agricultural land use, development, and collection, and are at risk of extinction. Conservation of these species through habitat preservation and in ex situ collections is needed to prevent extinction. To provide a tool for conservation of Magnolia species, microsatellite markers developed previously for Magnolia ashei were tested in 10 other species of Magnolia to determine their transferability across species. Of the 64 primer pairs tested, 21 amplified alleles in the expected size range in all samples; 11 primer pairs amplified clean products in most, but not all, species; 18 primer pairs consistently amplified a polymerase chain reaction (PCR) product in most species, but had either low peak height or other amplification issues; and 14 primers showed excessive stutter, nonspecific amplification, or no amplification. Cluster analysis using the 129 alleles amplified by these 21 simple sequence repeat (SSR) primer pairs generated groups that corresponded to the known taxonomic relationships in this genus. z Species authority and classification are according to the U.S Department of Agriculture, Agricultural Research Service (2018) and Kim and Suh (2013). All species are in subgenus Magnolia except M. acuminata, which is in subgenus Yulania (Spach) Rchb. y Ploidy based on Parris et al. (2010). x M. sharpii and M. tamaulipana are classified as endangered (Rivers et al., 2016).
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