Sequencing and annotation of the chloroplast DNAs and identification of polymorphisms distinguishing normal male-fertile and male-sterile cytoplasms of onion

Christopher Von Kohn , Agnieszka Kiełkowska , Michael J. Havey

Abstract

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.
Author Christopher Von Kohn
Christopher Von Kohn,,
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, Agnieszka Kiełkowska ( / / O-KGHiN)
Agnieszka Kiełkowska,,
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, Michael J. Havey
Michael J. Havey,,
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Journal seriesGenome, ISSN 0831-2796, (A 20 pkt)
Issue year2013
Vol56
No12
Pages737-742
Publication size in sheets0.5
Keywords in EnglishAllium cepa, cytoplasmic male sterility, molecular markers
ASJC Classification1311 Genetics; 1312 Molecular Biology; 2700 General Medicine; 1305 Biotechnology
DOIDOI:10.1139/gen-2013-0182
URL http://pubag.nal.usda.gov/pubag/downloadPDF.xhtml?id=58396&content=PDF
Internal identifierWBIO/2013/116
Languageen angielski
Score (nominal)20
Score sourcejournalList
Publication indicators WoS Citations = 21; Scopus SNIP (Source Normalised Impact per Paper): 2013 = 0.841; WoS Impact Factor: 2013 = 1.558 (2) - 2013=1.813 (5)
Citation count*6 (2016-04-26)
Additional fields
FinansowanieWe gratefully acknowledge the support of grant 2008-51180-04875 from the USDA Specialty Crops Research Initiative and SNP genotyping by Ag-Biotech, San Juan Bautista, California
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* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or Perish system.
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