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Oat–Maize Chromosome Addition Lines: a New System for Mapping the Maize Genome (Corn͞chromosome-Specific͞cosmid Library͞repetitive Dna͞cloning)

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Oat–Maize Chromosome Addition Lines: a New System for Mapping the Maize Genome (Corn͞chromosome-Specific͞cosmid Library͞repetitive Dna͞cloning) Proc. Natl. Acad. Sci. USA Vol. 94, pp. 3524–3529, April 1997 Agricultural Sciences Oat–maize chromosome addition lines: A new system for mapping the maize genome (cornychromosome-specificycosmid libraryyrepetitive DNAycloning) EVGUENI V. ANANIEV*, OSCAR RIERA-LIZARAZU*, HOWARD W. RINES*†, AND RONALD L. PHILLIPS*‡ *Department of Agronomy and Plant Genetics and Plant Molecular Genetics Institute, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN 55108; and †Plant Sciences Research Unit, U.S. Department of Agriculture–Agricultural Research Service, St. Paul, MN 55108 Contributed by Ronald L. Phillips, February 10, 1997 ABSTRACT Novel plants with individual maize chromo- that will assist in the construction of physical maps for maize somes added to a complete oat genome have been recovered via chromosomes. The approach is based on cloning genomic embryo rescue from oat (Avena sativa L., 2n 5 6x 5 42) 3 DNA of an oat–maize chromosome-addition line in an appro- maize (Zea mays L., 2n 5 20) crosses. An oat–maize disomic priate vector and subsequent use of maize-specific dispersed addition line possessing 21 pairs of oat chromosomes and one repetitive DNA sequences as detection probes to isolate clones maize chromosome 9 pair was used to construct a cosmid carrying maize genomic DNA. Such an approach was success- library. A multiprobe (mixture of labeled fragments used as a fully applied to the isolation of human-specific DNA fragments probe) of highly repetitive maize-specific sequences was used in cosmid libraries constructed from DNA of human-rodent to selectively isolate cosmid clones containing maize genomic hybrid cell lines carrying individual human chromosomes. In DNA. Hybridization of individual maize cosmid clones or their those experiments the probes included Alu-repeats (21), a subcloned fragments to maize and oat genomic DNA revealed Cot1 DNA fraction (22), or labeled total human DNA (23). that most high, middle, or low copy number DNA sequences Plant repetitive sequences that are apparently species- are maize-specific. Such DNA markers allow the identification specific were first isolated from rye (24, 25) and later found in of maize genomic DNA in an oat genomic background. Chi- many other species (26). Comparative studies revealed a strong meric cosmid clones were not found; apparently, significant correlation between the proportion of species-specific re- exchanges of genetic material had not occurred between the peated families in a genome and phylogenetic relationships maize-addition chromosome and the oat genome in these novel (27, 28). About 90–95% of all randomly tested genomic plants or in the cloning process. About 95% of clones selected repeated sequences from barley were detected in wheat and at random from a maize genomic cosmid library could be rye (27). According to DNA reassociation studies, less-related detected by the multiprobe. The ability to selectively detect species such as maize and wheat have less than 10% nucleotide maize sequences in an oat background enables us to consider sequences in common (28). The success of isolating maize oat as a host for the cloning of specific maize chromosomes or DNA from oat–maize chromosome-addition lines depends on maize chromosome segments. Introgressing maize chromo- how many maize-specific (relative to oat) high-copy-number some segments into the oat genome via irradiation should dispersed nucleotide sequences are found in the maize ge- allow the construction of a library of overlapping fragments nome. Genome analysis in grasses, including maize and oat, for each maize chromosome to be used for developing a reveals that a major portion of genomic DNA consists of physical map of the maize genome. families of repetitive sequences dispersed throughout the genome (26, 29, 30). According to DNA–DNA renaturation Chromosome addition lines of different plant species (1–5) data in maize (28), unique sequences of average length 2,100 have been generated to introgress valuable genes from wild or bp are interspersed with mid-repetitive sequences. Direct cultivated relatives into host plant species. Alien chromosome analysis of sequences adjacent to several maize genes reveals additions have been used for gene mapping (2, 6, 7) and serve that these genes are flanked by highly repetitive DNA se- as an enriched source of markers for positional cloning and quences (31). Thus, maize large DNA inserts cloned in an constructing physical maps of specific chromosomes. The appropriate vector will likely carry some kind of dispersed discovery of maize-chromosome retention in oat ‘‘haploids’’ maize-specific nucleotide sequence. A cosmid vector was after oat 3 maize crosses and the recovery of stable maize chosen for this project because of the high cloning efficiency chromosome-addition oat lines (8, 9) should allow the devel- and relatively large insertion size. Because the oat genome is opment of a system of chromosome analysis similar to that about 11,300 Mb, an added maize chromosome with median available in mammalian hybrid-cell systems (10–12). Such a size of about 250 Mb would constitute about 2–4% of the total system may be used for gene assignment, isolation of chromo- nuclear DNA of an oat–maize chromosome addition line. some-specific probes (13), flow sorting (14) and microdissec- We found that the major part of the maize genome consists tion of chromosomes (15), development of chromosome- of nucleotide sequences that do not cross-hybridize to oat specific ‘‘paints’’ of fluorochrome-labeled DNA fragments genomic sequences under standard hybridization conditions. (16–18), physical mapping, and selective isolation and map- This predominant nonhomology between oat and maize ping of cDNAs of a particular chromosome (19, 20). genomic sequences means that many maize genomic sequences In this paper we describe an approach for isolating clones can be directly used for Southern blot hybridization on DNA containing large-fragment maize DNA of a single-chromo- from oat–maize chromosome addition lines to selectively some origin from the oat–maize chromosome addition lines detect sequences of maize origin. A mixture of highly repetitive dispersed DNA sequences of maize was used as a maize- The publication costs of this article were defrayed in part by page charge specific multiprobe to screen a cosmid library of the chromo- payment. This article must therefore be hereby marked ‘‘advertisement’’ in some addition line. A group of maize-specific cosmids with accordance with 18 U.S.C. §1734 solely to indicate this fact. Copyright q 1997 by THE NATIONAL ACADEMY OF SCIENCES OF THE USA Abbreviation: RFLP, restriction fragment length polymorphism; Mb, 0027-8424y97y943524-6$2.00y0 megabase(s). PNAS is available online at http:yywww.pnas.org. ‡To whom reprint requests should be addressed. 3524 Downloaded by guest on September 29, 2021 Agricultural Sciences: Ananiev et al. Proc. Natl. Acad. Sci. USA 94 (1997) 3525 inserts from only maize chromosome 9 was isolated and RESULTS characterized. Based on the large difference in nucleotide sequence composition between oat and maize and the means Cloning of Maize-Specific Repetitive Sequences. When la- to efficiently isolate and identify maize DNA fragments from beled maize total genomic DNA was used as a probe in blot a chromosome addition line, we propose oat as an effective hybridization, little cross-hybridization to oat genomic DNA occurred under standard conditions (65 Cin6 SSC) in host for the cloning of maize DNA segments to construct 8 3 comparison with strong hybridization to maize genomic DNA physical maps for maize chromosomes. (data not shown). This hybridization pattern indicated that a significant portion of the repeated nucleotide sequences of MATERIALS AND METHODS maize and oat are not shared. To isolate maize repeated DNA sequences specific to maize relative to oat (hereafter referred Maize and Oat Strains. Oat–maize disomic addition lines to simply as ‘‘maize-specific’’ sequences) a maize plasmid for maize chromosomes 2, 3, 4, 7, and 9 were derived from genomic library was constructed with fragments from a com- plants recovered following sexual crosses of oat by maize (8, 9). plete Sau3A digest and screened with labeled total maize In these crosses about one-third of the recovered plants DNA. Clones were isolated that gave a high signal with total contained a haploid set of 21 oat chromosomes plus one or labeled maize DNA as the probe. Labeled oat genomic DNA more maize chromosomes as a result of incomplete maize- hybridized only to a small extent to the same set of clones on chromosome elimination during early embryo development. a replica filter. Purified plasmids with Sau3A insertions, Partial self-fertility due to the production of unreduced ga- together with a group of maize repetitive DNA sequences in metes by these plants yielded disomic maize-chromosome- plasmids (see Materials and Methods), were cut with appro- n addition oat plants (2 5 42 1 2). The presence of maize priate restriction enzymes to release insertions. They were chromosomes was verified cytologically for each plant in the screened by blot hybridization with labeled maize and oat current study. The chromosome addition lines, the maize DNA. Clones showing a high signal similar to the signal of an parent lines Seneca 60 and A188, and the oat parent lines 18S–26S rDNA sequence were considered as highly repetitive. Starter-1 and Sun II were used for DNA extraction. From this screening, 15 plasmids from the Sau3A maize Isolation and Analysis of DNA. Leaves of 2- to 4-week-old genomic library, 6 Zpr clones (from Bennetzen), and the one seedlings grown in a growth chamber were used for nuclei 185-bp knob repeat clone were selected as highly repetitive isolation in pH 9.5 buffer according to the protocol of Liu and maize-specific nucleotide sequences. Insertions from these 22 Whitter (32). High molecular weight DNA was purified by selected plasmids were combined to form a composite multi- phenol extraction from nuclei after lysis of the nuclei suspen- probe.
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