Genetic, Physical, and Informatics Resources for Maize. On the Road to an Integrated Map

Cone, Karen C.; McMullen, Michael D.; Bi, I. Vroh; Davis, Gregory L.; Yim, Young Sun; Gardiner, Jack M.; Polacco, Mary L.; Sánchez-Villeda, Héctor; Fang, Zhiwei; Schroeder, Steven G.; Havermann, Seth A.; Bowers, John E.; Paterson, Andrew H.; Soderlund, Carol; Engler, Fred; Wing, Rod A.; Coe, E. H.

doi:10.1104/pp.012245

Cited by 108 publications

(84 citation statements)

References 20 publications

(13 reference statements)

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“…The final map comprising all 3,610 markers was calculated based on the ''neighbours'' map approach described by Cone et al (2002). A new improved version of JoinMap based on a faster algorithm (Jansen et al 2001) was kindly provided by Dr. van Ooyen (www.kyazma.nl).…”

Section: Construction Of the Ssr Consensus Mapmentioning

confidence: 99%

“…Subsequently, with the corrected segregation data and with correct bridge markers, the final consensus map was calculated following the ''neighbours'' map approach described by Cone et al (2002). In order to allow comparison of this map with other genetic maps, the barley BIN markers also have been integrated (Kleinhofs and Graner 2001;Marcel et al 2007).…”

Section: Accuracy Of the Consensus Ssr Mapmentioning

confidence: 99%

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A high density barley microsatellite consensus map with 775 SSR loci

Varshney

Marcel

Ramsay³

et al. 2007

Theor Appl Genet

303

234

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Section: Construction Of the Ssr Consensus Mapmentioning

confidence: 99%

Section: Accuracy Of the Consensus Ssr Mapmentioning

confidence: 99%

A high density barley microsatellite consensus map with 775 SSR loci

Varshney

Marcel

Ramsay³

et al. 2007

Theor Appl Genet

303

234

View full text Add to dashboard Cite

“…These noncontiguous genomic positions are consistent with the previously mapped loci in BSSS53. We also compared BAC clones to the maize-mapping project (12). Each clone set matched the corresponding finger printed contigs (FPC) (FPC no.…”

Section: Isolation Of Z1cmentioning

confidence: 99%

Gene expression of a gene family in maize based on noncollinear haplotypes

Song

Messing

2003

Proc. Natl. Acad. Sci. U.S.A.

243

215

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Genomic regions of nearly every species diverged into different haplotypes, mostly based on point mutations, small deletions, and insertions that do not affect the collinearity of genes within a species. However, the same genomic interval containing the z1C gene cluster of two inbred lines of Zea mays significantly lost their gene collinearity and also differed in the regulation of each remaining gene set. Furthermore, when inbreds were reciprocally crossed, hybrids exhibited an unexpected shift of expression patterns so that ''overdominance'' instead of ''dominance complementation'' of allelic and nonallelic gene expression occurred. The same interval also differed in length (360 vs. 263 kb). Segmental rearrangements led to sequence changes, which were further enhanced by the insertion of different transposable elements. Changes in gene order affected not only z1C genes but also three unrelated genes. However, the orthologous interval between two subspecies of rice (not rice cultivars) was conserved in length and gene order, whereas changes between two maize inbreds were as drastic as changes between maize and sorghum. Given that chromosomes could conceivably consist of intervals of haplotypes that are highly diverged, one could envision endless breeding opportunities because of their linear arrangement along a chromosome and their expression potential in hybrid combinations (''binary'' systems). The implication of such a hypothesis for heterosis is discussed. z1C zein gene cluster ͉ heterosis ͉ genomic organization ͉ overdominance ͉ transposition C orn or Zea mays is one of the most important crops in the world.Although wheat and rice surpass it as a staple and in acreage, no crop rivals its total grain yield and the diversity of its uses as processed food, for animal feed and sweetener in soft drinks, and its industrial applications such as fuel and adhesives. The preference of corn over other grains or legumes for such applications is because of the unusual properties of hybrids. When distant inbred lines are crossed, the resulting hybrids exhibit an unusual vigor (heterosis) that results in higher yields per acre than the parental lines would produce themselves (1). The premium exercised for the breeding of steadily improved maize inbreds customized for different geographic areas has generated a huge enterprise worldwide, particularly in the United States, yet the underlying molecular mechanism for hybrid vigor is not well understood. To decide between two models explaining ''dominance complementation'' or ''overdominance'' of heterozygotes, it will therefore be necessary to compare not only the genomic architecture of genes within an interval of several hundred kilobases but also the expression of these genes of two parental inbreds and their reciprocal hybrids.The fact that some gene families are highly clustered within such lengthy intervals rather than spread over the entire genome is the springboard for our study. One such interval encodes the 22-kDa ␣-zein storage proteins. These proteins accumulate d...

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“…The Y1 gene containing BAC contig was identified in the Mo17 physical map (Bailin Li, personal communication) on the basis of overgo probe hybridization data (11). Low copy or genic sequences were identified in the shotgun sequence of BAC 4 and in BAC-end sequences of BACs within the Y1-containing Mo17 contig ( Fig.…”

Section: Shotgun Sequencing Of Y1-containing Bacterial Artificial Chrmentioning

confidence: 99%

Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep

Palaisa

Morgante

Tingey

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

204

153

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Both yellow and white corn occurs among ancestral open pollinated varieties. More recently, breeders have selected yellow endosperm variants of maize over ancestral white phenotypes for their increased nutritional value resulting from the up-regulation of the Y1 phytoene synthase gene product in endosperm tissue. As a result, diversity within yellow maize lines at the Y1 gene is dramatically decreased as compared to white corn. We analyzed patterns of sequence diversity and linkage disequilibrium in nine low copy regions located at varying distances from the Y1 gene, including a homolog of the barley Mlo gene. Patterns consistent with a selective sweep, such as significant associations of informative single-nucleotide polymorphisms with endosperm color phenotype, linkage disequilibrium, and significantly reduced diversity within the yellow endosperm haplotypes, were observed up to 600 kb downstream of Y1, whereas the upstream region showed a more rapid recovery. The starch branching enzyme 1 (sbe1) gene is the first region downstream of Y1 that does not have a highly conserved haplotype in the yellow endosperm germplasm.S elective forces acting on allelic variants of genes have a profound effect on local levels of genetic diversity and linkage disequilibria (LD). Positive directional selection leads to reduced variability and increased LD in the respective region (1-6), and the so-called selective sweep regions provide clues to genes that have been subjects of evolutionary forces as well as selection by humans. Recently, Clark et al. (7) characterized a selective sweep in the promoter region of teosinte branched1 (tb1). The sweep extends 60-90 kb upstream of the gene and is indicative of the gene's role in the domestication of maize from teosinte between 6,000 and 10,000 years ago.The maize Y1 gene on chromosome 6 has undergone recent selection for endosperm color phenotype. A recent study (8) uncovered a dramatic reduction in diversity at this gene for the yellow endosperm maize inbred lines only, over the entire 6-kb gene region. This footprint of selection was characterized by a conserved yellow endosperm haplotype at the 5Ј end of the gene with evidence of recombination toward the 3Ј end. Strong haplotype conservation at the 5Ј end is suggestive of the location of the causal variant associated with the gain-of-function mutation to yellow endosperm and may be indicative of further extension of the selective sweep in the 5Ј direction. The presence of recombinants in the 3Ј UTR region, however, suggested that the extent of the selective sweep may be limited downstream of the coding region.The white endosperm lines did not show characteristics of a selective sweep (8), despite the fact that the white endosperm phenotype is also a target of selection due to human taste preference (9). This is because white is the predicted ancestral state of the gene (John Doebley, personal communication), and thus multiple haplotypes are associated with the white endosperm phenotype.Understanding the boundaries of the selective ...

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Genetic, Physical, and Informatics Resources for Maize. On the Road to an Integrated Map

Cited by 108 publications

References 20 publications

A high density barley microsatellite consensus map with 775 SSR loci

A high density barley microsatellite consensus map with 775 SSR loci

Gene expression of a gene family in maize based on noncollinear haplotypes

Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep

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