Quantitative trait loci for callus initiation and totipotency in maize (Zea mays L.).

Induction of embryogenic callus in culture is an important step in plant transformation procedures, but response is genotype specific and the genetics of the trait are not well understood. Quantitative trait loci (QTL) were mapped in a set of 126 recombinant inbred lines (RILs) of inbred H99 (high Type I callus response) by inbred Mo17 (low Type I callus response) that were evaluated over two years for Type I callus response. QTL were observed in a total of eleven bins on eight chromosomes, including eight QTL with main effects and three epistatic interactions. Many of the QTL were mapped to the same or bordering chromosomal bins as candidate genes for abscisic acid metabolism, indicating a possible role for the hormone in the induction of embryogenic callus, as has previously been indicated in microspore embryo induction. Further examinations of allelic variability for known candidate genes located near the observed QTL could be useful for expanding the understanding of the genetic basis of induction embryogenic callus. The QTL observed herein could also be used in a marker assisted selection (MAS) program to improve the response of agronomically useful inbreds, but only if the resources required for MAS are lower than those required for phenotypic selection.

Development of an integrated laboratory information management system for the maize mapping project.

MOTIVATION: The development of an integrated genetic and physical map for the maize genome involves the generation of an enormous amount of data. Managing this data requires a system to aid in genotype scoring for different types of markers coming from both local and remote users. In addition, researchers need an efficient way to interact with genetic mapping software and with data files from automated DNA sequencing. They also need ways to manage primer data for mapping and sequencing and provide views of the integrated physical and genetic map and views of genetic map comparisons. RESULTS: The MMP-LIMS system has been used successfully in a high-throughput mapping environment. The genotypes from 957 SSR, 1023 RFLP, 189 SNP, and 177 InDel markers have been entered and verified via MMP-LIMS. The system is flexible, and can be easily modified to manage data for other species. The software is freely available. AVAILABILITY: To receive a copy of the iMap or cMap software, please fill out the form on our website. The other MMP-LIMS software is freely available at http://www.maizemap.org/bioinformatics.htm.

Polymorphism of PCR-based markers targeting exons, introns, promoter regions, and SSRs in maize and introns and repeat sequences in oat.

Sequence databases could be efficiently exploited for development of DNA markers if it were known which gene regions reveal the most polymorphism when amplified by PCR. We developed PCR primer pairs that target specific regions of previously sequenced genes from Avena and Zea species. Primers were targeted to amplify 40 introns, 24 exons, and 23 promoter regions within 54 maize genes. We surveyed 48 maize inbred lines (previously assayed for simple-sequence repeat (SSR) polymorphism) for amplification-product polymorphism. We also developed primers to target 14 SSRs and 12 introns within 18 Avena genes, and surveyed 22 hexaploid oat cultivars and 2 diploid Avena species for amplification-product polymorphism. In maize, 67% of promoter markers, 58% of intron markers, and 13% of exon markers exhibited amplification-product polymorphisms. Among polymorphic primer pairs in maize, genotype diversity was highest for SSR markers (0.60) followed by intron markers (0.46), exon markers (0.42), and promoter markers (0.28). Among all Avena genotypes, 64% of SSR markers and 58% of intron markers revealed polymorphisms, but among the cultivars only, 21% of SSR markers and 50% of intron markers were polymorphic. Polymorphic-sequence-tagged sites for plant-breeding applications can be created easily by targeting noncoding gene regions.

Genetics of alpha-amylases in hexaploid oat species.

The inheritance of alpha-amylases was studied in six F2 populations of hexaploid oats (Avena sativa, A. byzantina, A. fatua, A. sterillis) using polyacrylamide gel electrophoresis. A total of 22 loci was identified and described. Three main linkages of four or five loci each and an additional two pairs of linked loci were detected. It seems likely that the three main linkage groups represent homeologous chromosomes. Matching of alpha-amylase profiles of hexaploid (AACCDD), tetraploid (AACC), and diploid (AA) species was made to assign the linkage groups to particular subgenomes in the hexaploid oat. It was proposed that Linkage 1 (Amy12-Amy10-1-Amy4-Amy13-Amy11) belongs to the D-subgenome; Linkage 2 (Amy10-2, Amy9-Amy8-Amy6) belongs to the A-subgenome; and Linkage 3 (Amy7-Amy3-Amy5-Amy2) belongs to the C-subgenome of the hexaploid oat. The "malt" and "green" alpha-amylases in hexaploid and tetraploid oats have been identified. Isozymes of "green" alpha-amylase were lower in electrophoretic mobility than other isozymes and were governed by loci assigned to the A- and D-subgenomes.

Inheritance and linkage relationships of seed peroxidase loci in hexaploid oat (Avena sativa L.).

Polyacrylamide gel electrophoresis has been used to investigate the inheritance and linkage relationships between anodal (PXA) and cathodal (PXC) seed peroxidases in hexaploid oat (Avena sativa L.). A total of 12 seed peroxidase loci (5 loci of PXA and 7 loci of PXC) were identified in three crosses. Only two Pxc loci (Pxc5 and Pxc7) were not linked to any peroxidase loci; the others were scored in three linkage groups. The order of the three loci assigned to one of the linkage groups was Pxc1-Pxa5-Pxc2. The order of loci in the other two linkages were Pxc4-Pxa1-Pxa3 and Pxc3-Pxa4-Pxa2. Also, the Pxc6 locus was shown to be linked to the Pxc3 locus. Considering that A. sativa is an allohexaploid, it can be proposed that the three peroxidase linkages represent homoeologous chromosomes.