The first genetic transcript map of the soybean genome was created by mapping one SNP in each of 1141 genes in one or more of three recombinant inbred line mapping populations, thus providing a picture of the distribution of genic sequences across the mapped portion of the genome. Singlenucleotide polymorphisms (SNPs) were discovered via the resequencing of sequence-tagged sites (STSs) developed from expressed sequence tag (EST) sequence. From an initial set of 9459 polymerase chain reaction primer sets designed to a diverse set of genes, 4240 STSs were amplified and sequenced in each of six diverse soybean genotypes. In the resulting 2.44 Mbp of aligned sequence, a total of 5551 SNPs were discovered, including 4712 single-base changes and 839 indels for an average nucleotide diversity of u ¼ 0.000997. The analysis of the observed genetic distances between adjacent genes vs. the theoretical distribution based upon the assumption of a random distribution of genes across the 20 soybean linkage groups clearly indicated that genes were clustered. Of the 1141 genes, 291 mapped to 72 of the 112 gaps of 5-10 cM in the preexisting simple sequence repeat (SSR)-based map, while 111 genes mapped in 19 of the 26 gaps .10 cM. The addition of 1141 sequence-based genic markers to the soybean genome map will provide an important resource to soybean geneticists for quantitative trait locus discovery and map-based cloning, as well as to soybean breeders who increasingly depend upon marker-assisted selection in cultivar improvement.
In the 1980s, DNA‐based molecular markers were identified as having the potential to enhance corn (Zea mays L.) breeding. Research has demonstrated the advantage of using molecular markers for selection of simply inherited traits, however only a few studies have evaluated the potential to enhance genetic gain for quantitative traits. In the late 1990s, Monsanto decided to implement marker assisted selection for quantitative traits in our global plant breeding programs. We built genotyping systems and information tools and developed marker assisted methodologies that increased the mean performance in elite breeding populations.
A population of Arabidopsis thaliana recombinant inbred lines was constructed and used to develop a high-density genetic linkage map containing 252 random amplified polymorphic DNA markers and 60 previously mapped restriction fragment length polymorphisms. Linkage groups were correlated to the classical genetic map by inclusion of nine phenotypic markers in the mapping cross. We also applied a technique for local mapping that allows targeting of markers to a selected genome region by pooling DNA from recombinant inbred lines based on their genotype. We conclude that random amplified polymorphic DNAs, used in coglunction with a recombinant inbred population, can facilitate the genetic and physical characterization of the Arabidopsis genome and that this method is generally applicable to other organisms for which appropriate populations either are available or can be developed.The crucifer Arabidopsis thaliana is a useful system for basic studies in plant molecular genetics due to its relatively small genome size, small amounts of dispersed repetitive DNA, and rapid generation time (1). These attributes have made Arabidopsis an attractive model system for the analysis of genome organization and the development and use of technology to clone genes known only through their genetic map position.High-density genetic maps based upon DNA markers can provide starting points for chromosome walking experiments. Markers closely linked to a mutation of interest can reduce the amounts of DNA to be cloned and help establish the direction of the chromosome walk. Restriction fragment length polymorphisms (RFLPs) have been used as markers to construct genetic maps (2) and as starting points for chromosome walking (3). To date, two different RFLP maps have been reported in Arabidopsis (4, 5).Recently another class of genetic markers [random amplified polymorphic DNAs (RAPDs)] has been described (6, 7), which relies on the observation that a single oligonucleotide primer, of arbitrary nucleotide sequence, will direct the amplification of discrete loci (for a more detailed description of this method, see ref. 8). We report here the use of RAPD markers to construct a genetic map of A. thaliana. This map has been constructed with unprecedented speed by using RAPD markers and a recombinant inbred (RI) population. For many mapping purposes RI populations are superior to F2 or backcross populations because they constitute a permanent population in which segregation is fixed (9). Additional markers scored on the same RI population are automatically integrated with the existing map, making map information cumulative (9).Near-isogenic lines have been used to target RFLP (10) or RAPD (11) markers to specific segments of a genome. However, construction of near-isogenic lines is time consuming, and unlinked portions of the donor genome remain even after several crosses to the recurrent parent (12). Pooling DNA based on phenotype has been used as a means of either identifying additional RFLP loci (13) or mapping existing RFLP loci (14) ...
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.