TITLE

Genetic marker anchoring by six-dimensional pools for development of a soybean physical map

AUTHOR(S)
Xiaolei Wu; Guohua Zhong; Findley, Seth D.; Cregan, Perry; Stacey, Gary; Nguyen, Henry T.
PUB. DATE
January 2008
SOURCE
BMC Genomics;2008, Vol. 9, Special section p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Integrated genetic and physical maps are extremely valuable for genomic studies and as important references for assembling whole genome shotgun sequences. Screening of a BAC library using molecular markers is an indispensable procedure for integration of both physical and genetic maps of a genome. Molecular markers provide anchor points for integration of genetic and physical maps and also validate BAC contigs assembled based solely on BAC fingerprints. We employed a six-dimensional BAC pooling strategy and an in silico approach to anchor molecular markers onto the soybean physical map. Results: A total of 1,470 markers (580 SSRs and 890 STSs) were anchored by PCR on a subset of a Williams 82 BstY I BAC library pooled into 208 pools in six dimensions. This resulted in 7,463 clones (~1x genome equivalent) associated with 1470 markers, of which the majority of clones (6,157, 82.5%) were anchored by one marker and 1106 (17.5%) individual clones contained two or more markers. This contributed to 1184 contigs having anchor points through this 6-D pool screening effort. In parallel, the 21,700 soybean Unigene set from NCBI was used to perform in silico mapping on 80,700 Williams 82 BAC end sequences (BES). This in silico analysis yielded 9,835 positive results anchored by 4152 unigenes that contributed to 1305 contigs and 1624 singletons. Among the 1305 contigs, 305 have not been previously anchored by PCR. Therefore, 1489 (78.8%) of 1893 contigs are anchored with molecular markers. These results are being integrated with BAC fingerprints to assemble the BAC contigs. Ultimately, these efforts will lead to an integrated physical and genetic map resource. Conclusion: We demonstrated that the six-dimensional soybean BAC pools can be efficiently used to anchor markers to soybean BACs despite the complexity of the soybean genome. In addition to anchoring markers, the 6-D pooling method was also effective for targeting BAC clones for investigating gene families and duplicated regions in the genome, as well as for extending physical map contigs.
ACCESSION #
38122864

 

Related Articles

  • Identification of single nucleotide polymorphisms and haplotypes associated with yield and yield components in soybean ( Glycine max) landraces across multiple environments. Hao, Derong; Cheng, Hao; Yin, Zhitong; Cui, Shiyou; Zhang, Dan; Wang, Hui; Yu, Deyue // Theoretical & Applied Genetics;Feb2012, Vol. 124 Issue 3, p447 

    Genome-wide association analysis is a powerful approach to identify the causal genetic polymorphisms underlying complex traits. In this study, we evaluated a population of 191 soybean landraces in five environments to detect molecular markers associated with soybean yield and its components...

  • Seed and agronomic QTL in low linolenic acid, lipoxygenase-free soybean (Glycine max (L.) Merrill) germplasm. Reinprecht, Yarmilla; Poysa, Vaino W.; Kangfu Yu; Rajcan, Istvan; Ablett, Gary R.; Pauls, K. Peter // Genome;Dec2006, Vol. 49 Issue 12, p1510 

    Linolenic acid and seed lipoxygenases are associated with off flavours in soybean products. F5 recombinant inbred lines (RILs) from a cross between a low linolenic acid line (RG10) and a seed lipoxygenase-free line (OX948) were genotyped for simple sequence repeats (SSR), random amplified...

  • Glycine max non-nodulation locus rj1: a recombinogenic region encompassing a SNP in a lysine motif receptor-like kinase ( GmNFR1α). Lee, Woo; Jeong, Namhee; Indrasumunar, Arief; Gresshoff, Peter; Jeong, Soon-Chun // Theoretical & Applied Genetics;Mar2011, Vol. 122 Issue 5, p875 

    The rj1 mutation of soybean is a simple recessive allele in a single line that arose as a spontaneous mutation in a population; it exhibits non-nodulation with virtually all Bradyrhizobium and Sinorhizobium strains. Here, we described fine genetic and physical mapping of the rj1 locus on soybean...

  • Exact word matches in rice pseudomolecules. Liu, Shaolin; Tinker, Nicholas A.; Mather, Diane E. // Genome;Aug2006, Vol. 49 Issue 8, p1047 

    Using pseudomolecules of assembled genomic sequence, we computed the frequencies of 6 to 24 bp oligonucleotide (oligo) "words" across the genome of rice (Oryza sativa L. subsp. japonica). All oligos of 10 or fewer basepairs were repeated at least 12 times in the genome. The percentage of unique...

  • Multiplex single nucleotide polymorphism (SNP) assay for detection of soybean mosaic virus resistance genes in soybean. Shi, Ainong; Chen, Pengyin; Vierling, Richard; Zheng, Cuming; Li, Dexiao; Dong, Dekun; Shakiba, Ehsan; Cervantez, Innan // Theoretical & Applied Genetics;Feb2011, Vol. 122 Issue 2, p445 

    Soybean mosaic virus (SMV) is one of the most destructive viral diseases in soybean ( Glycine max). Three independent loci for SMV resistance have been identified in soybean germplasm. The use of genetic resistance is the most effective method of controlling this disease. Marker assisted...

  • A first linkage map of olive (Olea europaea L.) cultivars using RAPD, AFLP, RFLP and SSR markers. la Rosa, R.; Angiolillo, A.; Guerrero, C.; Pellegrini, M.; Rallo, L.; Besnard, G.; Bervillé, A.; Martin, A.; Baldoni, L. // Theoretical & Applied Genetics;May2003, Vol. 106 Issue 7, p1273 

    The first linkage map of the olive (Olea europaea L.) genome has been constructed using random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphisms (AFLP) as dominant markers and a few restriction fragment length polymorphisms (RFLP) and simple-sequence repeats (SSR) as...

  • Fine mapping of theFT1locus for soybean flowering time using a residual heterozygous line derived from a recombinant inbred line. Yamanaka, Naoki; Watanabe, Satoshi; Toda, Kyoko; Hayashi, Masaki; Fuchigami, Hiroki; Takahashi, Ryoji; Harada, Kyuya // Theoretical & Applied Genetics;Feb2005, Vol. 110 Issue 4, p634 

    Fine-mapping of loci related to complex quantitative traits is essential for map-based cloning. A residual heterozygous line (RHL) of soybean (Glycine max) derived from a recombinant inbred line (RIL) was used for fine-mappingFT1, which is a major quantitative trait locus (QTL) responsible for...

  • Molecular Mapping of the Male-Sterile, Female-Sterile Mutant Gene (st8) in Soybean. Kato, K. K.; Palmer, R. G. // Journal of Heredity;Sep/Oct2003, Vol. 94 Issue 5, p425 

    Soybean male-sterile, female-sterile mutant genes have been identified by genetic and cytological studies. The St8 gene has been identified as an asynaptic mutation resulting in male and female sterility. This mutant gene was derived from a gene-tagging study using the soybean w4-mutabte line....

  • Evaluation of High-Resolution Melting for Gene Mapping in Rice. Li, Jinshan; Wang, Xuming; Dong, Ruixian; Yang, Yong; Zhou, Jie; Yu, Chulang; Cheng, Ye; Yan, Chengqi; Chen, Jianping // Plant Molecular Biology Reporter;Dec2011, Vol. 29 Issue 4, p979 

    In this study, high-resolution melting (HRM) analysis was evaluated for gene mapping in rice with sequence-tagged site (STS) and simple sequence repeat (SSR) markers. A total of 103 out of 353 normal STS and SSR markers revealed polymorphic melting curves among the parental genotypes, and 12 of...

Share

Read the Article

Courtesy of NEW JERSEY STATE LIBRARY

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics