**7. References**


locus precisely. We developed manual large-scale genotyping of seeds, in which powdered cotyledon was obtained by drilling a hole on the surface of seed without any damage to the embryonic axis. Recombinants carrying crossovers in the target region were selected based on genotypes of DNA markers around the region. Genotypes of the flowering time locus of recombinants were determined by progeny test and identified the cosegregated region based on these genotypes. Physical contigs were constructed with BAC/TAC clones screened by SCAR markers converted from these AFLP fragments. By sequencing the BAC contig covering the cosegregated region, we identified the candidate genes. Confirmation of the responsible gene was performed by investigation of association between natural and induced variation of the candidate gene structures and flowering time. Mutant screening was carried out with TILLING using X-ray irradiated or EMS treated mutant libraries. The interactions between the identified genes were analyzed using several NILs and segregating population for the *E* loci. A tentative flowering time network in soybean was proposed taking into consideration the possible functions of responsible genes for *E1*, *E2*, *E3* and *E4* loci and *GmFT*s. Further characterization of other *E* loci is necessary to reveal the molecular

Recently, soybean genome sequence has been reported (Shumutz et al., 2010) and a large number of SSR (Song et al., 2010) and SNP (Hyten et al., 2010a; Lam et al., 2010) markers has been developed. New high-throughput sequencing technologies, and multiplex assays for genotyping a huge number of SNPs have become available. These technologies and information will accelerate the identification of responsible genes for agriculturally important loci. But methods and materials to precisely locate the target loci in the genome are still important. Moreover, variation of regional genome structure and gene content (Kim et al., 2010 ; William et al., 2010; Xia et al., unpublished) will need the sequencing of genome

We thank Dr. S. Sato and Dr. S. Tabata at the Kazusa DNA Research Institute, for nucleotide sequencing of BAC and TAC clones, Dr. H. Kanamori at the Institute of the Society for Techno-innovation of Agriculture and Dr. Y. Katayose at the National Institute of Agrobiological Sciences for nucleotide sequencing of the *E3* genes, and Dr. R. L. Nelson at the U. S. Department of Agriculture, University of Illinois, for supplying seeds of the Harosoy, Harosoy-*E1,* -*E2* and -*e3*. This study was partly supported by the Programs for the Promotion of Basic Research Activities for Innovative Biosciences, Research Fellowships from the Japan Society for the Promotion of Science for Young Scientists (17-2554), a grant from Ministry of Agriculture, Forestry and Fisheries of Japan (Genomics for Agricultural

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**4** 

*1,3USA 2Egypt* 

**Changes in the Expression of Genes in Soybean** 

Benjamin F. Matthews1, Heba M.M. Ibrahim1,2 and Vincent P. Klink3 *1United States Department of Agriculture, Agricultural Research Service, Soybean* 

*3Department of Biological Sciences, Mississippi State University, Mississippi State, MS* 

Plant parasitic nematodes cause severe damage to plants and are responsible for billions of dollars of losses worldwide (Koenning et al. 2007). Soybean cyst nematode (SCN; *Hederodera glycines*; Fig. 1a ) and root-knot nematode (RKN; *Meloidogyne* spp.; Fig. 1b) are sedentary obligate parasites of plants. SCN is the major pest of soybean and causes an estimated one billion dollars in losses annually in the US (Wrather & Koenning 2006). RKN is a major pest of vegetables and can become a serious problem on soybean, especially on edible soybean planted in areas used to grow vegetables (Adegbite & Adesiyan 2005). The genera *Meloidogyne* is widespread and is considered, economically and agriculturally, as a very important group of plant pathogens. The host range of *Meloidogyne* is very wide as it attacks almost all plant species (Sasser 1980). Both SCN and RKN are sedentary endoparasites and they cause dramatic morphological and physiological changes in plant cells while inflicting severe decreases on yield. Chemical methods of nematode control are costly and can damage the environment, especially with contamination of ground water. Therefore, the preferred method of nematode control is the use of resistant or tolerant varieties, when available. Unfortunately, a plant with resistance to one population of nematode is often susceptible to a different population due to the wide genetic variation of nematode

When a plant parasitic nematode infects a plant root, the nematode and the plant enters an intricate interactive relationship with the host that is attempting to inhibit nematode development, while the nematode's goal is to develop and reproduce. The life cycle of SCN and cellular responses of soybean to SCN infection have been documented and reviewed extensively (Bird & Koltai 2000; Endo 1964; Endo, 1965; Endo, 1992; Goverse *et al*. 2000; Lilley *et al*. 2005; Mitchum & Baum 2008; Niblack *et al*. 2006; Williamson & Gleason 2003; Abad & Williamson 2010; Klink *et al.* 2011a). The SCN egg can be found in soil and within the mature female. The second stage juvenile (J2) hatches from the egg, searches for a root of a plant host, penetrates the root epidermis, and migrates intracellularly, using its stylet and

enzyme secretions to disrupt cells and force its way toward the vascular tissue.

**1. Introduction** 

populations.

**1.1 Plant nematodes** 

**Roots Infected by Nematodes** 

*Genomics and Improvement Laboratory, Beltsville, 1,2Genetics Department, Cairo University, Cairo,* 

Yano, M., Katayose, Y., Ashikari, M., Yamanouchi, U., Monna, L., Taguchi, F., Baba, T., Yamamoto, K., Umehara, Y., Nagamura, Y. & Sasaki, T. (2000). *Hd1*, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene *CONSTANS*. *The Plant Cell*, Vol. 12, pp. 2473-2483
