An Informative Linkage Map of Soybean Reveals QTLs for Flowering Time, Leaflet Morphology and Regions of Segregation Distortion

Abstract

A genetic linkage map covering a large region of the genome with informative markers is essential for plant genome analysis, including identification of quantitative trait loci (QTLs), map-based cloning, and construction of a physical map. We constructed a soybean genetic linkage map using 190 F2 plants derived from a single cross between the soybean varieties Misuzudaizu and Moshidou Gong 503, based on restriction-fragment-length polymorphisms (RFLPs) and simple-sequence-repeat polymorphisms (SSRPs). This linkage map has 503 markers, including 189 RFLP markers derived from expressed sequence tag (EST) clones, and consists of 20 major linkage groups that may correspond to the 20 pairs of soybean chromosomes, covering 2908.7 cM of the soybean genome in the Kosambi function. Using this linkage map, we identified 4 QTLs--FT1, FT2, FT3, and FT4--for flowering time, the QTLs for the 5 largest principal components determining leaflet shape, 6 QTLs for single leaflet area, and 18 regions of segregation distortion. All 503 analyzed markers identified were located on the map, and almost all phenotypic variations in flowering time were explained by the detected QTLs. These results indicate that this map covers a large region of the soybean genome.

Genetic Redundancy in Soybean Photoresponses Associated With Duplication of the Phytochrome A Gene

“…None of the classical major genes controlling flowering and maturing times that have been mapped so far is located in LG O. Many QTL influencing the flowering and maturing times have been allocated to various LGs (Keim et al 1990;Mansur et al 1993;Lee et al 1996;Orf et al 1999;Tasma et al 2001;Yamanaka et al 2001;Chapman et al 2003;Watanabe et al 2004;Zhang et al 2004;Funatsuki et al 2005;Liu et al 2007). However, only a maturitycontrolling QTL has been located in LG O (Zhang et al 2004).…”

Map-Based Cloning of the Gene Associated With the Soybean Maturity Locus E3

“…Of these, the E1, E3, and E4 loci have been suggested to be related to photoperiod sensitivity under various light conditions (Saidon et al 1989;Cober et al 1996b;Abe et al 2003). In previous studies, using the same populations as in this study, three flowering-time quantitative trait loci (QTL)-FT1, FT2, and FT3 loci-were identified and considered to be identical with the maturity loci E1, E2, and E3, respectively (Yamanaka et al 2001;Watanabe et al 2004). Although many loci related to soybean flowering and maturity have been identified, and some candidate genes were recognized using near isogenic lines (NILs) (Tasma and Shoemaker 2003), most of the genes responsible for these loci have not yet been isolated except for the E4 gene.…”

Identification of quantitative trait loci for resistance against soybean sudden death syndrome caused by Fusarium tucumaniae

“…Misuzudaizu is a Japanese cultivar and Moshidou Gong 503 is a Chinese half-wild line, and populations derived from this cross contain many highly polymorphic DNA markers and have been used to discover numerous QTL for diverse characteristics (Yamanaka et al, , 2001Tajuddin et al, 2003;Watanabe et al, 2004). As expected, progenies of this cross were useful for identifying QTL for resistance against F. tucumaniae.…”

“…In order to confirm the homozygosis of RH1-73 (except for the region of RSDS1), the genotype data of the DNA markers used for previous map construction were utilized (Yamanaka et al, 2001;Watanabe et al, 2004). A segregating population of 42 individuals (F 10 ) was obtained by selfing of a single F 9 plant, which was heterozygous for the simple sequence repeat (SSR) marker Satt599, the nearest marker to RSDS1.…”

“…The PCR assay conditions were described by Hossain et al (2000). To analyze the genomic composition of line RH1-73, the genotype of this line was checked in each marker region by using the known genotypes of 526 markers in a F 2 map, and of 360 markers in a RIL map (Yamanaka et al, , 2001Watanabe et al, 2004).…”