Fine mapping of quantitative trait loci for seed size traits in soybean

Quantitative trait loci (QTL) for soybean seed size traits were stably detected in marker interval Satt640–Satt422 (approximately 25.5 cM) on chromosome 6 in our previous studies. However, little is known about whether these loci are derived from one major QTL or multiple linked QTL. To resolve this issue, 504 recombinant inbred lines (RILs, F7:8) from the direct and reciprocal crosses of Lishuizhongzihuang with Nannong493-1 and 265 cultivars in China were used to fine-map the QTL. Inserted in the target interval were 22 simple sequence repeat markers in the RILs and 160 single nucleotide polymorphism markers in the cultivar population. As a result, seed length was associated with markers X40, X53, X83–X85 and X92, seed width was associated with markers X40, X53 and X83–X85, seed thickness was associated with markers X53, X83–X85 and X92, and 100-seed weight was associated with markers X40, X53, X83–X85 and X90–X92. This means that at least two common QTL among seed length, width and thickness were observed, and that the QTL for 100-seed weight was derived from those for its component traits, indicating their similar genetic bases. Using annotation project database and gene expression profile data, eight candidate genes were predicted. Of these genes, Glyma06g07200 (SNP097), Glyma06g07400, Glyma06g07400, Glyma06g07400 (SNP111), Glyma06g09650 (SNP332), Glyma06g08830 and Glyma06g08860 (X90–X92) may be involved in the process of seed development, and Glyma06g08800 (X83–X85) encodes ARM repeat superfamily protein, which is involved in the ubiquitination pathway regulating the development of seed size.