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Background  The root system provides nutrient absorption and is closely related to abiotic stress tolerance, but it is difficult to study the roots under field conditions. This study was conducted to identify quantitative trait loci (QTL) associated with primary root length (PRL) during soybean seedling growth in hydroponic conditions. A total of 103 F 7  recombinant inbred lines (RILs) derived from a cross between K099 (short primary root) and Fendou 16 (long primary root) were used to identify QTL for PRL in soybean. The RIL population was genotyped with 223 simple sequence repeats markers covering 20 chromosomes. Phenotyping for primary root length was performed for 3-weeks plants grown in hydoponic conditions. The identified QTL was validated in near isogenic lines and in a separate RIL population.    Results  QTL analysis using inclusive composite interval mapping method identified a major QTL on Gm16 between SSR markers Sat_165 and Satt621, explaining 30.25 % of the total phenotypic variation. The identified QTL,  qRL16.1 , was further confirmed in a segregating population derived from a residual heterozygous line (RHLs-98). To validate  qRL16.1  in a different genetic background, QTL analysis was performed in another F 6  RIL population derived from a cross between Union (medium primary root) and Fendou 16, in which a major QTL was detected again in the same genomic region as  qRL16.1 , explaining 14 % of the total phenotypic variation for PRL. In addition, the effect of  qRL16.1  was confirmed using two pair of near-isogenic lines (NILs). PRL was significantly higher in NILs possessing the  qRL16.1  allele from Fendou 16 compared to allele from K099.    Conclusions  The  qRL16.1  is a novel QTL for primary root length in soybean which provides important information on the genetic control of root development. Identification of this major QTL will facilitate positional cloning and DNA marker-assisted selection for root traits in soybean.

Mapping and validation of a major QTL for primary root length of soybean seedlings grown in hydroponic conditions