Phosphorous (P) deficiency of soils is one of the major yield-limiting factors worldwide. The most economic and efficient strategy for sustainable agriculture is to breed varieties with P-deficiency tolerance. The objective of this study was to map QTLs for P-deficiency tolerance in soybean, which could lay theoretical foundation on molecular marker assisted selection in soybean with improved P-deficiency tolerance. A population consisting of 180 F2:3 lines derived from P-deficiency sensitive soybean variety Kenjian4 and P-deficiency tolerant soybean variety Fengshou24 was developed for mapping QTLs for P-deficiency tolerance. Five agronomic traits of plant height (HT), length of main root (RL), ratio of weight of dry root (DRW) to weight of dry shoot (DSW) (R/S), chlorophyll content in leaves(CHL), and phosphorus uptake of the whole plant (PC) were investigated at seedling stage under P deficiency(-P) and sufficiency(+P) condition in pot trial. All traits segregated continuously in the population under the two conditions. A genetic linkage map consisting of 15 linkage groups was constructed using 86 polymorphic SSR primers. The genetic map spanned 1510.3 cM in length with an average interval of 16.04 cM between adjacent markers. The linkage groups in our study ranged from 211.2 cM in MLG A1 to 10.8 cM in MLG A1, and the number of markers ranged from 10 markers in MLG D1a, MLG D2 and MLG D1b to 2 markers in MLG N. A total of six QTLs associated with P-deficiency tolerance was detected and mapped on MLG D1a, MLG F and MLG O linkage groups for the five traits of HT, LR, CHL, R/S, and PC. Among them, two QTLs had LOD score more than three. All the QTLs explained more than 10% of the total variation, and the additive gene of five QTLs came from Kenjian 4 and that of one QTL from Fengshou 24. An average of 1-2 QTLs were detected for traits related to P-deficiency tolerance using composite interval mapping.
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