One of the overarching goals of soybean breeding is to develop lines that combine increased yield with improved quality characteristics. High-density-marker QTL mapping can serve as an effective strategy to identify novel genomic information to facilitate crop improvement. In this study, we genotyped a recombinant inbred line (RIL) population (Zhonghuang 24 × Huaxia 3) using a restriction-site associated DNA sequencing (RAD-seq) approach. A high-density soybean genetic map was constructed and used to identify several QTLs that were shown to influence six yield-related and two quality traits. A total of 47,472 single-nucleotide polymorphisms (SNPs) were detected for the RILs that were integrated into 2639 recombination bin units, with an average distance of 1.00 cM between adjacent markers. Forty seven QTLs for yield-related traits and 13 QTLs for grain quality traits were found to be distributed on 16 chromosomes in the 2 year studies. Among them, 18 QTLs were stable, and were identified in both analyses. Twenty six QTLs were identified for the first time, with a single QTL (qNN19a) in a 56 kb region explaining 32.56% of phenotypic variation, and an additional 10 of these were novel, stable QTLs. Moreover, 8 QTL hotpots on four different chromosomes were identified for the correlated traits. With RAD-sequencing, some novel QTLs and important QTL clusters for both yield-related and quality traits were identified based on a new, high-density bin linkage map. Three predicted genes were selected as candidates that likely have a direct or indirect influence on both yield and quality in soybean. Our findings will be helpful for understanding common genetic control mechanisms of co-localized traits and to select cultivars for further analysis to predictably modulate soybean yield and quality simultaneously.

Multidrug and toxic compound extrusion (MATE) transporters, which exist widely in plants, function as crucial regulators in plant resistance to aluminum (Al) toxicity by inducing citrate efflux. However, the functions of most MATE family members in soybean (Glycine soja) remain to be elucidated. Expression pattern analysis showed that GsMATE was constitutively expressed in different soybean organs, with the highest level in root compared with those in stem, leaf and cotyledon. In addition, Al stress induced expression of GsMATE in soybean. Temporal analysis indicated that GsMATE expression was greatly enhanced by increasing concentrations of aluminum [Al3+] after short exposure, reaching the high levels detected in the BW69 (Al-resistant) and the JW81 (Al-sensitive) lines of Glycine soja of wild soybean at 6 h and 8 h, respectively. Furthermore, transient GsMATE expression in Arabidopsis protoplasts showed that GsMATE protein localized to the plasma membrane. Overexpression of GsMATE on an Arabidopsis columbia-0 (Col-0) background resulted in increased Al tolerance in transgenic plants. Analysis of hematoxylin staining showed that the roots of GsMATE transgenic lines were stained less intensely than those of the wild-type exposured to the same AlCl3 concentrations. Therefore, GsMATE enhanced the resistance of transgenic plants to Al toxicity by reducing Al accumulation in Arabidopsis roots. In summary, our results indicate that GsMATE is responsive to aluminum stress and may participate in the regulation of sensitivity to Al toxicity in Arabidopsis. In addition, the GsMATE protein is an Al-induced citrate transporter of the MATE family and exerts an essential role in Al tolerance in Glycine soja.

The different leaf type associated traits of soybean (Glycine max L.) including leaf area, leaf length, leaf width, leaf shape and petiole length are considered to be associated with seed yield. In order to identify quantitative trait loci (QTLs) affecting leaf type traits, two advanced recombinant inbred line (RIL, ZH, Zhonghuang 24 × Huaxia 3; GB, Guizao 1 × Brazil 13) populations were introduced to score phenotypic values in plants across nine different environments (years, seasons, locations and soybean growth stages). Two restriction site-associated DNA sequencing (RAD-seq) based high-density genetic linkage maps with an average distance of 1.00 centimorgan (cM) between adjacent bin markers were utilized for QTL fine mapping. Correlation analysis showed that most of the traits were correlated with each other and regulated both by hereditary and environmental factors. A total of 190 QTLs were identified for leaf type associated traits in the two populations, of which 14 loci were found to be environmentally stable. Moreover, these detected QTLs were categorized into 34 QTL hotspots, and four important QTL hotspots with phenotypic variance ranging from 3.89–23.13% were highlighted. Furthermore, Glyma04g05840, Glyma19g37820, Glyma14g07140 and Glyma19g39340 were predicted in the intervals of the stable loci and important QTL hotspots for leaf type traits by adopting Gene Ontology (GO) enrichment analysis. Our findings of the QTLs and the putative genes will be beneficial to gain new insights into the genetic basis for soybean leaf type traits and may further accelerate the breeding process for reasonable leaf type soybean.

Astragalus sinicus L. (milk vetch), one of the most widespread green manure species, is widely planted in the temperate zone. Eleusine indica L. (goosegrass), a serious annual weed in the world, has evolved resistance to some non-selective herbicides. The use of milk vetch as green manure for weed control in paddy fields was proposed. Aqueous extracts of milk vetch are known to exert a different level of phytotoxicity on weeds and crops. Phytotoxic substances contained in green manure were released into the soil by leaching at the initial stage and decomposition at the later stage after the return of green manure. Considering the need for searching new sustainable strategies for weed control, a question arises: “if milk vetch could be applied in goosegrass control, which stage is the most important to control goosegrass after milk vetch returned to the field, and at the same time, will the subsequent crop, corn (Zea mays L.), be affected by the side effects from milk vetch phytotoxicity?” In this study, the potential of milk vetch for goosegrass control was approached by repeated laboratory experiments, which include the aqueous extract experiment, decomposed experiment, and pot experiment. The effects of milk vetch returning to the field on maize were simulated by a pot experiment. The extract of milk vetch could significantly inhibit the germination of goosegrass at 2% concentration, and the inhibition enhanced with the increase of concentration. In the decomposed liquid experiment, decay time within 15 days, with the increase of decay days or concentration, goosegrass inhibition effect of decomposed liquid was enhanced. When decay time was more than 15 days, the inhibition ability of the decomposed liquid to goosegrass decreased. According to the RI accumulated value, aqueous extract and decomposed liquid have a “hormesis effect” on the germination and growth of goosegrass. Pot experiment proved that the addition of 1–10% (w/w) of milk vetch significantly reduced the germination and growth of goosegrass. On the contrary, the comprehensive analysis showed that the participation of milk vetch was conducive to the growth of corn. Our results constitute evidence that the incorporation of milk vetch into the soil could be a feasible practice to reduce weed infarctions in the corn-based cropping system.