Globally, soybean is a major protein and oil crop. Enhancing our understanding of the soybean domestication and improvement process helps boost genomics-assisted breeding efforts. Here we present a genome-wide variation map of 10.6 million single-nucleotide polymorphisms and 1.4 million indels for 781 soybean individuals which includes 418 domesticated (Glycine max), 345 wild (Glycine soja), and 18 natural hybrid (G. max/G. soja) accessions. We describe the enhanced detection of 183 domestication-selective sweeps and the patterns of putative deleterious mutations during domestication and improvement. This predominantly selfing species shows 7.1% reduction of overall deleterious mutations in domesticated soybean relative to wild soybean and a further 1.4% reduction from landrace to improved accessions. The detected domestication-selective sweeps also show reduced levels of deleterious alleles. Importantly, genotype imputation with this resource increases the mapping resolution of genome-wide association studies for seed protein and oil traits in a soybean diversity panel.
The potential of near infra-red spectroscopy (NIRS) for predicting the sprouting capacity of potato (Solanum tuberosum L.) tubers was investigated. The experiment was conducted for 2 years using 'Superior' and 'Atlantic' potatoes. A total of 380 potato tubers (200, Superior; 180, Atlantic) weighing 100-200 g were scanned by NIRS, and the sample sets were divided into four groups; three groups were classified based on the cultivars or years as follows: 'Superior', 2004; 'Superior', 2005; 'Atlantic', 2005; the fourth group contained the total number of samples. The reference value for the sprouting capacities was measured by determining the sprout weight after 30 days of incubation at 20°C. The first derivative transformation equation for raw optical data was standardized by applying standard normal variate (SNV) and detrending (DT) algorithms, and calibration equations between them were developed by modified partial least square (MPLS) regression. The coefficient of determination (r 2 ) ranged from 0.868 to 0.965 with a standard error of calibration (SEC) from 0.31 to 0.40 for the calibration sets; r 2 ranged from 0.724 to 0.904 with a standard error of prediction (SEP) from 0.532 to 0.602 for the four validation sets. These results indicate that the calibration model obtained from this experiment is applicable to all the different cultivars for different years, and the NIRS method is a powerful tool for the predictive assessment of the sprouting capacity of potato tubers.
The resveratrol-producing rice (Oryza sativa L.) inbred lines, Iksan 515 (I.515) and Iksan 526 (I.526), developed by the expression of the groundnut (Arachis hypogaea) resveratrol synthase 3 (AhRS3) gene in the japonica rice cultivar Dongjin, accumulated both resveratrol and its glucoside, piceid, in seeds. Here, we investigated the effect of the AhRS3 transgene on the expression of endogenous piceid biosynthesis genes (UGTs) in the developing seeds of the resveratrol-producing rice inbred lines. Ultra-performance liquid chromatography (UPLC) analysis revealed that I.526 accumulates significantly higher resveratrol and piceid in seeds than those in I.515 seeds and, in I.526 seeds, the biosynthesis of resveratrol and piceid reached peak levels at 41 days after heading (DAH) and 20 DAH, respectively. Furthermore, RNA-seq analysis showed that the expression patterns of UGT genes differed significantly between the 20 DAH seeds of I.526 and those of Dongjin. Quantitative real-time PCR (RT-qPCR) analyses confirmed the data from RNA-seq analysis in seeds of Dongjin, I.515 and I.526, respectively, at 9 DAH, and in seeds of Dongjin and I.526, respectively, at 20 DAH. A total of 245 UGTs, classified into 31 UGT families, showed differential expression between Dongjin and I.526 seeds at 20 DAH. Of these, 43 UGTs showed more than 2-fold higher expression in I.526 seeds than in Dongjin seeds. In addition, the expression of resveratrol biosynthesis genes (PAL, C4H and 4CL) was also differentially expressed between Dongjin and I.526 developing seeds. Collectively, these data suggest that AhRS3 altered the expression pattern of UGT genes, and PAL, C4H and 4CL in developing rice seeds.
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