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In cluster III, five probe sets showed down-regulation in good quality varieties in all three seed developmental stages.
In cluster III, the probe sets showed down-regulation in good quality varieties at early stage i.e. 7 DAA.
In cluster II, the majority of the probe sets showed up-regulation in good quality varieties at later stages of seed development (14 and 28 DAA).
In cluster V, the majority of the probe sets showed up-regulation in good quality varieties at early stage of seed development.
The genes of photo systems (light reactions) and Calvin cycle were down-regulated in early stage of seed development (7 DAA) in good quality varieties.
In cluster IV, the probe sets showed up-regulation in good quality varieties at later stage of seed development (28 DAA).
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Total of 110 probe sets were identified for quality which showed at least ten-fold differential expression between good and poor quality varieties in at least one of the three condition pairs ('Good-7 DAA' vs 'Poor-7 DAA', 'Good-14 DAA' vs 'Poor-14 Dand, and 'Good-28 DAA' vs 'Poor-28 DAA') (Tables 2 and 3, see Additional file 3, Figures 1 and 2A).
Total 219 probe sets were identified for seed development whose expression changed at least ten-fold between good and poor quality varieties in at least one of the three condition pairs ('Good-7 DAA' vs 'Poor-7 DAA', 'Good-14 DAA' vs 'Poor-14 Dand, and 'Good-28 DAA' vs 'Poor-28 DAA') (Table 2, see Additional file 3, Figures 1 and 2B).
Using gene-specific two-way ANOVA analysis, 110 probe sets were identified for processing quality showing at least 10-fold differential expression between good and poor quality varieties.
Genome-wide transcriptome analysis was done between good and poor quality varieties at three seed developmental stages (7, 14, and 28 DAA) to identify the candidate genes whose expressions changed due to quality, development, and interaction (quality x development).
In this study a high increase in differential expression of GBSS from early (about 7-fold at 7 DAA) to late maturity (about 93 fold at 28 DAA) was observed between good and poor quality varieties.
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