Changes in gene expression between a soybean F₁ hybrid and its parents are associated with agronomically valuable traits

<div><p>Soybean [<i>Glycine max</i> (L.) Merr.] genetic diversity is limited because domesticated soybean has undergone multiple genetic bottlenecks. Its progenitor, the wild soybean [<i>Glycine soja</i> Siebold & Zucc], has not undergone the same intense selection and is much more genetically diverse than domesticated soybean. However, the agronomic importance of diversity in wild soybean is unclear, and its weedy nature makes assessment difficult. To address this issue, we chose for study a highly selected, adapted F₄-derived progeny of wild soybean, NMS4-44-329. This breeding line is derived from the hybridization between <i>G</i>. <i>max</i> cultivar N7103 and <i>G</i>. <i>soja</i> PI 366122. Agronomic comparisons were made among N7103, NMS4-44-329 and their F₁ and F₂ progeny in replicated yield trials at two North Carolina locations. Significant F₁ mid-parent heterosis was observed at each location for seed yield (189 and 223 kgha^-1, P<0.05 and P<0.10, respectively), seed protein content (1.1g/100g, P<0.01) and protein production per hectare (101 and 100 kgha^-1, P<0.01 and P<0.06, respectively). Increased yield, seed protein content and protein production per hectare in the hybrids suggested that wild soybean has the potential to improve agronomic traits in applied breeding. Comparisons of differentially-expressed genes in the hybrid vs. parents identified genes associated with N metabolism. Non-additive changes in gene expression in the hybrids relative to the parents could reasonably explain the improved protein levels in the F₁ hybrids. Changes in gene expression were influenced by environmental effects; however, allele specific bias in the hybrids were well correlated between environments. We propose that changes in gene expression, both additive and non-additive, and changes in allele specific expression bias may explain agronomic traits, and be valuable tools for plant breeders in the assessment of breeding populations.</p></div

Contrast table for agronomic data.

<p>Contrast table for agronomic data.</p

Enriched ontologies.

<p>Enriched ontologies.</p

Gene counts from gene expression study.

<p>Gene counts from gene expression study.</p

The distribution of the bias of alternative SNPs.

<p>The fraction of the alternative allele is shown as the percent of total SNPS. Panel A shows the alternative allele (relative to the reference genome) from NMS4-44-329 and Panel B Shows the alternative alleles derived from N7103. Low values (>0.5) indicate higher levels of expression of the SNP from NMS4-44-329.</p

Changes in gene expression between a soybean F₁ hybrid and its parents are associated with agronomically valuable traits - Table 1

Changes in gene expression between a soybean F₁ hybrid and its parents are associated with agronomically valuable traits - Table

Non-additive gene expression in Clayton.

<p>Non-additive gene expression in Clayton.</p

Agronomic data.

<p>Agronomic data.</p

Non-additive gene expression in Kinston.

<p>Non-additive gene expression in Kinston.</p