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

Authors: Taliercio, Earl; EICKHOLT, DAVID - North Carolina State University; ROUF, RAKIN - North Carolina State University; Carter Jr, Thomas

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/5/2017
Publication Date: 5/11/2017
Citation: Taliercio, E.W., Eickholt, D., Rouf, R., Carter Jr, T.E. 2017. Changes in gene expression between a soybean F1 hybrid and its parents are associated with agronomically valuable traits. PLoS One. doi.org/10.1371/journal.pone.0177225.

Interpretive Summary: Mid-parent Heterosis, better performance of an F1 hybrid than its average for the parents, has been reported for a cross between the soybean lines N7103 and NMS4-44-329. One parent of NMS4-44-329 is the wild soybean accession PI366122. A detailed agronomic evaluation comparing the performance of the F1 hybrid with the two parents showed that protein content and seed size are increased in the hybrid relative to the parents. Yield over all was slightly elevated in the F1 hybrid, but importantly was more stable in the hybrid than the parents. Highly replicated genomic analyses of these field grown materials identified genes that are likely to be associated with the improved protein content of the hybrid as well as candidate genes for yield improvement. The evaluation of this cross has identified a source of improved seed protein content that does not appear to reduce yield.

Technical Abstract: Plant breeding consists of creating phenotypic and genetic diversity by hybridizing diverse parents and selecting progeny which have new combinations of targeted traits. Soybean [Glycine max (L.) Merr.] genetic diversity is limited because domesticated soybean has undergone multiple genetic bottlenecks in its evolution as a row crop. Its progenitor wild soybean [Glycine soja Siebold & Zucc] has not undergone the intense selection experienced by domesticated soybean. As a consequence of reduced selection, analyses with genetic markers have shown that wild soybean is much more genetically diverse than domesticated soybean. To assess the value of diversity in wild soybean to the elite Glycine domesticated germplasm, we chose for study an adapted and highly selected F4-derived breeding line, NMS4-44-329, which derives 50% of its pedigree from wild soybean. NMS4-44-329 was chosen instead of the wild progenitor because, hybrid progeny from NMS4-44-329 are agronomically adapted, unlike most hybrid progeny from wild soybean. NMS4-44-329, a progeny of max cultivar N7103 x soja PI 366122, was hybridized with its domesticated parent N7103. Agronomic comparisons were made among N7103, NMS4-44-329 and their F1 and F2 progeny. Over two North Carolina locations and 10 replications in typical agronomic plots, the F1 hybrid out-yielded the parental mean by 181 kg ha-1 (P=0.15). Mid-parent heterosis was also observed for seed size and seed protein content in the F1 hybrid. Both seed yield and seed protein content were greater than the midparent value, suggesting that both yield and seed protein content can be improved simultaneously in progeny from N7103 x NMS4-44-329. RNAseq analyses performed on the F1 hybrids and the parents demonstrated changes in expression of genes known to be associated with N metabolism, which could reasonably explain the improved protein levels in the F1 hybrids. We propose that changes in gene expression, both additive and non-additive, and changes in allele specific expression bias may explain improved yield and seed composition and be valuable tools for plant breeders to assess crosses.