An epigenetic breeding system in soybean for increased yield and stability

Abstract

SummaryEpigenetic variation has been associated with a wide range of adaptive phenotypes in plants, but there exist few direct means for exploiting this variation. RNAi suppression of the plant‐specific gene, MutS HOMOLOG1 (MSH1), in multiple plant species produces a range of developmental changes accompanied by modulation of defence, phytohormone and abiotic stress response pathways along with methylome repatterning. This msh1‐conditioned developmental reprogramming is retained independent of transgene segregation, giving rise to transgene‐null ‘memory’ effects. An isogenic memory line crossed to wild type produces progeny families displaying increased variation in adaptive traits that respond to selection. This study investigates amenability of the MSH1 system for inducing agronomically valuable epigenetic variation in soybean. We developed MSH1 epi‐populations by crossing with msh1‐acquired soybean memory lines. Derived soybean epi‐lines showed increase in variance for multiple yield‐related traits including pods per plant, seed weight and maturity time in both glasshouse and field trials. Selected epi‐F2:4 and epi‐F2:5 lines showed an increase in seed yield over wild type. By epi‐F2:6, we observed a return of MSH1‐derived enhanced growth back to wild‐type levels. Epi‐populations also showed evidence of reduced epitype‐by‐environment (e × E) interaction, indicating higher yield stability. Transcript profiling of epi‐lines identified putative signatures of enhanced growth behaviour across generations. Genes related to cell cycle, abscisic acid biosynthesis and auxin response, particularly SMALL AUXIN UP RNAs (SAURs), were differentially expressed in epi‐F2:4 lines that showed increased yield when compared to epi‐F2:6. These data support the potential of MSH1‐derived epigenetic variation in plant breeding for enhanced yield and yield stability.

Epigenomic plasticity of Arabidopsismsh1mutants under prolonged cold stress

“…The lower yield penalty under mild heat stress in the three epi-lines, coupled with the enhanced salt and cold tolerance, provides an indicator of greater yield stability and lower environmental effects on the MSH1 growth-enhanced phenotype (Fig 2B). These results resemble the higher yield stability observed in soybean MSH1 epi-lines grown across four different locations in Nebraska (Raju et al, 2017).…”

“…MSH1 phenotypes are conserved between monocots and eudicots. This conservation is evidenced in the RNAi suppression phenotypes, and the consistent observation that subsequent MSH1-RNAi transgene segregation gives rise to transgenerational msh1 memory in sorghum, pearl millet, tomato, tobacco and soybean (de la Rosa Santamaria et al, 2014; Raju et al, 2017; Xu et al, 2011; Xu et al, 2012; Yang et al, 2015).…”

“…It is possible that circadian regulation may resynchronize following the crossing of msh1 mutants with wild type, which is known to influence freezing tolerance in plants (Maibam et al, 2013). In comparable soybean epi-F 4 lines, circadian genes GI and PRR3/5/7 were up-regulated (Raju et al, 2017), suggesting that modulation of circadian regulators follows crosses with msh1 .…”

“…Derived epi-lines have been shown to display higher yield stability through reduced epitype-by-environment effect in soybean multi-location field trials (Raju et al, 2017). In Arabidopsis, we likewise observed a lower yield penalty under mild heat stress in epi-lines compared to wild type (Fig 2B), implying higher buffering across environments.…”

Conventional and Molecular Techniques from Simple Breeding to Speed Breeding in Crop Plants: Recent Advances and Future Outlook

“…Breeders using the DH system unintentionally practice many selections for loci, increasing the success rate of this approach [140], but this might limit genetic variation in the breeding populations in responsive genome regions. Another approach is the RNAi suppression of plant genes (for instance, the MutS HOMOLOG1 (MSH1) gene) in multiple plant species, which produces a variety of developmental modifications accompanied by adjustments in plant defense, phytohormones, and abiotic stress response pathways combined with methylome repatterning [141].…”