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We consider two practical constraints to successful QTL identification for the suite of transient, dynamic traits associated with stem NSC.The first issue is that the experimental design parameters needed to effectively evaluate NSC for genetic studies have not been systematically explored.

While some document a significant contribution of stem reserves to final yield (up to 40%) (Van Dat and Peterson, 1983;, Samonte , 1994).

Several studies show evidence of enhanced contribution to grain-filling during suboptimum conditions (e.g.

For (cultivated Asian rice), knowledge about stem NSC’s direct link to yield performance and the genetic controls that underlie its dynamics are still superficial.

Rice stems preferentially store starch and sucrose prior to heading, but lose these reserves rapidly following panicle exertion when grain-filling is prioritized energetically; these data support the idea that the stem experiences a sink-to-source transition at heading (Cock and Yoshida, 1972;, Chen and Wang, 2008).

Here we conducted three pilot experiments to lay the groundwork for large-scale diversity studies on rice stem NSC.

We assessed the relationship of stem NSC components with 21 agronomic traits in large-scale, tropical yield trials using 33 breeder-nominated lines, established an appropriate experimental design for future genetic studies using a Bayesian framework to sample sub-datasets from highly replicated greenhouse data using 36 genetically diverse genotypes, and used 434 phenotypically divergent rice stem samples to develop two partial least-squares (PLS) models using near-infrared (NIR) spectra for accurate, rapid prediction of rice stem starch, sucrose, and total non-structural carbohydrates.

We find evidence that stem reserves are most critical for short-duration varieties and suggest that pre-heading stem NSC is worthy of further experimentation for breeding early maturing rice.

Stem non-structural carbohydrates (NSCs) have long elicited interest from physiologists and breeders across a diversity of economically important grass species.

The MSUv7 genome assembly ( has been annotated with gene models across the 12 rice chromosomes, and over 100 predicted enzyme-coding genes have putative catalytic involvement in starch and sucrose biosynthesis, degradation, and transport (Dharmawardhana , 2013).

Despite these candidates and other genes involved in related developmental pathways (e.g.

water deficit or heat stress) coordinated with more rapid grain-filling and leaf senescence (Yang , 2011;, Morita and Nakano, 2011). heavy nitrogen application) seem to have the opposite effect and suppress translocation of stem reserves, in effect decreasing their grain-filling contribution (Hirano , 2012), studies on rice have not been able to clearly define aspects of stem reserves that are genetically tractable or capable of optimization and thereby valuable for varietal improvement.

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