Alternative Splicing (AS) is a mechanism that generates different mature transcripts from precursor mRNAs (pre-mRNAs) of the same gene. In plants, a wide range of physiological and metabolic events are related to AS, as well as fast responses to changes in temperature. AS is present in around 60% of intron-containing genes in Arabidopsis, 46% in rice, and 38% in maize and it is widespread among the circadian clock genes. Little is known about how AS influences the circadian clock of C4 plants, like commercial sugarcane, a C4 crop with a complex hybrid genome. This work aims to test if the daily dynamics of AS forms of circadian clock genes are regulated by environmental factors, such as temperature, in the field. A systematic search for AS in five sugarcane clock genes, ScLHY, ScPRR37, ScPRR73, ScPRR95, and ScTOC1 using different organs of sugarcane sampled during winter, with 4 months old plants, and during summer, with 9 months old plants, revealed temperature-and organ-dependent expression of at least one alternatively spliced isoform in all genes. Expression of AS isoforms varied according to the season. Our results suggest that AS events in circadian clock genes are correlated with temperature.

Most research in plant chronobiology has been done in laboratory conditions. However, laboratories usually fail to mimic natural conditions and their slight fluctuations, highlighting or obfuscating rhythmicity. High-density crops, such as sugarcane (Saccharum hybrid), generate field microenvironments with specific light and temperature regimes resulting from mutual shading.We measured the metabolic and transcriptional rhythms in the leaves of 4-month-old (4 mo) and 9 mo field-grown sugarcane. Most of the assayed rhythms in 9 mo sugarcane peaked >1 h later than in 4 mo sugarcane, including rhythms of the circadian clock gene, LATE ELONGATED HYPOCOTYL (LHY).We hypothesized that older sugarcane perceives dawn later than younger sugarcane as a consequence of self-shading. As a test, we measured LHY rhythms in plants on the east and the west sides of a field. We also tested if a wooden wall built between lines of sugarcane plants changed their rhythms. The LHY peak was delayed in the plants in the west of the field or beyond the wall; both shaded at dawn.We conclude that plants in the same field may have different phases resulting from field microenvironments, impacting important agronomical traits, such as flowering time, stalk weight and number.

20Alternative Splicing (AS) is a mechanism that generates different mature transcripts from 21 precursor mRNAs (pre-mRNAs) of the same gene. In plants, a wide range of 22 physiological and metabolic events are related to AS, as well as fast responses to changes 23 in temperature. AS is present in around 60% of intron-containing genes in Arabidopsis, 2446% in rice and 38% in maize and it is widespread among the circadian clock genes. Little 25 is known about how AS influences the circadian clock of C4 plants, like commercial 26 sugarcane, a C4 crop with a complex hybrid genome. This work aims to test if the daily 27 dynamics of AS forms of circadian clock genes are regulated by environmental factors, 28 such as temperature, in the field. A systematic search for AS in five sugarcane clock 29 genes, ScLHY, ScPRR37, ScPRR73, ScPRR95 and ScTOC1 using different organs of 30 sugarcane sampled during winter, with 4 months old plants, and during summer, with 9 31 months old plants, revealed temperature-and organ-dependent expression of at least one 32 alternatively spliced isoform in all genes. Expression of AS isoforms varied according to 33 the season. Our results suggest that AS events in circadian clock genes are correlated with 34 temperature. 35 36

Most research in plant chronobiology was done in laboratory conditions. However, they usually fail to mimic natural conditions and their nuanced fluctuations, highlighting or obfuscating rhythmicity. High-density crops, such as sugarcane (Saccharum hybrid), generate field microenvironments that have specific light and temperature, as they shade each other. Here, we measured the metabolic and transcriptional rhythms in the leaves of 4-month-old (4 mo.) and 9 mo. sugarcane grown in the field. Most of the assayed rhythms in 9 mo. sugarcane peaked >1 h later than in 4 mo. sugarcane, including rhythms of the circadian clock gene, LATE ELONGATED HYPOCOTYL (LHY), but not TIMING OF CAB EXPRESSION (TOC1). We hypothesized that older sugarcane perceives dawn later than younger sugarcane, due to self-shading. As a test, we measured LHY rhythms in plants on the east and the west side of a field. We also tested if a wooden wall built between lines of sugarcane also changed their rhythms. In both experiments, the LHY peak was delayed in the plants shaded at dawn. We conclude that plants in the same field may have different phases due to field microenvironments, which may impact important agronomical traits, such as flowering time, stalk weight and number.