Integration of small RNA, degradome and proteome sequencing in Oryza sativa reveals a delayed senescence network in tetraploid rice seed

Abstract

Seed of rice is an important strategic resource for ensuring the security of China's staple food. Seed deterioration as a result of senescence is a major problem during seed storage, which can cause major economic losses. Screening among accessions in rice germplasm resources for traits such as slow senescence and increased seed longevity during storage is, therefore, of great significance. However, studies on delayed senescence in rice have been based mostly on diploid rice seed to date. Despite better tolerance have been verified by the artificial aging treatment for polyploid rice seed, the delayed senescence properties and delayed senescence related regulatory mechanisms of polyploid rice seed are rarely reported, due to the lack of polyploid rice materials with high seed set. High-throughput sequencing was applied to systematically investigate variations in small RNAs, the degradome, and the proteome between tetraploid and diploid rice seeds. Degradome sequencing analysis of microRNAs showed that expression of miR-164d, which regulates genes encoding antioxidant enzymes, was changed significantly, resulting in decreased miRNA-mediated cleavage of target genes in tetraploid rice. Comparisons of the expression levels of small RNAs (sRNAs) in the tetraploid and diploid libraries revealed that 12 sRNAs changed significantly, consistent with the findings from degradome sequencing. Furthermore, proteomics also showed that antioxidant enzymes were up-regulated in tetraploid rice seeds, relative to diploids.

Identification of Known and Novel Arundo donax L. MicroRNAs and Their Targets Using High-Throughput Sequencing and Degradome Analysis

“…In the present study, small RNAs from A. donax plants were sequenced and known as well as candidate novel miRNAs were identified. The obtained sRNA profiles were consistent with the typical ones reported for rice, wheat, and other monocots [ 43 , 49 , 50 , 51 ], where the 24-nt sRNAs are the most abundant and heterogeneous class of small non-coding RNAs in the sRNAs libraries, while the 21-nt sRNAs, being mostly miRNA sequences, show a low level of redundancy. Consistently with the general characteristic of miRNAs [ 39 ] and with previous reports on A. donax [ 48 ] and other plants [ 43 , 52 ], we observed a miRNA length distribution with a prevalence of 21-nt sequences followed by those of 20-nt in length.…”

Melatonin delays dark‐induced leaf senescence by inducing miR171b expression in tomato

“…By analyzing the microRNAs degradome sequencing results in O. sativa , researchers found that the expression of miR164d has changed significantly in tetraploid rice. miR164d regulates the antioxidant enzyme gene through its target gene Os12g0610600 (NAC domain‐containing protein 21/22), and Os12g0610600 interact with gene Os04g0573200 (copper chaperone for superoxide dismutase, chloroplastic‐like, CCS), which may be the reason for the delayed senescence of polyploid rice seeds 60 . Moreover, miR164 delayed the senescence of strawberry fruit ( Fragaria ananassa ) under low temperature by negatively regulating the expression of NAC transcription factor genes 61 .…”

A Comparative Study of Morphology, Photosynthetic Physiology, and Proteome between Diploid and Tetraploid Watermelon (Citrullus lanatus L.)

“…Proteomics research has shown that the translation of multiple genes is changed in the tetraploid genotype compared with the diploid genotype [ 39 , 40 ]. For example, compared to diploid rice, tetraploid rice had more CAT proteins, peroxidase P7, and catalase isozyme A [ 41 ]. Autotetraploid P. australis exhibited a higher expression of protein genes related to glutathione metabolism, cell division, and chlorophyll, cellulose, and lignin synthesis than the diploid genotype [ 42 ].…”