Gene Expression Dynamics in Rice Peduncles at the Heading Stage

Abstract

Improving grain yield in the staple food crop rice has been long sought goal of plant biotechnology. One of the traits with significant impact on rice breeding programs is peduncle elongation at the time of heading failing which leads to significant reduction in grain yield due to incomplete panicle exsertion. To decipher transcriptional dynamics and molecular players underlying peduncle elongation, we performed RNA sequencing analysis of elongating and non-elongating peduncles in two Indian cultivars, Swarna and Pokkali, at the time of heading. Along with genes associated with cell division and cell wall biosynthesis, we observed significant enrichment of genes associated with auxins, gibberellins, and brassinosteroid biosynthesis/signaling in the elongating peduncles before heading in both the genotypes. Similarly, genes associated with carbohydrate metabolism and mobilization, abiotic stress response along with cytokinin, abscisic acid, jasmonic acid, and ethylene biosynthesis/signaling were enriched in non-elongating peduncles post heading. Significant enrichment of genes belonging to key transcription factor families highlights their specialized roles in peduncle elongation and grain filling before and after heading, respectively. A comparison with anther/pollen development-related genes provided 76 candidates with overlapping roles in anther/pollen development and peduncle elongation. Some of these are important for carbohydrate remobilization to the developing grains. These can be engineered to combat with incomplete panicle exsertion in male sterile lines and manipulate carbohydrate dynamics in grasses. Overall, this study provides baseline information about potential target genes for engineering peduncle elongation with implications on plant height, biomass composition and grain yields in rice.

Effects of Water Isotope Composition on Stable Isotope Distribution and Fractionation of Rice and Plant Tissues

“…Heading and filling stages are critical periods for the formation and development of rice grains. , Excess photoassimilates, accumulated in the form of sucrose and starch in rice stems before the heading stage occurs, are mobilized to the panicles after the heading stage to supplement grain filling . In the rice filling stage, grains require a large number of photosynthetic products sourced via leaf photosynthesis, which is more active at this time.…”

Gene Expression in the Developing Seed of Wild and Domesticated Rice

“…A few studies have aimed to better understand the dynamics of key genes and regulatory mechanisms in rice associated with morphology [ 22 ], physiology [ 23 ], abiotic and biotic stress mechanisms [ 24 , 25 , 26 ]. Transcriptional control of nutrients during grain filling in rice has been studied by designing a GeneChip microarray covering half of the rice genome to understand the effect of genes participating in nutrient partitioning on starch quality [ 27 ].…”

“…Using quantitative real-time RT-PCR, the gene expression of 27 starch synthesis-related genes have been evaluated in O. sativa seeds at different times after flowering [ 28 ]. Gene expression dynamics of peduncle development at heading stages in two indica rice cultivars were also investigated using RNA-Seq data [ 22 ]. Molecular and cellular events associated with rice embryogenesis at three embryo development stages: 3–5 DAP (days after pollination), 7 DAP, and 14 DAP have been investigated in the indica rice transcriptome [ 8 ]).…”