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Lee, S. Leaf Senescence in Rice. Encyclopedia. Available online: https://encyclopedia.pub/entry/9983 (accessed on 25 April 2024).
Lee S. Leaf Senescence in Rice. Encyclopedia. Available at: https://encyclopedia.pub/entry/9983. Accessed April 25, 2024.
Lee, Sichul. "Leaf Senescence in Rice" Encyclopedia, https://encyclopedia.pub/entry/9983 (accessed April 25, 2024).
Lee, S. (2021, May 24). Leaf Senescence in Rice. In Encyclopedia. https://encyclopedia.pub/entry/9983
Lee, Sichul. "Leaf Senescence in Rice." Encyclopedia. Web. 24 May, 2021.
Leaf Senescence in Rice
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This entry is adapted from the peer-reviewed paper 10.3390/ijms22094515

Leaf senescence, which is the last developmental phase of plant growth, is controlled by multiple genetic and environmental factors. Leaf yellowing is a visual indicator of senescence due to the loss of the green pigment chlorophyll. During senescence, the methodical disassembly of macromolecules occurs, facilitating nutrient recycling and translocation from the sink to the source organs, which is critical for plant fitness and productivity. Leaf senescence is a complex and tightly regulated process, with coordinated actions of multiple pathways, responding to a sophisticated integration of leaf age and various environmental signals. Many studies have been carried out to understand the leaf senescence-associated molecular mechanisms including the chlorophyll breakdown, phytohormonal and transcriptional regulation, interaction with environmental signals, and associated metabolic changes. The metabolic reprogramming and nutrient recycling occurring during leaf senescence highlight the fundamental role of this developmental stage for the nutrient economy at the whole plant level. The strong impact of the senescence-associated nutrient remobilization on cereal productivity and grain quality is of interest in many breeding programs.

rice leaf senescence productivity chlorophyll breakdown stay-green transcription factors phytohormones nitrogen remobilization

1. Introduction

Leaf senescence is easily observed because Chl degradation leads to leaf yellowing [1]. Stay-green is the heritable delayed senescence phenotype observed in comparison with a reference genotype, and stay-green mutants refer to genotypes that retain green leaves during senescence [2][3]. Maintaining leaf Chl levels and active photosynthetic capacity extends the time for assimilation processes and grain development, thereby increasing crop yield [4][5]. The genetic and physiological ways to obtain seemingly similar stay-green phenotypes are diverse, and five types of stay-green plants have been reported [2]. Their differences are based on the Chl behavior during senescence and their photosynthetic activities [2][6].

2. Development

The Type A stay-green plants initiate senescence lately but lose Chl at a normal rate. In Type B stay-green plants, senescence is started on schedule, but thereafter, the decline of the photosynthetic activity is comparatively slower than in WT. In Type C stay-green plants, Chl may be retained more or less indefinitely because of defects in pigment breakdown, but functional senescence occurs on a normal time-scale beneath the cosmetic surface of retained pigmentation. Therefore, Type C stay-greens are named cosmetic stay-green. The Type D stay-greens are described as pseudo-stay-greens because their leaves die before or in the middle of the senescence process as if freezing, and subsequently, the plant still appears green after death. The Type E stay-green plants accumulate higher levels of Chl in photosynthetic tissues, resulting in a delay of senescence and the conservation of green tissue. However, the photosynthetic capacity of Type E stay-greens follows the normal ontogenetic pattern. Both Type A and B stay-green plants are termed functional stay-greens as the duration of the photosynthetic capacity is extended. These stay-green types are sought by breeders as they can result in higher yield. Several studies have reported a synergistic effect by combining functional stay-green and other useful traits such as tolerance to drought and heat stress [7]. On the contrary, the Type C, D, and E plants are categorized as non-functional stay-green that retain greenness due to the impairment of Chl catabolism but lack the maintenance of leaf functionality during senescence [2][8]. Most CCE mutants in rice display a stay-green phenotype during senescence but lack an extended photosynthetic capacity and grain yield advantage; therefore, these mutants are regarded as non-functional stay-green plants.
Due to the high importance of maintaining photosynthesis longer and/or in promoting nutrient recycling and mobilization throughout the plant, the stay-green traits were investigated in many plant species, including rice, maize, Arabidopsis, soybean, barley, tomato, pepper, and wheat, and they were used as markers in plant breeding programs [9][10][11][12][13][14][15].
Several studies report that the Chl content in rice is regulated by a quantitative trait locus (QTL) [10][16][17][18]. Analyses of Chl content and the degree of greenness in the flag and second leaves identified 46 QTLs that were associated with delayed senescence [16]. Cha et al. mapped the stay-green (sgr) locus, which is responsible for maintaining greenness during leaf senescence, but not photosynthetic activity, to the long arm of chromosome 9 [10]. Further studies identified SGR as a senescence-associated gene encoding a novel chloroplast protein and Mg2+-dechetalase mediating Chl breakdown, which confirmed that sgr was a cosmetic stay-green locus [19][20].
A total of six QTLs (csfl2/tcs2, tcs4, tcs5, csfl6, csfl9/tcs9, and csfl12) were identified in recombinant inbred line populations derived from intra- and inter-subspecific crosses of rice varieties [21]. The functional stay-green japonica rice ‘SNU-SG1′ is mapped on chromosome 9. The presence of SNU-SG1 improved grain yield by maintaining photosynthetic activity in the flag and second leaves during grain filling, and by increasing sink strength due to high seed-setting rate [17]. Fine mapping performed by Lim et al. identified eleven main-effect loci in the japonica rice SNU-SG1 that were responsible for functional SG phenotypes [22]. Fifteen strong candidate genes were identified that explained these main-effect QTLs using the whole-genome sequence [22]. All these genes represent interesting candidates for further plant breeding. The qCC2 major QTL for Chl content was identified using a population derived from an interspecific cross between O. sativa and O. grandiglumi [18]. The GW2 gene that encodes an E3 ubiquitin ligase is located in the qCC2 region and is responsible for leaf senescence through the transcriptional regulation of phytohormone signaling pathways [18]. Whether the qCC2 QTL is explained by GW2 allelic variations in O. sativa and O. grandiglumi remains to be determined. Ten stable QTL regions for six delayed senescence traits have been identified [23]. Expression analysis of five candidate genes displayed the differential transcript levels, suggesting their strong association with the senescence pattern in the flag and second leaves and possible contribution in enhancing grain yield through genomics-assisted breeding.
A genome-wide association study (GWAS) of a diverse worldwide collection of rice accessions identified forty-six significant association loci in natural variation of Chl content (CC) [24]. Among them, the Grain number, plant height, and heading date7 (Ghd7) was a major locus for natural variations of Chl content that was involved in the repression of Chl and chloroplast biosynthetic genes [24]. As indicated by its name, this locus is a functional stay-green locus that controls also grain number, plant height, and heading date. Another candidate revealed by GWAS is Narrow leaf1 (NAL1) [24]. A high degree of polymorphism in the 5′ UTR and four non-synonymous single nucleotide polymorphisms (SNPs) in the coding region of NAL1 was shown to confer natural variations of Chl content [24]. Whether pleiotropic effects of NAL1 in regulating flag leaf width and spikelet number per panicle might be helpful for rice breeding remains to be determined. In another GWAS study, 25 known genes for CC and stay-green (SG) traits were identified in natural rice variations [25]. Non-synonymous SNPs were detected in six of the genes and three SNPs in the promoter region of OsSG1 [25]. Another GWAS revealed fourteen regions associated with CC and strong SG phenotypes [25]. From them, twenty-five candidate genes identified around the GWAS signals are genes with known important roles in CC and SG phenotypes. This suggests that these genes could be involved in the genetic variation of CC or SG. Non-synonymous SNPs within six of these genes, and three SNPs in the promoter of OsSG1, were unveiled. The impact of each of these genes on plant performance remains to be explored.
Two representative rice subspecies, japonica and indica, display distinct morphological and physiological features as well as clear variation in genomic sequences [26]. Furthermore, indica displays early leaf senescence, whereas japonica displays late leaf senescence [27]. Then, QTL mapping was conducted to determine the genetic factors responsible for the differential senescence patterns between indica and japonica [20]. Results showed that allelic polymorphisms in the OsSGR promoter in indica result in higher and earlier induction of OsSGR, thereby triggering earlier senescence. The introgression of japonica OsSGR alleles into elite indica cultivars produced near isogenic lines (NILs) with delayed leaf senescence and extended photosynthetic competence, leading to improved grain filling rate and yield. Then, the japonica OsSGR alleles represent technical solutions for a beneficial breeding strategy in rice.
In addition to QTL and GWAS approaches, experiments leading to the characterization of mutants were carried out. The screen of ethyl methansulphonate (EMS)-induced rice mutants led to the identification of three stay-green mutants that also displayed drought tolerance [28]. Amongst them, SGM-3 was characterized as a novel functional stay-green mutant with extended photosynthetic capacity during senescence, increased harvest index, and higher grain yield under irrigated as well as drought conditions which can be further used for the development of high-yielding lines [28]. The exact function of SGM-3 remains to be determined.

3. conclusion

In summary, we can see that both the quantitative genetics and mutagenesis approaches successfully identified several functional stay-green genes that play a role in plant productivity. Although the function of many of these genes and loci still remains to be elucidated, their positive alleles could be used in marker-assisted plant breeding programs.

References

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