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Song H, Wang T, Li L, Xing L, Xie HF, Feng BL, Liu JR. Comparative transcriptome analysis provides insights into grain filling commonalities and differences between foxtail millet [ Setaria italica (L.) P. Beauv.] varieties with different panicle types. PeerJ 2022; 10:e12968. [PMID: 35198264 PMCID: PMC8860066 DOI: 10.7717/peerj.12968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 01/28/2022] [Indexed: 01/11/2023] Open
Abstract
Grain filling affects grain weight and quality and is among the most critical factors in determining the yield and quality of cereal crops. Though hybrids have larger panicles and numerous spikelets with a larger sink capacity than conventional varieties, data on the grain filling commonalities and differences between foxtail millet varieties with different panicle types remain sparse. In this study, we found that "Zhang Gu 13" (ZG, large panicle) exhibits a significantly higher panicle weight than "Yu Gu 18" (YG, conventional panicle) at the early stage of grain filling, but the weight of YG increased rapidly and gradually overtook ZG during the middle stages. A temporal expression pattern analysis demonstrated that the genes involved in photosynthesis, metabolic pathways, and phenylpropanoid biosynthesis were downregulated, while those related to peroxisome function, purine metabolism, and zeatin biosynthesis were upregulated during grain filling in both varieties. A total of 6,832 differentially expressed genes (DEGs) were identified in both varieties, with the majority identified at the early and late stages. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis further revealed that the upregulated DEGs in YG were associated with gibberellin (GA) biosynthesis, ATP-binding cassette (ABC) transporters, and plant hormone signal transduction. Photosynthesis-related DEGs, such as photosystem and antenna proteins, were significantly upregulated in ZG. This study provides preliminary insights into the differences in gene expression and molecular mechanisms of grain filling between ZG and YG in the North China summer-sowing region.
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Affiliation(s)
- Hui Song
- Anyang Academy of Agriculture Sciences, Anyang, Henan, China
| | - Tao Wang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, Henan, China,Innovation and Practice Base for Postdoctors, Anyang Institute of Technology, Anyang, Henan, China
| | - Long Li
- Anyang Academy of Agriculture Sciences, Anyang, Henan, China
| | - Lu Xing
- Anyang Academy of Agriculture Sciences, Anyang, Henan, China
| | - Hui fang Xie
- Anyang Academy of Agriculture Sciences, Anyang, Henan, China
| | - Bai li Feng
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, China
| | - Jin rong Liu
- Anyang Academy of Agriculture Sciences, Anyang, Henan, China
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Pasion EA, Badoni S, Misra G, Anacleto R, Parween S, Kohli A, Sreenivasulu N. OsTPR boosts the superior grains through increase in upper secondary rachis branches without incurring a grain quality penalty. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1396-1411. [PMID: 33544455 PMCID: PMC8313136 DOI: 10.1111/pbi.13560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 12/29/2020] [Accepted: 01/19/2021] [Indexed: 06/02/2023]
Abstract
To address the future food security in Asia, we need to improve the genetic gain of grain yield while ensuring the consumer acceptance. This study aimed to identify novel genes influencing the number of upper secondary rachis branches (USRB) to elevate superior grains without compromising grain quality by studying the genetic variance of 310 diverse O. sativa var. indica panel using single- and multi-locus genome-wide association studies (GWAS), gene set analyses and gene regulatory network analysis. GWAS of USRB identified 230 significant (q-value < 0.05) SNPs from chromosomes 1 and 2. GWAS targets narrowed down using gene set analyses identified large effect association on an important locus LOC_Os02g50790/LOC_Os02g50799 encoding a nuclear-pore anchor protein (OsTPR). The superior haplotype derived from non-synonymous SNPs identified in OsTPR was specifically associated with increase in USRB with superior grains being low chalk. Through haplotype mining, we further demonstrated the synergy of offering added yield advantage due to superior allele of OsTPR in elite materials with low glycaemic index (GI) property. We further validated the importance of OsTPR using recombinant inbred lines (RILs) population by introgressing a superior allele of OsTPR into elite materials resulted in raise in productivity in high amylose background. This confirmed a critical role for OsTPR in influencing yield while maintaining grain and nutritional quality.
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Affiliation(s)
- Erstelle A. Pasion
- Applied Functional Genomics ClusterGrain Quality and Nutrition CentreStrategic Innovation PlatformInternational Rice Research InstituteLos BañosPhilippines
| | - Saurabh Badoni
- Applied Functional Genomics ClusterGrain Quality and Nutrition CentreStrategic Innovation PlatformInternational Rice Research InstituteLos BañosPhilippines
| | - Gopal Misra
- Applied Functional Genomics ClusterGrain Quality and Nutrition CentreStrategic Innovation PlatformInternational Rice Research InstituteLos BañosPhilippines
| | - Roslen Anacleto
- Applied Functional Genomics ClusterGrain Quality and Nutrition CentreStrategic Innovation PlatformInternational Rice Research InstituteLos BañosPhilippines
| | - Sabiha Parween
- Applied Functional Genomics ClusterGrain Quality and Nutrition CentreStrategic Innovation PlatformInternational Rice Research InstituteLos BañosPhilippines
| | - Ajay Kohli
- Applied Functional Genomics ClusterGrain Quality and Nutrition CentreStrategic Innovation PlatformInternational Rice Research InstituteLos BañosPhilippines
| | - Nese Sreenivasulu
- Applied Functional Genomics ClusterGrain Quality and Nutrition CentreStrategic Innovation PlatformInternational Rice Research InstituteLos BañosPhilippines
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Sekhar S, Kumar J, Mohanty S, Mohanty N, Panda RS, Das S, Shaw BP, Behera L. Identification of novel QTLs for grain fertility and associated traits to decipher poor grain filling of basal spikelets in dense panicle rice. Sci Rep 2021; 11:13617. [PMID: 34193914 PMCID: PMC8245594 DOI: 10.1038/s41598-021-93134-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023] Open
Abstract
High grain number is positively correlated with grain yield in rice, but it is compromised because of poor filling of basal spikelets in dense panicle bearing numerous spikelets. The phenomenon that turns the basal spikelets of compact panicle sterile in rice is largely unknown. In order to understand the factor(s) that possibly determines such spikelet sterility in compact panicle cultivars, QTLs and candidate genes were identified for spikelet fertility and associated traits like panicle compactness, and ethylene production that significantly influences the grain filling using recombinant inbred lines developed from a cross between indica rice cultivars, PDK Shriram (compact, high spikelet number) and Heera (lax, low spikelet number). Novel QTLs, qSFP1.1, qSFP3.1, and qSFP6.1 for spikelet fertility percentage; qIGS3.2 and qIGS4.1 for panicle compactness; and qETH1.2, qETH3.1, and qETH4.1 for ethylene production were consistently identified in both kharif seasons of 2017 and 2018. The comparative expression analysis of candidate genes like ERF3, AP2-like ethylene-responsive transcription factor, EREBP, GBSS1, E3 ubiquitin-protein ligase GW2, and LRR receptor-like serine/threonine-protein kinase ERL1 associated with identified QTLs revealed their role in poor grain filling of basal spikelets in a dense panicle. These candidate genes thus could be important for improving grain filling in compact-panicle rice cultivars through biotechnological interventions.
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Affiliation(s)
- Sudhanshu Sekhar
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, 753006, India.
| | - Jitendra Kumar
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, 753006, India
| | - Soumya Mohanty
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, 753006, India
| | - Niharika Mohanty
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, 753006, India
| | - Rudraksh Shovan Panda
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, 753006, India
| | - Swagatika Das
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, 753006, India
| | | | - Lambodar Behera
- Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, 753006, India.
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Characterization and Grouping of All Primary Branches at Various Positions on a Rice Panicle Based on Grain Growth Dynamics. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10020223] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Grain filling can directly influence rice yield. However, there is limited information on the growth relationship among grains at different positions on the entire panicle during grain filling. In this study, field experiments were conducted in 2014–2015 to compare the growth dynamics of grains at various positions for two rice cultivars (Nongle 1 and Guifeng 2). The results showed that a high similarity and a slow–fast–slow trend of dry-matter accumulation occurred in all primary branches. However, the maximum grain growth rates of the top primary branches were 86% and 44% higher than basal primary branches of Nongle 1 and Guifeng 2, respectively. Similarly, the maximum final grain weights were 32% and 18% greater in the top primary branches than in the basal primary branches of Nongle 1 and Guifeng 2, respectively. In contrast, the active grain filling duration was 1.5 and 1.3 times longer in the basal primary branches than the top primary branches of Nongle 1 and Guifeng 2, respectively. The time to reach the maximum rate of grain growth of the basal primary branches for Nongle 1 and Guifeng 2 was 2.2 and 2.5 times longer than those of the top primary branches, respectively. Based on cluster analysis of growth characteristics of all primary branches, Group I (superior primary-branches) was considered to be the fastest for grain filling and greatest for dry matter weight, followed by Group II (medium primary-branches). The poorest growth occurred in Group III (inferior primary-branches). Therefore, the yield of poor-filling grains at the basal panicle could be achieved primarily by improving the growth of Group III.
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Panigrahi R, Kariali E, Panda BB, Lafarge T, Mohapatra PK. Controlling the trade-off between spikelet number and grain filling: the hierarchy of starch synthesis in spikelets of rice panicle in relation to hormone dynamics. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:507-523. [PMID: 30961785 DOI: 10.1071/fp18153] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 02/13/2019] [Indexed: 06/09/2023]
Abstract
The advent of dwarf statured rice varieties enabled a major breakthrough in yield and production, but raising the ceiling of genetically determined yield potential even further has been the breeding priority. Grain filling is asynchronous in the rice panicle; the inferior spikelets particularly on secondary branches of the basal part do not produce grains of a quality suitable for human consumption. Of the various strategies being considered, the control of ethylene production at anthesis has been a valuable route to potentially enhance genetic yield level of rice. The physiology underlying spikelet development has revealed spikelet position-specific ethylene levels determine the extent of grain filling, with higher levels resulting in ill-developed spikelet embodying poor endosperm starch content. To break the yield barrier, breeders have increased spikelet number per panicle in new large-panicle rice plants. However, the advantage of panicles with numerous spikelets has not resulted in enhanced yield because of poor filling of inferior spikelets. High spikelet number stimulates ethylene production and downgrading of starch synthesis, suggesting a trade-off between spikelet number and grain filling. High ethylene production in inferior spikelets suppresses expression of genes encoding endosperm starch synthesising enzymes. Hence, ethylene could be a retrograde signal that dictates the transcriptome dynamics for the cross talk between spikelet number and grain filling in the rice panicle, so attenuation of its activity may provide a solution to the problem of poor grain filling in large-panicle rice. This physiological linkage that reduces starch biosynthesis of inferior kernels is not genetically constitutive and amenable for modification through chemical, biotechnological, surgical and allelic manipulations. Studies on plant genotypes with different panicle architecture have opened up possibilities of selectively improving starch biosynthesis of inferior spikelets and thereby increasing grain yield through a physiological route.
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Affiliation(s)
- Rashmi Panigrahi
- School of Life Sciences, Sambalpur University, Jyoti vihar, Sambalpur, 768019, India
| | - Ekamber Kariali
- School of Life Sciences, Sambalpur University, Jyoti vihar, Sambalpur, 768019, India
| | - Binay Bhusan Panda
- Environmental Biotechnology Laboratory, Institute of Life Science, Bhubaneswar, 751023, India
| | - Tanguy Lafarge
- CIRAD, UMR AGAP, F-34398 Montpellier, France; and AGAP, University of Montpellier, CIRAD, INRA, INRIA, Montpellier SupAgro, Montpellier, France
| | - Pravat Kumar Mohapatra
- School of Life Sciences, Sambalpur University, Jyoti vihar, Sambalpur, 768019, India; and Corresponding author. Emails:
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Li R, Li M, Ashraf U, Liu S, Zhang J. Exploring the Relationships Between Yield and Yield-Related Traits for Rice Varieties Released in China From 1978 to 2017. FRONTIERS IN PLANT SCIENCE 2019; 10:543. [PMID: 31134107 PMCID: PMC6514245 DOI: 10.3389/fpls.2019.00543] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 04/09/2019] [Indexed: 05/20/2023]
Abstract
Despite evidence from previous case studies showing that agronomic traits partially determine the resulting yield of different rice (Oryza sativa L.) varieties, it remains unclear whether this is true at the ecotype level. Here, an extensive dataset of the traits of 7686 rice varieties, released in China from 1978 to 2017, was used to study the relationship between yield and other agronomic traits. We assessed the association between yield and other agronomic traits for four different rice ecotypes, i.e., indica inbred, indica hybrid, japonica inbred, and japonica hybrid. We found that associations between agronomic traits and yield were ecotype-dependent. For both the indica inbred and indica hybrid ecotypes, we found that greater values of certain traits, including the filled grain number per panicle, 1000-grain-weight, plant height, panicle length, grains per panicle, seed setting rate, long growth period, low panicle number per unit area, and low seed length/width ratio, have accounted for high grain yield. In the japonica inbred and japonica hybrid ecotypes, we found that only high panicle number per unit area and long growth period led to high grain yield. Indirectly, growth period consistently had a positive effect on yield in all ecotypes, and plant height had a positive effect on yield for the indicas and japonica inbred only. Plant height had a negative effect for the japonica hybrid. Altogether, our findings potentially have valuable implications for improving the breeds of rice ecotypes.
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Affiliation(s)
- Ronghua Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
| | - Meijuan Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
| | - Umair Ashraf
- Department of Botany, University of Education (Lahore), Faisalabad-Campus, Faisalabad, Pakistan
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Shiwei Liu
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
| | - Jiaen Zhang
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
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Shade tolerance in Swarnaprabha rice is associated with higher rate of panicle emergence and positively regulated by genes of ethylene and cytokinin pathway. Sci Rep 2019; 9:6817. [PMID: 31048729 PMCID: PMC6497668 DOI: 10.1038/s41598-019-43096-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 03/06/2019] [Indexed: 12/27/2022] Open
Abstract
This study identifies characteristics of seedling, mature plant phenotypes, changes at genetic and genomic level associated with Swarnaprabha (SP) rice grown under prolonged shade and compared with Nagina 22 (N22). Coleoptile length under low red/far-red was intermediate between that in dark and red light in a 7-days growth frame. Whereas, highest rootlet number was discriminating in seedlings grown for 28 days in hydroponics. In shade, SP and N22 both showed several tolerant mature plant phenotypes, except the panicle length, yield per plant and % grain filling, which were higher in SP. Percentage decrease in yield / plant in shade showed significant positive correlation with increase in NDVI, decrease in panicle length and % grain filling (p ≤ 0.01). Rate of panicle emergence in shade was higher in SP than N22. Expression patterns of PHYTOCHROME INTERACTING FACTOR LIKE-13 and PHYTOCHROME B were contrasting in SP and N22 seedlings under continuous red or red/far-red. Microarray analysis revealed the up-regulation of most of the ethylene and cytokinin pathway genes in shade grown panicles of SP. Significant up-regulation of ETHYLENE RESPONSE ELEMENT BINDING PROTEIN-2, MOTHER OF FLOWERING TIME 1, and SHORT PANICLE1 genes in shade grown panicles of SP could explain its sustainable higher yield in shade.
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