scholarly journals Deciphering the genetics basis of lodging resistance in wild rice O. longistaminata

2019 ◽  
Author(s):  
Weixiong Long ◽  
Dong Dan ◽  
Zhengqing Yuan ◽  
Yunping Chen ◽  
Jie Jin ◽  
...  
Keyword(s):  
Wild Rice ◽  
High Throughput Sequencing ◽  
Breaking Strength ◽  
Chromosome 8 ◽  
Stem Diameter ◽  
Chromosome 1 ◽  
Stem Length ◽  
Cultivated Rice ◽  
Lodging Resistance ◽  
Major Qtl

Abstract The abuse of fertilizer results in tall rice plants that are susceptible to lodging and reduced plant yield. Hence, it is important to identify and utilize the QTLs/genes for lodging resistance breeding. O. longistaminata exhibited a strong stem and high biomass productively, which could be the candidate gene pool for cultivars lodging resistance improvement. However, most of previous studies have focused on cultivated rice and few reports on wild rice. Here, a set of 152 BC 2 F 20 lines derived from a cross between 93-11 and O. longistaminata were evaluated for lodging resistance. QTL mapping analysis combined with SNP marker derived from high-throughput sequencing identified 12 QTLs for stem diameter (SD), 11 QTLs for stem length (SL) and 3 QTLs for breaking strength (BS). Of which, 14 QTLs were firstly identified from O. longistaminata. A major QTL, qLR1 which was delimited to a region about 80 Kb on chromosome 1, increased stem diameter, stem length and breaking strength. And another major QTL, qLR8 that was delimited in an interval about 100 Kb on chromosome 8, significantly enhanced the breaking strength. These results provide evidence that the O. longistaminata can be exploited to develop lodging resistant rice lines.

scholarly journals Identification of Candidate Gene for Internode Length in Rice to Enhance Resistance to Lodging Using QTL Analysis

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1369
Author(s):  
Dan-Dan Zhao ◽  
Ju-Hyeong Son ◽  
Muhammad Farooq ◽  
Kyung-Min Kim
Keyword(s):  
Candidate Genes ◽  
Qtl Analysis ◽  
Middle Part ◽  
Internode Length ◽  
Stem Diameter ◽  
Chromosome 1 ◽  
Doubled Haploid Population ◽  
Lodging Resistance ◽  
Cytochrome P450 Family ◽  
Uppermost Internode

Internode length and stem diameter are the primary traits affecting the lodging resistance of rice. Traits related to the length of the panicle (LP), uppermost internode (LUI), second internode (LSI), third internode (LTI), fourth internode (LFI), lowest internode (LLI) as well as stem diameter at the uppermost internode (SDUI), second internode (SDSI), third internode (SDTI), fourth internode (SDFI), and lowest internode (SDLI) in 120 Cheongcheong/Nagdong doubled haploid population were investigated using a quantitative trait locus (QTL) analysis. Thirty-four QTL regions affected LP and the length of each internode. Twenty-six QTL regions were associated with the stem diameter of each internode. RM12285-RM212 on chromosome 1 contained 10 QTLs related to the internode length, which have overlapped for over 2 years. Twenty-three candidate genes were screened using mark interval. Among the candidate genes, Os01g0803900, named OsCYPq1, which is in the Cytochrome P450 family, might be involved in gibberellins (GA) synthesis. GA is an essential plant growth regulator that affects plant height. OsCYPq1 catalyzes oxidation steps in the middle part of the GA pathway. OsCYPq1 is expected to provide valuable information to improve the marker assessment for target traits and QTL gene cloning in rice.

scholarly journals Wild rice harbors more root endophytic fungi than cultivated rice in the F1 offspring after crossbreeding

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Lei Tian ◽  
Enze Wang ◽  
Xiaolong Lin ◽  
Li Ji ◽  
Jingjing Chang ◽  
...  
Keyword(s):  
Endophytic Fungi ◽  
Wild Rice ◽  
High Throughput Sequencing ◽  
Sequencing Data ◽  
Cultivated Rice ◽  
The Core ◽  
Bacterial Genus ◽  
Wild Rice Species ◽  
Root Endophytic Fungi ◽  
Bacteria And Fungi

Abstract Background Rice, which serves as a staple food for more than half of the world’s population, is grown worldwide. The hybridization of wild and cultivated rice has enabled the incorporation of resistance to varying environmental conditions. Endophytic microbiota are known to be transferred with their host plants. Although some studies have reported on the endophytic microbiota of wild and cultivated rice, the inheritance from wild and cultivated rice accessions in next generations, in terms of endophytic microbiota, has not been examined. Results In the present study, the endophytic microbial community structures of Asian and African wild and cultivated rice species were compared with those of their F1 offspring. High-throughput sequencing data of bacterial 16S rDNA and fungal internal transcribed spacer regions were used to classify the endophytic microbiota of collected samples of rice. Results indicated that when either African or Asian wild rice species were crossed with cultivated rice accessions, the first generation harbored a greater number of root endophytic fungi than the cultivated parent used to make the crosses. Network analysis of the bacterial and fungal operational taxonomic units revealed that Asian and African wild rice species clustered together and exhibited a greater number of significant correlations between fungal taxa than cultivated rice. The core bacterial genus Acidovorax and the core fungal order Pleosporales, and genera Myrothecium and Bullera connected African and Asian wild rice accessions together, and both the wild rice accessions with their F1 offspring. On the other hand, the core bacterial genus Bradyrhizobium and the core fungal genera Dendroclathra linked the African and Asian cultivated rice accessions together. Conclusions This study has theoretical significance for understanding the effect of breeding on the inheritance of endophytic microbiota of rice and identifying beneficial endophytic bacteria and fungi among wild and cultivated rice species, and their F1 offspring.

scholarly journals A Dwarfing Gene sd1-d (Dee-geo-woo-gen dwarf) on Lodging Resistance and Related Traits in Rice

2021 ◽  
Vol 7 ◽  
pp. 1-9
Author(s):  
Mukunda Bhattarai ◽  
Misa Kamimukai ◽  
Birendra Bahadur Rana ◽  
Hiroki Oue ◽  
Shinji Matsumura ◽  
...  
Keyword(s):  
Breaking Strength ◽  
Chromosome 1 ◽  
Marine Science ◽  
Dominant Allele ◽  
Panicle Length ◽  
Lodging Resistance ◽  
Dwarfing Gene ◽  
Indica Variety ◽  
Isogenic Lines ◽  
Indica And Japonica Subspecies

A dwarfing allele at the sd1 locus on chromosome 1 in rice, sd1-d, has been playing important role for developing lodging-resistant and high-yielding indica varieties IR8 and IR36. The dominant allele SD1 for long culm at the locus is differentiated into SD1-in and SD1-ja that are harbored in indica and japonica subspecies, respectively. The sd1-d of IR36 was substituted with SD1-in or SD1-ja by 17 backcrosses with IR36, and two isogenic tall lines were developed by using an indica variety IR5867 and a japonica one ‘Koshihikari’ as donors, which were denoted by “5867-36” and “Koshi-36’’, respectively. The present study was conducted to examine the effect of dwarfing gene sd1-d on lodging resistance and related traits, compared with SD1-in and SD1-ja. Two isogenic lines and IR36 were cultivated in the field of the Faculty of Agriculture and Marine Science, Kochi University, Japan during 2017. Regarding index of lodging (g·cm/g × 100), genotypes were in the order: 5867-36 (97.4) > Koshi-36 (74.1) > IR36 (46.0) on the 21st-day after 80%-heading, and they were in the same order on 10th-day after 80%-heading. The 4th-panicle length (cm) was in the order: 5867-36 (118.7) > Koshi-36 (97.6) > IR36 (78.6). Similarly, the 4th-top weight (g) was in the order: 5867-36 (12.2) > Koshi-36 (10.2) > IR36 (9.6). The highest breaking strength (g) was recorded in IR36 (1649) followed by 5867-36 (1493) whereas the lowest breaking strength (g) was recorded in Koshi-36 (1360). Consequently, it is inferred that sd1-d enhances lodging resistance due to the decreases in the length and weight above the 4th-internode as well as the increase of breaking strength. The effect of SD1-in on lodging resistance is lower than that of SD1-ja.

Comparative RFLP mapping of a wild rice, Oryza officinalis, and cultivated rice, O. sativa

Genome ◽  
1994 ◽  
Vol 37 (3) ◽  
pp. 382-389 ◽  
Author(s):  
K. K. Jena ◽  
G. S. Khush ◽  
G. Kochert
Keyword(s):  
Gene Order ◽  
High Frequency ◽  
Wild Rice ◽  
Chromosome 1 ◽  
Rflp Markers ◽  
Chromosome 11 ◽  
Cultivated Rice ◽  
Oryza Officinalis ◽  
Rflp Map ◽  
Comparative Maps

A comparative RFLP map was constructed in a wild rice, Oryza officinalis, by using 139 genomic and cDNA probes that had been used previously to map RFLPs in O. sativa. Nine of the 12 chromosomes of O. officinalis were highly homosequential to those of O. sativa. A major rearrangement of gene order was detected in chromosome 1 and small inversions were found in chromosomes 3 and 11. Fourteen translocated RFLP markers were found, and chromosome 11 contained a high frequency of such translocated segments. Results were consistent with meiotic and trisomie analysis, which suggested that the genomes of O. officinalis and O. sativa were similar. Applications of comparative maps in plant breeding and gene cloning are discussed.Key words: Oryza, rice, wild rice, RFLP, genetic map.

Vernalization Accelerates Flowering of Lysimachia clethroides Duby

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 508b-508
Author(s):  
Pamela M. Lewis ◽  
Alan M. Armitage ◽  
Jim M. Garner
Keyword(s):  
Stem Diameter ◽  
Stem Length ◽  
Cut Flower ◽  
Bud Formation ◽  
Flower Production ◽  
Sphagnum Peat ◽  
Potting Media ◽  
Lysimachia Clethroides ◽  
Shoot Emergence

The effect of vernalization method and duration on off-season cut flower production of Lysimachia clethroides Duby was examined. Rhizomes harvested in October were cooled for 0, 4, 6, 8, 10 or 12 weeks at 4 ± 1 °C in crates with unmilled sphagnum peat or in 3.75-L pots with potting media prior to forcing in a warm greenhouse. After 6 or more weeks of cooling, shoots emerged from crate-cooled rhizomes in higher percentages than from pot-cooled rhizomes. However, only the duration of cooling, not the method, affected the rate of shoot emergence, visible bud formation and anthesis of the first bud in the raceme. As cooling increased from 0 to 12 weeks, the greenhouse days required for shoot emergence, visible bud formation and anthesis decreased linearly. The number of flowering flushes and flowering stems varied quadratically with cooling duration, and the highest yields occurred when rhizomes received between 4 and 10 weeks of cooling. As the number of successive flowering flushes increased, the stem length increased linearly while the stem diameter decreased linearly. High numbers of flowers were produced rapidly after 10 weeks of cooling.

Improvement of lodging resistance with QTLs for stem diameter in rice (Oryza sativa L.)

2008 ◽  
Vol 117 (5) ◽  
pp. 749-757 ◽  
Author(s):  
Takayuki Kashiwagi ◽  
Eiji Togawa ◽  
Naoki Hirotsu ◽  
Ken Ishimaru
Keyword(s):  
Oryza Sativa ◽  
Oryza Sativa L ◽  
Stem Diameter ◽  
Lodging Resistance

scholarly journals Transcriptomic and proteomic responses to herbivory in cultivated, Bt-transgenic and wild rice

2020 ◽  
Author(s):  
Yongbo Liu ◽  
Weiqing Wang ◽  
Yonghua Li ◽  
Fang Liu ◽  
Weijuan Han ◽  
...  
Keyword(s):  
Transgenic Rice ◽  
Wild Rice ◽  
Crop Production ◽  
Brown Planthopper ◽  
Hierarchical Cluster ◽  
Nilaparvata Lugens ◽  
Cultivated Rice ◽  
Kegg Pathways ◽  
Itraq Analysis ◽  
Go Terms

Abstract Background: Strategies are still employed to decrease insect damage in crop production, including conventional breeding with wild germplasm resources and transgenic technology with the insertion of foreign genes, while the insect-resistant mechanism of these strategies remains unclear. Results: Under the feeding of brown planthopper (Nilaparvata lugens), cultivated rice (WT) showed less DEGs (568) and DAPs (4) than transgenic rice (2098 and 11) and wild rice CL (1990 and 39) and DX (1932 and 25). Hierarchical cluster of DEGs showed gene expression of CL and DX were similar, slightly distinct to GT, and clearly different from WT. DEGs assigned to the GO terms were less in WT rice than GT, CL and DX, and “Metabolic process”, “cellular process”, “response to stimulus” were dominant. Wild rice CL significantly enriched in KEGG pathways of “Metabolic pathways”, “biosynthesis of secondary metabolites”, “plant-pathogen interaction” and “plant hormone signal transduction”. The iTRAQ analysis confirmed the results of RNA-seq, which showing the least GO terms and KEGG pathways responding to herbivory in the cultivated rice. Synthesize conclusions: This study demonstrated that similarity in the transcriptomic and proteomic response to herbivory for the wild rice and Bt-transgenic rice, while cultivated rice lack of enough pathways in response to herbivory. Our results highlighted the importance of conservation of crop wild species.

scholarly journals Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAs

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Chenna Swetha ◽  
Anushree Narjala ◽  
Awadhesh Pandit ◽  
Varsha Tirumalai ◽  
P. V. Shivaprasad
Keyword(s):  
Metabolic Pathways ◽  
Wild Rice ◽  
Regulation Of Gene Expression ◽  
Genome Integrity ◽  
Cultivated Rice ◽  
Mrna Targets ◽  
Ribonucleoprotein Complexes ◽  
The Poor ◽  
Rna Targets ◽  
Secondary Wall Formation

Abstract Background Small non-coding (s)RNAs are involved in the negative regulation of gene expression, playing critical roles in genome integrity, development and metabolic pathways. Targeting of RNAs by ribonucleoprotein complexes of sRNAs bound to Argonaute (AGO) proteins results in cleaved RNAs having precise and predictable 5` ends. While tools to study sliced bits of RNAs to confirm the efficiency of sRNA-mediated regulation are available, they are sub-optimal. In this study, we provide an improvised version of a tool with better efficiency to accurately validate sRNA targets. Results Here, we improvised the CleaveLand tool to identify additional micro (mi)RNA targets that belong to the same family and also other targets within a specified free energy cut-off. These additional targets were otherwise excluded during the default run. We employed these tools to understand the sRNA targeting efficiency in wild and cultivated rice, sequenced degradome from two rice lines, O. nivara and O. sativa indica Pusa Basmati-1 and analyzed variations in sRNA targeting. Our results indicate the existence of multiple miRNA-mediated targeting differences between domesticated and wild species. For example, Os5NG4 was targeted only in wild rice that might be responsible for the poor secondary wall formation when compared to cultivated rice. We also identified differential mRNA targets of secondary sRNAs that were generated after miRNA-mediated cleavage of primary targets. Conclusions We identified many differentially targeted mRNAs between wild and domesticated rice lines. In addition to providing a step-wise guide to generate and analyze degradome datasets, we showed how domestication altered sRNA-mediated cascade silencing during the evolution of indica rice.

scholarly journals Genetic Divergence in Indigenous Wild and Cultivated Rice Species of Manipur Valley

ISRN Genetics ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
K. Medhabati ◽  
K. Rajiv Das ◽  
M. Rohinikumar ◽  
H. Sunitibala ◽  
Th. Dikash Singh
Keyword(s):  
Genetic Divergence ◽  
Wild Rice ◽  
Flag Leaf ◽  
Cluster Formation ◽  
Leaf Length ◽  
Cultivated Rice ◽  
And Performance ◽  
Flag Leaf Length ◽  
The Individual ◽  
Hybridization Programme

Genetic divergence of 32 indigenous rice germplasms and five wild rice of which three from Manipur and two wild rice procured from IRRI, Philippines was investigated using Mahalanobis, D2 statistic. Based on twelve agromorphological characters, the thirty-seven germplasms both wild and cultivated were grouped into five clusters based on the relative magnitudes of D2 values following Tocher's method of cluster formation. Based on the rank totals, the characters which contributed maximum towards genetic divergence in the present studies were grain yield/plant, spikelet/panicle, 100 grain weight, grain length, days to 50% flowering, ear bearing tillers/plant, and flag leaf length. In the present study, maximum intercluster distance was estimated between cluster III and (D2=14.09) which was closed followed by clusters II and V (D2=12.50). On the basis of their greater intercluster distance, high value of cluster mean according to the character to be improved and performance of the individual germplasms for the character, the germplasms could be used in hybridization programme for improvement of different plant characters in the rice germplasms of Manipur.

Sign in / Sign up

Export Citation Format

Share Document