RAPD analysis of jasmine rice-specific genomic structure

Genome ◽  
2006 ◽  
Vol 49 (6) ◽  
pp. 716-719 ◽  
Author(s):  
Y J Wu ◽  
Y Chen ◽  
J Wang ◽  
C X Zhu ◽  
B L Xu
Keyword(s):  
Oryza Sativa L ◽  
Genomic Structure ◽  
Pcr Amplification ◽  
Disease Resistance Gene ◽  
Japonica Rice ◽  
Rice Seed ◽  
Specific Sequence ◽  
First Intron ◽  
Jasmine Rice ◽  
True Relation

Total genomic DNA was extracted from 29 samples of rice seed, including jasmine rice Oryza sativa L. subsp indica 'KDML105', 'KDML105'-derived varieties, nonaromatic Thailand rice, and japonica rice. Polymorphism in RAPD profiles was analyzed to explore the genomic structure specific to jasmine rice. The degree of band sharing was used to evaluate genetic distance between varieties and to construct a phylogenetic tree. RD15, CNTLR85033, and CNT87040 were found to be closest to 'KDML105', which was consistent with the true relation among them. Four RAPD fragments that cooperatively distinguished jasmine rice from others were cloned and sequenced. PCR amplification using pairs of primers designed specifically further confirmed the credibility of the RAPD result. Comparison through Genbank revealed that a 454 bp RAPD band was similar to the first intron of a putative Cf2/Cf5 disease resistance gene and a 1107 bp RAPD band similar to a wall-associated kinase (wak) gene sequence.Key words: Jasmine rice, RAPD, specific sequence.

Organization, Expression and Evolution of a Disease Resistance Gene Cluster in Soybean

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1961-1977
Author(s):  
Michelle A Graham ◽  
Laura Fredrick Marek ◽  
Randy C Shoemaker
Keyword(s):  
Disease Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Developmental Stages ◽  
Gene Evolution ◽  
Pcr Amplification ◽  
Disease Resistance Genes ◽  
Disease Resistance Gene ◽  
R Genes ◽  
Specific Primers

Abstract PCR amplification was previously used to identify a cluster of resistance gene analogues (RGAs) on soybean linkage group J. Resistance to powdery mildew (Rmd-c), Phytophthora stem and root rot (Rps2), and an ineffective nodulation gene (Rj2) map within this cluster. BAC fingerprinting and RGA-specific primers were used to develop a contig of BAC clones spanning this region in cultivar “Williams 82” [rps2, Rmd (adult onset), rj2]. Two cDNAs with homology to the TIR/NBD/LRR family of R-genes have also been mapped to opposite ends of a BAC in the contig Gm_Isb001_091F11 (BAC 91F11). Sequence analyses of BAC 91F11 identified 16 different resistance-like gene (RLG) sequences with homology to the TIR/NBD/LRR family of disease resistance genes. Four of these RLGs represent two potentially novel classes of disease resistance genes: TIR/NBD domains fused inframe to a putative defense-related protein (NtPRp27-like) and TIR domains fused inframe to soybean calmodulin Ca2+-binding domains. RT-PCR analyses using gene-specific primers allowed us to monitor the expression of individual genes in different tissues and developmental stages. Three genes appeared to be constitutively expressed, while three were differentially expressed. Analyses of the R-genes within this BAC suggest that R-gene evolution in soybean is a complex and dynamic process.

scholarly journals Detection of QTLs for Outcrossing-Related Traits in CSSL Population Derived from Primitive Japonica Accession Ludao in the Genetic Background of O. sativa spp. Japonica Restorer C-bao Using RSTEP-LRT Method

Agronomy ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 28
Author(s):  
Lal Bux ◽  
Dalu Li ◽  
Muhammad Faheem ◽  
Nour Ali ◽  
Muzafar Hussain Sirohi ◽  
...  
Keyword(s):  
Seed Production ◽  
Hybrid Rice ◽  
Oryza Sativa L ◽  
Flag Leaf ◽  
Leaf Angle ◽  
Ratio Test ◽  
Phenotypic Variance ◽  
Rice Seed ◽  
Hybrid Seed Production ◽  
Cms Line

The outcrossing traits in rice (Oryza sativa L.) affect the yield of hybrid seed production. Using a cytoplasmic male sterile (CMS) line with good outcrossing traits, such as short flag leaf length (FLL), narrow flag leaf width (FLW), wide flag leaf angle (FLA), and elongated panicle neck length (PNL), for hybrid rice seed production, it is possible to avoid the procedure of cutting flag leaves and make the supplementary pollination feasible by machine. In this study, a japonica restorer C-bao as the receptor parent and a primitive japonica accession Ludao as the donor parent were used to construct a chromosome segment substitution line (CSSL) population. The CSSL population was used to detect quantitative trait loci (QTLs) for the four outcrossing traits using a likelihood ratio test based on the stepwise regression (RSTEP-LRT) method. The CSSL population constructed consisted of 163 lines covering 90.7% of the donor genome. Among the seven QTLs detected in the CSSL population, four QTLs were detected in both years. qFLL-4 explained 6.70% of the two-year-averaged phenotypic variance, and the alleles from Ludao decreased FLL 5.1 cm. qFLA-1.1 and qFLA-1.2 explained 7.85% and 21.29% of the 2-year-averaged phenotypic variance respectively, and the alleles from Ludao increased FLA 17.38° and 31.50°. qPNL-8 explained 8.87% of the 2-year-averaged phenotypic variance, and the alleles from Ludao increased PNL 4.44 cm. These favorable alleles identified could be used to improve the outcrossing traits of parents for hybrid rice seed production in rice.

Trypanosomatidae:PhytomonasDetection in Plants and Phytophagous Insects by PCR Amplification of a Genus-Specific Sequence of the Spliced Leader Gene

1999 ◽  
Vol 91 (3) ◽  
pp. 268-279 ◽  
Author(s):  
Myrna G. Serrano ◽  
Luiz R. Nunes ◽  
Marta Campaner ◽  
Gregory A. Buck ◽  
Erney P. Camargo ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Phytophagous Insects ◽  
Specific Sequence ◽  
Spliced Leader

scholarly journals Evaluation of japonica rice (Oryza sativa L.) varieties and their improvement in terms of stability, yield and cooking quality by pure-line selection in Thailand

ScienceAsia ◽  
2020 ◽  
Vol 46 (2) ◽  
pp. 157
Author(s):  
Pawat Nakwilai ◽  
Sulaiman Cheabu ◽  
Possawat Narumon ◽  
Chatree Saensuk ◽  
Siwaret Arikit ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Cooking Quality ◽  
Oryza Sativa L ◽  
Pure Line ◽  
Japonica Rice ◽  
Line Selection

scholarly journals A Novel Mutation of the NARROW LEAF 1 Gene Adversely Affects Plant Architecture in Rice (Oryza sativa L.)

2020 ◽  
Vol 21 (21) ◽  
pp. 8106
Author(s):  
Prasanta K. Subudhi ◽  
Richard S. Garcia ◽  
Sapphire Coronejo ◽  
Teresa B. De Leon
Keyword(s):  
Signaling Pathways ◽  
Plant Architecture ◽  
Oryza Sativa L ◽  
Novel Mutation ◽  
Bulked Segregant Analysis ◽  
Photosynthetic Apparatus ◽  
Pcr Amplification ◽  
Genetic Network ◽  
Rice Cultivar ◽  
Weedy Rice

Plant architecture is critical for enhancing the adaptability and productivity of crop plants. Mutants with an altered plant architecture allow researchers to elucidate the genetic network and the underlying mechanisms. In this study, we characterized a novel nal1 rice mutant with short height, small panicle, and narrow and thick deep green leaves that was identified from a cross between a rice cultivar and a weedy rice accession. Bulked segregant analysis coupled with genome re-sequencing and cosegregation analysis revealed that the overall mutant phenotype was caused by a 1395-bp deletion spanning over the last two exons including the transcriptional end site of the nal1 gene. This deletion resulted in chimeric transcripts involving nal1 and the adjacent gene, which were validated by a reference-guided assembly of transcripts followed by PCR amplification. A comparative transcriptome analysis of the mutant and the wild-type rice revealed 263 differentially expressed genes involved in cell division, cell expansion, photosynthesis, reproduction, and gibberellin (GA) and brassinosteroids (BR) signaling pathways, suggesting the important regulatory role of nal1. Our study indicated that nal1 controls plant architecture through the regulation of genes involved in the photosynthetic apparatus, cell cycle, and GA and BR signaling pathways.

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