Development and utilization of novel intron length polymorphic markers in foxtail millet (Setaria italica (L.) P. Beauv.)

Genome ◽  
2011 ◽  
Vol 54 (7) ◽  
pp. 586-602 ◽  
Author(s):  
Sarika Gupta ◽  
Kajal Kumari ◽  
Jyotirmoy Das ◽  
Charu Lata ◽  
Swati Puranik ◽  
...  
Keyword(s):  
Expressed Sequence Tag ◽  
Gene Diversity ◽  
Foxtail Millet ◽  
Subtractive Hybridization ◽  
Intron Length ◽  
Setaria Italica ◽  
Sequence Information ◽  
Mrna Maturation ◽  
Average Gene ◽  
High Level

Introns are noncoding sequences in a gene that are transcribed to precursor mRNA but spliced out during mRNA maturation and are abundant in eukaryotic genomes. The availability of codominant molecular markers and saturated genetic linkage maps have been limited in foxtail millet (Setaria italica (L.) P. Beauv.). Here, we describe the development of 98 novel intron length polymorphic (ILP) markers in foxtail millet using sequence information of the model plant rice. A total of 575 nonredundant expressed sequence tag (EST) sequences were obtained, of which 327 and 248 unique sequences were from dehydration- and salinity-stressed suppression subtractive hybridization libraries, respectively. The BLAST analysis of 98 EST sequences suggests a nearly defined function for about 64% of them, and they were grouped into 11 different functional categories. All 98 ILP primer pairs showed a high level of cross-species amplification in two millets and two nonmillets species ranging from 90% to 100%, with a mean of ∼97%. The mean observed heterozygosity and Nei’s average gene diversity 0.016 and 0.171, respectively, established the efficiency of the ILP markers for distinguishing the foxtail millet accessions. Based on 26 ILP markers, a reasonable dendrogram of 45 foxtail millet accessions was constructed, demonstrating the utility of ILP markers in germplasm characterizations and genomic relationships in millets and nonmillets species.

Molecular Characterization and Genetic Diversity Study in F3 Population of Rice

2013 ◽  
Vol 20 (1-2) ◽  
pp. 1-8
Author(s):  
MM Rahman ◽  
L Rahman ◽  
SN Begum ◽  
F Nur
Keyword(s):  
Genetic Distance ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Polymorphic Loci ◽  
Rice Genotypes ◽  
High Level ◽  
Genetic Diversity Study ◽  
Diversity Study

Random Amplified Polymorphic DNA (RAPD) assay was initiated for molecular genetic analysis among 13 F3 rice lines and their parents. Four out of 15 decamer random primers were used to amplify genomic DNA and the primers yielded a total of 41 RAPD markers of which 37 were considered as polymorphic with a mean of 9.25 bands per primer. The percentage of polymorphic loci was 90.24. The highest percentage of polymorphic loci (14.63) and gene diversity (0.0714) was observed in 05-6 F3 line and the lowest polymorphic loci (0.00) and gene diversity (0.00) was found in 05-12 and 05-15 F3 lines. So, relatively high level of genetic variation was found in 05-6 F3 line and it was genetically more diverse compared to others. The average co-efficient of gene differentiation (GST) and gene flow (Nm) values across all the loci were 0.8689 and 0.0755, respectively. The UPGMA dendrogram based on the Nei’s genetic distance differentiated the rice genotypes into two main clusters: PNR-519, 05-19, 05-14, 05-12 and 05-17 grouped in cluster 1. On the other hand, Baradhan, 05-9, 05-13, 05-11, 05-5, 05-6, 05-1, 05-4, 05-15 and 05-25 were grouped in cluster 2. The highest genetic distance (0.586) was found between 05-4 and 05-17 F3 lines and they remain in different cluster.DOI: http://dx.doi.org/10.3329/pa.v20i1-2.16839 Progress. Agric. 20(1 & 2): 1 – 8, 2009

Variation and Correlation Analysis of Hay Forage Quality Traits of Foxtail Millet [Setaria italica (L.) Beauv.]

2013 ◽  
Vol 38 (5) ◽  
pp. 800-807
Author(s):  
Hui ZHI ◽  
Zhen-Gang NIU ◽  
Guan-Qing JIA ◽  
Yang CHAI ◽  
Wei LI ◽  
...  
Keyword(s):  
Correlation Analysis ◽  
Foxtail Millet ◽  
Forage Quality ◽  
Setaria Italica ◽  
Quality Traits

Genetic Studies with Foxtail Millet, Setaria Italica (L.) Beauv. 1

1940 ◽  
Vol 32 (6) ◽  
pp. 426-438 ◽  
Author(s):  
H. W. Li ◽  
J. C. Meng ◽  
C. H. Li
Keyword(s):  
Foxtail Millet ◽  
Setaria Italica ◽  
Genetic Studies

Restriction Fragment Length Polymorphism and Divergence in the Genomic Regions of High and Low Recombination in Self-Fertilizing and Cross-Fertilizing Aegilops Species

Genetics ◽  
1998 ◽  
Vol 148 (1) ◽  
pp. 423-434
Author(s):  
Jan Dvorřák ◽  
Ming-Cheng Luo ◽  
Zu-Li Yang
Keyword(s):  
Related Species ◽  
Gene Diversity ◽  
Single Copy ◽  
Species Variation ◽  
Recombination Rates ◽  
Distal Chromosome ◽  
Phylogenetic Status ◽  
Average Gene ◽  
Genomic Regions ◽  
Chromosome Regions

Abstract RFLP was investigated at 52 single-copy gene loci among six species of Aegilops, including both cross-fertilizing and self-fertilizing species. Average gene diversity (H) was found to correlate with the level of outcrossing. No relationship was found between H and the phylogenetic status of a species. In all six species, the level of RFLP at a locus was a function of the position of the locus on the chromosome and the recombination rate in the neighborhood of the locus. Loci in the proximal chromosome regions, which show greatly reduced recombination rates relative to the distal regions, were significantly less variable than loci in the distal chromosome regions in all six species. Variation in recombination rates was also reflected in the haplotype divergence between closely related species; loci in the chromosome regions with low recombination rates were found to be diverged less than those in the chromosome regions with high recombination rates. This relationship was not found among the more distantly related species.

scholarly journals Establishing in planta haploid inducer line by edited SiMTL in foxtail millet ( Setaria italica )

2021 ◽  
Author(s):  
Zixiang Cheng ◽  
Yao Sun ◽  
Suhua Yang ◽  
Hui Zhi ◽  
Tao Yin ◽  
...  
Keyword(s):  
Foxtail Millet ◽  
Setaria Italica ◽  
In Planta ◽  
Haploid Inducer

scholarly journals Plant-based milk Developed from Soy (Glycine max) Milk and Foxtail Millet (Setaria italica)

2021 ◽  
Vol 807 (2) ◽  
pp. 022063
Author(s):  
Dzul Fadly ◽  
Wiwi Ulfairah Sutarno ◽  
Yuges Saputri Muttalib ◽  
Masturi Muhajir ◽  
Fatimah Fitriani Mujahidah
Keyword(s):  
Glycine Max ◽  
Foxtail Millet ◽  
Setaria Italica

scholarly journals Genetic Interactions WithCLF1Identify Additional Pre-mRNA Splicing Factors and a Link Between Activators of Yeast Vesicular Transport and Splicing

Genetics ◽  
2003 ◽  
Vol 164 (3) ◽  
pp. 895-907 ◽  
Author(s):  
Kevin Vincent ◽  
Qiang Wang ◽  
Steven Jay ◽  
Kathryn Hobbs ◽  
Brian C Rymond
Keyword(s):  
Mrna Splicing ◽  
Splicing Factors ◽  
Sequence Information ◽  
Specific Sequence ◽  
Synthetic Lethal ◽  
Growth Defects ◽  
Mrna Maturation ◽  
Assembly Factor ◽  
Gtpase Activation ◽  
Synthetic Growth

AbstractClf1 is a conserved spliceosome assembly factor composed predominately of TPR repeats. Here we show that the TPR elements are not functionally equivalent, with the amino terminus of Clf1 being especially sensitive to change. Deletion and add-back experiments reveal that the splicing defect associated with TPR removal results from the loss of TPR-specific sequence information. Twelve mutants were found that show synthetic growth defects when combined with an allele that lacks TPR2 (i.e., clf1Δ2). The identified genes encode the Mud2, Ntc20, Prp16, Prp17, Prp19, Prp22, and Syf2 splicing factors and four proteins without established contribution to splicing (Bud13, Cet1, Cwc2, and Rds3). Each synthetic lethal with clf1Δ2 (slc) mutant is splicing defective in a wild-type CLF1 background. In addition to the splicing factors, SSD1, BTS1, and BET4 were identified as dosage suppressors of clf1Δ2 or selected slc mutants. These results support Clf1 function through multiple stages of the spliceosome cycle, identify additional genes that promote cellular mRNA maturation, and reveal a link between Rab/Ras GTPase activation and the process of pre-mRNA splicing.

scholarly journals Phytolith Analysis for Differentiating between Foxtail Millet (Setaria italica) and Green Foxtail (Setaria viridis)

PLoS ONE ◽  
2011 ◽  
Vol 6 (5) ◽  
pp. e19726 ◽  
Author(s):  
Jianping Zhang ◽  
Houyuan Lu ◽  
Naiqin Wu ◽  
Xiaoyan Yang ◽  
Xianmin Diao
Keyword(s):  
Foxtail Millet ◽  
Setaria Italica ◽  
Setaria Viridis ◽  
Phytolith Analysis ◽  
Green Foxtail
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