Identification of YAC clones containing the mutable slender glume locus slg in rice (Oryza sativa L.)

Genome ◽  
2001 ◽  
Vol 44 (1) ◽  
pp. 1-6 ◽  
Author(s):  
M Teraishi ◽  
H Hirochika ◽  
Y Okumoto ◽  
A Horibata ◽  
H Yamagata ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Gamma Ray ◽  
Yeast Artificial Chromosome ◽  
Oryza Sativa L ◽  
Artificial Chromosome ◽  
Rice Cultivar ◽  
Inverse Pcr ◽  
Polymorphism Analysis ◽  
Japonica Rice ◽  
Yac Contig

A mutable slender glume gene slg, which often reverts to the wild-type state, was induced by gamma-ray irradiation of seeds of the japonica rice cultivar 'Gimbozu'. The final goal was to understand whether the slender glume mutation was associated with the insertion of a transposable element, utilizing map-based cloning techniques. The RFLP (restriction fragment length polymorphism) analysis revealed that the slg locus was located between two RFLP loci, XNpb33 and R1440, on chromosome 7 with recombination values of 3.1% and 1.0%, respectively. Using these two RFLP loci as probes, five YAC (yeast artificial chromosome) clones containing either of these two loci were selected from a YAC library. Subsequently, both end fragments of these YAC clones, amplified by the inverse PCR (IPCR) method, were used to select new YAC clones more closely located to the slg locus. After repeating such a procedure, we successfully constructed a 6-cM YAC contig, and identified four overlapping YAC clones, Y1774, Y3356, Y5124, and Y5762, covering the slg locus. The chromosomal location of the slg was narrowed down to the region with a physical distance of less than 280 kb between the right-end fragments of Y1774 and Y3356.Key words: Oryza sativa, mutable gene, slender glume mutation, YAC contig.

scholarly journals Structure of the Chromosome VII Centromere Region in Neurospora crassa: Degenerate Transposons and Simple Repeats

1998 ◽  
Vol 18 (9) ◽  
pp. 5465-5477 ◽  
Author(s):  
Edward B. Cambareri ◽  
Rafael Aisner ◽  
John Carbon
Keyword(s):  
Neurospora Crassa ◽  
Yeast Artificial Chromosome ◽  
Fragment Length Polymorphism ◽  
Artificial Chromosome ◽  
Polymorphism Analysis ◽  
Dna Repeats ◽  
Centromere Region ◽  
Simple Repeats ◽  
Restriction Fragment Length ◽  
Repeat Induced Point Mutation

ABSTRACT DNA from the centromere region of linkage group (LG) VII ofNeurospora crassa was cloned previously from a yeast artificial chromosome library and was found to be atypical ofNeurospora DNA in both composition (AT rich) and complexity (repetitive). We have determined the DNA sequence of a small portion (∼16.1 kb) of this region and have identified a cluster of three new retrotransposon-like elements as well as degenerate fragments from the 3′ end of Tad, a previously identified LINE-like retrotransposon. This region contains a novel full-length but nonmobilecopia-like element, designated Tcen, that is only associated with centromere regions. Adjacent DNA contains portions of a gypsy-like element designated Tgl1. A third new element, Tgl2, shows similarity to theTy3 transposon of Saccharomyces cerevisiae. All three of these elements appear to be degenerate, containing predominantly transition mutations suggestive of the repeat-induced point mutation (RIP) process. Three new simple DNA repeats have also been identified in the LG VII centromere region. While Tcenelements map exclusively to centromere regions by restriction fragment length polymorphism analysis, the defective Tad elements appear to occur most frequently within centromeres but are also found at other loci including telomeres. The characteristics and arrangement of these elements are similar to those seen in theDrosophila centromere, but the relative abundance of each class of repeats, as well as the sequence degeneracy of the transposon-like elements, is unique to Neurospora. These results suggest that the Neurospora centromere is heterochromatic and regional in character, more similar to centromeres of Drosophila than to those of most single-cell yeasts.

A physical map with yeast artificial chromosome (YAC) clones covering 63% of the 12 rice chromosomes

Genome ◽  
2001 ◽  
Vol 44 (1) ◽  
pp. 32-37 ◽  
Author(s):  
Shoko Saji ◽  
Yosuke Umehara ◽  
Baltazar A Antonio ◽  
Hiroko Yamane ◽  
Hiroshi Tanoue ◽  
...  
Keyword(s):  
Genetic Map ◽  
Dna Markers ◽  
Yeast Artificial Chromosome ◽  
Physical Map ◽  
Genome Structure ◽  
Rice Genome ◽  
Artificial Chromosome ◽  
Physical Length ◽  
Rice Chromosomes ◽  
Yac Contig

A new YAC (yeast artificial chromosome) physical map of the 12 rice chromosomes was constructed utilizing the latest molecular linkage map. The 1439 DNA markers on the rice genetic map selected a total of 1892 YACs from a YAC library. A total of 675 distinct YACs were assigned to specific chromosomal locations. In all chromosomes, 297 YAC contigs and 142 YAC islands were formed. The total physical length of these contigs and islands was estimated to 270 Mb which corresponds to approximately 63% of the entire rice genome (430 Mb). Because the physical length of each YAC contig has been measured, we could then estimate the physical distance between genetic markers more precisely than previously. In the course of constructing the new physical map, the DNA markers mapped at 0.0-cM intervals were ordered accurately and the presence of potentially duplicated regions among the chromosomes was detected. The physical map combined with the genetic map will form the basis for elucidation of the rice genome structure, map-based cloning of agronomically important genes, and genome sequencing.Key words: physical mapping, YAC contig, rice genome, rice chromosomes.

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 Kualitas Fisik Beras (Oryza sativa L.) Mutan M4 Hasil Iradiasi Sinar Gamma

2020 ◽  
Vol 4 (1) ◽  
pp. 32-42
Author(s):  
Nanda Funna Ledita ◽  
Efendi Efendi ◽  
Rita Hayati
Keyword(s):  
Oryza Sativa ◽  
Gamma Ray ◽  
Amylose Content ◽  
Oryza Sativa L ◽  
Mutant Line ◽  
Milled Rice ◽  
Physical Quality ◽  
Significant Difference ◽  
Gamma Ray Irradiation

Abstrak.  Beras (Oryza sativa L.) merupakan salah satu tanaman pangan yang berfungsi sebagai tanaman pokok selain gandum dan jagung di Indonesia, dikarenakan mengandung nutrisi yang dibutuhkan tubuh seperti karbohidrat, protein, air  dan lemak. Meningkatnya jumlah penduduk maka permintaan terhadap beras semakin meningkat. Permintaan tersebut sangat ditentukan oleh selera konsumen yang dipengaruhi oleh kualitas beras yaitu mutu fisik (ukuran dan bentuk butiran, rendemen dan pengapuran), mutu tanak (kadar amilosa dan suhu gelatinisasi) dan mutu rasa (tekstur dan aroma). Penelitian ini bertujuan untuk mengetahui kualitas beberapa galur padi mutan M4 hasil iradiasi sinar gamma. Penelitian ini dilaksanakan di Laboratorium Ilmu dan Teknologi Benih, Laboratorium Analisis Pangan dan Hasil Pertanian, Laboratorium Ilmu Nutrisi dan Teknologi Pakan dan Laboratorium Fisiologi Tumbuhan Fakultas Pertanian Universitas Syiah Kuala, serta Laboratorium Departemen Ilmu dan Teknologi Pangan Fakultas Teknologi Pertanian Institut Pertanian Bogor, yang berlangsung pada bulan April hingga Juli 2018. Rancangan yang digunakan dalam penelitian ini adalah Rancangan Acak Lengkap (RAL) pola non faktorial dengan 3 ulangan. Perlakuan penelitian ini berupa galur (G) dengan 5 taraf, yaitu i-Snb (G0) kontrol, O-39e (G1), O-57d (G2), O-57e (G3) dan O-88j (G4). Parameter yang diamati yaitu sifat fisik beras (densitas kamba, derajat sosoh, dimensi beras rendemen beras giling, dan warna). Hasil penelitian menunjukkan bahwa galur  mutan M4 berpengaruh sangat nyata terhadap kualitas sifat fisik rendemen beras giling dan warna nilai L (kecerahan). Rendemen beras giling terbaik galur O-39e (70,33%) dan warna nilai L (kecerahan) galur O-88j (117,90).  Perlakuan terbaik secara kumulatif  untuk sifat fisik beras yaitu pada i-Snb.. Physical Quality of Rice (Oryza sativa L. ) M4  Mutant Results of Gamma Ray IrradiationAbstract. Rice (Oryza sativa L.) is one of main food which the function is to be staple food beside wheat and corn in Indonesia because it contains nutrients such as carbohydrates, protein, water, and fat. Towards the increasing populations, the demand of rice is increasing as well. The demand is largerly depends on the consumer taste affected by the quality of rice which are physical quality (size and grain shape, rendemen, and calcification), cooked quality (amylose content and gelatinization temperature) and flavor quality (texture and smell). The purpose of this research was to investigate the quality of rice from several M4 mutant line resulting from gamma ray irradiation. This research was conducted at the Laboratory of Seed Science and Technology and Laboratory of Food and Agricultural Analysis, Faculty of Agriculture, Syiah Kuala University, Banda Aceh, from the month April to July 2018. The design used in this study was based on a non-factorial completely randomize design with 3 replications and continued with the Least Significant Difference Test (LSD) level of 5% on a significant F test results. The results showed that the M4 mutant line had a very significant effect on the quality of physical properties, the yield of milled rice and the best color L (brightness), namely on the O-88j and O-39e line.

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