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Use of methylation filtration and Cot fractionation for analysis of genome composition and comparative genomics in bread wheat

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Journal of Genetics and Genomics 2011年第7期38卷 315-325页

作者： Rajib Bandopadhyay Sachin Rustgi Rajat Kanti Chaudhuri Paramjit Khuran Jitendra Paul Khurana Akhilesh Kumar Tyagi harindra singh balyan Andreas Houben Pushpendra Kumar Gupta Department of Genetics & Plant Breeding Ch. Charan Singh University Meerut 250004 India Department of Biotechnology Birla Institute of Technology Mesra 835215 Ranchi India Department of Crop & Soil Sciences Washington State University Pullman 99163 USA Department of Botany University of Calcutta Kolkata 700019 India Department of Plant Molecular Biology University of Delhi South Campus New Delhi 110021 India Leibniz Institute of Plant Genetics and Crop Plant Research Corrensstrasse-03 Gatersleben 06466 Germany

We investigated the compositional and structural differences in sequences derived from different fractions of wheat genomic DNA obtained using methylation filtration and Cot fractionation. Comparative analysis of these sequences revealed large compositional and structural variations in terms of GC content, different structural elements including repeat sequences （e.g., transposable elements and simple sequence repeats）, protein coding genes, and non-coding RNA genes. A correlation between methylation status [determined on the basis of selective inclusion/ exclusion in methylation-filtered （MF） library] of different repeat elements and expression level was observed. The expression levels were determined by comparing MF sequences with expressed sequence tags （ESTs） available in the public domain. Only a limited overlap among ME high Cot （HC）, and ESTs was observed, suggesting that these sequences may largely either represent the low-copy non-transcribed sequences or include genes with low expression levels. Thus, these results indicated a need to study MF and HC sequences along with ESTs to fully appreciate complexity of wheat gene space.

关键词： Methylation--filtration Cot fractionation Transposable elements Gene-rich regions

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QTL analysis for some quantitative traits in bread wheat

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2007年第11期8卷 807-814页

作者： PUSHPENDRA Kumar Gupta harindra singh balyan PAWAN Laxminarayan Kulwal NEERAJ Kumar AJAY Kumar REYAZUL Rouf Mir AMITA Mohan JITENDRA Kumar Molecular Biology Laboratory Department of Genetics and Plant BreedingChaudhary Charan Singh UniversityMeerut 250 004India

Quantitative trait loci (QTL) analysis was conducted in bread wheat for 14 important traits utilizing data from four different mapping populations involving different approaches of QTL analysis. Analysis for grain protein content (GPC) sug- gested that the major part of genetic variation for this trait is due to environmental interactions. In contrast, pre-harvest sprouting tolerance (PHST) was controlled mainly by main effect QTL (M-QTL) with very little genetic variation due to environmental interactions; a major QTL for PHST was detected on chromosome arm 3AL. For grain weight, one QTL each was detected on chromosome arms 1AS, 2BS and 7AS. QTL for 4 growth related traits taken together detected by different methods ranged from 37 to 40; nine QTL that were detected by single-locus as well as two-locus analyses were all M-QTL. Similarly, single-locus and two-locus QTL analyses for seven yield and yield contributing traits in two populations respectively allowed detection of 25 and 50 QTL by composite interval mapping (CIM), 16 and 25 QTL by multiple-trait composite interval mapping (MCIM) and 38 and 37 QTL by two-locus analyses. These studies should prove useful in QTL cloning and wheat improvement through marker aided selection.

关键词： Quantitative trait loci (QTL) analysis Grain quality traits Grain protein content Pre-harvest sprouting tolerance(PHST) Grain weight Mapping populations Bread wheat

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