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Ashkani S.,University Putra Malaysia | Ashkani S.,Islamic Azad University at Tehran | Yusop M.R.,University Putra Malaysia | Shabanimofrad M.,University Putra Malaysia | And 5 more authors.
Current Issues in Molecular Biology | Year: 2015

Allele mining is a promising way to dissect naturally occurring allelic variants of candidate genes with essential agronomic qualities. With the identification, isolation and characterisation of blast resistance genes in rice, it is now possible to dissect the actual allelic variants of these genes within an array of rice cultivars via allele mining. Multiple alleles from the complex locus serve as a reservoir of variation to generate functional genes. The routine sequence exchange is one of the main mechanisms of R gene evolution and development. Allele mining for resistance genes can be an important method to identify additional resistance alleles and new haplotypes along with the development of allele-specific markers for use in marker-assisted selection. Allele mining can be visualised as a vital link between effective utilisation of genetic and genomic resources in genomics-driven modern plant breeding. This review studies the actual concepts and potential of mining approaches for the discovery of alleles and their utilisation for blast resistance genes in rice. The details provided here will be important to provide the rice breeder with a worthwhile introduction to allele mining and its methodology for breakthrough discovery of fresh alleles hidden in hereditary diversity, which is vital for crop improvement. © 2015, Caister Academic Press. All rights reserved. Source


Ashkani S.,University Putra Malaysia | Ashkani S.,Islamic Azad University at Tehran | Rafii M.Y.,University Putra Malaysia | Rahim H.A.,Malaysian Nuclear Agency | And 2 more authors.
Biotechnology Letters | Year: 2013

Malaysian rice, Pongsu Seribu 2, has wide-spectrum resistance against blast disease. Chromosomal locations conferring quantitative resistance were detected by linkage mapping with SSRs and quantitative trait locus (QTL) analysis. For the mapping population, 188 F3 families were derived from a cross between the susceptible cultivar, Mahsuri, and a resistant variety, Pongsu Seribu 2. Partial resistance to leaf blast in the mapping population was assessed. A linkage map covering ten chromosomes and consisting of 63 SSR markers was constructed. 13 QTLs, including 6 putative and 7 putative QTLs, were detected on chromosomes 1, 2, 3, 5, 6, 10, 11 and 12. The resulting phenotypic variation due to a single QTL ranged from 2 to 13 %. These QTLs accounted for approx. 80 % of the total phenotypic variation within the F3 population. Therefore, partial resistance to blast in Pongsu Seribu 2 is due to combined effects of multiple loci with major and minor effects. © 2013 Springer Science+Business Media Dordrecht. Source


Ashkani S.,University Putra Malaysia | Ashkani S.,Islamic Azad University at Tehran | Rafii M.Y.,University Putra Malaysia | Rahim H.A.,Malaysian Nuclear Agency | And 2 more authors.
Molecular Biology Reports | Year: 2013

Rice blast is one of the major fungal diseases that badly reduce rice production in Asia including Malaysia. There is not much information on identification of QTLs as well as linked markers and their association with blast resistance within local rice cultivars. In order to understanding of the genetic control of blast in the F3 families from indica rice cross Pongsu seribu2/Mahsuri, an analysis of quantitative trait loci against one of the highly virulent Malaysian rice blast isolate Magnaporthe oryzae, P5.0 was carried out. Result indicated that partial resistance to this pathotype observed in the present study was controlled by multiple loci or different QTLs. In QTL analysis in F3 progeny fifteen QTLs on chromosomes 1, 2, 3, 5, 6, 11 and 12 for resistance to blast nursery tests was identified. Three of detected QTLs (qRBr-6.1, qRBr-11.4, and qRBr-12.1) had significant threshold (LOD >3) and approved by both IM and CIM methods. Twelve suggestive QTLs, qRBr-1.2, qRBr-2.1, qRBr-4.1, qRBr-5.1, qRBr-6.2, qRBr-6.3, qRBr-8.1, qRBr-10.1, qRBr-10.2, qRBr-11.1, qRBr-11.2 and qRBr-11.3) with Logarithmic of Odds (LOD) <3.0 or LRS <15) were distributed on chromosomes 1, 2, 4, 5, 6, 8, 10, and 11. Most of the QTLs detected using single isolate had the resistant alleles from Pongsu seribu 2 which involved in the resistance in the greenhouse. We found that QTLs detected for deferent traits for the using isolate were frequently located in similar genomic regions. Inheritance study showed among F3 lines resistance segregated in the expected ratio of 15: 1 for resistant to susceptible. The average score for blast resistance measured in the green house was 3.15, 1.98 and 29.95 % for three traits, BLD, BLT and % DLA, respectively. © 2012 Springer Science+Business Media Dordrecht. Source


Ashkani S.,University Putra Malaysia | Ashkani S.,Islamic Azad University at Tehran | Rafii M.Y.,University Putra Malaysia | Shabanimofrad M.,University Putra Malaysia | And 4 more authors.
Critical Reviews in Biotechnology | Year: 2016

Rice blast disease, which is caused by the fungal pathogen Magnaporthe oryzae, is a recurring problem in all rice-growing regions of the world. The use of resistance (R) genes in rice improvement breeding programmes has been considered to be one of the best options for crop protection and blast management. Alternatively, quantitative resistance conferred by quantitative trait loci (QTLs) is also a valuable resource for the improvement of rice disease resistance. In the past, intensive efforts have been made to identify major R-genes as well as QTLs for blast disease using molecular techniques. A review of bibliographic references shows over 100 blast resistance genes and a larger number of QTLs (∼500) that were mapped to the rice genome. Of the blast resistance genes, identified in different genotypes of rice, ∼22 have been cloned and characterized at the molecular level. In this review, we have summarized the reported rice blast resistance genes and QTLs for utilization in future molecular breeding programmes to introgress high-degree resistance or to pyramid R-genes in commercial cultivars that are susceptible to M. oryzae. The goal of this review is to provide an overview of the significant studies in order to update our understanding of the molecular progress on rice and M. oryzae. This information will assist rice breeders to improve the resistance to rice blast using marker-assisted selection which continues to be a priority for rice-breeding programmes. © 2014 Informa Healthcare USA, Inc. Source


Hashemi F.S.G.,University Putra Malaysia | Rafii M.Y.,University Putra Malaysia | Ismail M.R.,University Putra Malaysia | Mahmud T.M.M.,University Putra Malaysia | And 6 more authors.
Critical Reviews in Plant Sciences | Year: 2013

One of the most valuable traits in high-quality rice is aroma or fragrance, which is important for consumer preference and global trade. Aromatic rice is unique and recognized as a badge of honor and an asset in many countries. Among more than 100 volatile components, 2-acetyl-1-pyrroline (2AP) is believed to be the main aromatic compound in rice. The principal gene contributing to 2AP is badh2, which was mapped on chromosome 8 by map-based cloning. A deletion in this gene truncates and makes non-functional the BADH2 protein. Thus, the mutant badh2 transcript leads to 2AP accumulation in aromatic rice. The discovery of the gene has led to the clarification of the biochemistry, molecular genetics and evolution of fragrant rice. The breeding of fragrant rice is now faster because of marker assisted selection (MAS), which is based on recognized genes. For a more extensive elucidation of all effective and fundamental factors contributing to rice fragrance, it is essential to further explore target quantitative trait loci (QTLs) and their inheritance and locations. © 2013 Copyright Taylor and Francis Group, LLC. Source

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