Browsing by Author "Rahman, M."

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Characterization of Ascochyta rabiei for population structure, mating type and pathogenic variability from Pakistan and United States
(III international Ascochyta workshop, Cordoba, Spain, 2012) Hinaali, A.S.S.; Attanayake, R.N.; Rahman, M.; Chen, W.
Chickpea production is greatly hampered by blight causing fungal pathogen Ascochyta rabiei (AR) in chickpea growing regions of the world. Genetic variability and mating type frequency of thirty two AR isolates from six geographical regions of Pakistan were compared with a US-AR population. Pakistani AR (PAR) population had an apparent skewed (3 Mat1-2: 1 Mat1-1) distribution, although Chi-square tests showed non significant deviation from equal distribution due to small sample sizes and the US-population showed a 1:1 distribution. The results showed that sexual reproduction is rare in PAR due to either unavailability of both mating types or lack of conductive environment but statistical analysis showed panmixia which may be due to past recombinational events. Genetic variation at six microsatellite loci was assessed and each isolate was assigned to a microsatellite haplotype. Population structure using Bayesian analyses differentiated isolates into three distinct clusters, two clusters of PAR and one of the US isolates. However, few isolates from US shared same genetic background with one cluster of the PAR isolates, providing a link of inter-continental migration of the pathogen due to import of seeds. Additionally, the two clusters of Pak-isolates are not strictly linked to the geographic locations in Pakistan, suggesting frequent gene flow of AR among different locations. Pathogenic variability of nineteen PAR collected from two different provinces was assessed. The results based on the reaction of isolates with differential lines showed that aggressive and highly aggressive pathotypes II and III respectively are prevalent in Pakistan as compared to least aggressive pathotype I. It is interesting to note that highly aggressive pathotypes III and IV have only beenreported from Syria and Pakistan where we assume less frequency of sexual reproduction due to predominance of one mating type, in contrast to other countries where both mating types are present in equal ratio hence, this issue needs further investigations.
Population structure and mating type distribution of the chickpea blight pathogen Ascochytarabiei form Pakistan and the United States
(Journal of plant pathology, 2012) Ali, H.; Alam, S.S.; Attanayake, R.N.; Rahman, M.; Chen, W.
Ascochyta blight caused by the fungus Ascochyta rabiei (AR) depresses chickpea production in Pakistan and worldwide. Thirty two AR isolates representing six geographical regions of Pakistan were compared with a US-AR population for mating type frequency and genetic variation. Mating type results showed that the Pakistani AR (PAR) population had an apparent skewed (3 Mat1-2: 1 Mat1-1) distribution, although Chi-square tests showed non-significant deviation from equal distribution due to small sample sizes. The US population showed a 1:1 distribution of the two mating types. The uneven distribution of mating types indicates that sexual reproduction among the PAR is rare due to either unavailability of both mating types or lack of conducive environment, but statistical analysis showed that panmixia is there reflecting past recombinational events. Genetic variation at six microsatellite loci was assessed and each isolate was assigned to a microsatellite haplotype. Population structure of the isolates was inferred using Bayesian analyses implemented in the structure software which differentiated isolates into three distinct clusters, two clusters of PAR and one of the US isolates. However, few isolates from the US shared the same genetic background with one cluster of the PAR isolates, providing a link of inter-continental migration of the pathogen. Additionally, the two clusters of PAR-isolates are not strictly associated with geographic locations in Pakistan, suggesting frequent gene flow of AR among different locations. Future studies should extend the sampling of representative populations to overcome the limitations of the small sample size for more accurate assessment of population structure.
Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation
(Nature Publishing Company, 2015) Kato, N.; Loh, M.; Takeuchi, F.; Verweij, N.; Wang, X.; Zhang, W.; Kelly, T.N.; Saleheen, D.; Lehne, B.; Leach, I.M.; Drong, A.W.; Abbott, J.; Wahl, S.; Tan, S.T.; Scott, W.R.; Campanella, G.; Chadeau-Hyam, M.; Afzal, U.; Ahluwalia, T.S.; Bonder, M.J.; Chen, P.; Dehghan, A.; Edwards, T.L.; Esko, T.; Go, M.J.; Harris, S.E.; Hartiala, J.; Kasela, S.; Kasturiratne, A.; Khor, C.C.; Kleber, M.E.; Li, H.; Mok, Z.Y.; Nakatochi, M.; Sapari, N.S.; Saxena, R.; Stewart, A.F.; Stolk, L.; Tabara, Y.; Teh, A.L.; Wu, Y.; Wu, J.Y.; Zhang, Y.; Aits, I.; Da Silva Couto Alves, A.; Das, S.; Dorajoo, R.; Hopewell, J.C.; Kim, Y.K.; Koivula, R.W.; Luan, J.; Lyytikäinen, L.P.; Nguyen, Q.N.; Pereira, M.A.; Postmus, I.; Raitakari, O.T.; Bryan, M.S.; Scott, R.A.; Sorice, R.; Tragante, V.; Traglia, M.; White, J.; Yamamoto, K.; Zhang, Y.; Adair, L.S.; Ahmed, A.; Akiyama, K.; Asif, R.; Aung, T.; Barroso, I.; Bjonnes, A.; Braun, T.R.; Cai, H.; Chang, L.C.; Chen, C.H.; Cheng, C.Y.; Chong, Y.S.; Collins, R.; Courtney, R.; Davies, G.; Delgado, G.; Do, L.D.; Doevendans, P.A.; Gansevoort, R.T.; Gao, Y.T.; Grammer, T.B.; Grarup, N.; Grewal, J.; Gu, D.; Wander, G.S.; Hartikainen, A.L.; Hazen, S.L.; He, J.; Heng, C.K.; Hixson, J.E.; Hofman, A.; Hsu, C.; Huang, W.; Husemoen, L.L.; Hwang, J.Y.; Ichihara, S.; Igase, M.; Isono, M.; Justesen, J.M.; Katsuya, T.; Kibriya, M.G.; Kim, Y.J.; Kishimoto, M.; Koh, W.P.; Kohara, K.; Kumari, M.; Kwek, K.; Lee, N.R.; Lee, J.; Liao, J.; Lieb, W.; Liewald, D.C.; Matsubara, T.; Matsushita, Y.; Meitinger, T.; Mihailov, E.; Milani, L.; Mills, R.; Mononen, N.; Müller-Nurasyid, M.; Nabika, T.; Nakashima, E.; Ng, H.K.; Nikus, K.; Nutile, T.; Ohkubo, T.; Ohnaka, K.; Parish, S.; Paternoster, L.; Peng, H.; Peters, A.; Pham, S.T.; Pinidiyapathirage, M.J.; Rahman, M.; Rakugi, H.; Rolandsson, O.; Rozario, M.A.; Ruggiero, D.; Sala, C.F.; Sarju, R.; Shimokawa, K.; Snieder, H.; Sparso, T.; Spiering, W.; Starr, J.M.; Stott, D.J.; Stram, D.O.; Sugiyama, T.; Szymczak, S.; Tang, W.H.; Tong, L.; Trompet, S.; Turjanmaa, V.; Ueshima, H.; Uitterlinden, A.G.; Umemura, S.; Vaarasmaki, M.; van Dam, R.M.; van Gilst, W.H.; van Veldhuisen, D.J.; Viikari, J.S.; Waldenberger, M.; Wang, Y.; Wang, A.; Wilson, R.; Wong, T.Y.; Xiang, Y.B.; Yamaguchi, S.; Ye, X.; Young, R.D.; Young, T.L.; Yuan, J.M.; Zhou, X.; Asselbergs, F.W.; Ciullo, M.; Clarke, R.; Deloukas, P.; Franke, A.; Franks, P.W.; Franks, S.; Friedlander, Y.; Gross, M.D.; Guo, Z.; Hansen, T.; Jarvelin, M.R.; Jorgensen, T.; Jukema, J.W.; Kähönen, M.; Kajio, H.; Kivimaki, M.; Lee, J.Y.; Lehtimäki, T.; Linneberg, A.; Miki, T.; Pedersen, O.; Samani, N.J.; Sorensen, T.I.; Takayanagi, R.; Toniolo, D.; BIOS-consortium; CARDIo GRAMplusCD; LifeLines Cohort Study; InterAct Consortium; Ahsan, H.; Allayee, H.; Chen, Y.T.; Danesh, J.; Deary, I.J.; Franco, O.H.; Franke, L.; Heijman, B.T.; Holbrook, J.D.; Isaacs, A.; Kim, B.J.; Lin, X.; Liu, J.; März, W.; Metspalu, A.; Mohlke, K.L.; Sanghera, D.K.; Shu, X.O.; van Meurs, J.B.; Vithana, E.; Wickremasinghe, A.R.; Wijmenga, C.; Wolffenbuttel, B.H.; Yokota, M.; Zheng, W.; Zhu, D.; Vineis, P.; Kyrtopoulos, S.A.; Kleinjans, J.C.; McCarthy, M.I.; Soong, R.; Gieger, C.; Scott, J.; Teo, Y.Y.; He, J.; Elliott, P.; Tai, E.S.; van der Harst, P.; Kooner, J.S.; Chambers, J.C.
We carried out a trans-ancestry genome-wide association and replication study of blood pressurephenotypes among up to 320,251 individuals of East Asian, European and South Asian ancestry. We find genetic variants at 12 new loci to be associated with blood pressure (P = 3.9 × 10(-11) to 5.0 × 10(-21)). The sentinel blood pressure SNPs are enriched for association with DNAmethylation at multiple nearby CpG sites, suggesting that, at some of the loci identified, DNAmethylation may lie on the regulatory pathway linking sequence variation to blood pressure. The sentinel SNPs at the 12 new loci point to genes involved in vascular smooth muscle (IGFBP3, KCNK3, PDE3A and PRDM6) and renal (ARHGAP24, OSR1, SLC22A7 and TBX2) function. The new and known genetic variants predict increased left ventricular mass, circulating levels of NT-proBNP, and cardiovascular and all-cause mortality (P = 0.04 to 8.6 × 10(-6)). Our results provide new evidence for the role of DNA methylation in blood pressure regulation.