Person:
Shah, T.

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Shah
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Shah, T.
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0000-0002-0091-7981

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    Q&A: Methods for estimating genetic gain in sub-Saharan Africa and achieving improved gains
    (CSSA, 2024) Dieng, I.; Gardunia, B.W.; Covarrubias-Pazaran, G.; Gemenet, D.; Trognitz, B.; Ofodile, S.; Fowobaje, K.; Ntukidem, S.; Shah, T.; Imoro, S.; Leena Tripathi; Mushoriwa, H.; Mbabazi, R.; Salvo, S.; Derera, J.
    Publication
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    Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L.)
    (Public Library of Science, 2011) Thudi, M.; Abhishek Bohra; Nayak, S.N.; Varghese, N.; Shah, T.; Penmetsa, R.V.; Thirunavukkarasu, N.; Gudipati, S.; Gaur, P.; Kulwal, P.L.; Upadhyaya, H.D.; Kavikishor, P.B.; Winter, P.; Kahl, G.; Town, C.D.; Kilian, A.; Cook, D.; Varshney, R.K.
    Publication
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    An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for tetraploid groundnut (arachis hypogaea l.)
    (Public Library of Science, 2012) Gautami, B.; Foncéka, D.; Pandey, M.K.; Moretzsohn, M.C.; Sujay, V.; Hongde Qin; Yanbin Hong; Faye, I.; Xiaoping Chen; Bhanuprakash, A.; Shah, T.; Gowda, M.V.C.; Nigam, S.N.; Xuanqiang Liang; Hoisington, D.A.; Baozhu Guo; Bertioli, D.; Rami, J.F.; Varshney, R.K.
    Publication
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    The generation challenge programme platform: Semantic standards and workbench for crop science
    (Hindawi Publishing Corporation :, 2008) Bruskiewich, R.; Senger, M.; Davenport, G.; Ruíz, M.; Rouard, M.; Hazekamp, T.; Takeya, M.; Koji Doi; Kouji Satoh; Costa, M.; Simon, R.; Jayashree, B.; Akinnola Nathaniel Akintunde; Mauleon, R.; Wanchana, S.; Shah, T.; Anacleto, M.; Portugal, A.; Ulat, V.J.; Thongjuea, Supat; Braak, K.; Ritter, S.; Dereeper, A.; Skofic, M.; Rojas, E.; Martins, N.; Pappas, G.; Alamban, R.; Almodiel,, R.; Barboza, L.H.; Detras, J.; Manansala, K.; Mendoza, M.J.; Morales, J.; Peralta, B.; Valerio, R.; Yi Zhang; Gregorio, S.; Hermocilla, J.; Echavez, M.; Yap, J.M.; Farmer, A.; Schiltz, G.; Lee, J.; Casstevens, T.; Jaiswal, P.; Meintjes, A.; Wilkinson, M.D.; Good, B.; Wagner, J.; Morris, J.; Marshall, D.S.; Collins, A.; Kikuchi, S.; Metz, T.; McLaren, C.; van Hintum, T.
    Publication
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    Genetic diversity and population structure of soybean lines adapted to Sub-Saharan Africa using single nucleotide polymorphism (SNP) markers
    (MDPI, 2021) Chander, S.; Garcia-Oliveira, A.L.; Gedil, M.; Shah, T.; Otusanya, G.O.; Asiedu, R.; Chigeza, G.
    Publication
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    Genetic analysis and QTL mapping for multiple biotic stress resistance in cassava
    (Public Library of Science, 2020) Garcia-Oliveira, A.L.; Kimata, B.; Kasele, S.; Kapinga, F.; Masumba, E.; Mkamilo, G.; Sichalwe, C.; Bredeson, J.V.; Lyons, J.B.; Shah, T.; Satoru Muranaka; Katari, M.S.; Ferguson, M.
    Publication
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    Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa
    (Wiley, 2011) Hiremath, P.J.; Farmer, A.; Cannon, S.B.; Woodward, J.; Kudapa, H.; Tuteja, R.; Kumar, A.; Bhanuprakash, A.; Mulaosmanovic, B.; Gujaria, N.; Krishnamurthy, L.; Gaur, P.; Kavikishor, P.B.; Shah, T.; Srinivasan, R.; Lohse, M.; Yongli Xiao; Town, C.D.; Cook, D.; May, G.D.; Varshney, R.K.
    Publication
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    Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.)
    (Springer, 2011) Gujaria, N.; Kumar, A.; Dauthal, P.; Dubey, A.; Hiremath, P.J.; Prakash, A.B.; Farmer, A.; Bhide, M.; Shah, T.; Gaur, P.; Upadhyaya, H.D.; Bhatia, S.; Cook, D.; May, G.D.; Varshney, R.K.
    Publication
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    Comparative SNP and haplotype analysis reveals a higher genetic diversity and rapider LD decay in tropical than temperate germplasm in maize
    (Public Library of Science, 2011) Yanli Lu; Shah, T.; Zhuanfang Hao; Taba, S.; Shihuang Zhang; Shibin Gao; Jian Liu; Moju Cao; Jing Wang; A. Bhanu Prakash; Tingzhao Rong; Yunbi Xu
    Understanding of genetic diversity and linkage disequilibrium (LD) decay in diverse maize germplasm is fundamentally important for maize improvement. A total of 287 tropical and 160 temperate inbred lines were genotyped with 1943 single nucleotide polymorphism (SNP) markers of high quality and compared for genetic diversity and LD decay using the SNPs and their haplotypes developed from genic and intergenic regions. Intronic SNPs revealed a substantial higher variation than exonic SNPs. The big window size haplotypes (3-SNP slide-window covering 2160 kb on average) revealed much higher genetic diversity than the 10 kb-window and gene-window haplotypes. The polymorphic information content values revealed by the haplotypes (0.436?0.566) were generally much higher than individual SNPs (0.247?0.259). Cluster analysis classified the 447 maize lines into two major groups, corresponding to temperate and tropical types. The level of genetic diversity and subpopulation structure were associated with the germplasm origin and post-domestication selection. Compared to temperate lines, the tropical lines had a much higher level of genetic diversity with no significant subpopulation structure identified. Significant variation in LD decay distance (2?100 kb) was found across the genome, chromosomal regions and germplasm groups. The average of LD decay distance (10?100 kb) in the temperate germplasm was two to ten times larger than that in the tropical germplasm (5?10 kb). In conclusion, tropical maize not only host high genetic diversity that can be exploited for future plant breeding, but also show rapid LD decay that provides more opportunity for selection.
    Publication
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    Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers
    (Public Library of Science, 2009) Jianbing Yan; Shah, T.; Warburton, M.; Buckler, E.; McMullen, M.D.; Crouch, J.H.
    A newly developed maize Illumina GoldenGate Assay with 1536 SNPs from 582 loci was used to genotype a highly diverse global maize collection of 632 inbred lines from temperate, tropical, and subtropical public breeding programs. A total of 1229 informative SNPs and 1749 haplotypes within 327 loci was used to estimate the genetic diversity, population structure, and familial relatedness. Population structure identified tropical and temperate subgroups, and complex familial relationships were identified within the global collection. Linkage disequilibrium (LD) was measured overall and within chromosomes, allelic frequency groups, subgroups related by geographic origin, and subgroups of different sample sizes. The LD decay distance differed among chromosomes and ranged between 1 to 10 kb. The LD distance increased with the increase of minor allelic frequency (MAF), and with smaller sample sizes, encouraging caution when using too few lines in a study. The LD decay distance was much higher in temperate than in tropical and subtropical lines, because tropical and subtropical lines are more diverse and contain more rare alleles than temperate lines. A core set of inbreds was defined based on haplotypes, and 60 lines capture 90% of the haplotype diversity of the entire panel. The defined core sets and the entire collection can be used widely for different research targets.
    Publication