TY  - JA
AU  - Yanli Lu
AU  - Shah,T.
AU  - Zhuanfang Hao
AU  - Taba,S.
AU  - Shihuang Zhang
AU  - Shibin Gao
AU  - Jian Liu
AU  - Moju Cao
AU  - Jing Wang
AU  - Prakash,A.B.
AU  - Tingzhao Rong
AU  - Yunbi Xu
TI  - Comparative SNP and haplotype analysis reveals a higher genetic diversity and rapider LD decay in tropical than temperate germplasm in maize
SN  - 1932-6203
PY  - 2011///
CY  - San Francisco, CA (USA)
PB  - Public Library of Science
KW  - Maize
KW  - AGROVOC
KW  - Biodiversity
KW  - Plant breeding
KW  - Nucleotide sequence
KW  - Population genetics
KW  - Molecular genetics
N1  - Peer-review: Yes - Open Access: Yes|http://science.thomsonreuters.com/cgi-bin/jrnlst/jlresults.cgi?PC=MASTER&ISSN=1932-6203; Peer review; Open Access
N2  - 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
UR  - http://hdl.handle.net/10883/1855
DO  - https://doi.org/10.1371/journal.pone.0024861
T2  - PLoS ONE
ER  -