Genetic diversity and population structure of a diverse set of rice germplasm for association mapping

被引:195
作者
Jin, Liang [1 ,2 ]
Lu, Yan [1 ,2 ]
Xiao, Peng [1 ,2 ]
Sun, Mei [3 ]
Corke, Harold [3 ]
Bao, Jinsong [1 ,2 ]
机构
[1] Zhejiang Univ, Inst Nucl Agr Sci, Key Lab Zhejiang Prov, Hangzhou 310029, Zhejiang, Peoples R China
[2] Zhejiang Univ, Chinese Minist Agr Nucl Agr Sci, Hangzhou 310029, Peoples R China
[3] Univ Hong Kong, Sch Biol Sci, Hong Kong, Hong Kong, Peoples R China
关键词
STARCH PHYSICOCHEMICAL PROPERTIES; SINGLE NUCLEOTIDE POLYMORPHISMS; QUANTITATIVE TRAIT LOCUS; MULTILOCUS GENOTYPE DATA; ORYZA-SATIVA L; LINKAGE DISEQUILIBRIUM; SYNTHESIZING GENES; NONWAXY RICE; SSR MARKERS; VISCOSITY;
D O I
10.1007/s00122-010-1324-7
中图分类号
S3 [农学(农艺学)];
学科分类号
0901 ;
摘要
Germplasm diversity is the mainstay for crop improvement and genetic dissection of complex traits. Understanding genetic diversity, population structure, and the level and distribution of linkage disequilibrium (LD) in target populations is of great importance and a prerequisite for association mapping. In this study, 100 genome-wide simple sequence repeat (SSR) markers were used to assess genetic diversity, population structure, and LD of 416 rice accessions including landraces, cultivars and breeding lines collected mostly in China. A model-based population structure analysis divided the rice materials into seven subpopulations. 63% of the SSR pairs in these accessions were in LD, which was mostly due to an overall population structure, since the number of locus pairs in LD was reduced sharply within each subpopulation, with the SSR pairs in LD ranging from 5.9 to 22.9%. Among those SSR pairs showing significant LD, the intrachromosomal LD had an average of 25-50 cM in different subpopulations. Analysis of the phenotypic diversity of 25 traits showed that the population structure accounted for an average of 22.4% of phenotypic variation. An example association mapping for starch quality traits using both the candidate gene mapping and genome-wide mapping strategies based on the estimated population structure was conducted. Candidate gene mapping confirmed that the Wx and starch synthase IIa (SSIIa) genes could be identified as strongly associated with apparent amylose content (AAC) and pasting temperature (PT), respectively. More importantly, we revealed that the Wx gene was also strongly associated with PT. In addition to the major genes, we found five and seven SSRs were associated with AAC and PT, respectively, some of which have not been detected in previous linkage mapping studies. The results suggested that the population may be useful for the genome-wide marker-trait association mapping. This new association population has the potential to identify quantitative trait loci (QTL) with small effects, which will aid in dissecting complex traits and in exploiting the rich diversity present in rice germplasm.
引用
收藏
页码:475 / 487
页数:13
相关论文
共 50 条
  • [21] An SNP caused loss of seed shattering during rice domestication
    Konishi, Saeko
    Izawa, Takeshi
    Lin, Shao Yang
    Ebana, Kaworu
    Fukuta, Yoshimichi
    Sasaki, Takuji
    Yano, Masahiro
    [J]. SCIENCE, 2006, 312 (5778) : 1392 - 1396
  • [22] Rice domestication by reducing shattering
    Li, CB
    Zhou, AL
    Sang, T
    [J]. SCIENCE, 2006, 311 (5769) : 1936 - 1939
  • [23] PowerMarker: an integrated analysis environment for genetic marker analysis
    Liu, KJ
    Muse, SV
    [J]. BIOINFORMATICS, 2005, 21 (09) : 2128 - 2129
  • [24] Population structure and long-range linkage disequilibrium in a durum wheat elite collection
    Maccaferri, M
    Sanguineti, MC
    Noli, E
    Tuberosa, R
    [J]. MOLECULAR BREEDING, 2005, 15 (03) : 271 - 289
  • [25] A mixed-model approach to association mapping using pedigree information with an illustration of resistance to Phytophthora infestans in potato
    Malosetti, M.
    van der Linden, C. G.
    Vosman, B.
    van Eeuwijk, F. A.
    [J]. GENETICS, 2007, 175 (02) : 879 - 889
  • [26] The extent of linkage disequilibrium in rice (Oryza sativa L.)
    Mather, Kristie A.
    Caicedo, Ana L.
    Polato, Nicholas R.
    Olsen, Kenneth M.
    McCouch, Susan
    Purugganan, Michael D.
    [J]. GENETICS, 2007, 177 (04) : 2223 - 2232
  • [27] Maurer HP, 2006, MAYDICA, V51, P269
  • [28] Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.)
    McCouch, SR
    Teytelman, L
    Xu, YB
    Lobos, KB
    Clare, K
    Walton, M
    Fu, BY
    Maghirang, R
    Li, ZK
    Xing, YZ
    Zhang, QF
    Kono, I
    Yano, M
    Fjellstrom, R
    DeClerck, G
    Schneider, D
    Cartinhour, S
    Ware, D
    Stein, L
    [J]. DNA RESEARCH, 2002, 9 (06) : 199 - 207
  • [29] ACCURACY OF ESTIMATED PHYLOGENETIC TREES FROM MOLECULAR-DATA .2. GENE-FREQUENCY DATA
    NEI, M
    TAJIMA, F
    TATENO, Y
    [J]. JOURNAL OF MOLECULAR EVOLUTION, 1983, 19 (02) : 153 - 170
  • [30] Evaluation of genetic diversity in rice subspecies using microsatellite markers
    Ni, J
    Colowit, PM
    Mackill, DJ
    [J]. CROP SCIENCE, 2002, 42 (02) : 601 - 607