基于株高性状的玉米EST序列与水稻基因组的比较研究

Comparative Analyses between EST Sequences Concerning Plant Height of Maize and Sequences of Rice Genome Database

从已公布的玉米分子标记中 ,挑选出均匀覆盖玉米全基因组、平均间距小于 10cM的 2 2 4个SSR和RFLP分子标记 ,从NCBI上查找这些标记所在的玉米EST或基因的原始序列 ,逐一与水稻数据库的序列信息进行同源性比较。结果表明 :在PN<1e 5水平上 ,从水稻数据库中共找到 16 939段同源序列 ,平均每段玉米的序列可以在水稻数据库中找到75 .6段同源序列 ;在PN<1e 10水平上 ,一共找到 785 3段同源序列 ,将其中 2 72 9段序列与水稻的物理图谱和分子标记连锁图进行比对定位 ,最终将 896段同源序列整合在水稻分子标记连锁图上 ,形成了在序列水平上的玉米和水稻的比较基因组图谱。基于这一图谱 ,对已定位的玉米和水稻株高QTL的分子标记进行了比较基因组的定位分析。 10个玉米株高QTL紧密连锁的 18个分子标记中有 10个标记在与之同源的水稻染色体区域也定位了控制水稻株高的QTL或基因 ,暗示有相当一部分控制玉米和水稻株高的QTL是同源的。但进一步的分析表明 ,玉米与水稻基因组的连续共线性区域可能低于预期估计 ;在此基础上提出了一种利用水稻基因组数据进行禾本科植物比较基因组 ,发掘新分子标记和克隆大基因组植物基因的策略。

Homology comparisons were investigated between EST or genetic sequences of maize searched from NCBI, which corresponded to 224 of SSR and RFLP markers covering whole maize genome with average distance about 10 cM, and sequences searched from rice genome database. By BLASTn, 16 939 sequences from rice genome database were found to be homologic with sequences of those maize molecular marker at P_N (P Value Cutoff)<1e-5, i.e. averagely one those maize sequence was corresponding to 75.6 fragment sequences of rice genome database. At P_N<1e-10, 7 853 sequences from rice genome database were searched out to be of correspondance with those maize sequences. Comparing with rice physical map, 2 729 sequences of maize were found to have their relative locations. Moreover, comparing rice physical map with rice molecular marker linkage map, 896 hits of those 2 729 sequences were also found to have their relative locations on rice molecular marker linkage map. Then, a comparative map between rice and maize were developed at sequence level. Based on this map, 11 of 18 molecular markers which were closely linked to 10 QTLs mapped for plant height in maize were corresponded to chromosome regions where were locations of QTLs or genes concerning rice plant height. It indicated that QTLs controlling rice and maize plant height were considerably homologous, though syntenic group could possibly smaller than that expected. Hence it could be proposed that comparative studies of cereal genomes by application of rice genome database could develop new molecular markers and isolate genes from plants with larger genomes.