| In maize, heterosis is particularly evident and has been used commercially with great benefit. And also maize is a model system for the investigation of genetic and molecular basis of heterosis. Root systems of terrestrial plants serve many important tasks such as anchorage of the plant, uptake of water plus nutrients. Root performance also influence grain yield of maize directly or indirectly. To understand the genetic basis of heterosis for complex quantitative traits, it is a good choice to start from root because it may be a relative simple organ to other materials. The aim of this study is to analyze the expression profile of hybrid and its parents at the same root developmental stage in order to explore the molecular basis of heterosis.In this study, forward and reverse subtractive cDNA libraries were constructed using Suppression Subtractive Hybridization (SSH) method, with seedling roots of an elite maize hybrid (Yuyu22) and its two parents as materials. After differential screening, sequencing and removing redundant sequences, 295 differential ESTs were obtained from 530 positive clones. According to BLASTX search results, 45% of the differential expressed genes were unknown function or new ESTs; the rest which had significant homology with known genes were 13% basic metabolism related, 9% transcription and regulation related (involving 6.4% transcription factors), 6% signal transduction related, 4% cell growth and division related, 5% protein processing and destination related genes.Expression analysis of fourteen differential expressed genes which were functionally related to transcription regulation, cell division, and signal transduction etc were confirmed by RT-PCR analysis, among which seven genes showed the same expression patterns as SSH. Four genes were up-regulated in hybrid to both parents; One expressed in hybrid between the level of two parents; Four expressed in hybrid as a lower parent; Among the genes expressed in hybrid as a higher parent, four were as higher as parent Zong3, one was as 87-1. Real-time PCR analysis demonstrated that CR2B06 and CR4C09 had the same expression patterns as SSH, which expressed in hybrid as a lower parent Zong3 and up-regulated in hybrid to both parents, respectively.Using CAPS or STS method, 12 differential expressed EST were mapped on maize chromosome 1, 2, 4, 6, 7, 9 and 10. With the 12 markers added to the genetic linkage map constructed in our lab, eight QTLs affecting maize seedling roots were mapped based on composite interval mapping method. It was found that the position of differential expressed EST CR2E08 was located within the interval of QTL controlling total root length, root surface area and root volume of seedling 4 days after germination. And importantly with marker CR2E08 added to the map, the LOD value and the contribution to phenotypic variation of the QTL for root volume increased both.Based on EST sequence AI770808 which expressed differentially between hybrid and inbred lines on a maize cDNA chip, two MYB transcription factors with same open reading frames (ZmMYBLI and ZmMYBL2) were obtained by RT-PCR. Sequence analysis revealed that ZmMYBLI encoded a typical R2R3-MYB protein. According to southern blot analysis, ZmMYBLI may be a single copy gene belonging to a multi-gene family in the maize genome. Expression analysis showed that ZmMYBLI transcripts accumulated in all examined tissues with different levels. Also it was expressed atrelatively lower level in root, stem and leaf in the hybrid than that in the parents. ZmMYBLI was mapped on maize chromosome bin7.03 between SSR markers, bnlg339 and umcl865 using Yuyu22 recombinant inbred line (RIL) population. A QTL for root average diameter of maize seedling was also localized on the corresponding region of chromosome7 with the interval ZmMYBLI-umc 1865. Expression analysis of R2R3-MYB transcription factors showed that other members of the family participated in the differential expression between hybrid and parents.
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