| Selecting elite parents is of paramount importance in conventional breeding and cross breeding programs. However, the selection of parents from a phalanx of inbred lines is extremely time consuming and often no better than a random process. Furthermore, parents with excellent agronomic traits do not always transmit those traits to their progeny. Thus, Sprague and Tatum proposed the concepts of general combining ability (GCA) and specific combining ability (SCA) to evaluate breeding parents and the parent combination, respectively. Since then, GCA has been widely and successfully used as criteria to evaluate elite parents in conventional breeding and in cross breeding practices. However, the genetic and molecular basis of GCA has been largely overlooked.To explore the genetic basis of GCA, we first analyzed GCA using a diallelcross population including six rice indica varieties, Zhenshan97(ZS), Aijiaonante (AJ), Guangluai#4(GL),93-11and Teqing (TQ), and15F1hybrids that mated from these parents. The diallel cross population were planted in three seasons: the summers of2008and2009in Wuhan and the winter of2009in Hainan Island. In each season, triplicates of30plants were grown. Three agronomic traits mainly contributed to rice yield, plant height (PH), heading date (HD) and grain number of per panicle (GP), were measured. The general combining ability (GCA) for each parent was calculated according to Griffing.For the further analysis of genetic basis of GCA, we constructed a F2population with the parents GL and TQ, which exhibited significantly difference on GCA for all the three traits. To evaluate the genetic base of GCA, total of700hybrids derived from the five test parents mating with140individual plants in the F2population of GLxTQ. A genetic map for GCA loci was made using the GCA score of individuals in the F2population. To further study the molecular basis of GCA, we did the transcriptome sequencing of GL, TQ and93-11, and their F1hybrids GLxTQ, GLx93-11and93-11xTQ. The main results as follows:1, We found that the GCA effects about the three agronomic traits of the parents tested appeared significantly difference. The GCA effects of93-11and TQ exhibited positive GCA effects, while ZS, AJ and GL exhibited negative GCA effects.2, We also found that the GCA effects does not be significantly affected by the environmental conditions in Wuhan and Hainan Island.3, A total of121polymorphic SSR markers were used for genetic linkage analysis of the GCA using140individuals of the F2population of GLxTQ. Two major QTLs were detected from the genetic mapping of the GCA for the three traits. One QTL controlling the GCA of GN with a Lod score5.7located between RM3148and RM462on chromosome1; the other QTL located near the RM1306on chromosome7, which has pleiotropism on controlling the GCA of three traits, HD, PH and GP, exhibited the Lod scores of35.5,12.9and12.5, respectively. These results indicated the concept of GCA derived from statistical analysis was controlled by QTLs.4, We found that the three agronomic traits from the F1hybrids were always similar to93-11and TQ in the diallel cross population, when either93-11or TQ was used as one parent in the hybrids. The correlation analysis for the three agronomic traits between Fl hybrids and the parents showed significant correlation with the parents of93-11and TQ (r>0.97, P<3.80E-07), but less significant correlation with the parents of GL, ZS and AJ (r=0.81, P<1.33E-03). These results indicated that the parents with higher GCA effects would make more contibutions to the phenotypes of F1hybrids than that of the parents with lower GCA effects.5, To explore the machanism of the agronomic traits in F1hybrids always biased to the high GCA parents, the transcriptome sequencing of the leaves at the development stage of secondary branch meristem from three F1hybrids, GLx93-11, GLxTQ and93-11XTQ, and their parents were accomplished. The results revealed that the global transcriptome profiles of F1hybrids were biased to the positive GCA effect parents.6, The transcriptome of F1hybrids biased to the positive GCA effect parents were validated by analyzing the gene expression patterns of the GA and flowering pathways that are corresponding for plant height and flowering time. In long day condition, the up-regulation of Ehdl, Ehd2, Hd3a, RFT1will induce rice flowering, these gene expression levels were obviously lower in GLx93-11, GLxTQ,93-11and TQ than that of in GL; while these gene expression levels of Hdl, OsPRR1and Ghd7that depressed the flowering in rice were significantly down-regulated in GL. In the GA regulation pathway, the gene expression levels of OsCPSl and OsKAO that enhance the GA synthesis were up-regulated in GLx93-11, GLxTQ,93-11and TQ. The similar results were obtained from expression anyalysis of GA2ox. While the expression level of GA3ox and GA20ox that feedbackly regulated by high level of GA were down-regulated.7, To explore the molecular basis of heterosis and the relationship between allelic expression and heterosis, we chose three F1hybrids, GLxTQ and GLx93-11, exhibited high heterosis, and the third,93-11XTQ, low heterosis and their parents GL, TQ and93-11for the transcriptome sequencing and allele-specific expression analysis.17.7-27.7of rice genome coverage were obtained from three parents to satisfy the minimum requirement for obtaining more than90%SNPs and a total of89.5to114.1million reads (90bp per read) were obtained from analogous tissue from the three F1hybrids used for the further allele-specific study. For the three F1hybrids, the sequencing depths were rached to8.6-11.9reads per SNP, repectively.8, We found that3.4to3.9%of the genes were classified as monoallelic expression (MAE),23.5to24.2%as preferential allelic expression (PAE) and72.0to73.0%as biallelic expression (BAE) from the three F1hybrids by the allele-specific expression analysis. The correlation analysis indcicated that correlation coefficients ranging from0.70to0.76(P<2.2E-16) in three F1hybrids between gene expression in the parents and the ASE in the F1hybrids, respectively. A higher correlation coefficient was obtained from the same analysis with ASE genes in the F1hybrids (r>0.80, P<2.2E-16). These results imply a cis-regulatory mechanism contributed to the allele-specific expression in rice hybrids.9, By comparing the allelic expression pattern of monoallelic and preferential allelic expression genes in reciprocal hybrids, we found the allelic expression pattern of all the genes tested biased to the high GCA effect parents. This allelic expression pattern was different from the three types of monoallelic expression genes that have well studied in mammals, so we designate this type of monoallelic expression gene as genotype-dependent monolallelic expression gene.10, We found80.7-94.6%expressed genes were regulated as cis-regulated mechanism in F1hybrids, while5.4-19.3%expressed genes regulated as trans-regulated effects through the gene expression level analysis. The results showed79.7%genes exhibited complementary effects, which were resulted from allele-specific expression. Our results revealed the categories of the expression activated and enhanced in the F1hybrids mainly resulted in complementary effects of superior alleles from both parents.11, The further analysis between allele-specific expression and differentially expressed genes occurred in F1hybrids indicated that these genes exhibiting allele-specific expression comprised42.4%of the genes differentially expressed between F1hybrids and their parents in average. Allele-specific expression accounted for79.8%of the genes displaying more than a10-fold expression level difference between an F1and its parents, and almost all (97.3%) of the genes expressed in F1, but non-expressed in one parent. |
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