Comparative Analysis Of Genes Encoding Enzymes Of C₄ Photosynthetic Pathway In Five Gramineae Crops And Genome-wide Mining Of Genes Regulating Yield And Quality Traits In Bread Wheat

Bread wheat(Triticum aestivum.L)is one of the most important food crops worldwide,and provides rich protein,dietary fiber and energy for human beings.Therefore,ensuring the continuous improvement of wheat yield and quality is essential to global food security.Improving the photosynthetic capacity of C3 crops such as wheat and rice through the C4 photosynthetic pathway,and mining excellent genetic sites for regulating yield and quality traits in the existing wheat varieties and excellent germplasm resources are important directions for further improvement of wheat yield.In this study,the C4 photosynthetic key enzyme genes of C3 crops wheat and rice and C4 crops of millet,maize and sorghum were identified and comparative analyzed,and the important genes and genetics loci for yield and quality traits of wheat were mined by Meta-QTL analysis and genome-wide association study(GWAS),which will promote germplasm innovation and genetic improvement of wheat yield and quality traits.The main results obtained are as follows:1.Genome-wide identification and comparative analyses of key genes involved in C4 photosynthesis in five main gramineous cropsHere,the genes encoding six C4 photosynthetic pathway key enzymes in the genomes of five important Gramineous crops(C4: maize,foxtail millet,sorghum;C3: rice,wheat)were systematically identified and compared.Based on sequence features,evolutionary relationships,subcellular localization and expression characteristics,their C4 functional copies were accurately distinguished from non-photosynthetic functional copies,and the non-photosynthetic functions were predicted in detail.Comparing the gene structures,protein sequences and expression patterns of C4-homologous genes in C3 crops and C4 genes in C4 crops,an I/N mutation at the N-terminal protein binding site of the Rubisco small subunit(Rbc S)in C4 crops may cause the change of C4-type Rubisco carboxylase function,and an A/G mutation at the C-termimus of C4 crop PEPC enhancing the tolerance to malic acid may be another key to the conversion of C4-type PEPC.Comparative analysis of expressin levels,expression localizations and promoter region sequences of C4/C4-homologous genes,found that the key to the C4-type CA? cytoplasmic localization is the deletion of the N-terminal chloroplast transit peptide,and the specific accumulation of C4-type Rbc S in bundle sheath cell is mainly determined by the 600bp-upstream sequence of the start condon.Comparing the expression synergy of C4 and C4-homologous genes in C4 and C3 crop leaves,showed that increasing the expression levels of PEPC,MDH,ME and PPDK is the first step for the C4-photosynthetic transformation of C3 crops,while the C4 transformation of Rbc S and CA? mainly lies in the change of cellular and subcellular localization.These results provide a certain basis for the C4-transformation of C3 crops.2.Large-scale integration of meta-QTL and genome-wide association study discovers the genomic regions and candidate genes for yield and yield-related traits in bread wheatA comprehensive meta-QTL analysis was conducted on 2230 QTL of yield-related traits obtained from 119 QTL studies.These QTL were refined into 145 meta-QTL(MQTL),and 89 MQTL were verified by GWAS with different natural populations.The average confidence interval(CI)of these MQTL was 2.92 times less than that of the initial QTL.Furthermore,76 core MQTL regions with a physical distance less than 25 Mb were detected.Based on the homology analysis and expression patterns,237 candidate genes in the MQTL involved in photoperiod response,grain development,multiple plant growth regulator pathways,carbon and nitrogen metabolism and spike and flower organ development were determined.A novel candidate gene Ta KAO-4A was confirmed to be significantly associated with grain size,and a CAPS marker was developed based on its dominant haplotype.In summary,this study clarified a method based on the integration of meta-QTL,GWAS and homology comparison to reveal the genomic regions and candidate genes that affect important yield-related traits in wheat.This work will help to lay a foundation for the identification,transfer and aggregation of these important QTL or candidate genes in wheat high-yield breeding.3.Genome-wide association study of important quality traits in bread wheatTo understand the genetic basis of key quality traits of wheat,two single-locus and five multi-locus GWAS models were performed for six grain quality traits and three dough rheological properties based on 19,254 SNPs in 267 bread wheat accessions.As a result,299 quantitative trait nucleotides(QTNs)within 105 regions were identified to be associated with these quality traits in four environments.Of which,40 core QTN regions were stably detected in at least three environments,19 of which were novel.Compared with the previous studies,these novel QTN regions explained smaller phenotypic variation,which verified the advantages of the multi-locus GWAS models in detecting important small effect QTNs associated with complex traits.After characterization of the function and expression in-depth,67 core candidate genes involved in protein/sugar synthesis,histone modification and the regulation of transcription factor were observed to be associated with the formation of grain quality,which showed that multi-level regulations influenced wheat grain quality.Finally,a preliminary network of gene regulation that may affect wheat quality formation was inferred.This study verified the power and reliability of multi-locus GWAS methods in wheat quality trait research,and increased the understanding of wheat quality formation mechanisms.The detected QTN regions and candidate genes in this study could be further used for gene cloning and marker-assisted selection in highquality breeding of bread wheat.